Individual Loci Research Articles

Three-dimensional localization and tracking of chromosomal loci throughout the Escherichia coli cell cycle.

The intracellular position of genes may impact their expression, but it has not been possible to accurately measure the 3D position of chromosomal loci. In 2D, loci can be tracked using arrays of DNA-binding sites for transcription factors (TFs) fused with fluorescent proteins. However, the same 2D data can result from different 3D trajectories. Here, we have developed a deep learning method for super-resolved astigmatism-based 3D localization of chromosomal loci in live E. coli cells which enables a precision better than 61 nm at a signal-to-background ratio of ~4 on a heterogeneous cell background. Determining the spatial localization of chromosomal loci, we find that some loci are at the periphery of the nucleoid for large parts of the cell cycle. Analyses of individual trajectories reveal that these loci are subdiffusive both longitudinally (x) and radially (r), but that individual loci explore the full radial width on a minute time scale.

Single Nucleotide Recognition and Mutation Site Sequencing Based on a Barcode Assay and Rolling Circle Amplification

Single nucleotide polymorphisms (SNPs) present significant challenges in microbial detection and treatment, further raising the demands on sequencing technologies. In response to these challenges, we have developed a novel barcode-based approach for highly sensitive single nucleotide recognition. This method leverages a dual-head folded complementary template probe in conjunction with DNA ligase to specifically identify the target base. Upon recognition, the system triggers rolling circle amplification (RCA) followed by the self-assembly of CdSe quantum dots onto polystyrene microspheres, enabling a single-particle fluorescence readout. This approach allows for precise base identification at individual loci, which are then analyzed using a bio-barcode array to screen for base changes across multiple sites. This method was applied to sequence a drug-resistant mutation site in Helicobacter pylori (H. pylori), demonstrating excellent accuracy and stability. Offering high precision, high sensitivity, and single nucleotide resolution, this approach shows great promise as a next-generation sequencing method.

The Meaning and Measure of Concordance Factors in Phylogenomics.

As phylogenomic datasets have grown in size, researchers have developed new ways to measure biological variation and to assess statistical support for specific branches. Larger datasets have more sites and loci and therefore less sampling variance. While we can more accurately measure the mean signal in these datasets, lower sampling variance is often reflected in uniformly high measures of branch support-such as the bootstrap and posterior probability-limiting their utility. Larger datasets have also revealed substantial biological variation in the topologies found across individual loci, such that the single species tree inferred by most phylogenetic methods represents a limited summary of the data for many purposes. In contrast to measures of statistical support, the degree of underlying topological variation among loci should be approximately constant regardless of the size of the dataset. "Concordance factors" (CFs) and similar statistics have therefore become increasingly important tools in phylogenetics. In this review, we explain why CFs should be thought of as descriptors of topological variation rather than as measures of statistical support, and argue that they provide important information about the predictive power of the species tree not contained in measures of support. We review a growing suite of statistics for measuring concordance, compare them in a common framework that reveals their interrelationships, and demonstrate how to calculate them using an example from birds. We also discuss how measures of topological variation might change in the future as we move beyond estimating a single "tree of life" toward estimating the myriad evolutionary histories underlying genomic variation.

Epigenetic trajectory predicts development of clinical rheumatoid arthritis in ACPA+ individuals: Targeting Immune Responses for Prevention of Rheumatoid Arthritis (TIP-RA).

The presence of autoantibodies to citrullinated protein antigens (ACPAs) in the absence of clinically-apparent inflammatory arthritis (IA) identifies individuals "at-risk" for developing future clinical rheumatoid arthritis (RA). However, it is unclear why some ACPA+ individuals convert to clinical RA while others do not. We explored the possibility in the Targeting Immune Responses for Prevention of Rheumatoid Arthritis (TIP-RA) study that epigenetic remodeling is part of the trajectory from an at-risk state to clinical disease and identifies novel biomarkers associated with conversion to clinical RA. ACPA-Controls, ACPA+ At-Risk, and Early RA individuals were followed for up to 5 years, including obtaining blood samples annually and at RA diagnosis. Peripheral blood mononuclear cells (PBMCs) were separated into CD19+ B cells, memory CD4+ T cells, and naïve CD4+ T cells using antibodies and magnetic beads. Genome-wide methylation within each cell lineage was assayed using the Illumina MethylationEPIC v1.0 beadchip. ACPA+ At-Risk participants who did or did not develop RA were designated "Pre-RA" or "Non-converters", respectively.Differentially methylated loci (DML) were selected using the Limma software package. Using the Caret package, we constructed machine learning models in test and validation cohorts and identified the most predictive loci of clinical RA conversion. Cross-sectional differential methylation analysis at baseline revealed DMLs that distinguish the Pre-RA methylome from ACPA+ Non-converters, the latter which closely resembled ACPA-Controls. Genes overlapping these DMLs correspond to aberrant NOTCH signaling and DNA repair pathways in B cells. Longitudinal analysis showed that ACPA-Control and ACPA+ Non-converter methylomes are relatively constant. In contrast, the Pre-RA methylome remodeled along a dynamic "RA methylome trajectory" characterized by epigenetic changes in active regulatory elements. Clinical conversion to RA, defined based on diagnosis, marked an epigenetic inflection point for cell cycle pathways in B cells and adaptive immunity pathways in naïve T cells. Machine learning revealed individual loci associated with RA conversion. This model significantly outperformed autoantibodies plus acute phase reactants as predictors of RA conversion. DNA methylation is a dynamic process in ACPA+ individuals at-risk for developing RA that eventually transition to clinical disease. In contrast, non-converters and controls have stable methylomes. The accumulation of epigenetic marks over time prior to conversion to clinical RA conforms to pathways that are associated with immunity and can be used to identify potential pathogenic pathways for therapeutic targeting and/or use as prognostic biomarkers.

Взаємозв’язок поліморфізму генетико-біохімічних систем з показниками молочної продуктивності сучасних українських порід великої рогатої худоби

DNA typing technologies make it possible to detect alleles and their frequencies in biochemical systems of proteins and enzymes, including specific PCR sequences, restriction enzymes and actually single nucleotide polymorphisms. The development of breed-specific SNPs is necessary for genotyping and mapping of associations with milk productivity traits, which will make it possible to identify the most valuable genotypes for their further use in selection and breeding work. The purpose of the study is to determine the allelic and genotypic frequencies, genetic diversity and polymorphism of hemoglobin (HB), ceruloplasmin (CP), posttransferrin (pTf), amylase (Am-1) and the receptor for vitamin D (calcitriol) (GS) to identify the relationship breed-specific features of their genetic structure. The results of the research revealed the influence of the breed of cows on their genetic structure according to the genetic-biochemical systems pTf, GS, HB, CP and Am-1. A clear influence of the genotype factor at the posttransferrin locus was observed, among the studied breeds of cows, on the manifestation of the content and amount of protein in milk. In addition, a probable effect of ceruloplasmin on the parameters of fat and protein in milk was established, depending on the breed of cows. The assessment of the genetic-biochemical system based on the amylase locus established a clear influence of the genotype on the manifestation of milk yield, milk fat and the amount of protein in milk. Thus, the use of polymorphism of individual loci of proteins and blood enzymes in the conduct of selection and breeding work will not only contribute to the improvement of breeding work, but also to the improvement of dairy cattle in general. Therefore, the perspective of breeding work with Holstein cattle should be the assessment of the diversity of the allelogen according to the polymorphic system of proteins and enzymes, which will allow to identify the best genotypes not only in terms of productivity, but also in genetic terms.

Identification of potential biomarkers for lung adenocarcinoma: a study based on bioinformatics analysis combined with validation experiments.

The prognosis for lung adenocarcinoma (LUAD) remains dismal, with a 5-year survival rate of <20%. Therefore, the purpose of this study was to identify potentially reliable biomarkers in LUAD by machine learning combination with Mendelian randomization (MR). TCGA-LUAD, GSE40791, and GSE31210 were employed this study. Key module differential genes were identified through differentially expressed analysis and weighted gene co-expression network analysis (WGCNA). Furthermore, candidate biomarkers were derived from protein-protein interaction network (PPI) and machine learning. Ultimately, biomarkers were confirmed using MR analysis. In addition, immunohistochemistry was used to detect the expression levels of genes that have a causal relationship to LUAD in the LUAD group and the control group. Cell experiments were conducted to validate the effect of screening genes on proliferation, migration, and apoptosis of LUAD cells. The correlation between the screened genes and immune infiltration was determined by CIBERSORT algorithm. In the end, the gene-related drugs were predicted through the Drug-Gene Interaction database. In total, 401 key module differential genes were obtained by intersecting of 5,702 differentially expressed genes (DEGs) and 406 key module genes. Thereafter, GIMAP6, CAV1, PECAM1, and TGFBR2 were identified. Among them, only TGFBR2 had a significant causal relationship with LUAD (p=0.04, b=-0.06), and it is a protective factor for LUAD. Subsequently, sensitivity analyses showed that there were no heterogeneity and horizontal pleiotropy in the univariate MR results, and the results were not overly sensitive to individual SNP loci, further validating the reliability of univariate Mendelian randomization (UVMR) results. However, no causal relationship was found between them by reverse MR analysis. Meanwhile, TGFBR2 expression was decreased in LUAD group through immunohistochemistry. TGFBR2 can inhibit proliferation and migration of lung adenocarcinoma cell line A549 and promote apoptosis of A549 cells. Immune infiltration analysis suggested a potential link between TGFBR2 expression and immune infiltration. Finally, Irinotecan and Hesperetin were predicted through DGIDB database. In this study, TGFBR2 was identified as a biomarker of LUAD, which provided a new idea for the treatment strategy of LUAD and may aid in the development of personalized immunotherapy strategies.

Mendelian Randomization Reveals Serum Copper as a Micronutrient is a Risk Factor for Erectile Dysfunction.

The cause and effect between serum micronutrients and erectile dysfunction (ED) is not clear. The purpose of this study was to evaluate the causal relationship between micronutrients and ED by Mendelian randomization (MR) analysis. We used the published genome-wide association study (GWAS) data for two-sample MR analysis. This study utilized inverse variance weighted (IVW), MR egger, weighted median, simple mode, and weighted mode method to assess the causal relationship between serum micronutrients and ED. IVW is considered the standard method for MR analysis. We used Cochran's Q tests to evaluate the heterogeneity. To investigate horizontal pleiotropy, this study employed the MR Egger method. Additionally, leave-one-out analysis was used to evaluate the influence of individual genetic loci on the results. The results showed that there was a causal relationship between serum copper and ED, and it was positively correlated with ED (OR = 1.115, CI = 1.00-1.24, p = 0.014). There was no significant correlation between other micronutrients and ED. Sensitivity analysis results indicated that our findings exhibit no heterogeneity or pleiotropy, thereby strengthening our conclusions. Serum copper is a risk factor for ED, which provides a new idea for the diagnosis and treatment of ED in the future. However, further experiments are needed to elucidate the underlying mechanisms.

RAD51 regulates eukaryotic chromatin motions in the absence of DNA damage.

In yeasts and higher eukaryotes, chromatin motions may be tuned to genomic functions, with transcriptional activation and the DNA damage response both leading to profound changes in chromatin dynamics. The RAD51 recombinase is a key mediator of chromatin mobility following DNA damage. As functions of RAD51 beyond DNA repair are being discovered, we asked whether RAD51 modulates chromatin dynamics in the absence of DNA damage and found that inhibition or depletion of RAD51 alters chromatin motions in undamaged cells. Inhibition of RAD51 increased nucleosome clustering. Predictions from polymer models are that chromatin clusters reduce chain mobility and, indeed, we measured reduced motion of individual chromatin loci in cells treated with a RAD51 inhibitor. This effect was conserved in mammalian cells, yeasts, and plant cells. In contrast, RAD51 depletion or inhibition increased global chromatin motions at the microscale. The results uncover a role for RAD51 in regulating local and global chromatin dynamics independently from DNA damage and highlight the importance of considering different physical scales when studying chromatin dynamics.

Divine Control Beliefs, Health Locus of Control, and Subjective Life Expectancy in the United States.

Little evidence has considered the extent to which feelings of health-related control may arise from religious beliefs to influence survival expectations. Moreover, research on the linkages between religion and sense of control has yielded mixed results. Using CHAPS (2021) data, this study examines whether divine control beliefs predict subjective life expectancy (SLE), and whether this link is mediated by an individual's health locus of control (HLC). Findings support a mediational model and show that individuals who place more dependence on God report a greater sense of control over their health, which in turn results in greater longevity expectations. Our findings offer insight into the mechanisms that underlie the association between divine control beliefs and SLE and add to the body of literature documenting religion's salutary role in promoting both a sense of empowerment and greater survival expectations.

Unraveling the key role of chromatin structure in cancer development through epigenetic landscape characterization of oral cancer

Epigenetic alterations, such as those in chromatin structure and DNA methylation, have been extensively studied in a number of tumor types. But oral cancer, particularly oral adenocarcinoma, has received far less attention. Here, we combined laser-capture microdissection and muti-omics mini-bulk sequencing to systematically characterize the epigenetic landscape of oral cancer, including chromatin architecture, DNA methylation, H3K27me3 modification, and gene expression. In carcinogenesis, tumor cells exhibit reorganized chromatin spatial structures, including compromised compartment structures and altered gene-gene interaction networks. Notably, some structural alterations are observed in phenotypically non-malignant paracancerous but not in normal cells. We developed transformer models to identify the cancer propensity of individual genome loci, thereby determining the carcinogenic status of each sample. Insights into cancer epigenetic landscapes provide evidence that chromatin reorganization is an important hallmark of oral cancer progression, which is also linked with genomic alterations and DNA methylation reprogramming. In particular, regions of frequent copy number alternations in cancer cells are associated with strong spatial insulation in both cancer and normal samples. Aberrant methylation reprogramming in oral squamous cell carcinomas is closely related to chromatin structure and H3K27me3 signals, which are further influenced by intrinsic sequence properties. Our findings indicate that structural changes are both significant and conserved in two distinct types of oral cancer, closely linked to transcriptomic alterations and cancer development. Notably, the structural changes remain markedly evident in oral adenocarcinoma despite the considerably lower incidence of genomic copy number alterations and lesser extent of methylation alterations compared to squamous cell carcinoma. We expect that the comprehensive analysis of epigenetic reprogramming of different types and subtypes of primary oral tumors can provide additional guidance to the design of novel detection and therapy for oral cancer.

An ultra-dense linkage map identified quantitative trait loci corresponding to fruit quality- and size-related traits in red goji berry.

Goji berries are a small-fruited shrub with industrial importance whose fruit considered beneficial in both fresh and dried forms. Current germplasms of goji berries include small fruits with a short shelf life, less sweet and bitter taste, and a lack of appropriate genetic information. This study aimed to employ whole genome resequencing to generate an ultra-dense bin linkage map and to elucidate the genetic basis of goji fruit quality and size using quantitative trait loci (QTL) mapping analysis in a cross-pollinated hybrid population. To achieve this goal, human sensory tests were carried out to determine the bitter taste (BT) and sweet taste (ST), and to quantify the soluble solid content (SSC), fruit firmness (FF), and fruit size-related traits of fresh goji fruits over three or four years. The results revealed that the goji bin linkage map based on resequencing spanned a total length of 966.42 cM and an average bin interval of 0.03 cM. Subsequent variant calling and ordering resulted in 3,058 bins containing 35,331 polymorphic markers across 12 chromosomes. A total of 99 QTLs, with individual loci in different environments explaining a phenotypic variance of 1.21-16.95% were identified for the studied traits. Ten major effects, including colocalized QTLs corresponding to different traits, were identified on chromosomes 1, 3, 5, 6, 7, and 8, with a maximum Logarithm of Odds (LOD) of 29.25 and 16.95% of explained phenotypic variance (PVE). In addition, four stable loci, one for FF, one for fruit weight (FW), and two for fruit shape index (FSI), were mainly mapped on chromosomes 5, 6, and 7, elucidating 2.10-16.95% PVE. These findings offer valuable insights into the genetic architecture of goji fruit traits along with identified specific loci and markers to further improve and develop sweeter, less bitter and larger fruited goji berry cultivars with extended shelf life.

Providing biological context for GWAS results using eQTL regulatory and co-expression networks in Populus.

Our study utilized genome-wide association studies (GWAS) to link nucleotide variants to traits in Populus trichocarpa, a species with rapid linkage disequilibrium decay. The aim was to overcome the challenge of interpreting statistical associations at individual loci without sufficient biological context, which often leads to reliance solely on gene annotations from unrelated model organisms. We employed an integrative approach that included GWAS targeting multiple traits using three individual techniques for lignocellulose phenotyping, expression quantitative trait loci (eQTL) analysis to construct transcriptional regulatory networks around each candidate locus and co-expression analysis to provide biological context for these networks, using lignocellulose biosynthesis in Populus trichocarpa as a case study. The research identified three candidate genes potentially involved in lignocellulose formation, including one previously recognized gene (Potri.005G116800/VND1, a critical regulator of secondary cell wall formation) and two genes (Potri.012G130000/AtSAP9 and Potri.004G202900/BIC1) with newly identified putative roles in lignocellulose biosynthesis. Our integrative approach offers a framework for providing biological context to loci associated with trait variation, facilitating the discovery of new genes and regulatory networks.

Cadmium Exposure in Male Rats Results in Ovarian Granulosa Cell Apoptosis in Female Offspring and Paternal Genetic Effects.

The aim of this study was to investigate whether the damage to male offspring induced by cadmium (Cd) exposure during embryonic period leads to the apoptosis of ovarian granulosa cells (OGCs) in the next generation of female offspring, and whether this apoptosis in the offspring was due to paternal genetic effects. Pregnant Sprague-Dawley (SD) rats were exposed to CdCl2 (0, 0.5, 2.0, or 8.0 mg/kg) by gavage daily for 20 days to produce the filial 1 (F1) generation. F1 males were mated with newly purchased females to produce the F2 generation, and the F3 generation was generated in the same way. No apoptotic bodies were observed in the OGCs of either the F2 or F3 generation as shown by electron microscopy, and a reduced OGC apoptosis rate (detected by flow cytometry) was observed in F2 OGCs from the Cd-exposed group. Moreover, the mRNA (qRT-PCR) levels of Bax and Bcl-2 and the protein (western blotting) level of pro-caspase-8 increased in the F2 generation (p < 0.05). The expression of apoptosis-related miRNAs (qRT-PCR) and methylation of apoptosis-related genes (determined via bisulfite-sequencing PCR) in OGCs were further determined. Compared with those of the controls, the expression patterns of microRNAs (miRNAs) in the F2 offspring were different in the Cd-exposed group. The miR-92a-2-5p expression levels were decreased in both the F2 and F3 generations (p < 0.05), while the average methylation level of apoptosis-related genes did not change significantly (except for individual loci). In summary, this study showed that the paternal genetic intergenerational effect of male Cd exposure during embryonic period induced apoptosis of OGCs in the offspring was weakened, and the transgenerational effect disappeared; nevertheless, intergenerational and transgenerational changes in apoptosis-related genes, epigenetic modifications, DNA methylation, and miRNAs were observed, and may be important for understanding the homeostatic mechanisms of the body to alleviate the intergenerational transmission of Cd-induced damage.

Single-mitochondrion sequencing uncovers distinct mutational patterns and heteroplasmy landscape in mouse astrocytes and neurons

BackgroundMitochondrial (mt) heteroplasmy can cause adverse biological consequences when deleterious mtDNA mutations accumulate disrupting “normal” mt-driven processes and cellular functions. To investigate the heteroplasmy of such mtDNA changes, we developed a moderate throughput mt isolation procedure to quantify the mt single-nucleotide variant (SNV) landscape in individual mouse neurons and astrocytes. In this study, we amplified mt-genomes from 1645 single mitochondria isolated from mouse single astrocytes and neurons to (1) determine the distribution and proportion of mt-SNVs as well as mutation pattern in specific target regions across the mt-genome, (2) assess differences in mtDNA SNVs between neurons and astrocytes, and (3) study co-segregation of variants in the mouse mtDNA.Results(1) The data show that specific sites of the mt-genome are permissive to SNV presentation while others appear to be under stringent purifying selection. Nested hierarchical analysis at the levels of mitochondrion, cell, and mouse reveals distinct patterns of inter- and intra-cellular variation for mt-SNVs at different sites. (2) Further, differences in the SNV incidence were observed between mouse neurons and astrocytes for two mt-SNV 9027:G > A and 9419:C > T showing variation in the mutational propensity between these cell types. Purifying selection was observed in neurons as shown by the Ka/Ks statistic, suggesting that neurons are under stronger evolutionary constraint as compared to astrocytes. (3) Intriguingly, these data show strong linkage between the SNV sites at nucleotide positions 9027 and 9461.ConclusionsThis study suggests that segregation as well as clonal expansion of mt-SNVs is specific to individual genomic loci, which is important foundational data in understanding of heteroplasmy and disease thresholds for mutation of pathogenic variants.

COMPARATIVE STUDY ON MORAL VALUES AND LOCUS OF CONTROL BETWEEN ATHEISTS AND THEISTS

The degree to which individuals feel they have control over the events and circumstances that impact their lives is known as their locus of control, a psychological concept. Guidelines that help a person distinguish between good and wrong are known as moral values. The study aims to compare the relationship between Locus of Control and Moral Identity among Atheists and Theists, determining the influence of religious belief on these factors. Atheism believes in the absence of deities, using scientific data and logical justifications to explain human life. Theism is the belief in a superior reality, often called God in Judaism, Christianity, and Islam. Understanding religious beliefs can help us understand human nature and religion's impact on values and behaviors. A sample of 211 individuals was included, including male and female participants from various geographical areas. The study used socio-demographic data collection tools, such as the Moral Identity Questionnaire and Rotter's Locus of Control Scale, and collected data for statistical analysis. The study maintains confidentiality and uses T-tests to examine significant relationships and gender differences. The research found that no significant difference exists between theists and atheists on their locus of control and moral values, and higher morality levels lower an individual's locus of control. KEYWORDS: Locus of control, Atheism, Theism, Moral values, Religio

Drivers of genomic diversity and phenotypic development in early phases of domestication in Hermetia illucens.

The black soldier fly (BSF), Hermetia illucens, has the ability to efficiently bioremediate organic waste into usable bio-compounds. Understanding the impact of domestication and mass rearing on fitness and production traits is therefore important for sustainable production. This study aimed to assess patterns of genomic diversity and its association to phenotypic development across early generations of mass rearing under two selection strategies: selection for greater larval mass (SEL lines) and no direct artificial selection (NS lines). Genome-wide single nucleotide polymorphism (SNP) data were generated using 2bRAD sequencing, while phenotypic traits relating to production and population fitness were measured. Declining patterns of genomic diversity were observed across three generations of captive breeding, with the lowest diversity recorded for the F3 generation of both selection lines, most likely due to founder effects. The SEL cohort displayed statistically significantly greater larval weight com the NS lines with pronounced genetic and phenotypic directional changes across generations. Furthermore, lower genetic and phenotypic diversity, particularly for fitness traits, were evident for SEL lines, illustrating the trade-off between selecting for mass and the resulting decline in population fitness. SNP-based heritability was significant for growth, but was low or non-significant for fitness traits. Genotype-phenotype correlations were observed for traits, but individual locus effect sizes where small and very few of these loci demonstrated a signature for selection. Pronounced genetic drift, due to small effective population sizes, is likely overshadowing the impacts of selection on genomic diversity and consequently phenotypic development. The results hold particular relevance for genetic management and selective breeding for BSF in future.

Extended genome-wide association study employing the African genome resources panel identifies novel susceptibility loci for Alzheimer's disease in individuals of African ancestry.

Despite a two-fold risk, individuals of African ancestry have been underrepresented in Alzheimer's disease (AD) genomics efforts. Genome-wide association studies (GWAS) of 2,903 AD cases and 6,265 controls of African ancestry. Within-dataset results were meta-analyzed, followed by functional genomics analyses. A novel AD-risk locus was identified in MPDZ on chromosome (chr) 9p23 (rs141610415, MAF=0.002, p=3.68×10-9). Two additional novel common and nine rare loci were identified with suggestive associations (P<9×10-7). Comparison of association and linkage disequilibrium (LD) patterns between datasets with higher and lower degrees of African ancestry showed differential association patterns at chr12q23.2 (ASCL1), suggesting that this association is modulated by regional origin of local African ancestry. These analyses identified novel AD-associated loci in individuals of African ancestry and suggest that degree of African ancestry modulates some associations. Increased sample sets covering as much African genetic diversity as possible will be critical to identify additional loci and deconvolute local genetic ancestry effects. Genetic ancestry significantly impacts risk of Alzheimer's Disease (AD). Although individuals of African ancestry are twice as likely to develop AD, they are vastly underrepresented in AD genomics studies. The Alzheimer's Disease Genetics Consortium has previously identified 16 common and rare genetic loci associated with AD in African American individuals. The current analyses significantly expand this effort by increasing the sample size and extending ancestral diversity by including populations from continental Africa. Single variant meta-analysis identified a novel genome-wide significant AD-risk locus in individuals of African ancestry at the MPDZ gene, and 11 additional novel loci with suggestive genome-wide significance at p<9×10-7. Comparison of African American datasets with samples of higher degree of African ancestry demonstrated differing patterns of association and linkage disequilibrium at one of these loci, suggesting that degree and/or geographic origin of African ancestry modulates the effect at this locus. These findings illustrate the importance of increasing number and ancestral diversity of African ancestry samples in AD genomics studies to fully disentangle the genetic architecture underlying AD, and yield more effective ancestry-informed genetic screening tools and therapeutic interventions.

Temporal Changes in Geographic Range and Population Size of the Santa Cruz Black Salamander

Abstract The Santa Cruz black salamander Aneides niger is a priority 3 California species of special concern with a restricted geographic range confined to the Santa Cruz Mountains. Anecdotal observations suggest that the species was relatively abundant in the early 1900s, but it has become more difficult to find in the past few decades. To better understand if the species has undergone population size fluctuations, we analyzed mitochondrial and nuclear sequence data to examine levels of genetic variation and phylogeographic structure, and test for signatures of population size change. We then reconstructed the climatic suitability for the species to 1) determine if past climate fluctuations could have influenced range size and genetic diversity, and 2) estimate the effects of future climate change on geographic range suitability as a proxy for possible future population size change. Genetic analyses detected low levels of genetic variation and a general lack of genetic structuring, suggesting a recent genetic bottleneck. While neutrality tests of individual loci were nonsignificant, skyline plot and isolation-with-migration analyses detected a relatively recent reduction in population size. Interpretation of these genetic results should consider the limited number of localities and individuals sampled for this species. Climatic suitability for Santa Cruz black salamanders was much lower during the last glacial maximum, which could be the cause of the detected historical change in population size. Future projections of climatic suitability under a high-emission scenario suggest a dramatic geographic range restriction to coastal areas. These projections highlight the need for the protection of coastal habitat patches to preserve existing coastal populations, and to maintain connectivity between coastal and inland habitats to allow the westward movement of populations and genes in response to climate change.

Single-Mitochondrion Sequencing Uncovers Distinct Mutational Patterns and Heteroplasmy Landscape in Mouse Astrocytes and Neurons.

Mitochondrial (mt) heteroplasmy can cause adverse biological consequences when deleterious mtDNA mutations accumulate disrupting 'normal' mt-driven processes and cellular functions. To investigate the heteroplasmy of such mtDNA changes we developed a moderate throughput mt isolation procedure to quantify the mt single-nucleotide variant (SNV) landscape in individual mouse neurons and astrocytes In this study we amplified mt-genomes from 1,645 single mitochondria (mts) isolated from mouse single astrocytes and neurons to 1. determine the distribution and proportion of mt-SNVs as well as mutation pattern in specific target regions across the mt-genome, 2. assess differences in mtDNA SNVs between neurons and astrocytes, and 3. Study cosegregation of variants in the mouse mtDNA. 1. The data show that specific sites of the mt-genome are permissive to SNV presentation while others appear to be under stringent purifying selection. Nested hierarchical analysis at the levels of mitochondrion, cell, and mouse reveals distinct patterns of inter- and intra-cellular variation for mt-SNVs at different sites. 2. Further, differences in the SNV incidence were observed between mouse neurons and astrocytes for two mt-SNV 9027:G>A and 9419:C>T showing variation in the mutational propensity between these cell types. Purifying selection was observed in neurons as shown by the Ka/Ks statistic, suggesting that neurons are under stronger evolutionary constraint as compared to astrocytes. 3. Intriguingly, these data show strong linkage between the SNV sites at nucleotide positions 9027 and 9461. This study suggests that segregation as well as clonal expansion of mt-SNVs is specific to individual genomic loci, which is important foundational data in understanding of heteroplasmy and disease thresholds for mutation of pathogenic variants.

A Constitutive Heterochromatic Region Shapes Genome Organization and Impacts Gene Expression in Neurospora crassa.

Genome organization is essential for proper function, including gene expression. In metazoan genome organization, chromatin loops and Topologically Associated Domains (TADs) facilitate local gene clustering, while chromosomes form distinct nuclear territories characterized by compartmentalization of silent heterochromatin at the nuclear periphery and active euchromatin in the nucleus center. A similar hierarchical organization occurs in the fungus Neurospora crassa where its seven chromosomes form a Rabl conformation, where heterochromatic centromeres and telomeres independently cluster at the nuclear membrane, while interspersed heterochromatic loci in Neurospora aggregate across megabases of linear genomic distance for forming TAD-like structures. However, the role of individual heterochromatic loci in normal genome organization and function is unknown. Here, we examined the genome organization of a Neurospora strain harboring a ~47.4 kilobase facultative (temporarily silent) heterochromatic region deletion, as well as the genome organization of a strain deleted of a 110.6 kilobase permanently silent constitutive heterochromatic region. While the facultative heterochromatin deletion had little effect on local chromatin structure, the constitutive heterochromatin deletion altered local TAD-like structures, gene expression, and the predicted 3D genome structure by qualitatively repositioning genes into the nucleus center. Our work elucidates the role of individual heterochromatic regions for genome organization and function.