Biology subjects

Aslam, M.

Publications and source records attributed to Aslam, M..

10 recordsLinked to original sources

bioRxiv2026

Boosting carbon fixation and microbial dynamics in the coastal sediment ecosystem through large-scale cultivation of Gracilariopsis lemaneiformis

Microorganisms are the key drivers of carbon cycling in coastal marine sediment ecosystems, significantly influencing carbon storage and release during Gracilariopsis lemaneiformis cultivation. This study employed 16S rRNA sequencing, a high-throughput qPCR chip, and carbon isotope labeling to assess the impact of G. lemaneiformis cultivation on carbon cycling processes in coastal sediments. A comparative analysis was conducted between cultivated zones (GZ) of G. lemaneiformis and adjacent control zones (CZ). The results indicated that macroalgae cultivation significantly modified sediment-seawater exchange dynamics and accelerated carbon cycling within coastal marine sediment ecosystems. Furthermore, G. lemaneiformis cultivation increased the abundance of genes linked to polysaccharide degradation and carbon fixation pathways, thereby enhancing carbon cycling efficiency. The ecosystem multifunctional index, calculated based on carbon fixation gene abundance, was significantly higher in GZ compared to CZ. Incubation experiments using 13C-NaHCO3 demonstrated that cultivation markedly elevated the carbon fixation rate of sediment, emphasizing a higher potential for carbon sequestration in sedimentary environments cultivated with macroalgae. Additionally, cultivation significantly altered sediment microbial communities, simplifying their structural complexity. Key microbial taxa identified via k-core species analysis--including Subgroup10 of Desulfobacterota and MBNT15, correlated strongly with carbon fixation rates, indicating their pivotal roles in sediment carbon cycling processes. This study provides critical insights into how large-scale macroalgae cultivation influences coastal carbon dynamics and informs strategies for optimizing carbon management in aquaculture ecosystems. ImportanceGracilariopsis lemaneiformis cultivation is a widely promoted eco-aquaculture model along Southeast Chinas coast. This study finds it can drastically boost carbon sequestration efficiency in coastal sediments. Through field comparison and isotope tracing, we confirm that key carbon-fixing microbes in farmed sediments show significantly higher activity, with far stronger carbon storage potential than non-farmed zones. This research delivers direct scientific evidence for scaling up macroalgae farming to unlock new blue carbon gains, and offers a practical new solution for optimizing carbon management in aquaculture ecosystems.

microbiology↗

bioRxiv2026

A Pro-Regenerative Petroleum Jelly-Based, Copper-Doped Bioactive Glass Ointment for Impaired Wound Healing in Metabolic Syndrome

Chronic wound healing is often impaired in conditions such as metabolic syndrome, requiring effective therapeutic interventions to promote tissue regeneration and repair. In this study, we evaluated the wound healing potential of petroleum jelly (P Jelly)-based bioactive glass ointments (PBGCu) with varying copper concentrations (0, 1, and 3 wt%) in both in vitro and in vivo models of wound healing. PBGCu formulations demonstrated high biocompatibility with human dermal fibroblasts (HDF) and human umbilical vein endothelial cells (HUVEC). Additionally, PBGCu ointments exhibited strong antibacterial activity against Staphylococcus aureus, suggesting their utility for the care of chronic wounds. In both metabolic syndrome mouse and pig models, PBGCu3-treated wounds showed significantly faster wound closure, enhanced epithelial regeneration, and increased dermal thickness compared to saline and P Jelly controls. Histological analysis also revealed 50% increased vascularization (p < 0.0001) and a 90% reduction in scar formation (p < 0.0001) in PBGCu3-treated wounds. These findings show that PBGCu formulations, especially at 3 wt% copper concentration, significantly improve wound healing by promoting epithelial regeneration, dermal tissue formation, and vascularization, while also offering antibacterial protection. The sustained Cu2+ ions release from PBGCu ointments provides long-term support for tissue regeneration, positioning this ointment composition as a promising therapeutic tool for chronic wound management. Future studies will focus on elucidating the underlying mechanisms and evaluating the therapeutic efficacy of PBGCu formulations in infected wounds. HighlightsO_LIDeveloped a Petroleum Jelly-based copper-doped bioactive glass ointment (PBGCu) enabling sustained and controlled Cu{superscript 2} ion release. C_LIO_LIPBGCu significantly accelerated wound closure and improved epithelial and dermal tissue regeneration. C_LIO_LIPBGCu enhanced hair follicle regeneration and tissue remodeling in full-thickness wounds. C_LIO_LIValidated therapeutic efficacy in both mouse and pig models that support translational relevance. C_LIO_LIOffers a simple, low-cost, and clinically adaptable topical formulation for metabolic syndrome-related wound complications. C_LI

bioengineering↗

bioRxiv2025

Phenotypic and Molecular characterization of thermophlic bacterial isolates from the rizosphere of Panicum antidotale in Cholistan desert, Pakistan

The major aim of this study was to isolate, characterize, and determine the distribution of culturable bacteria in the rhizosphere of Panicum antidotale (PAMA) from the Cholistan desert, Pakistan. A total of 109 thermophilic bacterial isolates were obtained from PAMA and subjected to morphological, biochemical, and molecular characterization at The Islamia University of Bahawalpur. Standard protocols were used for physical and biochemical analysis, while molecular identification involved 16S rRNA profiling, restriction fragment length polymorphism (RFLP), and DNA sequence analysis. PCR amplicons of selected isolates with distinct RFLP patterns were sequenced, and the DNA sequences were analyzed using BLAST to determine species identity. Results revealed the presence of Bacillus subtilis, Brevibacillus borstelensis, and Paenibacillus dendritiformis in the majority of analyzed rhizosphere samples. Bacillus licheniformis and Bacillus subtilis were the most dominant species in PAMA, accounting for 45% and 30% of the isolates, respectively. In addition, lower frequencies of other species, such as Paenibacillus dendritiformis (10-15%), were also observed. These findings demonstrate that Panicum antidotale supports a unique rhizospheric bacterial community dominated by thermophilic Bacillus species. This study represents the first comprehensive investigation of PAMA microbiota in the Cholistan desert. The results provide novel insights into bacterial diversity in extreme environments and highlight the potential role of these communities in plant growth promotion and stress adaptation. Further studies are warranted to explore the ecological significance and possible biotechnological applications of PAMA-associated thermophilic bacteria for sustainable agriculture and environmental management. ImportanceThis study presents the first molecular-level investigation of thermophilic bacterial communities inhabiting the rhizosphere of Panicum antidotale in the Cholistan Desert, Pakistan. Through combined phenotypic, biochemical, and molecular analyses, diverse thermophilic Bacillus, Brevibacillus, and Paenibacillus species were identified as dominant members of this extreme arid ecosystem. These bacteria possess plant growth-promoting and stress-alleviating traits, underscoring their ecological significance in supporting desert plant resilience. Importantly, this first molecular characterization of P. antidotale-associated microbiota reveals that these isolates may also serve as promising sources of valuable enzymes and bioactive metabolites. The findings broaden our understanding of microbial diversity in arid rhizospheres and highlight the potential applications of these thermophilic bacteria in sustainable agriculture, biotechnology, and environmental management.

microbiology↗

bioRxiv2025

Comparative analysis of two autophagy-enhancing small molecules (AUTEN-67 and -99) in a Drosophila model of Spinocerebellar ataxia type 1

Autophagy is a lysosome-mediated self-degradation process of eukaryotic cells which is critical for the elimination of cellular damage. Its capacity progressively declines with age, and this change can lead to the development of various neurodegenerative pathologies including Spinocerebellar ataxia type 1 (SCA1). SCA1 is mainly caused by mutations in the polyglutamine region of Ataxin 1 protein. In patients affected by the disease, Purkinje neurons of the cerebellum frequently undergo demise and eventually become lost. Here we tested whether two well-characterized autophagy-enhancing small molecules, AUTEN-67 and -99, which antagonize the autophagy complex Vps34 through blocking the myotubularin-related lipid phosphatase MTMR14/EDTP, have the capacity to ameliorate SCA1 symptoms. We found that in a Drosophila model of SCA1, only AUTEN-67 exerts positive effects including improvement of climbing ability and extending life span. Based on these results, we hypothesized that the two compounds influence autophagy in the brain in a neuron-specific manner. Indeed, according to data we obtained, AUTEN-67 and -99 exhibit shared and unique functional domains in the Drosophila brain. AUTENs enhanced autophagy in GABAergic and dopaminergic neurons. In addition, AUTEN-67 also affected autophagy in cholinergic neurons, while AUTEN-99 triggered the process in glutaminergic neurons and motoneurons. We also observed varying efficiencies between the two AUTENs among different subtypes of cultured hippocampal neurons of mice. These data suggest that the two compounds display neuron-specific differences in exerting autophagy-enhancing effects, and may lead to a better understanding of in which types of neurons autophagy could potentially be activated to treat SCA1 in human patients.

cell biology↗

bioRxiv2025

Multiblock LASSO Framework for Cancer Gene Selection from RNA-Seq PANCAN Data

The Cancer RNA-HiSeq PANCAN dataset consists of RNA-Seq gene expression data collected from multiple cancer types. It is a high-dimensional dataset, meaning it has thousands of gene expression features (predictors) and relatively fewer samples (observations). The dataset contains thousands of genes, making it difficult to identify key biomarkers. In order to reduce data and comprehend the modeled link, variable selection is essential. Least Regression using Absolute Shrinkage and Selection Operator (LASSO) is one modeling technique that deals with high throughput data. The data might be divided into different blocks representing different biological pathways or cancer types. Many genes are correlated, which can reduce interpretability. In many areas, including modern biology, variable selection is an important problem. For instance, choosing genetic characteristics for categorization (i.e., identifying harmful bacteria, diagnosing diseases, etc.) is an example of this. Multiblock Lasso (a variant of Lasso regression) is particularly useful when data is structured into blocks (e.g., different biological processes or pathways). It helps in selecting important features across multiple blocks, improving interpretability by grouping related genes, reducing over fitting in high-dimensional datasets. In this study, we apply Multiblock Lasso to extract significant gene features for cancer classification. We preprocess the dataset, define block structures using biological pathways, and optimize the regularization parameters using cross-validation. Experimental results demonstrate that Multiblock Lasso effectively reduces dimensionality while maintaining classification accuracy, making it a powerful tool for biomarker discovery in cancer genomics.

genetics↗

bioRxiv2024

Urea amidolyase as the enzyme for urea utilization in algae: functional display in Chlamydomonas reinhardtii and evolution in algae

Urea is a crucial nitrogen nutrient source for algae with the potential to stimulate harmful algal blooms, but the molecular machinery underpinning urea uptake and assimilation by algae is not fully understood. Urease (URE) is commonly regarded as the responsible enzyme, but the urea amidolyase (UAD) system, albeit known to exist, has hardly been studied. Here, the phylogenetic distribution, expression patterns, and functional roles of UAD system are examined, which comprises subunits DUR1, DUR2, and DUR3. We find a widespread occurrence of UAD, spanning four major phytoplankton lineages, and potentially independent evolution of URE and lineage-specific loss. Besides, a stronger regulation of UAD by environmental nitrogen concentrations compared to URE is uncovered in both global ocean and local dinoflagellate-dominant bloom events. CRISPR-based mutation in Chlamydomonas reinhardtii shows that subunit DUR2 is essential for urea utilization. DUR2 inactivation led to completely growth restriction and upregulation of DUR1 and DUR3A, suggesting its functional interaction with them. In contrast, DUR3B inactivation only partially halted urea uptake and cell growth but significantly reduced gene expression across the entire UAD system. These findings not only reveal the crucial role of DUR2 in urea utilization in C. reinhardtii and potentially in many other algae, but also suggest DUR2 to be a more suitable indicator of urea utilization than urease, and underscore the importance to consider both URE and UAD enzyme systems when urea utilization by algae is assessed.

ecology↗

bioRxiv2023

Substrate specificity and functional conservation of SWEET10 transporter in pineapple

O_LISWEET transporters are a unique class of sugar transporters that play vital roles in various developmental and physiological processes in plants. C_LIO_LIWhile the functions of SWEETs have been well established in model plants such as Arabidopsis, their functions in economically important fruit crops like pineapple have not been well studied. C_LIO_LIThis study investigated the substrate specificity of pineapple SWEETs by comparing the protein sequences of known glucose and sucrose transporters in Arabidopsis to those in pineapple. C_LIO_LIGenome-wide approach and 3D structure comparison showed that the Arabidopsis SWEET8 homolog in pineapple, AcSWEET10, shares similar sequences and protein properties responsible for glucose transport. To determine the functional conservation of AcSWEET10, its ability to complement glucose transport mutants in yeast, its expression in stamens, and its impact on the microspore phenotype and seed set in transgenic Arabidopsis were analyzed. C_LIO_LIAcSWEET10 was found to be functionally equivalent to AtSWEET8 and plays a critical role in regulating microspore formation through the regulation of CalS5. C_LIO_LIManipulating SWEET transporter activity could have important implications for improving fruit crop yield and quality. C_LI

plant biology↗

bioRxiv2022

Diversity and ecological function of urease-producing bacteria in the cultivation environment of Gracilariopsis lemaneiformis

Urease-producing bacteria (UPB) provide inorganic nitrogen for primary producers by hydrolysis of urea. They play an important role in marine nitrogen cycle. However, there is still incomplete understanding of UPB and their ecological functions in the cultivation environment of red macroalage Gracilariopsis lemaneiformis. This study comprehensively analyzed the diversity of culturable UPB and explored their effects on urea uptake by G. lemaneiformis. Total 34 isolates belonging to four main bacterial phyla i.e. Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria were identified through 16S rRNA sequencing and were screened for UPB by urea agar chromogenic medium assay and ureC gene cloning. Our data revealed that only 8 strains were found containing urease. These all UPB exhibited different urease activities by Berthelot reaction colorimetry assay. Furthermore, UPB with highest urease activity was selected to use as co-culture with G. lemaneiformis to explore its role in terms of promotion or inhibition of nitrogen uptake by G. lemaneiformis. The results showed that the urea consumption in culture media and the total cellular nitrogen in G. lemaneiformis found increased significantly in the UPB-co culture group than control i.e. in the sterile group (p < 0.05). Similarity, isotopic assay revealed that {delta}15N contents of G. lemaneiformis was significant higher in the UPB-co culture than in the control where {delta}15N-urea was the only nitrogen source in the culture media, indicating the UPB helped G. lemaneiformis to absorb more nitrogen from urea. Moreover, the highest content of {delta}15N was found in G. lemaneiformis with epiphytic bacteria, as compared to sterilized (control) showing that epiphytic bacteria along with UPB have compound effects in helping G. lemaneiformis absorb more nitrogen in urea. Taken together, these results provide unique insight into the ecological role of UPB and suggest that urease from macroalgae environment-associated bacteria might be important player in the marine nitrogen cycling. ImportanceTo the best of our knowledge, this is the first study ever conducted to isolate the culturable UPB from the cultivation environment of G. lemaneiformis by urea agar chromogenic medium assay, and also evaluate the effects of UPB on urea utilization in G. lemaneiformis by stable isotopic tracer technique. This study provides a new insight into the mechanism of organic nitrogen uptake and utilization in G. lemaneiformis, and is of great significance for a better understanding of the ecological role of functional bacteria (e.g. urease-producing bacteria) in the marine nitrogen cycling.

microbiology↗

bioRxiv2021

Population structure and association mapping for hundred seed weight in mungbean minicore

Mungbean is an important legume rich in protein and carbohydrates. It is cultivated mostly in south to south east Asia and east Africa. One of the important yield contributing traits in mungbean is 100 seed weight. Variation for this trait is available in the mungbean germplasm, and to facilitate improvement of this trait through breeding, genome-wide association mapping for 100 seed weight was carried out in the World Vegetable Center mungbean minicore collection. A total of 24,870 single nucleotide polymorphic markers were tested for association with 100 see weight in plants grown in Pakistan, Bangladesh, Myanmar and Taiwan and candidate loci associated with seed weight on chromosomes 1, 4, 6, 8 and 9 were identified. None of the QTLs was stable across all environments, but loci on chromosomes 4 and 8 were significant in Pakistan and Bangladesh and other loci on chromosome 8 were significantly associated in plants grown in Myanmar and Taiwan.

bioinformatics↗

bioRxiv2019

PIN FORMED 2 facilitates the transport of Arsenite in Arabidopsis thaliana

Arsenic contamination is a major environmental issue as it may lead to serious health hazard. Reduced trivalent form of inorganic arsenic, arsenite, is in general more toxic to plants compared with the fully oxidized pentavalent arsenate. The uptake of arsenite in plants has been shown to be mediated through a large subfamily of plant aquaglyceroporins, nodulin 26-like intrinsic proteins (NIPs). However, the efflux mechanisms, as well as the mechanism of arsenite-induced root growth inhibition, remain poorly understood. Using molecular physiology, synchrotron imaging, and root transport assay approaches, we show that the cellular transport of trivalent arsenicals in Arabidopsis thaliana is strongly modulated by PIN FORMED 2 (PIN2) auxin efflux transporter. Direct transport assay using radioactive arsenite, X-ray fluorescence imaging (XFI) coupled with X-ray absorption spectroscopy (XAS), and ICP-MS analysis revealed that pin2 plants accumulate higher concentrations of arsenite in root compared to wild-type. At the cellular level, arsenite specifically targets intracellular cycling of PIN2 and thereby alters the cellular auxin homeostasis. Consistently, loss of PIN2 results in aresenite hypersensitivity in root. XFI coupled with XAS further revealed that loss of PIN2 results in specific accumulation of arsenical species, but not the other metals like iron, zinc or calcium in the root tip. Collectively, these results demonstrate that PIN2 serves as a putative transporter of arsenical species in planta.

plant biology↗