N Biotechnol. 2023 Nov 29:S1871-6784(23)00066-3. doi: 10.1016/j.nbt.2023.11.003. Online ahead of print.

ABSTRACT

Cells, both of prokaryotic and eukaryotic origin, have developed dedicated molecular mechanisms to tightly control expression levels of their genes where the specific transcriptomic signature across all genes eventually determines the cell phenotype. Modulating cellular phenotypes is of major interest, either to study their role in disease or to reprogram cells for the manufacture of recombinant products, such as biopharmaceuticals. For the latter, cells of mammalian origin, such as Chinese hamster ovary (CHO) and Human embryonic kidney 293 (HEK293) cells, are most commonly employed to produce therapeutic proteins. Altering their phenotype is often achieved randomly by subcloning and selection of appropriate behavior or by genetic engineering. In both cases, the objective is to obtain expression systems that generate the desired product with the highest possible quality and quantity. Early genetic engineering approaches have often been attempted by "uncontrolled" overexpression or knock-down/-out of specific genetic factors. Many studies in the past years, however, have highlighted that a controlled manipulation of transgene expression, by rationally regulating and fine-tuning the strength of overexpression or knock-down to an optimum level, can adjust phenotypic traits with much greater precision than such "uncontrolled" approaches. To control and (fine-)tune the expression level of one or multiple transgenes or endogenous genes, synthetic biology tools inspired by naturally occurring gene regulation mechanisms have been generated to develop novel, molecular toolboxes that enable (fine-)tunable and/or inducible control of gene expression. In this review, we discuss various molecular tools that have been established in mammalian cell lines and group them by their mode of action: transcriptional, post-transcriptional, translational and post-translational regulation. Major emphasis is placed on studies in which such tools were employed to engineer recombinant protein production in CHO or other mammalian cell factories. We discuss the advantages and disadvantages of using these tools for each cell regulatory layer and with respect to cell line engineering approaches. This review highlights the existence of a plethora of synthetic toolboxes that could be employed, alone or in combination, to optimize cellular systems and eventually gain enhanced control over the cellular phenotype to equip mammalian cell factories with the tools required for efficient production of emerging, more difficult-to-express biologics formats.

PMID:38040288 | DOI:10.1016/j.nbt.2023.11.003

Int J Biol Macromol. 2023 Nov 29:128503. doi: 10.1016/j.ijbiomac.2023.128503. Online ahead of print.

ABSTRACT

The process of wound healing involves complex interplay of systems biology, dependent on coordination of various cell types, both intra and extracellular mechanisms, proteins, and signaling pathways. To enhance these interactions, drugs must be administered precisely and continuously, effectively regulating the intricate mechanisms involved in the body's response to injury. Controlled drug delivery systems (DDS) play a pivotal role in achieving this objective. A proficient DDS shields the wound from mechanical, oxidative, and enzymatic stress, against bacterial contamination ensuring an adequate oxygen supply while optimizing the localized and sustained delivery of drugs to target tissue. A pH-sensitive SPH was designed by blending two natural polysaccharides, Opuntia mucilage and carrageenan, using microwave irradiation and optimized according to swelling index at pH 1.2, 7.0, and 8.0 and % porosity. Optimized grade was analyzed for surface hydrophilicity-hydrophobicity using OCA. Analytical characterizations were performed using FTIR, TGA, XRD, DSC, reflecting semicrystalline behavior. Mechanical property confirmed adequate strength. In vitro drug release study with ciprofloxacin-HCL as model drug showed 97.8 % release within 10 h, fitting to the Korsmeyer-Peppas model following diffusion and erosion mechanism. In vitro antimicrobial, anti-inflammatory assays, zebrafish toxicity, and animal studies in mice with SPH concluded it as a novel biomaterial.

PMID:38040152 | DOI:10.1016/j.ijbiomac.2023.128503

Autoimmun Rev. 2023 Nov 29:103486. doi: 10.1016/j.autrev.2023.103486. Online ahead of print.

ABSTRACT

Anti-Saccharomyces cerevisiae antibodies (ASCA) are human antibodies that can be detected using an enzyme-linked immunosorbent assay involving a mannose polymer (mannan) extracted from the cell wall of the yeast S. cerevisiae. The ASCA test was developed in 1993 with the aim of differentiating the serological response in two forms of inflammatory bowel disease (IBD), Crohn's disease and ulcerative colitis. The test, which is based on the detection of anti-oligomannosidic antibodies, has been extensively performed worldwide and there have been hundreds of publications on ASCA. The earlier studies concerned the initial diagnostic indications of ASCA and investigations then extended to many human diseases, generally in association with studies on intestinal microorganisms and the interaction of the micro-mycobiome with the immune system. The more information accumulates, the more the mystery of the meaning of ASCA deepens. Many fundamental questions remain unanswered. These questions concern the heterogeneity of ASCA, the mechanisms of their generation and persistence, the existence of self-antigens, and the relationship between ASCA and inflammation and autoimmunity. This review aims to discuss the gray areas concerning the origin of ASCA from an analysis of the literature. Structured around glycobiology and the mannosylated antigens of S. cerevisiae and Candida albicans, this review will address these questions and will try to clarify some lines of thought. The importance of the questions relating to the pathophysiological significance of ASCA goes far beyond IBD, even though these diseases remain the preferred models for their understanding.

PMID:38040100 | DOI:10.1016/j.autrev.2023.103486

Immunity. 2023 Nov 29:S1074-7613(23)00484-3. doi: 10.1016/j.immuni.2023.11.003. Online ahead of print.

ABSTRACT

Commensal microbes induce cytokine-producing effector tissue-resident CD4+ T cells, but the function of these T cells in mucosal homeostasis is not well understood. Here, we report that commensal-specific intestinal Th17 cells possess an anti-inflammatory phenotype marked by expression of interleukin (IL)-10 and co-inhibitory receptors. The anti-inflammatory phenotype of gut-resident commensal-specific Th17 cells was driven by the transcription factor c-MAF. IL-10-producing commensal-specific Th17 cells were heterogeneous and derived from a TCF1+ gut-resident progenitor Th17 cell population. Th17 cells acquired IL-10 expression and anti-inflammatory phenotype in the small-intestinal lamina propria. IL-10 production by CD4+ T cells and IL-10 signaling in intestinal macrophages drove IL-10 expression by commensal-specific Th17 cells. Intestinal commensal-specific Th17 cells possessed immunoregulatory functions and curbed effector T cell activity in vitro and in vivo in an IL-10-dependent and c-MAF-dependent manner. Our results suggest that tissue-resident commensal-specific Th17 cells perform regulatory functions in mucosal homeostasis.

PMID:38039966 | DOI:10.1016/j.immuni.2023.11.003

Exp Mol Med. 2023 Dec 1. doi: 10.1038/s12276-023-01133-7. Online ahead of print.

ABSTRACT

Cells at the site of an infection experience numerous biochemical signals that vary in amplitude, space, and time. Despite the diversity of dynamic signals produced by pathogens and sentinel cells, information-processing pathways converge on a limited number of central signaling nodes to ultimately control cellular responses. In particular, the NF-κB pathway responds to dozens of signals from pathogens and self, and plays a vital role in processing proinflammatory inputs. Studies addressing the influence of stimulus dynamics on NF-κB signaling are rare due to technical limitations with live-cell measurements. However, recent advances in microfluidics, automation, and image analysis have enabled investigations that yield high temporal resolution at the single-cell level. Here, we summarize the recent research which measures and models the NF-κB response to pulsatile and fluctuating stimulus concentrations, as well as different combinations and sequences of signaling molecules. Collectively, these studies show that the NF-κB network integrates external inflammatory signals and translates these into downstream transcriptional responses.

PMID:38040923 | DOI:10.1038/s12276-023-01133-7

Sci Data. 2023 Dec 1;10(1):849. doi: 10.1038/s41597-023-02598-x.

ABSTRACT

Understanding the molecular mechanisms underlying frontotemporal dementia (FTD) is essential for the development of successful therapies. Systematic studies on human post-mortem brain tissue of patients with genetic subtypes of FTD are currently lacking. The Risk and Modyfing Factors of Frontotemporal Dementia (RiMod-FTD) consortium therefore has generated a multi-omics dataset for genetic subtypes of FTD to identify common and distinct molecular mechanisms disturbed in disease. Here, we present multi-omics datasets generated from the frontal lobe of post-mortem human brain tissue from patients with mutations in MAPT, GRN and C9orf72 and healthy controls. This data resource consists of four datasets generated with different technologies to capture the transcriptome by RNA-seq, small RNA-seq, CAGE-seq, and methylation profiling. We show concrete examples on how to use the resulting data and confirm current knowledge about FTD and identify new processes for further investigation. This extensive multi-omics dataset holds great value to reveal new research avenues for this devastating disease.

PMID:38040703 | DOI:10.1038/s41597-023-02598-x

Brief Bioinform. 2023 Nov 22;25(1):bbad421. doi: 10.1093/bib/bbad421.

ABSTRACT

RNA biology has risen to prominence after a remarkable discovery of diverse functions of noncoding RNA (ncRNA). Most untranslated transcripts often exert their regulatory functions into RNA-RNA complexes via base pairing with complementary sequences in other RNAs. An interplay between RNAs is essential, as it possesses various functional roles in human cells, including genetic translation, RNA splicing, editing, ribosomal RNA maturation, RNA degradation and the regulation of metabolic pathways/riboswitches. Moreover, the pervasive transcription of the human genome allows for the discovery of novel genomic functions via RNA interactome investigation. The advancement of experimental procedures has resulted in an explosion of documented data, necessitating the development of efficient and precise computational tools and algorithms. This review provides an extensive update on RNA-RNA interaction (RRI) analysis via thermodynamic- and comparative-based RNA secondary structure prediction (RSP) and RNA-RNA interaction prediction (RIP) tools and their general functions. We also highlighted the current knowledge of RRIs and the limitations of RNA interactome mapping via experimental data. Then, the gap between RSP and RIP, the importance of RNA homologues, the relationship between pseudoknots, and RNA folding thermodynamics are discussed. It is hoped that these emerging prediction tools will deepen the understanding of RNA-associated interactions in human diseases and hasten treatment processes.

PMID:38040490 | DOI:10.1093/bib/bbad421

Bull Math Biol. 2023 Dec 1;86(1):5. doi: 10.1007/s11538-023-01232-6.

ABSTRACT

Systems biology utilizes computational approaches to examine an array of biological processes, such as cell signaling, metabolomics and pharmacology. This includes mathematical modeling of CAR T cells, a modality of cancer therapy by which genetically engineered immune cells recognize and combat a cancerous target. While successful against hematologic malignancies, CAR T cells have shown limited success against other cancer types. Thus, more research is needed to understand their mechanisms of action and leverage their full potential. In our work, we set out to apply information theory on a mathematical model of NFκB signaling initiated by the CAR following antigen encounter. First, we estimated channel capacity for CAR-4-1BB-mediated NFκB signal transduction. Next, we evaluated the pathway's ability to distinguish contrasting "low" and "high" antigen concentration levels, depending on the amount of variability in protein concentrations. Finally, we assessed the fidelity by which NFκB activation reflects the encountered antigen concentration, depending on the prevalence of antigen-positive targets in tumor population. We found that in most scenarios, fold change in the nuclear concentration of NFκB carries a higher channel capacity for the pathway than NFκB's absolute response. Additionally, we found that most errors in transducing the antigen signal through the pathway skew towards underestimating the concentration of encountered antigen. Finally, we found that disabling IKKβ deactivation could increase signaling fidelity against targets with antigen-negative cells. Our information-theoretic analysis of signal transduction can provide novel perspectives on biological signaling, as well as enable a more informed path to cell engineering.Kindly check and confirm whether the corresponding affiliation is correctly identified.this is correct.

PMID:38038772 | DOI:10.1007/s11538-023-01232-6

Plant Reprod. 2023 Dec 1. doi: 10.1007/s00497-023-00488-1. Online ahead of print.

ABSTRACT

The VAMP721, VAMP722, SYP121, SYP122 and SNAP33 SNAREs are required in the Arabidopsis stigma for pollen hydration, further supporting a role for vesicle trafficking in the stigma's pollen responses. In the Brassicaceae, the process of accepting compatible pollen is a key step in successful reproduction and highly regulated following interactions between the pollen and the stigma. Central to this is the initiation of secretion in the stigma, which is proposed to provide resources to the pollen for hydration and germination and pollen tube growth. Previously, the eight exocyst subunit genes were shown to be required in the Arabidopsis stigma to support these pollen responses. One of the roles of the exocyst is to tether secretory vesicles at the plasma membrane for membrane fusion by the SNARE complex to enable vesicle cargo release. Here, we investigate the role of Arabidopsis SNARE genes in the stigma for pollen responses. Using a combination of different knockout and knockdown SNARE mutant lines, we show that VAMP721, VAMP722, SYP121, SYP122 and SNAP33 are involved in this process. Significant disruptions in pollen hydration were observed following pollination of wildtype pollen on the mutant SNARE stigmas. Overall, these results place the Arabidopsis SNARE complex as a contributor in the stigma for pollen responses and reaffirm the significance of secretion in the stigma to support the pollen-stigma interactions.

PMID:38038738 | DOI:10.1007/s00497-023-00488-1

Am J Physiol Heart Circ Physiol. 2023 Dec 1. doi: 10.1152/ajpheart.00553.2023. Online ahead of print.

ABSTRACT

Cardiac ion currents may compensate for each other when one is compromised by a congenital or drug-induced defect. Such redundancy contributes to a robust repolarization reserve that can prevent the development of lethal arrhythmias. Most efforts made to describe this phenomenon have quantified contributions by individual ion currents. However, it is important to understand the interplay between all major ion channel conductances, as repolarization reserve is dependent on the balance between all ion currents in a cardiomyocyte. Here, a genetic algorithm was designed to derive profiles of nine ion-channel conductances that optimize repolarization reserve in a mathematical cardiomyocyte model. Repolarization reserve was quantified using a previously defined metric, repolarization reserve current, i.e., the minimum constant current to prevent normal action potential repolarization in a cell. The optimization improved repolarization reserve current up to 84 \% compared to baseline in a human adult ventricular myocyte model and increased resistance to arrhythmogenic insult.The optimized conductance profiles were characterized by increased repolarizing current conductances, but also uncovered a previously unreported behavior by the late sodium current. Simulations demonstrated that upregulated late sodium increased action potential duration, without compromising repolarization reserve current. The finding was generalized to multiple models. Ultimately, this computational approach in which multiple currents were studied simultaneously illuminated mechanistic insights into how the metric's magnitude could be increased, and allowed for the unexpected role of late sodium to be elucidated.

PMID:38038718 | DOI:10.1152/ajpheart.00553.2023

Nano Lett. 2023 Dec 1. doi: 10.1021/acs.nanolett.3c03484. Online ahead of print.

ABSTRACT

Phase contrast imaging techniques enable the visualization of disparities in the refractive index among various materials. However, these techniques usually come with a cost: the need for bulky, inflexible, and complicated configurations. Here, we propose and experimentally demonstrate an ultracompact meta-microscope, a novel imaging platform designed to accomplish both optical and digital phase contrast imaging. The optical phase contrast imaging system is composed of a pair of metalenses and an intermediate spiral phase metasurface located at the Fourier plane. The performance of the system in generating edge-enhanced images is validated by imaging a variety of human cells, including lung cell lines BEAS-2B, CLY1, and H1299 and other types. Additionally, we integrate the ResNet deep learning model into the meta-microscope to transform bright-field images into edge-enhanced images with high contrast accuracy. This technology promises to aid in the development of innovative miniature optical systems for biomedical and clinical applications.

PMID:38038680 | DOI:10.1021/acs.nanolett.3c03484

J Immunol. 2023 Dec 1:ji2200835. doi: 10.4049/jimmunol.2200835. Online ahead of print.

ABSTRACT

The 2'3'-cyclic GMP-AMP (cGAMP) synthase (cGAS)-stimulator of IFN genes (STING) pathway can sense infection and cellular stress by detecting cytosolic DNA. Upon ligand binding, cGAS produces the cyclic dinucleotide messenger cGAMP, which triggers its receptor STING. Active STING initiates gene transcription through the transcription factors IFN regulatory factor 3 (IRF3) and NF-κB and induces autophagy, but whether STING can cause changes in the metabolism of macrophages is unknown. In this study, we report that STING signaling activates ATP-citrate lyase (ACLY) by phosphorylation in human macrophages. Using genetic and pharmacologic perturbation, we show that STING targets ACLY via its prime downstream signaling effector TANK (TRAF family member-associated NF-κB activator)-binding kinase 1 (TBK1). We further identify that TBK1 alters cellular metabolism upon cGAMP treatment. Our results suggest that STING-mediated metabolic reprogramming adjusts the cellular response to DNA sensing in addition to transcription factor activation and autophagy induction.

PMID:38038390 | DOI:10.4049/jimmunol.2200835

Small. 2023 Dec 1:e2308390. doi: 10.1002/smll.202308390. Online ahead of print.

ABSTRACT

Compartments are a fundamental feature of life, based variously on lipid membranes, protein shells, or biopolymer phase separation. Here, this combines self-assembling bacterial microcompartment (BMC) shell proteins and liquid-liquid phase separation (LLPS) to develop new forms of compartmentalization. It is found that BMC shell proteins assemble at the liquid-liquid interfaces between either 1) the dextran-rich droplets and PEG-rich continuous phase of a poly(ethyleneglycol)(PEG)/dextran aqueous two-phase system, or 2) the polypeptide-rich coacervate droplets and continuous dilute phase of a polylysine/polyaspartate complex coacervate system. Interfacial protein assemblies in the coacervate system are sensitive to the ratio of cationic to anionic polypeptides, consistent with electrostatically-driven assembly. In both systems, interfacial protein assembly competes with aggregation, with protein concentration and polycation availability impacting coating. These two LLPS systems are then combined to form a three-phase system wherein coacervate droplets are contained within dextran-rich phase droplets. Interfacial localization of BMC hexameric shell proteins is tunable in a three-phase system by changing the polyelectrolyte charge ratio. The tens-of-micron scale BMC shell protein-coated droplets introduced here can accommodate bioactive cargo such as enzymes or RNA and represent a new synthetic cell strategy for organizing biomimetic functionality.

PMID:38037673 | DOI:10.1002/smll.202308390

ACS Appl Nano Mater. 2023 Nov 6;6(22):21245-21257. doi: 10.1021/acsanm.3c04357. eCollection 2023 Nov 24.

ABSTRACT

Theranostic materials research is experiencing rapid growth driven by the interest in integrating both therapeutic and diagnostic modalities. These materials offer the unique capability to not only provide treatment but also track the progression of a disease. However, to create an ideal theranostic biomaterial without compromising drug encapsulation, diagnostic imaging must be optimized for improved sensitivity and spatial localization. Herein, we create a protein-engineered fluorinated coiled-coil fiber, Q2TFL, capable of improved sensitivity to 19F magnetic resonance spectroscopy (MRS) detection. Leveraging residue-specific noncanonical amino acid incorporation of trifluoroleucine (TFL) into the coiled-coil, Q2, which self-assembles into nanofibers, we generate Q2TFL. We demonstrate that fluorination results in a greater increase in thermostability and 19F magnetic resonance detection compared to the nonfluorinated parent, Q2. Q2TFL also exhibits linear ratiometric 19F MRS thermoresponsiveness, allowing it to act as a temperature probe. Furthermore, we explore the ability of Q2TFL to encapsulate the anti-inflammatory small molecule, curcumin (CCM), and its impact on the coiled-coil structure. Q2TFL also provides hyposignal contrast in 1H MRI, echogenic signal with high-frequency ultrasound and sensitive detection by 19F MRS in vivo illustrating fluorination of coiled-coils for supramolecular assembly and their use with 1H MRI, 19F MRS and high frequency ultrasound as multimodal theranostic agents.

PMID:38037605 | PMC:PMC10682962 | DOI:10.1021/acsanm.3c04357

Nephrol Dial Transplant. 2023 Nov 30:gfad254. doi: 10.1093/ndt/gfad254. Online ahead of print.

ABSTRACT

BACKGROUND AND HYPOTHESIS: Glucocorticoids are the treatment of choice for proteinuric patients with minimal-change disease (MCD) and primary focal and segmental glomerulosclerosis (FSGS). Immunosuppressive as well as direct effects on podocytes are believed to mediate their actions. In this study, we analyzed the anti-proteinuric effects of inhibition of the glucocorticoid receptor (GR) in glomerular epithelial cells, including podocytes.

METHODS: We employed genetic and pharmacological approaches to inhibit the GR. Genetically, we used Pax8-Cre/GRfl/fl mice to specifically inactivate the GR in kidney epithelial cells. Pharmacologically, we utilized a glucocorticoid antagonist called mifepristone.

RESULTS: Genetic inactivation of GR, specifically in kidney epithelial cells, using Pax8-Cre/GRfl/fl mice, ameliorated proteinuria following protein overload. We further tested the effects of pharmacological GR inhibition in three models and species: the puromycin-aminonucleoside-induced nephrosis model in rats, the protein overload model in mice and the inducible transgenic NTR/MTZ zebrafish larvae with specific and reversible podocyte injury. In all three models, both pharmacological GR activation and inhibition consistently and significantly ameliorated proteinuria. Additionally, we translated our findings to humans, where three nephrotic adult patients with MCD or primary FSGS with contraindications or insufficient responses to corticosteroids, were treated with mifepristone. This treatment resulted in a clinically relevant reduction of proteinuria.

CONCLUSIONS: Thus, across multiple species and proteinuria models, both genetic and pharmacological GR inhibition was at least as effective as pronounced GR activation. While, the mechanism remains perplexing, GR inhibition may be a novel and targeted therapeutic approach to treat glomerular proteinuria potentially bypassing adverse actions of steroids.

PMID:38037533 | DOI:10.1093/ndt/gfad254

J Mol Cell Biol. 2023 Nov 30:mjad069. doi: 10.1093/jmcb/mjad069. Online ahead of print.

ABSTRACT

Obesity is closely related to non-alcoholic fatty liver disease (NAFLD). Although sex differences in body fat distribution have been well demonstrated, little is known about the sex-specific associations between adipose tissue and the development of NAFLD. Using community-based cohort data, we evaluated the associations between magnetic resonance imaging-quantified areas of abdominal adipose tissue, including visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT), and incident NAFLD in 2830 participants (1205 males and 1625 females) aged 55-70 years. During a 4.6-year median follow-up, the cumulative incidence rates of NAFLD increased with areas of VAT and SAT both in males and females. Further analyses showed that the abovementioned positive associations were stronger in males than in females, especially in participants under 60 years old. In contrast, these sex differences disappeared in those over 60 years old. Furthermore, the risk of developing NAFLD increased nonlinearly with increasing fat area in a sex-specific pattern. Additionally, sex-specific potential mediators, such as insulin resistance, lipid metabolism, inflammation, and adipokines, may exist in the associations between adipose tissue and NAFLD. This study showed that the associations between abdominal fat and the risk of NAFLD were stratified by sex and age, highlighting the potential need for sex- and age-specific management of NAFLD.

PMID:38037475 | DOI:10.1093/jmcb/mjad069

Biotechnol Appl Biochem. 2023 Nov 30. doi: 10.1002/bab.2542. Online ahead of print.

ABSTRACT

Ongoing mutations of SARS-CoV-2 present challenges for vaccine development, promising renewed global efforts to create more effective vaccines against coronavirus disease (COVID-19). One approach is to target highly immunogenic viral proteins, such as the spike receptor binding domain (RBD), which can stimulate the production of potent neutralizing antibodies. This study aimed to design and test a subunit vaccine candidate based on the RBD. Bioinformatics analysis identified antigenic regions of the RBD for recombinant protein design. In silico analysis identified the RBD region as a feasible target for designing a recombinant vaccine. Bioinformatics tools predicted the stability and antigenicity of epitopes, and a 3D model of the RBD-angiotensin-converting enzyme 2 complex was constructed using molecular docking and codon optimization. The resulting construct was cloned into the pET-28a (+) vector and successfully expressed in Escherichia coli BL21DE3. As evidenced by sodium dodecyl-polyacrylamide gel electrophoresis and Western blotting analyses, the affinity purification of RBD antigens produced high-quality products. Mice were immunized with the RBD antigen alone or combined with aluminum hydroxide (AlOH), calcium phosphate (CaP), or zinc oxide (ZnO) nanoparticles (NPs) as adjuvants. Enzyme-linked immunosorbent assay assays were used to evaluate immune responses in mice. In-silico analysis confirmed the stability and antigenicity of the designed protein structure. RBD with CaP NPs generated the highest immunoglobulin G titer compared to AlOH and ZnO after three doses, indicating its effectiveness as a vaccine platform. In conclusion, the recombinant RBD antigen administered with CaP adjuvant NPs induces potent humoral immunity in mice, supporting further vaccine development. These results contribute to ongoing efforts to develop more effective COVID-19 vaccines.

PMID:38037222 | DOI:10.1002/bab.2542

Front Zool. 2023 Dec 1;20(1):37. doi: 10.1186/s12983-023-00516-w.

ABSTRACT

Suckermouth armoured catfish (Loricariidae) are a highly speciose and diverse freshwater fish family, which bear upper and lower lips forming an oral disc. Its hierarchical organisation allows the attachment to various natural surfaces. The discs can possess papillae of different shapes, which are supplemented, in many taxa, by small horny projections, i.e. unculi. Although these attachment structures and their working mechanisms, which include adhesion and interlocking, are rather well investigated in some selected species, the loricariid oral disc is unfortunately understudied in the majority of species, especially with regard to comparative aspects of the diverse oral structures and their relationship to the ecology of different species. In the present paper, we investigated the papilla and unculi morphologies in 67 loricariid species, which inhabit different currents and substrates. We determined four papilla types and eight unculi types differing by forms and sizes. Ancestral state reconstructions strongly suggest convergent evolution of traits. There is no obvious correlation between habitat shifts and the evolution of specific character states. From handling the structures and from drying artefacts we could infer some information about their material properties. This, together with their shape, enabled us to carefully propose hypotheses about mechanisms of interactions of oral disc structures with natural substrates typical for respective fish species.

PMID:38037029 | DOI:10.1186/s12983-023-00516-w

Nat Genet. 2023 Nov 30. doi: 10.1038/s41588-023-01586-6. Online ahead of print.

ABSTRACT

The human leukocyte antigen (HLA) locus plays a critical role in complex traits spanning autoimmune and infectious diseases, transplantation and cancer. While coding variation in HLA genes has been extensively documented, regulatory genetic variation modulating HLA expression levels has not been comprehensively investigated. Here we mapped expression quantitative trait loci (eQTLs) for classical HLA genes across 1,073 individuals and 1,131,414 single cells from three tissues. To mitigate technical confounding, we developed scHLApers, a pipeline to accurately quantify single-cell HLA expression using personalized reference genomes. We identified cell-type-specific cis-eQTLs for every classical HLA gene. Modeling eQTLs at single-cell resolution revealed that many eQTL effects are dynamic across cell states even within a cell type. HLA-DQ genes exhibit particularly cell-state-dependent effects within myeloid, B and T cells. For example, a T cell HLA-DQA1 eQTL ( rs3104371 ) is strongest in cytotoxic cells. Dynamic HLA regulation may underlie important interindividual variability in immune responses.

PMID:38036787 | DOI:10.1038/s41588-023-01586-6

Nat Genet. 2023 Nov 30. doi: 10.1038/s41588-023-01524-6. Online ahead of print.

ABSTRACT

Deep learning methods have recently become the state of the art in a variety of regulatory genomic tasks1-6, including the prediction of gene expression from genomic DNA. As such, these methods promise to serve as important tools in interpreting the full spectrum of genetic variation observed in personal genomes. Previous evaluation strategies have assessed their predictions of gene expression across genomic regions; however, systematic benchmarking is lacking to assess their predictions across individuals, which would directly evaluate their utility as personal DNA interpreters. We used paired whole genome sequencing and gene expression from 839 individuals in the ROSMAP study7 to evaluate the ability of current methods to predict gene expression variation across individuals at varied loci. Our approach identifies a limitation of current methods to correctly predict the direction of variant effects. We show that this limitation stems from insufficiently learned sequence motif grammar and suggest new model training strategies to improve performance.

PMID:38036778 | DOI:10.1038/s41588-023-01524-6