Biology subjects

Hoque, A.

Publications and source records attributed to Hoque, A..

11 recordsLinked to original sources

bioRxiv2026

SpectroVQ: Noise-Aware Compression of Proteomics Data via Vector-Quantized Deep Learning improves MS/MS data storage and Peptide Identification

The amount of proteomics data generated has dramatically grown for the past decade due to the wider accessibility to mass spectrometers and technological advances. Current data storage and compression techniques largely treat mass spectra as meaningless series of numbers, wasting storage on useless noise and limiting the compression ratio. Here, we present SpectroVQ, a noise-aware vector-quantized autoencoder to compress and denoise peptide tandem mass spectra without any prior annotation by exploiting peptide fragmentation pattern using deep-learning Evaluation results showed that SpectroVQ can preferentially retain useful signals in spectra from diverse peptide ions, including those in unseen datasets. SpectroVQ achieved over 3-fold increase in compression ratio over mzMLb while maintaining over 0.9 in average cosine similarity and 90% agreement in peptide identifications. In addition, we develop a novel strategy to increase peptide identifications by ~15% via ordinary library searching, by leveraging the tuneable denoising capability of SpectroVQ.

bioinformatics↗

bioRxiv2026

Fine tuning energy metabolism in skeletal muscle: Discovery of a novel autoinhibitory mechanism in the N-terminal extension of AMPKγ3

AMP-activated protein kinase (AMPK) regulates metabolism in response to metabolic stress that includes stimulating glucose uptake in skeletal muscle independently of the canonical insulin signalling pathway, positioning it as an attractive therapeutic target for insulin resistance and type 2 diabetes mellitus (T2DM). AMPK is an {beta}{gamma} heterotrimer, with multiple isoforms for each subunit enabling the formation of 12 different complexes with distinct tissue expression profiles. Among these, the 2{beta}2{gamma}3 complex is predominantly expressed in skeletal muscle, the major site of glucose disposal and a highly desirable therapeutic target for T2DM. Here, we characterise the functional role of a unique, 182 residue N-terminal extension (NTE) within {gamma}3 subunit. Deletion of the {gamma}3-NTE from 2{beta}2{gamma}3 complex increases basal AMPK activity without affecting activation by AMP or pharmacological AMPK activators, demonstrating the {gamma}3-NTE performs an autoinhibitory function. Using complementary biophysical techniques, including hydrogen-deuterium exchange-mass spectrometry, surface plasmon resonance, chemical crosslinking and co-pulldowns, we identified a 39-residue sequence in the {gamma}3-NTE (residues 129-168), that directly interacts with the C-helix of the AMPK kinase domain small lobe, a key regulatory element in many protein kinases. Using AlphaFold3, we probe the interaction predicted to take place between a {gamma}3-NTE -helix ({gamma}3-iHelix; [~]T142-E154) and the C-helix in the 2{beta}2{gamma}3 complex. These findings provide the groundwork for developing novel T2DM therapies that target AMPK activation selectively in skeletal muscle involving reversal of the {gamma}3 autoinhibition.

biochemistry↗

bioRxiv2026

DishCam: an open-source 3D-printed darkfield imager for microbial colonies and small organisms on Petri dishes

Petri dishes are routinely photographed using handheld cameras under reflected light. While adequate for large, distinct colonies, this approach fails to capture individual organisms or colonies that are transparent, do not reflect light well, or have fine structures, and is unsuitable for high quality timelapses. Darkfield illumination provides superior contrast for organisms on agar surfaces, but existing solutions rely on improvised setups with inconsistent lighting, or on large and expensive benchtop instruments that cannot be housed inside incubators. We present DishCam, an open-source device consisting entirely of 3D-printed parts and inexpensive off-the-shelf electronics, controlled by a Raspberry Pi running custom open-source software. DishCam produces high-contrast darkfield images using angled LED illumination beneath a Petri dish. All components used are off-the-shelf or easily 3D-printed. The camera and lights can be fully controlled through Raspberry Pi using our software. We demonstrate the device across multiple biological systems: Klebsiella aerogenes colonies of differing densities, Trypanosoma brucei colonies doing social motility, Dictyostelium discoideum streaming aggregation, and Caenorhabditis elegans on feeding substrates. The total cost of the basic device is approximately {pound}166 or $222, with the upgraded configuration costing approximately {pound}413 or $552, which includes a high-quality telephoto lens, SSD storage and incubator-compatible cables.

microbiology↗

bioRxiv2026

L-type channel voltage-dependent facilitation results from asymmetric π-H and π-π quadrangle interactions at DI-DII domains

Voltage-dependent facilitation (VDF) is a unique phenomenon observed in L-type voltage-gated calcium (CaV) channels, in which depolarized prepulse voltages increase inward current by several fold, contributing to neuronal firing, neurotransmitter release, cardiac automaticity, and muscle contraction. Despite three decades of research, the molecular origin and biophysical mechanisms underlying VDF in L-type (CaV1.1-CaV1.4) channels remain elusive. A serendipitous observation that solutions stored in polypropylene tubes eliminated CaV1.2 and CaV1.3 L-type channel VDF led us to identify the leachable 2,4-di-tert-butylphenol (2,4-DTBP) as a selective VDF inhibitor. Docking and molecular dynamics simulations of 2,4-DTBP revealed a previously unreported {pi}-H and {pi}-{pi} interdomain quadrangle interaction, asymmetrically positioned at the DI-DII pore-domain (PD) interface of L-type channels. Point mutagenesis disrupted these quadrangle interactions and abolished the VDF, as confirmed by whole-cell and single-channel recordings of CaV1.2. Remarkably, introducing this {pi}-H and {pi}-{pi} quadrangle interaction into the DIIS6 segment of non-VDF-displaying CaV2.1 channels induced robust VDF. In conclusion, this study provides the first molecular evidence for the VDF endpoint: L-type channel-specific interdomain quadrangle interactions asymmetrically positioned at the DI-DII PD interface.

biophysics↗

bioRxiv2025

Lower Airway Dysbiosis in NTM+ Bronchiectasis is Associated with NET-Predominant Severe Phenotypes

RationaleThe discoveries of neutrophilic inflammation and Pseudomonas-dominant pulmonary dysbiosis have helped pave the way for host-directed therapy in bronchiectasis. Substantial knowledge gaps remain about the interplay between neutrophilic signatures and microbes in non-tuberculous mycobacterial lung disease (NTM-LD), a phenotypically diverse lung infection that is increasingly prevalent in the United States and other parts of the world. ObjectivesEvaluate the lower airway microbiota and neutrophilic traits in NTM- and NTM+ bronchiectasis. Methods16S rRNA gene sequencing, cell counts and neutrophil extracellular trap (NET) immunoassays were performed on bronchoscopic lower airway samples in 200 bronchiectasis subjects (108 NTM-, 92 NTM+). A preclinical model of oral commensal micro-aspiration and NTM infection was used to profile the murine lower airways with flow cytometry and a NET assay. Measurements and Main ResultsLower airways of NTM+ bronchiectasis patients were enriched with Mycobacterium and oral commensals (e.g., Veillonella, Prevotella). NET levels were higher in NTM+ BAL. Mycobacterium and oral commensals co-occurred with NET and neutrophils in network studies. Distinct oral commensal taxa associated with severe disease phenotypes such as cavitary disease and exacerbators. In a murine micro-aspiration model, the combination of oral commensals and Mycobacterium led to a sustained pro-inflammatory immune response marked by an increase in Th17, {gamma}8T cells, PD-1+ T lymphocytes as well as higher NET levels. ConclusionsOur analyses showed that distinct microbiome features beyond the primary pathogen can contribute to neutrophilic inflammation and severe disease phenotypes in bronchiectasis/ NTM-LD.

immunology↗

bioRxiv2025

Deletion of KLHDC3, an E3 ubiquitin ligase complex substrate receptor, leads to obesity in mice.

Protein ubiquitination is a critical post-translational modification that regulates protein stability and cellular homeostasis. KLHDC3 is a substrate recognition receptor within the recently identified C-terminal degron-mediated DesCEND ubiquitination pathway. It has been characterised to selectively bind proteins with C-terminal RxxxG motifs, targeting them for degradation. Unlike the well-characterised N-terminal degron pathway, the physiological roles of C-terminal degrons remain poorly understood. To investigate KLHDC3 function in vivo, we generated Klhdc3-deficient (Klhdc3-/-) mice. These mice exhibited sub-Mendelian birth rates and progressive postnatal lethality, with a median survival of 136 days and maximum survival observed of [~]1 year of age. Early growth retardation was apparent, followed by a normalisation of body mass with age. However, as Klhdc3-/- mice aged they developed pronounced obesity at the expense of lean mass, with some individuals reaching fat mass exceeding 50% of total body weight. Combined transcriptomic and proteomic analyses of Klhdc3-/- embryonic fibroblasts revealed significant changes in protein expression with minimal impact on transcript levels, consistent with KLHDC3s role in post-translational regulation. Among the upregulated proteins, HINT1 was identified as a novel KLHDC3 substrate, possessing a C-terminal degron motif. Protein stability assays and immunoblotting confirmed HINT1 as a direct target of KLHDC3. These findings establish a new in vivo physiological role for the DesCEND pathway and highlight KLHDC3 as a key regulator of development, survival, and adiposity in mice.

developmental biology↗

bioRxiv2025

Lateral hypothalamus directs stress-induced modulation of acute and psoriatic itch

Stress and anxiety are well-known modulators of both physiological and pathological itch. Acute stress suppresses itch, while chronic stress exacerbates it. These effects are mediated by neural circuits within the brain, though the precise mechanisms remain poorly understood. In this study, we investigate the role of neurons in the stress-sensitive lateral hypothalamic area (LHA) in modulating itch. Using neural activity-dependent genetic labeling and chemogenetic tools, we selectively engaged a population of LHA neurons (LHAstress-TRAP neurons) responsive to stress. Transient stimulation of these neurons induced anxiety-like behaviors, conditioned place aversion, and suppressed acute (chloroquine-induced) and chronic (psoriatic) itch. Conversely, the inhibition of the LHAstress-TRAP neurons enhanced acute and chronic itch. Interestingly, LHAstress-TRAP neurons did not respond to acute itch stimuli, but their activity was temporally correlated with scratching episodes in mice with psoriasis. Ex vivo whole-cell patch-clamp recordings revealed that these neurons exhibit heightened excitability in psoriatic animals. Anterograde viral tracing demonstrated that LHAstress-TRAP neurons project to brainstem regions implicated in itch modulation, including the periaqueductal gray (PAG), rostral ventromedial medulla (RVM), and lateral parabrachial nucleus (LPBN). Furthermore, chemogenetic activation and optogenetic silencing of LHAstress-TRAP axon terminals revealed that bidirectional modulation of itch is primarily mediated through projections to the PAG. Together, these findings identify a previously unrecognized central mechanism by which stress modulates itch, centered on a specific population of LHA neurons and their downstream brainstem targets.

neuroscience↗

bioRxiv2022

N-Terminomic Changes of Neurons During Excitotoxicity Reveals Proteolytic Events Associated with Synaptic Dysfunctions and Potential Targets for Neuroprotection

Excitotoxicity is a neuronal death process initiated by over-stimulation of ionotropic glutamate receptors. Although dysregulation of proteolytic signaling networks is critical for excitotoxicity, the identity of affected proteins and mechanisms by which they induce neuronal cell death remain unclear. To address this, we used quantitative N-terminomics to identify proteins modified by proteolysis in neurons undergoing excitotoxic cell death. We found that most proteolytically processed proteins in excitotoxic neurons are likely substrates of calpains, including key synaptic regulatory proteins such as CRMP2, doublecortin-like kinase I, Src tyrosine kinase and calmodulin-dependent protein kinase II{beta} (CaMKII{beta}). Critically, calpain-catalyzed proteolytic processing of these proteins generates stable truncated fragments with altered activities that potentially contribute to neuronal death by perturbation of synaptic organization and function. Blocking calpain-mediated proteolysis of one of these proteins, Src protected against neuronal loss in a rat model of neurotoxicity. Extrapolation of our N-terminomic results led to the discovery that CaMKII, an isoform of CaMKII{beta} undergoes differential processing in mouse brains under physiological conditions and during ischemic stroke. In summary, our findings inform excitotoxic neuronal death mechanism and suggest potential therapeutic strategies for neuroprotection. In BriefAmeen, et al. used a proteomic method called N-terminomics to identify proteolytic events occurring in neurons during excitotoxicity. They found that most proteolytic processing is mediated by calpains, resulting in the generation of stable truncated fragments with the potential to induce synaptic dysfunction and loss, eventually leading to neuronal death. They further showed that some of these proteolytic processed proteins, such as the protein kinases Src and CaMKII, are potential targets for neuroprotection. HighlightsO_LIIdentification of over 300 neuronal proteins cleaved by calpains to form stable truncated fragments during excitotoxicity. C_LIO_LIThe calpain cleavage sites of these proteins unveil for the first time the preferred cleavage sequences of calpains in neurons. C_LIO_LIThese pathological proteolytic events potentially induce synaptic dysfunction and loss, which likely contribute to excitotoxic neuronal death. C_LIO_LISome of the neuronal proteins proteolyzed by calpains are potential targets of neuroprotection. C_LI Graphical abstract: Pathological proteolytic events in neurons during excitotoxicity unveiled by N-terminomic analyses(A) N-terminomic and global proteomic analyses identified neo-N-terminal sites and neuronal proteins undergoing significant abundance changes during excitotoxicity. (B) Informatic analysis of the proteomic results predicted (i) the preferred sequences of proteolytic processing of neuronal proteins catalyzed by calpains during excitotoxicity and (ii) perturbation of synaptic organization and functions as the major consequence of calpain-mediated proteolytic events. (C) Validation of these predictions and further experimentations unveiled: (i) calpain-mediated cleavage of proteins associated with synaptic damage in excitotoxic neurons, (ii) a new mechanism of dysregulation of CaMKII and CaMKII{beta}, which are key protein kinases governing synaptic dysfunctions and excitotoxic neuronal death and (iii) potential therapeutic targets such as the protein kinases Src and CaMKII for neuroprotection O_FIG O_LINKSMALLFIG WIDTH=194 HEIGHT=200 SRC="FIGDIR/small/484119v2_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1c69873org.highwire.dtl.DTLVardef@142db3forg.highwire.dtl.DTLVardef@481521org.highwire.dtl.DTLVardef@6359e2_HPS_FORMAT_FIGEXP M_FIG C_FIG One Sentence SummaryProteolytic events in neurons during excitotoxicity inform neuronal death mechanism and potential therapeutic strategies for neuroprotection.

neuroscience↗

bioRxiv2021

Novel torin1-sensitive phosphorylation sites on the metabolic regulator AMPK revealed by label-free mass spectrometry

AMPK and mTORC1 are nutrient-sensitive protein kinases that form a fundamental negative feedback loop that governs cell growth and proliferation. AMPK is an {beta}{gamma} heterotrimer that is directly phosphorylated by mTORC1 on 2S345 to suppress AMPK activity and promote cell proliferation under nutrient stress conditions. Using mass spectrometry, we generated precise phosphorylation profiles of all 12 AMPK complexes expressed in proliferating human cells. Of the 18 phosphorylation sites detected, seven were sensitive to pharmacological mTORC1 inhibition, including four in the AMPK {gamma}2 isoform NH2-terminal domain and 2S377 which is located in the nucleotide-sensing motif. In particular, {beta}1S182 and {beta}2S184 were found to be mTORC1 substrates in vitro and near-maximally or substantially phosphorylated under cellular growth conditions. {beta}S182 phosphorylation was elevated in 1-containing complexes, relative to 2, an effect partly attributable to the non-conserved -subunit serine/threonine-rich loop. While mutation of {beta}1S182 to a non-phosphorylatable Ala had no effect on basal and ligand-stimulated AMPK activity, {beta}2-S184A mutation increased nuclear AMPK activity and enhanced cell proliferation under nutrient stress. We conclude that mTORC1 governs the nuclear activity of AMPK to regulate transcription factors involved in metabolism and cell survival during nutrient shortage.

biochemistry↗

bioRxiv2021

Linkage disequilibrium and population structure in a core collection of Brassica napus (L.)

Estimation of genetic diversity in rapeseed/canola is important for sustainable breeding program to provide an option for the development of new breeding lines. The objective of this study was to elucidate the patterns of genetic diversity within and among different structural groups, and measure the extent of linkage disequilibrium (LD) of 383 globally distributed rapeseed/canola germplasm using 8,502 single nucleotide polymorphism (SNP) markers. The germplasm accessions were divided into five subpopulations (P1 to P5) with obvious geographic and growth habit-related patterns. All subpopulations showed moderate genetic diversity (average H = 0.22 and I = 0.34). The pairwise Fst comparison revealed a great degree of divergence (Fst > 0.24) between most of the combinations. The rutabaga type showed highest divergence with spring and winter types. Higher divergence was also found between winter and spring types. Overall, mean linkage disequilibrium was 0.03 and it decayed to its half maximum within < 45 kb distance for whole genome. The LD decay was slower in C genome (< 93 kb), relative to the A genome (< 21 kb) which was confirmed by availability of larger haplotype blocks in C genome than A genome. To maximize genetic gain, hybridization between rutabaga and other types are potentially the best option. Hybridization between spring and winter, semi-winter type is also helpful to maximize the diversity in subsequent populations. Low genetic differentiation between both spring type subpopulations (P4 and P3) will accelerate favorable allele accumulation for specific traits in elite lines. The Neighbor-Joining tree and kinship matrix will assist to identify distantly related genotypes from subpopulations to utilize in hybridization. The low levels of LD and population structure make the core collection an important resource for association mapping efforts to identify genes useful in crop improvement as well as for selection of parents for hybrid breeding.

genomics↗

bioRxiv2020

An Atlas of Phosphorylation and Proteolytic Processing Events During Excitotoxic Neuronal Death Reveals New Therapeutic Opportunities

Excitotoxicity, a neuronal death process in neurological disorders, is initiated by over-stimulation of neuronal ionotropic glutamate receptors. The over-stimulated receptors dysregulate proteases, protein kinases and phosphatases, which in turn modify target neuronal proteins to induce cell death. To decipher this cell death mechanism, we used quantitative proteomics, phosphoproteomics and N-terminomics to identify modified proteins in excitotoxic neurons. Data, available in ProteomeXchange (identifiers: PXD019527 and PXD019211), enabled us to identify over one thousand such proteins with calpains, cathepsins and over twenty protein kinases as their major modifiers. These protein modification events can potentially perturb signalling pathways governing cell survival, synaptogenesis, axonal guidance and mRNA processing. Importantly, blocking the modification of Src protein kinase, a signalling hub in excitotoxic neurons, protected against neuronal loss in vivo in a rat model of neurotoxicity. Besides offering new insights into excitotoxic neuronal death mechanism, our findings suggest potential neuroprotective therapeutic targets for treating neurological disorders. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/151456v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@1f0191forg.highwire.dtl.DTLVardef@17ba2org.highwire.dtl.DTLVardef@15c0848org.highwire.dtl.DTLVardef@123d28b_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMulti-dimensional proteomic analysis identified proteins modified by proteolysis and altered phosphorylation in neurons undergoing excitotoxic cell death. C_LIO_LICalpains, cathepsins and over twenty protein kinases are major modifiers of these proteins. C_LIO_LIThese protein modification events are predicted to impact cell survival, axonal guidance, synaptogenesis and mRNA processing. C_LIO_LIBlocking modification of an identified protein Src, which acts as a major signalling hub in neurons, was protective against excitotoxic injury in vivo. C_LI In BriefUsing multidimensional proteomic approaches, Ameen, et al. mapped the changes of proteome, phosphoproteome and N-terminome of cultured primary neurons during excitotoxicity, a crucial neuronal death process in neurological disorders. These proteomic changes document new excitotoxicity-associated molecular events, and offer insights into how these events are organized to induce neuronal death. Potential therapeutic relevance of these molecular events is illustrated by the demonstration that in vivo blockade of one of these events could protect against excitotoxic neuronal loss.

biochemistry↗