bluuebunny/crossref_metadata_2025 huggingface dataset:
Are Current National Review Board Downstaging Protocols for Hepatocellular Carcinoma Too Restrictive?
Authors: Ahmed Ola , Vachharajani Neeta , Croome Kris P , Tabrizian Parissa , Agopian Vatche , Halazun Karim , Hong Johnny C , Dageforde Leigh Anne , Chapman William C , Doyle MB Majella ,   for the Primary Liver Tumor Study Group
Published: April 2022

BACKGROUND:

Liver transplantation (LT) is an effective strategy for patients with unresectable hepatocellular carcinoma (HCC). To qualify for standardized LT model for end-stage liver disease exception points, the United Network for Organ Sharing National Liver Review Board (NLRB) requires that the presenting and final HCC tumor burden be within the University of California San Francisco criteria, which were recently expanded (within expanded UCSF [W-eUCSF]). Current NLRB criteria may be too restrictive because it has been shown previously that the initial burden does not predict LT failure when tumors downstage to UCSF. This study aims to assess LT outcomes for HCC initially presenting beyond expanded UCSF (B-eUCSF) criteria in a large multicenter collaboration.

STUDY DESIGN:

Comparisons of B-eUCSF and W-eUCSF candidates undergoing LT at seven academic institutions between 2001 and 2017 were made from a multi-institutional database. Survival outcomes were compared by Kaplan-Meier and Cox regression analyses.

RESULTS:

Of 1,846 LT recipients with HCC, 86 (5%) met B-eUCSF criteria at initial presentation, with the remainder meeting W-eUCSF criteria. Despite differences in tumor burden, B-eUCSF candidates achieved comparable 1-, 5- and 10-year overall (89%, 70%, and 55% vs 91%, 74%, and 60%, respectively; p = 0.2) and disease-free (82%, 60%, and 53% vs 89%, 71%, and 59%, respectively; p = 0.07) survival to patients meeting W-eUCSF criteria after LT. Despite increased tumor recurrence in B-eUCSF vs W-eUCSF patients (24% vs 10%, p = 0.0002), post-recurrence survival was similar in both groups (p = 0.69).

CONCLUSION:

Transplantation for patients initially presenting with HCC B-eUSCF criteria offers a survival advantage similar to those with tumors meeting W-eUCSF criteria at presentation. The current NLRB policy is too stringent, and considerations to expand criteria should be discussed.
Comparison of Vibrio coralliilyticus virulence in Pacific oyster larvae and corals
Authors: Ushijima Blake , Saw Jimmy H. , Videau Patrick , Häse Claudia C.
Published: April 2022

The bacterium

Vibrio coralliilyticus

has been implicated in mass mortalities of corals and shellfish larvae. However, using corals for manipulative infection experiments can be logistically difficult compared to other model organisms, so we aimed to establish oyster larvae infections as a proxy model. Therefore, this study assessed the virulence of six wild-type

V. coralliilyticus

strains, and mutants of one strain with deletions of known virulence factors, between Pacific oyster larvae (Crassostrea gigas) and Hawaiian rice coral (Montipora capitata) infection systems. The wild-type strains tested displayed variable virulence in each system, but virulence levels between hosts were not necessarily comparable. Strains RE98 and OCN008 maintained a medium to high level of virulence across hosts and appeared to be more generalist pathogens. Strain H1, in contrast, was avirulent towards coral but displayed a medium level of virulence towards oyster larvae. Interestingly, the BAA-450 type strain had a medium level of virulence towards coral and was the least virulent to oyster larvae. A comparison of known virulence factors determined that the flagellum, motility or chemotaxis, all of which play a significant role in coral infections, were not crucial for oyster infections with strain OCN008. A genomic comparison of the newly sequenced strain H1 with the other strains tested identified 16 genes potentially specific to coral pathogens that were absent in H1. This is both the first comparison of various

V. coralliilyticus

strains across infection systems and the first investigation of a strain that is non-virulent to coral. Our results indicate that the virulence of

V. coralliilyticus

strains in coral is not necessarily indicative of virulence in oyster larvae, and that the set of genes tested are not required for virulence in both model systems. This study increases our understanding of the virulence between

V. coralliilyticus

strains and helps assess their potential threat to marine environments and shellfish industries.
Haemolysis detection in microRNA-seq from clinical plasma samples
Authors: Smith Melanie D. , Leemaqz Shalem Y. , Jankovic-Karasoulos Tanja , McAninch Dale , McCullough Dylan , Breen James , Roberts Claire T. , Pillman Katherine A.
Published: April 2022

The abundance of cell-free microRNA (miRNA) has been measured in many body fluids, including blood plasma, which has been proposed as a source with novel, minimally invasive biomarker potential for several diseases. Despite improvements in quantification methods for plasma miRNAs, there is no consensus on optimal reference miRNAs or to what extent haemolysis may affect plasma miRNA content. Here we propose a new method for the detection of haemolysis in miRNA high-throughput sequencing (HTS) data from libraries prepared using human plasma. To establish a miRNA haemolysis signature in plasma we first identified differentially expressed miRNAs between samples with known haemolysis status and selected miRNA with statistically significant higher abundance in our haemolysed group. Given there may be both technical and biological reasons for differential abundance of signature miRNA, and to ensure the method developed here was relevant outside of our specific context, that is women of reproductive age, we tested for significant differences between pregnant and non-pregnant groups. Here we report a novel 20 miRNA signature (miR-106b-3p, miR-140-3p, miR-142-5p, miR-532-5p, miR-17-5p, miR-19b-3p, miR-30c-5p, miR-324-5p, miR-192-5p, miR-660-5p, miR-186-5p, miR-425-5p, miR-25-3p, miR-363-3p, miR-183-5p, miR-451a, miR-182-5p, miR-191-5p, miR-194-5p, miR-20b-5p) that can be used to identify the presence of haemolysis, in silico, in high throughput miRNA sequencing data. Given the potential for haemolysis contamination, we recommend that assay for haemolysis detection become standard pre-analytical practice and provide here a simple method for haemolysis detection.
Frequent Cocaine Use is Associated with Larger HIV Latent Reservoir Size
Authors: Aouizerat Bradley E. , Garcia Josephine N. , Domingues Carlos V. , Xu Ke , Quach Bryan C. , Page Grier P. , Konkle-Parker Deborah , Bolivar Hector H. , Lahiri Cecile D. , Golub Elizabeth T. , Cohen Mardge H. , Kassaye Seble G. , DeHovitz Jack , Kuniholm Mark H. , Archin Nancie M. , Tien Phyllis C. , Hancock Dana B. , Johnson Eric Otto
Published: April 2022

Background

With the success of combination antiretroviral therapy, HIV is now treated as a chronic disease, including among drug users. Cocaine—one of the most frequently abused illicit drugs among persons living with HIV (PLWH)— slows the decline of viral production after ART, and is associated with higher HIV viral load, more rapid HIV progression, and increased mortality. We examined the impact of cocaine use on the CD4+ T-cell HIV Latent Reservoir (HLR) in virally suppressed PLWH.

Methods

CD4+ T-cell genomic DNA was isolated from peripheral blood mononuclear cells collected from 434 women of diverse ancestry (i.e., 75% Black, 14% Hispanic, 12% White) who self-reported cocaine use (i.e., 160 cocaine users, 59 prior users, 215 non-users). Participants had to have an undetectable HIV RNA viral load measured by commercial assay for at least 6 months. The Intact Proviral HIV DNA Assay (IPDA) provided estimates of intact provirus per 106 CD4+ T-cells.

Results

The HLR size differed by cocaine use (i.e., median [interquartile range]: 72 [14, 193] for never users, for prior users 165 [63, 387], 184 [28, 502] for current users), which was statistically significantly larger in both prior (p=0.023) and current (p=0.001) cocaine users compared with never users.

Conclusion

Our study is the first to provide evidence that cocaine use may contribute to a larger replication competent HLR in CD4* T-cells among virologically suppressed women living with HIV. Our findings are important, because women are under-represented in HIV reservoir studies and in studies of the impact of cocaine use on outcomes among PLWH.
Framework for prioritizing variants of unknown significance from clinical genetic testing in kidney disease – utility of multidisciplinary approach to gather evidence of pathogenicity for Hepatocyte Nuclear Factor-1β (HNF1B) p.Arg303His
Authors: Mirshahi Uyenlinh L. , Bhan Ahana , Tholen Lotte E. , Fang Brian , Chen Guoli , Moore Bryn , Cook Adam , Mohan Prince , Patel Kashyap , Igarashi Peter , de Baaij Jeroen H.F. , Ferrè Silvia , Hoenderop Joost G.J. , Carey David J. , Chang Alexander R.
Published: April 2022

Monogenic causes in over 300 kidney-associated genes account for roughly 12% of end stage kidney disease (ESKD) cases. Advances in next generation sequencing, and large customized panels enable the diagnosis of monogenic kidney disease noninvasively at relatively low cost, allowing for more precise management for patients and their families. A major challenge is interpreting rare variants, many of which are classified as variants of unknown significance (VUS). We present a framework in which we thoroughly evaluated and provided evidence of pathogenicity for HNF1B-p.Arg303His, a VUS returned from clinical genetic testing for a kidney transplant candidate. This blueprint, designed by a multi-disciplinary team of clinicians, molecular biologists, and diagnostic geneticists, includes using a health system-based cohort with genetic and clinical information to perform deep phenotyping of VUS carriers, examination of existing genetic databases, as well as functional testing. With our approach, we demonstrate evidence for pathogenicity for HNF1B-p.Arg303His by showing similar burden of kidney manifestations in this variant to known HNF1B pathogenic variants, and greater burden compared to non-carriers. Determination of a molecular diagnosis for the example family allows for proper surveillance and management of HNF1B-related manifestations such as kidney disease, diabetes, and hypomagnesemia with important implications for safe living-related kidney donation. The candidate gene-variant pair also allows for clinical biomarker testing for aberrations of linked pathways. This working model may be applicable other diseases of genetic etiology.
Linking hubness, embryonic neurogenesis, transcriptomics and diseases in human brain networks
Authors: Diez Ibai , Garcia-Moreno Fernando , Carral-Sainz Nayara , Stramaglia Sebastiano , Nieto-Reyes Alicia , D’Amato Mauro , Cortes Jesús Maria , Bonifazi Paolo
Published: April 2022

Understanding the architectural principles that shape human brain networks is a major challenge for systems neuroscience. We hypothesize that the centrality of the different brain circuits in the human connectome is a product of their embryogenic age, such that early-born nodes should become stronger hubs than those born later. Using a human brain segmentation based on embryogenic age, we observed that nodes’ structural centrality correlated with their embryogenic age, fully confirming our hypothesis. Distinct trends were found at different resolutions on a functional level. The difference in embryonic age between nodes inversely correlated with the probability of existence of links and their weights. Brain transcriptomic analysis revealed strong associations between embryonic age, structure-function centrality, and the expression of genes related to nervous system development, synapse regulation and human neurological diseases. Our results highlight two key principles regarding the wiring of the human brain, “preferential age attachment” and “the older gets richer”.
Climate and competition combine to set elevational distributions of tropical rainforestDrosophila
Authors: Chen Jinlin , Lewis Owen T.
Published: April 2022

Species turnover with elevation is a widespread phenomenon and provides valuable information on why and how ecological communities might reorganize as the climate warms. Tropical mountains typically have pronounced thermal gradients and intense species interactions, providing a testing ground for investigating the relationship between thermal tolerances and biotic interactions as the proximate factors influencing species’ distributions. We investigated temperature and interspecific competition as causes of species turnover and abundance changes of the nine most abundant species ofDrosophilaalong elevational gradients in the Australian Wet Tropics. Thermal performance curves revealed that species’ distributions were better explained by their performance at extreme temperatures, rather than their thermal optima. Upper thermal limits varied less among species than lower thermal limits. Nonetheless, these small differences were associated with differences in centred elevation of distribution, consistent with environmental sorting as a driver of community composition at low-elevation sites. In contrast, community composition at cool, high elevations was driven by temperature-dependent interspecific competition rather than tolerance to low temperatures. These results run counter to common assumptions about the role of abiotic and biotic factors in structuring communities along thermal gradients, and indicate that tropical insects may be highly vulnerable to future warming. Our study illustrates the importance of experimental, quantitative tests across biological levels (i.e., individuals to populations) and temporal scales (i.e., within-generation to multi-generation) for characterizing effects of climate on a guild of closely-interacting species.
LENS: Landscape of Effective Neoantigens Software
Authors: Vensko Steven P. , Olsen Kelly , Bortone Dante , Smith Christof C. , Chai Shengjie , Beckabir Wolfgang , Fini Misha , Jadi Othmane , Rubinsteyn Alex , Vincent Benjamin G.
Published: April 2022

Motivation

Elimination of cancer cells by T cells is a critical mechanism of anti-tumor immunity and cancer immunotherapy response. T cells recognize cancer cells by engagement of T cell receptors with peptide epitopes presented by major histocompatibility complex (MHC) molecules on the cancer cell surface. Peptide epitopes can be derived from antigen proteins coded for by multiple genomic sources. Bioinformatics tools used to identify tumor-specific epitopes via analysis of DNA and RNA sequencing data have largely focused on epitopes derived from somatic variants, though a smaller number have evaluated potential antigens from other genomic sources.

Results

We report here an open-source workflow utilizing the Nextflow DSL2 workflow manager, Landscape of Effective Neoantigen Software (LENS), which predicts tumor-specific and tumor-associated antigens from single nucleotide variants, insertions and deletions, fusion events, splice variants, cancer testis antigens, overexpressed self-antigens, viruses, and endogenous retroviruses. The primary advantage of LENS is that it expands the breadth of genomic sources of discoverable tumor antigens using genomics data. Other advantages include modularity, extensibility, ease of use, and harmonization of relative expression level and immunogenicity prediction across multiple genomic sources. We present an analysis of 115 acute myeloid leukemia (AML) samples to demonstrate the utility of LENS. We expect LENS will be a valuable platform and resource for T cell epitope discovery bioinformatics, especially in cancers with few somatic variants where tumor-specific epitopes from alternative genomic sources are an elevated priority.

Availability

More information about LENS, including workflow documentation and instructions, can be found athttps://gitlab.com/landscape-of-effective-neoantigens-software

Contact

steven_vensko@med.unc.edu,benjamin_vincent@med.unc.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
Speed-dependent biomechanical changes vary across individual gait metrics post-stroke relative to neurotypical adults
Authors: Kettlety Sarah A. , Finley James M. , Reisman Darcy S. , Schweighofer Nicolas , Leech Kristan A
Published: April 2022

Background

Gait training at fast speeds is recommended to reduce walking activity limitations post-stroke. Fast walking may also reduce gait kinematic impairments post-stroke. However, the magnitude of speed-dependent kinematic impairment reduction in people post-stroke relative to neurotypical adult walking patterns is unknown.

Objective

To determine the effect of faster walking speeds on gait kinematics post-stroke relative to neurotypical adults walking at similar speeds.

Methods

We performed a secondary analysis with data from 28 people post-stroke and 50 neurotypical adults treadmill walking at multiple speeds. We evaluated the effects of speed and group on individual spatiotemporal and kinematic metrics and performed k-means clustering with all metrics at self-selected and fast speeds

Results

People post-stroke decreased step length asymmetry and trailing limb angle impairment, reducing between-group differences at fast speeds. Speed-dependent changes in peak swing knee flexion, hip hiking, and temporal asymmetries exaggerated between-group differences. Our clustering analyses revealed two clusters. One represented neurotypical gait behavior, composed of neurotypical and post-stroke participants. The other characterized stroke gait behavior, comprised entirely of participants post-stroke. Cluster composition was largely consistent at both speeds, and the distance between clusters increased at fast speeds

Conclusions

The biomechanical effect of fast walking post-stroke varied across individual gait metrics. For participants within the stroke gait behavior cluster, speed-dependent changes did not lead to an overall gait pattern more similar to neurotypical adults. This suggests that combining fast walking with an approach to strategically target gait metrics with smaller speed-dependent changes may potentiate the biomechanical benefits of fast walking.
Active vision during prey-capture in wild marmoset monkeys
Authors: Ngo Victoria , Gorman Julia C. , De la Fuente María Fernanda , Souto Antonio , Schiel Nicola , Miller Cory T.
Published: April 2022

Here, we examined prey-capture in wild common marmosets (Callithrix jacchus) to explicate the active role of primate vision for high-precision, goal-directed motor actions in challenging natural environments. We observed distinct marmoset hunting strategies that each relied on the close integration of visual processes and dynamic biomechanical motor movements, but differed based on several factors including prey size/speed, substrate, and their relative distance to the prey. Marmoset positional behavior in these complex arboreal settings often involves extending the body, including inversions, while relying on vision to guide prey capture. Applying markerless pose estimation technology, analyses revealed details of how primate vision both guides and corrects rapid motor actions in real-time during prey-capture in the wild. These findings illustrate the significance of active vision during primate ethological behaviors in response to the very challenges the visual system evolved to solve.
Principal component analysis- and tensor decomposition-based unsupervised feature extraction to select more suitable differentially methylated cytosines: Optimization of standard deviation versus state-of-the-art methods
Authors: Taguchi Y-H. , Turki Turki
Published: April 2022

In contrast to RNA-seq analysis, which has various standard methods, no standard methods for identifying differentially methylated cytosines (DMCs) exist. To identify DMCs, we tested principal component analysis and tensor decomposition-based unsupervised feature extraction with optimized standard deviation, which has been shown to be effective for differentially expressed gene (DEG) identification. The proposed method outperformed certain conventional methods, including those that assume beta-binomial distribution for methylation as the proposed method does not require this, especially when applied to methylation profiles measured using high throughput sequencing. DMCs identified by the proposed method also significantly overlapped with various functional sites, including known differentially methylated regions, enhancers, and DNase I hypersensitive sites. The proposed method was applied to data sets retrieved from The Cancer Genome Atlas to identify DMCs using American Joint Committee on Cancer staging system edition labels. This suggests that the proposed method is a promising standard method for identifying DMCs.
Evolutionary responses of a reef-building coral to climate change at the end of the last glacial maximum
Authors: Zhang Jia , Richards Zoe T. , Adam Arne A. S. , Chan Cheong Xin , Shinzato Chuya , Gilmour James , Thomas Luke , Strugnell Jan M. , Miller David J. , Cooke Ira
Published: April 2022

Climate change threatens the survival of coral reefs on a global scale, primarily through mass bleaching and mortality as a result of marine heatwaves. While these short-term effects are clear, predicting the fate of coral reefs over the coming century is a major challenge. One way to understand the longer-term effects of rapid climate change is to examine the response of coral populations to past climate shifts. Coastal and shallow-water marine ecosystems such as coral reefs have been reshaped many times by sea-level changes during the Pleistocene, yet, few studies have directly linked this with its consequences on population demographics, dispersal, and adaptation. Here we use powerful analytical techniques, afforded by haplotype phased whole-genomes, to establish such links for the reef-building coral,Acropora digitifera. We show that three genetically distinct populations are present in northwestern Australia, and that their rapid divergence since the last glacial maximum (LGM) can be explained by a combination of founder-effects and restricted gene flow. Signatures of selective sweeps, too strong to be explained by demographic history, are present in all three populations and overlap with genes that show different patterns of functional enrichment between inshore and offshore habitats. In contrast to rapid divergence in the host, we find that photosymbiont communities are largely undifferentiated between corals from all three locations, spanning almost 1000 km, indicating that selection on host genes and not acquisition of novel symbionts, has been the primary driver of adaptation for this species in northwestern Australia.
Emergence of distinct neural subspaces in motor cortical dynamics during volitional adjustments of ongoing locomotion
Authors: Xing David , Truccolo Wilson , Borton David A.
Published: April 2022

3

The brain is capable of simultaneously carrying out multiple functions, such as making different types of movements at the same time. One example is how we are able to both carry out stereotyped walking or running movements, while concurrently performing precise, target-directed movements such as kicking a ball in a soccer match. Recently, research has shown that different computations within the same population of neurons can be carried out without disrupting each other by confining the processes into separate subspaces. Whether this strategy is used to precisely control our limbs while maintaining locomotion is still an open question. Here, we recorded the activity of primary motor cortex in nonhuman primates during obstacle avoidance on a treadmill. We found that the same neural population was active during both basic unobstructed locomotion and volitional obstacle avoidance movements. Additionally, we identified the neural modes spanning the subspace of the low-dimensional dynamics in M1 using both supervised and unsupervised techniques. We found that motor cortex employs a subspace that consistently maintains the same cyclic activity throughout obstacle stepping, despite large changes in the movement itself. All the variance corresponding to the large change in movement during the obstacle avoidance is confined to its own distinct subspace. Our findings suggest that M1 utilizes different activity subspaces to coordinate the maintenance of ongoing locomotor-related neural dynamics and fast volitional gait adjustments during complex locomotion.

4

Significance Statement

Our ability to modulate our ongoing walking gait with precise, voluntary adjustments is what allows us to navigate complex terrains. Locomotion and precise, goal-directed movements, such as reaching are two distinct movement modalities and have been shown to have differing requirements of motor cortical input. It is unknown how these two movements are represented in M1 low dimensional dynamics when both are carried out at the same time, such as during obstacle avoidance. We developed a novel obstacle avoidance paradigm in freely-moving non-human primates and discovered that the strategy employed by motor cortex is to confine the rhythmic locomotion-related dynamics and the voluntary, gait-adjustment movement into separate subspaces.
Exon Elongation Added Intrinsically Disordered Regions to the Encoded Proteins and Facilitated the Emergence of the Last Eukaryotic Common Ancestor
Authors: Fukuchi Satoshi , Noguchi Tamotsu , Anbo Hiroto , Homma Keiichi
Published: April 2022

Most prokaryotic proteins consist of a single structural domain (SD) with little intrinsically disordered regions (IDRs) that by themselves do not adopt stable structures, while the typical eukaryotic protein is comprised of multiple SDs and IDRs. How eukaryotic proteins evolved to differ from prokaryotic proteins has not been fully elucidated. Here, we found that the longer internal exons are, the more frequently they encode IDRs in eight eukaryotes including vertebrates, invertebrates, a fungus, and plants. Based on this observation, we propose the “small bang” model from the proteomic viewpoint: the protoeukaryotic genes had no introns and mostly encoded one SD each, but a majority of them subsequently divided into multiple exons (step 1). Many exons unconstrained by SDs elongated to encode IDRs (step 2). The elongated exons encoding IDRs frequently facilitated the acquisition of multiple SDs to make the last common ancestor of eukaryotes (step 3). One prediction of the model is that long internal exons are mostly unconstrained exons. Analytical results of the eight eukaryotes are consistent with this prediction. In support of the model, we identified cases of internal exons that elongated after the rat-mouse divergence and discovered that the expanded sections are mostly in unconstrained exons and preferentially encode IDRs. The model also predicts that SDs followed by long internal exons tend to have other SDs downstream. This prediction was also verified in all the eukaryotic species analysed. Our model accounts for the dichotomy between prokaryotic and eukaryotic proteins and proposes a selective advantage conferred by IDRs.
Neuronal nuclear calcium signaling suppression of microglial reactivity is mediated by osteoprotegerin after traumatic brain injury
Authors: Fröhlich Albrecht , Heuvel Florian olde , Rehman Rida , Krishnamurthy Sruthi Sankari , Li Shun , Li Zhenghui , Bayer David , Conquest Alison , Hagenston Anna M. , Ludolph Albert , Huber-Lang Markus , Boeckers Tobias , Knöll Bernd , Morganti-Kossmann Maria Cristina , Bading Hilmar , Roselli Francesco
Published: April 2022

Background

Traumatic Brain Injury (TBI) is characterized by massive changes in neuronal excitation, from acute excitotoxicity to chronic hyper- or hypoexcitability. Nuclear calcium signaling pathways are involved in translating changes in synaptic inputs and neuronal activity into discrete transcriptional programs which not only affect neuronal survival and synaptic integrity, but also the crosstalk between neurons and glial cells. Here we report the effects of blunting neuronal nuclear calcium signals in the context of TBI.

Methods

We used AAV vectors to express the genetically-encoded and nuclear-targeted calcium buffer parvalbumin (PV.NLS.mCherry) or the calcium/calmodulin buffer CaMBP4.mCherry in neurons only. Upon TBI, the extent of neuroinflammation, neuronal death and synaptic loss were assessed by immunohistochemistry and targeted transcriptome analysis. Modulation of the overall level of neuronal activity was achieved by PSAM/PSEM chemogenetics targeted to parvalbumin interneurons. The functional impact of neuronal nuclear Calcium buffering in TBI was assessed by quantification of spontaneous whisking.

Results

Buffering neuronal nuclear calcium unexpectedly resulted in a massive and long-lasting increase in the recruitment of reactive microglia to the injury site, which was characterised by a disease-associated and phagocytic phenotypes. This effect was accompanied by a substantial surge in synaptic loss and significantly reduced whisking activity. Transcriptome analysis revealed a complex effect of TBI in the context of neuronal nuclear calcium buffering, with upregulation of complement factors, chemokines and interferon-response genes, as well as the downregulation of synaptic genes and epigenetic regulators compared to control conditions. Notably, nuclear calcium buffering led to a substantial loss in neuronal osteoprotegerin (OPG). Whereas stimulation of neuronal firing induced OPG expression. Viral re-expression of OPG resulted in decreased microglial recruitment and synaptic loss. OPG upregulation was also observed in the CSF of human TBI patients, underscoring its translational value.

Conclusion

Neuronal nuclear calcium signals regulate the degree of microglial recruitment and reactivity upon TBI via, among others, osteoprotegerin signals. Our findings support a model whereby neuronal activity altered after TBI exerts a powerful impact on the neuroinflammatory cascade, which in turn contributes to the overall loss of synapses and functional impairment.
T cell-mediated development of stromal fibroblasts with an immune-enhancing chemokine profile
Authors: Yan Ran , Fearon Douglas T.
Published: April 2022

Stromal fibroblasts reside in inflammatory tissues that are characterized by either immune suppression or immune activation, but whether these cells adapt to these contrasting microenvironments is not known. Cancer-associated fibroblasts (CAFs) mediate immune quiescence by producing the chemokine CXCL12 that coats cancer cells to suppress T cell infiltration. We examined whether CAFs can adopt an immune-promoting chemokine profile. Single-cell RNA-sequencing of CAFs from mouse pancreatic adenocarcinomas identified a sub-population with decreased expression of CXCL12 and increased expression of the T cell-attracting chemokine, CXCL9, that was expanded when tumors were infiltrated with T cells. Conditioned media from activated CD8+ T cells containing TNFα and IFNγ converted the chemokine profile of stromal fibroblasts from a CXCL12+/CXCL9- immune suppressive phenotype into a CXCL12-/CXCL9+ immune-activating phenotype. Studies with recombinant cytokines showed that TNFα acted synergistically with IFNγ to induce CXCL9 expression, and alone was mainly responsible for suppressing CXCL12 expression. This coordinated chemokine switch demonstrates that stromal fibroblasts have a phenotypic plasticity that allow their adaptation to contrasting immune tissue microenvironments.

It is unclear whether and how stromal fibroblasts adapt and contribute to varying tissue microenvironments. This study shows immune-suppressive cancer-associated fibroblasts (CAFs) have the capacity to develop an immune-promoting chemokine profile in response to cytokines from infiltrating T cells.
Transcriptional Heterogeneity and Cell Cycle Regulation as Central Determinants of Primitive Endoderm Priming
Authors: Perera Marta , Nissen Silas B. , Proks Martin , Pozzi Sara , Monteiro Rita S. , Trusina Ala , Brickman Joshua M.
Published: April 2022

During embryonic development cells acquire identity at the same time as they are proliferating, implying that an intrinsic facet of cell fate choice requires coupling lineage decisions to rates of cell division. How is the cell cycle regulated to promote or suppress heterogeneity and differentiation? We explore this question combining time lapse imaging with single cell RNA-seq in the contexts of self-renewal, priming and differentiation of embryonic stem cells (ESCs) towards the Primitive Endoderm lineage (PrE). Since ESCs are derived from the Inner Cell Mass of the mammalian blastocyst, ESCs in standard culture conditions are transcriptionally heterogeneous containing subfractions that are primed for either of the two ICM lineages, Epiblast and PrE. These subfractions represent dynamic states that can readily interconvert in culture, and the PrE subfraction is functionally primed for endoderm differentiation. Here we find that differential regulation of cell cycle can tip the balance between these primed populations, such that naïve ESC culture conditions promote Epiblast-like expansion and PrE differentiation stimulates the selective proliferation of PrE-primed cells. In endoderm differentiation, we find that this change is accompanied by a counter-intuitive increase in G1 length that also appears replicatedin vivo. While FGF/ERK signalling is a known key regulator of ESCs and PrE differentiation, we find it is not just responsible for ESCs heterogeneity, but also cell cycle synchronisation, required for the inheritance of similar cell cycles between sisters and cousins. Taken together, our results point to a tight relationship between transcriptional heterogeneity and cell cycle regulation in the context of lineage priming, with primed cell populations providing a pool of flexible cell types that can be expanded in a lineage-specific fashion while allowing plasticity during early determination.
A sleep-active neuron can promote survival while sleep behavior is disturbed
Authors: Busack Inka , Bringmann Henrik
Published: April 2022

Sleep is controlled by neurons that induce behavioral quiescence and physiological restoration. It is not known, however, how sleep neurons link sleep behavior and survival. InCaenorhabditis elegans, the sleep-active RIS neuron induces sleep behavior and is required for survival of starvation and wounding. Sleep-active neurons such as RIS might hypothetically promote survival primarily by causing sleep behavior and associated conservation of energy. Alternatively, RIS might provide a survival benefit that does not depend on behavioral sleep. To probe these hypotheses, we tested how activity of the sleep-active RIS neuron inCaenorhabditis eleganscontrols sleep behavior and survival during larval starvation. To manipulate the activity of RIS, we expressed constitutively active potassium channel (twk-18gfandegl-23gf) or sodium channel (unc-58gf) mutant alleles in this neuron. Low levels ofunc-58gfexpression in RIS increased RIS calcium transients and sleep. High levels ofunc-58gfexpression in RIS elevated baseline calcium activity and inhibited calcium activation transients, thus locking RIS activity at a high but constant level. This manipulation caused a nearly complete loss of sleep behavior but increased survival. Long-term optogenetic activation also caused constantly elevated RIS activity and a small trend towards increased survival. Disturbing sleep by lethal blue-light stimulation also overactivated RIS, which again increased survival. FLP-11 neuropeptides were important for both, induction of sleep behavior and starvation survival, suggesting that FLP-11 might have divergent roles downstream of RIS. These results indicate that promotion of sleep behavior and survival are separable functions of RIS. These two functions may normally be coupled but can be uncoupled during conditions of strong RIS activation or when sleep behavior is impaired. Through this uncoupling, RIS can provide survival benefits under conditions when behavioral sleep is disturbed. Promoting survival in the face of impaired sleep might be a general function of sleep neurons.

Author Summary

The sleep neuron RIS inCaenorhabditis elegansis required to induce sleep behavior and to promote survival upon stress. Here we show that RIS can provide survival benefits even when sleep is disturbed.
Species-typical chemical signals mediate reproductive isolation in a teleost fish
Authors: Holland Christopher , Rosenthal Gil G.
Published: April 2022

The authors have withdrawn their manuscript because they can no longer stand by the behavioral data set and corresponding manuscript as submitted to bioRxiv. A colleague downloaded the data and noted seven instances where pairs of values were duplicated across trials for different pairs of stimuli (data set with duplicated values highlighted is available as supplementary data). While omitting these values from the data set does not qualitatively change the conclusions presented, we have no means to validate the remaining data and therefore feel the best course of action is to treat the whole dataset as invalid. Consequently, analyses and conclusions based wholly or partly on behavioral data are invalid as well. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Microglia Detect Externalized Phosphatidylserine on Synapses for Elimination via TREM2 in Alzheimer’s Disease Models
Authors: Rueda-Carrasco Javier , Sokolova Dimitra , Lee Sang-Eun , Childs Thomas , Jurčáková Natália , De Schepper Sebastiaan , Ge Judy Z. , Lachica Joanne I. , Toomey Christina E. , Freeman Oliver J. , Hardy John , Stevens Beth , Lashley Tammaryn , Chang Sunghoe , Hong Soyon
Published: April 2022

Genetic studies implicate phagocytosis pathways in microglia to be a major Alzheimer’s disease (AD)-associated process. Microglia phagocytose synapses in AD mouse models, suggesting a role for microglia in region-specific synapse loss, a pathological hallmark of AD. However, whether specific synapses are targeted for elimination, and if so, how, remains to be elucidated. Here, we show that synapses externalize phosphatidylserine (PtdSer) upon challenge by β-amyloid oligomers, which are then selectively engulfed by microglia. Mechanistically, we find that Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) is critical for microglia to sense and preferentially engulf AD synapses. In brains of mice and humans, TREM2 dysfunction leads to exacerbation of apoptotic synapses. Our work altogether suggests a fundamental role for microglia as brain-resident macrophages to remove damaged synapses in AD. We provide mechanistic insight into how TREM2 variants associated with increased risk of developing AD may contribute to defective microglia-synapse function.

One-Sentence summary

Microglia selectively engulf synapses in Alzheimer-like mouse brains via PtdSer-TREM2 signaling.
Cholinergic stimulation modulates the functional composition of CA3 cell types in the hippocampus
Authors: Puhl Christopher Jon , Wefelmeyer Winnie , Burrone Juan
Published: April 2022

The functional heterogeneity of hippocampal CA3 pyramidal neurons has emerged as a key aspect of circuit function. Here, we explored the effects of long-term cholinergic activity on the functional heterogeneity of CA3 pyramidal neurons in organotypic slices. Application of agonists to either acetylcholine receptors (AChRs) generally, or muscarinic AChRs (mAChRs) specifically, induced robust increases in network activity in the low-gamma range. Prolonged AChR stimulation for 48 hrs uncovered a population of hyperadapting CA3 pyramidal neurons that typically fired a single, early action potential in response to current injection. Although these neurons were present in control networks, their proportions were dramatically increased following long-term cholinergic activity. Characterised by the presence of a strong M-current, the hyperadaptation phenotype was abolished by acute application of either M-channel antagonists or the re-application of AChR agonists. We conclude that long-term mAChR activation modulates the intrinsic excitability of a subset of CA3 pyramidal cells, uncovering a highly plastic cohort of neurons that are sensitive to chronic ACh modulation. Our findings provide evidence for the activity-dependent plasticity of functional heterogeneity in the hippocampus.
Detection and molecular characterization of a phytoplasma associated with Cucumber (Cucumis sativus) and its first report from India
Authors: Muttappagol Mantesh , Kumar H. D. Vinay , Hiremath Shridhar , Nandan M. , Basha C. R. Jahir , Shankarappa K. S. , Venkataravanappa V. , Reddy C. N. Lakshminarayana
Published: April 2022

Cucumber (Cucumis sativus) plants exhibiting typical phyllody symptoms were collected from farmers field of Chintamani, Chickballapur districts of Karnataka (India). Disease incidence of phyllody was 2-3%. The etiology of the cucumber phyllody phytoplasma (CuPP) was confirmed by amplifying 16S rRNA gene from symptomatic plants using PCR followed by nested PCR using universal primers pairs P1/P7 and R16F2n/R16R2. After general detection the non-ribosomal SecY and rp (ribosomal protein) genes was amplified using specific primers. The PCR amplified products 16SrRNA (1.2 kb), SecY (1.6 kb) rp gene (1.2 kb) was cloned and sequenced. Sequence and phylogenetic analyses of 16S rRNA, secY and rp genes revealed that the detected phytoplasma is a member of the 16SrI group (Candidatus Phytoplasma asteris). Further on the basis of computer-simulated RFLP (= in silico RFLP) analysis of amplified F2n/R2 region of 16S rRNA gene indicates that, the detected phytoplasma was belongs to the subgroup X (16SrII-X). This is the first report on phytoplasma associated with phyllody disease of cucumber in India.
Transmembrane helices 5 and 12 control transport dynamics, substrate affinity and specificity in the elevator-type UapA transporter
Authors: Dimakis Dimitris , Pyrris Yiannis , Diallinas George
Published: April 2022

An increasing number of solute transporters have been shown to function with the so-called sliding-elevator mechanism. Despite structural and functional differences all elevator-type transporters use a common mechanism of substrate translocation via reversible movements of a mobile core domain (the elevator) hosting the substrate binding site along a rigid scaffold domain stably anchored in the plasma membrane via homodimerization. One of the best studied elevator transporters is the UapA uric acid-xanthine/H+ symporter of the filamentous fungus Aspergillus nidulans. Here, we present a novel genetic analysis for deciphering the role of transmembrane segments (TMS) 5 and 12 in UapA transport function. We show that specific residues in both TMS5 and TMS12 control, negatively or positively, the dynamics of transport, but also substrate binding affinity and specificity. More specifically, mutations in TMS5 can lead to increased rate of transport, but also to an inactive transporter due to high-affinity substrate-trapping, whereas mutations in TMS12 lead to apparently uncontrolled sliding, and thus broadened specificity and UapA-mediated purine toxicity. Our findings shed new light on how elevator transporters function or how their transport characteristics might be altered genetically or have been modified in the course of evolution.
Community adaptation to temperature explains abrupt soil bacterial community shift along a geothermal gradient on Iceland
Authors: Weedon James T. , Bååth Erland , Rijkers Ruud , Reischke Stephanie , Sigurdsson Bjarni D. , Oddsdottir Edda , van Hal Jurgen , Aerts Rien , Janssens Ivan A. , van Bodegom Peter M.
Published: April 2022

Understanding how and why soil microbial communities respond to temperature changes is important for understanding the drivers of microbial distribution and abundance. A unique area in Iceland, where soil temperatures have increased due to geothermic activity four years prior to sampling, creating a stable gradient of ambient to +40°C, allowed us to investigate the shape of the response to warming of soil bacterial communities, and their associated community temperature adaptation. We used 16S rRNA amplicon sequencing to profile bacterial communities, and bacterial growth based assays (3H Leu-incorporation) to characterize community adaptation using a temperature sensitivity index (SI, log (growth at 40°C/4°C)). Samples were taken from ≥9 levels of warming (covering almost up to +40°C above ambient soil temperature), under both grassland (Agrostis capillaris) and forest (Picea sitchensis) vegetation. The soils had very different community composition, but temperature adaptation was the same. Both diversity and community composition as well SI showed similar threshold dynamics along the soil temperature gradient. There were no significant changes up to soil warming of approx. 6-9 °C, beyond which all indices shifted in parallel. The consistency of these responses gives strong support for a decisive role for direct temperature effects in driving bacterial community shifts along soil temperature gradients.
Prey resources are more important than climatic conditions for predicting the distribution of a broad-ranged apex predator
Authors: Sutton Luke J. , Anderson David L. , Franco Miguel , McClure Christopher J.W. , Miranda Everton B.P. , Vargas F. Hernán , de Vargas González José J. , Puschendorf Robert
Published: April 2022

A current biogeographic paradigm states that climate regulates species distributions at continental scales and that biotic interactions are undetectable at coarse-grain extents. However, recent advances in spatial modelling show that incorporating food resource distributions are important for improving model predictions at large distribution scales. This is particularly relevant to understand the factors limiting distribution of widespread apex predators whose diets are likely to vary across their range. The harpy eagle (Harpia harpyja) is a large raptor, whose diet is largely comprised of arboreal mammals, such as sloths and primates, all with broad distributions across Neotropical lowland forest. Here, we used a hierarchical modelling approach to determine the relative importance of abiotic factors and prey resource distribution on harpy eagle range limits. Our hierarchical approach consisted of the following modelling sequence of explanatory variables: (a) abiotic covariates, (b) prey resource distributions predicted by an equivalent modelling for each prey, (c) the combination of (a) and (b), and (d) as in (c) but with prey resources considered as a single prediction equivalent to prey species richness. Incorporating prey distributions improved model predictions but using solely these biotic covariates still resulted in a high performing model. In the Abiotic model, Climatic Moisture Index (CMI) was the most important predictor, contributing 80 % to model prediction. Three-toed sloth (Bradypus spp.) was the most important prey resource, contributing 57 % in a combined Abiotic-Biotic model, followed by CMI contributing 29 %. Harpy eagle distribution had moderate to high environmental overlap across all prey distributions in geographic space when measured individually, but overlap was substantially lower in environmental space when prey distributions were combined. With strong reliance on prey distributions across its range, harpy eagle conservation programs must therefore consider its most important food resources as a key element in the protection of this threatened raptor.