Biology subjects

Sarkar, A.

Publications and source records attributed to Sarkar, A..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Role of m6A RNA methylation in dosage compensation

In therian mammals, inactivation of one of the X-chromosomes in females balances the dosage of X-linked gene expression between the sexes. On the other hand, upregulation of active-X balances the dosage of monoallelically expressed X-linked genes with biallelic autosomal genes (AA). Factors and mechanisms involved in the maintenance of X-chromosome inactivation (XCI) and X to autosome dosage compensation remain underexplored. Recently, it has been implicated that N6-methyladenosine (m6A) RNA modification contributes to XCI and X to autosome dosage compensation. Here, we have investigated the role of m6A RNA methylation in the maintenance of XCI and X to autosome dosage compensation in early embryonic lineages. Surprisingly, we find that the depletion of m6A RNA methylation does not affect the maintenance of inactive-X gene silencing in mouse epiblast stem cells (EpiSC), trophoblast stem cells (TSC) and extraembryonic endoderm stem cells (XEN). On the other hand, we show that m6A marks are less enriched on X-linked transcripts than the autosomal transcripts in early embryonic lineages. It is believed that less enrichment of m6A in X-linked transcript increases the stability of the X-linked transcript and thereby contributes to the X to autosome dosage compensation. Interestingly, we find that while X-linked transcripts without m6A are fully dosage compensated, transcripts with m6A undergo partial X to autosome dosage compensation in EpiSC, TSC and XEN. However, we find that the depletion of m6A has a minor effect on the X to autosome dosage compensation. Taken together, our study provides significant insight into the role of m6A RNA methylation in dosage compensation of early embryonic lineages.

genetics↗

bioRxiv2024

Confinement in fibrous environments positions and orients mitotic spindles

Accurate positioning of the mitotic spindle within the rounded cell body is critical to physiological maintenance. Adherent mitotic cells encounter confinement from neighboring cells or the extracellular matrix (ECM), which can cause rotation of mitotic spindles and, consequently, titling of the metaphase plate (MP). To understand the positioning and orientation of mitotic spindles under confinement by fibers (ECM-confinement), we use flexible ECM-mimicking nanofibers that allow natural rounding of the cell body while confining it to differing levels. Rounded mitotic bodies are anchored in place by actin retraction fibers (RFs) originating from adhesion clusters on the ECM-mimicking fibers. We discover the extent of ECM-confinement patterns RFs in 3D: triangular and band-like at low and high confinement, respectively. A stochastic Monte-Carlo simulation of the centrosome (CS), chromosome (CH), membrane interactions, and 3D arrangement of RFs on the mitotic body recovers MP tilting trends observed experimentally. Our mechanistic analysis reveals that the 3D shape of RFs is the primary driver of the MP rotation. Under high ECM-confinement, the fibers can mechanically pinch the cortex, causing the MP to have localized deformations at contact sites with fibers. Interestingly, high ECM-confinement leads to low and high MP tilts, which mechanistically depend upon the extent of cortical deformation, RF patterning, and MP position. We identify that cortical deformation and RFs work in tandem to limit MP tilt, while asymmetric positioning of MP leads to high tilts. Overall, we provide fundamental insights into how mitosis may proceed in fibrous ECM-confining microenvironments in vivo.

biophysics↗

bioRxiv2024

Inactivation of a non-canonical gp130 signaling arm attenuates chronic systemic inflammation and multimorbidity induced by a high-fat diet.

Interleukin-6 (IL-6) is a major pro-inflammatory cytokine for which the levels in plasma demonstrate a robust correlation with age and body mass index (BMI) as part of the senescence-associated secretory phenotype. IL-6 cytokines also play a crucial role in metabolic homeostasis and regenerative processes, primarily via the canonical STAT3 pathway. Thus, selective modulation of IL-6 signaling may offer a unique opportunity for therapeutic interventions. Recently, we discovered that a non-canonical signaling pathway downstream of tyrosine (Y) 814 within the intracellular domain of gp130, the IL-6 co-receptor, is responsible for the recruitment and activation of SRC family of kinases (SFK). Mice with constitutive genetic inactivation of gp130 Y814 (F814 mice) show accelerated resolution of inflammatory response and superior regenerative outcomes in skin wound healing and posttraumatic models of osteoarthritis. The current study was designed to explore if selective genetic or pharmacological inhibition of the non-canonical gp130-Y814/SFK signaling reduces systemic chronic inflammation and multimorbidity in a high-fat diet (HFD)-induced model of accelerated aging. F814 mice showed significantly reduced inflammatory response to HFD in adipose and liver tissue, with significantly reduced levels of systemic inflammation compared to wild type mice. F814 mice were also protected from HFD-induced bone loss and cartilage degeneration. Pharmacological inhibition of gp130-Y814/SFK in mice on HFD mirrored the effects observed in F814 mice on HFD; furthermore, this pharmacological treatment also demonstrated a marked increase in physical activity levels and protective effects against inflammation-associated suppression of neurogenesis in the brain tissue compared to the control group. These findings suggest that selective inhibition of SFK signaling downstream of gp130 receptor represents a promising strategy to alleviate systemic chronic inflammation. Increased degenerative changes and tissue senescence are inevitable in obese and aged organisms, but we demonstrated that the systemic response and inflammation-associated multi-morbidity can be therapeutically mitigated.

cell biology↗

bioRxiv2024

Experimental type 1 diabetes metabolically rejuvenates CD8+ T cells for improved control of tumor growth through an IGF1-IGF1R axis

AbstractEpidemiological studies suggest that patients with pre-existing type 1 diabetes (T1D) have a decreased risk of developing melanoma, prostate cancer, and breast cancer, although the underlying mechanism remains to be elucidated. In translational modelling, we observed that streptozotocin (STZ) induced T1D mice exhibited restricted melanoma and carcinoma (mammary, lung and colon) growth in association with extended overall survival. Tumor-infiltrating CD8+ T cells were found to be responsible for tumor growth restriction. Tumor infiltrating CD8+ T cells but not tumor cells themselves exhibited higher glycolytic and cytotoxic activities in T1D hosts. Such improved anti-tumor T cell function was linked to selective upregulated expression of insulin-like growth factor 1, insulin-like growth factor 1 receptor, and phospho-mTOR in CD8+ T cells in the TME. T1D patient derived CD8+ T cells displayed superior activation in vitro after tumor antigen stimulation vs. non-diabetic CD8+ T cells. Activation of T1D patient derived CD8+ T cells was sensitive to targeted antagonism of IGF1R and mTOR, supporting the operational involvement of the IGF1R-mTOR signaling axis. Our results suggest that selective activation of the intrinsic IGF1R-mTOR signaling axis in CD8+ T cells represents a preferred endpoint to achieving more effective immunotherapy outcomes and improved cancer patient management. SignificanceExperimental type 1 diabetes decelerates tumor growth through metabolic activation of cytotoxic T cells dependent on an IGF1R-mTOR signaling pathway. CD8+IGF1R+IGF1+ T cells play a crucial role in T1D dependent tumor control.

cancer biology↗

bioRxiv2024

Design and Assembly of a Cargo-agnostic Hollow Two-lidded DNA Box for Drug Delivery

DNA origami, a method of folding DNA into precise nanostructures, has emerged as a powerful tool to design complex nanoscale shapes with movable parts. DNA origami has great potential as a drug delivery system that can encapsulate and protect a range of cargos spanning small molecules through large proteins, while remaining stable in a variety of ex vivo processing conditions and in vivo environments. DNA origami has been utilized for drug delivery applications, but the vast majority of these structures have been flexible, flat 2D or solid 3D nanostructures. There is a crucial need for a hollow and completely enclosed design capable of holding any type of cargo. In this paper, we present the design and assembly of a hollow DNA origami "box" with two actuatable lids. We characterize isothermal conditions for structural assembly in minutes that eliminates the need for a thermocycler. The stability of these structures is outstanding, remaining stable at body temperature and low pH for weeks and in the presence of solvents and biological fluids over several days. We demonstrate that passive loading of small molecules is charge dependent. We also outline an approach to design staple extensions pointing into the cavity or outside of the hollow DNA origami, allowing for either active loading of protein or the potential for decoration with passivating or targeting molecules. Future work includes fitting this hollow DNA origami structure with alternative lid opening mechanisms to release a variety of different cargos in response to environmental cues. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/586853v1_ufig1.gif" ALT="Figure 1"> View larger version (19K): org.highwire.dtl.DTLVardef@97179corg.highwire.dtl.DTLVardef@18f0b46org.highwire.dtl.DTLVardef@2d390eorg.highwire.dtl.DTLVardef@fcf35c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2024

Comprehensive analysis of CXXX sequence space reveals that S. cerevisiae GGTase-I mainly relies on a2X substrate determinants

Many proteins undergo a post-translational lipid attachment, which increases their hydrophobicity, thus strengthening their membrane association properties or aiding in protein interactions. Geranylgeranyltransferase-I (GGTase-I) is an enzyme involved in a three-step post-translational modification (PTM) pathway that attaches a 20-carbon lipid group called geranylgeranyl at the carboxy-terminal cysteine of proteins ending in a canonical CaaL motif (C - cysteine, a - aliphatic, L - often leucine, but can be phenylalanine, isoleucine, methionine, or valine). Genetic approaches involving two distinct reporters were employed in this study to assess S. cerevisiae GGTase-I specificity, for which limited data exists, towards all 8000 CXXX combinations. Orthogonal biochemical analyses and structure-based alignments were also performed to better understand the features required for optimal target interaction. These approaches indicate that yeast GGTase-I best modifies the Cxa[L/F/I/M/V] sequence that resembles but is not an exact match for the canonical CaaL motif. We also observed that minor modification of non-canonical sequences is possible. A consistent feature associated with well-modified sequences was the presence of a non-polar a2 residue and a hydrophobic terminal residue, which are features recognized by mammalian GGTase-I. These results thus support that mammalian and yeast GGTase-I exhibit considerable shared specificity. Article SummaryThis work investigates yeast GGTase-I specificity through genetics, high throughput sequencing, and two distinct reporter systems. This approach allows for comprehensive evaluation of all CXXX sequence space, which has not been possible with earlier approaches. We identified CXXX sequences supporting geranylgeranylation that differ from the historically defined CaaL sequence often cited in the literature as the GGTase-I target motif, and our results indicate that the last two amino acids of the target motif largely dictate GGTase-I specificity.

genetics↗

bioRxiv2023

Fluoxetine treatment during postnatal and juvenile temporal epochs evokes diametrically opposing changes in anxio-depressive behaviors, gene expression, mitochondrial function, and neuronal architecture in the medial prefrontal cortex

BackgroundThe selective serotonin reuptake inhibitor, fluoxetine is reported to evoke distinct effects on anxio-depressive behaviors based on the temporal window of administration. Here, we systematically addressed the influence of postnatal or juvenile fluoxetine treatment on anxio-depressive behavior, gene expression, mitochondrial biogenesis, and neuronal cytoarchitecture in adulthood. MethodsRat pups received postnatal fluoxetine (PNFlx) or juvenile fluoxetine (JFlx) treatment from postnatal day 2 (P2)-P21 or P28-48 respectively, and were assessed for changes in anxio-depressive behaviors, global gene expression, mitochondrial biogenesis/function, and dendritic cytoarchitecture in the medial prefrontal cortex (mPFC) in adulthood. ResultsPNFlx evoked long-lasting increases in anxio-depressive behaviors, whereas JFlx elicited persistent decreases in anxio-depressive behavior, accompanied by differential and minimally overlapping transcriptional changes in the mPFC in adulthood. We noted opposing changes in mitochondrial function and dendritic cytoarchitecture in the mPFC of PNFlx and JFlx animals, with a decline observed following PNFlx and an increase in response to JFlx treatment. Furthermore, the enhanced despair-like behavior in the PNFlx cohort was reversed by adult-onset treatment with nicotinamide, a precursor for NAD+ which enhances mitochondrial bioenergetics. ConclusionsFluoxetine treatment in early postnatal versus juvenile windows evokes opposing and persistent effects on anxio-depressive behavior in adult male rats, along with differential effects on gene expression, mitochondrial function, and dendritic morphology in the mPFC. Collectively, our findings highlight two distinct temporal windows in which fluoxetine exposure programs starkly differing outcomes in mood-related behavior, and posits a role for altered bioenergetics within the mPFC in contributing to these distinctive changes in emotionality.

neuroscience↗

bioRxiv2023

Video-Microscopy-Based Automated Trajectory Determination for High-Velocity, Densely Clustered, Indistinguishable Objects Moving in A Directed Force Field

We present a method for tracking densely clustered, high-velocity, indistinguishable objects being spawned at a high rate and moving in a directed force field using only object centroids as inputs and no other image information. The algorithm places minimal restrictions on the velocities or accelerations of the objects being tracked and uses a methodology based on a scoring function and a back-tracking refinement process. This combination leads to successful tracking of hundreds of particles in challenging environments even when the displacement of the individual objects at successive times approaches the separation between neighboring objects in any one frame. We note that these cases can be particularly difficult to handle by existing methods. The performance of the algorithm is methodically examined by comparison to simulated trajectories which vary the temporal and spatial densities, velocities, and accelerations of the objects in motion, as well as the signal-to-noise ratio. Also, we demonstrate its capability by analyzing data from experiments with superparamagnetic microspheres moving in an inhomogeneous magnetic field in aqueous buffer at room temperature. Our method should be widely applicable since trajectory determination problems are ubiquitous in video microscopy applications in biology, materials science, physics, and engineering.

biophysics↗

bioRxiv2023

Selective refueling of CAR T cells using ADA1 and 1 CD26 boosts antitumor immunity

CAR T cell therapy has revolutionized the treatment of hematologic malignancies, but its efficacy in solid tumors remains limited due to the immunosuppressive nature of the tumor microenvironment and the inability of T cells to persist and traffic to the tumor site. While current strategies focus on enhancing CAR T cell activity through costimulatory molecules and cytokines, a critical yet often overlooked factor is the competition for nutrients between tumor cells and T cells in the nutrient-deprived tumor microenvironment. To address this challenge, we employed a selective metabolic refueling (MR) strategy by providing T cells with inosine as an alternative fuel source for growth and functionality. In this study, we engineered CAR T cells to co-express a membrane-bound CD26 and a cytoplasmic adenosine deaminase 1 (ADA1) fused to an anti-CD3 scFv. ADA1 irreversibly converts both intracellular and extracellular adenosine to inosine, overcoming adenosine-mediated immunosuppression and providing T cells with inosine for growth. The inclusion of an anti-CD3 scFv fusion partner and overexpressing CD26 boosts ADA1 capture in a membrane proximal manner, providing inosine for T cells and minimizing feeding the tumor cells. We demonstrate that ADA1 is conditionally secreted only in stress conditions and that it activates CAR T cells through trans-signaling in a tumor-specific manner. In addition, we show that, compared to unmodified CAR T cells, CD26-overexpressing CAR T cells have better migration capacity and are less susceptible to TGF-{beta}1 suppression. Finally, we found that, in mice models of human hepatocellular carcinoma (GPC3-MR-CAR) and human non-small cell lung cancer (HER2-MR-CAR), metabolically refueled CAR T cells (MR-CAR) are more efficient in reducing tumor growth than unmodified CAR T cells. Thus, selective refueling CAR T cells using ADA1 and CD26 holds promise for improving the efficacy of CAR T cell therapy of solid tumors.

immunology↗

bioRxiv2023

A Humanized Yeast System for Evaluating the Protein Prenylation of a Wide Range of Human and Viral CaaX Sequences

The C-terminal CaaX sequence (cysteine-aliphatic-aliphatic-any of several amino acids) is subject to isoprenylation on the conserved cysteine and is estimated to occur in 1-2% of proteins within yeast and human proteomes. Recently, non-canonical CaaX sequences in addition to shorter and longer length CaX and CaaaX sequences have been identified that can be prenylated. Much of the characterization of prenyltransferases has relied on the yeast system because of its genetic tractability and availability of reporter proteins, such as the a-factor mating pheromone, Ras GTPase, and Ydj1 Hsp40 chaperone. To compare the properties of yeast and human prenyltransferases, including the recently expanded target specificity of yeast farnesyltransferase, we have developed yeast strains that express human farnesyltransferase or geranylgeranyltransferase-I in lieu of their yeast counterparts. The humanized yeast strains display robust prenyltransferase activity that functionally replaces yeast prenyltransferase activity in a wide array of tests, including the prenylation of a wide variety of canonical and non-canonical human CaaX sequences, virus encoded CaaX sequences, non-canonical length sequences, and heterologously expressed human proteins HRas and DNAJA2. These results reveal highly overlapping substrate specificity for yeast and human farnesyltransferase, and mostly overlapping substrate specificity for GGTase-I. This yeast system is a valuable tool for further defining the prenylome of humans and other organisms, identifying proteins for which prenylation status has not yet been determined. Summary StatementWe report yeast engineered to express human prenylation enzymes with which prenylation can be investigated for established and novel CaaX sequences associated with proteins involved in human disease.

biochemistry↗

bioRxiv2023

A first comprehensive analysis of Transcribed Ultra Conserved Regions uncovers important regulatory functions of novel non-coding transcripts in gliomas.

Transcribed Ultra-Conserved Regions (TUCRs) represent a severely understudied class of putative non-coding RNAs (ncRNAs) that are 100% conserved across multiple species. We performed the first-ever analysis of TUCRs in glioblastoma (GBM) and low-grade gliomas (LGG). We leveraged large human datasets to identify the genomic locations, chromatin accessibility, transcription, differential expression, correlation with survival, and predicted functions of all 481 TUCRs, and identified TUCRs that are relevant to glioma biology. Of these, we investigated the expression, function, and mechanism of action of the most highly upregulated intergenic TUCR, uc.110, identifying it as a new tumor enhancer. Uc.110 was highly overexpressed in GBM and LGG, where it promoted malignancy and tumor growth. Uc.110 activated the WNT pathway by upregulating the expression of membrane frizzled-related protein (MFRP), by sponging the tumor suppressor microRNA miR-544. This pioneering study shows important roles for TUCRs in gliomas and provides an extensive database and novel methods for future TUCR research.

cancer biology↗

bioRxiv2023

A benzoxazolylurea inhibits VraS and enhances antimicrobials against vancomycin intermediate-resistant Staphylococcus aureus

Vancomycin intermediate-resistant Staphylococcus aureus (VISA) is a pathogen of concern. VraS, a histidine kinase, facilitates the VISA phenotype. Here, we reveal a benzoxazolylurea that directly inhibits VraS and enhances vancomycin to below the clinical breakpoint against an archetypal VISA strain. To the best of our knowledge, this is the first direct VraS inhibitor ever reported that shows significant enhancement of vancomycin against VISA.

pharmacology and toxicology↗

bioRxiv2023

A glucanotransferase that uses two sub-sites and four catalytic aspartates/glutamates to disproportionate oligosaccharides ranging in length from maltotriose to starch

PF0272 (PfuAmyGT) from Pyrococcus furiosus is a 656 residues-long, homodimeric, three-domain GH57 glycoside hydrolase [homologous to TLGT from Thermococcus litoralis (PDB ID: 1K1X)]. It is proposed to be either an -amylase (EC 3.2.1.1), or a 4--glucanotransferase (EC 2.4.1.25). We demonstrate that PfuAmyGT is an exo-amylase-cum-glucanotransferase capable of transferring glucose, and dis-proportionating oligosaccharides, by excising glucose from malto-oligosaccharides (ranging in length from maltotriose to amylose/starch), and transferring it to malto-oligosaccharides (ranging in length from glucose to maltoheptaose and, possibly, even longer lengths). Convention holds that glucanotransferases transfer sugars through the serial and alternating binding of donors and acceptors to the same site, with covalent retention of excised sugars between such bindings. We present evidence of multiple behaviors in PfuAmyGT that challenge this view: (i) Production of free glucose, indicating scope for release of excised glucose; (ii) Higher activity with longer donors, indicating processivity; (iii) Accelerated activity with shorter acceptors, indicating a dependence upon rapid acceptor turnover; and (iv) Evidence of four catalytic glutamates/aspartates (E131, D222, E224, D362), indicating possible separation of excision and ligation functions. These behaviours collectively indicate the binding of donors and acceptors to separate sub-sites that have different substrate length preferences, supporting our own previous proposal regarding separate tunnel (internal) and groove (surface) binding sites. Although PfuAmyGTs mechanism of function remains to be fully elucidated, this paper definitively demonstrate coupling of exo-amylase and glucanotransferase functions involving separate sub-sites for donor and acceptor binding.

biochemistry↗

bioRxiv2023

Differences in the activities of domain-swapped chimeras of two homologous GH57 glucanotransferases suggest that a glucan-binding DUF could influence donor substrate specificity

Five enzymes of the archaeal hyperthermophilic family of disproportionating GH57 4--glucanotransferases have been studied till date. Our focus here lies upon three homologous members of this family: (i) PfuAmyGT from Pyrococcus furiosus (PF0272), (ii) TonAmyGT from Thermococcus onnurenius (B6YUX8), and (iii) TliAmyGT (TLGT) from Thermococcus litoralis (O32462). The polypeptide chain of each of these enzymes is approximately 655 residues long, folded into three distinct domains (1, 2 and 3), and assembled into a homodimer. Domain 1 is a beta/alpha barrel containing an aspartate known to function as a catalytic nucleophile in TLGT. Domain 2 (which is helical) and domain 3 (made up of beta sheets) are thought to be domains of unknown function (or DUFs). In PfuAmyGT and TonAmyGT, we have recently identified a catalytically-important aspartate upon a loop in domain 2. In PfuAmyGT, we demonstrate the presence of two additional catalytically-important (glutamate) residues in domain 1, in a companion paper. In this paper, our focus lies upon domain 3 which hosts a second binding site (SBS) for a glucan, at its domain-domain interface with domain 2. Using strategies involving studies of both (a) domains (or pairs of contiguous domains) extracted from PfuAmyGT, and (b) chimeric three-domain enzymes recombining analogous domains between PfuAmyGT and TonAmyGT, we demonstrate that domain 3 determines the choice of the preferred glucan that acts as a donor in the glucan transfer reaction.

biochemistry↗

bioRxiv2023

Combined, yet Separate: cocktails of carriers (not drugs) for α-particle therapy of solid tumors expressing moderate-to-low levels of targetable markers

Alpha-particle radionuclide-antibody conjugates are being clinically evaluated against solid cancers expressing moderate levels of the targeted markers, with promising results. These findings are attributed to the high killing power of alpha-particles in spite of the expected decrease in antibody tumor uptake, that reduces tumor absorbed doses. However, when tumor absorbed doses are reduced, addressing the heterogeneities in delivery of alpha-particles within solid tumors (i.e. enabling uniform irradiation patterns) becomes critical: to maintain efficacy, the fewer alpha-particles delivered within tumors need to traverse/hit as many different cancer cells as possible. This proof-of-concept study describes an approach to complement the antibody- targeted radiotherapy by using a separate carrier to deliver a fraction of the injected radioactivity to tumor regions geographically different than those affected by the antibody; collectively, the two carriers should distribute the alpha-particle emitters, Actinium-225 in particular, more uniformly within tumors maintaining efficacy. MethodsWe monitored the extent(s) of tumor growth inhibition, onset delay of spontaneous metastases and/or survival on orthotopic MDA-MB-213 and MDA-MB-436 triple negative breast cancer mouse models and on an ectopic BxPC3 pancreatic cancer mouse model, treated systemically with the two separate carriers. Tumors were chosen to express different (but low) levels of HER1, utilized as a model antibody-targeted marker. ResultsIndependent of tumor origin and/or resistance to chemotherapy, the two separate carriers: (a) improved the primary tumor growth inhibition, (b) eliminated the formation of spontaneous metastases, and/or (c) prolonged survival, at lower or comparable tumor delivered doses relative to the antibody alone, without noticeable off-target toxicities. ConclusionThis tumor-agnostic strategy is timely and could be used to enhance the efficacy of existing alpha-particle radionuclide-antibody treatments without increasing, possibly even reducing, the total administered radioactivity.

bioengineering↗

bioRxiv2023

Analytical code sharing practices in biomedical research

Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71x10-9). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10-07). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

scientific communication and education↗

bioRxiv2023

Interpreting structure in sequence count data with differential expression analysis allowing for grades of membership

Parts-based representations, such as non-negative matrix factorization and topic modeling, have been used to identify structure from single-cell sequencing data sets, in particular structure that is not as well captured by clustering or other dimensionality reduction methods. However, interpreting the individual parts remains a challenge. To address this challenge, we extend methods for differential expression analysis by allowing cells to have partial membership to multiple groups. We call this grade of membership differential expression (GoM DE). We illustrate the benefits of GoM DE for annotating topics identified in several single-cell RNA-seq and ATAC-seq data sets.

genomics↗

bioRxiv2023

Yeast Farnesyltransferase has broad reactivity with CXXX sequences

The current understanding of farnesyltransferase (FTase) specificity was pioneered through investigations of reporters like Ras and Ras-related proteins that possess a C-terminal CaaX motif that consists of 4 amino acid residues: Cysteine - aliphatic1 - aliphatic2 - variable (X). These studies led to the finding that proteins with the CaaX motif are subject to a 3-step post-translational modification pathway involving farnesylation, proteolysis, and carboxylmethylation. Emerging evidence indicates, however, that FTase can farnesylate sequences outside the CaaX motif and that these sequences do not undergo the canonical 3-step pathway. In this work, we report a comprehensive evaluation of all possible CXXX sequences as FTase targets using the reporter Ydj1, an Hsp40 chaperone that only requires farnesylation for its activity. Our genetic and high throughput sequencing approach reveals an unprecedented profile of sequences that yeast FTase can recognize in vivo, which effectively expands the potential target space of FTase within the yeast proteome. We also document that yeast FTase specificity is majorly influenced by restrictive amino acids at a2 and X positions as opposed to the resemblance of CaaX motif as previously regarded. This first complete evaluation of CXXX space expands the complexity of protein isoprenylation and marks a key step forward in understanding the potential scope of targets for this isoprenylation pathway.

genetics↗