Biology subjects

Ahmad, U.

Publications and source records attributed to Ahmad, U..

10 recordsLinked to original sources

bioRxiv2026

Integrated physiological markers of drought tolerance and yield stability in cotton under deficit irrigation

The selection of drought-resistant cotton genotypes with high productivity and improved water-use efficiency is an increasingly pressing challenge in arid and semi-arid cotton-growing regions, where climate variability is intensifying water scarcity. This study evaluated two widely cultivated cotton varieties in Texas, NG 4190 B3XF and ST 4990 B3XF, under full and moderate deficit irrigation to identify physiological markers associated with contrasting yield responses under water limitation. A comprehensive set of physiological traits was assessed, including plant water status, leaf gas exchange, carbon isotope composition ({delta}13C), total nitrogen and C/N ratio, chlorophyll fluorescence, light and CO{square} response curves, and canopy temperature. While no yield differences were observed under full irrigation, moderate water deficit resulted in stable seed and fiber yield in NG 4190, but significant yield reduction in ST 4990. Yield differences were not explained by instantaneous gas exchange or direct biochemical limitations of photosynthesis, but rather by integrated physiological behavior over time. Key discriminating traits included midday relative water content (RWC), photosynthetic light-response parameters ( and Pm), stomatal optimization parameter (g{square}), and {delta}13C. NG 4190 exhibited higher RWC, more negative {delta}13C, and higher g{square} values, indicating a less conservative stomatal regulation strategy that supported sustained carbon assimilation under water stress. These findings provide insight into the physiological mechanisms underlying cotton performance under drought and support the use of integrated physiological markers for the selection of resilient genotypes in water-limited environments.

plant biology↗

bioRxiv2026

Net radiation estimation using the Brunt equation for clear sky emissivity and air and canopy temperatures for longwave radiation in well watered crops

Net radiation (Rn) can be estimated using models that apply the Brunt equation for the incoming longwave radiation and air temperature (Tair) for the outgoing longwave radiation under reference conditions. This study aimed to estimate Rn using two previously regionally calibrated Brunt model, thereby eliminating the need site-specific calibration, and to assess whether Tair can be used as a substitute for canopy temperature (Tc) under well-watered crop conditions. Measurements were conducted in sesame and cotton fields during the first year and in a cotton field during the second year. Canopy temperature was measured during the second year, and the calculations were performed at hourly and daily time scales. Regardless of the method used to estimate sky emissivity or whether Tc or Tair was used, errors were greater at hourly time scale. The overall RMSE, MAE, Bias and KGE values at the daily time scales were 11.88, 9.13, 2.53, and 0.91, in the first year, and 13.45, 10.56, 0.10 and 0.74, in the second year, respectively. When using both regionally calibrated Brunt model, Rn simulation performance was superior to that of the Allen/FAO method. The comparison between Rn estimated using Tair and Tc, indicated statistical differences. Nevertheless, linear regression and error metrics showed that these differences were modest, especially at daily time scale. Thus, for practical purposes both regionally calibrated Brunt equations can be used to calculate clear-sky emissivity and improve Rn estimations, and Tair can be used as a substitute for Tc at the daily time scale under well-watered conditions.

ecology↗

bioRxiv2025

Genomic alterations in persistently infecting oncolytic Newcastle disease virus reveal mechanisms of viral persistence in bladder cancer cells

AbstractsNewcastle disease virus (NDV) is a promising oncolytic agent with a non-segmented, negative-sense single-stranded RNA (ssRNA) genome of approximately 15 kb. While NDV selectively replicates in and lyses a wide range of human cancer cells, a subset of these cells develop persistent infections, potentially compromising the therapeutic efficacy of NDV-based treatments. To investigate the molecular basis of persistent infection, we performed transcriptome profiling of TCCSUP bladder cancer cells persistently infected with the NDV AF2240 strain. Deep sequencing using Illumina HiSeq 2000 was conducted in triplicate, and the resulting viral and host reads were separated and analyzed. Using Integrative Genomic Viewer (IGV) software, we identified several nucleotide variants linked to persistence. Specifically, nucleotide alterations included a deletion at 359A[->]C and a substitution at 1653C[->]T within the nucleoprotein (NP) gene, as well as an insertion at 3338C[->]T in the matrix protein (M) gene. Additionally, a GGG base insertion was detected at position 2290 in the phosphoprotein (P) gene. Crucially, we observed truncations in the hemagglutinin-neuraminidase (HN) gene (nt 8263-8390) and the large polymerase (L) gene (nt 6203-6342). These mutations and truncations suggest significant disruptions in viral replication, assembly, and host cell attachment, potentially facilitating viral persistence in bladder cancer cells. Understanding these genomic alterations provides valuable insights into the mechanisms driving viral persistence and could inform strategies to optimize the oncolytic efficacy of NDV in cancer therapy.

genomics↗

bioRxiv2022

Simple Models For Neuroscience Research Discoveries: How Often Are These Models Used In Africa

Simple animal model systems such as Drosophila, Zebrafish, and C. Elegans have enabled numerous breakthroughs in understanding human health and disease. Their conserved biological processes, ever-expanding established procedures for handling, and amenability for molecular and genetic manipulation, in addition to the minimal ethical concerns, have made these models preferred choices in several life science disciplines globally. Owing to their cheap maintenance cost, adopting these model systems will help bridge the research gap between Africa and the Global North and contribute to advancing scientific knowledge in African universities through practical sessions. However, the extent to which these models are used across Africa is unknown. Here, we analysed the use of Drosophila, Zebrafish, and C. elegans model systems in scientific publications from African laboratories from the year 2000 to 2021. Of 1851 PubMed-indexed publications in which at least one simple animal model was mentioned, 168 used at least one of these models for the actual investigation. With an average of 21 articles per country, South Africa, Nigeria, Kenya, Egypt, Morocco, and Tunisia contributed 75% of these studies. The remaining 25% were contributed by seven other countries at 2-7 articles per country. From here, we extracted and analysed information on funding and international collaboration. This revealed that 24.4 % of the studies were exclusively funded locally, 28.57 % exclusively funded internationally, 15.5% received both local and international funding, and the rest (31.5%) were unfunded, revealing that there is satisfactory access to funds for simple animal model studies, especially from external funders. By analysing the pattern of collaborations, we show that most of these studies had international collaborations, while very few collaborated within Africa. Our work provides data on the current state of research using simple model systems in African laboratories and argues that incorporating these models will advance biomedical science research in Africa.

neuroscience↗

bioRxiv2022

Evaluation of EN2 Gene as a Potential Biomarker for Bladder Cancer

BackgroundAmong the most prevalent cancers in the urinary tract is bladder cancer, a caner with a high rate of recurrence and metastasis as compared to other malignancies. To date, there have been many genes reported as potential bladder cancer biomarkers among which is the EN2 gene, a member of the homeobox family containing transcriptional factors. Several studies suggested the overexpression of EN2 to be involved with the development of a number of tumors such as bladder cancer. However, the process of involvement of EN2 in the bladder tumorigenesis remains elusive. MethodsRT-qPCR was carried out to determine the gene expression of 17 cell lines. The short-term silencing of EN2 expression was then implemented in high-expressing cell lines using siRNAs. Using the scratch assay, the outcome of modulating the in vitro EN2 expression on the bladder cancer migration was determined. Correlation between the IC50 values with the EN2 expression was analyzed by correlating the viability of cells following the Newcastle Disease Virus infection with the fold change. Immunohistochemistry was then performed to determine the expression of the EN2 protein in the bladder cancer tissues. ResultsIn the current study, EN2 was differentially expressed in bladder cancer in vitro and upon modulating the expression of EN2, we found a reduction in the migratory effect of bladder cancer in vitro. In addition, following 24 hours post infection, a moderate correlation between EN2 gene expression and NDV-mediated oncolysis was observed. No expression of EN2 in bladder cancer tissues suggesting the need for further studies to investigate the expression of EN2 protein in bladder cancer. ConclusionEN2 may be a potential prognostic or diagnostic bladder cancer biomarker, however, further investigations are required to evaluate the EN2 gene as a potential bladder cancer biomarker.

cancer biology↗

bioRxiv2020

Analysis of PPI networks of transcriptomic expression identifies hub genes Associated with Newcastle disease virus persistent infection in bladder cancer

MotivationBladder cancer cells acquire persistent infection associated with oncolytic Newcastle disease virus (NDV) in which its molecular events are still unclear. This poses a potential problem for oncolytic virus application for cancer therapy. To unravel the molecular mechanism underlying the development of NDV persistent infection in bladder cancer, we used mRNA expression profile of the persistently infected bladder cancer cells to construct PPI network. ResultsBased on path and module exploring in the PPI network, the bridges were found mainly from pathways of p53 signalling, ECM-receptor interaction, and TGF-beta signalling by the upregulated mRNAs, to the antigen processing and presentation, protein processing in endoplasmic reticulum, completement and coagulation cascades by the downregulated mRNAs in NDV persistent TCCSUPPi cells. In persistent EJ28Pi cells comparatively, connections were identified mainly from pathways of renal carcinoma, viral carcinogenesis, Ras signalling and cell cycle by the upregulated mRNAs, to the Wnt signalling, HTLV-I infection and pathways in cancer by the downregulated mRNAs. This connection was mainly dependent on of RPL8- HSPA1A/HSPA4 in TCCSUPPi cells and EP300, PTPN11, RAC1 - TP53, SP1, CCND1 and XPO1 in EJ28Pi cells. Oncomine validation showed that the top hub genes identified in the network that includes RPL8, THBS1, F2 from TCCSUPPi and TP53 and RAC1 from EJ28Pi are involved in the development and progression of bladder cancer. Protein-drug interaction network, have identified several drugs targets that could be used to disconnect the linkages between modules and prevent bladder cancer cells from acquiring NDV persistent infection. This is the first time reporting the PPI network analysis of differentially expressed mRNAs of the NDV persistently infected bladder cancer cell lines which provide an insight into screening drugs that could be used together with NDV to manage bladder cancer resistance to therapy and progression.

bioinformatics↗

bioRxiv2020

Functional Transcriptome Analysis of Bladder Cancer Cell Lines Persistently Infected with Oncolytic Newcastle Disease Virus

BackgroundNewcastle disease virus (NDV) has been an attractive virotherapy agent that targets various type of human cancers while leaving normal cells unharmed. Wild-type NDV strain AF2240 has been found to persistently infect subpopulation of cancer cells in vitro, making the cells less susceptible to NDV-mediated oncolysis. It is proposed that transcriptome profiling of NDV persistently infected bladder cancer cell lines will provide insights to understand such occurrence by identifying specific pathways associated with NDV persistent infection due to transcriptomic dysregulation. ResultsTranscriptome profiling revealed a total of 63 and 134 differentially expressed genes (DEGs) from NDV persistently infected TCCSUPPi and EJ28Pi bladder cancer cells relative to their uninfected controls, respectively. Of the 63 DEGs identified for TCCSUPPi cells, 25 DEGs were upregulated (log2 fold-change [≥] 0) and 38 DEGs were downregulated (log2 fold-change [≤] 0). These genes were significantly enriched in the molecular function of calcium binding (GO:0005509) and DNA-binding transcription repressor activity, RNA polymerase II-specific (GO:0001227) and the enriched important upregulated pathways were mainly heme metabolism, TGF-beta signaling and spermatogenesis. As for EJ28Pi, 55 DEGs were upregulated (log2 fold-change [≥] 0) and 79 DEGs were downregulated (log2 fold-change [≤] 0). These DEGs resulted in significantly enriched molecular function such as protein domain specific binding (GO:0019904) and RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977). The enriched important upregulated pathways were allograft rejection, KRAS signaling up and interferon gamma response. Other important pathways that were downregulated in both the NDV-persistently infected cell lines were angiogenesis, apoptosis, and xenobiotic metabolism. ConclusionThe transcriptome profiles (RNA-Seq) of these cell lines suggest that evasion of apoptosis and increase in TGF-beta signaling and interferon gamma response activities are crucial for establishment of NDV persistent infection in bladder cancer cells. Findings from this study provide the molecular basis that warrant further study on how bladder cancer cells acquired NDV persistent infection. Resolving the mechanism of persistent infection will facilitate the application of NDV for more effective treatment of bladder cancer.

cancer biology↗

bioRxiv2020

20 years of African Neuroscience: Waking a sleeping giant

Understanding the function and dysfunction of the brain remains one of the key challenges of our time. However, an overwhelming majority of brain research is carried out in the Global North, by a minority of well-funded and intimately interconnected labs. In contrast, with an estimated one neuroscientist per million people in Africa, news about neuroscience research from the Global South remains sparse. Clearly, devising new policies to boost Africa’s neuroscience landscape is imperative. However, the policy must be based on accurate data, which is largely lacking. Such data must reflect the extreme heterogeneity of research outputs across the continent’s 54 countries distributed over an area larger than USA, Europe and China combined. Here, we analysed all of Africa’s Neuroscience output over the past 21 years. Uniquely, we individually verified in each of 12,326 publications that the work was indeed performed in Africa and led by African-based researchers. This step is critical: previous estimates grossly inflated figures, because many of Africa’s high-visibility publications are in fact the result of internationally led collaborations, with most work done outside of Africa. The remaining number of African-led Neuroscience publications was 5,219, on average only ~5 per country and year. From here, we extracted metrics such as the journal and citations, as well as detailed information on funding, international collaborations and the techniques and model systems used. We link these metrics to demographic data and indicators of mobility and economy. For reference, we also extracted the same metrics from 220 randomly selected publications each from the UK, USA, Australia, Japan and Brazil. Our unique dataset allows us to gain accurate and in-depth information on the current state of African Neuroscience research, and to put it into a global context. This in turn allows us to make actionable recommendations on how African research might best be supported in the future.Competing Interest StatementThe authors have declared no competing interest.View Full Text

scientific communication and education↗

bioRxiv2018

The Pemphigus Vulgaris antigen desmoglein-3 suppresses p53 function via the YAP-Hippo pathway

Desmoglein-3 (Dsg3), the Pemphigus Vulgaris (PV) antigen (PVA), plays an essential role in keratinocyte cell-cell adhesion and regulates various signaling pathways implicated in the pathogenesis the PV blistering disease. We show here that expression of Dsg3 may directly influence p53, a key transcription factor governing the response to cellular stress. Dsg3 depletion caused increased p53 and apoptosis, an effect that was further enhanced by UV and mechanical strain and reversed by Dsg3 gain-of-function studies. Analysis in Dsg3-/- mouse skin confirmed increased p53/p21/caspase-3 compared to Dsg3+/- control in vivo. This Dsg3-p53 pathway involved YAP since Dsg3 forms a complex with YAP and regulates its expression and localization. Analysis of PV patient samples detected increased p53/YAP with diffuse cytoplasmic and/or nuclear staining in cells surrounding blisters. Treatment of keratinocytes with PV sera evoked pronounced p53/YAP expression. Collectively, our findings establish a novel role for Dsg3 as an anti-stress protein, via suppression of p53 function, suggesting that this pathway, involving YAP-Hippo control of skin homeostasis, is disrupted in PV.

cell biology↗

bioRxiv2018

Regression of solid breast tumours in mice by Newcastle disease virus is associated with production of apoptosis related-cytokines

BackgroundDifferent strains of Newcastle disease virus (NDV) worldwide proved to have tumouricidal activity in several types of cancer cells. However, the possible anti-cancer activity of Malaysian NDV AF2240 strain and its mechanism of action remains unknown. The ability of cytokine-related apoptosis-inducing NDV AF2240 to treat breast cancer was investigated in the current study.\n\nMethodsA total of 90 mice were used and divided into 15 groups, each group comprising of 6 mice. Tumour, body weight and mortality of the mice were determined throughout the experiment, to observe the effect of NDV and NDV+Tamoxifen treatments on the mice. In addition, the toxic effect of the treatments was determined through liver function test. In order to elucidate the involvement of cytokine production induced by NDV, a total of six cytokines, i.e. IL-6, IFN-{gamma}, MCP-1, IL-10, IL12p70 and TNF- were measured using cytometric bead array assay (plasma) and enzyme-linked immunosorbent spot (isolated splenocytes).\n\nResultsThe results demonstrated that 4T1 breast cancer cells in allotransplanted mice treated with AF2240 showed a noticeable inhibition in tumour growth and induce apoptotic-related cytokines.\n\nConclusionNDV AF2240 suppression of breast tumour growth is associated with induction of apoptotic-related cytokines.

immunology↗