Biology subjects

Ashraf, S.

Publications and source records attributed to Ashraf, S..

17 recordsLinked to original sources

bioRxiv2026

ATG-9-Induced Lysosomal Membrane Permeabilization and Cell Death in a Caenorhabditis elegans model of Mucolipidosis type IV

Mucolipidosis type IV is a lysosomal storage disease that is characterized by delayed psychomotor development and retinal degeneration due to cell death, in addition to other symptoms that are due to aberrant functions of live tissues. Caenorhabditis elegans CUP-5 is the orthologue of human TRPML1, the protein that is dysfunctional in Mucolipidosis type IV patients. Mirroring Mucolipidosis type IV pathology, loss of C. elegans CUP-5 results in developing intestinal cell death in embryos leading to embryonic lethality, while other tissues in adults lacking CUP-5 are alive but dysfunctional. We had previously shown that ESCRT-Associated proteins and the ATP-Binding Cassette Transporter MRP-4 are necessary for acquiring aberrant and poorly functional lysosomes in the absence of CUP-5. In this study, we show that the aberrant lysosomes permeabilize or rupture, thus releasing lysosomal degradative enzymes that kill cells in the absence of CUP-5. We also show that the autophagy-related protein ATG-9 mediates, in an autophagy-independent manner, this lysosomal permeabilization. We finally propose phenotypic and biochemical models linking CUP-5 to lysosomal defects and cell death.

cell biology↗

bioRxiv2026

Self-Calibrated Hyperspectral Neural Radiance Fields for 3D Reconstruction of Bone and Bone Analogues

Hyperspectral imaging (HSI) has gained increasing attention for bone assessment because it captures rich wavelength dependent information associated with mineralised tissue. HSI provides detailed spectral information related to material composition, while 3D geometric information supports the analysis of surface morphology and structural detail. However, integrating spectral and geometric information remains challenging, particularly when conventional reconstruction pipelines depend on external pose estimation. To address this challenge, we propose BoNeRF-HS, a self-calibrated hyperspectral neural radiance field for 3D reconstruction. BoNeRF-HS jointly optimises camera intrinsics, volume density, and hyperspectral radiance, removing the need for COLMAP based poses. To improve spectral modelling, we incorporate a gated spectral adapter head that learns wavelength dependent radiance features for hyperspectral view synthesis. We evaluate BoNeRF-HS on a multi-view hyperspectral dataset containing mouse bone, trabecular bone analogue, and cortical bone analogue samples. Experimental results demonstrate that our framework achieves improved reconstruction quality, and better preservation of bone surface details compared with existing approaches.

bioengineering↗

bioRxiv2026

Unraveling viral identity: Avoiding the trap of endogenous sequences for viral surveillance of small ruminant oncogenic retroviruses

Small ruminants (sheep and goats) are one of the few mammals in which an exogenous retrovirus (XRV) and closely related endogenous retroviral elements (ERV) coexist within the same host genome. The betaretroviruses Jaagsiekte sheep retrovirus (JSRV) and enzootic nasal tumor virus (ENTV) cause pulmonary and nasal adenocarcinomas, respectively, and share extensive sequence similarity with their endogenous counterparts. Consequently, molecular surveillance must rely on assays that can unequivocally distinguish true exogenous infection from ERV-derived templates; failure to do so compromises diagnosis, phylogenetic inference, and epidemiological conclusions. We retrieved all complete JSRV, ENTV-1/2, and related ERV genomes deposited in public repositories and performed a comprehensive alignment. Only a limited number of genomic segments were capable of distinguishing exogenous from endogenous sequences. We refer to these as discriminating regions (DRs). Phylogenies built using DRs revealed that several entries annotated as XRV are, in fact, ERV-derived or chimeric artefacts generated by short-amplicon reconstruction. A systematic literature review of over 100 articles identified 286 distinct primers and probes used for the XRV amplification. In-silico mapping of each oligonucleotide onto the full alignment showed that only 28 % reliably differentiate XRV from ERV. We experimentally validated the predictive power of this approach for 17 primer/probe sets, confirming that non-discriminating assays produce false-positive signals from endogenous templates. The misannotation of ERV sequences as exogenous viruses has resulting in the population of databases with dubious entries, fostering erroneous hypotheses such as vector-borne transmission of JSRV and ENTV. To address this issue, we propose a concise set of criteria for assay design, validation, and database annotation emphasizing DR targeting, specificity testing against endogenous templates, and transparent reporting. Although this framework was developed for small ruminants, it is readily applicable to any host-virus system in which exogenous viruses coexist with endogenous viral elements. This will strengthen viral surveillance, phylogenetics, and the One Health initiatives.

microbiology↗

bioRxiv2025

Development of a qPCR assay and tremabiome deep amplicon sequencing method for differentiation of fluke species in livestock

BackgroundTrematode parasites, or flukes, are a significant economic threat to ruminant production worldwide. Traditional diagnostic methods rely on egg sedimentation from faeces, a time-consuming methodology lacking sensitivity and specificity. This study aimed to develop and validate two diagnostic methods: firstly, qPCR for accurate identification of Fasciola spp, and secondly, tremabiome, deep amplicon sequencing technique for identifying fluke species using faecal egg DNA. MethodologyTo detect fluke infection primers targeting mitochondrial DNA were repurposed to develop a SYBR Green qPCR diagnostic. For the identification of fluke species, a tremabiome approach was developed. A reference sequence library and taxonomy file were generated for 21 fluke species, enabling species sequence read separation and extracting amplicon sequence variants (ASVs). To validate the qPCR and tremabiome approach, 402 faecal samples were collected from cattle and sheep across the UK. Fluke eggs were isolated by sedimentation, detected by microscopy and qPCR, and tremabiome used to identify fluke eggs to species level. ResultsqPCR demonstrated high analytical sensitivity, detecting Fasciola hepatica DNA down to 19.2fg and F. gigantica down to 6.4fg, with no cross-amplification of other flukes. Tremabiome was able to detect as few as five F. hepatica and Calicophoron daubneyi eggs and identify mixed infections. High levels of co-infection (14.4%) of F. hepatica and C. daubneyi were observed in faecal samples, followed by single infections with C. daubneyi (12.6%) and F. hepatica (3.2%). Notably, tremabiome detected F. hepatica in 20 samples missed by qPCR. Data analysis identified 55 and 32 ASVs for F. hepatica and C. daubneyi, respectively, with phylogenetic clustering within their respective clades. ConclusionThis study developed qPCR assay for Fasciola detection and validated a tremabiome deep amplicon sequencing for fluke species differentiation. These approaches have improved capacity to identify fluke species compared to microscopy and are valuable tools for enhancing fasciolosis surveillance and control. Author SummaryFlukes are flatworm parasites that cause disease domestic and wild animals and humans. The main species infecting cattle and sheep globally are the liver flukes F. hepatica and F. gigantica, with other species including the rumen fluke Calicophoron daubneyi locally important or emerging. Infections result in serious economic losses. The traditional method of diagnosing fluke infection involves observation of eggs in faecal samples under the microscope, but this can be time-consuming and error prone, since the eggs of different species often look similar. In this study, we developed and validated two methods to improve detection: qPCR, a sensitive DNA-based test to identify Fasciola infections, and tremabiome, a DNA sequencing technique that can accurately differentiate between different fluke species. We tested these methods using faecal samples collected from cattle and sheep across the UK. The qPCR could detect small amounts of Fasciola DNA, while tremabiome was more sensitive, identifying different fluke species from as few as five eggs. Our study found that co-infections of F. hepatica and C. daubneyi are common in the UK. The approaches we have developed could be valuable tools for to improve fluke diagnosis and enable better control of this important parasitic disease.

molecular biology↗

bioRxiv2025

Acinetobacter enrichment shapes composition and function of the bacterial microbiota of field-grown tomato plants

Tomato is a staple crop and an excellent model to study host-microbiota interactions in the plant food chain. In this study we describe a lab-in-the-field approach to investigate the microbiota of field-grown tomato plants. High-throughput amplicon sequencing revealed a three-microhabitat partition, phyllosphere, rhizosphere and root interior, differentiating host-associated communities from the environmental microbiota. An individual bacterium, classified as Acinetobacter sp., emerged as a dominant member of the microbiota at the plant-soil continuum. To gain insights into the functional significance of this enrichment, we subjected rhizosphere specimens to shotgun metagenomics. Similar to the amplicon sequencing survey, a microhabitat effect defined by a set of rhizosphere-enriched functions was identified. Mobilisation of mineral nutrients, as well as adaptation to salinity and polymicrobial communities, including antimicrobial resistance genes (ARGs), emerged as a functional requirement sustaining metagenomic diversification. A metagenome-assembled genome (MAG) representative of Acinetobacter calcoaceticus was retrieved and metagenomic reads associated to this species identified a functional specialisation for plant-growth promotion traits (PGPTs), such as phosphate solubilization, siderophores production and reactive oxygen species detoxification, which were similarly represented in across tomato genotype-independent fashion. Our results revealed that the enrichment of a beneficial bacterium capable of alleviating plants abiotic stresses appears decoupled from ARGs facilitating microbiota persistence at the root-soil interface. IMPORTANCETomatoes are at centre-stage in global food security due to their high nutritional value, widespread cultivation, and versatility. Tomatoes provide essential vitamins and minerals, contribute to diverse diets, and support farmer livelihoods, making them a cornerstone of sustainable food systems. Beyond direct dietary benefits, the intricate relationship between tomatoes, their associated microbiota, and ARG is increasingly recognised. Tomato plants host diverse microbial communities in association with their organs, which influence plant health and productivity. Crop management impacts on composition and function of these communities, contributing to the prevalence of ARG in the soil and on the plants themselves. These genes can potentially transfer to human pathogens, posing a food safety and public health risk. Understanding these complex interactions is critical for developing sustainable agricultural practices capable of mitigating the impact of climatic modifications and the global threat of antimicrobial resistance.

plant biology↗

bioRxiv2025

You Only Look Once (YOLO) Based Machine Learning Algorithm for Real-Time Detection of Loop-Mediated Isothermal Amplification (LAMP) Diagnostics

Loop-mediated isothermal amplification (LAMP) is a widely used rapid and affordable molecular DNA amplification method with minimal resource requirements. However, visual interpretation of results is subjective and prone to errors, leading to potential false-positive and negative results. To address this limitation, a machine-learning approach is proposed for automated LAMP classification based on digital images. The approach utilizes You Only Look Once (YOLOv8), a fast and robust object detection algorithm to locate and classify tubes within LAMP images, enabling automated categorization as positive or negative. The trained model achieved a high overall accuracy of 95.5% in classifying LAMP images into positive or negative. Additionally, the approach had a 98.0% precision and 92.7% recall for positive cases and 93.4% precision and 98.2% recall for negative cases, demonstrating its potential for real-time LAMP diagnosis and enhanced assay performance. This project demonstrated the platforms suitability for real-time testing, offering an easy operation and rapid results.

microbiology↗

bioRxiv2023

Mosquito virus diversity in Western and North-western Uganda

IntroductionSurveillance for mosquito borne arboviruses in Sub Saharan Africa has largely focussed on known viruses including Yellow fever virus (YFV), Rift Valley fever virus (RVFV), Chikungunya virus (CHIKV), West Nile virus (WNV) and Dengue viruses (DENV). Routine surveillance and outbreak investigations traditionally rely on serology, PCR and cell culture. Although such methods are useful, they are do not detect novel or unexpected viruses. MethodsThis study employed unbiased metagenomic next generation sequencing (MNGS) to characterise viruses circulating in mosquitoes of Arua and Kasese districts of Uganda collected systematically as part the ArboViral Infection (AVI) study. Adult mosquito sampling was carried out from multiple sites using light traps baited with solid carbon dioxide (indoors) and pyrethrum spray (outdoors). 10,026 mosquitoes were identified using appropriate morphological identification keys and separated into 96 pools by species and location of collection. Viral RNA extracted from homogenised mosquitoes was reverse transcribed to complimentary DNA and sequenced on the flow cell of an Illumina NextSeq platform. Bioinformatic analysis was performed using a customized in-house metagenomics pipeline. Downstream analyses were carried out in R version 4.2.1. Results97 viruses from 24 families and 31 genera were detected in 96 mosquito pools from Arua and Kasese districts. The abundance of viruses in different families was in the order Rhabdoviridae (33), Flaviviridae (28), Orthomyxoviridae (13), Mesoniviridae (9), Piconarviridae (9), Peribunyaviridae (9), Phasmaviridae (9), Iflaviridae (8), Phenuiviridae (7), Nodaviridae (5), Xinmoviridae (4), Reoviridae (4), Virusidae (2), Nairoviridae (2), Qinviridae (2), Togaviridae (2), Alphatetraviridae (2), Picornaviralesidae (2), Iridoviridae, (1), Nudiviridae (1), Parvoviridae (1), Permutetraviridae (1) and 22 viruses from different families remain unclassified. The Flaviviridae, Togaviridae, Rhabdoviridae, Peribunyaviridae, Phenuiviridae, Nairoviridae, Nodaviridae and Orthomyxoviridae harbor viruses that cause disease in humans and other mammals. Viruses from insect-specific virus families that were detected included the Chuviridae, Iflaviridae, Phasmaviridae and Alphatetraviridae. 92/173 (53%) of the viral genomes had full opening reading frames (ORFs) and diverged by >30% nucleotide pairwise distance from the nearest reference genome. ConclusionThe majority of viruses detected were novel species described for the first time with unknown potential to cause disease. The diversity of virus species in mosquitoes from Uganda, a hotspot for emerging arboviruses has been only partially characterized. This study, carried out in Western and North West Uganda illustrates the scale of richness and virus diversity in the region and the need to further characterise the virome in mosquitoes, especially those with a propensity to feed from human and animal hosts.

genomics↗

bioRxiv2023

In Silico Analysis of Drug Off-Target Effects on Diverse Isoforms of Cervical Cancer for Enhanced Therapeutic Strategies

Cervical cancer is a severe medical issue as 500,000 new cases of cervical cancer are identified in the world every year. The selection and analysis of the suitable gene target are the most crucial in the early phases of drug design. The emphasis at one protein while ignoring its several isoforms or splice variations may have unexpected therapeutic or harmful side effects. In this work, we provide a computational analysis of interactions between cervical cancer drugs and their targets that are influenced by alternative splicing. By using open-accessible databases, we targeted 45 FDA-approved cervical cancer drugs targeting various genes having more than two distinct protein-coding isoforms. Binding pocket interactions revealed that many drugs do not have possible targets at the isoform level. In terms of size, shape, electrostatic characteristics, and structural analysis have shown that various isoforms of the same gene with distinct ligand-binding pocket configurations. Our results emphasized the risks of ignoring possibly significant interactions at the isoform level by concentrating just on the canonical isoform and promoting consideration of the impacts of cervical cancer drugs on- and off-target at the isoform level to further research.

bioinformatics↗

bioRxiv2023

Ticks; a reservoir for virus emergence at the human-livestock interface in Uganda

BackgroundUganda is one of the most biodiverse regions on the planet and a hotspot for virus emergence. In particular, the warm-humid lowlands favour tick population growth with the associated risk of tick-borne disease. The prevalent tick species Rhipicephalus appendiculatus, R. evertsi evertsi and Amblyomma variegatum harbour a diverse range of viruses, from harmless to highly pathogenic. Notably, the orthonairoviruses cause human outbreaks of Crimean-Congo haemorrhagic fever (CCHF) regularly within the cattle corridor of Uganda, a region spanning from the south-west to the north-east of the country. MethodsIn the ArboViral Infection (AVI) study, the first to explore the virome of ticks in Uganda using next generation sequencing (NGS), we collected ticks from three geographically diverse areas and subjected these to target-enrichment (TE) NGS. Viral genomes were detected by de novo assembly, mapping and BLASTn. ResultsWe analyzed a total of 2,754 ticks collected from 31 livestock farms in the districts of Arua, Nakaseke and Lyantonde. These were combined into 219 pools by site of collection and tick species, including R. appendiculatus, R. evertsi evertsi, A. variegatum and Hyalomma rufipes. We detected partial or near-complete viral genomes in 163 tick pools; 110 (67%) of which were from Arua, 39 (24%) from Nakaseke and 12 (7%) from Lyantonde districts. 2 pools (2%) were from Arua/Lyantonde. These included 22 species of virus, representing 15 genera and 9 families, including the Nairoviridae, Retroviridae, Orthomyxoviridae, Chuviridae, Rhabdoviridae, Phenuiviridae, Parvoviridae, Poxviridae and Flaviviridae. There were 8 viral species known to be pathogens of humans or animals and 5 highly divergent genomes detected, representing novel virus species. A high abundance of orthonairoviruses was notable, including CCHFV, Dugbe virus and a novel Orthonairovirus species that we have named Macira virus. InterpretationTicks in Uganda are an important reservoir of diverse virus species, many of which remain uncharacterised and of unknown pathogenic potential. Author SummaryTicks are parasitic arachnids that may transmit a spectrum of viral diseases to humans and animals. Uganda is a hotspot for such tick-borne diseases. In this study, we sequenced ticks collected from three geographically diverse regions of Uganda using a semi-agnostic next- generation sequencing method in order to detect viruses from all known virus families. We collected and analyzed 2,754 ticks from 31 farms across the country. Within these ticks, we detected 22 species of virus from 15 genera and 9 viral families, including 8 animal or human pathogens and 5 new novel virus species. Notably, orthonairoviruses, including the highly pathogenic Crimean-Congo haemorrhagic fever virus, were highly prevalent in the ticks. The researchers suggest that ticks in Uganda serve as an important reservoir for diverse viruses, many of which have significant pathogenic potential. This information will inform public health efforts to prevent and control tick-borne diseases in Uganda and other similar regions.

microbiology↗

bioRxiv2022

Senescent response in inner annulus fibrosus cells in response to TNFα, H2O2, and TNFα-induced nucleus pulposus senescent secretome

Senescence, particularly in the nucleus pulposus (NP) cells, has been implicated in the pathogenesis of disc degeneration, however, the mechanism(s) of annulus fibrosus (AF) cell senescence is still not well understood. Both TNF and H2O2, have been implicated as contributors to the senescence pathways, and their levels are increased in degenerated discs when compared to healthy discs. Thus the objective of this study is to identify factor(s) that induces inner AF (iAF) cell senescence. Under TNF exposure, at a concentration that can induce senescence in NP cells, bovine iAF cells did not undergo senescence, indicated by their ability to continue to proliferate as demonstrated by Ki67 staining and growth curves and lack of expression of the senescent markers, p16 and p21. Unlike iAF cells, NP cells treated with TNF accumulated more intracellular ROS and secreted more H2O2. Following TNF treatment, only iAF cells had increased expression of the superoxide scavengers SOD1 and SOD2 whereas NP cells had increased NOX4 gene expression, an enzyme that can generate H2O2. Treating iAF cells with low dose H2O2 (50 M) induced senescence, however unlike TNF, H2O2 did not induce degenerative-like changes as there was no difference in COL2, ACAN, MMP13, or IL6 gene expression or number of COL2 and ACAN immunopositive cells compared to untreated controls. The latter result suggests that iAF cells have distinct degenerative and senescent phenotypes. To evaluate paracrine signalling, iAF and TNF-treated NP cells were co-cultured. In contact co-culture the NP cells did induce iAF senescence. Thus, senescent NP cells may secrete soluble factors that induce degenerative and senescent changes within the iAF. This may contribute to a positive feedback loop of disc degeneration. It is possible these factors may include H2O2 and cytokines (TNF). Further studies will investigate if human disc cells respond similarly.

cell biology↗

bioRxiv2021

PanClassif: Improving pan cancer classification of single cell RNA-seq using machine learning

Cancer is one of the major causes of human death per year. In recent years, cancer identification and classification using machine learning have gained momentum due to the availability of high throughput sequencing data. Using RNA-seq, cancer research is blooming day by day and new insights of cancer and related treatments are coming into light. In this paper, we propose PanClassif, a method that requires a very few and effective genes to detect cancer from RNA-seq data and is able to provide performance gain in several wide range machine learning classifiers. We have taken 22 types of cancer samples from The Cancer Genome Atlas (TCGA) having 8287 cancer samples and 680 normal samples. Firstly, PanClassif uses k-Nearest Neighbor (k-NN) smoothing to smooth the samples to handle noise in the data. Then effective genes are selected by Anova based test. For balancing the train data, PanClassif applies an oversampling method, SMOTE. We have performed comprehensive experiments on the datasets using several classification algorithms. Experimental results shows that PanClassif out-perform existing state-of-the-art methods available and shows consistent performance for two single cell RNA-seq datasets taken from Gene Expression Omnibus (GEO). PanClassif improves performances of a wide variety of classifiers for both binary cancer prediction and multi-class cancer classification. PanClassif is available as a python package (https://pypi.org/project/panclassif/). All the source code and materials of PanClassif are available at https://github.com/Zwei-inc/panclassif.

bioinformatics↗

bioRxiv2021

Potential of fungicides, botanicals and biocontrol agents to induce physio-biochemical tolerance on Curcuma longa impaired by Colletotrichum gloeosporioides

Necrotic leaf spot of Curcuma longa (turmeric) limits the chief physio-biochemical activity for maintaining the plant health and productivity. In the present study, polyhouse and open field trials were conducted to estimate the pathogenicity of C. gloeosporioides on turmeric and to evaluate the foliar efficiency of propiconazole @ RD and copper oxychloride, extracts of A. indica, A. sativum and O. sanctum @ 40%, and culture filtrates of T. viride, T. harzianum and T. virens @ 4x106 cfu/ml in inducing physio-biochemical tolerance of pathogen inoculated and non-inoculated plants. In both the trials, these three agents yielded the highest efficiency to enhance the physio-biochemical traits. The induced physio-biochemical tolerance in treated turmeric plants showed variation in the elevation of plant health and immunity in response to pathogen aggressiveness or disease severity. However, phytophenol content was quite higher in infected plants than non-infected plants due to initiation of defense reaction in response of pathogenic elicitors. Thus, the present study demonstrated the novelty of physio-biochemical tolerance induction on turmeric plants by using fungicides, biocontrol agents and phytoextracts. HighlightsO_LIFoliar treatments improve desirable plant physio-biochemical traits against pathogen. C_LIO_LIPhysio-biochemical variation induces the innate plant defense system. C_LIO_LIHigh phytophenol accumulation counteracts the pathogenic stress. C_LIO_LITurmeric plants health and yield enhance by the reduction of disease intensity. C_LI

pathology↗

bioRxiv2020

Microtubule-independent movement of the fission yeast nucleus

Movement of the cell nucleus typically involves the cytoskeleton and either polymerization-based pushing forces or motor-based pulling forces. In fission yeast Schizosaccharomyces pombe, nuclear movement and positioning are thought to depend on microtubule polymerization-based pushing forces. Here we describe a novel, microtubule-independent, form of nuclear movement in fission yeast. Microtubule-independent nuclear movement is directed towards growing cell tips, and it is strongest when the nucleus is close to a growing cell tip, and weakest when the nucleus is far from that tip. Microtubule-independent nuclear movement requires actin cables but does not depend on actin polymerization-based pushing or myosin V-based pulling forces. Vesicle-associated membrane protein (VAMP)-associated proteins (VAPs) Scs2 and Scs22, which are critical for endoplasmic reticulum-plasma membrane contact sites in fission yeast, are also required for microtubule-independent nuclear movement. We also find that in cells in which microtubule-based pushing forces are present, disruption of actin cables leads to increased fluctuations in interphase nuclear positioning and subsequent altered septation. Our results suggest two non-exclusive mechanisms for microtubule-independent nuclear movement, which may help illuminate aspects of nuclear positioning in other cells.

cell biology↗

bioRxiv2020

An in vitro assessment of anti-SARS-CoV-2 activity of oral preparations of iodine complexes (RENESSANS)

Since the emergence of CoVID-19 pandemic in China in late 2019, scientists are striving hard to explore non-toxic, viable anti-SARS-CoV-2 compounds or medicines. We determined In Vitro anti-SARS-CoV-2 activity of oral formulations (syrup and capsule) of an Iodine-complex (Renessans). A monolayer of vero cells were exposed to SARS-CoV-2 in the presence and absence of different concentrations (equivalent to 50, 05 and 0.5 g/ml of I2) of Renessans. Anti-SARS-CoV-2 activity of each of the formulation was assessed in the form of cell survival, SARS-CoV-2-specific cytopathic effect (CPE) and genome quantization. With varying concentrations of syrup and capsule, a varying rate of inhibition of CPE, cells survival and virus replication was observed. Compared to 0.5 g/ml concentration of Renessans syrup, 5 and 50 g/ml showed comparable results where there was a 100% cell survival, no CPEs and a negligible viral replication ({Delta}CT= 0.11 and 0.13, respectively). This study indicates that Renessans, containing iodine, may have potential activity against SARS-CoV-2 which needs to be further investigated in human clinical trials.

microbiology↗

bioRxiv2020

Evaluation of Antimicrobial, Antioxidant, Total Phenolic, Total Flavonoids, Metal Content and Proximate Potential of Solanum xanthocarpum L. (Solanaceae)

The current research work is focused on screening of antimicrobial, antioxidant, total phenolic, total flavonoid, metal estimation and proximate potential of four parts (fruits, leaves, stem bark and root bark) of S. xanthocarpum. Antimicrobial potential of dried crude extracts of S. xanthocarpum were evaluated against two gram positive bacteria (S. aureus, P. vulgaris), three gram negative bacteria (P. aeruginosa, K. pneumonia, E. coli), three fungi (A. flavus, F. solani, stolonifer) and two yeasts (S. cerevisiae, C. albicans) by using disc diffusion assay. Five organic solvents ranging from non-polar to highly polar were used for extraction of active metabolites. Amongst all the parts of S. xanthocarpum tested, antimicrobial activity of methanol extract of fruits (14.67{+/-}0.33) against P. aeruginosa, ethanolic extract of leaves against P. vulgaris (14{+/-}0.58), stem bark methanolic extract against S. aureus (13{+/-}0.58) and stem bark methanolic extract against P. vulgaris (17.67{+/-}0.33) were found to be more significant. All other extracts also showed promising antimicrobial activity against bacterial pathogens. Among fungal pathogens, R. stolonifer and S. cerevisiae were found to be more sensitive to extracts of S. xanthocarpum. Gram negative bacteria exhibited more resistance than gram positive bacteria. However, fungi were found to be more resistant than bacteria. All the extracts showed antioxidant activity. However, methanol extract of stem bark of S. xanthocarpum with IC50 value of 0.323102 mg mL-1 showed maximum antioxidant potential. Total phenolic contents ranged from 12.3541{+/-}1.73 to 23.2942{+/-}1.33 Pmol GA/ug. However, highest flavonoid content was found in the stem bark extract (17.8480{+/-}1.75 ugRutin/ug) and lowest in leaves extract of S. xanthocarpum (2.4806{+/-}0.59 ugRutin/ug). Total metal contamination in four parts of Solanum xanthocarpum (fruits, leaves, stem bark and root bark) was estimated by atomic absorption spectroscopy and results showed Cadmium contamination in its stem bark and root bark, Chromium contamination in leaves, stem bark and root bark, Copper and Magnesium contamination in all parts of S. xanthocarpum and Maganese contamination in leaves critically above the standard permissible limits. The proximate analysis of the Solanum xanthocarpum revealed that stem bark is a poor source of lipid (3.42%) and high carbohydrate (50.07%) and ash (16.50%) contents. Whereas, root bark has highest wet moisture content (65%), dry moisture content (20%) and lowest fiber (13%). Highest energy (285.455%), protein (8.32%), fat (9.79%) and lowest amount of ash (13%) was found in fruits. This composition shows that the Solanum xanthocarpum could be considered as a good source of carbohydrate, moisture and energy. These results revealed that over all, methanolic extract of the S. xanthocarpum is richest in phenolic, flavonoid and nutritional contents as well as most potent against bacterial and fungal pathogens. Therefore, further investigation is recommended to isolate, screen and characterize their active metabolites.

plant biology↗

bioRxiv2019

Architecture of the Mto1/2 microtubule nucleation complex

Proteins that contain a Centrosomin Motif 1 (CM1) domain are key regulators of{gamma} -tubulin complex-dependent microtubule nucleation, but how they are organized in higher-order structures is largely unknown. Mto1[bonsai], a truncated functional version of the Schizosaccharomyces pombe CM1 protein Mto1, interacts with Mto2 to form an Mto1/2[bonsai] complex in vivo. Here we show that recombinant Mto1/2[bonsai] forms higher-order multimers in vitro and that Mto2 alone can also multimerize. We demonstrate that Mto2 multimerization involves two separate homodimerization domains, the near N-terminal domain (NND) and the twin-cysteine domain (TCD). The TCD crystal structure reveals a stable homodimer with a novel dimerization interface. While the NND homodimer is intrinsically less stable, using crosslinking mass spectrometry we show that within Mto1/2[bonsai] complexes, it can be reinforced by additional cooperative interactions involving both Mto2 and Mto1[bonsai]. We propose a model for Mto1/2[bonsai] complex architecture that is supported by functional analysis of mutants in vivo.

cell biology↗

bioRxiv2018

In vivo fate of free and encapsulated iron oxide nanoparticles after injection of labelled stem cells

Nanoparticle contrast agents are useful tools to label stem cells and monitor the in vivo bio-distribution of labeled cells in pre-clinical models of disease. In this context, understanding the in vivo fate of the particles after injection of labelled cells is important for their eventual clinical use as well as for the interpretation of imaging results. We examined how the formulation of superparamagnetic iron oxide nanoparticles (SPIONs) impacts the labelling efficiency, magnetic characteristics and fate of the particles by comparing individual SPIONs with polyelectrolyte multilayer capsules containing SPIONs. At low labelling concentration, encapsulated SPIONs served as an efficient labelling agent for stem cells. The bio-distribution after intra-cardiac injection of labelled cells was monitored longitudinally by MRI and as an endpoint by inductively coupled plasma-optical emission spectrometry. The results suggest that, after being released from labelled cells after cell death, both formulations of particles are initially stored in liver and spleen and are not completely cleared from these organs 2 weeks post-injection.

biochemistry↗