Biology subjects

Singh, S.

Publications and source records attributed to Singh, S..

At least 181 records · Page 10Linked to original sources

bioRxiv2024

A reconstruction of the mammalian secretory pathway identifies mechanisms regulating antibody production

The secretory pathway processes >30% of mammalian proteins, orchestrating their synthesis, modification, trafficking, and quality control. However, its complexity-- spanning multiple organelles and dependent on coordinated protein interactions--limits our ability to decipher how protein secretion is controlled in biomedical and biotechnological applications. To advance such research, we present secRecon--a comprehensive reconstruction of the mammalian secretory pathway, comprising 1,127 manually curated genes organized within an ontology of 77 secretory process terms, annotated with functional roles, subcellular localization, protein interactions, and complex composition. Using secRecon to integrate multi-omics data, we identified distinct secretory topologies in antibody-producing plasma cells compared to CHO cells. Genes within proteostasis, translocation, and N-glycosylation are deficient in CHO cells, highlighting them as potential engineering targets to boost secretion capacity. Applying secRecon to single-cell transcriptomics and SEC-seq data, we uncovered secretory pathway signatures underlying secretion diversity among IgG-secreting plasma cells. Different transcriptomic clusters had unique secretory phenotypes characterized by variations in the unfolded protein response (UPR), endoplasmic reticulum-associated degradation (ERAD), and vesicle trafficking pathways. Additionally, we discovered specific secretory machinery genes as new markers for plasma cell differentiation. These findings demonstrate secRecon can identify mechanisms regulating protein secretion and guide diverse studies in biomedical research and biotechnology. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=73 SRC="FIGDIR/small/623668v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@f9f865org.highwire.dtl.DTLVardef@122db7forg.highwire.dtl.DTLVardef@1788a1aorg.highwire.dtl.DTLVardef@b2b2bd_HPS_FORMAT_FIGEXP M_FIG C_FIG

systems biology↗

bioRxiv2024

Systematic benchmarking of mass spectrometry-based antibody sequencing reveals methodological biases

The circulating antibody repertoire is crucial for immune protection, holding significant immunological and biotechnological value. While bottom-up mass spectrometry (MS) is the most widely used proteomics technique for profiling the sequence diversity of circulating antibodies (Ab-seq), it has not been thoroughly benchmarked. We quantified the replicability and robustness of Ab-seq using six monoclonal antibodies with known protein sequences in 70 different combinations of concentration and oligoclonality, both with and without polyclonal serum IgG background. Each combination underwent four protease treatments and was analyzed across four experimental and three technical replicates, totaling 3,360 LC-MS/MS runs. We quantified the dependence of MS-based Ab-seq identification on antibody sequence, concentration, protease, background signal diversity, and bioinformatics setups. Integrating the data from experimental replicates, proteases, and bioinformatics tools enhanced antibody identification. De novo peptide sequencing showed similar performance to database-dependent methods for higher antibody concentrations, but de novo antibody reconstruction remains challenging. Our work provides a foundational resource for the field of MS-based antibody profiling.

immunology↗

bioRxiv2024

Fibril fragmentation generates diversity in seed population

Neurodegenerative diseases are characterised by the formation and accumulation of protein fibrils. The mechanism underlaying this aggregation process remains poorly understood. Fibril fragmentation, resulting in seed generation, plays a role in toxicity. Here we provide a quantitative picture of the impact of ultrasound on patient-derived and recombinant fibrils from various diseases. Fragmentation of recombinant Tau fibrils and patient-derived fibrils from Alzheimers Disease, Corticobasal Degeneration and Frontotemporal Dementia generates amyloid and non-amyloid species. Interestingly, patient-derived fibrils are more susceptible to ultrasound than artificial fibrils. Understanding fibril fragmentation and the generation and nature of seeds may provide insights to the molecular mechanism of the disease progression, contributing to the development therapeutic approaches.

biochemistry↗

bioRxiv2024

miRNA Biomarkers in Prostate Cancer: Leveraging Machine Learning for Improved Diagnostic Accuracy

Prostate cancer (PCa) diagnosis often relies on prostate-specific antigen (PSA) testing, but its high false-positive rates often lead to unnecessary biopsies. MicroRNAs (miRNAs) have emerged as promising non-invasive biomarkers for cancer detection due to their stability in biological fluid and disease specificity. Despite their potential, the clinical translation of miRNAs as non-invasive cancer biomarkers is hindered by several challenges - population-based variability, environmental Factors, methodological Inconsistencies, lack of standardization, normalization Issues, and complexity of the biological System. These factors significantly impact the consistency of miRNA expression readouts, particularly in terms of Ct-values, across different studies, which in turn affects the determination of cutoff values that are crucial in a diagnostic setup. This preliminary study offers a pilot demonstration for integrating miRNA biomarker expression with machine learning (ML), which can help identify patterns and improve classification, potentially reducing the reliance on fixed cutoff values in certain contexts and pave the path to wider clinical translation. We analyzed the expression of key miRNAs (miR-21-5p, miR-221-3p, and miR-141-3p) in blood samples from patients with PCa and benign prostatic hyperplasia (BPH). Utilizing a Random Forest classifier, we achieved an accuracy of 77.42%, a precision of 86.21%, a recall of 71.43%, and an AUC-ROC score of 0.78. The application of ML enabled us to leverage complex features, such as combinations and ratios of miRNA expression data, which enhanced the robustness and reliability of the diagnostic model. Additionally, bioinformatics analysis of the preferential features identified by the ML model confirmed the biological relevance of these miRNAs in PCa-related pathways, further supporting their potential as clinical biomarkers. In the future, ML is poised to significantly enhance diagnostic performance compared to traditional linear analyses of a limited set of biomarkers. While our study did not explore multiple populations or the effects of methodological variables, it highlights the potential of ML by demonstrating improved accuracy and eliminating the need for cutoff values. This capability could broaden the applicability of miRNA-based diagnostics, making them more reliable and actionable in clinical settings. However, to fully realize this potential, further validation with larger and more diverse cohorts is essential. Overall, this study lays the groundwork for utilizing ML-enhanced miRNA panels as powerful tools for the early and non-invasive diagnosis of PCa in future clinical practice. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/618146v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@2eddd9org.highwire.dtl.DTLVardef@e6d6c8org.highwire.dtl.DTLVardef@11eea0forg.highwire.dtl.DTLVardef@989c15_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2024

Syzygium cumini (L.) Skeels has Thermostable and Selective Anti-Bacillus anthracis Activity

IntroductionGastrointestinal (GI) anthrax caused by Bacillus anthracis remains a neglected disease in many parts of the Americas, Asia, and Africa. The symptoms include dysentery, stomachache, bloating of the stomach, vomiting, fever, chills, etc. Current study evaluated several edible plants traditionally indicated for GI disease/symptoms in the Indian subcontinent for their anti-B. anthracis activity. Materials & MethodsAqueous extracts of plant parts were assessed for anti-B. anthracis activity using standard antimicrobial susceptibility testing assays. Most promising extracts were evaluated for desirable activity under conditions relevant to their usage, including extremes of temperature, pH, presence of bile salt, impact on gut microflora, and interaction with FDA-approved drugs for anthrax treatment. The bioactive components separated by bioactivity-guided thin-layer-chromatography were subjected to GC-MS characterization. ResultsAqueous Syzygium cumini (L.) Skeels or Jamun extract (AJE) was most potent and reduced the viable colony-forming units (CFU) by 6-logs within 2 hours of exposure at [≥]1.9%w/v concentration. It displayed both desirable selectivity towards gut microflora and thermostability (>90% and [~]80% of anti-B. anthracis activity were retained on incubation at 50{degrees}C for 20 days and at 95{degrees}C for 12h, respectively). AJE and FDA-approved antibiotics for anthrax displayed synergy. GC-MS analysis of AJE identified various previously-identified antimicrobials belonging to categories of alkaloids, flavonoids, phenols, etc. ConclusionAJE has potent and selective anti-B. anthracis activity with the desired degree of thermotolerance, compatibility with gut microflora, and recommended antibiotics. Further studies exploring the bioactive components in AJE and their potential application in preventing anthrax and anthrax-like diseases may be undertaken.

microbiology↗

bioRxiv2024

Model-based fed-batch cultivation of Viola odorata plant cells exhibiting antimalarial and anticancer activity

Viola odorata is used in the indigenous medicine to treat respiratory tract disorders and is limited in availability. Bioprocess principles can be applied to develop sustainable methods to produce high-quality V. odorata biomass. To this effect, a modified stirred tank reactor and a balloon-type bubble column reactor were used to improve biomass production. Nutrient feeding strategies were developed using first principle-based mathematical modelling to achieve higher cell density in the reactor. Experimental validation of the fed-batch model-predicted strategy resulted in a two-fold enhancement in biomass production (32.2 g DW L-1) at the bioreactor level. Also, bioreactor-cultivated biomass extracts were tested for in vitro hemolytic, cytotoxic, anti-inflammatory, and in vivo antiplasmodial activities. This is the first report on fed-batch cultivation in bioreactors and the antiplasmodial activity of V. odorata. Overall, the bioactive potential of the in vitro-generated biomass extracts is found to be similar to that in the natural plant biomass extracts. HighlightsO_LICultivation of V. odorata cell suspension culture using a modified stirred tank and balloon-type bubble column bioreactors. C_LIO_LIBatch kinetic models were developed and extrapolated into a fed-batch model. C_LIO_LIEnhanced biomass production (32.2 g DW L-1) in bioreactors using a nutrient-feeding strategy. C_LIO_LIExtracts showed anti-inflammatory effects and up to 80 % inhibition of parasite growth, with no hemolytic activity. C_LIO_LIConfirmed antiplasmodial activity in vivo, effective alongside artesunate. C_LIO_LIIn vitro-generated biomass extracts showed comparable bioactive potential to that of natural plants. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/618783v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@171c39aorg.highwire.dtl.DTLVardef@1e0eda5org.highwire.dtl.DTLVardef@121eddorg.highwire.dtl.DTLVardef@1a86215_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

The Spc105-Kre28 complex promotes mitotic error correction by outer kinetochore recruitment of the Ipl1/Aurora B kinase

Kinetochores link chromosomes to dynamic microtubules of the mitotic spindle. To ensure equal chromosome segregation, sister chromatids must achieve biorientation. The conserved kinase Aurora B phosphorylates outer kinetochore proteins on attachments lacking tension, allowing re-establishment of new connections until biorientation is achieved. Aurora B localizes to the centromere as part of the chromosomal passenger complex (CPC), but the underlying recruitment pathways can be eliminated without disrupting biorientation. It therefore remains unclear how the kinase operates during error correction. Here, we identify the conserved Spc105/Kre28 complex as an outer kinetochore receptor of the Aurora kinase Ipl1 and its activator Sli15 in Saccharomyces cerevisiae. We show that mutations in the helix bundle domain of Spc105/Kre28 impair mitotic error correction, resembling the effects of ipl1 or sli15 mutants. The defects can be suppressed by artificial recruitment of Ipl1. In biochemical experiments Ipl1/Sli15 directly associates with Spc105/Kre28, and a conserved segment in the Sli15 central domain is crucially involved in the binding mechanism. These results have important implications for the mechanism of tension-dependent error correction during chromosome biorientation.

cell biology↗

bioRxiv2024

Properties of rhythmogenic currents in spinal Shox2 interneurons across postnatal development

Locomotor behaviors are performed by organisms throughout life, despite developmental changes in cellular properties, neural connectivity, and biomechanics. The basic rhythmic activity in the central nervous system that underlies locomotion is thought to be generated via a complex balance between network and intrinsic cellular properties. Within mature mammalian spinal locomotor circuitry, we have yet to determine which properties of spinal interneurons (INs) are critical to rhythmogenesis and how they change during development. Here, we combined whole cell patch clamp recordings, immunohistochemistry, and RNAscope targeting lumbar Shox2 INs in mice, which are known to be involved in locomotor rhythm generation. We focused on the properties of putatively rhythmogenic ionic currents and the expression of corresponding ion channels across postnatal time points in mice. We show that subsets of Shox2 INs display voltage-sensitive conductances, in addition to respective ion channels, which may contribute to or shape rhythmic bursting. Persistent inward currents, M-type potassium currents, slow afterhyperpolarization, and T-type calcium currents are enhanced with age. In contrast, the hyperpolarization-activated and A-type potassium currents were either found with low prevalence in subsets of neonatal, juvenile, and adult Shox2 INs or did not developmentally change. We show that Shox2 INs become more electrophysiologically diverse by juvenile and adult ages, when locomotor behavior is weight-bearing. These results suggest a developmental shift in the magnitude of rhythmogenic ionic currents and the expression of corresponding ion channels that may be important for mature, weight-bearing locomotor behavior.

neuroscience↗

bioRxiv2024

Cryo-EM structures of human GPR155 elucidate its regulatory and transport mechanisms

GPR155 is a polymodal lysosomal membrane "transceptor" comprising both a transporter domain and a GPCR domain, predominantly expressed in brain. GPR155 facilitates cholesterol-dependent mTORC1 signaling and is implicated in neurological disorders like Huntingtons disease. The GPCR domain likely does not bind extracellular ligands canonically, and the functional relationship between GPR155 domains remains unclear. Here, we report the first structures of monomeric human GPR155 and two distinct dimers, revealing an inward-open transporter domain and an inactivated GPCR domain with a unique luminal loop 7 conformation occupying orthosteric pocket. The dimeric assembly is cholesterol-sensitive: at low cholesterol, the transporter domain resembles plant PIN transporters and transports auxin molecules; at high cholesterol, it forms a unique dimer stabilized by cholesterol. Altogether, these findings have implications for uncovering new lysosomal signaling pathways.

biochemistry↗

bioRxiv2024

Synonymous and single nucleotide changes facilitate the adaptation of a horizontally transferred gene.

The movement of genes between microbial species, or horizontal gene transfer, is common. While this process speeds up adaptation, the functionality of horizontally transferred genes is highly constrained in the new hosts due to several reasons, and protein localization is one of them. In this study, we ask what is the minimum number of mutations that can resolve a localization problem faced by a horizontally transferred protein in a new host. Using a directed-evolution approach, we show that SNPs and a synonymous mutation can change the localization patterns of an ammonia transporter (AmtA) moved from Dictyostelium discoideum to Saccharomyces cerevisiae. Interestingly, the mutations that cause this change in localization, confer different fitness effects, are spread throughout the gene, and do not cause a uniform change in amino acids. In a novel attempt, we show how SNPs or a synonymous mutation can alter the membrane affinity of proteins, and as a result, aiding protein evolution and functional diversification.

evolutionary biology↗

bioRxiv2024

Design and immunogenicity of an HIV-1 clade C pediatric envelope glycoprotein stabilized by multiple platforms

Various design platforms are available to stabilize soluble HIV-1 envelope (Env) trimers, which can be used as antigenic baits and vaccine antigens. However, stabilizing HIV-1 clade C trimers can be challenging. Here, we stabilized an HIV-1 clade C trimer based on an Env isolated from a pediatric elite-neutralizer (AIIMS_329) using multiple platforms, including SOSIP.v8.2, ferritin nanoparticles (NP) and an I53-50 two-component NP, followed by characterization of their biophysical, antigenic, and immunogenic properties. The stabilized 329 Envs showed binding affinity to trimer-specific HIV-1 broadly neutralizing antibodies (bnAbs), with negligible binding to non-neutralizing antibodies (non-nAbs). Negative-stain electron microscopy (nsEM) confirmed the native-like conformation of the Envs. Multimerization of 329 SOSIP.v8.2 on ferritin and two-component I53-50 NPs improved the overall affinity to HIV-1 bnAbs and immunogenicity in rabbits. These stabilized HIV-1 clade C 329 Envs demonstrate the potential to be used as antigenic baits and as components of multivalent vaccine candidates in future.

immunology↗

bioRxiv2024

Enhancing NADPH to Restore Redox Homeostasis and Lysosomal Function in G6PD-Deficient Microglia

Microglia, the residential immune cells in the central nervous system (CNS) exhibited in multiple states from resting to activated, play a significant role in neurogenesis, myelination, synaptic transmission, immune surveillance, and neuroinflammation. The aggravated inflammatory response by microglia triggers the generation of superoxide, which often causes the degeneration of neurons, leading to the development of Parkinsons and Alzheimers. The oxidative stress is key to many neurological disorders, often regulated by many genes. The terminal neutralization of oxidative stress is mediated by NADPH and glutathione. The cytosolic NADPH level is majorly contributed by a key enzyme called glucose-6-phosphate dehydrogenase (G6PD). The deficiency of G6PD is associated with hemolytic anemia, diabetes, cardiovascular, autoimmune, and neurological disorders. Our recent study indicated that G6PD deficiency decreases cytosolic NADPH levels and alters redox homeostasis and lysosomal function in microglia. Therefore, replenishment of NADPH is crucial for targeting G6PD deficiency-mediated microglial dysfunctions. This research promotes alternate metabolic pathways by targeting the expression and activity of enzymes such as isocitrate dehydrogenase 1 (IDH1) and malic enzyme 1 (ME1), which are responsible for cytoplasmic NADPH production. Metabolites like citric and malic acid supplementation promote NADPH production and reduce microglial oxidative stress. Additionally, using another group of small-molecule metabolites, such as dieckol and resveratrol, enhances the expression of IDH1 and ME1 enzymes to resolve potential tissue heterogeneity. Finally, combining these metabolites supplementation increased NADPH production and restored redox homeostasis and lysosomal function in G6PD deficient microglia, indicating their further use as potential therapeutics against G6PD deficiency disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/607918v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@5e69f2org.highwire.dtl.DTLVardef@7d9015org.highwire.dtl.DTLVardef@17e5500org.highwire.dtl.DTLVardef@fe9bc5_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

Lessons learned during the journey of data: from experiment to model for predicting kinase affinity, selectivity, polypharmacology, and resistance

Recent advances in machine learning (ML) are reshaping drug discovery. Structure-based ML methods use physically-inspired models to predict binding affinities from protein:ligand complexes. These methods promise to enable the integration of data for many related targets, which addresses issues related to data scarcity for single targets and could enable generalizable predictions for a broad range of targets, including mutants. In this work, we report our experiences in building KinoML, a novel framework for ML in target-based small molecule drug discovery with an emphasis on structure-enabled methods. KinoML focuses currently on kinases as the relative structural conservation of this protein superfamily, particularly in the kinase domain, means it is possible to leverage data from the entire superfamily to make structure-informed predictions about binding affinities, selectivities, and drug resistance. Some key lessons learned in building KinoML include: the importance of reproducible data collection and deposition, the harmonization of molecular data and featurization, and the choice of the right data format to ensure reusability and reproducibility of ML models. As a result, KinoML allows users to easily achieve three tasks: accessing and curating molecular data; featurizing this data with representations suitable for ML applications; and running reproducible ML experiments that require access to ligand, protein, and assay information to predict ligand affinity. Despite KinoML focusing on kinases, this framework can be applied to other proteins. The lessons reported here can help guide the development of platforms for structure-enabled ML in other areas of drug discovery.

biophysics↗

bioRxiv2024

Live Cell Painting: image-based profiling in live cells using Acridine Orange

Image-based profiling has been used to analyze cell health, drug mechanism of action, CRISPR-edited cells, and overall cytotoxicity. Cell Painting is a broadly used image-based assay that uses morphological features to capture how cells respond to treatments. However, this method requires cell fixation for staining, which prevents examining live cells. To address this limitation, here we present Live Cell Painting (LCP), a high-content method based on Acridine orange, a metachromatic dye that labels different organelles and cellular structures. We began by showing that LCP can be applied to follow acidic vesicle redistribution of cells exposed to acidic vesicles inhibitors. Next, we show that LCP can identify subtle changes in cells exposed to silver nanoparticles that are not detected by techniques such as MTT assay. In drug treatments, LCP was helpful in assessing the dose-response relationship and creating profiles that allow clustering of drugs that cause liver injury. Here, we present an affordable and easy-to-use image-based assay capable of assessing overall cell health and showing promise for use in various applications such as assessing drugs and nanoparticles. We envisage the use of Live Cell Painting as an initial screening of overall cell health while providing insights into new biological questions.

cell biology↗

bioRxiv2024

FibrilPaint targets amyloid fibrils for ubiquitination

Failure of the Protein Quality Control (PQC) System to control the Tau protein leads to amyloid fibrils that are at the basis of various Tauopathies, including Alzheimers Disease (AD). Reinstating the PQC for Tau is desirable. Here we show that the PROTAC peptide FibrilPaint20 (FP20) recruits the ubiquitination system to Tau amyloid fibrils. We reconstituted the ubiquitin-proteasome cascade and monitored the stepwise ubiquitin transfer using the microfluidics technique FIDA. To direct ubiquitination specifically to amyloids, we discovered FP20, a bifunctional peptide that connects amyloid fibrils to the E3 ligase CHIP. FP20 mediated ubiquitination of recombinant and patient derived fibrils from various tauopathies, ultimately enabling the 26S proteasome to target CHIP-ubiquitinated Tau fibrils. This shows that FP20 cooperates with the PQC system and can initiate fibril cleavage. This offers a strategy to target amyloid diseases by cooperation with the PQC system exploiting key cellular systems.

biochemistry↗

bioRxiv2024

Fibril Paint: a class of amyloid-targeting peptides

Amyloid fibrils are a common pathological hallmark in multiple neurodegenerative diseases, yet molecular tools to selectively recognise and manipulate them remain scarce. We report FibrilPaints, a family of modular peptides designed for selective amyloid binding and adaptable chemical functionality. The degenerative amyloid-targeting unit of FibrilPaints, W5P4H3R2, has a high content of {pi}-stacking and aromatic side chains. Systematic sequence variation, altering charge, termini, and residue order, revealed the importance of the composition of the amyloid-targeting unit for high-affinity binding across Tau and Huntingtin fibrils. Importantly, sequence changes outside this unit do not preclude fibril binding, which permits attachment of fluorophores or E3-recruiting motifs for targeted protein degradation. This work establishes FibrilPaint as a modular peptide system for the detection and modulation of amyloids. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/609586v4_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@1e9cadborg.highwire.dtl.DTLVardef@50f9eorg.highwire.dtl.DTLVardef@446ee8org.highwire.dtl.DTLVardef@cd47a2_HPS_FORMAT_FIGEXP M_FIG Figure of content The modular design of FibrilPaints enables systematic evaluation of their functionality by testing the binding capacity of each variant (FibrilPaintX) to distinct amyloid fibrils. Successful binding results in visible painting of the fibrils, facilitating their detection and downstream research. C_FIG

biochemistry↗

bioRxiv2024

Type-B response regulators MaRR_B9 and MaRR_B12 coordinate cytokinin-mediated negative regulation of anthocyanin biosynthesis in banana fruits

O_LIAnthocyanins are pigments responsible for vibrant plant colors and play vital roles in plant physiology. Comparing two banana varieties, grand naine (GN) and red banana (RB), which display significant contrast in anthocyanin pigmentation. C_LIO_LITranscriptomic analysis of GN and RB peel and pulp tissue highlighted cytokinin-specific response regulators, MaRR_B9 and MaRR_B12, as regulators of anthocyanin biosynthesis. C_LIO_LIThrough a combination of physiological, molecular, and biochemical analyses, we demonstrate that MaRR_B9 and MaRR_B12 exert direct regulatory control over key structural genes of anthocyanin biosynthesis, dihydroflavanol reductase (MaDFR) and anthocyanidin synthase (MaANS). MaRR_B9 and MaRRB_12 interact with the promoters of MaDFR and MaANS, repressing the concerned genes in vivo. Overexpression of MaRR_B9 and MaRR_B12 in banana fruits leads to a reduction in anthocyanin content, particularly that of the cyanidin derivative, along with altered expression patterns of MaDFR and MaANS. C_LIO_LIThus, the present study identifies novel regulators of anthocyanin biosynthesis in banana and provides further evidence that the cytokinin regulatory network modifies anthocyanin accumulation in plants. In conclusion, our findings reveal new molecular targets, in the form of MaRRs for the genetic manipulation of anthocyanin content and thereby for the development of stress-resilient and nutritionally enriched crop plants. C_LI

plant biology↗

bioRxiv2024

Exploring ancestry inference of the Middle East

The capability to infer biogeographic ancestry with curated panels of ancestry informative markers (AIMs) is a critical component to DNA intelligence. There are many AIM panels that resolve population differentiation at a continental level. Of late, several studies have directed marker discovery to the Middle East because of the difficulties for AIM panels to resolve this region amongst populations in Eurasia. The AIM discovery process has remained largely unchanged, except for the most recent additions of whole-genome sequence (WGS) data repositories which now include Middle Eastern individuals. Here, the latest WGS data from 1000 Genomes Project and Human Genome Diversity Project was paired with novel Middle Eastern population data from Lebanon for AIMs discovery. An unbiased genetic clustering approach was employed for selecting population clusters for allelic frequency comparisons. Two candidate AIMs were reported, compared, and evaluated together with the autosomal AIMs from the VISAGE Enhanced Tool. These comparisons involved a validation dataset from Middle Eastern WGS data published by the Wellcome Sanger Institute and resulted in slight gains of Middle Eastern ancestry proportions for several Middle Eastern samples with varying levels of co-ancestries. The validation samples also underwent an unsupervised worldwide ADMIXTURE analysis alongside previously mentioned WGS datasets using nearly two million markers (r2 < 0.1) to establish a ground truth population membership. Lastly, a novel application of the deep learning dimensional reduction algorithm popVAE is provided as an open-source web tool to illustrate the AIM panels variance among these population clusters within two dimensions for easy global ancestry visualization in addition to providing a closest population membership metric.

genetics↗