Biology subjects

Sharif, S.

Publications and source records attributed to Sharif, S..

11 recordsLinked to original sources

bioRxiv2026

Computational Identification of Candidate Gene Families for Volatile Sulfur Compound Biosynthesis in Cannabis sativa Using Profile Hidden Markov Models

Cannabis is well known for its pungent, skunk-like aroma. Recent chemical studies have identified prenylated and C6 volatile sulfur compounds as contributors to its skunky and citrus-like aromas, but the pathways that produce these compounds remain unknown. This gap limits efforts to explain variation in sulfur-aroma traits and to selectively enhance or reduce those traits. To address this gap, we used the known chemistry of sulfur-containing volatiles in Cannabis and characterized sulfur and volatile biosynthetic pathways in other plant species to select candidate enzyme groups. Because the GMO cultivar is anecdotally associated with a pronounced sulfurous aroma, reference protein sequences and profile hidden Markov models were used to search its version 1 (v1) primary high-confidence protein set of 55,790 sequences. These searches recovered 975 unique proteins. Sequence screening retained 941 candidates across 20 reporting categories; 939 contained all expected domains, while the two candidates assigned to the methionine gamma-lyase (MGL)-nearest category had no category-specific expected-domain rule. The largest reporting category comprised 359 proteins containing a cytochrome P450 domain, recovered through a search motivated by cytochrome P450 family 74 (CYP74) enzymes involved in oxylipin and plant volatile formation. Thirteen of these proteins were also recovered by at least one full-length CYP74 reference search. Other large reporting categories included 218 sugar-transferase, 83 glutathione-transferase, and 61 alcohol dehydrogenase candidates. Comparison with the Cannabis Expression Atlas linked 168 candidates to 128 annotated genes through 100%-identity amino-acid matches spanning at least 80% of each GMO v1 candidate protein. Twenty-nine genes were tissue-specific, including 13 root-specific and 6 trichome-specific genes. These results define candidates for biochemical testing and direct searches for additional enzymes acting upstream and downstream in Cannabis sulfur-volatile pathways.

plant biology↗

bioRxiv2026

Gas uptake stoichiometry governs carbon partitioning in syngas-fermenting Clostridium autoethanogenum

Given the current global environmental challenges, waste biomass is an attractive renewable resource for circular economies. Gasification of biomass yields syngas (CO, CO2, and H2) that is a suitable feedstock for gas fermentation in biomanufacturing of fuels and chemicals using acetogen microbes. While it is generally known that syngas composition influences both acetogen growth and process performance, we are lacking a consistent dataset quantifying these effects under controlled fermentation conditions. Here, we mapped the metabolic response of the model-acetogen Clostridium autoethanogenum to seven synthetic syngas mixtures during exponential batch growth in bioreactor fermentations. Notably, distinct gas compositions resulted in different fermentation profiles, affecting both growth and metabolite production. Maximum specific growth rates ranged within 0.05-0.13 h-1, with slower growth for low-CO mixtures. While acetate and ethanol production yields varied between 20-133 and 76-353 mmol per gram dry cell weight, respectively, minor production of 2,3-butanediol was detected. All syngas mixtures supported co-utilization of CO and H2, though gas uptake stoichiometry only moderately correlated with syngas content. Importantly, gas uptake stoichiometry strongly influenced carbon partitioning, with higher relative H2 uptake reducing CO2 loss or even realizing CO2 fixation together with increasing carbon flow towards metabolites. Interestingly, higher syngas H2 content favored ethanol and 2,3-butanediol production, while higher H2:CO uptake ratios increased total flux through the Wood-Ljungdahl pathway rather than selectively favoring reduced by-products. Our results are valuable for a better understanding of syngas composition effects on the acetogen biocatalyst and for process engineering towards optimizing gas fermentation performance.

microbiology↗

bioRxiv2026

Acquired resistance to the PRMT5 inhibitor confers collateral sensitivity to MEK inhibition in MTAP-null non-small cell lung cancer

Protein arginine methyltransferase 5 (PRMT5) is a synthetic lethal target in methylthioadenosine phosphorylase-deleted (MTAP-null) cancers. Second-generation MTA-cooperative PRMT5 inhibitors preferentially target MTAP-null cells while largely sparing MTAP-wildtype (MTAP-WT) cells, thereby improving tumor selectivity over first-generation PRMT5 inhibitors. Despite encouraging efficacy and safety signals in early clinical studies, the modest objective response rates (ORRs) observed with these inhibitors suggest that intrinsic or acquired resistance may limit their clinical benefit. Here, we investigated mechanisms of acquired resistance to the MTA-cooperative PRMT5 inhibitor BMS-986504/MRTX1719 in MTAP-null non-small cell lung cancer (NSCLC) cells and sought to identify therapeutic vulnerabilities that emerge upon resistance. Using multiple in vitro-derived resistant models, we found that acquired resistance was not fully explained by alterations in PRMT5 activity or reduced MTA levels. Instead, resistance was associated with collateral sensitivity to MEK inhibition and enrichment of MAPK-related transcriptional programs. Together, these findings identify MEK inhibition as an actionable collateral vulnerability in MTAP-null NSCLC cells that acquire resistance to PRMT5 inhibition.

cancer biology↗

bioRxiv2026

Multi-compartment spatiotemporal metabolic modeling of the chicken gut guides dietary intervention design

Understanding the interactions between diet and the gut microbiome is critical for identifying dietary interventions that support gut health. This is of particular importance for poultry where the elimination of antibiotic growth promoters has resulted in an alarming rise in enteric infections with significant economic consequences. While the application of computational models capable of dissecting the metabolic interactions supporting gut communities has shown promise, they remain limited, largely ignoring the physiological and geographical considerations of the poultry gastrointestinal tract. To address these limitations, we developed the first multi-compartment, spatiotemporally-resolved metabolic model of the chicken gastrointestinal tract. Our six-compartment framework integrates avian-specific physiological features including bidirectional flow, feeding-fasting cycles, and compartment-specific environmental parameters. The model captured distinct metabolic specialization along the gut, with upper compartments enriched for biosynthetic pathways and lower compartments specialized for fermentation. In silico screening of 34 dietary supplements revealed context-dependent metabolic responses and predicted cellulose, starch, and L-threonine as robust enhancers of short-chain fatty acid production. A controlled feeding trial validated key predictions, particularly for butyrate, with prediction accuracy further improved through integration of trial-specific microbial community data. Our findings demonstrate that community composition is a major driver of metabolic outcomes and underscore the need for context-specific modeling. Our framework provides a mechanistic platform for rational dietary intervention design and is broadly adaptable to other animal or human gastrointestinal systems.

bioinformatics↗

bioRxiv2025

Uncovering a new player in ischemic stroke: a study of intra-arterial interferon-gamma-producing monocytes in hyperacute stroke

Stroke triggers a rapid and complex immune response that is not yet fully understood, especially within hours after an ischemic infarct. Our previous study in stroke patients revealed a significant increase in interferon- gamma (IFN-{gamma}) immediately (hyperacute) and downstream of the ischemic ictus, within the arterial compartment. The present study investigated the source, inciting factors, and role of IFN-{gamma} in a preclinical murine model. Stroke was produced using transient middle cerebral artery occlusion, and immune cells within the arterial vasculature distal to the occlusion (pre- and post-occlusion) were characterized using flow cytometry. Compared with the control samples, the post-occlusion samples presented an increase in IFN-{gamma}+ and CD69+ cells, whereas no significant increase was detected in IL17+, IL4+, and CD25+ cells. Further analysis of the IFN-{gamma}+ population revealed two novel attributes. First, interrogation of the identity of these IFN-{gamma}+ cells revealed that the increase in IFN-{gamma} production was largely driven by CD14+ cells in the post- occlusion sample, with negligible contributions from other canonical IFN-{gamma}-producing cells (CD4, CD8). Second, the IFN-{gamma}+ cells exhibited two distinct clusters, an IFN-{gamma}low and an IFN-{gamma}hi population. Further analysis revealed that the IFN-{gamma} low population was largely composed of CD14+ cells, whereas the IFN-{gamma}hi population was dominated by CD4+ T-cells. To explore the conditions driving IFN-{gamma} production, an in vitro ischemia model involving oxygen-glucose deprivation (OGD) was employed. Co-culturing of naive splenocytes with OGD-treated CNS cells and OGD-derived supernatant resulted in a significant increase in IFN-{gamma}+CD14+ cells, as compared to normoxic controls, an effect that coincided with marked loss of DAPI+ and NeuN+DAPI+ cells in mixed cortical (neuronal and glial) cultures. In summary, this study identified intra-arterial CD14+ monocytes as novel early sources of IFN-{gamma} in the hyperacute phase of stroke, a role traditionally attributed to adaptive immune cells. Using in vivo and in vitro ischemia models, the findings reveal that injury-associated signals from CNS cells are sufficient to directly induce IFN-{gamma} production in CD14+ cells, redefining early stroke immunopathology and uncovering a potential target for timely immunomodulation.

immunology↗

bioRxiv2022

Mice lacking dopamine production in neurotensin receptor 1 neurons voluntarily undergo time-restricted feeding of high fat diet and resist obesity

The introduction of processed foods high in fat and sugars has caused a dramatic increase in obesity in humans. Diet-induced obesity (DIO) can be modeled in laboratory mice by increasing the fat content of their diet. Previously, it was determined that mice lacking dopamine receptor 1 (Drd1) are completely resistant to DIO and do not eat as much food during the day as control mice. Surprisingly, when Drd1 is restored to the suprachiasmatic nucleus (SCN), which is the central regulator of circadian rhythms, these mice increase day-eating and become obese. The source of dopamine in the SCN is the ventral tegmental area (VTA), but the genetic identity of the dopamine neurons is unknown. Here we create conditional deletion mutants for tyrosine hydroxylase (TH) using neurotensin receptor 1 (Ntsr1) Cre and other Cre drivers and measure feeding and body weight homeostasis on standard and high fat diets. Control mice were susceptible to DIO and overate during the day whereas Ntsr1-Cre conditional knockouts for TH mice did not increase day-eating, nor did they gain much weight on HFD. We used an adeno-associated virus to selectively restore TH to the VTA Ntsr1 neurons and observed an increase in body weight and increased day-eating of HFD. These results implicate VTA Ntsr1 dopamine neurons as promoting out-of-phase feeding behavior on a high fat diet that could be an important contributor to diet-induced obesity.

neuroscience↗

bioRxiv2020

Development Optimization and Validation of RT-LAMP based COVID-19 Facility in Pakistan

The pandemic SARS-CoV-2 (Severe acute respiratory syndrome coronavirus 2) has created a widespread panic across the globe especially in the developing countries like Pakistan. The lack of resources and technical staff are causing havoc challenges in the detection and prevention of this global outbreak. Therefore, a less expensive and massive screening of suspected individuals for COVID-19 is required. In this study, a user-friendly technique of reverse transcription-loop mediated isothermal amplification (RT-LAMP) was designed and validated to suggest a potential RT-qPCR alternate for rapid testing of COVID-19 suspected individuals. A total of 12 COVID-19 negative and 72 COVID-19 suspected individuals were analyzed. Both RT-qPCR and RT-LAMP assays were performed for all the individuals using open reading frame (ORF 1ab), nucleoprotein (N) and Spike (S) genes. All 12 specimens which were negative using RT-qPCR were also found negative using RT-LAMP assay. Overall 62 out of 72 positive samples (detected using RT-qPCR) were found COVID-19 positive using RT-LAMP assay. Interestingly all samples (45) having Ct values less than 30 showed 100% sensitivity. However, samples with weaker Ct values (i.e., => 35) showed 54% concordance, suggesting potential false negatives or false positives in RT-LAMP or RT-qPCR results, respectively. Overall comparative assessment showed that RT-LAMP assay showed strong sensitivity and specificity and can be used as an alternative strategy for rapid COVID-19 testing. Hence, based on fast processing time, minimal risk of specimens transfer and utilizing available resources, LAMP based detection of COVID-19 is strongly advocated especially for developing countries.

molecular biology↗

bioRxiv2020

Rapid and sensitive direct detection and identification of poliovirus from stool and environmental surveillance samples using nanopore sequencing

Global poliovirus surveillance involves virus isolation from stool and environmental samples, intratypic differential (ITD) by PCR and sequencing of the VP1 region to distinguish vaccine (Sabin), vaccine-derived and wild-type polioviruses and ensure an appropriate response. This cell-culture algorithm takes 2-3 weeks on average between sample receipt and sequencing. Direct detection of viral RNA using PCR allows faster detection but has traditionally faced challenges related to poor sensitivity and difficulties in sequencing common samples containing poliovirus and enterovirus mixtures. We present a nested PCR and nanopore sequencing protocol that allows rapid (<3 days) and sensitive direct detection and sequencing of polioviruses in stool and environmental samples. We developed barcoded primers and a real-time analysis platform that generate accurate VP1 consensus sequences from multiplexed samples. The sensitivity and specificity compared with cell-culture were 90.9% (95% Confidence Interval: 75.7-98.1%) and 99.2% (95.5-100.0%) for wild-type 1 poliovirus, 92.5% (79.6-98.4%) and 98.7% (95.4-99.8%) for vaccine and vaccine-derived serotype 2 poliovirus, and 88.3% (81.2-93.5%) and 93.2% (88.6-96.3%) for Sabin 1 and 3 poliovirus alone or in mixtures when tested on 155 stool samples in Pakistan. Variant analysis of sequencing reads also allowed identification of polioviruses and enteroviruses in artificial mixtures and was able to distinguish complex mixtures of polioviruses in environmental samples. The median identity of consensus nanopore sequences with Sanger or Illumina sequences from the same samples was >99.9%. This novel method shows promise as a faster and safer alternative to cell-culture for the detection and real-time sequencing of polioviruses in stool and environmental samples.

microbiology↗

bioRxiv2019

Accumulation of genetic variants associated with immunity in the selective breeding of broilers

To satisfy an increasing demand for dietary protein, the poultry industry has employed genetic selection to increase the growth rate of broilers by over 400% in the past 50 years. Although modern broilers reach a marketable weight of [~]2 kg in a short span of 35 days, a speed twice as fast as a broiler 50 years ago, the expedited growth has been associated with several negative detrimental consequences. Aside from heart and musculoskeletal problems, which are direct consequences of additional weight, the immune response is also thought to be altered in modern broilers. Given that identifying the underlying genetic basis responsible for a less sensitive innate immune response would be economically beneficial for poultry breeding, we decided to compare the genomes of two unselected meat control strains that are representative of broilers from 1957 and 1978, and a current commercial broiler line. Through analysis of genetic variants, we developed a custom prioritization strategy to identify genes and pathways that have accumulated genetic changes and are biologically relevant to immune response and growth performance. Our results highlight two genes, TLR3 and PLIN3, with genetic variants that are predicted to enhance growth performance at the expense of immune function. Placing these new genomes in the context of other chicken lines, reveal genetic changes that have specifically arisen in selective breeding programs that were implemented in the last 50 years.

genomics↗

bioRxiv2018

The impact of 10-valent Pneumococcal Conjugate Vaccine on the incidence of radiologically-confirmed pneumonia and clinically-defined pneumonia in Kenyan children.

BackgroundPneumococcal conjugate vaccines (PCV) are highly protective against invasive pneumococcal disease caused by vaccine serotypes but the burden of pneumococcal disease in developing countries is dominated by pneumonia, most of which is non-bacteraemic. We examined the impact of PCV on pneumonia incidence.\n\nMethodsWe linked prospective hospital surveillance for clinically-defined WHO severe or very-severe pneumonia at Kilifi County Hospital from 2002-2015 to population surveillance at Kilifi Health and Demographic Surveillance System, comprising 45,000 children aged <5 years. Chest radiographs were read according to a WHO standard. A 10-valent pneumococcal non-typeable Haemophilus influenzae protein D conjugate vaccine (PCV10) was introduced in Kenya in January 2011. In Kilifi, there was a catch-up campaign for children aged <5 years. We estimated the impact of PCV10 on pneumonia incidence through interrupted time series analysis accounting for seasonal and temporal trends.\n\nFindingsThe incidence of admission with clinically-defined pneumonia in 2002/3 was 21{middle dot}7/1000/year in children aged 2-59 months. This declined progressively over 13 years. By the end of March 2011, 61{middle dot}1% of children aged 2-11 months received [≥]2 doses and 62{middle dot}3% of children aged 12-59 months received [≥]1 dose of PCV10. Adjusted incidence rate ratios for admissions with radiologically-confirmed pneumonia, clinically-defined pneumonia, and diarrhoea (control condition), associated with PCV10 introduction, were 0{middle dot}52 (95% CI 0{middle dot}32-0{middle dot}86), 0{middle dot}73 (95% CI 0{middle dot}54-0{middle dot}97) and 0{middle dot}63, (95% CI 0{middle dot}31-1{middle dot}26), respectively. The annual incidence of clinically-defined pneumonia in December 2010 was 12{middle dot}2/1000; this was reduced by 3{middle dot}3/1000 with PCV10 introduction.\n\nInterpretationOver 13 years, hospitalisations for clinically-defined pneumonia declined progressively at Kilifi County Hospital but fell abruptly by 27% in association with PCV10 introduction. The incidence of radiologically-confirmed pneumonia fell by 48%. The burden of childhood pneumonia in Kilifi, Kenya, has been reduced substantially by PCV10.\n\nFundingGavi, Wellcome Trust

epidemiology↗

bioRxiv2018

Impact of 10-valent pneumococcal conjugate vaccine on invasive pneumococcal disease and nasopharyngeal carriage in Kenya

Background10-valent pneumococcal conjugate vaccine (PCV10), delivered at 6, 10 and 14 weeks of age, was introduced in Kenya in January 2011, accompanied by a catch-up campaign in Kilifi County for children <5 years. Coverage with [≥]2 PCV10 doses in children 2-11 months was 80% in 2011 and 84% in 2016; coverage with [≥]1 dose in children 12-59 months was 66% and 87%, respectively.\n\nMethodsClinical and microbiological surveillance for invasive pneumococcal disease (IPD) among admissions of all ages at Kilifi County Hospital was linked to the Kilifi Health and Demographic Surveillance System from 1999-2016. We calculated the incidence rate ratio (IRR) comparing the pre-vaccine and post-vaccine eras, adjusted for confounding, and reported percent reduction in IPD as 1-IRR. Annual cross-sectional surveys of nasopharyngeal carriage were conducted from 2009-2016.\n\nFindingsSurveillance identified 667 IPD cases in 3,211,403 person-years of observation. IPD incidence in children <5 years fell sharply in 2011 following PCV10 introduction, and remained low (PCV10-type IPD: 60{middle dot}8 vs 3{middle dot}2/100,000 [92% reduction; 95%CI: 78, 97]; overall IPD: 81{middle dot}6 vs 15{middle dot}3/100,000 [68% reduction; 95%CI: 40, 83]; 1999-2010 vs 2012-2016). PCV10-type IPD also declined significantly in unvaccinated age groups (<2 months, 5-14 years, [≥]15 years), with estimated reductions of 100%, 74%, and 81%, respectively. There was no significant change in the incidence of non-PCV10 type IPD. In children aged <5 years, PCV10-type carriage declined by 74% and non-PCV10-type carriage increased by 71%.\n\nInterpretationIntroduction of PCV10 in Kenya resulted in a substantial reduction in PCV10-type IPD in children and adults without significant replacement disease. These findings suggest that routine infant PCV10 immunization programmes with catch-up campaigns will provide substantial direct and indirect protection in low-income settings in tropical Africa.

epidemiology↗