bluuebunny/crossref_metadata_2025 huggingface dataset:
Chemical screen of Arabidopsis zygote and proteomics in tobacco BY-2 cells identify general plant cell division inhibitors
Authors: Kimata Yusuke , Yamada Moé , Murata Takashi , Kuwata Keiko , Sato Ayato , Suzuki Takamasa , Kurihara Daisuke , Hasebe Mitsuyasu , Higashiyama Tetsuya , Ueda Minako
Published: May 2022

Cell division is essential for growth and development and involves events such as spindle assembly, chromosome separation, and cell plate formation. In plants, the tools used to control these events at the desired time are still poor because the genetic approach is ineffective owing to a high redundancy and lethality, as well as harmful side effects. Accordingly, we screened cell division-affecting compounds, with a focus on Arabidopsis thaliana zygotes, which individually develop in maternal ovules; the cell division was reliably traceable without time-lapse observations. We then identified the target events of the identified compounds using tobacco BY-2 cells for live-cell imaging and proteomics. As a result, we isolated two compounds, PD-180970 and PP2. PD-180970 disrupts microtubule (MT) organization and, thus, nuclear separation, presumably by inhibiting MT-associated proteins (MAP70). PP2 affected class II Kinesin-12 localization at the phragmoplast emerging site and impaired cytokinesis. Moreover, neither chemical caused irreversible damage to viability but they were effective in multiple plant species such as cucumber (Cucumis sativus) and moss (Physcomitrium patens). We propose that the combination of chemical screening based on Arabidopsis zygotes and target event specification focusing on tobacco BY-2 cells can be used to effectively identify novel tools and transiently control specific cell division events that are conserved in diverse plant species.
Benchmark of tools for in silico prediction of MHC class I and class II genotypes from NGS data
Authors: Claeys Arne , Staut Jasper , Merseburger Peter , Marchal Kathleen , Van den Eynden Jimmy
Published: May 2022

The Human Leukocyte Antigen (HLA) genes are a group of highly polymorphic genes that are located in the Major Histocompatibility Complex (MHC) region on chromosome 6. The HLA genotype affects the presentability of tumour antigens to the immune system. While knowledge of these genotypes is of utmost importance to study differences in immune responses between cancer patients, gold standard, PCR-derived genotypes are rarely available in large Next Generation Sequencing (NGS) datasets. Therefore, a variety of methods for in silico NGS-based HLA genotyping have been developed, bypassing the need to determine these genotypes with separate experiments. However, there is currently no consensus on the best performing tool. Here, we compiled a list of 13 HLA callers and evaluated their accuracy on three different datasets. Based on these results, best-practice guidelines were constructed, and consensus HLA allele predictions were made for DNA and RNA samples from The Cancer Genome Atlas (TCGA).
The Repeating, Modular Architecture of the HtrA Proteases
Authors: Merski Matthew , Macedo-Ribeiro Sandra , Wieczorek Rafal M. , Górna Maria W.
Published: May 2022

A conserved, 26 residue sequence [AA(X2)[A/G][G/L](X2)GDV[I/L](X2)[V/L]NGE(X1)V(X6)] and corresponding structure repeating module was identified within the HtrA protease family using a non-redundant set (N=20) of publically available structures. While the repeats themselves were far from sequence perfect they had notable conservation to a statistically significant level with three or more repetitions identified within one protein at a level that would be expected to randomly occur only once per 1031 residues. This sequence repeat was associated with a six stranded antiparallel β-barrel module, two of which are present in the core of the structures of the PA clan of serine proteases, while a modified version of this module could be identified in the PDZ-like domains. Automated structural alignment methods had difficulties in superimposing these β-barrels but use of a target human HtrA2 structure showed that these modules had an average RMSD across the set of structures of less than 2 Å (mean and median). Our findings support Dayhoff’s hypothesis that complex proteins arose through duplication of simpler peptide motifs and domains.
Systematic analysis of alternative splicing in time course data using Spycone
Authors: Lio Chit Tong , Louadi Zakaria , Fenn Amit , Baumbach Jan , Kacprowski Tim , List Markus , Tsoy Olga
Published: May 2022

During disease progression or organism development, alternative splicing (AS) may lead to isoform switches (IS) that demonstrate similar temporal patterns and reflect the AS co-regulation of such genes. Tools for dynamic process analysis usually neglect AS. Here we propose Spycone (https://github.com/yollct/spycone), a splicing-aware framework for time course data analysis. Spycone exploits a novel IS detection algorithm and offers downstream analysis such as network and gene set enrichment. We demonstrate the performance of Spycone using simulated and real-world data of SARS-CoV-2 infection.
Pre-T cell receptor Self-MHC Sampling Restricts Thymocyte Dedifferentiation
Authors: Duke-Cohan Jonathan S. , Akitsu Aoi , Mallis Robert J. , Messier Cameron M. , Lizotte Patrick H. , Hwang Wonmuk , Lang Matthew J. , Reinherz Ellis L.
Published: May 2022

Summary paragraph

Programming T lymphocytes to distinguish self from non-self is a vital, multi-step process arising in the thymus1–4. Signalling through the pre-T cell receptor (preTCR), a CD3-associated heterodimer comprising an invariant pTα chain and a clone-specific β chain, constitutes a critical early checkpoint in thymocyte development within the αβ T-cell lineage5, 6. Recent work demonstrates that preTCRs arrayed on double negative (DN) thymocytes, like αβ TCRs appearing on double positive (DP) thymocytes, ligate peptides bound to MHC molecules (pMHC) on thymic stroma but via a different molecular docking strategy7–10. Here we show the consequences of those distinctive interactions for thymocyte progression, using synchronized fetal thymic progenitor cultures differing in the presence or absence of pMHC on support stroma, determining single cell transcriptomes at key thymocyte developmental transitions. Although MHC negative stroma fosters αβ T lymphocyte differentiation, the absence of pMHC-preTCR interplay leads to deviant thymocyte transcriptional programming associated with de-differentiation. Highly proliferative DN and DP subsets with antecedent characteristics of T cell lymphoblastic and myeloid malignancies emerge. Thus, at least in vitro, beyond fostering β chain repertoire broadening for subsequent αβ TCR utilization, preTCR-pMHC interaction limits cellular plasticity to facilitate normal thymocyte differentiation and proliferation that, if absent, introduces significant developmental vulnerabilities.
Complete sequences of six Major Histocompatibility Complex haplotypes, including all the major MHC class II structures
Authors: Houwaart Torsten , Scholz Stephan , Pollock Nicholas R , Palmer William H. , Kichula Katherine M. , Strelow Daniel , Le Duyen B , Belick Dana , Lautwein Tobias , Wachtmeister Thorsten , Henrich Birgit , Köhrer Karl , Parham Peter , Guethlein Lisbeth A , Norman Paul J , Dilthey Alexander T
Published: May 2022

Accurate and comprehensive immunogenetic reference panels are key to the successful implementation of population-scale immunogenomics. The 5Mbp Major Histocompatibility Complex (MHC) is the most polymorphic region of the human genome and associated with multiple immune-mediated diseases, transplant matching and therapy responses. Analysis of MHC genetic variation is severely complicated by complex patterns of sequence variation, linkage disequilibrium and a lack of fully resolved MHC reference haplotypes, increasing the risk of spurious findings on analyzing this medically important region. Integrating Illumina and ultra-long Nanopore sequencing as well as bespoke bioinformatics, we completed five of the alternative MHC reference haplotypes of the current (B38) build of the human reference genome and added one other. The six assembled MHC haplotypes encompass the DR1 and DR4 haplotype structures in addition to the previously completed DR2 and DR3, as well as six distinct classes of the structurally variable C4 region. Analysis of the assembled haplotypes showed that MHC class II sequence structures, including repeat element positions, are generally conserved within the DR haplotype supergroups, and that sequence diversity peaks in three regions around HLA-A, HLA-B+C, and the HLA class II genes. Demonstrating the potential for improved short-read analysis, the number of proper read pairs recruited to the MHC was found to be increased by 0.32% – 0.69% in a 1000 Genomes Project read re-mapping experiment with seven diverse samples. Furthermore, the assembled haplotypes can serve as references for the community and provide the basis of a structurally accurate genotyping graph of the complete MHC region.
Developmental changes of opsin gene expression in ray-finned fishes (Actinopterygii)
Authors: Lupše Nik , Kłodawska Monika , Truhlářová Veronika , Košátko Prokop , Kašpar Vojtěch , Bitja Nyom Arnold Roger , Musilova Zuzana
Published: May 2022

Fish often change their habitat and trophic preferences during development. Dramatic functional differences between embryos, larvae, juveniles and adults also concern sensory systems, including vision. Here we focus on the photoreceptors (rod and cone cells) in the retina and their gene expression profiles during the development. Using comparative transcriptomics on 63 species, belonging to 23 actinopterygian orders, we report general developmental patterns of opsin expression, mostly suggesting an increased importance of the rod opsin (RH1) gene and the long-wavelength sensitive (LWS) cone opsin, and a decreasing importance of the shorter wavelength sensitive cone opsin throughout development. Furthermore, we investigate in detail ontogenetic changes in 14 selected species (from Polypteriformes, Acipenseriformes, Cypriniformes, Aulopiformes and Cichliformes), and we report examples of expanded cone opsin repertoires, cone opsin switches (mostly within RH2) and increasing rod:cone ratio as evidenced by the opsin and phototransduction cascade genes. Our findings provide molecular support for developmental stage-specific visual palettes of ray-finned fishes and shifts between, which most likely arose in response to ecological, behavioural and physiological factors.
A novel computational approach to identify cancer cells in scRNA-seq data
Authors: Gasper William , Rossi Francesca , Ligorio Matteo , Ghersi Dario
Published: May 2022

Single-cell RNA-seq is an invaluable research tool that allows for the investigation of gene expression in heterogeneous cancer cell populations in ways that bulk RNA-seq cannot. However, normal (i.e., non tumor) cells in cancer samples have the potential to confound the downstream analysis of single-cell RNA-seq data. Several existing methods for identifying tumor cells use copy number variation inference. This work aims to extend existing approaches for identifying cancer cells in single-cell RNA-seq samples by incorporating putative driver alterations. We found that putative driver alterations can be detected in single-cell RNA-seq data and that a subset of cells in tumor samples are enriched in putative driver alterations as compared to normal cells. Furthermore, we show that the number of putative driver alterations and inferred copy number variation are not correlated in all samples. Taken together, our findings suggest that combining copy number variation inference with putative driver mutation load can augment the number of tumor cells that can be confidently included in downstream analyses of single-cell RNA-seq datasets.
Sex-Specific Effects of Psychedelic Drug Exposure on Central Amygdala Reactivity and Behavioral Responding
Authors: Effinger DP , Quadir SG , Ramage MC , Cone MG , Herman MA
Published: May 2022

Psilocybin, and its active metabolite psilocin, have been shown to elicit rapid and long-lasting symptom improvements in a variety of affective psychiatric illnesses. However, the region-specific alterations underlying these therapeutic effects remain relatively unknown. The central amygdala (CeA) is a primary output region within the extended amygdala that is dysregulated in affective psychiatric disorders. Here, we measured CeA activity using the activity marker c-Fos and CeA reactivity using fiber photometry paired with an aversive air-puff stimulus. We found that psilocin administration acutely increased CeA activity in both males and females and increased stimulus specific CeA reactivity in females, but not males. In contrast, psilocin produced time-dependent decreases in reactivity in males, but not females as early as 2-days and lasting to 28-days post administration. We also measured behavioral responses to the air-puff stimulus and found sex-dependent changes in threat responding but not exploratory behavior or general locomotion. Repeated presentations of the auditory component of the air-puff were also performed and sex-specific effects of psilocin on CeA reactivity to the auditory-alone stimulus were also observed. This study provides new evidence that a single dose of psilocin produces sex-specific, time-dependent, and enduring changes in CeA reactivity and behavioral responding to specific components of an aversive stimulus.
A Unifying Statistical Framework to Discover Disease Genes from GWAS
Authors: McManus Justin N.J. , Lovelett Robert J. , Lowengrub Daniel , Christensen Sarah
Published: May 2022

Genome-wide association studies (GWAS) identify genomic loci associated with complex traits, but it remains an open challenge to identify the genes underlying the association signals. Here, we extend the equations of statistical fine-mapping, to compute the probability that each gene in the human genome is targeted by a causal variant, given a particular trait. Our computations are enabled by several key innovations. First, we partition the genome into optimal linkage disequilibrium blocks, enabling genome-wide detection of trait-associated genes. Second, we unveil a comprehensive mapping that associates genetic variants to the target genes they affect. The combined performance of the map on high-throughput functional genomics and eQTL datasets supersedes the state of the art. Lastly, we describe an algorithm which learns, directly from GWAS data, how to incorporate prior knowledge into the statistical computations, significantly improving their accuracy. We validate each component of the statistical framework individually and in combination. Among methods to identify genes targeted by causal variants, this paradigm rediscovers an unprecedented proportion of known disease genes. Moreover, it establishes human genetics support for many genes previously implicated only by clinical or preclinical evidence, and it discovers an abundance of novel disease genes with compelling biological rationale.
Divergence of trafficking and polarization mechanisms for PIN auxin transporters during land plant evolution
Authors: Tang Han , Lu Kuan-Ju , Zhang YuZhou , Cheng You-Liang , Tu Shih-Long , Friml Jiří
Published: May 2022

The phytohormone auxin and its directional transport through tissues play a fundamental role in development of higher plants. This polar auxin transport predominantly relies on PIN-FORMED (PIN) auxin exporters. Hence, PIN polarization is crucial for development, but its evolution during the rise of morphological complexity in land plants remains unclear. Here, we performed a cross-species investigation by observing the trafficking and localization of endogenous and xenologous PINs in two bryophytes,Physcomitrium patensandMarchantia polymorpha, and in the flowering plantArabidopsis thaliana. We confirmed that the GFP fusion did not compromise the auxin export function of all examined PINs by using radioactive auxin export assay and by observing the phenotypic changes in transgenic bryophytes. Endogenous PINs polarize to filamentous apices, while xenologous Arabidopsis PINs distribute symmetrically on the membrane in both bryophytes. In Arabidopsis root epidermis, bryophytic PINs show no defined polarity. Pharmacological interference revealed a strong cytoskeleton dependence of bryophytic but not Arabidopsis PIN polarization. The divergence of PIN polarization and trafficking is also observed within the bryophyte clade and between tissues in individual species. These results collectively reveal a divergence of PIN trafficking and polarity mechanisms throughout land plant evolution and a co-evolution of PIN sequence-based and cell-based polarity mechanisms.
Regenerating axolotl retinas regrow diverse cell types with modulation by Notch signaling and reconnect to the brain
Authors: Yandulskaya Anastasia S. , Miller Melissa N. , Ansaripour Ronak , Carrier Rebecca L. , Monaghan James R.
Published: May 2022

Some species successfully repair retinal injuries in contrast to non-regenerative mammalian retina. We show here that the Mexican axolotl salamander regrows its excised retina even in adulthood. During early regeneration, cell proliferation occurred in the retinal pigment epithelium (RPE). All dividing cells expressed Vimentin, and some also expressed Müller glia and neural progenitor cell marker Glast (Slc1a3), suggesting that regeneration is driven by RPE-derived retinal progenitor cells. Bulk RNA sequencing showed that genes associated with the extracellular matrix and angiogenesis were upregulated in early-to-mid retinal regeneration. The fully regenerated retina re-established nerve projections to the brain and contained all the original retinal cell types, including Müller glia. Regeneration of cellular diversity may be modulated by Notch signaling, as inhibiting Notch signaling in early regeneration promoted production of rod photoreceptors. Our study highlights the axolotl salamander as an advantageous model of adult tetrapod retinal regeneration and provides insights into its mechanisms.

We demonstrate that adult Mexican axolotl salamanders regenerate retinas after a retinectomy. We also show some cellular and molecular mechanisms that drive axolotl retinal regeneration.
Smoke exposed roots causes reduced whole-plant vascular sectoriality
Authors: Benoit Mary , Waller Spenser , Wilder Stacy L. , Schueller Michael J. , Ferrieri Richard A.
Published: May 2022

While photosynthates are partitioned by the relative strength of young developing leaves and roots as sinks for carbon-based resources, many plants also show a close relationship between partitioning, phyllotaxy and vascular connectivity, yielding sectorial patterns of allocation. We examined whether smoke influences phloem vascular sectoriality in a model plant, sunflower (Helianthis annuus L.). Using radioactive 11CO2 administered to single photosynthetically active source leaves, we examined the transport behavior and allocation patterns of 11C-photosynthates using gamma counting and autoradiography. Soil treated with liquid smoke caused significant reductions in phloem sectoriality involving young sink leaves and roots. The resulting increase in vascular connectivity could benefit young plant performance by allowing a more uniform allocation of nutrients and/or stress signal molecules at a critical time of their growth.

One-Sentence Summary

Smoke-exposed roots exhibit a significant reduction in phloem sectoriality involving carbon transport to young sink leaves and roots.
Actin-regulated Siglec-1 nanoclustering influences HIV-1 capture and virus-containing compartment formation in dendritic cells
Authors: Gutiérrez-Martínez Enric , Benet Susana , Mateos Nicolas , Erkizia Itziar , Nieto-Garai Jon Ander , Lorizate Maier , Manzo Carlo , Campelo Felix , Izquierdo-Useros Nuria , Martinez-Picado Javier , Garcia-Parajo Maria F.
Published: May 2022

The immunoglobulin-like lectin receptor CD169 (Siglec-1) mediates the capture of HIV-1 by activated dendritic cells (DC) through binding to sialylated ligands. These interactions result in a more efficient virus capture as compared to resting DCs, although the underlying mechanisms are poorly understood. Using a combination of super-resolution microscopy, single particle tracking and biochemical perturbations we studied the nanoscale organization of Siglec-1 on activated DCs and its impact on viral capture and its trafficking to a single viral-containing compartment. We found that activation of DCs leads to Siglec-1 basal nanoclustering at specific plasma membrane regions where receptor diffusion is constrained by Rho-ROCK activation and formin-dependent actin polymerization. Using liposomes with varying ganglioside concentrations, we further demonstrate that Siglec-1 nanoclustering enhances the receptor avidity to limiting concentrations of gangliosides carrying sialic ligands. Binding to either HIV-1 particles or ganglioside-bearing liposomes lead to enhanced Siglec-1 nanoclustering and global actin rearrangements characterized by a drop in RhoA activity, facilitating the final accumulation of viral particles in a single sac-like compartment. Overall, our work provides new insights on the role of the actin machinery of activated DCs in regulating the formation of basal Siglec-1 nanoclustering, being decisive for the capture and actin-dependent trafficking of HIV-1 into the virus-containing compartment.
Partial refuges from biological control due to intraspecific variation in protective host traits: a case study with the egg parasitoidTrissolcus japonicus
Authors: Abram Paul K. , Haye Tim , Clarke Peggy , Grove Emily , Thiessen Jason , Gariepy Tara D.
Published: May 2022

Predicting how much of a host or prey population may be attacked by their natural enemies is fundamental to several subfields of applied ecology, particularly biological control of pest organisms. Hosts or prey can occupy refuges from natural enemy attack, but habitat or ecological refuges are challenging or impossible to predict in a laboratory setting – which is often where efficacy and specificity testing of candidate biological control agents is done. Here we explore how intraspecific variation in continuous traits that confers some protection from natural enemy attack – even after the natural enemy has encountered the prey – could provide partial refuges. The size of these trait-based refuges should depend on the relationship between trait values and host/prey susceptibility to natural enemy attack, and on how common different trait values are within a host/prey population. These can be readily estimated in laboratory testing of natural enemy impact on target or non-target prey or hosts as long as sufficient host material is available. We provide a general framework for how intraspecific variation in protective host traits could be integrated into biological control research, specifically with reference to non-target testing as part of classical biological control programs. As a case study, we exposed different host clutch sizes of target (pest) and non-target (native species) stink bug (Hemiptera: Pentatomidae) species to a well-studied exotic biocontrol agent, the egg parasitoidTrissolcus japonicus(Hymenoptera: Scelionidae). Although we observed several behavioural and reproductive responses to variation in host egg mass size byT. japonicus, they did not translate to increases in predicted refuge size (proportion host survival) large enough to change the conclusions of non-target testing. We encourage researchers to investigate intraspecific variation in a wider variety of protective host and prey traits and their consequences for refuge size.
Sorting single T cells based on secreted cytokines and surface markers using hydrogel nanovials
Authors: Koo Doyeon , Dimatteo Robert , Lee Sohyung , de Rutte Joseph , Di Carlo Dino
Published: May 2022

Immune cell function is intrinsically linked to secreted factors which enable cells to communicate with neighboring or distant cells to coordinate a response. The ability to secrete cytokines also can help define the population of cells with therapeutic potential in emerging cell therapies, such as chimeric antigen receptor (CAR)-T cell therapies. Polyfunctional cells that can secrete more than one cytokine have been found to play an outsized role in therapeutic efficacy. While there are a variety of techniques to analyze cellular secretions from individual polyfunctional cells, there are no widely-available approaches to sort viable cells based on this phenotype. Here, we apply lab on a particle technology to the analysis and sorting of T cells based on a combination of secreted factors, interferon gamma (IFN-γ), tumor necrosis factor alpha (TNF-α) and interleukin 2 (IL-2) and surface markers (CD8+ and CD4+). Cells are selectively loaded into the antibody-functionalized cavity of micro-hydrogel particles, called nanovials, where secreted cytokines are captured and fluorescently stained. By leveraging standard fluorescence activated cell sorters and using fluorescence pulse area/height information we can distinguish between fluorescence signals on the nanovial cavities and on cells, and are able to process greater than 1 million nanovials in one hour of sorting. The frequency of multi-cytokine secreting cells was correlated with surface marker expression, and biased towards CD4+ T cells. CD8+ cells that secreted more than one cytokine, were biased towards IFN-γ and TNF-α with fewer CD8+ cells secreting IL-2. The majority of cells with a polyfunctional phenotype that were sorted remained viable and regrew following sorting. This nanovial cytokine secretion assay can be applied to sort antigen-specific T cells or CAR-T cells based on their functional engagement with cognate antigens or peptide-major histocompatibility complexs (MHCs), enabling discovery of functional CARs or T cell receptors and deeper investigation into the molecular underpinnings of single T cell function.
BMAL1 loss in oligodendroglial lineage cells dysregulates myelination and sleep
Authors: Rojo Daniela , Badner Anna , Dal Cengio Louisa , Kim Samuel , Sakai Noriaki , Greene Jacob , Eisinger Ella , Arellano-Garcia Caroline , Mehl Lindsey C. , Gumma Mohammad E. , Soyk Rebecca L. , Ransom Julia , Weigel Maya K. , Yalçın Belgin , Jones Samuel E. , Ollila Hanna M. , Nishino Seiji , Gibson Erin M.
Published: May 2022

Myelination depends on maintenance of oligodendrocytes that arise from oligodendrocyte precursor cells (OPCs). We show that the dynamic nature of oligodendroglia and myelination are regulated by the circadian transcription factor BMAL1. Bmal1 knockdown in OPCs during development – but not adulthood – decreases OPC proliferation, whereas BMAL1 regulates OPC morphology throughout life. OPC-specific Bmal1 deficiency impairs remyelination in an age-dependent manner, suggesting that age-associated decrements in circadian regulation of oligodendroglia may contribute to the deficient remyelination potential in demyelinating diseases like multiple sclerosis (MS). This oligodendroglial dysregulation and dysmyelination increase sleep fragmentation in OPC-specific Bmal1 knockout mice, and sleep fragmentation is causally associated with MS. These findings have broad mechanistic and therapeutic implications for numerous brain disorders that include both myelin and sleep phenotypes.

One-Sentence Summary

BMAL1 regulates the homeostatic maintenance of oligodendroglia and myelin, that subsequently controls sleep architecture.
Hyperimmune bovine colostrum containing lipopolysaccharide antibodies (Imm124-E) has a non-detrimental effect on gut microbial communities in unchallenged mice
Authors: Gore Rachele , Mohsenipour Mitra , Wood Jennifer L , Balasuriya Gayathri K , Hill-Yardin Elisa L , Franks Ashley E
Published: May 2022

1

EnterotoxigenicEscherichia coli(ETEC) is a leading cause of bacterial diarrhea in travelers, military personnel and children in developing countries. Infection has the potential to cause long-term gastrointestinal dysfunction. Preventative treatments for ETEC-induced diarrhea exist, yet the effects of these treatments on gastrointestinal commensals in healthy individuals is unclear. Whether administration of a prophylactic preventative treatment for ETEC-induced diarrhea causes specific shifts in gut microbial populations in controlled environments is also unknown. Here we studied the effects of a hyperimmune bovine colostrum (IMM-124E) used in the manufacture of Travelan® (AUST L 106709) on gastrointestinal bacteria in healthy C57BL/6 mice. Using next generation sequencing, we aimed to test the onset and magnitude of potential changes to the mouse gut microbiome in response to the anti-diarrheagenic hyperimmune bovine colostrum product, rich in immunoglobulins against select ETEC strains (Travelan®, Immuron Ltd). We engineered changes in mouse fecal and cecal bacterial communities by delivering lipopolysaccharide (LPS) antibodies derived from bovine colostrum via dietary supplementation. Holstein Friesian and Jersey cows between 28- and 35-weeks’ gestation stimulated by subcutaneous delivery of three important pathogenic and antigenic determinants; LPS, flagella, and colonization factor antigen (CFA), produced a hyperimmune colostrum (IMM-124E) with demonstrated beneficial effects on health via modulation of metabolic pathways and immune function. We show that in mice administered colostrum containing LPS antibodies there was an increased abundance of potentially gut-beneficial bacteria, such asAkkermansiaandDesulfovibrio, without disrupting the underlying ecology of the gastrointestinal tract. Compared to controls, there was no difference in overall weight gain, body or cecal weights or small intestine length following LPS antibody colostrum supplementation. Overall, dietary supplementation with colostrum containing LPS antibodies produced subtle alterations in gut bacterial composition of mice. Primarily, Travelan® LPS antibody treatment decreased the ratio of Firmicutes/Bacteroidetes in gut microbial populations in unchallenged healthy mice. Further studies are required to examine the effect of Travelan® LPS antibody treatment to engineer the microbiome in a diseased state and during recovery.
Early steps of embryo implantation are regulated by exchange of extracellular vesicles between the embryo and the endometrium
Authors: Szuszkiewicz Joanna , Myszczynski Kamil , Reliszko Zaneta P , Heifetz Yael , Kaczmarek Monika M
Published: May 2022

In early pregnancy, as the embryo arrives in the uterus, intensive communication between the embryo and uterus begins. Hundreds of molecules are known to be involved, but despite numerous findings, full understanding of the complexity of the embryo–maternal dialog remains elusive. Recently, extracellular vesicles, nanoparticles able to transfer functionally active cargo between cells, have emerged as important players in cell–cell communication, and as such, they have gained great attention over the past decade also in reproductive biology. Here we use a domestic animal model (Sus scrofa) with an epitheliochorial, superficial type of placentation because of its advantage in studding uterine luminal fluid extracellular vesicles. We show that during early pregnancy, the uterine lumen is abundant with extracellular vesicles that carry a plethora of miRNAs able to target genes involved in embryonic and organismal development. These extracellular vesicles, upon the delivery to primary trophoblast cells, affect genes governing development as well as cell-to-cell signaling and interactions, consequently having an impact on trophoblast cell proliferation, migration, and invasion. We conclude that exchange of a unique population of extracellular vesicles and their molecular cargo at the maternal–embryo interface is the key to the success of embryo implantation and pregnancy.
The capsid precursor protein of astrovirus VA1 is proteolytically processed intracellularly
Authors: Aguilera-Flores Catalina , López Tomás , Zamudio Fernando , Sandoval-Jaime Carlos , Pérezc Edmundo I. , López Susana , DuBois Rebecca , Arias Carlos F.
Published: May 2022

Human astrovirus VA1 has been associated with neurological disease in immunocompromised patients, and its recent propagation in cell culture has opened the possibility to study its biology. Unlike classical human astroviruses, VA1 growth was found to be independent of trypsin during virus replication in vitro. In this work, we show that despite its independence on trypsin activation for cell infection, the VA1 capsid precursor protein, of 86 kDa (VP86), is processed intracellularly, and this proteolytic processing is important for astrovirus VA1 infectivity. Antibodies raised against different regions of the capsid precursor showed that the polyprotein can be processed starting at either its amino-or carboxy-terminal end, and they allowed us to identify that proteins of about 33 (VP33) and 38 (VP38) kDa constitute the core and the spike proteins of the mature infectious virus particles, respectively. The amino-terminal end of the spike protein was found to be Thr-348. Whether the protease involved in intracellular cleavage of the capsid precursor is of viral or cellular origin remains to be determined, but the cleavage is independent of caspases. Also, trypsin is able to degrade the capsid precursor but has no effect on VP34 and VP38 proteins when assembled into virus particles. These studies provide the basis for advancement of the knowledge of astrovirus VA1 cell entry and replication.

IMPORTANCE

Human astrovirus VA1 has been associated with neurological disease in immunocompromised patients. Its recent propagation in cell culture has facilitated the study of its biology. In this work, we show that despite the ability of this virus to grow in the absence of trypsin, a marked feature of human classical astroviruses, the capsid precursor protein of astrovirus VA1 is cleaved intracellularly to yield the mature infectious particles, formed by two polypeptides, VP33 that constitutes the core domain of the virus particle, and V38 that forms the spike of the virus. These studies provide a platform to advance our knowledge on astrovirus VA1 cell entry and replication.
‘Erythritol’, a safe natural sweetener exhibits multi-stage anti-malarial activity by blocking Plasmodium falciparum membrane transporter ‘aquaporin’
Authors: Kumari Jyoti , Kumar Vikash , Behl Ankita , Sah Raj Kumar , Garg Swati , Pati Soumya , Samby Kirandeep , Burrows Jeremy , Mohandas Narla , Singh Shailja
Published: May 2022

The increased resistance of human malaria parasite Plasmodium falciparum to currently used drugs necessities the development of novel anti-malarials. In the present study, we examine the potential of erythritol, a sugar substitute, for therapeutic intervention that target a multifunctional transporter protein Plasmodium aquaglyceroporin (PfAQP) responsible for maintaining hydro-homeostasis. We show that erythritol effectively inhibited growth and progression of asexual blood stage malaria parasite by suppressing invasion and egress processes. It inhibited the liver stage (sporozoites) and transmission stage parasite (gametocytes) development that suggest its multi-stage, transmission-blocking potential. Interestingly, erythritol inhibited in vivo growth of malaria parasite in mouse experimental model. It was more effective in inhibiting parasite growth both in vivo and in vitro when tested together with a known anti-malarial ‘artesunate’. No Evans blue staining in treated mice indicated erythritol mediated protection of blood–brain barrier integrity in mice infected with P. berghei. Additionally, erythritol showed cytokine-modulating effect which suggest its direct effect on the host immune system. Our results of cellular thermal shift assay and ammonia detection assay demonstrate that erythritol binds with PfAQP and reduce the amount of ammonia release across the parasite respectively. We performed functional complementation assays which suggest that PfAQP expression in yeast mutant restores its growth in hyperosmotic conditions but showed reduced growth in the presence of erythritol, suggesting erythritol as an inhibitor of PfAQP. Overall, our data bestow erythritol as a promising new lead compound with an attractive antimalarial profile and could possibly be combined with known drugs without losing its efficacy.
Implementation strategies for telemental health: a systematic review
Authors: Appleton Rebecca , Barnett Phoebe , San Juan Norha Vera , Tuudah Elizabeth , Lyons Natasha , Parker Jennie , Roxburgh Emily , Spyridonidis Spyros , Tamworth Camilla , Worden Minnie , Yilmaz Melisa , Sevdalis Nick , Lloyd-Evans Brynmor , Needle Justin J , Johnson Sonia
Published: May 2022

Background

The COVID-19 pandemic resulted in a rapid shift from traditional face-to-face care provision towards delivering mental health care remotely through telecommunications, often referred to as telemental health care. However, the manner and extent of telemental health implementation have varied considerably across settings and areas, and substantial barriers are encountered. There is, therefore, now a need to identify what works best for service users and staff and establish the key mechanisms for efficient integration into routine care.

Objective

We aimed to identify investigations of pre-planned strategies intended to achieve or improve effective and sustained implementation of telemental health approaches, and to evaluate how different strategies influence implementation outcomes.

Methods

A systematic review was conducted, with five databases searched for relevant literature using any methodological approach, published between January 2010 and July 2021. Studies were eligible for inclusion if they took place in secondary or tertiary mental health services and focused on pre-planned strategies for achieving or improving delivery of mental health care through remote communication between mental health professionals or between mental health professionals and service users, family members, unpaid carers, or peer supporters. All included studies were assessed for risk of bias. Data were synthesised using the Expert Recommendations for Implementing Change (ERIC) compilation of implementation strategies and the taxonomy of implementation outcomes.

Results

A total of 14 studies were identified which met the inclusion criteria. A variety of implementation strategies were identified, the most commonly reported being ‘Train and educate stakeholders’. All studies reported using a combination of several implementation strategies.

Conclusions

Using a combination of implementation strategies appears to be a helpful method of supporting the implementation of telemental health. Further research is needed to test the impact of specific implementation strategies on implementation outcomes.
“Similar performances but markedly different triaging thresholds in three CAD4TB versions risk systematic errors in TB screening programs”
Authors: Fehr Jana , Wong Emily B.
Published: May 2022

Tuberculosis (TB) screening programs may apply computer-aided diagnostic (CAD) tools on chest radiographs to select people for microbiological sputum examination using a pre-selected triaging threshold. CAD software-updates are frequently introduced and it is unknown whether their use requires adjustment of triaging thresholds. In a community-based screening program in South Africa, we compared the scores between the three recent CAD4TB versions (v5, v6, and v7) and assessed their performance to identify microbiologically-confirmed TB. The performance of all versions was similar (v5: AUC 0.78, v6: AUC 0.79, v7: AUC 0.80; p-values>0.05), but along a 0-100 point scale, each had markedly different score distributions and optimal triaging thresholds (v5: 40, v6: 47, v7: 20). This has the potential to cause confusion within TB screening programs as these tools are increasingly adopted and new versions released. Independent guidance for adapting CAD triaging thresholds for frequently released software updates is needed.
Effects of gender-affirming hormone therapy on gray matter density, microstructure and monoamine oxidase A levels in transgender subjects
Authors: Handschuh PA , Reed MB , Murgaš M , Vraka C , Kaufmann U , Nics L , Klöbl M , Ozenil M , Konadu ME , Patronas EM , Spurny-Dworak B , Hahn A , Hacker M , Spies M , Baldinger-Melich P , Kranz GS , Lanzenberger R
Published: May 2022

MAO-A catalyzes the oxidative degradation of monoamines and is thus implicated in sex-specific neuroplastic processes that influence gray matter (GM) density (GMD) and microstructure (GMM). Given the exact monitoring of plasma hormone levels and sex steroid intake, transgender individuals undergoing gender-affirming hormone therapy (GHT) represent a valuable cohort to potentially investigate sex steroid-induced changes of GM and concomitant MAO-A density. Here, we investigated the effects of long-term GHT over a median time period of 4.5 months on GMD and GMM as well as MAO-A distribution volume. To this end, 20 cisgender women, 11 cisgender men, 20 transgender women and 10 transgender men underwent two MRI scans in a longitudinal design. PET scans using [11C]harmine were performed before each MRI session in a subset of 35 individuals. GM changes determined by diffusion weighted imaging (DWI) metrics for GMM and voxel based morphometry (VBM) for GMD were estimated using repeated measures ANOVA. Regions showing significant changes of both GMM and GMD were used for the subsequent analysis of MAO-A density. These involved the fusiform gyrus, rolandic operculum, inferior occipital cortex, middle and anterior cingulum, bilateral insula, cerebellum and the lingual gyrus (post-hoc tests: pFWE+Bonferroni< 0.025). In terms of MAO-A distribution volume, no significant effects were found. Additionally, the sexual desire inventory (SDI) was applied to assess GHT-induced changes in sexual desire, showing an increase of SDI scores among transmen. Changes in the GMD of the bilateral insula showed a moderate correlation to SDI scores (rho = −0.62, pBonferroni= 0.047). The present results are indicative of a reliable influence of gender-affirming hormone therapy on 1) GMD and GMM following an interregional pattern and 2) sexual desire specifically among transmen.

Highlights

Gender-affirming hormone therapy led to significant changes in gray matter density and microstructure in various brain regions

Gray matter changes found after gender-affirming hormone therapy were not reflected by monoamone oxidase A density changes in the brain.

Masculinizing gender-affirming hormone therapy resulted in increased sexual desire in transgender men.
Plasma membrane topography governs the three-dimensional dynamic localization of IgM B cell receptor clusters
Authors: Saltukoglu Deniz , Özdemir Bugra , Holtmannspötter Michael , Reski Ralf , Piehler Jacob , Kurre Rainer , Reth Michael
Published: May 2022

B lymphocytes recognize bacterial or viral antigens via different classes of the B cell antigen receptor (BCR). Protrusive structures termed microvilli cover lymphocyte surfaces and are thought to perform sensory functions in screening antigen-bearing surfaces. Here, we have studied the cell surface features of Ramos B cells and the spatiotemporal organization of the IgM-BCR using lattice light sheet microscopy in combination with tailored custom-built 4D image analysis. Ramos B cell surfaces were found to form dynamic networks of elevated ridges bridging individual microvilli. A proportion of membrane-localized IgM-BCR was found in clusters, which were associated with the ridges and the microvilli. The dynamic ridge network organization and the IgM-BCR cluster mobility were linked and both were controlled by Arp2/3 complex activity. Our results suggest that topographical features of the cell surface govern the distribution and dynamic localization of IgM-BCR clusters to facilitate antigen screening.
TET1 attenuates human pluripotency-related heterogeneities and enhances differentiation capabilities
Authors: Motono Makoto , Hiraki-Kamon Keiko , Kamon Masayoshi , Kiyosawa Hidenori , Kondo Yoichi , Kato Hidemasa
Published: May 2022

Human induced pluripotent stem cells (hiPSCs) offer transformative potential for developmental research and therapeutic discovery; however, their variable characteristics are a significant barrier to their broader application. We reprogrammed hiPSCs by adding TET1, a DNA-demethylating dioxygenase, to produce TET1-iPSCs (T-iPSCs) with enhanced epithelialization and differentiation capabilities. A default differentiation survey—designed and implemented in our hiPSC-production pipeline—revealed considerable variation in differentiation capacity across qualitatively pluripotent iPSC clones. By comparing high- differentiation T-iPSCs and conventional iPSCs (C-iPSCs) at the single-cell level, we identified a subpopulation of C-iPSCs in the G0/G1 phase (CDKN2A-positive) exhibiting lowTET1expression and an elevated extraembryonic mesenchymal gene signature. The extraembryonic mesenchymal gene signature is common to iPSCs and quantitatively correlates to default differentiation results. Deviation of C-iPSCs from the cell-cycling embryonic epithelial gene profile was accompanied by DNA hypermethylation concomitant withTET1insufficiency and the accompanying derepression of poised and Polycomb-repressed enhancers, leading to the derepression of senescence-associated and extraembryonic genes. TET1-facilitated reprogramming can ameliorate these deviations. This study provides a standardized hiPSC- production pipeline and discovers an aspect of TET1 for establishing human pluripotency by remedying the inherent heterogeneities resulting from C-iPSC reprogramming.
Core genome sequencing and genotyping ofLeptospira interrogansin clinical samples by target capture sequencing
Authors: Grillova Linda , Cokelaer Thomas , Mariet Jean-François , da Fonseca Juliana Pipoli , Picardeau Mathieu
Published: May 2022

The life-threatening pathogenLeptospira interrogansis the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are circulating worldwide due to the fastidious nature of the bacteria and its difficulty to be culture isolated. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material.

Here, to elucidate the genomic diversity ofLeptospiracirculating strains, hybridization capture followed by Illumina sequencing of the core genome was performed directly from 20 biological samples that were PCR positive for pathogenicLeptospira. A set of samples subjected to capture with RNA probes covering theL. interroganscore genome resulted in 72 to 13,000-fold increase in pathogen reads when compared to standard sequencing without capture. A SNP analysis of the genomes sequenced from the biological samples using 273Leptospirareference genome was then performed in order to determine the genotype of the infecting strain. For samples with sufficent coverage (19/20 samples with coverage >8X), we could unambigously identifyL. interroganssv Icterohaemorrhagiae (14 samples),L. kirschnerisv Grippotyphosa (4 samples) andL. interroganssv Pyrogenes (1 sample) as the infecting strain.

In conclusion, we obtained for most of our biological samples high quality genomic data at suitable coverage for confident core genome genotyping of the agent of leptospirosis. The ability to generate culture-free genomic data opens new opportunities to better understand the epidemiology and evolution of this fastidious pathogen.