Biology subjects

Kashif, M.

Publications and source records attributed to Kashif, M..

8 recordsLinked to original sources

bioRxiv2026

Multi-Scale Contextual Attention for Robust Crop and Pest Image Classification

Image-based crop and pest recognition is considered useful for reducing the delay and cost of manual field scouting, therefore supporting timely intervention in precision-agriculture workflows. However, the real field imagery remains challenging due to the cluttered backgrounds, occlusions, illumination changes, and strong scale variation that are frequently observed across crops. The symptoms are often small or low-contrast, and pests may be partially hidden, which reduces the reliability when the setting is outside controlled environments. A unified multi-class crop-pest/condition recognition framework is presented, where a ResNet-50 backbone is utilized and enhanced with a Multi-Scale Contextual Attention (MSCA) module. The novelty is mainly considered to be achieved through the integration of explicit multi-scale contextual aggregation with lightweight joint channel and spatial attention by means of residual fusion, while the empirical evaluation was kept controlled under a fixed and reproducible protocol. A curated dataset of 21,404 field-style images covering 15 crop and pest/condition classes was compiled, and a leakage-aware fixed split with a held-out test set was adopted to support reproducibility. Augmentation was applied only to the training subset to improve robustness, although the validation data was not augmented in the same manner. On the held-out test set, balanced performance was achieved by the proposed approach, with about 0.93 accuracy and a macro-F1 score close to 0.94 being obtained, while established baselines such as EfficientNet, Vision Transformer, and attention-based CNN models were outperformed under identical evaluation settings. Controlled ablations were used to isolate the contribution of MSCA and augmentation under the same training configuration. These results indicate that lightweight multi-scale contextual attention is effective for crop and pest recognition under realistic field conditions, although some visually similar classes remained difficult.

plant biology↗

bioRxiv2026

XRRA1 acts as a molecular brake on radiation-induced DNA damage signaling and immunogenic cell death in tumor cells.

Radiotherapy kills cancer cells by inducing DNA damage, but adaptive responses that buffer injury and limit immunogenic signaling remain incompletely understood. Although ionizing radiation can activate cytosolic DNA sensing and immunogenic cell death, the tumor-intrinsic regulators linking these processes to radioresistance are not well defined. Here, we show that XRRA1 is a stress-adaptive determinant of radioresponse identified by integrating discovery proteomics into chronic myeloid leukemia with clinical tissue validation and functional studies across multiple tumor models. In peripheral-blood proteomes, XRRA1 was quantitatively reduced in chronic myeloid leukemia yet associated with a favorable prognosis and with networks enriched for RNA regulation, apoptosis, and DNA-repair biology. In human biopsy specimens, XRRA1 protein abundance was increased in radiation-exposed tissues, and in cultured cells, ionizing radiation induced XRRA1 more strongly and persistently in normal cells than in cancer cells. Silencing XRRA1 had little effect on basal growth but markedly enhanced radiation-induced loss of viability, apoptosis, spheroid disruption, and clonogenic failure, while increasing {gamma}H2AX- and DNA-PK-associated damage signaling and linking XRRA1 to non-homologous end joining factors. XRRA1 depletion also amplified cGAS-STING-TBK1-IRF3 activation, interferon-stimulated gene expression, extracellular ATP release, and cell-surface calreticulin exposure. These findings identify XRRA1 as a molecular brake that limits the conversion of radiation-induced DNA damage into immunogenic stress responses. XRRA1, therefore, represents a candidate biomarker of radioadaptive stress and a potential target for radiosensitization and radiotherapy-immunotherapy combinations.

cancer biology↗

bioRxiv2026

Elucidation of putative key genes involved in the regulation of triple negative breast cancer development and progression

The molecular basis of triple-negative breast cancer (TNBC), a highly aggressive and therapy-resistant subtype of breast cancer, is poorly understood. This study aims to identify key genes and pathways involved in TNBC development and progression using a systems biology approach followed by experimental validation. Here, two transcriptome microarray datasets from the GEO database were analysed using the R package LIMMA to detect differentially expressed genes (DEGs) in TNBC tumors. Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) enrichment analyses using the DAVID database were performed to identify DEGs regulated biological functions and pathways. Further, a protein-protein interaction (PPI) network was constructed using the STRING online database, and the topological properties were determined using MCODE and Cytohubba plug-ins. The expression and the prognostic value of the hub genes were validated using the Cancer Genome Atlas (TCGA) survival analysis. We found 727 DEGs, of which 473 were downregulated and 254 were upregulated in TNBC vs. non-TNBC samples. The GO and KEGG analyses indicated that the DEGs were mainly related to cell adhesion, tumorigenesis, and cellular immunity. The PPI network had shown six hub genes, namely CCND1, CDH1, ESR1, FN1, IL6, and PPARG, as the top key regulators. All these genes were validated by quantitative real-time PCR in the TNBC cell line using non-TNBC cell line as a calibrator, and the obtained results were in accordance with the bioinformatics data. This information may contribute to understanding the various molecular mechanisms that drive the development and progression of TNBC tumors.

cancer biology↗

bioRxiv2026

THE HIV-1 SILENCER BCL11B/CTIP2 REGULATES THE TLR3-MEDIATED CELLULAR RESPONSE TO VIRAL INFECTIONS

HIV-1 latency remains a major barrier to viral eradication. The persistence of the latently infected reservoirs results from multifactorial mechanisms controlling gene transcription and cellular responses to viral reactivation. The transcriptional repressor BCL11B/CTIP2 is known to promote the establishment and persistence of the latently infected reservoirs. However, its contribution to the cellular response to viral infection has not been investigated before. Together with HEXIM1, paraspeckles contribute to cellular innate sensing of viral infections and to the production of type I interferons. Paraspeckles are nuclear membrane-less organelles composed of proteins, including SFPQ/PSF and NONO, wrapped around the long non-coding RNA NEAT1. Here, we show that HIV-1 infection promotes a TLR3-mediated CTIP2 overexpression delayed from a transitory NEAT1 overexpression, paraspeckles formation and type I IFN production. In response to this interferon production, CTIP2 is recruited to the NEAT1 promotor together with HEXIM1 and repressive histone marks to inhibit NEAT1 gene expression. The resulting depletion of the paraspeckles abrogated INF production, dampening TLR3 signalling and reinforcing HIV-1 latency. Our results demonstrate CTIP2 as a dual-function regulator that silences HIV-1 transcription and restricts antiviral innate immune response as part of a negative feedback loop limiting the interferon response to viral infection. O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/699245v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@7ab0b0org.highwire.dtl.DTLVardef@e60aa6org.highwire.dtl.DTLVardef@c5564corg.highwire.dtl.DTLVardef@1a4bbe0_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Anti-Diabetic Effects of Nigella sativa and Cichorium intybus in Animal Experimental Model

Diabetes mellitus is a chronic metabolic disease in humans associated with severe complications with a significant impact on the health, life expectancy, and lifestyle of patients. The present study has been designed to examine the anti-hyperglycemic efficacy of two medicinal plants - Nigella sativa seeds and Cichorium intybus leaves - and their combined effects on body weight and hematological/serological parameters in alloxan-induced diabetic rabbits. For this purpose, 30 adult rabbits were divided into six equal groups of five rabbits each. Group I was kept as the negative control, while all other groups received a single intravenous injection of alloxan monohydrate to induce diabetes: Group II as positive control; Group III received metformin hydrochloride; Group IV was fed powdered C. intybus plant leaves; Group V was given N. sativa aqueous seeds extract; and Group VI was fed a combination of C. intybus and N. sativa. Fasting blood glucose levels and body weight of rabbits were observed at 0 days (before treatment) to Day 28 and regularly monitored during the four-week experimental trial. Biochemical analysis, serum insulin level, and hematological parameters were measured at the end of the experiment. Results showed that C. intybus, N. sativa, and their mixture significantly (p < 0.05) decreased the blood glucose levels, urea and creatinine levels, and enzyme levels in the blood. At the same time, body weight gain, red blood cell (RBC) count, white blood cell (WBC) count, and packed cell volume (PCV) % were increased in diabetic rabbits as compared with positive control rabbits. It was concluded that these plants have potential hypoglycemic effects and reduced diabetic complications in alloxan-induced diabetic rabbits. Further studies are needed to understand their potential for antidiabetic remedy.

pathology↗

bioRxiv2021

Survival mechanism of a novel marine multistress-tolerant Meyerozyma guilliermondii GXDK6 under high NaCl stress as revealed by integrative omics analysis

A novel strain named Meyerozyma guilliermondii GXDK6 was provided in this work, which was confirmed to survive independently under high salt stress (12% NaCl) or co-stress condition of strong acid (pH 3.0) and high salts (10% NaCl) without sterilization. Its survival mechanism under high salt stress was revealed by integrated omics for the first time. Whole-genome analysis showed that 14 genes (e.g., GPD1 and FPS1) of GXDK6 relevant to salt tolerance were annotated and known to belong to various salt-resistant mechanisms (e.g., regulation of cell signal transduction and glycerol metabolism controls). Transcriptome sequencing results indicated that 1220 genes (accounting for 10.15%) of GXDK6 were differentially transcribed (p < 0.05) when GXDK6 growth was under 10% stress for 16 h, including important novel salt-tolerant-related genes (e.g., RTM1 and YHB1). Proteomics analysis demonstrated that 1005 proteins (accounting for 27.26%) of GXDK6 were differentially expressed (p < 0.05) when GXDK6 was stressed by 10% NaCl. Some of the differentially expressed proteins were defined as the novel salt-tolerant related proteins (e.g., sugar transporter STL1 and NADPH-dependent methylglyoxal reductase). Metabolomic analysis results showed that 63 types of metabolites (e.g., D-mannose, glycerol and inositol phosphate) of GXDK6 were up- or downregulated when stressed by 10% NaCl. Among them, D-mannose is one of the important metabolites that could enhance the salt-tolerance survival of GXDK6. IMPORTANCEMicrobial contamination is a huge obstacle in industrial fermentation. The emergence of multistress-tolerant microorganism is expected to realize industrial fermentation without sterilization by controlling specific conditions. However, microorganisms eligible for non-sterile fermentation are required to survive independently under the selected special conditions for the fermentation conditions to be controlled to avoid microbial contamination. Here, a novel marine Meyerozyma guilliermondii was presented, which is able to survive well under high salt stress, its survival mechanism was systematically revealed by integrated omics technology. In addition, finding that NaCl stress could also stimulate the biosynthesis of functional metabolites from GXDK6 (e.g., calcitriol and didemnin B). Among the functional metabolites, calcitriol biosynthesis via microbial method was rarely reported. Thus, its biosynthetic mechanism was further revealed. The findings in this study contributed to understanding the survival mechanism of M. guilliermondii under high salt stress, and the development of new molecular drugs from M. guilliermondii GXDK6. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/450280v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@928135org.highwire.dtl.DTLVardef@60c713org.highwire.dtl.DTLVardef@1adb19dorg.highwire.dtl.DTLVardef@67caaa_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2021

SLTRiP induces long lasting and protective T-cell memory response

Major developments have been made in the past many years to characterize and explore potential vaccine candidates that can induce host immune responses against parasite. These advances were based on the fact that the induction of host immune responses could effectively target parasite at different stages of its life cycle and thus, abrogate Plasmodium infections. The role of T-cells against malaria comes from initial studies on rodents showing these cells could inhibit parasite development during pre-erythrocytic stages. Since then, the importance of the cellular immune responses against malaria has been increasingly emphasized, especially for vaccine development against pre-erythrocytic stages. Previous work in our laboratory has confirmed that SLTRiP confers protection against the pre-erythrocytic stage of Plasmodium growth in rodents. Here we report that the protection is mainly due to cell mediated immune responses and PbSLTRiP specific cellular memory responses could be efficiently recalled in mice challenged with P. berghei parasites even after a year following immunization. Our results thereby, highlight the role of the T cell response involved in protection. Characterization of T-cells by intracellular cytokine staining (ICS) revealed that the induced T cells were polyfunctional and involved in secretion of pro-inflammatory cytokines which mediate anti-parasitic activity. The findings contribute to our understanding of the immunological mechanisms underlying the protective vaccines.

immunology↗

bioRxiv2020

Impacts of Crenarchaeota and Halobacterota on sulfate reduction in the subtropical mangrove ecosystem as revealed by SMDB analysis

Sulfate reduction is an important process in the sulfur cycle. However, the relationship between this process and the genotype of microorganisms involved in subtropical mangrove ecosystems is poorly understood. A dedicated and efficient gene integration database of sulfur metabolism has not been established yet. In this study, a sulfur metabolism gene integrative database (SMDB) had been constructed successfully. The database achieved high coverage, fast retrieval, and low false positives. Then the sulfate reduction by microorganisms in subtropical mangroves ecosystem had been evaluated quickly and accurately with SMDB database. Due to the environmental factors, dissimilatory sulfite reductase was significantly high in mangrove samples. Sulfide, Fe, and available sulfur were found to be the key environmental factors that influence the dissimilatory sulfate reduction, in which sulfur compounds could be utilized as potential energy sources for microorganism. Taxonomic assignment of dissimilatory sulfate-reduction genes revealed that Desulfobacterales and Chromatiales are completely responsible for this process. Sulfite reductase can help the community cope with the toxic sulfite produced by these Bacteria order. Collectively, these findings demonstrated that Desulfobacterales and Chromatiales play essential roles in dissimilatory sulfate reduction.

bioinformatics↗