bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional characterization of two glycosyltransferases fromWithania somniferailluminates their role in withanosides biosynthesis and defence against bacteria
Authors: Anjali P , Narayanan Ananth Krishna , Parihar Durgesh , Patil Anusha , Nagegowda Dinesh A.
Published: February 2024

The medicinal properties of Ashwagandha (Withania somniferaL. Dunal) are attributed to the presence of unique class of natural products called as withanolides and their glycosylated forms, withanosides. Withanosides are proposed to be formed from withanolides by the action of glycosyltransferases (GTs). This study reports the functional characterization of two GTs (WsGT4andWsGT6) fromW. somniferathat exhibited induced expression in response to methyl jasmonate treatment and showed highest expression in leaves compared to other tissues. Biochemical assays with recombinant WsGT proteins showed that WsGT4 and WsGT6 formed glycosylated products with four and one of the seven tested withanolides substrates, respectively. WsGT4 catalyzed product formation using withanolide A, withanolide B, withanone, and 12-deoxywithastramonolide as substrates, with UDP-glucose serving as the glucose donor, while WsGT6 catalyzed the product formation only with withaferin A as substrate employing either UDP-glucose or UDP-galactose as sugar donors. Moreover,in plantastudies through virus-induced gene silencing and transient overexpression ofWsGT4andWsGT6inW. somniferaleaves modulated the levels of withanolides and withanosides, indicating their role in withanosides biosynthesis. Furthermore, while individual silencing of bothWsGT4andWsGT6inW. somniferareduced the tolerance toPseudomonas syringaeDC3000 growth, their overexpression enhanced the tolerance to the bacterium inW. somnifera. Taken together, these results shed light on the roles of WsGT4 and WsGT6 in withanoside biosynthesis and defence against model bacterial pathogen inW. somnifera.
Controlling for polygenic genetic confounding in epidemiologic association studies
Authors: Zhao Zijie , Yang Xiaoyu , Miao Jiacheng , Dorn Stephen , Barcellos Silvia H. , Fletcher Jason M. , Lu Qiongshi
Published: February 2024

Epidemiologic associations estimated from observational data are often confounded by genetics due to pervasive pleiotropy among complex traits. Many studies either neglect genetic confounding altogether or rely on adjusting for polygenic scores (PGS) in regression analysis. In this study, we unveil that the commonly employed PGS approach is inadequate for removing genetic confounding due to measurement error and model misspecification. To tackle this challenge, we introduce PENGUIN, a principled framework for polygenic genetic confounding control based on variance component estimation. In addition, we present extensions of this approach that can estimate genetically-unconfounded associations using GWAS summary statistics alone as input and between multiple generations of study samples. Through simulations, we demonstrate superior statistical properties of PENGUIN compared to the existing approaches. Applying our method to multiple population cohorts, we reveal and remove substantial genetic confounding in the associations of educational attainment with various complex traits and between parental and offspring education. Our results show that PENGUIN is an effective solution for genetic confounding control in observational data analysis with broad applications in future epidemiologic association studies.
A spring-loaded and leakage-tolerant synthetic gene switch for in-vitro detection of DNA and RNA
Authors: Gupta Krishna , Krieg Elisha
Published: February 2024

Nucleic acid tests (NATs) are essential for biomedical diagnostics. Traditional NATs, often complex and expensive, have prompted the exploration of Toehold-Mediated Strand Displacement (TMSD) circuits as an economical alternative. However, the wide application of TMSD-based reactions is limited by ‘leakage’—the spurious activation of the reaction leading to high background signals and false positives. Here we introduce a new TMSD cascade that recognizes a custom nucleic acid input and generates an amplified output. The system is based on a pair of thermodynamically spring-loaded DNA modules. The binding of a predefined nucleic acid target triggers an intermolecular reaction that activates a T7 promoter, leading to the perpetual transcription of a fluorescent aptamer that can be detected by a smartphone camera. The system is designed to permit the selective depletion of leakage byproducts to achieve high sensitivity and zero-background signal in the absence of the correct trigger. Using Zika virus (ZIKV)- and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-derived nucleic acid sequences, we show that the assay generates a reliable target-specific readout. Native RNA can be directly detected under isothermal conditions, without requiring reverse transcription, with a sensitivity as low as 200 attomole. The modularity of the assay allows easy re-programming for the detection of other targets by exchanging a single sequence domain. This work provides a low-complexity and high-fidelity synthetic biology tool for point-of-care diagnostics and for the construction of more complex biomolecular computations.
Quantitative analysis of MHC class II peptide exchange reveals pivotal role of peptide association rate
Authors: Günther Matthias , Sticht Jana , Freund Christian , Höfer Thomas
Published: February 2024

MHC-II presents antigenic peptides to T helper cells, thus shaping adaptive immune responses. Peptide loading of MHC-II in endosomes is shaped by the susceptibility of the peptide-MHC-II complex to dissociation by the catalyst HLA-DM. For a given MHC-II allotype, experimental data reveal an enormous range of HLA-DM susceptibilities of different peptides – more than five orders of magnitude. To understand the underlying mechanisms, we develop a coarse-grained kinetic model and confront it with experimental data. The model explains the observed variation of HLA-DM susceptibility with the peptide-MHC-II binding energy by an allosteric competition mechanism. Paradoxically, however, certain peptides are resistant to dissociation by HLA-DM regardless of their binding energy. Our model predicts that this resistance is linked with fast peptide association to MHC-II in the absence of HLA-DM. In sum, our data-based theoretical analysis identifies two distinct molecular mechanisms that shape antigen presentation by MHC-II.
Ultraviolet attenuates centromere-mediated meiotic genome stability and alters gametophytic ploidy consistency in flowering plants
Authors: Fu Huiqi , Zhong Jiaqi , Zhao Jiayi , Huo Li , Wang Chong , Ma Dexuan , Pan Wenjing , Sun Limin , Ren Ziming , Fan Tianyi , Wang Ze , Wang Wenyi , Lei Xiaoning , Yu Guanghui , Li Jing , Zhu Yan , Geelen Danny , Liu Bing
Published: February 2024

Ultraviolet (UV) radiation influences development and genome stability in organisms; however, its impacts on meiosis, a special cell division essential for the delivery of genetic information over generations in eukaryotes, remain not yet elucidated. In this study, we demonstrate that UV attenuates the centromere-mediated meiotic chromosome stability and induces unreduced gametes inArabidopsis thaliana. We show that UV reduces crossover (CO) rate but does not interfere with meiotic chromosome integrity. Functional centromere-specific histone 3 (CENH3) is required for the obligate CO formation, and plays a role in protection of homolog synapsis and sister-chromatid cohesion under UV stress. Moreover, UV specifically alters the orientation and organization of spindles and phragmoplasts at meiosis II, resulting in meiotic restitution and unreduced gametes. Further, we determine that UV-induced meiotic restitution does not rely on the UV Resistance Locus8-mediated UV perception and the Tapetal Development and Function1- and Aborted Microspores-dependent tapetum development, but occurs possibly via impacted JASON function and downregulated Parallel Spindle1. This study sheds light on the impacts of UV on meiotic genome stability and gametophytic ploidy consistency, which thus may influence genome evolution in flowering plants.
Proteolytic Cleavage of the ENaC γ Subunit – Impact Upon Na+and K+Handling
Authors: Ray Evan C. , Nickerson Andrew , Sheng Shaohu , Carrisoza-Gaytan Rolando , Lam Tracey , Marciszyn Allison , Zhang Lei , Jordahl Alexa , Bi Chunming , Winfrey Aaliyah , Kou Zhaohui , Gingras Sebastien , Kirabo Annet , Satlin Lisa M. , Kleyman Thomas R.
Published: February 2024

The ENaC gamma subunit is essential for homeostasis of Na+, K+, and body fluid. Dual subunit cleavage before and after a short inhibitory tract allows dissociation of this tract, increasing channel open probability (PO),in vitro. Cleavage proximal to the tract occurs at a furin recognition sequence (143RKRR146in mouse). Loss of furin-mediated cleavage preventsin vitroactivation of the channel by proteolysis at distal sites. We hypothesized that143RKRR146mutation to143QQQQ146(Q4) in 129/Sv mice would reduce ENaC PO, impair flow-stimulated flux of Na+(JNa) and K+(JK) in perfused collecting ducts, reduce colonic amiloride-sensitive short circuit current (ISC), and impair Na+, K+, and body fluid homeostasis. Immunoblot ofQ4/Q4mouse kidney lysates confirmed loss of a band consistent in size with the furin-cleaved proteolytic fragment. However,Q4/Q4male mice on a low Na+diet did not exhibit altered ENaC POor flow-induced JNa, though flow-induced JKmodestly decreased. Colonic amiloride-sensitive ISCinQ4/Q4mice was not altered.Q4/Q4males, but not females, exhibited mildly impaired fluid volume conservation when challenged with a low Na+diet. Blood Na+and K+were unchanged on a regular, low Na+, or high K+diet. These findings suggest that biochemical evidence of gamma subunit cleavage should not be used in isolation to evaluate ENaC activity. Further, factors independent of gamma subunit cleavage modulate channel POand the influence of ENaC on Na+, K+, and fluid volume homeostasis in 129/Sv mice,in vivo.
Discovering genotype-phenotype relationships with machine learning and the Visual Physiology Opsin Database (VPOD)
Authors: Frazer Seth A. , Baghbanzadeh Mahdi , Rahnavard Ali , Crandall Keith A. , Oakley Todd H.
Published: February 2024

Background

Predicting phenotypes from genetic variation is foundational for fields as diverse as bioengineering and global change biology, highlighting the importance of efficient methods to predict gene functions. Linking genetic changes to phenotypic changes has been a goal of decades of experimental work, especially for some model gene families including light-sensitive opsin proteins. Opsins can be expressed in vitro to measure light absorption parameters, including λmax - the wavelength of maximum absorbance - which strongly affects organismal phenotypes like color vision. Despite extensive research on opsins, the data remain dispersed, uncompiled, and often challenging to access, thereby precluding systematic and comprehensive analyses of the intricate relationships between genotype and phenotype.

Results

Here, we report a newly compiled database of all heterologously expressed opsin genes with λmaxphenotypes called the Visual Physiology Opsin Database (VPOD).VPOD_1.0contains 864 unique opsin genotypes and corresponding λmaxphenotypes collected across all animals from 73 separate publications. We useVPODdata anddeepBreaksto show regression-based machine learning (ML) models often reliably predict λmax, account for non-additive effects of mutations on function, and identify functionally critical amino acid sites.

Conclusion

The ability to reliably predict functions from gene sequences alone using ML will allow robust exploration of molecular-evolutionary patterns governing phenotype, will inform functional and evolutionary connections to an organism’s ecological niche, and may be used more broadly forde-novoprotein design. Together, our database, phenotype predictions, and model comparisons lay the groundwork for future research applicable to families of genes with quantifiable and comparable phenotypes.

Key Points

We introduce the Visual Physiology Opsin Database (VPOD_1.0), which includes 864 unique animal opsin genotypes and corresponding λmaxphenotypes from 73 separate publications.

We demonstrate that regression-based ML models can reliably predict λmax from gene sequence alone, predict non-additive effects of mutations on function, and identify functionally critical amino acid sites.

We provide an approach that lays the groundwork for future robust exploration of molecular-evolutionary patterns governing phenotype, with potential broader applications to any family of genes with quantifiable and comparable phenotypes.
Cell-free expression and biochemical characterization of polysaccharide-synthesizing glycosyltransferases
Authors: Jayachandran Dharanidaran , Parvate Amar D. , Brookreson Jory T. , Evans James E. , Chundawat Shishir P.S.
Published: February 2024

Polysaccharides are a major class of natural polymers found abundantly across all major life forms and play a critical role as structural, metabolic, or functional components in biomolecular processes. Some polysaccharides like cellulose and hyaluronan are synthesized by membrane-bound family-2 glycosyltransferases (GTs). Despite the fact that the GT-2 family has the maximum number of deposited sequences, the biochemistry of GT-2 family enzymes is still poorly understood due to difficulties associated with GT membrane protein expression, purification, and reconstitution in lipid carriers. Here, we chosePopulus tremula x tremuloidescellulose synthase 8 (PttCesA8) andStreptococcus equisimilishyaluronan synthase (SeHas) as putative family-2-GTs to be expressed in a wheat-germ-based cell-free expression (CFE) system as proteoliposomes. The cell-free products were obtained as reconstituted liposomes directly from CFE reactions at high yields and short processing times compared to other approaches. GT enzymes expression was confirmed using SDS-PAGE and immunoblotting, and the integration of GTs in lipid layers was observed using cryogenic electron microscopy. Both GTs tested were catalytically active when incubated with their respective substrates and cofactors. The Michalis-Menten kinetic constants, Kmfor PttCesA8, was 295.8 µM, and SeHas was 321.51 µM (toward UDP N-Acetyl Glucosamine) and 207.88 µM (toward UDP Glucuronic Acid), respectively. UDP was found to actively inhibit both these GTs with apparent inhibition constants of 10.08 µM and 24.38 µM. Mutation of specific conserved residues in structure-deficit SeHas confirmed the importance of lysine-139, glutamine-248, and threonine-283 residues in hyaluronan biosynthesis. In summary, wheat-germ-based CFE can be used to express functionally active and liposome-reconstituted family-2 GTs at high yields with relative ease to enable classical enzymology assays and will also enable more detailed structural studies in the near future.
Memory-boundk-mer selection for large and evolutionary diverse reference libraries
Authors: Şapcı Ali Osman Berk , Mirarab Siavash
Published: February 2024

Usingk-mers to find sequence matches is increasingly used in many bioinformatic applications, including metagenomic sequence classification. The accuracy of these down-stream applications relies on the density of the reference databases, which, luckily, are rapidly growing. While the increased density provides hope for dramatic improvements in accuracy, scalability is a concern. Referencek-mers are kept in the memory during the query time, and saving allk-mers of these ever-expanding databases is fast becoming impractical. Several strategies for subsampling have been proposed, including minimizers and finding taxon-specifick-mers. However, we contend that these strategies are inadequate, especially when reference sets are taxonomically imbalanced, as are most microbial libraries. In this paper, we explore approaches for selecting a fixed-size subset ofk-mers present in an ultra-large dataset to include in a library such that the classification of reads suffers the least. Our experiments demonstrate the limitations of existing approaches, especially for novel and poorly sampled groups. We propose a library construction algorithm called KRANK (K-mer RANKer) that combines several components, including a hierarchical selection strategy with adaptive size restrictions and an equitable coverage strategy. We implement KRANK in highly optimized code and combine it with the locality-sensitive-hashing classifier CONSULT-II to build a taxonomic classification and profiling method. On several benchmarks, KRANKk-mer selection dramatically reduces memory consumption with minimal loss in classification accuracy. We show in extensive analyses based on CAMI benchmarks that KRANK outperformsk-mer-based alternatives in terms of taxonomic profiling and comes close to the best marker-based methods in terms of accuracy.
Postdoctoral Scholar Recruitment and Hiring Practices in STEM: A Pilot Study
Authors: Heirwegh Meagan , Rees Douglas C. , Malcom-Piqueux Lindsey
Published: February 2024

Despite the importance of the postdoctoral position in the training of scientists for independent research careers, few studies have addressed recruiting and hiring of postdocs. We conducted a pilot study on postdoctoral hiring in the Division of Chemistry and Chemical Engineering at the California Institute of Technology to serve as a starting point to better understand postdoctoral recruiting and hiring processes. From this survey of both postdocs and faculty, together with the available literature, the picture emerges that the postdoc hiring process is more decentralized than either faculty hiring or graduate admissions. Postdoc positions are often filled through a passive process where the initial expression of interest from a prospective postdoc is through a “cold-call” contact to a prospective advisor. Individual faculty members are often responsible for developing and implementing their own outreach and recruitment plans and deciding who to hire into a postdoc position. The overall opacity of the processes and practices by which postdocs are identified, recruited, and hired make it difficult to pinpoint where interventions could be effective to ensure equitable hiring practices. Implementation of such practices is critical to training a diverse postdoc population and subsequently of the future STEM faculty recruited from this group.
Pathogen and pest risks to vegetatively propagated crops in humanitarian contexts: Toward a national plant health risk analysis for Cameroon and Ethiopia
Authors: Mouafo-Tchinda Romaric A. , Etherton Berea A. , Plex Sulá Aaron I. , Andrade-Piedra Jorge , Ogero Kwame , Omondi Bonaventure A. , McEwan Margaret A. , Tene Tayo Paul M. , Harahagazwe Dieudonné , Cherinet Mihiretu , Gebeyehu Setegn , Sperling Louise , Garrett Karen A.
Published: February 2024

Cameroon and Ethiopia face humanitarian crises that disrupt the production of key food security crops like banana and plantain, cassava, potato, and sweetpotato. In this study, we address seed degeneration in these crops, the reduction in planting material quality due to the accumulation of pathogens and pests. We consider the context of humanitarian crises, with the goal of developing an ongoing ‘national plant health risk analysis’, in this case to inform decisions about mitigating seed degeneration. We analyzed cropland density maps and applied network centrality metrics to identify locations that are candidates for disease and pest management and surveillance in Cameroon and Ethiopia. We used expert knowledge elicitation and global trade data to map pathogen and pest movement risks and characterize trade of crop-specific commodities and planting materials. We identified specific locations that may be important for pathogen and pest spread in in Cameroon and Ethiopia, given their roles in the cropland network, and the reported presence of pathogens and pests. This national plant health risk analysis can inform regional and national surveillance and management strategies and provide a baseline for more in-depth studies in Cameroon and Ethiopia. We discuss strategies for ongoing improvement of a national plant health risk analysis, to inform decision-making in the humanitarian sector for designing on-the-ground actions to avoid unintentional spread of pathogens and pests during agricultural recovery interventions.
A Specialized Centrosome-Proteasome Axis Mediates Proteostasis and Influences Cardiac Stress through Txlnb
Authors: McLendon Jared M. , Zhang Xiaoming , Stein Colleen S. , Baehr Leslie M. , Bodine Sue C. , Boudreau Ryan L.
Published: February 2024

Background

Centrosomes localize to perinuclear foci where they serve multifunctional roles, arranging the microtubule organizing center (MTOC) and anchoring ubiquitin-proteasome system (UPS) machinery. In mature cardiomyocytes, centrosomal proteins redistribute into a specialized perinuclear cage-like structure, and a potential centrosome-UPS interface has not been studied. Taxilin-beta (Txlnb), a cardiomyocyte-enriched protein, belongs to a family of centrosome adapter proteins implicated in protein quality control. We hypothesize that Txlnb plays a key role in centrosomal-proteasomal crosstalk in cardiomyocytes.

Methods

Integrative bioinformatics assessed centrosomal gene dysregulation in failing hearts. Txlnb gain/loss-of-function studies were conducted in cultured cardiomyocytes and mice. Txlnb’s role in cardiac proteotoxicity and hypertrophy was examined using CryAB-R120G mice and transverse aortic constriction (TAC), respectively. Molecular modeling investigated Txlnb structure/function.

Results

Human failing hearts show consistent dysregulation of many centrosome-associated genes, alongside UPS-related genes. Txlnb emerged as a candidate regulator of cardiomyocyte proteostasis that localizes to the perinuclear centrosomal compartment. Txlnb’s interactome strongly supports its involvement in cytoskeletal, microtubule, and UPS processes, particularly centrosome-related functions. Overexpressing Txlnb in cardiomyocytes reduced ubiquitinated protein accumulation and enhanced proteasome activity during hypertrophy. Txlnb-knockout (KO) mouse hearts exhibit proteasomal insufficiency and altered cardiac growth, evidenced by ubiquitinated protein accumulation, decreased 26Sβ5 proteasome activity, and lower mass with age. In Cryab-R120G mice, Txlnb loss worsened heart failure, causing lower ejection fractions. After TAC, Txlnb-KO mice also showed reduced ejection fraction, increased heart mass, and elevated ubiquitinated protein accumulation. Investigations into the molecular mechanisms revealed that Txlnb-KO did not affect proteasomal subunit expression but led to the upregulation of Txlna and several centrosomal proteins (Cep63, Ofd1, and Tubg) suggesting altered centrosomal dynamics. Structural predictions support Txlnb’s role as a specialized centrosomal-adapter protein bridging centrosomes with proteasomes, confirmed by microtubule-dependent perinuclear localization.

Conclusions

Together, these data provide initial evidence connecting Txlnb to cardiac proteostasis, hinting at the potential importance of functional bridging between specialized centrosomes and UPS in cardiomyocytes.
A Curated Cell Life Imaging Dataset of Immune-enriched Pancreatic Cancer Organoids with Pre-trained AI Models
Authors: Kulkarni Ajinkya , Ferreira Nathalia , Scodellaro Riccardo , Alves Frauke
Published: February 2024

Tumor organoids are three-dimensional in vitro models which can recapitulate the complex mutational landscape and tissue architecture observed in cancer patients, providing a realistic tumor microenvironment for testing novel therapies, including immunotherapies. A significant challenge in organoid research in oncology lies in developing efficient and reliable methods for segmenting organoid images, quantifying organoid growth, regression and response to treatments, as well as predicting the behavior of organoid systems. Up to now, a curated dataset of organoids co-cultured with immune cells is not available. To address this gap, we present a new public dataset, comprising both phase-contrast images of murine and patient-derived tumor organoids of one of the deadliest cancer types, the Pancreatic Ductal Adenocarcinoma, co-cultured with immune cells, and state-of-the-art algorithms for object detection and segmentation. Our dataset,OrganoIDNetData, encompassing 190 images with 33906 organoids, can be a potential common benchmark for different organoids segmentation protocols, moving beyond the current practice of training and testing these algorithms on isolated datasets.
Development and Validation of the Participation Questionnaire for Preschoolers with Autism Spectrum Disorder: A Focus on Structural Validity, Internal Consistency, and Construct Validity
Authors: Nakamura Takuto , Nagayama Hirofumi , Sasada Satoshi
Published: February 2024

Aim

To develop and validate the Participation Questionnaire for Preschoolers (PQP), a new disease-specific participation measurement tool for children with autism spectrum disorder (ASD)

Methods

In this cross-sectional study, questionnaires were distributed to caregivers of children through child development facilities and medical institutions. The sample comprised 180 children with ASD and 100 children with developmental disabilities without ASD. Additional participants with ASD were recruited through users of a developmental support website. Following item reduction based on the data from children with ASD, exploratory factor analysis was conducted, and Cronbach’s alpha coefficients were calculated. Correlations between PQP scores and age, symptom severity, sensory processing, and family functioning were evaluated to examine the construct validity. PQP scores for children with ASD were then compared with those for children with developmental disabilities.

Results

In total, 412 participants completed the questionnaire. Item reduction analysis led to the exclusion of seven items, revealing four factors. The PQP demonstrated high internal consistency and good construct validity, with observation of score differences based on the presence or absence of an ASD diagnosis.

Conclusion

The PQP appears to be an effective tool for children with ASD. However, further research is required to assess its longitudinal properties.
Liquid Biopsy for Detection of Pancreaticobiliary Cancers in Suspected Patients by Functional Enrichment and Immunofluorescent Profiling of Circulating Tumor Cells and their Clusters
Authors: Gaya Andrew , Rohatgi Nitesh , Limaye Sewanti , Shreenivas Aditya , Ajami Ramin , Akolkar Dadasaheb , Datta Vineet , Srinivasan Ajay , Patil Darshana
Published: February 2024

Background

Circulating tumor cells (CTCs) have historically been used for prognostication in oncology. We evaluate performance of liquid biopsy CTC assay as a diagnostic tool in suspected pancreaticobiliary cancers. The assay utilises functional enrichment of CTCs followed by immunofluorescent profiling of organ specific markers.

Methods

Multicentric case control study was followed by a prospective observational study. Adult patients undergoing tissue sampling for suspected pancreaticobiliary cancer were included in the studies. Blood samples for TruBlood® CTC assay were drawn before tissue sampling. Patients with a prior cancer treatment or cancer history were excluded. CTCs and their clusters were harvested by a unique functional enrichment method which is label-free, size independent and non-mechanical. The CTCs then underwent immunofluorescent profiling for CA19.9, Maspin, EpCAM, CK and CD45, blinded to the tissue histopathological diagnosis. TruBlood® malignant or non-malignant predictions were compared with tissue diagnoses to establish the sensitivity and specificity.

Results

The case-control study evaluated 360 participants including 188 cases diagnosed with pancreaticobiliary cancer and 172 healthy individuals. A subsequent prospective observational study included 88 individuals with suspicion of pancreaticobiliary malignancy. The test had 95.9% overall sensitivity (95% CI: 86.0% - 99.5%) and 92.3% specificity (95% CI: 79.13% to 98.38%) to differentiate pancreaticobiliary cancers (PBC) (n = 49) from benign PB conditions (n = 39).

Conclusions

The high accuracy of the CTC based TruBlood test demonstrates its potential clinical application as a diagnostic tool to assist effective detection of pancreaticobiliary cancers when tissue sampling is unviable or inconclusive. A confirmational prospective interventional studiy in patients with suspicion of pancreaticobiliary malignancy including those with unavailability of tissue diagnosis is warranted.
Chlamydomonas cells transition through distinct Fe nutrition stages within 48 h of transfer to Fe-free medium
Authors: Liu Helen W. , Urzica Eugen I. , Gallaher Sean D. , Blaby-Haas Crysten E. , Iwai Masakazu , Schmollinger Stefan , Merchant Sabeeha S.
Published: February 2024

Low iron (Fe) bioavailability can limit the biosynthesis of Fe-containing proteins, which are especially abundant in photosynthetic organisms, thus negatively affecting global primary productivity. Understanding cellular coping mechanisms under Fe limitation is therefore of great interest. We surveyed the temporal responses of Chlamydomonas (Chlamydomonas reinhardtii) cells transitioning from an Fe-rich to an Fe-free medium to document their short- and long-term adjustments. While slower growth, chlorosis and lower photosynthetic parameters are evident only after one or more days in Fe-free medium, the abundance of some transcripts, such as those for genes encoding transporters and enzymes involved in Fe assimilation, change within minutes, before changes in intracellular Fe content are noticeable, suggestive of a sensitive mechanism for sensing Fe. Promoter reporter constructs indicate a transcriptional component to this immediate primary response. With acetate provided as a source of reduced carbon, transcripts encoding respiratory components are maintained relative to transcripts encoding components of photosynthesis and tetrapyrrole biosynthesis, indicating metabolic prioritization of respiration over photosynthesis. In contrast to the loss of chlorophyll, carotenoid content is maintained under Fe limitation despite a decrease in the transcripts for carotenoid biosynthesis genes, indicating carotenoid stability. These changes occur more slowly, only after the intracellular Fe quota responds, indicating a phased response in Chlamydomonas, involving both primary and secondary responses during acclimation to poor Fe nutrition.
TSC22D,WNKandNRBPgene families exhibit functional buffering and evolved with Metazoa for macromolecular crowd sensing
Authors: Xiao Yu-Xi , Lee Seon Yong , Aguilera-Uribe Magali , Samson Reuben , Au Aaron , Khanna Yukti , Liu Zetao , Cheng Ran , Aulakh Kamaldeep , Wei Jiarun , Farias Adrian Granda , Reilly Taylor , Habsid Andrea , Brown Kevin R. , Chan Katherine , Mero Patricia , Huang Jie Qi , Billmann Maximilian , Rahman Mahfuzur , Myers Chad , Andrews Brenda J. , Youn Ji-Young , Yip Christopher M. , Rotin Daniela , Derry W. Brent , Forman-Kay Julie D. , Moses Alan M. , Pritišanac Iva , Gingras Anne-Claude , Moffat Jason
Published: February 2024

The ability to sense and respond to osmotic fluctuations is critical for the maintenance of cellular integrity. Myriad redundancies have evolved across all facets of osmosensing in metazoans, including among water and ion transporters, regulators of cellular morphology, and macromolecular crowding sensors, hampering efforts to gain a clear understanding of how cells respond to rapid water loss. In this study, we harness the power of gene co-essentiality analysis and genome-scale CRISPR-Cas9 screening to identify an unappreciated relationship betweenTSC22D2,WNK1andNRBP1in regulating cell volume homeostasis. Each of these genes have paralogs and are functionally buffered for macromolecular crowd sensing and cell volume control. Within seconds of hyperosmotic stress, TSC22D, WNK and NRBP family members physically associate into cytoplasmic biocondensates, a process that is dependent on intrinsically disordered regions (IDRs). A close examination of these protein families across metazoans reveals thatTSC22Dgenes evolved alongside a domain in NRBPs that specifically binds to TSC22D proteins, which we have termed NbrT (NRBPbinding region withTSC22D), and this co-evolution is concomitant with rapid IDR length expansion in WNK family kinases. Our study identifies functions for unrecognized components of the cell volume sensing machinery and reveals thatTSC22D,WNKandNRBPgenes evolved as cytoplasmic crowding sensors in metazoans to co-regulate rapid cell volume changes in response to osmolarity.
Common data models to streamline metabolomics processing and annotation, and implementation in a Python pipeline
Authors: Mitchell Joshua M. , Chi Yuanye , Thapa Maheshwor , Pang Zhiqiang , Xia Jianguo , Li Shuzhao
Published: February 2024

To standardize metabolomics data analysis and facilitate future computational developments, it is essential is have a set of well-defined templates for common data structures. Here we describe a collection of data structures involved in metabolomics data processing and illustrate how they are utilized in a full-featured Python-centric pipeline. We demonstrate the performance of the pipeline, and the details in annotation and quality control using large-scale LC-MS metabolomics and lipidomics data and LC-MS/MS data. Multiple previously published datasets are also reanalyzed to showcase its utility in biological data analysis. This pipeline allows users to streamline data processing, quality control, annotation, and standardization in an efficient and transparent manner. This work fills a major gap in the Python ecosystem for computational metabolomics.

Author Summary

All life processes involve the consumption, creation, and interconversion of metabolites. Metabolomics is the comprehensive study of these small molecules, often using mass spectrometry, to provide critical information of health and disease. Automated processing of such metabolomics data is desired, especially for the bioinformatics community with familiar tools and infrastructures. Despite of Python’s popularity in bioinformatics and machine learning, the Python ecosystem in computational metabolomics still misses a complete data pipeline. We have developed an end-to-end computational metabolomics data processing pipeline, based on the raw data preprocessor Asari [1]. Our pipeline takes experimental data in .mzML or .raw format and outputs annotated feature tables for subsequent biological interpretation. We demonstrate the application of this pipeline to multiple metabolomics and lipidomics datasets. Accompanying the pipeline, we have designed a set of reusable data structures, released as the MetDataModel package, which shall promote more consistent terminology and software interoperability in this area.
Knockdown resistance (kdr) Associated organochlorine Resistance in mosquito-borne diseases (Culex quinquefasciatus): Systematic study of reviews and meta-analysis
Authors: Abbasi Ebrahim , Daliri Salman
Published: February 2024

Introduction

Culex quinquefasciatusis one of the most important carriers of human pathogens. The use of insecticides is one of the most important methods of combating this vector. But the genetic resistance created inCulex quinquefasciatushas led to disruption in the fight against this pest. As a result, it is necessary to know the level of resistance in order to fight this vector. Based on this, the present study was conducted with the aim of investigating the prevalence of kdr resistance inCulex quinquefasciatusagainst organochlorine insecticides in the world.

Methods

This study was conducted by systematic review and meta-analysis on the prevalence of kdr resistance and mortality rate inCulex quinquefasciatusagainst organochlorine insecticides in the world. Based on this, during the search in the scientific databases Web of Science, PubMed, Scopus, biooan.org, Embase, ProQuest and Google scholar without time limit until the end of November 2023, all related articles were extracted and analyzed. Statistical analysis of the data was done using fixed and random effects model in meta-analysis,I2index, Cochran’s test and meta-regression by STATA version 17 software.

Results

Seventy articles were included in the meta-analysis process. Based on the findings, the prevalence of Kdr inCulex quinquefasciatusagainst organochlorine insecticide was estimated at 63.1%. Also, the mortality rate against the insecticide deltamethrin was 46%, DDT 18.5%, permethrin 42.6%, malathion 54.4% and lambdacyhalothrin 53%.

Conclusion

More than half of Cx. quinquefasciatus had Kdr. This vector was relatively resistant to DDT and permethrin insecticides and sensitive to malathion, deltamethrin and lambdacyhalothrin. As a result, it is necessary to use effective insecticides to fight this vector in order to prevent the increase of resistance to other insecticides.
HairSplitter: haplotype assembly from long, noisy reads
Authors: Faure Roland , Lavenier Dominique , Flot Jean-François
Published: February 2024

Motivation

Long-read assemblers face challenges in discerning closely related viral or bacterial strains, often collapsing similar strains into a single sequence. This limitation has been hampering metagenome analysis, as diverse strains may harbor crucial functional distinctions.

Results

We introduce a novel software, HairSplitter, designed to retrieve strains from a partially or totally collapsed assembly and long reads. The method uses a custom variant-calling process to operate with erroneous long reads and introduces a new read binning algorithm to recover an a priori unknown number of strains. On noisy long reads, HairSplitter recovers more strains while being faster than state-of-the-art tools, both in the cases of viruses and bacteria.

Availability

HairSplitter is freely available on GitHub atgithub.com/RolandFaure/HairSplitter.

Contact

roland.faure@irisa.fr
Data mining antibody sequences for database searching in bottom-up proteomics
Authors: Trinh Xuan-Tung , Freitag Rebecca , Krawczyk Konrad , Schwämmle Veit
Published: February 2024

Mass spectrometry (MS)-based proteomics allows identifying and quantifying thousands of proteins but suffers from challenges when measuring human antibodies due to their vast variety. The mainly used bottom-up proteomics approaches rely on database searches that compare experimental values of peptides and their fragments to theoretical values derived from protein sequences in a database. While the human body can produce millions of distinct antibodies, the current databases for human antibodies such as UniProtKB/Swiss-Prot are limited to only 1095 sequences (as of 2024 Jan). This limitation may hinder the identification of new antibodies using mass spectrometry. Therefore, extending the database for mass spectrometry is an important task for discovering new antibodies. Recent genomic studies have compiled millions of human antibody sequences publicly accessible through the Observed Antibody Space (OAS) database. However, this data has yet to be exploited to confirm the presence of these antibodies. In this study, we adopted this extensive collection of antibody sequences for conducting efficient database searches in publicly available proteomics data with a focus on the SARS-CoV-2 disease. Thirty million heavy antibody sequences from 146 SARS-CoV-2 patients in the OAS database were digestedin silicoto obtain 18 million unique peptides. These peptides were then used to create new databases for bottom-up proteomics. We used those databases for searching new antibody peptides in publicly available SARS-CoV-2 human plasma samples in the Proteomics Identification Database (PRIDE). This approach avoids false positives in antibody peptide identification as confirmed by searching against negative controls (brain samples) and employing different database sizes. We show that the found sequences provide valuable information to distinguish diseased from healthy and expect that the newly discovered antibody peptides can be further employed to develop therapeutic antibodies. The method will be broadly applicable to find characteristic antibodies for other diseases.
Characterization of a new lacrimal gland cell line in 2D and 3D cell culture models
Authors: Gleixner Sophie , Zahn Ingrid , Dietrich Jana , Singh Swati , Drobny Alice , Schneider Yanni , Schwendner Raphael , Socher Eileen , Blavet Nicolas , Bräuer Lars , Gostian Antoniu-Oreste , Balk Matthias , Schulze-Tanzil Gundula , Günther Claudia , Paulsen Friedrich , Arnold Philipp
Published: February 2024

The lacrimal gland produces the tear film’s aqueous component, which moistens and nourishes the ocular surface to maintain eye health. Reduced production of this component leads to dry eye disease, which affects over 250 million people worldwide. Despite the impact on patients, the availability of primary human material to study underlying disease mechanisms is severely limited and there is no cell model available for human lacrimal gland epithelial cells. After insertion of an SV40 antigen into primary human lacrimal gland epithelial cells, we selected, expanded, and characterized three epithelial cell clones from a female lacrimal gland donor. We show their epithelial character at genomic (PCR and RNAseq) and protein (immunofluorescence) levels and grow these cells in a 3D cell spheroid model. Here, we report the development of an immortalized human lacrimal gland epithelial cell line that improves accessibility to study the molecular pathogenesis mechanisms of dry eye disease and link them to causal treatments. We show the expression of typical lacrimal gland epithelial cell marker genes (e.g. PAX6, FOXC1, AQP5, CSTB, and CST6) and describe the feasibility of the cells to form 2D cell sheets and 3D cell spheroids.

We successfully established immortalized human lacrimal gland cells with epithelial character. In the future, the integration of these cells into larger studies holds great potential for advancing our understanding of dry eye disease and its underlying cellular mechanisms.
UBA1-CDK16: A Sex-Specific Chimeric RNA and Its Role in Immune Sexual Dimorphism
Authors: Shi Xinrui , Facemire Loryn , Singh Sandeep , Kumar Shailesh , Cornelison Robert , Liang Chen , Qin Fujun , Liu Aiqun , Lin Shitong , Tang Yue , Elfman Justin , Manley Thomas , Bullock Timothy , Haverstick Doris M. , Wu Peng , Li Hui
Published: February 2024

RNA processing mechanisms, such as alternative splicing and RNA editing, have been recognized as critical means to expand the transcriptome. Chimeric RNAs formed by intergenic splicing provide another potential layer of RNA diversification. By analyzing a large set of RNA-Seq data and validating results in over 1,200 blood samples, we identifiedUBA1-CDK16, a female-specific chimeric transcript. Intriguingly, both parental genes, are expressed in males and females. Mechanistically,UBA1-CDK16is produced by cis-splicing between the two adjacent X-linked genes, originating from the inactive X chromosome. A female-specific chromatin loop, formed between the junction sites, facilitates the alternative splicing of its readthrough precursor. This unique chimeric transcript exhibits evolutionary conservation, evolving to be female-specific from non-human primates to humans. Furthermore, our investigation reveals thatUBA1-CDK16is enriched in the myeloid lineage and plays a regulatory role in myeloid differentiation. Notably, female COVID-19 patients who tested negative for this chimeric transcript displayed higher counts of neutrophils, highlighting its potential role in disease pathogenesis. These findings support the notion that chimeric RNAs represent a new repertoire of transcripts that can be regulated independently from the parental genes, and a new class of RNA variance with potential implications in sexual dimorphism and immune responses.
TheTofumutation restores female fertility toDrosophilawith a nullBEAFmutation
Authors: McKowen J. Keller , Dassanayake Maheshi , Hart Craig M.
Published: February 2024

Compensatory mutations offer clues to deciphering the role of a particular protein in cellular processes. Here we investigate an unknown compensatory mutation, present in theBEAFNP6377fly line, that provides sufficient rescue of the defective ovary phenotype caused by nullBEAFalleles to allow maintenance of fly stocks lacking the chromatin domain insulator proteins Boundary Element-Associated Factors BEAF-32A and BEAF-32B. We call this mutationTofu. We employ both classical genetics and genomic sequencing to attempt to identify the mutation. We find evidence that points to a mutation in a predicted Polycomb response element upstream of theribbongene, which may lead to aberrantribexpression.
Repeated behavioral evolution is associated with targeted convergence of gene expression in cavity-nesting songbirds
Authors: Lipshutz Sara E , Hibbins Mark S , Bentz Alexandra B , Buechlin Aaron M , Empson Tara A , George Elizabeth M , Hauber Mark E , Rusch Douglas B , Schelsky Wendy M , Thomas Quinn K , Torneo Samuel J , Turner Abbigail M , Wolf Sarah E , Woodruff Mary J , Hahn Matthew W. , Rosvall Kimberly A
Published: February 2024

Uncovering the genomic bases of phenotypic adaptation is a major goal in biology, but this has been hard to achieve for complex behavioral traits. Here, we leverage the repeated, independent evolution of obligate cavity-nesting in birds to test the hypothesis that pressure to compete for a limited breeding resource has facilitated convergent evolution in behavior, hormones, and gene expression. We used an integrative approach, combining aggression assays in the field, testosterone measures, and transcriptome-wide analyses of the brain in wild-captured females and males. Our experimental design compared species pairs across five avian families, each including one obligate cavity-nesting species and a related species with a more flexible nest strategy. We find behavioral convergence, with higher levels of territorial aggression in obligate cavity-nesters, particularly among females. Across species, levels of testosterone in circulation were not associated with nest strategy, nor aggression. Phylogenetic analyses of individual genes and co-regulated gene networks revealed more shared patterns of brain gene expression than expected by drift, but the scope of convergent gene expression evolution was limited to a small percent of the genome. When comparing our results to other studies that did not use phylogenetic methods, we suggest that accounting for shared evolutionary history may reduce the number of genes inferred as convergently evolving. Altogether, we find that behavioral convergence in response to shared ecological pressures is associated with largely independent gene expression evolution across different avian families, punctuated by a narrow set of convergently evolving genes.