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8-18 yaş arası yelken sporcularında SLC6A4 genindeki 5-HTTLPR polimorfizminin genotip, kısa alel ve uzun alel dağılımları ile dürtüsellik, bilişsel esneklik ve kendini toparlama gücü arasındaki ilişkinin incelenmesi
Bu araştırmada 8-18 yaş arasında olan yelken sporcularında SLC6A4 genindeki 5-HTTLPR polimorfizminin genotip, kısa alel ve uzun alel dağılımları ile dürtüsellik, bilişsel esneklik ve kendini toparlama gücü arasındaki ilişki incelenmiştir. Kişisel Bilgi Formu, Barratt Dürtüsellik Ölçeği, Bilişsel Esneklik Envanteri ve Kendini Toparlama Gücü Ölçeği kullanılarak veriler toplanmış ve kan alımları gerçekleştirilmiştir. SLC6A4 geni 5-HTTLPR polimorfizmi genotip dağılımları izole edilen genomik DNA'dan polimeraz zincir reaksiyonu (PZR) tekniği ile tanımlanmıştır. Çalışmaya katılan 23 kız, 41 erkek sporcunun %39,1'inin LL, %34,4'ünün LS ve %26,5'inin SS genotiplerine sahip olduğu bulunmuştur. L aleli sıklığı %56, S aleli sıklığı %44 olarak tespit edilmiştir. Yelken sınıfının ve cinsiyet değişkeninin ölçek toplam puanlarına etkisinin olmadığı belirlenmiştir. LL, LS ve SS olup olmama ile Barratt Dürtüsellik Ölçeği (BDÖ) (Fmin=4,00; p<,05; Fmax=87,31; p<,001), toplam puanları ve alt ölçek toplam puanlarının tamamı için regresyon modelleri anlamlı bulunmuştur. Buna göre LL olup olmama BDÖ toplam puanları varyansının yaklaşık %9'unu; LS olup olmama yaklaşık %12'sini ve SS olup olmama ise yaklaşık %54'ünü açıklamaktadır. LL olup olmama Bilişsel Esneklik Envanteri (BEE) toplam puanlarının yaklaşık %7'sini; LS olup olmama BEE toplam puanlarının yaklaşık %12'sini; SS olup olmama BEE toplam puanlarının yaklaşık %51'ini açıklamaktadır. LL olup olmama Kendini Toparlama Gücü Ölçeği (KTÖ) toplam puanındaki varyansın yaklaşık %14'ünü; SS olup olmama KTÖ toplam puanındaki varyansın yaklaşık %45'ini açıklamaktadır. Bu çalışma yelken sporcularındaki LL genotip ve L alelinin daha yoğun olduğunu gösteren ilk rapor niteliğindedir.
Kuantum nokta temelli fotovoltaik arayüzlerle retinal ve nöral stimülasyon
Electrical stimulation of neural tissues is the one of the emerging technological areas in medicine. Although several attempts from various research groups, neuro-electronic interface technologies are still in infancy period. Especially in neurodegenerative situations, such as retinitis pigmentosa and age-related macular degeneration, neural stimulation could be effective rehabilitation method. For retina, photovoltaic surfaces are the pioneer concepts for recovery of sensation. The institutes, which are working on retinal prostheses, currently exploiting various photoactive electrical surfaces to stimulate bipolar and ganglion cells in the retina. However, they fail to fulfill functions of retinal prosthesis due to bio-incompatibility, external energy source necessity, lack of flexibility and mobility of prosthesis. Therefore, there is enormous necessity for innovative biomaterials at retinal prosthesis production. Quantum dot based photovoltaic devices are great candidates for nano-sized neural stimulators. Their working principle relies on photoelectric effect, which makes them possible replacement for rhodopsin based phototransduction mechanism in photoreceptor cells. For retinal implant production on flexible PET (polyethylene terephthalate) surface, various types of quantum dot-based photovoltaic interfaces could be used, such as Lead(II)sulfide (PbS), Aluminum antimonide (AlSb). The main concerns on these biointerfaces are biocompatibility and effective electrical charge capacity on neurons which induce action potential activity. Compared to other photoactive polymer-based interfaces in literature, quantum dots-based materials could induce photoelectrical neurostimulation under lower light intensities due to their nanocrystal content. Also compared to other silicon-based biointerfaces, they do not need an external energy source or complicated processor systems, thanks to the photo-capacitive current production. The aim of the study is to investigate various types of quantum dots-based structures to produce effective photovoltaic interface for neural stimulation, which could be used as retinal prosthesis in the rats with retinal degeneration. For this purpose, different type quantum dots were examined with in vitro biocompatibility and electrophysiology experiments. Then, selected quantum dots based neural interfaces implanted to the subretinal spaces of the rats with and without retinal degeneration. After implantation, electrophysiology (VEP-EEG and ERG) and behavioral tests conducted to understand biocompatibility and recovery of visual sensation. After in vivo studies, the animals were euthanized and changes in the retina after implantations and photoelectrical stimulations were observed. By this way, both functional recovery of vision and the structural integrity of the different cell types in retina were demonstrated. Different types of quantum dots-based interfaces induce action potentials in primary hippocampal neurons, which enables neuromodulation with biocompatible photoactive interfaces. In in vivo step, PbS and AlSb QDs based retinal prostheses also induce retinal stimulation with light pulses. Unfortunately, required light levels for neural stimulation with these devices are significantly higher than ocular safety limits. Also, both AlSb and PbS QDs based retinal prostheses induce gliosis and retinal damage in subretinal implantation area. Because of those reasons, further investigations are required for quantum dots based retinal stimulation systems.
The role of chronic stress on the development of Parkinson's Disease phenotype
Background Depression and anxiety, which are associated with chronic stress are core features of Parkinson's Disease (PD). Stress is suggested to affect onset and prognosis of PD. In this study, it had been hypothesized that exposure to chronic stress would lead to earlier onset of motor and non-motor symptoms of Parkinson's Disease (PD). Also, mice with PINK1-/- genotype would be more vulnerable to the effects of chronic stress in this manner. Methods To test this hypothesis, C57BL/6 Non-stress exposed (n=8), C57BL/6 Stress-exposed (n=11), PINK1-/- Non-stress exposed (n=6), PINK1-/- Stress-exposed (n=10), C57BL/6 Follow-up Non-stress exposed (n=16), PINK1-/- Follow-up Non-stress exposed (n=13) and PINK1-/- Follow-up Stress-exposed (n=6) groups were used. For stress-exposed groups, a chronic stress paradigm with three different stressors as rat exposure, tail suspension and restraint stress for the first 28 consecutive days were used. Behavioral tests were applied to assess anxiety (elevated plus maze), memory (spontaneous alternation test), and motor functions (grip and pole tests). The effect of aging in addition to chronic stress exposure was evaluated using both PINK1-/- and control mice aged for six more months. As a validation of the chronic stress procedure, adrenal gland weight, animal weight and plasma corticosterone levels were measured. Results It was found that chronic stress paradigm that was used, lead to significant weight differences, and increased relative adrenal gland weight. Weight at the 4th week was significantly increased by PINK1-/- genotype (B=2.875, p<0.001) and decreased by stress exposure (B=-1.982, p=0.003), when genotype and stress exposure were analyzed as factors in a multivariate linear regression model [F(2,69)=13.11, R2= 0.281, p<0.001]. When relative adrenal gland weights of the groups that were terminated after the first month were compared, it had been found that it was significantly increased by stress (B=3.587e-5, p=<0.001) but it did not depend on genotype (B=-3.961e-6, p=0.679), when genotype and stress exposure were analyzed as factors in a multivariate linear regression model [F(2,34)=6.943, R2=0.303, p=0.003]. When PINK1-/- follow-up non-stress exposed, PINK1-/- follow-up stress-exposed and C57BL/6 follow-up non-stress exposed groups were compared, as expected PINK1-/- Follow-up Stress-exposed group had significantly higher relative adrenal weight than both PINK1-/- Follow-up Non-exposed (p=0.001) and C57BL/6 Follow-up Non-exposed (p<0.01) groups. In follow-up groups' comparison, PINK1-/- follow-up stress-exposed group was shown to have significantly higher plasma corticosterone levels than PINK1-/- follow-up non-stress-exposed group (p=0.046). In the anxiety level assessments of PINK1-/- non-stress exposed, C57 non-stress exposed, PINK1-/- stress-exposed and C57 stress-exposed groups, anxiety levels were found to be significantly increased by PINK1-/- genotype (B=-0.085, p=0.003; B=0.099, p<0.001) but not depend on stress exposure (B=0.043, p=0.129; B=-0.025, p=0.322), when genotype and stress exposure were analyzed as factors in a multivariate linear model in both EPM ratio time [F(2,69)=5.552, R2=0.142, p=0.006] and number [F(2,69)=7.974, R2=0.192, p<0.001] respectively. In motor function assessments of PINK1-/- non-stress exposed, C57 non-stress exposed, PINK1-/- stress-exposed and C57 stress-exposed groups, required time to descent was found to be increased with stress exposure (B=3.555, p=0.022), but not depend on PINK1-/- genotype (B=-2.581, p=0.086); and required time to descent after rotation was found to be increased with both stress exposure (B=1.4, p=0.004) and with having C57BL/6 genotype (B=-1.255, p=0.007), when genotype and stress exposure were analyzed as factors in a multivariate linear model in time spent to descent [F(2,69)=3.743, R2=0.101, p=0.029] and time spent to descent after rotation [F(2,69)=7.3, R2=0.179, p=0.001] in the pole test. To assess effects of aging on psychopathology, mixed-effect regression analysis was used to compare PINK1-/- Follow up Non-stress exposed and Stress-exposed groups' 1st and 6th-month assessments by controlling for both time and stress effect and using animal IDs as cluster variable. EPM ratio number results were indicated that anxiety level was increased by stress (B=0.0501, p=0.015) and decreased by time (B=-0.0463, p=0.009). In grip test results, the time span of holding the wire is found to be decreased by time (B=-53.9, p=0.003). In the comparison of C57BL/6 Follow-up Non-stress exposed, PINK1-/- Follow-up Non-stress exposed and PINK1-/- Follow-up Stress-exposed groups, it was found that PINK1-/- Follow-up Stress-exposed group took longer time to rotate downward than both C57BL/6 Follow-up Non-stress exposed (p=0.021) and PINK1-/- Follow-up Non-stress exposed groups (p=0.029). Additionally, both PINK1 Follow-up Stress-exposed (p=0.001) and PINK1-/- Follow-up Non-stress exposed (p<0.001) groups were required higher distance to rotate than C57BL/6 Follow-up Non-stress exposed group. Conclusions These findings support that genetic predisposition to PD could lead to vulnerability for psychiatric symptomatology despite stress exposure and that chronic stress exposure may not lead to earlier onset of motor symptoms.
Validation of the modified berlin questionnaire for the diagnosis of obstructive sleep apnea in patients with COVID-19 infection
Obstructive sleep apnea (OSA) is a condition characterized by intermittent cessation of breathing and hypoxia during sleep. Less is known regarding the actual prevalence of OSA in COVID-19 patients, given that objective sleep studies with polysomnography are not accurate in the face of an active contagious respiratory infection. The Berlin Questionnaire (BQ) is a widely used survey to predict OSA, which includes 10 questions in three categories (snoring severity, daytime sleepiness, presence of hypertension and/or obesity). Considering the confounding effect of obesity and hypertension on the clinical course of COVID-19, we have recently developed a modified BQ (mBQ) for addressing the clinical outcomes in patients with high-risk vs low-risk OSA. The primary purpose of the current study was to validate this questionnaire. All cases with a history of COVID-19 infection between March 10 and June 22, 2020, and who completed the mBQ in our first study, were invited to participate. Participants refilled the questionnaires, and an attended polysomnography was conducted. The mBQ was validated based on the polysomnography results. A cut-off value of an apnea-hypopnea-index 15 events/hour was used for the OSA diagnosis. Out of 50, 22 participants (44%) were categorized as having high risk of OSA based on the mBQ. In all, 27 cases (54%) were categorized as positive on snoring intensity and/or snoring frequency, 7 cases (14%) on witnessed apneas, and 28 cases (56%) on the tiredness in the morning and/or during the whole day. According to the PSG results, 19 patients with high risk OSA (86.4%) and 2 patients with low risk (7.1%) were found to have AHI ≥15 events/h. Thus, the mBQ had a sensitivity of 90.5%, a specificity of 89.6%, a positive predictive value of 86.4%, a negative predictive value of 92.9%, and an accuracy of 90%. The area under the curve was 0.89 (95% CI 0.78 – 0.99) confirming a very good performance of the mBQ in screening for OSA for the AHI threshold 15 events/h. The Cronbach's alpha value was 0.70 indicating an acceptable internal reliability whereas the test-retest reliability was low (α = 0.44). The principal component analysis supported the three factor structures. The convergent validity was confirmed by a moderate agreement between the mBQ and the STOP-Bang. A strong discriminant validity was confirmed by the weak correlation between the mBQ and the Narcissistic Personality Inventory scores. A relatively good correlation between the total scores of mBQ and BQ supported the concurrent validity of the mBQ. To conclude, the mBQ is a practical, feasible, and cost-effective method to predict OSA in adults with a history of COVID-19 infection. It requires short administration time, and has a good level of diagnostic sensitivity, specificity and accuracy, suggesting that it can be used as a screening tool during COVID-19 pandemic. Moreover, the mBQ can be used in clinical management of cases with high-risk OSA in hospitals with long waiting lists for PSG, and to eliminate unnecessary PSG investigations for adults with low-risk OSA.
Deliryum patogenezinde astrositik glikojenin rolü
Background: Delirium is an acute neuropsychiatric syndrome that is very common in hospitalized patients. Also, a delirium episode independently increases the risk of post-discharge mortality and dementia. However, with this high prevalence and deleterious outcomes, the clear pathogenesis of delirium has not been explained yet. Systemic inflammation, hypoglycemia, and sleep deprivation can trigger delirium, among other causes, and the coexistence of multiple risk factors further increases the delirium risk. The brain astrocytic glycogen is a vital lactate donor for neurons under hypoglycemic conditions and glutamatergic excitation. And glycogen is necessary for synaptic plasticity and long-term memory formation. Sleep deprivation decreases the astrocytic glycogen content and is also a risk factor for delirium. Thus, the unavailability of astrocytic glycogen may induce or exacerbate a delirium episode. Aim: In this thesis project, we first aimed to investigate the role of astrocytic glycogen in delirium pathogenesis. Furthermore, we included a glucose treatment group to study if exogenous glucose replacement reverses the adverse effects of inhibition of glycogen degradation. Finally, we followed animals for one month to show if our model leads to late cognitive decline. Methods: Our study included 14 months old 74 male C57 mice. One week before the delirium model induction, an intracerebroventricular cannula was placed. The DAB+LPS group received 2µl of 5.9M DAB one hour before the intraperitoneal LPS (0.33mg/kg) challenge. The controls and LPS-only groups were injected with the same amount of sterile saline. Glucose treatment was done with 2mg/kg D-glucose with LPS injections and another dose after 2.5 hours. Open field, buried food, and Y-maze tests were conducted in the first 24 hours and repeated one month later with a novel object recognition test. Blood glucose, IL-1β, lactate, glucagon, insulin, amyloid β 1-41, and total and phosphorylated TAU levels were measured. Also, PAS staining was conducted to quantify glycogen, GFAP, and Neun immunofluorescence stainings for astrocyte and neuron numbers. Results: The DAB+LPS group show worse behavioral test performance at the first 3-6 hours of delirium model induction than the LPS-only group. And the glucose replacement mitigated the acute worsening due to DAB injection. The blood sugar was significantly lower in LPS treated groups than in controls in all the measurements up to 24 hours. Noteworthy, the solely DAB injection led to hyperglycemia in the 4th hour. The glucose replacement could not resolve but shortened the duration of LPS-induced hypoglycemia. The PAS-positive area was preserved in the DAB-only group. Moreover, not only the PAS-positive area was held, but the hippocampal lactic acid levels were also lower in the glucose treatment group. The plasma IL-1β levels were increased in the LPS-only group at the 24th hour. On the other hand, IL-1β levels were attenuated in all the DAB-received groups in the hippocampal homogenates. Finally, the GFAP expression in astrocytes was upregulated in the hippocampus and glia limitans except for controls. One month later, the DAB+LPS group showed cognitive impairments in memory tests compared to controls but not the LPS only or glucose treatment groups. We did not detect a significant decrease in the number of neurons (the percentage of Neun stained area), but they have a smaller hippocampus and an increased amount of Aβ 1-42 protein. Finally, the GFAP fluorescent intensity was still pronounced in the DAB+LPS group in glia limitans. Conclusion and Comment: This study demonstrated that inhibition of utilization of astrocytic glycogen increased the LPS-induced cognitive impairments in aged mice. One month later, the DAB+LPS group still had a worse cognitive profile than the controls, along with structural changes suggesting neurodegeneration. Glucose treatment reverses the DAB-induced cognition worsening in acute and chronic phases. Thus, the simultaneous presence of an inflammatory insult and glycogen-derived lactate insufficiency may lead to decompensation and permanent damage after a delirium episode.
Identification of novel clinical testing methods and sensor-based parameters for sensitive detection of gait and balance impairment in early multiple sclerosis
Gait and balance problems are considered to be rare in early multiple sclerosis (MS) as these problems can hardly be detected at this stage by using routine neurological examination. However, patients frequently complain of gait and balance problems in early MS, and these problems can be detected by digital analysis when challenging tasks are used. Moreover, quantitative sensor-based measurement methods have the potential for being used for following up of patients' annual progression. In this study, we aimed to define the sensor-based and clinical parameters and challenging task conditions that are sensitive for the detection of gait and balance problems in the early stages of MS. We designed a study protocol using APDM MobilityLab System in patients with MS. We grouped 56 patients into three subgroups, and 23 healthy people were gender and age-matched with the early stages of MS group. Patients and the healthy control group performed normal speed walk, The Timed 25-foot walking, tandem walk, and quiet stance for 30 seconds in several balance tests such as Clinical Test of Sensory Interaction and Balance, Modified Balance Error Scoring System, Tandem Stance with APDM OPAL sensors. Patients also completed several patient-reported outcome measures (PROMs), such as the 12-Item Multiple Sclerosis Walking Scale (MSWS-12), The Upper Extremity Functional Index (UEFI), and The Modified Fatigue Impact Scale 5-Item (MFIS-5), The EQ-5D-3L and The Beck Depression Inventory (BDI). We examined lower extremity muscle strength, spasticity, and upper extremity function with the 9 Hole Peg Test (9-HPT) as well as SARA and SPRS scales. There were significant differences in selected balance and gait parameters, MSWS-12, UEFI, and MFIS-5 between mild, moderate and severe affected MS groups. We found that tandem walk and normal stance are not sensitive tests for discriminate an impairment in the early stages of the disease. Standing on foam was a sensitive method for detection of balance impairment in early MS, especially when performed eyes closed. One limb stance eyes closed stance was the most sensitive challenging task to observe difference between groups. We found that even though patients could perform all the tasks above, there is a significant difference in many sensor-based gait and balance parameters during the normal speed walk, T25FW, tandem walk and quiet stance tests between the healthy controls and early MS patients, pointing out to their significant potential to be used as biomarkers for detecting disability since the earliest stage of MS.
Investigation of effects of Brimonidine tartrate loaded LMSC cells on in vitro injury model of neuron cells
Brimonidine tartrate (BT), with a proven neuroprotective effect, is an eyedrop that lowers intraocular pressure by functioning as a selector alpha-2 adrenoreceptor agonist. Although it is frequently used in glaucoma, there is no information on its effects on limbal mesenchymal stem cells (LMSCs) which reside in the corneoscleral part of the eye and have important roles in the support of the corneal surface. BT is a promising agent with neuroprotective effectiveness in müller cells, retinal epithelium cells and retinal ganglion cells (RGCs). The aim of the study was to determine the effects of Brimonidine tartrate loaded LMSC cells on in vitro injury models of neuron cells. LMSCs were isolated from corneoscleral rims and tissue explants were cultured for 3 weeks in Matrigel-coated plates. After checking characterization and their differentiation abilities stem cells are stored in order to use in further experiments. The optimum BT dos was determined with CTG cell viability assay. The role of BT treatment in the regulation of LMSC proliferation via which cellular signaling mechanisms was determined by immunofluorescence staining of the Ki67, the scratch assay, ROS assay, and RT-q-PCR. Also, the effect of BT-loaded LMSC on H2O2 injured primary hippocampal cells was shown with the expression of inflammatory genes upon co-culture experiments. BT and LMSC can be used for therapeutic purposes for the optic nerve injury, glaucoma model, and RGCs degeneration through their neuroprotective potentials. From this point of view, we hypothesized that intravitreally injection of Brimonidine tartrate-loaded limbal mesenchymal stem cells might be used as a protectant against cell death during recovery of retinal disorders Keywords: brimonidine tartrate, limbal mesenchymal stem cell, primary hippocampal cell, co-culture
Immune functions of human brain pericytes and fibroblasts during neuroinflammation
Neuroinflammation, directed by microglia and astrocytes or arising as peripheral leukocyte infiltration, has adverse consequences for brain activity and is present in most neurological disorders. Mural cells (pericyte and smooth muscle cells) and perivascular fibroblasts (PVF) around them are present in the structure of CNS microvessels. These cells have important roles in BBB formation and CNS immune homeostasis. The unique perivascular position of pericytes makes these cells ideally localized to check several aspects of the CNS immune response. Under normal conditions, peripheral immune cells (lymphocytes and macrophages) do not pass into the parenchyma, during neuroinflammation; the blood-brain barrier (BBB) is crossed as a result of the infiltration of these cells into the CNS. Pericytes and other perivascular cells are highly likely to contribute to the immune-related diseases. However, the exact contribution of these cell types to is not yet known. In the light of recent studies, we can say that pericytes are very sensitive cells against CNS inflammation. What is not yet known is how these cells interact with leukocytes during neuroinflammation, how they affect neuroinflammation and how they are affected. This is an important area to be explored. Recent studies have also shown that perivascular fibroblasts are also present in perivascular space and, like pericytes, they are PDGFRβ and CD13 positive. These features make it difficult to distinguish between fibroblasts and pericytes in vascular pathology studies. In this project, we aimed to examine the roles of brain vascular pericyte and fibroblast cells in CNS inflammation. For this purpose, we stimulated the human brain primary pericyte and fibroblast cell lines with certain cytokines, and then examined the inflammatory gene expressions and protein expression changes. In addition, we conducted a chemotaxis experiment to explore the pericyte-macrophage and fibroblast-macrophage interactions. Taken together, the data defines an extensive and unappreciated contribution of brain pericytes to neuroinflammation. Since neuroinflammation occurs in almost all neurological disorders, targeting different approaches of pericyte-mediated immune responses may offer therapeutic ways for the treatment or prevention of several neurological conditions.
Neuroprotective effects of n-acetylcysteine in an acute model of LPS induced neuroinflammation
Neuroinflammation has been a major focus for researchers in the fields of neurology and neuropathology, as it had proven to play a key role in triggering the pathogenesis of various neurodegenerative diseases like Alzheimer's disease, where inflammation, among many other interconnected factors including oxidative stress and mitochondrial dysfunction plays a crucial role in the pathological feedback loop contributing to disease progression. Therefore, there is an inevitable need for implicating variable models of neuroinflammation, and it remains promising to investigate potential therapeutics, those of a natural origin in particular. LPS induced neuroinflammation is a widely used model in animal research and is able to mimic intrinsic neuroinflammatory states seen in the human CNS by activating microglia and initiating the release of several proinflammatory cytokines. Numerous studies have pointed out the relevance of glial cells, like astrocytes and microglia to neuroinflammation, thus to possibly linked protein abnormalities like Tau fibrillary tangles and amyloid plaques. Moreover, recent works are focusing on the microglial activation derived perineuronal net disruptions in neurodegenerative and neuropsychiatric disorders. These disruptions might hold the answer to understanding the vulnerability of particular neuronal types to neuroinflammation. In this project, we investigated the neuroprotective role of N-Acetylcysteine, a well-known natural antioxidant, on an acute, 10-day model of centrally injected LPS rats. Animal Groups consisted of healthy controls, LPS-induced animals, NAC treated LPS-induced and a group treated with an additional prophylactic dose of NAC prior to model induction. We assessed the anti-inflammatory potential of NAC in terms of neuronal loss, perineuronal net degradation, glial cell activation, and protein aggregations, in addition to cognitive decline, using immunofluorescence stainings, ELISA and a behavioral test for working memory. Our results indicated that NAC was able to reduce LPS-induced Aβ1–42 accumulations in the brain and spinal cord, as well as to halt neuronal loss and inflammatory astrocytosis in variable regions of the hippocampus. Moreover, NAC administration clearly protected PNN structures and alleviated PNN density loss associated with LPS-induced microglial activation in the prefrontal cortex. These results indicate the potential neuroprotective and anti-inflammatory impact of NAC on early neuroinflammation-associated CNS pathologies and highlight the need for more in-depth investigation regarding the neuro-protective role of NAC in models of inflammatory neurodegeneration.
The effect of depleting the CNS Border associated macrophages at pre-symptomatic stage of ALS on neuroinflammation, symptoms, and survival
Background: Amyotrophic lateral sclerosis (ALS) is an incurable motor neuron disease characterized by progressive muscle atrophy, including respiratory muscles. Muscle weakness, wasting, cramps, and fasciculations result from the loss of lower motor neurons. Additionally, patients with ALS may experience extra-motor symptoms due to neuronal loss in the frontotemporal cortex. Survival typically ranges from 2 to 4 years after disease onset, with respiratory failure being the primary cause of death. ALS, the most common motor neuron disease in adults, has an incidence of 2 per 100,000 and a prevalence of 5.4 per 100,000. Despite extensive studies on ALS pathogenesis, the exact mechanism of neurodegeneration remains unclear. Perivascular macrophages (PVMs) are myeloid cells residing in the central nervous system (CNS) and are part of the larger group of macrophages known as CNS border-associated macrophages. In a healthy state, these cells phagocytize harmful substances that infiltrate from the vasculature and regulate immune responses. However, in an inflammatory state, they contribute to increased vascular permeability and subsequent neuroinflammation. Dysregulation of the blood-brain barrier (BBB) occurs well before the symptomatic stage of ALS and influences PVMs, leading to increased reactive oxygen species (ROS) generation and BBB permeability. Transformed PVMs, in collaboration with other brain myeloid cells, initiate proinflammatory processes. Aim: Our aim is to investigate the contribution of PVMs to ALS pathogenesis and their impact on neuroinflammation. To achieve this, we depleted PVMs at the presymptomatic stage of ALS and evaluated microglia activation, astrogliosis, BBB disruption, symptoms, and lifespan in an animal model. Methods: PVM depletion was achieved by injecting clodronate-loaded liposomes or PBS-loaded liposomes (as a control) into the cisterna magna of SOD1(G93A) mutated rats, an ALS animal model. The study included 59 SOD1 mutated rats (both male and female). Preliminary studies involved nine rats, while the remaining fifty rats received either clodronate-loaded liposomes (depleted group) or PBS-loaded liposomes (sham group) via cisternal injection. The clodronate concentration in the suspension was 5 mg/ml. Rats were divided into three experiments: early single injection (day 80 after birth), late single injection (day 160 after birth), and multiple injections (administered at day 80 after birth followed by two additional injections every 20 days). Rats were monitored until reaching the humane endpoint, when the rats cannot turn back after being placed on their side, with weight measured twice a week and locomotor activity tested weekly to assess neuromuscular strength, motor coordination, and balance. The locomotor activity test comprised gait analysis, tail elevation, balance beam test, paw-grip endurance, extension reflex, rearing behavior, and ladder rung test for paw placement accuracy during walking. Validation studies included wild-type (WT) rats from a Sprague Dawley background for comparison of PVMs between SOD1 and WT rats, injection point validation, and confirmation of PVM depletion. FITC-Albumin injection into the cisterna magna of two WT rats confirmed appropriate delivery to the brain and spinal cord. Immunofluorescent staining of astrocytes, microglia, and CD206+ cells in obtained tissues from sacrificed animal models was conducted using GFAP, Iba 1, and CD206 primary antibodies, respectively. Statistical methods were employed to analyze behavior scoring and weight change, as well as staining results, between depleted and sham groups in the three experiments. Results: Preliminary studies on CNS tissues from SOD1 and WT rats revealed upregulation of CD206+ cells in various brain and spinal cord regions of SOD1 mutated rats. FITC-Albumin injection confirmed delivery to the brain and spinal cord, colocalizing with PVMs, validating the injection point for subsequent studies. Immunofluorescence staining with CD206 for brain and spinal cord sections of WT rats showed downregulation of CD206+ cells in all regions of the depleted group, with significant results for the spinal cord in the multiple injection experiment. Weight change analysis indicated a delayed presymptomatic stage in the depleted group across all three experiments, with significant results for the multiple injection experiment. Behavioral studies confirmed milder or delayed symptomatic stages in the depleted groups, particularly in the multiple injection experiment. Immunofluorescence staining for PVMs, astrocytes, and microglia revealed upregulation of all three cell types in the ventral horn of the lumbar section of the spinal cord in the depleted group compared to the sham group in both the late single injection and multiple injection experiments. Conclusion: This study demonstrated that depleting perivascular macrophages at the presymptomatic stage of ALS can delay disease onset, particularly in animals receiving repetitive doses of clodronate-loaded liposomes. Locomotor activity tests and weight change records showed a delayed and milder symptomatic phase in these animals. The upregulation of CD206+ cells, microglia, and astrocytes at the endpoint in the ventral horn of the depleted group appears to be associated with the anti-inflammatory phenotype of CD206+ cells, astrocytes, and microglia, correlating with improved motor behavior in this group.
Butyrylcholinesterase as a potential depression biomarker: Insights from a translational study
Major depressive disorder, a prevalent psychiatric disorder, significantly impacts quality of life. Although several biological pathways and related biomarker candidates try to explain its complex pathomechanism and assess objectively its diagnosis and onset, biomarker research in depression is still in infancy. Recent studies showed that depression may be influenced by dysregulation of cholinergic transmission. Within these findings, while the role of acetylcholinesterase is commonly studied in depression pathomechanism, the role of butyrylcholinesterase (BChE) remains unclear. Recently, we developed a BChE-activatable chemiluminescent molecular sensor (BCC) for real-time visualization of BChE activity, demonstrating efficiency in vitro and in tumor-bearing mice. In this translational study, we employed BCC to investigate the association between BChE activity and depression. We first assessed BChE activity in patients with depression (32 unipolar depression, 20 bipolar disorders with depressive episodes) compared to healthy controls (n=48) and reassessed changes with respect to remission (n=15). Second, we evaluated BChE activity in rats exposed to chronic unpredictable mild stress (CUMS), CUMS with concurrent fluoxetine treatment, and controls. Lastly, we established cell models for psychological stress by mimicking the hypothalamic-pituitary-adrenal (HPA) axis outcomes with 200µM corticosterone for 24 hours and the sympatho-adrenomedullary (SAM) system outcomes with 1mM norepinephrine treatments for 24 hours and assessed their BChE activity compared to controls in PC-12 Adh cell. Results indicated that individuals with depression exhibited significantly lower BChE activity compared to controls (p<.001), with increased activity correlating with remission (p<.001). Rats exposed to CUMS showed a significant decrease in BChE levels (p=.011), while fluoxetine treatment showed an increasing trend but could not achieve significance (p=.345). Additionally, BChE activity significantly decreased with corticosterone exposure (p=.002) and increased with norepinephrine exposure (p=.002). Subsequent, 5µM fluoxetine treatment cell exposed to those psychological stresses showed increased BChE activity (p=.002 for both). This translational study demonstrates a decrease in BChE activity in both clinical populations and chronic stress animal models, and psychological stress model established cell models, with levels reversing upon symptom alleviation. Our findings ultimately suggest that BChE activity can be a promising biomarker for depression diagnosis and treatment outcome.
Comparative analysis of the molecular, spatial, and functional domains of vertebrate habenula
The habenula (Hb) is a diencephalic brain region implicated in adaptive behaviors and neuropsychiatric disorders. Two main Hb subdivisions, the lateral habenula and medial habenula, have been shown to play different roles in diverse behaviors, ranging from classical and operant learning to the prediction of outcomes, fear, addiction, and social interactions. However, our understanding of cytoarchitecture and topography of the vertebrate Hb, as well as how different Hb microcircuits are organized across species, remains limited. In this study, we utilized a combination of single-cell and spatial transcriptomic approaches across multiple species to investigate how habenular subdivisions are organized and how this organization compares across species in relation to Hb function. First, we demonstrated that habenular cell types are relatively conserved across species from fish to mice, with some exceptions. Subsequently, employing spatial transcriptomics at subcellular resolution, we identified numerous topographically organized subregions within the adult zebrafish and mouse Hb. Many of these subregions were found to be shared between both species. We also observed that while zebrafish Hb is known to be highly asymmetric across hemispheres, several habenular subdomains remain symmetric, resembling those of mouse Hb. Similarly, though the mouse habenula is traditionally considered highly symmetrical across hemispheres, we observed a few mouse Hb subregions with prominent asymmetries. These results suggest that the asymmetry of the vertebrate habenula exists on a continuum across species. Moreover, vertebrates share many cytoarchitectural similarities that are topographically organized. Our ongoing investigation aims to elucidate how the molecular topography of the zebrafish Hb relates to its functional architecture.
Investigating oligodendrocyte myelin glycoprotein as a novel autoantibody candidate in demyelinating disorders
Over the past decade, increasing studies of autoantibodies associated with inflammatory disorders of the central nervous system (CNS) have further expanded the spectrum of demyelinating diseases. The discovery of anti-AQP4 and anti-MOG antibodies has remarkably enabled differential diagnostic criteria formation for patients with Neuromyelitis Optica Spectrum Diseases and MOG-related Antibody Disease. Despite this, most patients in that spectrum are still either undiagnosed or misdiagnosed due to their atypical features, and the actual target of autoimmune responses is unknown. Associating relevant patients with novel autoantibodies to be discovered is crucial, particularly in the proper treatment decisions and showing improvement. Oligodendrocyte myelin glycoprotein (OMGp) is a promising autoantibody candidate because it is a glycoprotein explicitly expressed on the surfaces of CNS neurons and oligodendrocytes. In this study, the "live cell-based assay," a "gold standard" for numerous autoantibody detections, was first optimized and developed to detect anti-OMGp antibodies. Subsequently, the serum of 800 people, aged between 8 and 90, with a gender distribution of female: male with a 1.84 ratio were screened for anti-OMGp antibody positivity employing this test. The CSF of 86 patients out of these 800 people was also scanned using the same method. The cut-off value was determined using 30 healthy controls. While net positivity was detected in seventeen sera, all CSF samples were negative. All patients with positive anti-OMGp antibodies had negative anti-MOG and anti-AQP4 antibodies. The average age of positive cases is 46 (range 23-63), female-male ratio is 2.4. Atypical demyelinating traits were present in all positive patients except one. Some of those features were as follows: tumefactive lesion in five patients, brainstem lesions in eight patients, diffuse ADEM-like lesions in three patients, long segment transverse myelitis in two patients, and cortical lesion in three patients. Furthermore, in most positive cases, steroid response was limited during attacks, and treatments such as PLEX and IVIg were required. Thus, this study tested anti-OMGp antibodies in an atypical feature-rich demyelinating disease cohort for the first time in the literature; seventeen positive patients were identified. Atypical demyelinating disease features were detected in positive patients regarding clinical, radiological, and treatment response. Our findings indicate that anti-OMGp antibodies may cause a distinct disease entity and should be tested, especially in individuals with atypical demyelinating disease characteristics.
The genetic landscape of ALS/MND in Turkey and alsin protein-related motor neuron pathology in ipsc-derived cortical neurons
After Alzheimer's and Parkinson's diseases, Amyotrophic Lateral Sclerosis (ALS) is the third most common adult-onset neurodegenerative disease, characterized by progressive muscle weakness and atrophy due to the degeneration of both upper and lower motor neurons. ALS exhibits a broad spectrum of phenotypic variability and involves complex genetic factors. Approximately 10-15% of patients inherit the disease from their parents while the remainder appear sporadic. Monogenic mutations in various genes, particularly C9ORF72, SOD1, TARDBP and FUS, account for disease development in 70% of familial and 5-8% of sporadic cases worldwide, pointing to the strong genetic component in ALS pathophysiology. In the first part of this PhD thesis, the genetically heterogeneous, yet inbred Turkish population was investigated to explore and revisit the basis of ALS genetics. A cohort of 1200 index patients of Turkish origin were included in the study, 15% (176/1200) having familial ALS. Parental consanguinity was present in 14.1% (170/1200) of cases and in 26.5% (319/1200) of patients, the parents were from the same region. All patients were tested for C9ORF72 hexanucleotide repeat expansion. The HRE mutation was detected in 27% (47/176) of familial and 2% (23/1024) of sporadic cases. Further genetic analysis was conducted on 577 patients, using Next Generation Sequencing techniques. The most frequently implicated genes in the cohort were SOD1 (n=33), OPTN (n=18), TARDBP (n=10) and FUS (n=5), which, together with C9ORF72, explained 47% of familial and 4.7% sporadic cases. Additionally, 10% of the familial and 3% of sporadic cases were solved with rare ALS-associated genes, pointing to a strong locus heterogeneity among the Turkish cohort under study Genetic analysis in some families uncovered unique and previously unrecognized situations that diverge from the established inheritance patterns and phenotypic associations reported in other studies. These findings emphasize the significance of our research in revealing novel mechanisms and underscore the critical role of genetics in the pathophysiology of ALS. Homozygous loss of function (lof) mutations in the alsin Rho guanine nucleotide exchange factor ALS2 (ALS2) gene are responsible for three distinct juvenile motor neuron diseases: jALS, IAHSP and jPLS. The alsin protein, encoded by the ALS2 gene, contains three domains with putative guanine exchange factor activity for Ras superfamily GTPases. Disruptions in these domains have been shown to cause neuronal dysfunction, ultimately leading to neurodegeneration. In the second part of this thesis, a patient with a homozygous termination mutation in ALS2 gene was studied and the consequences of alsin lof in patient-derived iPSCs and induced cortical neurons were investigated. Our study revealed that alsin-deficient cell lines exhibit defects in endovesicular trafficking, along with significant impairments and delays in receptor-mediated endocytosis. Additionally, decreased activation of Rac1-GTPase and prominent morphological abnormalities were observed in these cells. This research is significant in presenting the alsin pathophysiology in patient-derived induced cortical cells for the first time.
The complex molecular landscape of Parkinson's disease in Turkey: Genotype-phenotype correlations in a potentially genetic cohort
Parkinson's Disease (PD) is the most common neurodegenerative movement disorder characterised by its cardinal motor signs, bradykinesia, rigidity, tremor, and postural instability. Since age is the significant risk factor, PD is expected to become a worldwide pandemic in 2040 because of rising life expectancy. The disease was considered as sporadic until the mutations in the SNCA gene were associated. Nowadays, it is known that 5-10% of PD cases can be genetically explained with monogenic inheritance. In this thesis, the molecular architecture of PD was investigated in the ethnically heterogeneous yet inbred Turkish population with a potentially genetic cohort comprising 195 index patients and 35 affected family members using state-of-the-art genetic technologies. Whole exome sequencing (WES) is a gold standard method to study PD genetics with a variable diagnostic yield that differs in distinct populations. In the framework of this thesis, WES revealed that 93 out of 230 patients have rare or novel variations in 27 different causative genes and/or known risk factors, GBA and GLUD2 genes. Seven out of 73 index patients were identified with oligogenic inheritance. Additionally, candidate risk factors, heterozygous PRKN/PINK1 and rare TENM4 variants, and the APOE E4 isoform were investigated in the thesis cohort. By re-annotating WES data and analysing two large data portals, AMP-PD and PPMI, ten possible candidate genes for PD were identified. Functional analyses will help to understand the accurate roles of these genes in the pathogenesis of PD. This thesis presents the distribution of mutations in PD-related genes in Turkey and demonstrates that the Turkish cohort under investigation represents with its specific features a mixture of European and Asian populations, further implicating a high gene/variant heterogeneity. The results of the thesis are expected to contribute to the knowledge about the genetic factors underlying Parkinson's disease in the Turkish population, paving the ways for accurate and early diagnosis and to the development of personalized treatments in the era of translational medicine.
The impact of non-alcoholic steatohepatitis on brain vasculature
Non-alcoholic fatty liver disease (NAFLD) and its more severe form, non-alcoholic steatohepatitis (NASH), are increasingly recognized as multi-system conditions with implications beyond the liver, including potential impacts on the brain. This study explores the relationship between NASH and cerebral vasculature using two different models in mice: the methionine- and choline-deficient (MCD) diet and carbon tetrachloride (CCl₄) injections. This thesis aimed to assess the effect of NASH on the blood-brain barrier (BBB) and perivascular fibrosis. Important differences were observed in the expression of CD13 and KDR in the MCD diet group, suggesting that NASH contributes to BBB disruption. Elevated LDL-H and LDL-C3 levels further indicated metabolic changes affecting brain health. However, liver enzyme markers like ALT and AST showed no significant changes, possibly due to the early NASH stage.. Additionally, increased perivascular pericyte activation, collagen IV, and fibronectin levels were noted, pointing to early BBB breakdown and fibrosis.This study highlights the complex relationship between NASH and brain health, emphasizing the need for further research to explore the mechanisms linking liver pathology to cerebral dysfunction.
Detection of suicidal ideation with machine learning using biopsychosocial and linguistic correlates
Suicide represents a global public health crisis, causing over 700,000 deaths annually. Traditional suicide risk assessment relies heavily on direct disclosure, which is often limited by stigma and shame. Individuals may deny suicidal ideation when directly asked by healthcare providers, with this rate reaching up to two-thirds in some studies. This dissertation presents three complementary machine learning studies that predict suicidal ideation without relying on directly suicide-related predictors (previous suicide attempts, explicit suicidal thoughts). This approach aims to overcome current assessment barriers while ensuring comprehensive coverage of dimensions of the biopsychosocial model. The first study used psychiatric symptom variables, the second study employed psychosocial factors outside of psychopathology, and the third study utilized variables obtained from linguistic analysis of autobiographical memory narratives cued by emotionally evocative words as predictors. In Study 1, an artificial neural network was trained using data from 924 university students with the DSM-5 Self-Rated Level 1 Cross-Cutting Symptom Measure, and external validation was tested with data from 361 university students. Study 2 examined 190 participants (clinical and control groups) using non-psychopathological measures including childhood adversities, attachment patterns, coping strategies, emotion regulation, and personality traits, with external validation on 84 participants. Study 3 investigated 190 participants' autobiographical memory narratives using Linguistic Inquiry and Word Count (LIWC-22) software with nested cross-validation. All studies employed explainable machine learning techniques (SHAP analysis) and multiple algorithms including neural networks, random forest, and support vector machines. Study 1 achieved AUC = 0.80 (external validation: 0.79), identifying personality functioning, depressed mood, and anxiety as top predictors. Study 2 demonstrated superior performance with AUC = 0.878 and F1 = 0.819, maintaining strong external validation (AUC = 0.791, F1 = 0.549), with loneliness as the strongest predictor alongside protective effects of conscientiousness and extraversion. Study 3 achieved the highest discriminative performance (AUC = 0.908, F1 = 0.727), revealing emotion-specific linguistic patterns including protective effects of impersonal pronouns in fear contexts and cognitive mechanisms in positive emotional memories. This dissertation demonstrates that suicidal ideation can be effectively predicted across multiple levels of the biopsychosocial framework without relying on direct suicide-related disclosure. The convergence of interpersonal disconnection as a critical factor across Studies 1 and 2, combined with Study 3's identification of cognitive processing patterns, provides comprehensive insights into suicide risk mechanisms. The performance hierarchy (linguistic analysis > psychosocial factors > psychiatric symptoms) suggests that novel approaches capturing complex behavioral patterns may offer superior predictive capability. These findings support the development of interpretable screening tools using multiple data sources. These findings demonstrate the importance of developing interpretable screening tools using multiple data sources. These tools can strengthen clinical assessment by reducing self-report limitations and contribute to early detection and prevention of suicidal behavior.
EML1'in mikrotübül organizasyonu ve hücre bölünmesindeki düzenleyici rolü
Microtubules and microtubule-associated proteins (MAPs) are crucial for regulating diverse cellular processes, including intracellular transport, spindle formation, and cell division, all of which are critical for ensuring proper brain development and cortical organization. Among these, EML1 is a MAP that has been associated with subcortical heterotopia, yet its molecular role in microtubule organization and the consequences of disease-associated mutations remain incompletely understood. To investigate the regulatory role of EML1, CRISPR-Cas9-mediated knockout in HeLa cells and Eml1 conditional knockout neural progenitors obtained from E14.5 mouse forebrain were used. Exogenous expression of GFP-tagged wild-type or disease-causing T243A mutant EML1 was employed to assess the impact of the mutation on microtubule binding and cellular phenotypes. A combination of microtubule pelleting assays, confocal immunofluorescence imaging, label-free quantitative proteomics, and live-cell imaging was applied to evaluate microtubule stability, MAP recruitment, spindle organization, and mitotic progression. Loss of EML1 resulted in a reduction of taxol-stabilized microtubules, an increase in soluble tubulin, reduced α-tubulin acetylation, and enhanced vulnerability to nocodazole-induced microtubule depolymerization. These changes were accompanied by diminished recruitment of other MAPs such as EML4 and SEPTIN2 to microtubules, despite unchanged total protein levels. EML1 was found to be required for EML4's association with the microtubule network; its absence led to a significant reduction in EML4 binding, potentially contributing to impaired microtubule organization and mitotic fidelity. Notably, mitotic abnormalities such as spindle disorganization and prolonged division time were rescued by wild-type EML1 but not by the T243A mutant, which exhibited impaired microtubule binding and aggregation. Cell cycle-specific proteomic analysis revealed that EML1 associates with partially distinct sets of proteins during interphase and mitosis, indicating dynamic regulation of its interactome throughout the cell cycle. In addition, NEK9, a mitotic kinase not previously reported as an EML1 interactor, was reproducibly identified in Eml1-GFP pull-down samples, suggesting a potential new association. Importantly, EML1 regulates the dynamic localization of EML4 during cell division. In EML1 knockout cells, EML4 shows aberrant accumulation on spindle and midzone microtubules, whereas Eml1-GFP rescue restores its normal distribution. Overall, EML1 is established as a central scaffold-like regulator of microtubule stability, MAP interactions, and mitotic organization. Loss or mutation of EML1 compromises cytoskeletal integrity and mitotic fidelity, providing mechanistic insight into the pathogenesis of EML1-related heterotopia and suggesting potential targets for therapeutic intervention.
Consequences of KIF13A and SLC49A3 variants in Brown-Vialetto-Van Laere Syndrome using patient-derived iPSCs and motor neurons
Motor neuron diseases (MNDs) constitute a clinically and genetically heterogeneous group of neurodegenerative disorders, characterized by the progressive degeneration of upper and/or lower motor neurons. This degeneration results in muscle weakness, paralysis, and premature death, as exemplified by amyotrophic lateral sclerosis (ALS). Brown–Vialetto–Van Laere (BVVL) syndrome is a rare childhood-onset motor neuron disorder and around half of the cases have been attributed to mutations in the riboflavin transporter genes SLC52A2 and SLC52A3. In the present study, we identified a family with BVVL syndrome negative for mutations in the riboflavin transporters. WES analysis revealed two novel candidate variants: 1) a homozygous single-nucleotide substitution in KIF13A (p. Glu1656Lys) and a heterozygous splice donor mutation in SLC49A3, a solute carrier gene with no prior OMIM association. To investigate their functional consequences, we generated patient-derived motor neurons from induced pluripotent stem cells (iPSCs) and performed molecular, cellular, and transcriptomic analyses. Overexpression assays in HEK293T and SH-SY5Y cells, as well as patient-derived motor neurons, revealed that wild-type KIF13A preferentially localized to dendrites, whereas the mutant variant exhibited reduced dendritic selectivity. Functionally, patient-derived motor neurons displayed significant reductions in neurite outgrowth, axonal elongation, and axonal branching. Transcriptomic profiling further demonstrated upregulation of developmental transcription factors and downregulation of genes involved in axonogenesis, presynaptic differentiation, and axon guidance, consistent with incomplete motor neuron maturation. Together, these results indicate defects in neuronal maturation and axonal elongation in BVVL, providing new mechanistic insights beyond riboflavin transporter deficiency.
Evaluation of paeonol as a neurorestoration agent in a rotenone-induced in vitro model of Parkinson's disease: Post-injury recovery of cell viability, migration, and pCREB signaling
Parkinson's disease (PD) is defined by progressive dopaminergic neurodegeneration involving a complex interplay of mitochondrial dysfunction, impaired redox homeostasis, and diminished cellular resilience. While most experimental models evaluate candidate agents in pre-treatment paradigms, clinically meaningful intervention requires the capacity to rescue already-injured cells. This study therefore investigated whether paeonol, a natural phenolic compound, could exert post-injury restorative effects in a rotenone-induced SH-SY5Y in vitro model of PD. A reproducible sub-lethal injury window was first established using MTT assays, identifying a rotenone paradigm (50 nM, 48 h) that induced significant but non-terminal metabolic suppression. To model a clinically realistic therapeutic scenario, paeonol was administered only after rotenone injury and washout. Cell viability and functional recovery were assessed using MTT and wound-healing assays; intracellular ROS was evaluated via DCFH-DA fluorescence; pCREB signalling was examined by immunofluorescence; and exploratory transcriptional changes in TH and SNCA were analysed by qPCR. Rotenone significantly impaired both cell viability and migration. Following washout, metabolic activity recovered spontaneously; however, paeonol post-treatment enhanced wound closure and restored pCREB signalling, indicating functional and molecular recovery beyond metabolic restoration.Contrary to classical expectations, rotenone did not elevate intracellular ROS; instead, total fluorescence was markedly reduced relative to controls, likely reflecting decreased cell density and metabolic suppression. Paeonol did not substantially modify ROS, suggesting that its restorative effects are not primarily mediated by bulk antioxidant activity. At the signalling level, rotenone markedly suppressed pCREB, whereas paeonol robustly restored pCREB expression (p < 0.0001), supporting a mechanism involving reactivation of pro-survival pathways rather than simple redox scavenging. Exploratory qPCR findings were interpreted cautiously due to methodological limitations and are presented as hypothesis-generating. Overall, paeonol demonstrates meaningful post-injury rescue effects, improving cellular viability, functional migration, and survival signalling in a rotenone-based PD model. These findings highlight paeonol as a promising modulator of cellular resilience and provide a strong rationale for further mechanistic and translational investigation.
SOX2 odak noktasında: SOX2 gen kopya sayısı varyosyonunun TCGA pancancer kümelerinde TP53 mutasyonu ile ilişkisi ve shiny uygulaması kullanılarak de novo SOX2 sentezi için kodon optimize tasarım
Recombinant proteins are crucial for diverse research applications such as biosensors and cancer studies. Proteins are engineered through de novo gene synthesis methods. Numerous tools and databases have emerged to facilitate the design of recombinant proteins, starting from the design of the gene sequence. De novo DNA synthesis enables the synthesis of custom-designed sequences, allowing codon optimization to enhance expression yield in heterologous systems. In cancer research, recombinant expression of proteins involved in tumorigenesis-related signaling pathways is employed for functional studies, potentially revealing new therapeutic targets. A notable example is the pivotal role of SOX2 expression in the formation of cancer stem cells (CSCs) across various cancer types. Previous studies highlight SOX2 expression functionally overlaps with TP53 expression on the PI3K/AKT signaling pathway. This association may stem from the p53-MDM2 interaction. This thesis investigates the association between SOX2 copy number gain and TP53 mutations within TCGA PanCancer cohorts. Fisher's exact test results reveal varying association, dependent on tissue type and specific driver mutations within each cancer type. The findings suggest the potential therapeutic relevance of SOX2 in cancer research. Furthermore, the thesis employs an in-silico approach to design de novo SOX2 synthesis, utilizing a novel shiny app that integrates codon optimization and primer design functionalities. The app enables simultaneous codon optimization for multiple expression systems and offers distance analysis through hierarchical clustering. Codon optimization feature provides control over the rate of replacement value for codon substitution which validated through a case study involving human insulin. Finally, app design set of overlapping primers with synchronized melting temperature to be used in PCR assembly for de novo SOX2 gene synthesis. Keywords: Recombinant Protein, Cancer, TCGA-PANCAN, SOX2, TP53, Association Analysis, Codon Optimization, PCR Assembly, Primer Design
CAP-RNAseq: Gen esansiyelliğine ve mRNA ve protein düzeyleri arasindaki uyuma dayalı RNA-seq veri kümeleme, annotasyon ve önceliklendirme için çevrimiçi bir platform
In recent years, there has been a remarkable growth in the application of RNA-seq in both clinical and molecular biology research contexts. The analysis and interpretation of these RNA-seq data demands a good knowledge of bioinformatics. Many different applications are available to perform the analysis, but more comprehensive applications are needed, especially for researchers without coding experience. Therefore, I developed an all-in-one novel RNA-seq analysis tool, CAP-RNAseq (http://konulabapps.bilkent.edu.tr:3838/CAPRNAseq/), which provide valuable analysis for co-expression cluster prioritization and annotation. CAP-RNAseq in particular performs clustering of the genes based on their expression patterns, annotates mirror clusters that display inverse patterns with a network-based visualizations before prioritization of clusters and/or genes based on "gene essentiality", protein levels and the degree of congruence between mRNA and protein levels of genes. Furthermore, for illustration of the use of CAP-RNAseq in this thesis, I reanalyzed a number of published RNA-seq datasets and identified novel pathways modulated by NTRK2 overexpression (GSE136868) in neural stem cells and also showed significance of the essential genes/pathways in senescent cell clearance focusing on NTRK2 (fibroblast; GSE190998) and THBD (Huh7, GSE228941) siRNA models. In addition, I analyzed our lab's novel RNA-seq data obtained from breast cancer cell lines in CAP-RNAseq; and the findings revealed a) the complex associations between steroid hormones; Drospirenone, Aldosterone, and Estrogen in hormone positive T47D and mineralocorticoid receptor-overexpressing MCF-7 cells; and b) significant differences in essential and non-essential gene expression of the isogenic MCF7 cells overexpressing wildtype or mutant TP53. I also studied a public breast cancer dataset (GSE201085) demonstrating CAP-RNAseq's ability to identify novel breast cancer markers exhibiting high mRNA-protein level correlations. In conclusion, this thesis not only demonstrates the use and power of CAP-RNAseq as a tool to identify essential genes and pathways by analyzing RNA-seq data, but also provides new insights into the roles of essential genes in glioma, senescence and breast cancer.
Yukarıdan aşağıya dikkat süreçlerinin eylem algısı ağı üzerinde etkisi
Action perception is one of the fundamental skills for survival and social interaction. In neuroscience literature, it is well-established that when an action is visually perceived, the Action Observation Network (AON) becomes active in the human brain. This network has three core brain regions: the posterior superior temporal sulcus (pSTS), parietal cortex, and premotor cortex. Recent studies in neuroscience have shown that action perception is not a passive process but is affected by top-down signals such as attention. In this study, we investigated the influence of attention on the AON by conducting a two-session fMRI experiment. The stimuli comprised eight videos of pushing actions, with each video featuring a unique combination of actor (female or male), effector (hand or foot), and target (object or human). In the active fMRI session, participants viewed the videos while performing three different tasks that directed their attention to distinct features of the action (actor, effector, target). In the passive fMRI session, participants viewed the same videos without performing any task. The data from the passive session was used to extract ROIs: pSTS, parietal, and premotor in each hemisphere. Univariate analysis, representational similarity analysis (RSA), and decoding analysis were performed. Univariate analysis showed that introducing attentional demands during video viewing elicited a significant increase in neural activity within both parietal and premotor cortices relative to passive viewing conditions. RSA results revealed significant correlations between neural activity patterns and task models across all ROIs, indicating top-down influence throughout the AON. Decoding analysis showed unique top-down effects in each ROI, depending on its hierarchical level and intrinsic selectivity. These findings demonstrate strong top-down modulation of the AON based on cognitive demands, highlighting the dynamic interplay of attention and action perception.
Farkli alt görevlerle ilişkili çalişma belleği ayri, müdahale etmeyen depolarda korunabilir
How can WM maintain more information when its capacity is only around 4 items? Here, we explore the possibility that information related to separate subtasks do not count towards this limit, perhaps, because they are maintained in non-interfering stores. Across the two experiments, we investigated if increasing the WM load related to one subtask interfered with the execution of a concurrent but distinct second subtask. In Experiment 1, participants first saw pictures that were to be kept in mind and used for a later subtask B. They then executed subtask A, while keeping in mind these subtask B pictures. Although subtasks A and B involved maintaining and updating identical sets of pictures, increasing the number of subtask B pictures did not interfere with subtask A execution, which was only affected when the number of pictures relevant to it was increased, suggesting that subtask A and B pictures were maintained in separate non-interfering stores. An objection might be that in Experiment 1, subtask B pictures were passively and not goal-directedly maintained. In Experiment 2, participants executed a more complex subtask that forced participants to maintain and update two separate sets of subtask B pictures while executing subtask A and subtask A also involved WM maintenance and updating of identical pictures. We found that even here increased load of subtask B pictures did not affect subtask A performance. Thus, at least in some multitasking situations, information related to distinct subtasks can be maintained in separate non-interfering stores.
Dss kaynakli er stresin ire1 ve jnk sinyal yolaklarinin fare serebral korteksinde incelenmesi̇
Endoplasmic reticulum (ER) stress plays a critical role in cellular homeostasis and is implicated in various neurodegenerative diseases. The inositol-requiring enzyme 1 (IRE1) is one of the arms of the unfolded protein response (UPR), which is activated in the presence of ER stress. IRE1 pathway activates c-Jun Nterminal kinase (JNK) downstream under prolonged stress. This thesis explores the activation of the IRE1 and JNK signaling pathways in the mouse cerebral cortex following DSS-induced colitis, focusing on their roles as markers of ER stress in the context of the gut-brain axis. While DSS-induced intestinal inflammation and ER stress are well-established, neurological effects remain less understood. Employing a murine model, the study explored ER stress markers in the cerebral cortex resulting from intestinal pathology. Despite evidence of DSS-triggered systemic inflammation and ER stress in intestinal tissues, our study revealed no significant differences in the expression levels of IRE1, p-IRE1, or the p-IRE1/IRE1, nor in JNK, p-JNK, or the p-JNK/JNK between the control and DSS-treated groups. Additionally, these results are supported with correlational and linear discriminant analyses (LDA). These findings suggest that acute DSS-induced colitis did not elicit a detectable ER stress response in the mouse cerebral cortex under the conditions used. Possible explanations include tissue-specific reactions to the ER stress, transient activation of the IRE1-JNK pathway that returned to baseline by the time of analysis, or potential survivor's bias. Despite its limitations, this thesis provides a novel investigation into the effects of DSS-induced colitis on ER stress in the cerebral cortex.
Algısal karar verme süreçlerinin altında yatan nöral dinamikler: Biyolojik hareket yön ayrımı deneyiyle bir EEG çalışması
Algısal kararlar çevreyle olan etkileşimlerimizin temelinde yer alır. Bu karar süreçleri, temel varsayımı gürültülü duyusal kanıtın belirli seviyeye kadar biriktirilmesi olan modeller aracılığıyla incelenmektedir. Algısal kararların altında yatan dinamikler insanlarda da EEG aracılığıyla gözlemlenmiş ve bu olaya ilişkin potansiyel centro-parietal pozitiflik (CPP) olarak isimlendirilmiştir. Bu varsayımlar ve CPP çeşitli deneylerle doğrulansa da biyolojik hareket algısı bağlamında henüz geniş kapsamlı incelenmemiştir. Bu çalışmada, ekranda süregelen bir görsel uyaranın olduğu ve hedef uyaranlara kesintisiz bir şekilde geçiş yapıldığı bir tasarım kullanılmıştır. Bu deney dizaynı, yaygın olarak kullanılan rastgele nokta hareketi deneylerinden esinlenilmiştir. Bu bağlamda, karıştırılmış hareketi takip eden nokta-ışık uyaran şeklinde insan hareketi gösterimleri kullanılmıştır. Katılımcıların iki alternatifli zorunlu seçim görevinde yürüme yönünü tayin etmeleri beklenmiştir. CPP'nin kanıt birikiminden ortaya çıkan karar değişkenini yansıttığı, duyusal kanıtın gücüyle ölçeklenen bir artış oranı ve karar bildirme zamanına yakın bir ortak genlik seviyesine ulaşmasıyla gösterilmiştir. Ek olarak, CPP deney içerisindeki doğru ve geçersiz cevaplar arasında ayrım göstermiş, karar süresini tahmin edebilmiş ve difüzyon-sürüklenme modeli çıktılarından sürüklenme oranı parametresiyle pozitif yönde ilişkilendirilmiştir. Ayrıca, hedef uyaran öncesi dikkat seviyeleri ve biyolojik hareket algısına özgü sinyaller incelenmiştir. Hedef öncesi dikkatin, takip eden gelişmiş görsel işleme arabulucuğuyla karar verme süreci üzerindeki etkisi görülmüştür. Sonuç olarak, çalışmamız CPP hakkındaki önceki bulguları biyolojik hareket literatürüne genişletmiş ve algısal kararların altında yatan farklı dinamikleri ortaya çıkarmıştır.
Sacsin'in glial ara filament organizasyonu ve inflamatuar sinyal yolağındaki rolünün erken dönem zebrafish gelişiminde araştırılması
Autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS) is a rare neurodegenerative disorder characterized by early-onset ataxia, spasticity, and peripheral neuropathy. While ARSACS has been primarily studied in neurons, recent findings implicate glial cells in disease pathology. Sacsin, the protein encoded by the SACS gene and mutated in ARSACS, is shown to be expressed in both astrocytes and microglia while playing key roles in cytoskeletal integrity and cellular stress signaling. When adding the growing recognition of ARSACS as a disorder with neurodevelopmental components, investigating glial contributions to the disease pathogenesis during early development is becoming a requirement. This study aimed to investigate the impact of sacsin deletion on developmental and glial markers in zebrafish embryos and larvae, using a sacs-null mutant model of ARSACS. To this end, we quantified gene and protein expression profiles of sacsin and key glial markers across developmental time points (60–180 hours post-fertilization, hpf). RT-qPCR was used to assess the expression of sacs, s100b (astrocytic inflammatory marker), and aif1l (microglial inflammatory marker IBA-1), while Western blotting was used to examine protein levels of STAT3 (developmental marker), vimentin (early glial intermediate filament marker), and GFAP (astrocytic intermediate filament marker). Zebrafish sacs-null mutants showed a significant decrease in sacs mRNA expression only at 180 hpf, while the lack of earlier differences is possibly due to the stable mutant transcripts. Among glial inflammatory markers, s100b expression was significantly upregulated in sacs-null mutants; however, aif1l showed no genotype-dependent changes, reflecting a compensatory response of astrocytes that may even occur earlier than the microglial response. Additionally, no significant correlations were found between sacs and these glial inflammatory markers, indicating selective, possibly indirect, molecular interactions. Vimentin protein expression was significantly higher in sacs-null mutants, supporting the notion that sacsin loss disrupts intermediate filament dynamics, not just structurally, but in quantity. However, GFAP expression did not differ between genotypes, unlike the literature based on cellular imaging, suggesting the necessity of anatomical tissue-specific assays. Together, these results demonstrate that sacsin loss leads to selective and temporally defined alterations in glial development, particularly affecting cytoskeletal and inflammatory markers. The zebrafish model effectively captured these dynamics, validating its utility for studying glial contributions to early-onset neurodegenerative diseases. In conclusion, this study advances our understanding of glial dysregulation in ARSACS and underscores the importance of considering non-neuronal mechanisms in early disease progression. In future studies, tissue-specific analyses based on the imaging of glial cells in the central nervous system will be of critical importance for uncovering the molecular foundations of glial involvement in ARSACS and related disorders.
Çoklu görev sırasında farklı görevlerin çalışan bellek yükünün etkileri farklılaşabilir: Bir fMRG çalışması
Multiple demand (MD) regions are well-known for their activation pattern in task-related events and are especially sensitive to working memory load (WM) conditions. Different WM loads deplete varying amounts of WM capacity and may lead to interference. However, whether MD regions are sensitive to precision in addition to cognitive load still remains unclear. This thesis investigates whether challenging multitasking induces interference and whether brain responses to demanding tasks are modulated by precision. Thirty healthy participants (M = 27.1) underwent two fMRI runs and completed a hierarchically nested visual WM task, where task A's items were maintained during task B under alternating high and low WM loads. Parametric modulation, whole-brain, and region-of-interest (ROI) analyses were performed. Results showed that MD regions were activated during the encoding phase of task B, whereas task A exhibited a deactivation pattern. However, tasks were not differentiated during their corresponding retrieval steps. Brain regions correlating with performance accuracy also did not differ. The Default Mode Network (DMN) showed sustained deactivation during recall, regardless of task type, indicating domain-general suppression mechanisms. These findings support hybrid WM models that allow flexible control mechanisms and discrete capacity limits. The MD network appears to adjust engagement depending on task context and phase, aligning with hierarchical models. Task-specific encoding but shared recall dynamics suggest that while storage may be selectively distributed, retrieval relies on generalized control. This enhances understanding of cognitive control–memory interactions and highlights the need to examine individual differences to inform interventions for WM-related disorders.
Motivasyonel koşulların zaman persepsiyonu üzerindeki etkisi bir tersine öğrenme paradigmasında
Time perception, a fundamental cognitive process, can be influenced by various external and internal factors such as adaptability, attentional control, and reinforcement learning. Understanding how motivation affects time perception is important in dynamic learning environments where participants must adapt to changing conditions and make timely decisions. To study the influence of food manipulation on participant's time perception, three experiments were designed in current study which involved reversal learning. Two food conditions; experimental and control. In one condition, a calorie-rich snack was provided at 10-minute intervals during breaks. No snack was offered in the control condition. The first experiment was conducted in a basketball court, where participants were rewarded by scoring the right basket. After a fixed interval, the basket changed, and scoring on the other side became correct. In the second experiment, there were two darts boards and participants threw darts at one of the two dartboards. After a fixed interval, the dartboard switched, and scoring on the other side became correct. In the third experiment, the task was to build houses of cards, with the correct table switching back and forth after a fixed interval. In all three experiments, participants were paid to score on the correct side. Our results suggest that food motivation influenced participant's time perception in the cards-based experiment but there was no effect of food manipulation on time perception of participant's in basketball and darts throwing experiment. Task difficulty affected time perception significantly and proficiency in the specific task being performed also affected time perception in all experiments. The interactions of food condition, proficiency and satiety was also checked which shows that even though food motivation was not significant in first two experiments, its interaction with other factors can be significant. This study extends the research on reversal learning and contributes to the understanding of various factors influencing human cognitive processes. It contributes to understanding how food manipulation interacts with adaptive decision-making and time perception under changing task requirements.
Düşüncenin bedensel haritaları: Düşünceler kafanın farklı bölgelerinde toplanır
The mind and body are tied together; research on embodied cognition shows that people feel the Self and emotions in the body. They are processed in the mind and perceived through the body template. Building on this notion, we asked whether thoughts are experienced in the body template similarly and whether different kinds of thoughts are located in different bodily regions. In a behavioral experiment, we gave participants short scenarios in five different categories and asked them to imagine/think about those scenarios. Then they were asked to locate their thoughts and images on head and full-body templates. We compared within-category distances to between-category distances, examined each category pair for distinctness, and checked whether any category stood out for being especially tight and consistent. Results showed that people do locate their thoughts on their body template, and different thoughts are located differently from each other. Specifically, thoughts on mental arithmetic and auditory imagery formed distinct groups on the head template compared to other categories. In a second behavioral experiment, we replicated the task with blind and deaf individuals and found that distinct mapping patterns for different thoughts exist in blind individuals, but not in deaf individuals. When compared to other categories, auditory thoughts in blind individuals revealed a very clear and distinct pattern, while visual imagery in deaf individuals showed a distinct localization that differed from other thoughts. Taken together, our findings show that thoughts are located in the body template, with different thoughts located distinctly from each other, and that these localizations are affected by visual and auditory loss.
Şizofreni genetik riskinin adolesan gelişimi boyunca üçlü ağ modeline haritalanması: Boylamsal bir çalışma
The Triple Network Model, which includes the Default Mode Network (DMN), Frontoparietal Network (FPN), and Salience Network (SN), is a core model for schizophrenia and explains all the positive, negative, and cognitive symptoms. Many studies demonstrated the importance of the Triple Network Model in schizophrenia; however, no longitudinal study has yet examined the between‑network connectivity among the three Triple Network systems in healthy adolescents. To address this gap, we conducted a one‑year investigation of between‑network functional connectivity during typical development and assessed how genetic liability to schizophrenia moderates these changes. In this thesis, 89 pairs of twins and siblings were recruited and underwent resting‑state fMRI at baseline and one‑year follow‑up, with ROI‑to‑ROI functional connectivity values computed separately for each session. Participants also completed the CAPE‑42 to assess subclinical psychotic symptoms and provided blood or saliva samples for genotyping to derive schizophrenia polygenic risk scores (PRS‑SCZ). Using linear mixed‑effects models, we evaluated (1) whether significant longitudinal connectivity changes occurred, (2) whether PRS‑SCZ moderated these longitudinal changes, and (3) whether connectivity changes were associated with subclinical psychotic symptom scores (total, positive, negative, and depressive). We found no significant time effect from baseline to follow‑up; however, PRS‑SCZ significantly moderated connectivity trajectories, with higher PRS‑SCZ associated with greater increases in FPN–SN, DMN–SN, and DMN–FPN connectivity. Specifically, PRS‑related enhancements were observed in the connections between left lateral prefrontal cortex (LPFC)–left supramarginal gyrus (SMG), left posterior parietal cortex (PPC)–right rostral prefrontal cortex (RPFC), right PPC–right SMG, left anterior insula (AI)–left lateral parietal cortex (LP), left PPC–left posterior cingultae cortex (PCC), and right PPC–right PCC. None of these PRS‑modulated connectivity changes, however, were significantly associated with changes in subclinical symptom scores. The PRS‑SCZ–related connectivity increases paralleled patterns observed in patients and other high‑risk groups, suggesting that these alterations may reflect early neurodevelopmental mechanisms underlying schizophrenia pathology before the emergence of clinical symptoms. These findings highlight the potential of Triple Network Model functional connectivity as an early biomarker of schizophrenia risk and underscore the need for extended longitudinal follow‑up to capture non‑linear developmental trajectories.
Eş seçimi bağlamında kıskançlık ve zihinselleştirmenin etkileşimi
Mate choice is a multifaceted decision mediated by mentalization and jeal- ousy, etc. Jealousy is conceptualized to alter attentional bias toward con- textual cues and recalibrate partners' valued traits. This thesis examined whether a jealousy induction, compared to a control group, alters perspec- tive taking, jealousy state, attentional bias, and preferred traits ranking. 48 participants completed: a dot-probe (image/words), MJS (Multidimensional Jealousy Scale), DMASC-MC (Double Movie for the Assessment of Social Cognition — Multiple Choice), a 12-item trait ranking, and the Draw E task. Drawing E was modeled using logistic regression. By filtering out in- valid/missing data, the analytic numbers were: MJS and trait-rating n=48 (Control=24, Experimental=24), DMASC-MC n=46 (Control=23, Experi- mental=23), and dot-probe n=45 (Control=21, Experimental=24). Results and discussion: for both Dot-Probe and DMASC-MC: baselines controlled, groups did not differ at post, rather pre-test covariations were highly predictive: Dot-probe: F (1,42) =0.21, p=.652; covariation F (1,42) =19.25, p<.001. Baseline total RTs were comparable (0.776 vs. 0.832 s); DMASC-MC: using ANCOVAs, (post Group + pre), no sig. between- groups posttest (Cognitive: F (1,43) = 0.05, p=.819; Count "N-Correct": F (1,43) = 0.56, p=.460); covariate F (1,43) = 20.97, p<.001). MJS: no discernible between group changes (Total t(46)=-1.05, p=.300, g=-0.30; Be- havioral t(46)=-0.28, p=.784, g=-0.08; Cognitive t (46) = -1.89, p=.065, g=-0.54; Emotional t(46)=-0.08, p=.939, g =-0.02; ). Trait-rating: Trait, Session, and Trait×Session, were significant (Trait: F (3.46,159.16) =155.59, p<.001, ω2≈.67; by Session (F (1,46) =145.94, p<.001, ω2≈.19); with change over Session varying by Trait (F (2.50,114.77) =162.81, p<.001, ω2≈.47)); Group showed no effects. Logistic regression: Age was a positive predictor of self-oriented E. Also, in our logistic modeling, the direction of writing, age, sex and their interaction improved the fitness of the prediction of self- oriented (∆χ2(4)=12.30, p=.015 (McFadden R2=.27; Nagelkerke R2≈.37; Tjur R2≈.33)). The priming manipulation did not yield condition-specific re- sults on the battery tests, suggesting more intense/prolonged manipulations. Nevertheless, the significant logistic results of age underpin a trajectory of intrapersonal differences in perspective-taking, offering further studies.
Yapılı çevrelerde huşu: Mimari stil ve bakış açısının görsel tanıma belleğine etkileri
In recent years, there has been a growing interest in neuroarchitecture. This emerging field integrates neuroscience, psychology, and architecture to investigate the built environment's impact on cognition, emotion, and behavior. Aesthetic and emotional responses to architecture, especially the experience of awe, are becoming more recognized as significant factors influencing cognitive processes, including attention, memory, and decision-making. However, the association between awe, components of architecture, and perceptual perspective is still insufficiently examined. The present study investigated the interactions among awe, architectural style, and viewing angle on visual recognition memory in built environments, employing a 2 (awe: awe-evoking vs. non-awe-evoking) × 2 (style: traditional vs. modern) × 2 (angle: eye-angle vs. low-angle) within-subjects design. Thirty-six participants participated in a visual recognition memory task involving real-life architectural imagery. Analyses of recognition sensitivity (d′) indicated that traditional architecture revealed higher recognition sensitivity than modern architecture, and eye-angle perspectives yielded better sensitivity than low-angle perspectives. Awe alone did not yield a significant main effect; however, it interacted with architectural style, diminishing discriminability for modern architecture while having no effect or a slight improvement on traditional architecture. Analyses of the response criterion (c) revealed that awe, style, and angle independently modulated decision thresholds, with awe‐evoking images eliciting a more liberal bias. This study contributes to the existing literature by establishing the contextual restrictions of awe's mnemonic effects, indicating that architectural stimuli's perceptual and stylistic characteristics moderate its influence on memory. The combination of affective science, neuroarchitecture, and signal detection theory provides a new framework for analyzing the interplay between aesthetic and perceptual factors in shaping memory within the built environment.
Ko-ekspresyon çiftleri ve modülleri (CoEX-PM): Bir Shiny aplikasyonu ve kromograninler üzerinde bir örnek olay incelemesi
Gene expression signatures have been proved to be effective biomarkers of tumorigenesis and metastasis especially when alternative methods are inconvenient or ineffective. Nevertheless, handling very large datasets obtained via high-throughput protocols to extract gene expression signatures may prove challenging. A great number of software packages that facilitate such analyses have been written in R programming language are publicly available and free. However, the relatively steep learning curve that is required to use R proficiently prevents the utilization of these packages. I have developed the Shiny application Co-expression Modules and Pairs (CoEX-PM) using R programming language and the R package shiny. The CoEX-PM application handles human Affymetrix microarray data and enables users to generate pairwise correlation plots, conduct meta-correlation analysis with user-selected GEO datasets along with co-expression module generation by WGCNA program for genes of interest. The CoEX-PM application provides the user with a GUI, therefore, does not require any coding knowledge to perform the analyses. Pheochromocytoma (PCC) and neuroblastoma (NB) are neural-crest derived tumors, common in adults and children, respectively and are both associated with high-rate of morbidity and mortality. In addition, both tumor types display neuroendocrine tumor (NET) characteristics. Chromogranin A (CgA) has been linked with NETs as a moderately sensitive and non-specific tumor marker. The chromogranin family consists of up to seven members, three of which are chromogranin (CgA), chromogranin B (CgB) and secretogranin II (SgII) or occasionally named as chromogranin C (CgC). However, it is not known whether chromogranin/secretogranin family members are differentially co-expressed in PCC and NB. Here, I investigate the degree of co-expression in gene networks by analyzing gene expression signatures of the chromogranin/secretogranin paralogous gene family using CoEX-PM application on neuroendocrine tumor datasets. The findings indicate the presence of concise and highly co-expressed functional components in PCC and NB driven by chromogranin expression signatures.
Kontrast ve büyüklüğün hareket algısındaki rolü: Kortikal bölge v1 ve MT'deki çevre ve merkez etkileşimlerinin fMRI ve davranışşal deneylerle incelenmesi
Behavioral experiments have demonstrated that observers' ability to discriminate the drift direction of a grating improves as its size increases if the grating has a low contrast, and deteriorates if it has a high contrast. It has been proposed that receptive field organization in middle temporal (MT+) visual area underlies this counter-intuitive perceptual effect. Supporting evidence for this proposal has been provided in literature. However, previous studies have not unequivocally showed that MT+ is the sole area whose activity underlies the perceptual effect. Here, we investigate the activity patterns of primary visual cortex (V1) and middle temporal (MT+) in response to drifting Gabor patches in differing size and contrast levels to elucidate the neural region involved in size-contrast interac- tion in motion perception. We first replicated the findings in the literature with a behavioral experiment, where small or large (1.67 and 8.05 degrees of visual angle) drifting gratings with either low (2%) or high (99%) contrast levels were presented at the periphery (centered 9.06 degrees of visual angle to left and right of fixation). We measured the duration thresholds (79%) for accurately discrim- inating the drift direction of gratings for eleven participants using an adaptive staircase and two-alternative forced choice (2AFC) design. In line with previous literature, we observed that increasing the size of the low-contrast stimuli resulted in decreased discrimination threshold, while for high-contrast stimuli, increasing the size resulted in increased discrimination threshold. In the second stage of the study, six observers participated in a block design fMRI study with the same spatial configuration and contrast levels used in the behavioral experiment. We first identified the region of interests (ROI) for visual area V1 and MT+ separately for all participants. Then, we identified a "sub-ROI" that corresponds to the region that was selectively responsive to the small sized stimuli (1.67 degrees) using an independent localizer. With this setup, we allowed for both large and small sized gratings to stimulate the sub-ROI throughout the entire scan. Therefore, changes in Blood Oxygenated Level Dependent (BOLD) response at the sub-ROI in response to large compared to small sized gratings indicated the influence of the surrounding region to the center of the gratings. In area MT+, we observed that increasing the size of the grating increases the BOLD activity if the stimuli have low contrast, compared to high contrast. In other words, surrounding region had a facilitative influence to the group of MT+ neurons encoding the center of the stimuli if the stimuli had low contrast. This neuronal facilitation observed with the neuroimaging data explain the enhance- ment of the performance with increasing the size of the low-contrasted stimuli observed at the behavioral experiment. In V1, however, increasing the size of the high-contrasted gratings increased the BOLD activity, compared to activity evoked by increasing the size of the low-contrasted gratings. On the whole, we show that center-surround interaction in V1 and MT were differentiated in re- sponse to peripherally viewed drifting Gabor patches at differing contrast and size levels, hence we provide further evidence that the perceptual size-contrast interaction effect is likely to originates at cortical area MT+.
Sağlıkla ilgili bilgiler üzerine yorumlama ve dikkat yanlılıklarının karşılıklı etkileri
tive processing biases to health-related information have been endorsed to be present in patients who are suffering from medical diseases. Attentional bias is one of the cognitive processes which facilitates the detection of health-threatening information. Interpretation bias is the other cognitive mechanism that makes patients attribute catastrophic meanings to ambiguous bodily sensations. Despite the literature demonstrating that attentional and interpretation biases increase negative emotions and challenge patients for adaptation to their health condition, the link between these two biases has remained unclear. While some theories claim that attentional and interpretation biases are interrelated, some state that they might be orthogonal components of cognitive processing. Therefore, this thesis aimed to investigate the relationship between interpretation and attentional biases to health-related information by modifying interpretation bias and studying its effect on attentional bias. One hundred undergraduate students who lack any medical or psychological problems were randomly allocated to Main-Modification or Placebo-Modification groups. All participants were asked to complete a battery of questionnaire including health anxiety inventory, Beck depression inventory, and Beck anxiety inventory in order to control between-group differences regarding these constructs. As the pre-modification assessment, participants' interpretation and attentional biases to health-related information were respectively measured using the Modified Version of Online Interpretation Bias and Dot-probe tasks. Then, the Main-Modification group underwent Main On-line Negative Interpretation Bias Modification Task aimed to impose unsafe and threatening interpretations for ambiguous health-related scenarios. the Placebo-modification group completed Placebo On-line Negative Interpretation Bias Modification Task. The modification phase was followed by post-modification measurements. Results revealed that the participants in the Main-Modification group experienced more post-test interpretation bias indexed by Unsafe valence of interpretations for ambiguous health-related situations compared to the Placebo group. The Post-test between-group difference, however, was not significant for interpretation bias indexed by reaction time. Main negative interpretation bias modification succeeded to amplify attentional bias toward Ambiguous images in the Main group but Placebo modification did not do so. Unlike Placebo modification, Main modification increased attentional bias to Health-Related images as well. However, this increase was not statistically significant. These results can be considered as the pieces of evidence endorsing the idea that interpretation and attentional biases are interrelated aspects of cognitive processing. Repeated exposure to negative interpretations for health-related situations might increase patients' accessibility to negative meanings for interpreting further ambiguous health-related situations. In turn, the new negative meanings might facilitate detection of ambiguous bodily sensations or another health-related information known as attentional bias
FMRG kan oksijen seviyesine bağımlı (bold) sinyalin insan birincil görme korteksinde zamansal ve konumsal nonlineerlikleri
It is generally assumed that fMRI BOLD response (i.e., functional magnetic resonance imaging blood-oxygen-level-dependent signal) is linear and time-invariant. In this study, we investigated spatial and temporal nonlinearities in fMRI BOLD response at different flickering durations (nearly instantaneous and 1 s). We presented participants two successive flickering checkerboard wedge stimuli with stimulus onset asynchrony (SOA) of 0 s, 0.5 s, 1.5 s, and 6 s. The spatial locations of the stimuli were categorized as the same location in the same hemifield, adjacent locations in the same hemifield, and between hemifields. We demonstrated that fMRI BOLD response behaves nonlinearly when the successive stimuli spatially and temporally were close to each other for both flickering durations. Nonlinearity between the successive stimuli was the highest for the same location in the same hemifield, higher in adjacent locations in the same hemifield, and the lowest in between hemifields. In addition, nonlinearity at the shorter SOAs (0 s, 0.5 s, and 1.5 s) was found to be higher than nonlinearity at SOA 6.
Korku duygusu içeren görsel uyaranların popülasyon alıcı alan tahminleri üzerindeki etkisi
Previous studies showed that the content of stimulus might affect the results of population receptive field (pRF) estimation method [1, 2, 3]. In addition, emotion might modulate visual processing in humans by increasing BOLD activity [4, 5]. Taken together, the stimulus with emotional cue might affect the pRF parameters. To investigate the effect of emotion on visual processing, we used the population receptive field (pRF) method [6], with simultaneous wedge and ring stimuli rendered with scrambled, neutral or emotional images. Results showed that the pRF estimations were affected by the stimulus content in visual areas hV4 and V3A, as well as lower retinotopic regions: V1, V2 and V3. Moreover, we showed the emotional content of stimulus might lead to the increased pRF sizes as well as a shift in pRF centers toward the eccentric side. We argue that the increased pRF size and the pRF shift might be a result of emotional modulation of visual processing.
İnsanların performansını karşılaştırmak ve 3D-konvoleksiyonel nöral ağlarda dinamik pişirme kullanılan malzeme anlayışı
There are numerous studies on material perception in humans. Similarly, there are various deep neural network models that are trained to perform different visual tasks such as object recognition. However, the intersection of material perception in humans and deep neural network models has not been investigated to our knowledge. Especially, the importance of the ability of deep neural networks in categorizing materials and also comparing human performance with the performance of deep convolutional neural networks has not been appreciated enough. Here we have built, trained and tested a 3D-convolutional neural network model that is able to categorize the animations of simulated materials. We have compared the performance of the deep neural network with that of humans and concluded that the conventional training of deep neural networks is not necessarily giving the optimal state of the network to be compared to the performance of the humans. In the material categorization task, the similarity between the performance of humans and deep neural networks increases and reaches the maximum similarity and then decreases as we train the network further. Also, by training the 3D-CNN on regular, temporally consistent animations and also training it on the temporally inconsistent animations and comparing the results we found out that the 3D-CNN model can use spatial information in order to categorize the material animations. In other words, we found out that the temporal, and consistent motion information is not necessary for the deep neural networks in order to categorize the material animations.
Zebrabalığı (Danıo rerio) modelinde yetişkin nörogenezi ve astositlerin yaşlanmaya bağlı değişimleri
Brain aging is marked by a decline in cognitive abilities and associated with neurodegenerative disorders. In order to identify appropriate interventions to change the course of brain aging and age-related neurological disorders, we should first understand the normal age-related changes. Previous studies claimed that there was a correlation between cognitive capacities and number of neurons. However, recent studies have shown no statistically significant change in total neuron number during healthy aging. Therefore, further studies are required to understand the reasons behind these changes in the brain. One possibility could be the age-related alterations in neuronal lineage and glial markers. Thus, this study aims to show the protein levels, distributions, and localizations of key neuronal lineage and glial markers, which include neural progenitor, early neuronal, immature neuron, and mature neuron and glial markers during healthy aging of the zebrafish brain. For this aim, we measured NeuN (Fox-3, Rbfox3, or Hexaribonucleotide Binding Protein-3), MAP-2 (Microtubule-associated protein 2), HuC (ELAV like neuron-specific RNA binding protein 3), DCAMKL-1 (Doublecortin-like kinase 1), and GFAP (Glial fibrillary acidic protein) with immunohistochemistry and western blot techniques. First, the immunohistochemistry technique was applied on two specific proliferation areas, pallium and optic tectum, to detect the changes in the number of neuronal lineages and glial marker. The results indicated no statistically significant changes between young and old groups. Secondly, we performed whole-brain immunohistochemistry of all markers and quantified every image by manually counting the positive signal. We found that aging did not have an effect on the distribution and expression of the markers, even in the whole brain. Finally, Western-blot was performed in whole brain lysates to compare neuron number and protein level changes. Western-blot results indicated an age-related statistically significant decline in immature neuron marker for specifically males and glial marker for specifically females. The protein level of neural progenitor marker showed the significant decline in males during aging but no change between two age groups. Results of the mature neuron antibody revealed that the protein levels were consistent through aging and did not show variation. Our results overall support the finding that the number of neurons and glia do not change during aging since the numbers of markers were not show statistically significant changes during the aging process in the proliferation areas of the zebrafish brain. However, protein levels showed changes between age and gender groups. Thus, this study shows that understanding changes in the number of cells need to count; protein level is not representative, and zebrafish is an appropriate model for brain aging studies.
Zebrabalığı dokularında ve insan beyin kanserlerinde telomerlerin sürdürülme mekanizmalarının incelenmesi
Telomeres are nucleoprotein complexes formed at each end of the chromosomes to protect these ends from deterioration. In each round of cellular division, telomeric sequences shorten due to the end replication problem of DNA polymerase. Progressive telomere shortening results in replicative senescence in healthy somatic cells. To evade replicative senescence, cells need to maintain their telomere length either by activating the telomerase enzyme or through the alternative lengthening of telomeres (ALT). Telomerase is a holoenzyme, which is composed of dyskerin, telomerase RNA subunit (TR or TERC), and telomerase catalytic subunit (TERT). Dyskerin and TR are constitutively expressed in all cells but TERT expression is silenced in adult somatic cells. Thus, telomerase activity is dependent on the expression of TERT. Current studies show that TERT re-activation is a common feature of cancer cells and 85-90% of cancers utilize telomerase enzyme in maintaining telomeres to become immortal. Remaining of cancer cells maintain their telomeres by the alternative lengthening of telomeres (ALT), which is a DNA repair pathway dependent mechanism. Current models suggest that ALT is achieved by homology-directed DNA repair, through the interaction of multiple proteins. DNA methylation is regarded as a key player in epigenetic silencing of transcription. DNA methyltransferase inhibitors are currently being used in cancer treatments. Recent studies show that DNA methyltransferases and their expression levels impact both telomerase- and ALT mediated lengthening of telomeres, and have different outcomes in different tissue types. In this study, we worked on the zebrafish brain and human brain cancer cell lines. In zebrafish brain, we observed differences in methylated regions at Sp1 binding site between young and old that can be associated with telomere shortening. By silencing DNMT1 and DNMT3B in brain cancer cell lines, we investigated the changes in gene expression levels of telomerase and ALT related genes, telomerase activity, population doubling time and replicative senescence status. To further investigate TERT regulation, we introduced mutations to the Sp1 binding sites in the promoter region and measured the promoter activity with luciferase assay. Our results show that Sp1 methylation sites in the telomerase promoter region are critical in brain aging, dependent on their position. We propose a therapeutical option for brain aging and tumorigenesis.
Görsel algısal öğrenme sürecinde insan korteksindeki fonksiyonel değişimler
In this study we assessed functional changes through visual perceptual learning with bisection discrimination task. Before learning, after third session of learning and after learning ended, behavioral threshold and fMRI data has been collected. Our results showed that while participants showed threshold decrease in the mid-learning session, the post-learning thresholds are turned to pre-learning levels. These results might be due to fatigue which caused by our experiment. Besides to training condition, we also tested location and task specificity. The results showed that only 150\degree polar angle location showed significant change between sessions. Along with the behavioral data, we collected task-based fMRI data while participants performing training and control conditions in the scanner. The analysis showed task-based BOLD response changed with session. However, post-hoc tests did not reveal significant results. The resting-state functional connectivity analysis showed that the functional connectivity between V1 and V2 regions is significantly increased. The Post Hoc analysis showed significant change in the 210 degree and 150 degree polar angle conditions. The changes in the behavioral and functional connectivity measurements at 150 degree polar angle conditions, these results might indicate the effect of the inter-hemispheric connections. Moreover, our analysis on resting state data also revealed that, while there is no change between pre-learning and mid-learning sessions, connectivity changes significantly in the post-learning session compared to other sessions. This finding supports the idea that functional connectivity changes related to perceptual learning might be occurring at the late phases of the learning. Overall, to rule out the confounds in the behavioral measurements and to link the behavioral data with the neural data, additional measurements should be taken in the future.
Probing sensory plasticity with rapid forms of motion adaptation
Perception is shaped by both immediate pattern of sensory inputs and previous experience with the external environment. Visual adaptation, a temporary change in perception following exposure to a stimulus, has been widely employed to understand how previous sensory experience on different timescales shapes perception. Visual motion adaptation is a powerful investigative tool to understand sensory plasticity and neural adaptation. However, the neural mechanisms underlying adaptation induced changes by visual motion are still subject to debate. In the present thesis, spatiotemporal dynamics, neural substrates, and the functional role of sensory plasticity in the human visual system were examined using rapid forms of motion adaptation paradigm combined with EEG. Specifically, how motion adaption-induced short-term sensory plasticity is reflected at the neural level and parallel with perceptual performance were explored. Participants were adapted to directional drifting gratings for either short (640 ms in Experiment 1; 188 ms in Experiments 2 and 3) or long (6.4 s in Experiment 1; 752 ms in Experiments 2 and 3) durations and used a counter-phase flickering (with constant polarity in experiments 1 and 2; polarity inverting within every step in Experiment 3) grating as a test pattern. Sinusoidal gratings of phi motion were employed in Experiment 1 whereas; square-wave gratings were used for phi and reverse-phi adaptations in experiments 2 and 3 to examine how ON and OFF pathways operate in the visual processing stream. Based on the EEG analyses in Experiment 1, the scalp sites relevant to motion adaptation were identified. Experiment 1 showed that both adapting durations led to significant motion aftereffects and EEG results showed that long adaptation produced stronger aftereffects than the short adaptation condition within 64-112 ms time range over occipital and parieto-occipital sites. Taken together, these findings provide important electrophysiological evidence that motion aftereffects reflect changes in cortical areas mediating low- and mid-level visual motion processing. They also suggest that adaptation is an active process that involves neural mechanisms operating at different time scales. In Experiments 2 and 3, the short-term adaptation induced changes over these identified scalp sites were further examined based on Experiment 1. Given that the phi and reverse-phi motion mainly engage within (ON or OFF) and across (ON and OFF) pathway mechanisms, the comparisons of adaptation induced changes across these motion types provided further insights into the nature of corresponding mechanisms over the visual cortex. The behavioral and EEG findings pointed to the efficient convergence of information provided by these pathways and some distinct characteristics of across pathway mechanisms.
Identification of preclinical implications for novel indole-benzimidazoles and phenothiazines using in vitro cancer cell line and in vivo zebrafish models
Meme kanseri (BC) ve hepatosellüler karsinom (HCC), kayda değer ölüm oranlarına sahip iki önemli sağlık sorunudur. İlaç tedavileri mevcut olmasına rağmen, terapötik başarı sınırlıdır. Düşük biyoyararlanım, yüksek toksisite ve tekrarlayan ilaç direnci nedeniyle yeni tedavi seçenekleri gereklidir. Bu tezde, BC ve HCC'de, sırası ile, yeni indol-benzimidazol ve fenotiyazinlerin anti-kanser etkilerini ve klinik öncesi potansiyellerini test etmek için farklı in vitro, in siliko ve in vivo yaklaşımlar uygulandı. Tezin ilk bileşeninde, in vitro kanser hatları, in vivo zebrabalığı embriyo ve larvaları ve in siliko karşılaştırmalı transkriptomik analizler kullanarak yeni indol-benzimidazol türevlerinin BC hücre hattı toksisitelerini ve östrojen reseptörü (ER) ile ilişkilerini değerlendirdim. İkinci bölümde ise antipsikotik bileşikler olan fenotiyazinler (PTZ), HCC tedavisi için yeniden konumlandırıldılar. Bu nedenle, tek başına veya sorafenib (SFB) ile kombinasyon halinde jenerik PTZ türevleri, in vitro kanser hatları, ardından zebrabalığı gelişim testleri ve embriyonik aşama zenograftları kullanılarak test edildiler. Ek olarak, RNAseq analizleri, ilaçların gen ekspresyon düzeyindeki sinerjistik/antagonistik etkilerini anlamak üzere trifluoperazin (TFP), SFB ve TFP + SFB kombinasyonu ile muamele edilen Hep3B hücreleri üzerinde gerçekleştirildi. Son olarak, yeni PTZ türevlerinin anti-HCC potansiyelleri, in vitro ve in vivo taramalarla araştırıldı. Ayrıca, yeni ve jenerik türevlerin nöral yolaklar üzerindeki etkileri, kolinesteraz testleri ve motor tepki ölçümleri ile değerlendirildi. Tezin bulguları, özgün BC ve HCC tedavilerine istinaden ileri klinik öncesi çalışmaların yürütülmesine potansiyel yol gösterici niteliktedir.
Değişen düzey ve farklı sürelerdeki kalori kısıtlamasının hücresel ve sinaptik proteinler ve dişi fare beyninin inflamatuvar durumu üzerine etkileri
Aging is an inevitable and complicated process leading to functional decline. Regarding brain aging, cognitive decline takes place in multiple domains, including learning, memory, executive functions, motor coordination, and language. At the cellular and molecular level, age-related cognitive decline is elucidated with certain hallmarks, including aberrant neuronal network, stem cell exhaustion, glial cell activation, and inflammation. Calorie restriction (CR) is a widely-utilized approach for coping with aging's detrimental effects even though there is no one agreed way for the application of CR. In this study, varying levels of CRs were applied for differing durations to MMTV-TGF-alpha female mice. The study initiated when mice were 10-weeks of age (Baseline) and carried out until 49/50 weeks of age and 81/82 weeks of age. There were four dietary groups named Ad-libitum (AL; control), Chronic Calorie Restriction (CCR), Intermittent Calorie Restriction - Restriction (ICR-R), and Intermittent Calorie Restriction -Refeed (ICR-RF). The study's first aim was to show age-related changes in the cellular and synaptic proteins and the inflammatory state of the female mice's brains. The second aim of the study is to demonstrate the effects of varying levels of CR implemented for the short-term and the long-term manner on the same hallmarks. Our findings showed both chronic- or intermittent- CR altered the synaptic integrity proteins against brain aging at the long-term period (81/82 weeks) compared to the short-term (49/50 weeks) period except for PSD-95. Similarly, both chronic- or intermittent- CR showed an attenuative impact on the pro-inflammatory markers, but IL-6 was affected only by CCR at the same periods. Furthermore, an age-related imbalance between neurogenesis and astrogliogenesis was shown based on DCX and GFAP. Both chronic- or intermittent- CR showed a compensatory effect on it acting through astrogliogenesis, even though it was not statistically significant.
Ergenlik-erken yetişkinlik döneminde dorsolateral prefrontal kortekste gerçekleşen dinamik alternatif gen kırpılma olayları ve şizofreni ile ilgili çıkarımlar
Alternative splicing (AS) or differential exon usage (DEU) is a regular process after gene expression and it contributes to the diversity of the genome by generating multiple protein isoforms. According to recent studies, the majority (92-94\%) of all human multi-exon genes undergo AS and the brain, especially the neocortex, has the highest number of AS events compared to other tissues. While contributing to the complexity of the brain, AS may lead to neuropsychiatric disorders such as schizophrenia or autism if dysregulated. Adolescence and young adulthood (AYA) period which nearly covers age range between 15 to 24 years old, is known to be a critical time to develop several neuropsychiatric disorders including schizophrenia and depression. Therefore, it is important to know developmental changes in AS events that occur in healthy brains in order to understand what is disrupted in a diseased brain. Although there are many studies investigating the possible roles of AS in the function of specific neuron types and during neurogenesis, there are only a few studies investigating AS changes in the human brain during different developmental periods. Therefore, in this study we first compared DEU that occur in the dorsolateral prefrontal cortex (DLPFC) of psychologically healthy individuals during AYA period to other developmental periods: infancy, early childhood, middle and late childhood, young adulthood, middle adulthood, and late adulthood. Additionally we compared DEU that occur in the DLPFC of schizophrenia patients to psychologically healthy individuals. Then we found exons that show both developmental and schizophrenia related DEU changes. Our results revealed 4 exons that belong to 3 different genes: AKAP7, BAIAP3 and SEMA3B. If further investigated, these exons can help us better understand the pathophysiology of schizophrenia and be possible early markers of the disease.
Algısal öğrenmenin görsel korteksin işlevi ve mikro yapısı üzerindeki etkilerinin araştırılması
Perceptual learning is the long-term improvement of the ability to process sensory stimuli through experience. Although an extensively studied field, the mechanism and locus of plasticity underlying visual perceptual learning is subject of debate. Here, we investigated the experience-dependent plasticity in the visual cortex across the time course of perceptual learning of bisection discrimination task. Population receptive field (pRF) analysis was used to examine functional architecture of the visual cortex. Microstructural properties of the visual cortex were characterized with neurite orientation dispersion and density imaging (NODDI). We compared pre-, mid-, and post-training values of pRF size, neurite density, and orientation dispersion in the trained location as well as in two control locations where no training has been received. The values in the trained location did not change with time and did not differ from control locations. In addition, we assessed the microstructural properties in the white matter tract between the training location and the mirror-symmetric control location and did not observe any change with training. In conclusion, we found no training-related changes in the early visual cortex (V1-V3). Our results are limited by the lack of performance improvement with training and the small sample size. Moreover, we were not able to identify visual areas beyond V1-V3 leaving high-level visual areas unexplored. Suggestions for further research include redesigning the behavioral training paradigm, optimization of pRF protocol to identify high-level visual areas, and repeating the study with a larger sample size.
Uzaysal destekli voksel-bazlı modelleme ve insan beyninde dinamik sahne kategorisi temsili
Humans have an impressive ability to rapidly process global information in natural scenes to infer their category. Yet, it remains unclear whether and how scene categories observed dynamically in the natural world are represented in cerebral cortex beyond few canonical scene-selective areas. To address this question, here we examined the representation of dynamic visual scenes by recording whole-brain blood oxygenation level-dependent (BOLD) responses while subjects viewed natural movies. We fit voxelwise encoding models to estimate tuning for scene categories that reflect statistical ensembles of objects and actions in the natural world. Voxelwise modeling (VM) is a powerful framework to predict single voxel responses evoked by a rich set of stimulus features present in complex natural stimuli. However, because VM disregards correlations across neighboring voxels, its sensitivity in detecting functional selectivity can be diminished in the presence of high levels of measurement noise. Here, we introduce spatially-informed voxelwise modeling (SPIN-VM) to take advantage of response correlations in spatial neighborhoods of voxels. To optimally utilize shared information, SPIN-VM performs regularization across spatial neighborhoods in addition to model features, while still generating single-voxel response predictions. Compared to VM, SPIN-VM yields higher prediction accuracies and better capture locally congruent information representations across cortex. We find that this scene-category model explains a significant portion of the response variance broadly across cerebral cortex. Cluster analysis of scene-category tuning profiles across cortex reveals nine spatially-segregated networks of brain regions consistently across subjects. These networks show heterogeneous tuning for a diverse set of dynamic scene categories related to navigation, human activity, social interaction, civilization, natural environment, non-human animals, motion-energy, and texture, suggesting that the organization of scene category representation is quite complex.
Nöropsikiyatrik belirtilerden önce pediatrik sistemik lupus eritematozus'ta yapısal bağlantı değişiklikleri
Systemic lupus erythematosus (SLE) is an autoimmune multi-system disorder affecting the central nervous system which may exhibit neuropsychiatric manifestations. Pediatric-onset SLE is rare and although there is an increased risk of neuropsychiatric symptoms, underlying pathological mechanisms remain poorly understood. This study explored the entire white matter network with brain structural connectivity and DTI tractography analysis to provide a better understanding of the probable connectivity alterations. Whole-brain structural connectivity and tractography of 17 pediatric-onset SLE patients without neuropsychiatric involvement (non-NPSLE) and 8 age and gender matched healthy controls were explored. To investigate the topological structure, graph theory analysis was applied. Global and nodal network features were derived by estimating structural connectivity matrices between 360 brain regions of the HCP atlas. Non-NPSLE patients demonstrated higher network characteristic path length and assortativity and lower density and global efficiency compared with healthy controls. The hubs were selected according to the strength of the nodes and their structure and distribution were changed in the patients. According to the altered hubs' network characteristics significant modifications between HCs and non-NPSLE, along with TBSS findings, altered regions were observed in the language, visual, auditory, and motor-related areas. These findings are in good agreement with WISC-IV VerbalComprehension Index. Compared to healthy controls non-NPSLE patients showed significantly lower scores according to WISC-IV score components. To conclude, from a network and connectivity perspective, our research demonstrated an altered topological structure of the brain in non-NPSLE patients. The findings of this study provide a better understanding of the structural alterations underlying pediatric-onset non-NPSLE patients' functional and neurocognitive abnormalities.
Dikkat yükü altında biyolojik hareket algısının nöral temelleri
Humans can detect and differentiate biological motion from non-biological motion stimuli effortlessly, even if the stimuli were shown as simplistic as a composition of moving dots (i.e. point-light displays [PLD]). Considering its survival and social significance, BM perception is assumed to occur automatically. Indeed, Thornton and Vuong (2004) showed that task-irrelevant BM in the periphery interfered with task performance at the fovea. However, the neural underpinnings of this bottom-up processing of BM lacks thorough examination in the field. Under selective attention, BM perception is supported by a network of regions including the occipito-temporal, parietal, and premotor cortices. A retinotopy mapping study on BM showed distinct maps for its processing under and away from selective attention (Saygın & Sereno, 2008). Based on these findings, we investigated how bottom-up perception of BM would be processed under attentional load when it was shown away from the focus of attention as a task-irrelevant stimulus. Participants (N=31) underwent an fMRI study in which they performed an attentionally demanding visual detection task at the fovea while intact or scrambled PLDs of BM were shown at the periphery. Our results showed the main effect of attentional load in fronto-parietal regions; as well as, the main effect of peripheral stimuli in occipito-temporal cortex. Both univariate and multivariate pattern analysis results support the attentional load modulation on BM. Lastly, ROI results on each core node of BM processing network expanded these findings by showing that the attentional load modulation on both intact and scrambled BM stimuli were the strongest in bilateral occipito-temporal regions as compared to parietal and premotor cortices. In conclusion, BM was processed within the motion sensitive regions in the occipito-temporal cortex when shown away from the selective attention, and was modulated by attentional load.