Biology subjects

Shaukat, A.

Publications and source records attributed to Shaukat, A..

9 recordsLinked to original sources

bioRxiv2026

Vision-Language Models for Image-Based Dietary Assessment: A Benchmark of Accuracy, Cost, and Prompt Strategies Across Ten Models

BackgroundDietary assessment is the cornerstone of clinical management and research studies evaluating diet and health. Traditional methods such as food diaries and 24-hour recalls can be burdensome, prone to recall bias, and difficult to adhere to. Image-based dietary assessment using vision-language models (VLMs) offers a potential solution. ObjectiveOur goal was to benchmark state-of-the-art VLMs for automated food recognition, weight estimation, and calorie estimation using Googles Nutrition5k dataset. MethodsWe evaluated 3,229 food images using ten approaches: proprietary VLMs (Gemini 2.0 Flash, 2.5 Flash, 3.0 Flash, and 3.1 Flash Lite; GPT- 4o, GPT-4o-mini, and GPT-5 Mini; and Claude Haiku 4.5), an open-source VLM (Qwen2-VL-7B), and a commercial food recognition API (FatSecret). We assessed calorie and weight estimation using Lins Concordance Correlation Coefficient (CCC) and component detection using Jaccard similarity. ResultsGemini 3.0 Flash achieved the best calorie estimation (CCC 0.767, MAE 80.7 kcal), while Gemini 3.1 Flash Lite offered very comparable accuracy (CCC 0.754) with the highest ingredient recognition (Jaccard 0.655) at the lowest cost among top-performing models ($0.59/1K images). Among earlier-generation models, Gemini 2.0 Flash remained competitive (CCC 0.742, Jaccard 0.621) at a fraction of the cost ($0.10/1K images). A human validation study in which four annotators reviewed 440 images revealed systematic omissions in the original Nutrition5k labels. After correction, the extrapolated ingredient-overlap score for Gemini 2.0 Flash increased from 0.62 to an estimated 0.82, suggesting that raw Jaccard scores substantially underestimate true model performance. ConclusionsCurrent VLMs can perform automated dietary assessment with reasonable accuracy from single overhead photographs. Our results inform model selection for dietary assessment applications and highlight remaining challenges in calorie estimation and component detection for complex, multi-item meals.

bioinformatics↗

bioRxiv2025

Mechanosensitive channel PIEZO1 enhances endometrial decidualization via BECN1-dependent autophagy

The mechanosensitive ion channel PIEZO1 plays critical roles in physiological and pathological processes in response to various types of mechanical forces, including shear stress, stretch, and extracellular matrix (ECM) stiffness. Decidualization is crucial for a successful pregnancy, characterized by the differentiation of fibroblastic endometrial stromal cells into round, secretory decidual cells, along with the rapid remodeling of the ECM. Herein, we report that PIEZO1 plays a crucial role in enhancing decidualization in response to extracellular matrix (ECM) stiffness and cell contraction. Uterine-specific knockout of Piezo1 using Pgr-Cre in mice results in subfertility due to decidualization impairment in mid-late pregnancy. Silencing of PIEZO1 in human endometrial stromal cells also results in impaired decidualization. Treatment with the PIEZO1 agonist Yoda1 enhances decidualization in both in vivo and in vitro models. Stromal cells growing on ECM with 25 kPa stiffness display a better decidualization response than cells seeded on softer 2 kPa surface or harder surface of the regulator petri dish, and this difference is abolished by null of Piezo1. Consistent with PIEZO1 as a Ca2+ modulator, blocking of intracellular Ca2+ or pCaMKII significantly inhibits Yoda1-enhanced decidualization. Further investigation reveals that BECN1-dependent autophagy acts as the downstream of PIEZO1. Silencing of Beclin1 abolishes Yoda1-induced decidualization, while Tat-BECN1 fully rescues impaired decidualization caused by the lack of PIEZO1. Finally, the lower expression of PIEZO1 is associated with impaired decidualization in the endometrium of endometriotic baboons. In conclusion, we have uncovered a novel mechanism of decidualization that is regulated by PIEZO1-mediated mechanotransduction, providing further insight into decidualization studies. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/668790v1_ufig1.gif" ALT="Figure 1"> View larger version (68K): org.highwire.dtl.DTLVardef@2d25faorg.highwire.dtl.DTLVardef@186e56org.highwire.dtl.DTLVardef@1f3f61borg.highwire.dtl.DTLVardef@1a26bb7_HPS_FORMAT_FIGEXP M_FIG C_FIG

physiology↗

bioRxiv2023

Supercharged Fluorescent Protein-Apoferritin Cocrystals for Lighting Applications

The design of lighting sources based on fluorescent proteins (FPs) has been limited by the lack of protocols to stabilize FPs under preparation (deposition techniques, organic solvents, etc.) and working (temperature, irradiation, etc.) conditions. As a critical bottleneck, photo-induced heat generation due to FP motion and quick heat transfer leads to working device temperatures of ca. 70 {degrees}C, resulting in a quick FP-denaturation and, in turn, a quick loss of the device performance. Herein, we showcase FP stabilization for lighting devices with an electrostatically self-assembled FP-apoferritin cocrystals embedded in a silicone-based color down-converting filter. This strategy highlights three major advances: i) engineering of positively supercharged FPs (+22) without losing photoluminescence and thermal stability compared to its native form, ii) a crystallization protocol resulting in highly emissive cocrystals keeping the photoluminescence features of the FPs, and iii) a 40-fold increase of the lighting device stability compared to reference devices due to the reduction of the device working temperatures to 40 {degrees}C. Thus, the success of this multidisciplinary approach contributes toward developing stable energy-related protein-based optoelectronics.

bioengineering↗

bioRxiv2022

Genome-wide binding of Drosophila Mask reveals its role in maintenance of gene activation by Trithorax group

The Trithorax group (trxG) proteins counteract repressive effect of Polycomb group (PcG) complexes and maintain transcriptional memory of active states of key developmental genes. Although, chromatin structure and modifications appear to play a fundamental role in this process, it is not clear how trxG prevents PcG-silencing and heritably maintain an active gene expression state. Here, we report a hitherto unknown role of Drosophila Multiple ankyrin repeats single KH domain (Mask), which emerged as one of the candidate trxG genes in our reverse genetic screen. The genome-wide binding profile of Mask correlates with known trxG binding sites across Drosophila genome. In particular, association of Mask at chromatin overlaps with CBP and H3K27ac, which are known hallmarks of actively transcribed genes by trxG. Importantly, Mask predominantly associates with actively transcribed genes in Drosophila. Depletion of Mask not only results in downregulation of trxG targets but also correlates with drastic reduction in H3K27ac levels and an increased H3K27me3 levels. The fact that MASK positively regulates H3K27ac levels in flies was also found to be conserved in human cells. Finally, strong suppression of Pc mutant phenotype by mutation in mask provides physiological relevance that Mask contributes to the anti-silencing effect of trxG, maintaining expression of key developmental genes. Since Mask is a downstream effector of multiple cell signaling pathways, we propose that Mask may connect cell signaling with chromatin mediated epigenetic cell memory governed by trxG.

genomics↗

bioRxiv2021

Interplay between BALL and CBP maintains H3K27 acetylation on active genes in Drosophila

CREB binding protein (CBP) is a multifunctional transcriptional co-activator that interacts with a variety of transcription factors and acts as a histone acetyltransferase. In Drosophila, CBP mediated acetylation of histone H3 lysine 27 (H3K27ac) is a known hallmark of gene activation regulated by trithorax group proteins (trxG). Recently, we have shown that a histone kinase Ballchen (BALL) substantially co-localizes with H3K27ac at trxG target loci and is required to maintain gene activation in Drosophila. Here, we report direct interaction between BALL and CBP, which positively regulates H3K27ac. Analysis of genome-wide binding profile of BALL and CBP reveals major overlap and their co-localization at actively transcribed genes. We show that BALL biochemically interacts with CBP and depletion of BALL results in drastic reduction in H3K27ac. Together, these results demonstrate a previously unknown synergy between BALL and CBP and reveals a potentially new pathway required to maintain gene activation during development.

genomics↗

bioRxiv2020

Kinome-wide RNAi screen uncovers role of Ballchen in maintenance of gene activation by trithorax group in Drosophila

Polycomb group (PcG) and trithorax group (trxG) proteins are evolutionary conserved factors that contribute to cell fate determination and maintenance of cellular identities during development of multicellular organisms. The PcG behaves as repressors to maintain heritable patterns of gene silencing and trxG act as anti-silencing factors by maintaining activation of cell type specific genes. Genetic and molecular analysis has revealed extensive details about how different PcG and trxG complexes antagonize each other to maintain cell fates, however the cellular signaling components that contribute to maintenance of gene expression by PcG/trxG remain elusive. Here, we report an ex vivo kinome-wide RNAi screen in Drosophila aimed to identify cell signaling genes that facilitate trxG to counteract PcG mediated repression. From the list of trxG candidates, Ballchen (BALL), a histone kinase, known to phosphorylate histone H2A at threonine 119 (H2AT119p), was characterized as a trxG regulator. The ball mutant exhibit strong genetic interaction with Polycomb (Pc) and trithorax (trx) mutants and loss of BALL also affects expressions of trxG target genes in ball mutant embryos. BALL co-localizes with Trithorax on chromatin and depletion of BALL results in increased H2AK118 ubiquitination, a histone mark central to PcG mediated gene silencing. Moreover, analysis of genome-wide binding profile of BALL shows an overlap with 85% known binding sites of TRX across the genome. Both BALL and TRX are highly enriched at actively transcribed genes, which also correlate with presence of H3K4me3 and H3K27ac. We propose that BALL mediated signal positively contributes to the maintenance of gene activation by trxG by counteracting the repressive effect of PcG.

molecular biology↗

bioRxiv2020

Genetic models suggest single and multiple origins of dihydrofolate reductase mutations in Plasmodium vivax

Pyrimethamine was first introduced for the treatment of malaria in Asia and Africa during the early 1980s, replacing chloroquine, and has become the first line of drugs in many countries. In recent years, development of pyrimethamine resistance in Plasmodium vivax has become a barrier to effective malaria control strategies. Here, we describe the use of meta-barcoded deep amplicon sequencing technology to assess the evolutionary origin of pyrimethamine resistance by analysing the flanking region of dihydrofolate reductase (dhfr) locus. The genetic modelling suggests that 58R and 173L single mutants and 58R/117N double mutants are present on a single lineage; suggesting a single origin of these mutations. The triple mutants (57L/58R/117N, 58R/61M/117N and 58R/117N/173L) share the lineage of 58R/117N, suggesting a common origin. In contrast, the 117N mutant is present on two separate lineages suggesting that there are multiple origins of this mutation. We characterised the allele frequency of the P. vivax dhfr locus. Our results support the view that the single mutation of 117N and double mutations of 58R/117N arise commonly, whereas the single mutation of 173L and triple mutations of 57L/58R/117N, 58R/61M/117N and 58R/117N/173L are less common. Our work will help to inform mitigation strategies for pyrimethamine resistance in P. vivax.

genetics↗

bioRxiv2019

Novel metabarcoded DNA sequencing tool for the detection of Plasmodium species in malaria positive patients

Various PCR based methods have been described for the diagnosis of malaria, but most depend on the use of Plasmodium species-specific probes and primers; hence only the tested species are identified and there is limited available data on the true circulating species diversity. Sensitive diagnostic tools and platforms for their use are needed to detect Plasmodium species in both clinical cases and asymptomatic infections that contribute to disease transmission. We have been recently developed for the first time a novel high throughput haemoprotobiome metabarcoded DNA sequencing method and applied it for the quantification of haemoprotozoan parasites (Theleria and Babesia) of livestock. Here, we describe a novel, high throughput method using an Illumina MiSeq platform to demonstrate the proportions of Plasmodium species in metabarcoded DNA samples derived from human malaria patients. Plasmodium falciparum and Plasmodium vivax positive control gDNA was used to prepare mock DNA pools of parasites to evaluate the detection threshold of the assay for each of the two species and to assess the accuracy of proportional quantification. We then applied the assay to malaria-positive human samples to show the species composition of Plasmodium communities in the Punjab province of Pakistan and in the Afghanistan-Pakistan tribal areas. The diagnostic performance of the deep amplicon sequencing method was compared to an immunochromatographic assay that is widely used in the region. Metabarcoded DNA sequencing showed better diagnostic performance, greatly increasing the estimated prevalence of Plasmodium infection. The next-generation sequencing method using metabarcoded DNA has potential applications in the diagnosis, surveillance, treatment, and control of Plasmodium infections, as well as to study the parasite biology.

genetics↗

bioRxiv2018

Selective sweep and phylogenetic models for the emergence and spread of pyrimethamine resistance mutations in Plasmodium vivax

Pyrimethamine resistance is a major concern for the control of human haemoprotozoa, especially Plasmodium species. Currently, there is little understanding of how pyrimethamine resistance developed in Plasmodium vivax in the natural field conditions. Here, we present first time the evidence of positive selection pressure on a dihydrofolate reductase locus and its consequences on the emergence and the spread of pyrimethamine resistance in P. vivax in the Punjab province of Pakistan. First, we examined the pyrimethamine resistance locus in 38 P. vivax populations to look for evidence of positive selection pressure in human patients. The S58R (AGA)/S117N (AAC) double mutation was most common, being detected in 10/38 populations. Single mutation S117N (AAC), I173L (CTT) and S58R (AGA) SNPs were detected in 8/38, 2/38 and 1/38 populations, respectively. The F57L/I (TTA/ATA) and T61M (ATG) SNPs were not detected in any population examined. Although both soft and hard selective sweeps have occurred with striking differences between populations, there was a predominance of hard sweeps. A single resistance haplotype was present at high frequency in 9/14 populations, providing a strong evidence for the single emergence of these mutations. In contrast, 5/14 populations carried multiple resistance haplotypes at high frequencies, providing an evidence of the emergence of resistance by recurrent mutations, characteristics of soft selective sweeps. Our phylogenetic relationship analysis suggests that S58R (AGA)/S117N (AAC) and S117N (AAC) mutations arose multiple times from a single origin and spread to multiple different cities in the Punjab province through gene flow. Interestingly, the I173L (CTT) mutation was present on a single haplotype, suggesting that it arises rarely and has not spread between cities. Our work shows the need for responsible use of exiting and new antimicrobial drugs and their combinations, control the movement of infected patients and mosquito vector control strategies.

evolutionary biology↗