Biology subjects

Ahmad, M.

Publications and source records attributed to Ahmad, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2023

Chemical inhibition of histidine biosynthesis curtails M. tuberculosis infection

To overcome the drug resistance crisis and shorten the current duration of human tuberculosis (TB) therapy, new anti-TB molecules is required. In an earlier study, we have shown that Mycobacterium tuberculosis (Mtb), the causative agent of TB, with a fractured de novo histidine biosynthesis fails to mount TB infection in mouse model, emboldening that disrupting the function of this pathway may constitute a novel strategy to curtailing TB infection. In this study, through a target based approach we have designed a number of triazole scaffold molecules specific to imidazole glycerol phosphate dehydratase (IGPD; HisB) of this pathway and have delineated atomic level interactions between the enzyme and inhibitors which pinpointed the specificity and the inhibitory mechanism. Importantly, these molecules exhibited significant potency against free as well as macrophage-internalized wild-type and drug-resistant clinical isolates in culture medium. Notably, a couple of these compounds showed efficacy in reducing the bacterial burden in Mtb-infected mouse model. The chemical inhibition of IGPD induces histidine auxotrophy in Mtb and brings in new prospects to the area of anti-TB drug discovery.

biochemistry↗

bioRxiv2022

O-GlcNAcylation promotes YTHDF1 cytosolic localization and colorectal cancer tumorigenesis

O-linked N-acetylglucosamine (O-GlcNAc) is an emerging post-translation modification that couples metabolism with cellular signal transduction by crosstalking with phosphorylation and ubiquitination to orchestrate various biological processes. Herein we show that it modifies the N6-methyladenosine (m6A)-mRNA reader YTHDF1 and fine-tunes its nuclear translocation by the exportin protein Crm1. First we present evidence that YTHDF1 interacts with the sole O-GlcNAc transferase (OGT). Second, we verified the YTHDF1 O-GlcNAcylation sites to be Ser196/Ser197/Ser198, as described in previous numerous chemoproteomic studies. Then we constructed the O-GlcNAc-deficient YTHDF1-S196AS197FS198A (AFA) mutants, which significantly attentuated O-GlcNAc signals. Moreover, we revealed that YTHDF1 is a nucleocytoplasmic protein, whose nuclear export is mediated by Crm1. Furthermore, O-GlcNAcylation increases the cytosolic portion of YTHDF1 by enhancing binding with Crm1, thus upregulating the downstream target (e.g. c-Myc) expression. Molecular dynamics simulations suggest that O-GlcNAcylation at S197 might promote the binding between the nuclear export signal motif and Crm1 through increasing hydrogen bonding. Mouse xenograft assays further demonstrate that YTHDF1-AFA mutants decreased the colon cancer mass and size via decreasing c-Myc expression. In sum, we found that YTHDF1 is a nucleocytoplasmic protein, whose cytosolic localization is dependent on O-GlcNAc modification. We propose that the OGT-YTHDF1-c-Myc axis might underlie colorectal cancer tumorigenesis.

biochemistry↗

bioRxiv2022

A Generalizable Nanopore Sensor for Highly Specific Protein Detection at Single-Molecule Precision

Protein detection and biomarker profiling have wide-ranging implications in many areas of basic research and molecular diagnostics. Substantial progress has been made in protein analytics using nanopores and the resistive-pulse technique. Yet, a long-standing challenge is implementing specific binding interfaces for detecting proteins without the steric hindrance of the pore interior. To overcome this technological difficulty, we formulate a new class of sensing elements made of a programmable antibody-mimetic binder fused to a monomeric protein nanopore. This way, such a modular design significantly expands the utility of nanopore sensors to numerous proteins while preserving their architecture, specificity, and sensitivity. We prove the power of this approach by developing and validating nanopore sensors for protein analytes that drastically vary in size, charge, and structural complexity. These analytes produce unique electrical signatures that depend on their identity and quantity and the binder-analyte assembly at the nanopore tip. From a practical point of view, our sensors unambiguously probe protein recognition events without the necessity of using any additional exogenous tag. The outcomes of this work will impact biomedical diagnostics by providing a fundamental basis and tools for protein biomarker detection in biofluids.

biophysics↗

bioRxiv2022

Low-cost and highly efficient: A method for high-quality nucleic acid isolation from cotton fibres

Gene expression analyses to study the development of cotton fibers require high-quality nucleic acid. The conventional methods of nucleic acid extraction results in sub-quality nucleic acids with low yields. Young fibers are rich in polyphenols and sugars that react with nucleic acid to form phenols and insoluble substances. Furthermore, mature fibers contain more than 95% cellulose, hindering the nucleic acid isolation. Cytoplasm collapse and cellulose deposition also result in a very low yield of nucleic acid. Three different methods of RNA isolation from different cotton tissues were compared in this study to determine the best and most efficient one. The integrity and quality of RNA were analyzed using UV spectrum, agarose gel electrophoresis, RIN values, PCR, and Northern blot hybridization. RNA of functional quality was observed when using the high ion and pH method, with an A260/A280 ratio up to 1.87 and an average yield of 0.68 mg g-1 from fiber cells. From leaves, we found an A260/A280 ratio of 2.02 and an average yield of 6.35 mg g-1, which is suitable for molecular biology experiments. The extraction buffer with a high ion density and pH value include Tris-HCl, LiCl, EDTA, SDS, sodium deoxycholate, Nonident P-40, mercaptoethanol, and PVP. The addition of sodium deoxycholate and Nonider-40 (NP-40) enhances the density of other salt compounds and elevates the pH value. The results depicted that the high ion and pH method is a simple and effective way to extract a copious amount of high-quality RNA from polysaccharide-rich tissues. This method is also suitable for the extraction of cotton genomic DNA with high purity. Genomic DNA extracted from cotton using this method showed an A260/A230 ratio up to 2.09 and a yield of 1.44 mg g-1. This method is useful for isolating DNA and RNA from cotton fibers and produces high yields and quality at a comparatively low cost.

genomics↗

bioRxiv2022

Evaluation of Association between CSN2 Genetic Marker 7:32016718C>A with A1/A2 Milk in Pakistani Buffaloes

Milk is an essential part of the diet that plays an important role in human growth and development due to the presence of different components like calcium, fats and proteins. Among six major proteins of the milk, {beta}-casein is one of them which is being investigated here due to the A1/A2 milk genetic variants and its associated gene of CSN2 in one of the valued species of Bubalus bubalis in Pakistan. Fifty buffalo samples were genotyped using the ARMS-PCR technique. CSN2 gene locus 32016718C>A is located on Chr.7 with CDS position c.350C>A on its 7th exon as per (GenBank transcript ID: XM_006071124.3). In {beta}-casein, 117th amino acid position where histidine (CAT) is responsible for A1 and proline (CCT) for A2 milk phenotype. A2 milk is considered to be healthy for human health due to the absence of bioactive peptide {beta}-casomorphin-7 (BCM7) in comparison with A1 milk. The current results showed that overall, 100% buffalo population is homozygous wild-type (CC) which means no mutant allele is detected in all studied samples therefore, Pakistani buffalo is exclusively producing A2 milk. Furthermore, this work may also be conducted on different buffalo breeds in Pakistan as well as other species of cattle, goat, sheep and camel to explore their genomic architecture for this valued trait.

genetics↗

bioRxiv2022

Rye: genetic ancestry inference at biobank scale

Biobank projects around the world are generating genomic data for many thousands and even millions of individuals. Computational methods are needed to handle these massive data sets, including tools for genetic ancestry (GA) inference. Current methods for GA inference are generally accurate, but they are slow and do not scale to biobank-size genomic datasets. Here we present Rye - a new algorithm for GA inference at biobank scale. We compare the accuracy and runtime performance of Rye to the widely used RFMix and ADMIXTURE programs, and we apply it to a dataset of 488,221 genome-wide variant samples from the UK Biobank. Rye infers GA based on principal component analysis (PCA) of genomic variant samples from ancestral reference populations and query individuals. The algorithms accuracy is powered by Metropolis-Hastings optimization and its speed is provided by non-negative least squares (NNLS) regression. Rye produces highly accurate GA estimates for three-way admixed populations - African, European, and Native American - compared to RFMix and ADMIXTURE (R2 = 0.998 - 1.00), and shows 50x runtime improvement compared to ADMIXTURE on the UK Biobank dataset. Rye analysis of UK Biobank samples demonstrates how it can be used to infer GA at different levels of relatedness. We discuss user consideration and options for the use of Rye; the program and its documentation are distributed on the GitHub repository: https://github.com/healthdisparities/rye.

bioinformatics↗

bioRxiv2022

The role of floral traits in community assembly process at high elevations in Lesser Himalaya

O_LIEcological theory postulates that plant trait research should consider multiple traits related to different organs and/or ontogenetic stages as such traits represent different ecological niche axes. Particularly, floral traits have been suggested to play an important role in assembling plant communities along environmental gradients as they determine the reproductive success, one of the key functions in plants. Yet, the predictive power of floral traits in community assembly research remains largely unverified empirically. C_LIO_LIWe analyzed the predictive power of six floral traits of 139 herbaceous species for inferring community assembly process in twenty-one sites located along an elevation gradient in Lesser Himalaya ranging from 2,000 to 4,000 meters above sea level. The floral trait variability along the gradient was analyzed using community-weighted trait mean (CWM) values and functional diversities (FD) calculated for each of the study communities. C_LIO_LIThe CWM values for onset of flowering and flower display area increased significantly with increasing elevation, whereas specific flower area showed an opposite pattern. In combination with convergence in onset of flowering and specific area (i.e., lower FD values in high elevation sites), these patterns suggest that abiotic filtering and plant-pollinator interactions affected the floral trait composition of the communities studied. Increasing low-temperature stress towards high-elevation sites selected for late-flowering species that produce resource-intensive flowers with larger display areas. C_LIO_LILow pollinator abundancy and activity in high elevation, could also explain why these traits were selected in the study communities. Delayed flowering with increasing elevations might facilitate the phenological overlap of plants and their pollinators, as pollinator activity at higher elevation peaks in the second half of the vegetation period. The dominance of species with low specific flower area and larger display area in high elevation communities were attributed to the increased flower longevity and attraction of pollinators, respectively, to maximize pollination success under pollinator scarcity. C_LIO_LISynthesis. Our study provides empirical support of the recent argument that floral traits contribute considerably to the assembly of plant communities along environmental gradients. Thus, such traits should be included into community assembly research agenda as they represent key growth and survival ecological functions. C_LI

ecology↗

bioRxiv2021

Functional Communication between IP3R and STIM2 at sub-threshold stimuli is a critical checkpoint for initiation of SOCE

Stromal interaction molecules, STIM1 and STIM2, sense decreases in the endoplasmic reticulum (ER) [Ca2+] ([Ca2+]ER) and cluster in ER-plasma membrane (ER-PM) junctions where they recruit and activate Orai1. While STIM1 responds when [Ca2+]ER is relatively low, STIM2 displays constitutive clustering in the junctions and is suggested to regulate basal Ca2+ entry. The cellular cues that determine STIM2 clustering under basal conditions is not known. By using gene editing to fluorescently tag endogenous STIM2, we report that endogenous STIM2 is constitutively localized in mobile and immobile clusters. The latter associate with ER-PM junctions and recruit Orai1 under basal conditions. Agonist stimulation increases immobile STIM2 clusters which co- ordinate recruitment of Orai1 and STIM1 to the junctions. Extended synaptotagmin (E-Syt)2/3 are required for forming the ER-PM junctions, but are not sufficient for STIM2 clustering. Importantly, inositol 1,4,5-triphosphate receptor (IP3R) function and local [Ca2+]ER are the main drivers of immobile STIM2 clusters. Enhancing, or decreasing, IP3R function at ambient [IP3] causes corresponding increase, or attenuation, of immobile STIM2 clusters. We show that immobile STIM2 clusters denote decreases in local [Ca2+]ER mediated by IP3R that is sensed by the STIM2-N terminus. Finally, under basal conditions, ambient PIP2-PLC activity of the cell determines IP3R function, immobilization of STIM2, and basal Ca2+ entry while agonist stimulation augments these processes. Together, our findings reveal that immobilization of STIM2 clusters within ER-PM junctions, a first response to ER-Ca2+ store depletion, is facilitated by the juxtaposition of IP3R and marks a checkpoint for initiation of Ca2+ entry. SignificanceSTIM proteins sense decreases in [Ca2+]ER and cluster in endoplasmic reticulum (ER)-plasma membrane (PM) junctions where they recruit and activate Orai1. While STIM1 clustering requires substantial [Ca2+]ER decrease, STIM2 displays pre-clustering under resting conditions and regulates basal Ca2+ entry. The mechanism(s) underlying constitutive clustering of STIM2 is not known. We show herein that endogenous STIM2 assembles as mobile and immobile clusters and that Orai1 is recruited to the latter. Anchoring of STIM2 clusters is triggered by decreases in local [Ca2+]ER that is mediated by ambient activity of IP3R and sensed by the STIM2 N-terminus. This functional link between IP3R and STIM2 governs constitutive STIM2 clustering and ensures coupling of [Ca2+]ER decrease at sub-threshold stimuli with activation of Ca2+ entry.

physiology↗

bioRxiv2021

Aβ toxicity rescued by protein retention in the ER

Accumulation of A{beta} in the brain is one of the hallmarks of Alzheimers disease (AD). In the adult Drosophila brain, human A{beta} over-expression is toxic and leads to deterioration of climbing ability and shortened lifespan. However, it remains unknown if A{beta} is inherently toxic or if it triggers toxic downstream pathways that lead to neurodegeneration. Here, we describe a novel, and previously unidentified, protective role of intracellular laminin chain accumulation. Despite high A{beta} levels, over-expression of the extracellular matrix protein subunit Laminin B1 (LanB1) resulted in a robust rescue of toxicity, highlighting a potential protective mechanism of resistance to A{beta}. Over-expression of other Laminin subunits and a Collagen IV subunit also significantly rescued A{beta} toxicity, while combining LanB1 with these subunits led to an even larger rescue. Imaging revealed that LanB1 was retained in the ER but had no effect on the secretion of A{beta} into the extracellular milieu. LanB1 rescued toxicity independently of the IRE1/XBP1-mediated branch of the ER stress response. Interestingly, over-expression of ER-targeted GFP also rescued A{beta} toxicity, indicating a potentially broader benefit of ER protein retention. Finally, in proof-of-principle lentiviral transduction experiments using murine organotypic hippocampal slice cultures, over-expression of mouse Lamb1 resulted in ER-retention in transduced cells, highlighting a conserved mechanism. Typically, retention of proteins in the ER is detrimental to cellular health, but in the context of neuronal A{beta} toxicity it may prove to be beneficial and a new therapeutic avenue for AD.

neuroscience↗

bioRxiv2021

Spatial and ecological drivers of population structure in Alkanna tinctoria (Boraginaceae), a polyploid medicinal herb

Background and AimsQuantifying genetic variation is fundamental to understand a species demographic trajectory and its ability to adapt to future changes. In comparison to diploids, however, genetic variation and factors fostering genetic divergence remains poorly studied in polyploids due to analytical challenges. Here, by employing a ploidy-aware framework, we investigated the genetic structure and its determinants in polyploid Alkanna tinctoria (Boraginaceae), an ancient medicinal herb that is the source of bioactive compounds known as alkannin and shikonin (A/S). From a practical perspective, such investigation can inform biodiversity management strategies. MethodsWe collected 14 populations of A. tinctoria within its main distribution range in Greece and genotyped them using restriction site-associated DNA sequencing (RAD-seq). As an outgroup, we included two populations of A. sieberi. By using a ploidy-aware genotype calling based on likelihoods, we generated a dataset of 16,107 high quality SNPs. Classical and model-based analysis was done to characterize the genetic structure within and between the sampled populations. Finally, to reveal the drivers of genetic structure, we searched for associations between allele frequencies and spatial and climatic variables. Key ResultsWe found support for a marked regional structure in A. tinctoria along a latitudinal gradient in line with phytogeographic divisions. Several analyses identified interspecific admixture affecting both mainland and island populations. Modelling of spatial and climatic variables further demonstrated a larger contribution of neutral processes and a lesser albeit significant role of selection in shaping the observed genetic structure in A. tinctoria. ConclusionsCurrent findings provide evidence of strong genetic structure in A. tinctoria mainly driven by neutral processes. The revealed natural genomic variation in Greek Alkanna can be used to further predict variation in A/S production, whereas our bioinformatics approach should prove useful for the study of other non-model polyploid species.

genomics↗

bioRxiv2021

Characterization of the NiRAN domain from RNA-dependent RNA polymerase provides insights into a potential therapeutic target against SARS-CoV-2

Apart from the canonical fingers, palm and thumb domains, the RNA dependent RNA polymerases (RdRp) from the viral order Nidovirales possess two additional domains. Of these, the function of the Nidovirus RdRp associated nucleotidyl transferase domain (NiRAN) remains unanswered. The elucidation of the 3D structure of RdRp from the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), provided the first ever insights into the domain organisation and possible functional characteristics of the NiRAN domain. Using in silico tools, we predict that the NiRAN domain assumes a kinase or phosphotransferase like fold and binds nucleoside triphosphates at its proposed active site. Additionally, using molecular docking we have predicted the binding of three widely used kinase inhibitors and five well characterized anti-microbial compounds at the NiRAN domain active site along with their drug-likeliness as well as DFT properties. For the first time ever, using basic biochemical tools, this study shows the presence of a kinase like activity exhibited by the SARS-CoV-2 RdRp. Interestingly, the proposed kinase inhibitors and a few of the predicted nucleotidyl transferase inhibitors significantly inhibited the aforementioned enzymatic activity. In line with the current global COVID-19 pandemic urgency and the emergence of newer strains with significantly higher infectivity, this study provides a new anti-SARS-CoV-2 drug target and potential lead compounds for drug repurposing against SARS-CoV-2.

bioinformatics↗

bioRxiv2020

Molecular basis of the logical evolution of the novel coronavirus SARS-CoV-2: A comparative analysis

A novel disease, COVID-19, is sweeping the world since end of 2019. While in many countries, the first wave is over, but the pandemic is going through its next phase with a significantly higher infectability. COVID-19 is caused by the novel Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) that seems to be more infectious than any other previous human coronaviruses. To understand any unique traits of the virus that facilitate its entry into the host, we compared the published structures of the viral spike protein of SARS-CoV-2 with other known coronaviruses to determine the possible evolutionary pathway leading to the higher infectivity. The current report presents unique information regarding the amino acid residues that were a) conserved to maintain the binding with ACE2 (Angiotensin-converting enzyme 2), and b) substituted to confer an enhanced binding affinity and conformational flexibility to the SARS-CoV-2 spike protein. The present study provides novel insights into the evolutionary nature and molecular basis of higher infectability and perhaps the virulence of SARS-CoV-2.

evolutionary biology↗

bioRxiv2020

B1 and B2 B cells are characterized by distinct CpG modification states at DNMT3A-maintained enhancers

We show that DNA methylation is a layered process in B lymphocytes. An underlying foundational methylome is stably established during B lineage commitment and overlaid with a DNMT3A-maintained dynamic methylome which is sculpted in distinct ways in B1 and B2 B cells during B cell development. An engineered loss of DNMT3A after commitment to the B lineage unmasks a foundational methylome that is shared in both B1 and B2 sub-lineages. The dynamic methylome is comprised of novel enhancers whose methylation state is maintained by DNMT3A but can be modulated in strikingly different ways in B1 and B2 B cells. During B1 B cell development, the dynamic methylome undergoes a prominent programmed demethylation event that is not observed during B2 B cell development. The methylation pattern of the dynamic methylome is determined by the coincident recruitment of DNMT3A and TET enzymes and it regulates the developmental expression of B1 and B2 lineage-specific genes.

immunology↗

bioRxiv2020

Potential short-term negative versus positive effects of olive mill-derived biochar on nutrient availability in a calcareous loamy sandy soil

In this study, a greenhouse pot experiment with maize (Zea mays L.) was conducted using treatments consisting of a control (CK), inorganic fertilizer of NPK (INF), and 1% and 3% (wt/wt) of olive mill solid waste (OMSW)-derived biochar (BC) at various pyrolytic temperatures (300-700 {degrees}C). The goal was to investigate potential negative versus positive effects of BC on pH, electrical conductivity (EC), and nutrient (P, K, Na, Ca, Mg, Fe, Mn, Zn, and Cu) availability in a calcareous loamy sandy soil. The results showed that application of OMSW-derived BC, especially with increasing pyrolysis temperature and/or application rate, significantly increased soil pH, EC, NH4OAc-extractable K, Na, Ca, and Mg, and ammonium bicarbonate-diethylenetriaminepentaacetic acid (AB-DTPA)-extractable Fe and Zn, while AB-DTPA-extractable Mn decreased. The application of 1% and 3% BC, respectively, increased the NH4OAc-extractable K by 2.5 and 5.2-fold for BC300, by 3.2 and 8.0-fold for BC500, and by 3.3 and 8.9-fold for BC700 compared with that of untreated soil. The results also showed significant increases in shoot content of K, Na, and Zn, while there were significant decreases in shoot content of P, Ca, Mg, and Mn. Furthermore, no significant effects were observed for growth of maize plants as a result of biochar BC addition. In conclusion, OMSW-derived BC can potentially have positive effects on the enhancement of soil K availability and its plant content but it reduced shoot nutrients, specifically P, Ca, Mg, and Mn; therefore, application of OMSW-derived BC to calcareous soil might be restricted.

bioengineering↗

bioRxiv2020

Disease-specific variant pathogenicity prediction significantly improves variant interpretation in inherited cardiac conditions

BackgroundAccurate discrimination of benign and pathogenic rare variation remains a priority for clinical genome interpretation. State-of-the-art machine learning tools are useful for genome-wide variant prioritisation but remain imprecise. Since the relationship between molecular consequence and likelihood of pathogenicity varies between genes with distinct molecular mechanisms, we hypothesised that a disease-specific classifier may outperform existing genome-wide tools. MethodsWe present a novel disease-specific variant classification tool, CardioBoost, that estimates the probability of pathogenicity for rare missense variants in inherited cardiomyopathies and arrhythmias, trained with variants of known clinical effect. To benchmark against state-of-the-art genome-wide pathogenicity classification tools, we assessed classification of hold-out test variants using both overall performance metrics, and metrics of high-confidence (>90%) classifications relevant to variant interpretation. We further evaluated the prioritisation of variants associated with disease and patient clinical outcomes, providing validations that are robust to potential mis-classification in gold-standard reference datasets. ResultsCardioBoost has higher discriminating power than published genome-wide variant classification tools in distinguishing between pathogenic and benign variants based on overall classification performance measures with the highest area under the Precision-Recall Curve as 91% for cardiomyopathies and as 96% for inherited arrhythmias. When assessed at high-confidence (>90%) classification thresholds, prediction accuracy is improved by at least 120% over existing tools for both cardiomyopathies and arrhythmias, with significantly improved sensitivity and specificity. Finally, CardioBoost improves prioritisation of variants significantly associated with disease, and stratifies survival of patients with cardiomyopathies, confirming biologically relevant variant classification. ConclusionsWe demonstrate that a disease-specific variant pathogenicity prediction tool outperforms state-of-the-art genome-wide tools for the classification of rare missense variants of uncertain significance for inherited cardiac conditions. To facilitate evaluation of CardioBoost, we provide pre-computed pathogenicity scores for all possible rare missense variants in genes associated with cardiomyopathies and arrhythmias (https://www.cardiodb.org/cardioboost/). Our results also highlight the need to develop and evaluate variant classification tools focused on specific diseases and clinical application contexts. Our proposed model for assessing variants in known disease genes, and the use of application-specific evaluations, is broadly applicable to improve variant interpretation across a wide range of Mendelian diseases.

genetics↗

bioRxiv2020

Extreme acid resistance of human cheek epithelial cells.

Human cheek epithelial cells, despite residing in an almost neutral environment of the mouth, are exposed to many acidic stimuli, so these cells may possess acid resistance. Our researchs objective is to find out if isolated human cheek epithelial cells can survive in highly acidic conditions, and whether there is any difference in acid resistance between cheek epithelial cells of males and females; and to establish a protocol. We collected 3 buccal swab samples from each male or female participant and gave following 3 different treatments to their samples: (i) Milli-Q water (ii) HCl with pH of -0.48 (iii) HCl with pH of - 0.48 and, then, rehydration with Milli-Q water. Staining and microscopic analysis showed that cheek epithelial cells did not burst after acid treatment. However, they slightly shrunk in size and were stained substantially darker. Moreover, cells that were rehydrated after acid treatment, provided further evidence of their survival because these cells, as a result of rehydration, had substantially regained bigger size as well as lighter staining. Furthermore, at pH of -0.48, no difference was observed in acid resistance of the cells from the two genders. Results of this study, which is the only one to incubate cheek epithelial cells at pH < 2.0, manifest that the human cheek epithelial cells, isolated from any of the two genders, are extremely acid-resistant and do not burst in highly acidic conditions. Besides, these cells may also be useful as model cells for the study of acid-resistant pathogens and acid-resistant cancer cells.

cell biology↗

bioRxiv2018

Relative Principal Components Analysis: Application to Analyzing Biomolecular Conformational Changes

A new method termed \"Relative Principal Components analysis\" (RPCA) is introduced that extracts optimal relevant principal components to describe the change between two data samples representing two macroscopic states. The method is widely applicable in data-driven science. Calculating the components is based on a unified physical framework which introduces the objective function, namely the Kullback-Leibler divergence, appropriate for quantifying the change of the macroscopic state as it is effected by the microscopic features. To demonstrate the applicability of RPCA, we analyze the thermodynamically relevant conformational changes of the protein HIV-1 protease upon binding to different drug molecules. In this case, the RPCA method provides a sound thermodynamic foundation for the analysis of the binding process. The relevant collective (global) conformational changes can be reconstructed from the informative latent variables to exhibit both the enhanced and the restricted conformational fluctuations upon ligand association. Moreover, RPCA characterizes the locally relevant conformational changes which can be presented on the structure of the protein.

biophysics↗

bioRxiv2018

Quantitative approaches to variant classification increase the yield and precision of genetic testing in Mendelian diseases: The case of hypertrophic cardiomyopathy

BackgroundInternational guidelines for variant interpretation in Mendelian disease set stringent criteria to report a variant as (likely) pathogenic, prioritising control of false positive rate over test sensitivity and diagnostic yield. Genetic testing is also more likely informative in individuals with well-characterised variants from extensively studied European-ancestry populations. Inherited cardiomyopathies are relatively common Mendelian diseases that allow empirical calibration and assessment of this framework.\n\nResultsWe compared rare variants in large hypertrophic cardiomyopathy (HCM) cohorts to reference populations to identify variant classes with high prior likelihoods of pathogenicity, as defined by etiological fraction (EF). Analysis of variant distribution identified regions in which variants are significantly enriched in cases and variant location was a better discriminator of pathogenicity than generic computational functional prediction algorithms. Non-truncating variant classes with an EF[≥]0.95, and therefore clinically actionable, were identified in 5 established HCM genes. Applying this approach leads to an estimated 14-20% increase in cases with actionable HCM variants.\n\nConclusionsWhen found in a patient confirmed to have disease, novel variants in some genes and regions are empirically shown to have a sufficiently high probability of pathogenicity to support a \"likely pathogenic\" classification, even without additional segregation or functional data. This could increase the yield of high confidence actionable variants, consistent with the framework and recommendations of current guidelines. The techniques outlined offer a consistent, unbiased and equitable approach to variant interpretation for Mendelian disease genetic testing. We propose adaptations to ACMG/AMP guidelines to incorporate such evidence in a quantitative and transparent manner.

genetics↗