Biology subjects

Amin, I.

Publications and source records attributed to Amin, I..

10 recordsLinked to original sources

bioRxiv2026

dbverse scales spatial omics analysis with embedded analytical databases

Spatial omics datasets are increasing in size and complexity, exceeding the memory of standard computers and thereby limiting data analysis. Here we present dbverse, a framework for larger-than-memory matrix, spatial and genomic data analysis in embedded analytical databases. Benchmarks show dbverse provides orders of magnitude runtime improvements relative to established in-memory and file-backed methods for core operations in single-cell and spatial omics analysis. We integrated dbverse with Giotto Suite, scaling end-to-end preprocessing of millions of cells and enabling spatial alternative polyadenylation analysis as demonstrated on a Visium HD 3' ovarian clear cell carcinoma sample. The dbverse framework provides an interoperable database foundation for larger-than-memory spatial omics analysis on ordinary computers.

bioinformatics↗

bioRxiv2026

Phagocytosis deficient glia display phagosome processing defects and macrophage recruitment to the brain of adult Drosophila melanogaster.

Efficient clearance of dying cells is essential for brain homeostasis, yet how partial defects in phagocytic processing affect neuroimmune interactions during aging remains unclear. In the adult Drosophila brain, glia function as professional phagocytes through the conserved engulfment receptor Draper (Drpr). Here, we show that glial loss of Drpr does not completely eliminate phagocytosis but instead leads to persistent, age-dependent inefficiency in corpse degradation. Using a genetically encoded pH-sensitive reporter to visualize acidified phagocytic compartments, we find that drpr-deficient glia retain residual engulfment activity but progressively accumulate enlarged, incompletely degraded phagocytic cargo. This chronic clearance defect coincides with altered immune dynamics at the central nervous system periphery, including increased recruitment and adhesion of peripheral hemocytes at the blood-brain barrier (BBB), without overt BBB disruption. Notably, hemocytes at the brain surface can phagocytose glial material in a Drpr-dependent manner, revealing a form of barrier-associated "border clearance". Together, these findings demonstrate that inefficient corpse degradation is sufficient to reshape neuroimmune interactions during aging. Main pointsO_LIDraper-deficient glia still engulf corpses but fail phagolysososomal degradation. C_LIO_LIImpaired glial clearance reshapes immune dynamics at the CNS periphery. C_LIO_LIWith intact BBB, hemocytes that accumulate on the aging brain surface engulf glial debris. C_LI

neuroscience↗

bioRxiv2026

New host and geographic range expansion of Lemuricola nycticebi in the Bengal slow loris

PurposeThe Bengal slow loris (Nycticebus bengalensis) is a globally Endangered nocturnal primate with limited health data across its South and Southeast Asian range. MethodsDuring necropsies of two deceased individuals from northeastern Bangladesh, numerous live adult pinworms were recovered. ResultsMorphological examination combined with mitochondrial cox1 gene sequencing identified the parasites as Lemuricola (Protenterobius) nycticebi. Both hosts exhibited severe gastrointestinal and peritoneal lesions consistent with high-intensity helminth infection. This represents the first confirmed record of L. nycticebi in the Bengal slow loris and extends the parasites known geographic range by approximately 3,400 km. ConclusionOur findings highlight an overlooked parasitic threat to slow lorises. Given that many Bengal slow lorises are rescued or confiscated from the illegal wildlife trade and forest-edge areas in Bangladesh every year and subsequently released into the wild, the results underscore the need for systematic health assessments, including parasitic screening, before repatriation into the wild.

zoology↗

bioRxiv2025

Clinical feasibility of spatial transcriptomics using discarded tissue from diagnostic breast biopsies

Spatial transcriptomics holds potential to transform cancer diagnostics, yet significant barriers still limit its clinical translation. First, access to primary patient tissue is often restricted by logistical challenges and patient hesitancy. Second, it remains uncertain whether high-quality spatial transcriptomics data can be generated from clinical biopsy sections as these are collected primarily for diagnostic purposes that do not prioritize RNA-quality. We investigated whether discarded tissue slices, generated during standard pathology procedures, could be repurposed for spatial transcriptomics and alleviate concerns about both tissue availability and quality. Here, we established a pipeline to collect and perform spatial in situ transcriptomics on discarded biopsy material from a breast cancer patient, and digitized matched pathology images, including hematoxylin and eosin and traditional histochemistry stains from adjacent sections. Our results show that spatial transcriptomics data from discarded tissue are concordant with the original pathology report, while also providing additional insights such as accurate cell type annotation, detailed spatial architecture, and quantification of biological processes relevant to breast cancer progression. Altogether, our approach using discarded pathology tissue sections provides a practical and scalable solution that would maximize the scientific value of existing clinical specimens and enable high-resolution tumor microenvironment mapping.

genomics↗

bioRxiv2023

Giotto Suite: a multi-scale and technology-agnostic spatial multi-omics analysis ecosystem

Emerging spatial omics technologies continue to advance the molecular mapping of tissue architecture and the investigation of gene regulation and cellular crosstalk, which in turn provide new mechanistic insights into a wide range of biological processes and diseases. Such technologies provide an increasingly large amount of information content at multiple spatial scales. However, representing and harmonizing diverse spatial datasets efficiently, including combining multiple modalities or spatial scales in a scalable and flexible manner, remains a substantial challenge. Here, we present Giotto Suite, a suite of open-source software packages that underlies a fully modular and integrated spatial data analysis toolbox. At its core, Giotto Suite is centered around an innovative and technology-agnostic data framework embedded in the R software environment, which allows the representation and integration of virtually any type of spatial omics data at any spatial resolution. In addition, Giotto Suite provides both scalable and extensible end-to-end solutions for data analysis, integration, and visualization. Giotto Suite integrates molecular, morphology, spatial, and annotated feature information to create a responsive and flexible workflow for multi-scale, multi-omic data analyses, as demonstrated here by applications to several state-of-the-art spatial technologies. Furthermore, Giotto Suite builds upon interoperable interfaces and data structures that bridge the established fields of genomics and spatial data science, thereby enabling independent developers to create custom-engineered pipelines. As such, Giotto Suite creates an immersive ecosystem for spatial multi-omic data analysis.

bioinformatics↗

bioRxiv2023

Comparative Analysis, Diversification and Functional Validation of Plant Nucleotide-Binding Site Domain Genes

Nucleotide-binding site (NBS) domain genes are one of a superfamily of resistance genes involved in plant responses to pathogens. The current study identified presumably identified 12,820 NBS-containing genes across 34 species covering from mosses to monocots and dicots. These identified genes classified into 168 classes with several novel domain architectures patterns encompassing significant diversity among plant species. Several classical (NBS, NBS-LRR, TIR-NBS, TIR-NBS-LRR etc.) and species-specific structural patterns (TIR-NBS-TIR-Cupin_1-Cupin_1, TIR-NBS-Prenyltransf, Sugar_tr-NBS etc.) were discovered. We observed 603 orthogroups (OGs) with some core (most common orthogroups; OG0, OG1, OG2 etc.) and unique (highly specific to species; OG80, OG82 etc) OGs with tandem duplications. The expression profiling presented the putative upregulation of OG2, OG6, and OG15 in different tissues under various biotic and abiotic stresses in susceptible and tolerant plants to CLCuD. The genetic variation between susceptible (Coker 312) and tolerant (Mac7) G. hirsutum accessions identified several unique variants in NBS genes of Mac7 (6,583 varaints) and Coker312 (5,173 variants). The protein-ligand and proteins-protein interaction showed a strong interaction of some putative NBS proteins with ADP/ATP and different core proteins of cotton leaf curl disease virus. The silencing of GaNBS (OG2) in resistant cotton through virus-induced gene silencing (VIGS) demonstrated its putative role in virus tittering. The presented study will be further helpful to understand the plant adaptation mechanism.

plant biology↗

bioRxiv2022

Fully Transient CRISPR/Cas12f system in plants capable of broad-spectrum resistance against Begomovirus

CRISPR/Cas system has emerged as the most efficient genome editing technology for both eukaryotic and prokaryotic cells. Recently, biologist have started using CRISPR/Cas9 as a defence machinery in plants against DNA viruses by targeting conserve regions of their genome. Considerable resistance requires formation of stable transgenic lines with multiple gRNAs, targeting specific viruses. Development of such transgenic plants is not only time consuming but also there will always be some uncertainty of their efficiency and off targets in plant genome. Newly discovered miniature CRISPR/Cas12f (Cas14a) system has unique ability to chop down every ssDNA fragment once activated through targeted cleavage. Here we report first fully functional transient CRISPR/Cas12f system in plants. We also show that Cas12f with just one gRNA is enough for substantial broad-spectrum resistance against Gemini viruses. Plant phenotype showed nearly complete recovery and qPCR results showed multifold decrease infection of CLCuV in CRISPR/Cas12f treated plants compare to the infected plants (infected with CLCuMuV and CLCuKV). Smaller size, broad range and more efficiency make Cas12f a superior alternative of Cas9 against diverse group of ssDNA viruses.

plant biology↗

bioRxiv2020

Improving COVID-19 Testing Efficiency using Guided Agglomerative Sampling

One of the challenges in the current COVID-19 crisis is the time and cost of performing tests especially for large-scale population surveillance. Since, the probability of testing positive in large population studies is expected to be small (<15%), therefore, most of the test outcomes will be negative. Here, we propose the use of agglomerative sampling which can prune out multiple negative cases in a single test by intelligently combining samples from different individuals. The proposed scheme builds on the assumption that samples from the population may not be independent of each other. Our simulation results show that the proposed sampling strategy can significantly increase testing capacity under resource constraints: on average, a saving of ~40% tests can be expected assuming a positive test probability of 10% across the given samples. The proposed scheme can also be used in conjunction with heuristic or Machine Learning guided clustering for improving the efficiency of large-scale testing further. The code for generating the simulation results for this work is available here: https://github.com/foxtrotmike/AS.

bioinformatics↗

bioRxiv2019

Genotyping Test Development and Genotyping Survey of Pakistani population of Holstein Friesian imported from Different Origins for A1/A2 SNP in Beta-casein Gene

Quality of milk is determined by multiple factors including microbial load, somatic cell score, content percentages and absence of adulterants. However, in term of genetics, milk quality can be linked with beta casein. Beta casein is a milk protein having genetic variants, one of which is believed to be linked with progression of many diseases including cardiovascular diseases, metabolic diseases and nervous disorders. As beta casein has genetic basis so milk quality can be elucidated by animal genotyping. But no such genotyping facility was available country wide for this purpose. Hence objective of this study is the development of diagnostic test using ARMS-PCR technology in Pakistan and genotyping of beta casein variants in Pakistani population of Holstein Friesian cattle. A total of 166 blood samples were collected from Holstein Friesian (imported from Holland, USA and Australia) and genotyped using ARMS-PCR. Validation of ARMS-PCR was confirmed by Sanger sequencing of beta casein gene from 78 animals. ARMS-PCR based test was then compared with parallel genotyping techniques in term of cost and time effectivity. Reproducibility of this test was tested and validation of this test was done by Sanger sequencing. This test is cost effective as well as time effective in compared to other techniques. Holstein Friesian originating from different countries have different percentages of beta casein variants. This test can be used routinely for genotyping of beta casein. In future there is a need to find out prevalence of beta casein variants of indigenous cattle as well as cross bred population of Pakistan and formulation of breeding policy, keeping in view health concerns of A1 genotype of {beta}-casein.\n\nNovelty StatementIn this study, a diagnostic test is developed to genotype beta casein variants in animal. This is the first report of its kind in Pakistan as before this report either sequencing or tedious and costly procedures were in use for genotyping of beta casein variants in Pakistan. Additionally, for the first time in Pakistan Holstein Friesian imported from Holland, United States and Australia were genotyped to elucidate their genotype status for beta casein polymorphism.

genetics↗

bioRxiv2018

Silencing cathepsin L expression reduces Myzus persicae protein content and the nutritional value as prey for Coccinella septempunctata

Gut-expressed aphid genes, which may be more easily inhibited by RNA interference (RNAi) constructs, are attractive targets for pest control efforts involving transgenic plants. Here we show that expression of cathepsin L, a cysteine protease that functions in aphid guts, can be reduced by expression of an RNAi construct in transgenic tobacco. The effectiveness of this approach is demonstrated by up to 80% adult mortality, reduced fecundity, and delayed nymph production of Myzus persicae (green peach aphids) when cathepsin L expression was reduced by plant-mediated RNAi. Consistent with the function of cathepsin L as a gut protease, M. persicae fed on the RNAi plants had a lower protein content in their bodies and excreted more protein in their honeydew. Larvae of Coccinella septempunctata (seven-spotted ladybugs) grew more slowly on aphids having reduced cathepsin L expression, suggesting that prey insect nutritive value, and not just direct negative effects of the RNAi construct, needs to be considered when producing transgenic plants for RNAi-mediated pest control.\n\nHighlightsO_LISilencing expression of cathepsin L by RNA interference reduces protein content of Myzus persicae (green peach aphid) bodies.\nC_LIO_LIHoneydew of aphids with cathepsin L silenced contains elevated protein.\nC_LIO_LICathepsin L is required for efficient protein uptake from phloem sap.\nC_LIO_LIAphids with cathepsin L expression silenced have increased mortality and fewer offspring.\nC_LIO_LICoccinella septempunctata (seven-spotted ladybugs) grow more slowly on aphids with expression of cathepsin L silenced.\nC_LI\n\n\n\nO_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=173 SRC=\"FIGDIR/small/451211_ufig1.gif\" ALT=\"Figure 1\">\nView larger version (26K):\norg.highwire.dtl.DTLVardef@5ee6d7org.highwire.dtl.DTLVardef@853fe8org.highwire.dtl.DTLVardef@26c2aborg.highwire.dtl.DTLVardef@b67e2b_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗