Genotypic Differences Research Articles

Deciphering ApoE Genotype-Driven Proteomic and Lipidomic Alterations in Alzheimer's Disease Across Distinct Brain Regions.

Alzheimer's disease (AD) is a neurodegenerative disease with a complex etiology influenced by confounding factors such as genetic polymorphisms, age, sex, and race. Traditionally, AD research has not prioritized these influences, resulting in dramatically skewed cohorts such as three times the number of Apolipoprotein E (APOE) ε4-allele carriers in AD relative to healthy cohorts. Thus, the resulting molecular changes in AD have previously been complicated by the influence of apolipoprotein E disparities. To explore how apolipoprotein E polymorphism influences AD progression, 62 post-mortem patients consisting of 33 AD and 29 controls (Ctrl) were studied to balance the number of ε4-allele carriers and facilitate a molecular comparison of the apolipoprotein E genotype. Lipid and protein perturbations were assessed across AD diagnosed brains compared to Ctrl brains, ε4 allele carriers (APOE4+ for those carrying 1 or 2 ε4s and APOE4- for non-ε4 carriers), and differences in ε3ε3 and ε3ε4 Ctrl brains across two brain regions (frontal cortex (FCX) and cerebellum (CBM)). The region-specific influences of apolipoprotein E on AD mechanisms showcased mitochondrial dysfunction and cell proteostasis at the core of AD pathophysiology in the post-mortem brains, indicating these two processes may be influenced by genotypic differences and brain morphology.

Morphological Diversity and Genetic Parameter of Okra (Abelmoschus esculentus L. Moench) Genotypes.

<b>Background and Objective:</b> Considering that the potential for okra as an anti-diabetic is very high, while okra productivity in Indonesia is still low, a plant breeding program through variety development is needed. One of the initial activities that needs to be carried out is the characterization of various genotypes, both quantitative and qualitative characters. This research aimed to obtain information on the diversity of morpho-agronomic characters in okra genotypes. <b>Materials and Methods:</b> The experiment was conducted as a randomized block design, one factor is genotype with three replications. The materials used in this research were 20 okra genotypes. The experimental units used in this research were 60 units. Each experimental unit consists of 10 sample plants. Analysis of quantitative character variations used PKBT-STAT 3.1. Cluster analysis was carried out with PBSTAT-CL 2.1.2 with the Gower dissimilarity and average linkage clustering methods. Furthermore, analysis was carried out using SAS OnDemand for Academics to see the distinguishing characteristics between clusters. <b>Results:</b> There were differences in okra genotypes based on qualitative and quantitative characteristics. The most diverse quantitative character is the yield component, which is the fruit character. Variance in genetic and heritability showed broad and high criteria, respectively. Based on cluster analysis results, okra genotypes were grouped into 3 clusters with a cophenetic distance value of 0.40. Cluster 1 consists of 9 genotypes. Cluster 2 consists of 10 genotypes. Cluster 3 consists of 1 genotype the Red Hill Country genotype. The grouping in cluster analysis was carried out based on leaf width, number of fruits, fruit weight, fruit diameter and carpel thickness character. <b>Conclusion:</b> This diversity of okra germplasm can facilitate plant breeding activities in the future by selecting genotypes to serve as parents according to the objectives carried out.

Survey of Rice Genotypes of Southern India for Seed Zinc Concentration to Explore its Seed Endophytic Microbial Diversity

Background: Rice is a vital staple food for a large part of the global population and zinc deficiency poses health risks, particularly in rice-dependent regions. Studying genotypic differences in rice seed zinc content is vital for breeding zinc enriched varieties to address malnutrition and enhance food security. In the plant microbe partnership exploring the role of seed bacterial endophytes in influencing the plant physiology holds promise for Zn accumulation contributing to the broader goals of enhancing food quality, nutrition and crop production in a world facing increasing agricultural demands and challenges. Methods: Rice genotypes were surveyed and their seed zinc content was analysed using non-destructive X-ray fluorescence spectrometry. Surface sterilization of rice seed samples was performed to isolate endophytic bacteria, involving a series of treatments with distilled water, ethanol and sodium hypochlorite to remove surface microflora. The sterilized seeds were then macerated and diluted to obtain a countable number of colonies, which were subsequently spread-plated on nutrient agar, tryptic soy agar and soil extract agar to enumerate the different nutritional types of seed endophytic microflora. Result: In this study, 34 different rice genotypes, comprising traditional landraces and modern cultivars, were collected and analysed for their inherent zinc content. One variety in each category of low, medium and high seed Zn content was selected. The occurrence of all nutritional types of bacterial and their population was highest in the genotype Karuppunel followed by CO51 and ADT 39. Nutrient agar was found to promote a higher count of culturable bacterial endophytes compared to Tryptic soy agar and Soil extract agar.

Evaluation of the participation of ABCA1 transporter in epicardial and mediastinal adipose tissue from patients with coronary artery disease.

Recent studies have shown a relationship between adipose tissue and coronary artery disease (CAD). The ABCA1 transporter regulates cellular cholesterol content and reverses cholesterol transport. The aim of this study was to determine the relationship between single nucleotide polymorphisms (SNPs) R230C, C-17G, and C-69T and their expression in epicardial and mediastinal adipose tissue in Mexican patients with CAD. The study included 71 patients with CAD and a control group consisting of 64 patients who underwent heart valve replacement. SNPs were determined using TaqMan probes. mRNA was extracted using TriPure Isolation from epicardial and mediastinal adipose tissue. Quantification and expression analyses were done using RT-qPCR. R230C showed a higher frequency of the GG genotype in the CAD group (70.4%) than the control group (57.8%) [OR 0.34, 95% CI (0.14-0.82) p = 0.014]. Similarly, C-17G (rs2740483) showed a statistically significant difference in the CC genotype in the CAD group (63.3%) in comparison to the controls (28.1%) [OR 4.42, 95% CI (2.13-9.16), p = 0.001]. mRNA expression in SNP R230C showed statistically significant overexpression in the AA genotype compared to the GG genotype in CAD patients [11.01 (4.31-15.24) vs. 3.86 (2.47-12.50), p = 0.015]. The results suggest that the GG genotype of R230C and CC genotype of C-17G are strongly associated with the development of CAD in Mexican patients. In addition, under-expression of mRNA in the GG genotype in R230C is associated with patients undergoing revascularization.

5-HT2A Receptor Knockout Mice Show Sex-Dependent Differences following Acute Noribogaine Administration.

Noribogaine (noribo) is the primary metabolite from ibogaine, an atypical psychedelic alkaloid isolated from the root bark of the African shrub Tabernanthe iboga. The main objective of this study was to test the hypothesis that molecular, electrophysiological, and behavioral responses of noribo are mediated by the 5-HT2A receptor (5-HT2AR) in mice. In that regard, we used male and female, 5-HT2AR knockout (KO) and wild type (WT) mice injected with a single noribo dose (10 or 40 mg/kg; i.p.). After 30 min., locomotor activity was recorded followed by mRNA measurements by qPCR (immediate early genes; IEG, glutamate receptors, and 5-HT2AR levels) and electrophysiology recordings of layer V pyramidal neurons from the medial prefrontal cortex. Noribo 40 decreased locomotion in male, but not female WT. Sex and genotype differences were observed for IEG and glutamate receptor expression. Expression of 5-HT2AR mRNA increased in the mPFC of WT mice following Noribo 10 (males) or Noribo 40 (females). Patch-clamp recordings showed that Noribo 40 reduced the NMDA-mediated postsynaptic current density in mPFC pyramidal neurons only in male WT mice, but no effects were found for either KO males or females. Our results highlight that noribo produces sexually dimorphic effects while the genetic removal of 5HT2AR blunted noribo-mediated responses to NMDA synaptic transmission.

Nutritional composition and mineral profile of leaves of Moringa oleifera provenances grown in Gaborone, Botswana

Although Moringa is an important vegetable crop elsewhere, its nutritional and non-food uses are not widely known in Botswana community. This study was conducted to determine the chemical composition and mineral contents of leaves of Moringa oleifera trees grown in Gaborone, Botswana. The leaf samples were collected from Moringa trees grown in the backyards of six different households in Gaborone city. They were dried separately at 55 ºC for 24 h and then ground to obtain a powder for analysis. The data on the proximate composition of the Moringa samples were subjected to Analysis of Variance to determine statistical differences among the mean values. The overall mean values of moisture, fat, protein, ash, fiber and total available carbohydrates of the leaves were 6.93 ± 0.16, 7.78 ± 0.13, 27.1 ± 0.43, 7.34 ± 0.31, 9.1 ± 1 and 46.5 ± 3%, respectively. The Moringa leaves contained average values of 520 ± 96.0, 7.7 ± 1.3, 30.1 ± 15.5, 0.8 ± 0.1, 82.6 ± 6.4, 1.7 ± 0.2, 1.6 ± 0.2 and 0.02 ± 0.00 mg/100g of Calcium, Iron, Sodium, Zinc, Magnesium, Aluminum, Manganese and Chromium, respectively. Significant differences were observed for moisture, fat, protein and ash contents among the six Moringa samples. The results showed that the leaves are rich in nutrients, particularly with high amounts of protein and ash. This suggests that Moringa leaf could serve as an important protein and mineral supplement in the diet and can be consumed as a vegetable in Botswana. The difference in composition observed between the Moringa leaf samples suggests a possible genotypic difference between the Moringa trees used in this experiment. Thus, there is a need for further study to verify this.Graphical

"Chamber #8" - a holistic approach of high-throughput non-destructive assessment of plant roots.

In the past years, it has been observed that the breeding of plants has become more challenging, as the visible difference in phenotypic data is much smaller than decades ago. With the ongoing climate change, it is necessary to breed crops that can cope with shifting climatic conditions. To select good breeding candidates for the future, phenotypic experiments can be conducted under climate-controlled conditions. Above-ground traits can be assessed with different optical sensors, but for the root growth, access to non-destructively measured traits is much more challenging. Even though MRI or CT imaging techniques have been established in the past years, they rely on an adequate infrastructure for the automatic handling of the pots as well as the controlled climate. To address both challenges simultaneously, the non-destructive imaging of plant roots combined with a highly automated and standardized mid-throughput approach, we developed a workflow and an integrated scanning facility to study root growth. Our "chamber #8" contains a climate chamber, a material flow control, an irrigation system, an X-ray system, a database for automatic data collection, and post-processing. The goals of this approach are to reduce the human interaction with the various components of the facility to a minimum on one hand, and to automate and standardize the complete process from plant care via measurements to root trait calculation on the other. The user receives standardized phenotypic traits and properties that were collected objectively. The proposed holistic approach allows us to study root growth of plants in a field-like substrate non-destructively over a defined period and to calculate phenotypic traits of root architecture. For different crops, genotypic differences can be observed in response to climatic conditions which have already been applied to a wide variety of root structures, such as potatoes, cassava, or corn. It enables breeders and scientists non-destructive access to root traits. Additionally, due to the non-destructive nature of X-ray computed tomography, the analysis of time series for root growing experiments is possible and enables the observation of kinetic traits. Furthermore, using this automation scheme for simultaneously controlled plant breeding and non-destructive testing reduces the involvement of human resources.

GENETIC VARIATION AND HERITABILITY ESTIMATES IN CHICKPEA SEEDLING TRAITS: IMPLICATIONS FOR BREEDING PROGRAMS

Chickpea, also known as Bengal gram, Channa, or garbanzo bean, is a vital pulse crop that offers wholesome food to the growing population. Originating from modern-day southeast Turkey and Syria, chickpea germplasm is abundant in Ethiopia, serving as a secondary centre of genetic diversity for various dietary legumes. Two main varieties are desi and Kabuli. A study at the University of Punjab Lahore found significant genetic variations in chickpea seedlings, with high genetic components and a broad-sense heritability of 87.04%. Root length showed a significant genotypic effect, with a PCV of 16.39% and a larger GCV than SL. The root-to-seedling length ratio showed a significant genotypic variance, with a heritability estimate of 69.98% and a genetic advance of 5.740%. Seedling biomass did not show significant genotypic variation. Leaf characteristics showed substantial genotypic differences, indicating extensive genetic heterogeneity. The correlation matrix showed substantial correlations between seven qualities in chickpea seedlings, suggesting genetic and physiological links between the qualities. These findings can inform breeding efforts, improve breeding programs, and generate new varieties with improved features.

Integrated transcriptome and metabolome analysis reveals the divergent evolution of low-P tolerance in cultivated and Tibetan wild barley

Most arable lands in the world are quite low in available phosphorus (P), becoming an important factor restricting crop yield. However, the genotypic difference of low-P tolerance in barley is rarely understood at molecular level. In this study, low-P responses of three barley genotypes were explored by physiological, transcriptomic and metabolomic analysis. The results showed that low-P-tolerant genotypes Zaoaibai (cultivar) and X130 (Tibetan wild accession) showed less growth inhibition compared to low-P-sensitive Salooni2 under low-P stress. Omics analysis showed that many genes involved in Pi acquisition and transport were more upregulated in Zaoaibai, which had relatively higher concentrations of shoot P and glucose-6-phosphate, indicating that enhancement of P acquisition, P translocation and P availability contributed to low-P tolerance in Zaoaibai. On the other hand, the genes and metabolites involved in biosynthesis of Pi-free lipids were highly expressed and more abundant in X130, suggesting that remodeling of membrane lipids by replacing phospholipids with Pi-free lipids is an important strategy for X130 in its adaptation to low-P stress. The divergent evolution of low-P tolerance in Zaoaibai and X130 could be driven by diverse ecological factors in Eastern China (low soil P) and Tibet Plateau (high soil P and low temperature), respectively.

Genotype Analysis of Respiratory Syncytial Virus Before and After the COVID-19 Pandemic Using Whole-Genome Sequencing: A Prospective, Single-Center Study in Korea From 2019 to 2022.

Respiratory syncytial virus (RSV), a highly transmissible virus, is the leading cause of lower respiratory tract infections. We examined molecular changes in the RSV genome before and after the coronavirus disease 2019 (COVID-19) pandemic in Korea, and investigated whether drug-resistant mutations were present. In this prospective, single-center study, RSV-positive respiratory samples were collected between September 2019 and December 2022. Long-read whole-genome sequencing (WGS) was performed, and the presence of known drug-resistant substitutions for palivizumab, nirsevimab, and suptavumab was investigated. Overall, 288 respiratory samples were collected from 276 children. WGS data were available for 133 samples (71 and 62 samples from the pre- and post-pandemic periods, respectively). All RSV-A strains (n = 56) belonged to the GA2.3.5 (ON1) genotype, whereas all RSV-B strains (n = 77) belonged to the GB5.0.5a (BA) genotype. No significant differences in genotypes were observed between the pre- and post-pandemic periods. In addition, no notable mutations related to nirsevimab or palivizumab resistance were detected in the F gene. However, the L172Q and S173L substitutions, which are known to confer resistance to suptavumab, were present in all RSV-B samples. Despite the unprecedented interruption of RSV seasonality, there were no significant molecular changes in circulating RSV strains in Korea related to nirsevimab or palivizumab resistance before and after the COVID-19 pandemic. However, RSV-specific drug-resistance substitutions for suptavumab were identified.

Association between Transcription Factor 7-Like 2 Gene Polymorphisms rs7903146 and rs12255372 with the Risk of Diabetic Nephropathy among South Indian Population

Abstract Introduction: Transcription factor 7-like 2 (TCF7L2) gene has been associated with the genetic predisposition of type 2 diabetes mellitus (T2DM) and diabetic nephropathy (DN) in different populations. The study aimed to explore the correlation between rs7903146 and rs12255372 polymorphisms of TCF7L2 gene and DN among the South Indian population. Methods: Polymerase chain reaction (PCR)-based direct sequencing method and allele-specific PCR were used to determine the genotypes of TCF7L2 polymorphisms in 20 normal glucose tolerance (NGT) participants, 35 T2DM patients without DN and 35 T2DM patients with DN. The differences in genotype and allelic distribution between the study groups were analyzed by Chi-square test and odds ratio (OR) with 95% confidence interval (CI) which were used to indicate the relative risk of DN. Results: The distribution of TCF7L2 gene polymorphism rs7903146 prevalence was as follows: in the NGT group, CC, 65%; CT, 30%; TT, 5%; in the T2DM without DN group, CC, 25.71%; CT, 62.86%; TT, 11.43%; and in the T2DM with DN group, CC, 31.43%; CT, 60.0%; TT, 8.57%. The distribution of rs12255372 was as follows: in the NGT group, GG, 80%; GT, 15%; TT, 5%; in the T2DM without DN group, GG, 42.86%; GT, 41.46%; TT, 8.57%; and in the T2DM with DN group, GG, 48.57%; GT, 40%; TT, 5.71%. The T allele of rs7903146 polymorphism was associated with an increased risk of T2DM without DN (OR = 3.0; 95% CI = 1.21–7.437; P = 0.010) and T2DM with DN (OR = 2.51; 95% CI = 1.00–6.252; P = 0.04), and the T allele of rs12255372 polymorphism was also associated with increased risk of T2DM without DN (OR = 3.42; 95% CI = 1.18–9.902; P = 0.018) and not with T2DM with DN when compared with NGT individuals. Conclusion: In our study, the T allele of the rs7903146 single-nucleotide polymorphism in the TCF7L2 gene confers the risk of developing DN in diabetes patients, but the T allele of the rs12255372 polymorphism in the TCF7L2 gene is associated with T2DM and its association with DN is arbitrated through T2DM.

Sex- and time-dependent role of insulin regulated aminopeptidase in lipopolysaccharide-induced inflammation.

The enzyme, insulin regulated aminopeptidase (IRAP), is expressed in multiple immune cells such as macrophages, dendritic cells and T cells, where it plays a role in regulating the innate and adaptive immune response. There is a genetic association between IRAP and survival outcomes in patients with septic shock where a variant of its gene was found to be associated with increased 28-day mortality. This study investigated the role for IRAP in a lipopolysaccharide (LPS)-induced inflammatory response which is thought to model facets of the systemic inflammation observed in the early stages of human gram-negative sepsis. The frequencies and activation of splenic immune cell populations were investigated in the IRAP knockout (KO) mice compared to the wildtype controls over a period of 4-, 24-, or 48-hours following LPS stimulation. Dendritic cells isolated from the spleen of female IRAP KO mice, displayed significant increases in the activation markers CD40, CD86 and MHCII at 24 hours after LPS induction. A modest heightened pro-inflammatory response to LPS was observed with increased expression of activation marker CD40 in M1 macrophages from male IRAP knockout mice. Observations in vitro in bone marrow-derived macrophages (BMDM) revealed a heightened pro-inflammatory response to LPS with significant increases in the expression of CD40 in IRAP deficient cells compared with BMDM from WT mice. The heightened LPS-induced response was associated with increased pro-inflammatory cytokine secretion in these BMDM cells. A genotype difference was also detected in the BMDM from female mice displaying suppression of the LPS-induced increases in the activation markers CD40, CD86, CD80 and MHCII in IRAP deficient cells. Thus, this study suggests that IRAP plays specific time- and sex-dependent roles in the LPS-induced inflammatory response in dendritic cells and macrophages.

Genotypic Differences in Photosynthetic Limitations to Carbon Assimilation in Peanut under Drought at the Onset of Flowering

Drought can greatly limit carbon assimilation in plants. However, different species have distinct photosynthetic components governing limitations to photosynthesis exposed to drought conditions. Furthermore, intra-species variations in photosynthetic response to drought is also expected. Information on underlying limitations to carbon assimilation in peanut (Arachis hypogaea L.) has been controversial. Therefore, this study aimed to verify potential drought tolerance associated with the photosynthetic process within ten diverse peanut genotypes grown under drought as well as to determine the limitation to carbon assimilation in these genotypes and identify parameter(s) that can be used as a reference indicator of photosynthesis response to drought intensity. Experiments were conducted in 2017 and 2018 using rainout shelters to impose drought for 40 days starting 34 days after planting. Ten peanut genotypes were planted in two blocks, one fully irrigated and one under drought stress during reproductive development. Photosynthetic measurements were taken at 25 and 40 days after onset of stress. C76-16 was identified as the most tolerant genotype due to improved plasticity by downregulating photosynthesis under mild drought stress (25 progressive days under drought) and upregulating multiple photosynthetic component processes under more severe drought (40 days under drought) to sustain photosynthesis. The primary limitation to photosynthesis across all peanut genotypes was stomatal conductance, whereas non-stomatal factors (photochemical reactions) were nearly unaffected by mild drought. In addition, stomatal conductance and electron flux to CO2 assimilation contributed most to drought tolerance in peanut genotypes. Moreover, these two photosynthetic component processes can be jointly used as reference indicators of photosynthetic status of peanut under varying drought intensities.

Deletion of arrestin-3 does not reduce drug-seeking behavior in a longitudinal paradigm of oral morphine self-administration.

Opioid drugs are potent analgesics that mimic the endogenous opioid peptides, endorphins and enkephalins, by activating the µ-opioid receptor. Opioid use is limited by side effects, including significant risk of opioid use disorder. Improvement of the effect/side effect profile of opioid medications is a key pursuit of opioid research, yet there is no consensus on how to achieve this goal. One hypothesis is that the degree of arrestin-3 recruitment to the µ-opioid receptor impacts therapeutic utility. However, it is not clear whether increased or decreased interaction of the µ-opioid receptor with arrestin-3 would reduce compulsive drug-seeking. We utilized three genotypes of mice with varying abilities to recruit arrestin-3 to the µ-opioid receptor in response to morphine in a novel longitudinal operant self-administration model. We also created a quantitative method to define compulsivity in drug-seeking based on a multi-variate analysis of several operant response variables. We demonstrate that arrestin-3 knockout and wild type mice have highly variable drug-seeking behavior with few genotype differences. In contrast, in mice where the µ-opioid receptor strongly recruits arrestin-3, drug-seeking behavior is much less varied. We found that mice lacking arrestin-3 were more likely to meet the criteria for compulsivity whereas mice with enhanced arrestin-3 recruitment did not develop a compulsive phenotype. These experiments show that a lack of arrestin-3 is not protective against the abuse liability of morphine in an operant self-administration context. Our data also suggest that opioids that engage both G protein and arrestin-3, recapitulating the endogenous signaling pattern, will reduce abuse liability.

Evaluation of gene-gene interaction between the interleukin (IL)-2 and IL-2RA gene polymorphisms in schizophrenia patients in the Turkish Population.

To evaluate the genetic polymorphisms in IL-2 and IL-2RA genes in schizophrenia (SCZ) patients by comparing them with healthy controls. A sample of 127 patients with SCZ and 100 healthy volunteers were included in the case-control study. These individuals were consecutively selected from the Malazgirt State Hospital Psychiatry Outpatient Clinic in Mus, Turkey, over the three months from October 2020 to December 2020. The Structured Clinical Interview for DSM-5 Disorders, Clinician Version (SCID-5-CV) was used to confirm the diagnosis according to the DSM-5 criteria. In addition, polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) was used to determine gene polymorphisms from DNA material. Our findings indicated significant differences in the IL-2 genotype and allele frequencies between SCZ patients and the healthy control group. Specifically, the frequency of the homozygous GG genotype was notably higher in SCZ patients compared to the control group. Conversely, when comparing the IL-2RA genotype and allele frequencies of SCZ patients with the control group, no statistically significant differences were observed between the 2 groups. When compared to individuals with other genotypes, interaction analysis indicated that carriers of the GG/AG (IL-2/IL-2RA) genotype demonstrated a significantly increased risk of SCZ. In light of the analyses, our study indicates that while the IL-2 genotype polymorphism may be considered a risk factor for developing SCZ, the IL-2RA variant was not associated with SCZ among Turkish patients.

Aldehyde Dehydrogenase 2 rs671 G/A and a/A Genotypes are Associated with the Risk of Acute Myocardial Infarction.

Aldehyde dehydrogenase 2 (ALDH2) is a key catalytic enzyme involved in the aldehyde metabolism that plays an important role in the occurrence and development of acute myocardial infarction (AMI). However, the relationship of ALDH2 polymorphism and susceptibility to AMI may differ among different regions and populations, and it has not yet been reported in Hakka population. The purpose of the present study was to investigate it in this population. Four hundred and nineteen AMI patients and 636 individuals without AMI were included in the present study. The ALDH2 rs671 polymorphism was genotyped using polymerase chain reaction (PCR)-microarray. Differences in ALDH2 rs671 genotypes and alleles between patients and controls were compared, and the relationship between ALDH2 rs671 genotypes and AMI risk was analyzed. Patients with AMI had a lower frequency of ALDH2 rs671 G/G genotype (43.2% vs 52.7%, p=0.003), and a higher G/A genotype (45.6% vs 38.5%, p=0.025) than controls. And AMI patients had a lower frequency of ALDH2 rs671 G allele (66.0% vs 71.9%), and a higher A allele (34.0% vs 28.1%) (p=0.004) than controls. Logistic regression analysis showed that overweight (body mass index (BMI)≥24.0 kg/m2 vs BMI 18.5-23.9 kg/m2: odds ratio (OR) 2.046, 95% confidence interval (CI): 1.520-2.754, p<0.001), history of hypertension (yes vs no: OR 3.464, 95% CI: 2.515-4.770, p<0.001), ALDH2 rs671 G/A genotype (G/A vs G/G: OR 1.476, 95% CI: 1.102-1.976, p=0.009), and A/A genotype (A/A vs G/G: OR 1.656, 95% CI: 1.027-2.668, p=0.038) maybe the independent risk factors for AMI. Overweight (BMI≥24.0 kg/m2), a history of hypertension, and ALDH2 rs671 G/A or A/A genotypes increased the risk of developing AMI in Hakka population.

Superoxide Dismutase (rs2070424, rs4880, rs2536512) and Catalase (rs794316, rs1001179) SNPs and their Association with Breast Cancer Risk: Findings from a Hospital Based Case-Control Study.

The antioxidant enzymes are important cellular components involved in detoxification of reactive oxygen species (ROS) and protect cells from ROS induced oxidative damage. Single nucleotide polymorphisms (SNPs) of antioxidant enzyme coding genes such as superoxide dismutase (SOD) and catalase (CAT) may alter the enzyme activity which can influence susceptibility towards carcinogenesis. Therefore, the present study was planned to investigate possible SNPs of SOD (SOD1 (Cu,Zn-SOD), SOD2(Mn-SOD), SOD3(EC-SOD) and CAT genes and their possible association with breast cancer risk in rural Indian women. In this case-control study, the association of SOD and CAT gene polymorphism was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. The study was conducted among 400 clinically breast cancer patients and 400 healthy women in a population of South-Western Maharashtra. The logistic regression analysis was carried out to calculate Odds ratio (OR) with 95% confidence interval and p-value, where p ≤0.05 was considered as statistically significant. The results of analysis of genotype frequency distribution showed significant association of rs4880 SNP of Mn-SOD with BC risk at homozygous variant (CC/CC) genotype (OR 2.46; 95%CI, 1.61-3.75; p<0.0001) and corresponding frequency of variant (C) allele (OR 1.53; 95%CI, 1.25-1.86; p<0.0001). In CAT gene polymorphisms the variant (T/T) was increased significantly in BC cases as compared to controls (OR 3.45; 95%CI, 2.17-5.50; p<0.0001) along with its variant (T) allele (OR 2.01; 95%CI, 1.63-2.48; p<0.0001). The results implied that, C/C genotype of SOD2-1183T/C polymorphism and T/T genotype of CAT-262 C/T polymorphism may be associated with an increased breast cancer risk. However, SOD1-251 A/G and SOD3-172 G/A polymorphisms did not show any significant difference in variant homozygous genotypes of patients compared to controls.

Sex differences in sleep architecture in a mouse model of Huntington's disease.

Sleep and circadian rhythm disturbances are common features of Huntington's disease (HD). HD is an autosomal dominant neurodegenerative disorder that affects men and women in equal numbers, but some epidemiological studies as well as preclinical work indicate there may be sex differences in disease presentation and progression. Since sex differences in HD could provide important insights to understand cellular and molecular mechanism(s), we used the bacterial artificial chromosome transgenic mouse model of HD (BACHD) to examine whether sex differences in sleep/wake cycles are detectable in an animal model of the disease. Electroencephalography/electromyography (EEG/EMG) was used to measure sleep/wake states and polysomnographic patterns in young adult (12-week-old) male and female wild-type and BACHD mice. Our findings show that male, but not female, BACHD mice exhibited increased variation in phases of the rhythms as compared to age- and sex-matched wild-types. For both rapid-eye movement (REM) and non-rapid eye movement (NREM) sleep, genotypic and sex differences were detected. In particular, the BACHD males spent less time in NREM sleep and exhibited a more fragmented sleep than the other groups. Finally, in response to 6 h of sleep deprivation, both genotypes and sexes displayed the predicted homeostatic responses to sleep loss. These findings suggest that females are relatively protected early in disease progression in this HD model.

The usefulness of anti-HCV signal to cut-off ratio in predicting hepatitis C viremia and the effect of genotype differences on signal to cut-off ratio.

In the hepatitis C virus (HCV) diagnostic algorithm, an anti-HCV screening test is recommended first. In countries with low HCV prevalence, anti-HCV testing can often give false-positive results. This may lead to unnecessary retesting, increased costs, and psychological stress for patients. In this study, the most appropriate S/Co (signal-cutoff) value to predict HCV viremia in anti-HCV test(+) individuals was determined, and the effect of genotype differences was evaluated. Of the 96,515 anti-HCV tests performed between 2020 and 2023, 934 were reactive. A total of 332 retests and 65 patients without HCV-ribonucleic acid (RNA) analysis were excluded. Demographic data were calculated for 537 patients, and 130 patients were included in the study. The average age of 537 patients was 55±18 years, and 57.1% were women. The anti-HCV positivity rate was 0.62% (602/96,515), and the actual anti-HCV positivity rate was 0.13% (130/96,515). Anti-HCV levels were higher in HCV-RNA(+) patients than in HCV-RNA-negative individuals (p<0.0001) (Table 1). Receiver operating characteristic curve analysis identified the optimal S/Co value to be 10.86 to identify true positive cases. Sensitivity was 96.1%, specificity was 61.2%, positive predictive value (PPV) was 44.2%, and negative predictive value (NPV) was 98% (Figure 2). A total of 107 (82.3%) of the patients were identified as GT1, and the most common subtype was GT1b (n=100). If anti-HCV S/Co is ≥10.86, direct HCV RNA testing may be recommended; However, the possibility of false positivity should be considered in patients with a S/Co value below 10.86.

Cotton morphological traits tracking through spatiotemporal registration of terrestrial laser scanning time-series data.

Understanding the complex interactions between genotype-environment dynamics is fundamental for optimizing crop improvement. However, traditional phenotyping methods limit assessments to the end of the growing season, restricting continuous crop monitoring. To address this limitation, we developed a methodology for spatiotemporal registration of time-series 3D point cloud data, enabling field phenotyping over time for accurate crop growth tracking. Leveraging multi-scan terrestrial laser scanning (TLS), we captured high-resolution 3D LiDAR data in a cotton breeding field across various stages of the growing season to generate four-dimensional (4D) crop models, seamlessly integrating spatial and temporal dimensions. Our registration procedure involved an initial pairwise terrain-based matching for rough alignment, followed by a bird's-eye view adjustment for fine registration. Point clouds collected throughout nine sessions across the growing season were successfully registered both spatially and temporally, with average registration errors of approximately 3cm. We used the generated 4D models to monitor canopy height (CH) and volume (CV) for eleven cotton genotypes over two months. The consistent height reference established via our spatiotemporal registration process enabled precise estimations of CH (R 2=0.95, RMSE = 7.6cm). Additionally, we analyzed the relationship between CV and the interception of photosynthetically active radiation (IPAR f ), finding that it followed a curve with exponential saturation, consistent with theoretical models, with a standard error of regression (SER) of 11%. In addition, we compared mathematical models from the Richards family of sigmoid curves for crop growth modeling, finding that the logistic model effectively captured CH and CV evolution, aiding in identifying significant genotype differences. Our novel TLS-based digital phenotyping methodology enhances precision and efficiency in field phenotyping over time, advancing plant phenomics and empowering efficient decision-making for crop improvement efforts.