bluuebunny/crossref_metadata_2025 huggingface dataset:
Kilometer-scale larval dispersal processes predict metapopulation connectivity pathways for Paramuricea biscaya in the northern Gulf of Mexico
Authors: Liu Guangpeng , Bracco Annalisa , Quattrini Andrea M. , Herrera Santiago
Published: October 2021

Fine-scale larval dispersal and connectivity processes are key to species survival, growth, recovery and adaptation under rapidly changing disturbances. Quantifying both are required to develop any effective management strategy. In the present work, we examine the dispersal pattern and potential connectivity of a common deep-water coral, Paramuricea biscaya, found in the northern Gulf of Mexico by evaluating predictions of physical models with estimates of genetic connectivity. While genetic approaches provide estimates of realized connectivity, they do not provide information on the dispersal process. Physical circulation models can now achieve kilometer-scale resolution sufficient to provide detailed insight into the pathways and scales of larval dispersal. A high-resolution regional ocean circulation model is integrated for 2015 and its advective pathways are compared with the outcome of the genetic connectivity estimates of corals collected at six locations over the continental slope at depths comprised between 1000 and 3000 meters. Furthermore, the likely interannual variability is extrapolated using ocean hindcasts available for this basin. The general connectivity pattern exhibits a dispersal trend from east to west following 1000 to 2000-meter isobaths, corresponding to the overall westward near-bottom circulation. The connectivity networks predicted by our model were mostly congruent with the estimated genetic connectivity patterns. Our results show that although dispersal distances of 100 km or less are common, depth differences between tens to a few hundred meters can effectively limit larval dispersal. A probabilistic graphic model suggests that stepping-stone dispersal mediated by intermediate sites provides a likely mechanism for long-distance connectivity between the populations separated by distances of 300 km or greater, such as those found in the DeSoto and Keathley canyons.
Identification of sex chromosomes using genomic and cytogenetic methods in a range-expanding spider, Argiope bruennichi (Araneae: Araneidae)
Authors: Sheffer Monica M , Cordellier Mathilde M , Forman Martin , Grewoldt Malte , Hoffmann Katharina , Jensen Corinna , Kotz Matěj , Král Jiří , Kuss Andreas W , Líznarová Eva , Uhl Gabriele
Published: October 2021

Differences between sexes in growth, ecology and behavior strongly shape species biology. In some animal groups, such as spiders, it is difficult or impossible to identify the sex of juveniles based on external morphology. This information would be useful for field surveys, behavioral experiments, and ecological studies on e.g. sex ratios and dispersal. In species with sex chromosomes, sex can be determined based on the specific sex chromosome complement. Additionally, information on the sequence of sex chromosomes provides the basis for studying sex chromosome evolution. We combined cytogenetic and genomic data to identify the sex chromosomes in the sexually dimorphic spider Argiope bruennichi, and designed RT-qPCR sex markers. We found that genome size and GC content of this spider falls into the range reported for the majority of araneids. The male karyotype is formed by 24 acrocentric chromosomes with an X1X20 sex chromosome system, with little similarity between X chromosomes, suggesting origin of these chromosomes by X chromosome fission or early duplication of an X chromosome and subsequent independent differentiation of the copies. Our data suggest similarly sized X chromosomes in A. bruennichi. They are smaller chromosomes of the complement. Our findings open the door to new directions in spider evolutionary and ecological research.
Software choice and depth of sequence coverage can impact plastid genome assembly – A case study in the narrow endemic Calligonum bakuense
Authors: Giorgashvili Eka , Reichel Katja , Caswara Calvinna , Kerimov Vuqar , Borsch Thomas , Gruenstaeudl Michael
Published: October 2021

Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequence coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense, which forms a distinct lineage in the genus Calligonum. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequence coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and three levels of sequence coverage (original depth, 2,000x, and 500x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic tree inference is also assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produced the most consistent assemblies for C. bakuense. Moreover, we found that a cap in sequence coverage can reduce both the sequence variability across assembly contigs and computation time. While no evidence was found that the sequence variability across assemblies was large enough to affect the phylogenetic position inferred for C. bakuense, differences among the assemblies may influence genotype recognition at the population level.
Range contractions of the Broad-winged Hawk in the Northeast United States
Authors: Pruitt Rachael , Goodrich Laurie , Shumar Matthew B. , Wilson Andrew M.
Published: October 2021

The Broad-winged Hawk (BWHA,Buteo platypterus)is a small, secretive hawk with distinguishing broad black tail bands that breeds in northeastern North America. The hawk nests in deciduous or mixed forest, often near water, and close to clearings or forest edges. Land conversion and fragmentation alters the landscape and reduces the area of contiguous forest used by BWHA. This study seeks to determine the landscape characteristics influencing the apparent breeding range declines of the BWHA at the landscape scale. Landscape characteristics and BWHA presence data from 18,684 Breeding Bird Atlas blocks (each about 25km2) from Ohio, West Virginia, Maryland, Pennsylvania, and New York for two atlas period (1st Atlas: 1980s, 2nd Atlas: 2000s) were analyzed. Bayesian latent Gaussian models were fitted using INLA to determine best fit model for predicting the landscape characteristics associated with BWHA presence. The best models included landscape changes in land cover, including forest, water, urban, barren, farmland, and wetland and fragmentation of the landscape. Trends in loss were especially prevalent around the region’s largest cities: New York, Philadelphia, Baltimore and Washington DC. Loss of BWHA at the block-level was associated with areas with less forest in the 2000s, a decline in size of largest forest patches, lower elevations and lower latitudes. We suggest that both habitat loss and climate change may be contributing to the range contraction of the Broad-winged Hawk in the northeast United States.
The endemic plant species of Bali Ngemba Forest Reserve, Bamenda Highlands Cameroon, with a new Endangered cloud-forest tree speciesVepris onanae(Rutaceae)
Authors: Cheek Martin , Hatt Sebastian , Onana Jean Michel
Published: October 2021

We revise and update the records of strict and near-endemic species of the Bali Ngemba Forest Reserve, the largest known surviving patch (c. 8 km2in area) of submontane or cloud forest in the Bamenda Highlands, Cameroon which have lost >96 % of their original forest due to human activities. Nine strict endemics, and 11 near endemics are now documented, a drop from the number recorded after the first survey in 2004, since when five of the provisionally named species have been formally published.

We test the hypothesis that a further one of the provisionally named putative Bali Ngemba new species,Veprissp. A, an 8 – 20 m tall tree from cloud forest in the 1310 – 1600 m altitudinal band, is indeed new to science. We compare it morphologically with other multicarpellate, apocarpous, trifoliolate Cameroon tree species formerly placed in the genusOriciaPierre until they were subsumed intoVeprisby Mziray (1992). These areVepris trifoliolata(Engl.) Mziray andV. gabonensis(Pierre) Mziray. We conclude thatVeprissp. A is a new undescribed species here named asVepris onanae. The new species is illustrated, mapped and its conservation status assessed as Endangered using the 2012 IUCN standard due to the threats of habitat clearance from agricultural pressures at its three locations all of which remain formally unprotected.

Vepris onanaeappears unique among the Guineo-Congolian African oricioid species ofVeprisin occurring in cloud forest, the other species, apart fromV. renieriiof the Albertine Rift, occurring in lowland forest. It also differs in the very broad, (7.8 –) 11.3 – 18 cm wide leaflets of the flowering stems which have a 6-18(−30) mm long, narrowly triangular acumen (vs leaflets <12 cm wide, acumen absent or short) and in having both subsessile and pedicellate (pedicels 0.25 – 0.3 mm long and 1(– 2) mm long) male flowers (vs male flower pedicels all sessile, or all c. 3 mm long).

We report for the first time on stage-dependent leaf heteromorphy inVeprisand characterise a level of sexual dimorphism more advanced than usual in the genus.

We highlight the importance of protecting Bali Ngemba and other forest patches in the Bamenda Highlands if species such asVepris onanaeare not soon to become extinct.
Automated Optimization of Residual Reduction Algorithm Parameters in Opensim
Authors: Sturdy Jordan T. , Silverman Anne K. , Pickle Nathan T.
Published: October 2021

The residual reduction algorithm (RRA) in OpenSim is designed to improve dynamic consistency of kinematics and ground reaction forces in movement simulations of musculoskeletal models. RRA requires the user to select numerous tracking weights for the joint kinematics to reduce residual errors. Selection is often performed manually, which can be time-consuming and is unlikely to yield optimal tracking weights. A multi-heuristic optimization algorithm was used to expedite tracking weight decision making to reduce residual errors. This method produced more rigorous results than manual iterations and although the total computation time was not significantly reduced, this method does not require the user to monitor the algorithm’s progress to find a solution, thereby reducing manual tuning. Supporting documentation and code to implement this optimization is freely provided to assist the community with developing movement simulations.
Auto-encoded Latent Representations of White Matter Streamlines for Quantitative Distance Analysis
Authors: Zhong Shenjun , Chen Zhaolin , Egan Gary
Published: October 2021

Parcellation of whole brain tractograms is a critical step to study brain white matter structures and connectivity patterns. The existing methods based on supervised classification of streamlines into predefined streamline bundle types are not designed to explore sub-bundle structures, and methods with manually designed features are expensive to compute streamline-wise similarities. To resolve these issues, we propose a novel atlas-free method that learns a latent space using a deep recurrent auto-encoder. The method efficiently embeds any length of streamlines to fixed-size feature vectors, named streamline embedding, for tractogram parcellation using unsupervised clustering in the latent space. The method was evaluated on the ISMRM 2015 tractography challenge dataset with discrimination of major bundles using unsupervised clustering and streamline querying based on similarity. The learnt latent streamline and bundle representations open the possibility of quantitative studies of arbitrary granularity of sub-bundle structures using generic data mining techniques.
Cervicovaginal microbiota predicts Neisseria gonorrhoeae clinical presentation
Authors: Lovett Angela , Seña Arlene C. , Macintyre Andrew N. , Sempowski Gregory D. , Duncan Joseph A. , Waltmann Andreea
Published: October 2021

Neisseria gonorrhoeae infection of the female lower genital tract can present with a spectrum of phenotypes ranging from asymptomatic carriage to symptomatic cervical inflammation, or cervicitis. The factors that contribute to the development of asymptomatic or symptomatic infections are largely uncharacterized. We conducted a pilot study to assess differences in the cervicovaginal microbial community of patients presenting with symptomatic vs. asymptomatic N. gonorrhoeae infections to a sexually transmitted infections (STI) clinic. DNA was isolated from cervicovaginal swab specimens from women who tested positive for N. gonorrhoeae infection using a clinical diagnostic nucleic acid amplification test. We performed deep sequencing of 16S ribosomal RNA gene amplicons, followed by microbiome analyses with QIIME, and species-specific real-time PCR to assess the composition of microbial communities cohabitating the lower genital tract with the infecting N. gonorrhoeae. Specimens collected from asymptomatic individuals with N. gonorrhoeae infection and no co-infection with Chlamydia trachomatis and/or Trichomonas vaginalis carried Lactobacillus-dominant microbial communities more frequently than symptomatic patients without co-infection. When compared to asymptomatic individuals, symptomatic women had microbial communities characterized by more diverse and heterogenous bacterial taxa, typically associated with bacterial vaginosis (BV) (Prevotella, Sneathia, Mycoplasma hominis and Bacterial Vaginosis-Associated Bacterium-1 (BVAB1)/”Candidatus Lachnocurva vaginae). Both symptomatic and asymptomatic N. gonorrhoeae patients with additional STI co-infection displayed a BV-like microbial community. We used a murine model of N. gonorrhoeae infection in mice pre-colonized with Lactobacillus crispatus to test whether pre-existing L. crispatus was protective from N. gonorrhoeae colonization or whether N. gonorrhoeae infection could drive the loss of L. crispatus during infection. Vaginal infection with either N. gonorrhoeae strain 1291 or an isogenic mutant known to exhibit lower inflammatory had no impact on Lactobacillus burden recovered from the mice. These data taken together suggest that Lactobacillus-dominant vaginal microbial community may protect individuals from developing symptoms during lower genital tract infection with N. gonorrhoeae.
Exo-enzymatic addition of diazirine-modified sialic acid to cell surfaces enables photocrosslinking of glycoproteins
Authors: Yarravarapu Nageswari , Reddy Konada Rohit Sai , Darabedian Narek , Pedowitz Nichole J. , Krishnamurthy Soumya N. , Pratt Matthew R. , Kohler Jennifer J.
Published: October 2021

Glycan binding often mediates extracellular macromolecular recognition events. Accurate characterization of these binding interactions can be difficult because of dissociation and scrambling that occur during purification and analysis steps. Use of photocrosslinking methods has been pursued to covalently capture glycan-dependent interactionsin situhowever use of metabolic glycan engineering methods to incorporate photocrosslinking sugar analogs is limited to certain cell types. Here we report an exo-enzymatic labeling method to add a diazirine-modified sialic acid (SiaDAz) to cell surface glycoconjugates. The method involves chemoenzymatic synthesis of diazirine-modified CMP-sialic acid (CMP-SiaDAz), followed by sialyltransferase-catalyzed addition of SiaDAz to desialylated cell surfaces. Cell surface SiaDAz-ylation is compatible with multiple cell types and is facilitated by endogenous extracellular sialyltransferase activity present in Daudi B cells. This method for extracellular addition of α2-6-linked SiaDAz enables UV-induced crosslinking of CD22, demonstrating the utility for covalent capture of glycan-mediated binding interactions.
Identification of Key Ischemic Stroke Genes by Computational Systems Biology
Authors: Yue Rongting , Dutta Abhishek
Published: October 2021

Stroke is one of the leading causes of death in humans. Even if patients survive from stroke, they may suffer sequelae such as disability. Treatment for strokes remains unsatisfactory due to an incomplete understanding of its mechanisms. This study investigates Ischemic Stroke (IS), a primary subtype of stroke, through analyses based on microarray data. Limma (in R)derives differentially expressed genes, and the protein-protein interaction (PPI) network is mapped from the database. Gene co-expression patterns are obtained for clustering gene modules by the Weighted Correlation Network Analysis (WGCNA), and genes with high connectivity in the significantly co-expressed modules are selected as key regulators. Common hubs are identified as Cdkn1a, Nes and Anxa2. Based on our analyses, we hypothesize that these hubs might play a key role in the onset and progression of IS. Result suggests the potential of identifying unexplored key regulators by the systemic method used in this work. Further analyses aim at expanding candidate genes for screening biomarkers for IS, and experimental validation is required on identified potential hubs.
Comparison Between Lotka-Volterra and Multivariate Autoregressive Models of Ecological Interaction Systems
Authors: Olivença Daniel V. , Davis Jacob D. , Voit Eberhard O.
Published: October 2021

Lotka-Volterra (LV) and Multivariate Autoregressive (MAR) models are computational frameworks with different mathematical structures that have both been proposed for the same purpose of extracting governing features of dynamic interactions among coexisting populations of different species from observed time series data.

We systematically compare the feasibility of the two modeling approaches, using four synthetically generated datasets and seven ecological datasets from the literature.

The overarching result is that LV models outperform MAR models in most cases and are generally superior for representing cases where the dependent variables deviate greatly from their steady states. A large dynamic range is particularly prevalent when the populations are highly abundant, change considerably over time, and exhibit a large signal-to-noise ratio. By contrast, MAR models are better suited for analyses of populations with low abundances and for investigations where the quantification of noise is important.

We conclude that the choice of either one or the other modeling framework should be guided by the specific goals of the analysis and the dynamic features of the data.

Availability of algorithms used

https://github.com/LBSA-VoitLab/Comparison-Between-LV-and-MAR-Models-of-Ecological-Interaction-Systems
Multi-omics analysis of multiple glucose-sensing receptor systems in yeast
Authors: Li Shuang , Li Yuanyuan , Rushing Blake R. , Harris Sarah E. , McRitchie Susan L. , Dominguez Daniel , Sumner Susan J. , Dohlman Henrik G.
Published: October 2021

The yeast Saccharomyces cerevisiae has long been used to produce alcohol from glucose and other sugars. While much is known about glucose metabolism, relatively little is known about the receptors and signaling pathways that indicate glucose availability. Here we compare the two glucose receptor systems in S. cerevisiae. The first is a heterodimer of transporter-like proteins (transceptors), while the second is a seven-transmembrane receptor coupled to a large G protein (Gpa2) and two small G proteins (Ras1 and Ras2). Through comprehensive measurements of glucose-dependent transcription and metabolism, we demonstrate that the two receptor systems have distinct roles in glucose signaling: the G protein-coupled receptor directs carbohydrate and energy metabolism, while the transceptors regulate ancillary processes such as ribosome, amino acids, cofactor and vitamin metabolism. The large G protein transmits the signal from its cognate receptor, while the small G protein Ras2 (but not Ras1) integrates responses from both receptor pathways. Collectively, our analysis reveals the molecular basis for glucose detection and the earliest events of glucose-dependent signal transduction in yeast.
Txn1 mutation causes epilepsy associated with vacuolar degeneration in the midbrain
Authors: Ohmori Iori , Ouchida Mamoru , Imai Hirohiko , Ishida Saeko , Toyokuni Shinya , Mashimo Tomoji
Published: October 2021

Thioredoxin (TXN), encoded by Txn1, acts as a critical antioxidant in the defense against oxidative stress by regulating the dithiol/disulfide balance of interacting proteins. The role of TXN in the central nervous system (CNS) is largely unknown. A phenotype-driven study of N-ethyl-N-nitrosourea-mutated rats with running seizures at around five-week of age revealed the relevance of Txn1 mutations to CNS disorders. Genetic mapping identified Txn1-F54L in epileptic rats. The insulin-reducing activity of Txn1-F54L rats was approximately one-third that of the wild-type. Vacuolar degeneration in the midbrain, mainly in the thalamus and the inferior colliculus, was observed in the Txn1-F54L rats. The lesions displayed neuronal and oligodendrocyte cell death. Neurons in Txn1-F54L rats showed morphological changes in the mitochondria. Vacuolar degeneration began at three weeks of age, and spontaneous repair began at seven weeks; a dramatic change from cell death to repair occurred in the midbrain during a restricted period. In conclusion, Txn1 is essential for the development of the midbrain in juvenile rats.
Assessing the Live Decellularized Renal Microvasculature Post-Transplantation Using Intravital Microscopy
Authors: Corridon Peter R. , Khan Anousha A.
Published: October 2021

Transplantation is the ideal solution for end-stage renal failure, but the growing mismatch between organ supply and demand accentuates the need for alternative solutions like the bioartificial kidney. Several approaches to developing this technology have been demonstrated, and whole organ decellularization appears to be a promising methodology. One major challenge to this strategy is maintaining vascular integrity and functionality post-transplantation. Most models to examine the microvasculature have primarily utilized in vitro or in vivo techniques that are incapable of providing adequate spatial and temporal resolution. Here, we show that decellularized scaffolds orthotopically transplanted into rats initially retain microvascular structure in vivo using intravital two-photon microscopy, as previously identified in vitro. Large molecular weight dextran molecules also provide real-time evidence of the onset of ischemia and increases in microvascular permeability, support substantial translocation of dextran macromolecules from glomerular and peritubular capillary tracks as early as 12 hours after transplantation. Macromolecular extravasation continued across a week, at which time the decellularized microarchitecture was significantly compromised. These results indicate that a in vivo method capable of tracking microvascular integrity represents a powerful interdisciplinary approach for studying scaffold viability and identifying ways to promote scaffold longevity and angiogenesis in bioartificial organs.
CircHIPK3 dysregulation of the miR-30c/DLL4 axis is essential for KSHV lytic replication
Authors: Harper Katherine L. , Mottram Timothy J. , Anene Chinedu A. , Foster Becky , Patterson Molly R. , McDonnell Euan , Macdonald Andrew , Westhead David , Whitehouse Adrian
Published: October 2021

Non-coding RNA (ncRNA) regulatory networks are emerging as critical regulators of gene expression. These intricate networks of ncRNA:ncRNA interactions modulate multiple cellular pathways and impact the development and progression of multiple diseases. Herpesviruses, including Kaposi’s sarcoma-associated herpesvirus, are adept at utilising ncRNAs, encoding their own as well as dysregulating host ncRNAs to modulate virus gene expression and the host response to infection. Research has mainly focused on unidirectional ncRNA-mediated regulation of target protein-coding transcripts; however, we have identified a novel host ncRNA regulatory network essential for KSHV lytic replication in B cells. KSHV-mediated upregulation of the host cell circRNA, circHIPK3, is a key component of this network, functioning as a competing endogenous RNA of miR-30c, leading to increased levels of the miR-30c target, DLL4. Dysregulation of this network highlights a novel mechanism of cell cycle control during KSHV lytic replication in B cells. Importantly, disruption at any point within this novel ncRNA regulatory network has a detrimental effect on KSHV lytic replication, highlighting the essential nature of this network and potential for therapeutic intervention.
Transgenic Drosophila lines for LexA-dependent gene and growth regulation
Authors: Chang Kathleen R. , Tsao Deborah D. , Bennett Celine , Wang Elaine , Floyd Jax F. , Tay Ashley S.Y. , Greenwald Emily , Kim Ella S. , Griffin Catherine , Morse Elizabeth , Chisholm Townley , Rankin Anne E. , Baena-Lopez Alberto , Lantz Nicole , Fox Elizabeth , Kockel Lutz , Kim Seung K. , Park Sangbin
Published: October 2021

Conditional expression of short hairpin RNAs (shRNAs) with binary genetic systems is an indispensable tool for studying gene function. Addressing mechanisms underlying cell-cell communication in vivo benefits from simultaneous use of two independent gene expression systems. To complement the abundance of existing Gal4/UAS-based resources in Drosophila, we and others have developed LexA/LexAop-based genetic tools. Here, we describe experimental and pedagogical advances that promote the efficient conversion of Drosophila Gal4 lines to LexA lines, and the generation of LexAop-shRNA lines to suppress gene function. We developed a CRISPR/Cas9-based knock-in system to replace Gal4 coding sequences with LexA, and a LexAop-based shRNA expression vector to achieve shRNA-mediated gene silencing. We demonstrate the use of these approaches to achieve targeted genetic loss-of-function in multiple tissues. We also detail our development of secondary school curricula that enable students to create transgenic flies, thereby magnifying the production of well-characterized LexA/LexAop lines for the scientific community. The genetic tools and teaching methods presented here provide LexA/LexAop resources that complement existing resources to study intercellular communication coordinating metazoan physiology and development.
Growth and development of trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata) reflects locomotor behavior, life-history, and neuromuscular development
Authors: Saers Jaap P.P. , Gordon Adam D. , Ryan Timothy M. , Stock Jay T.
Published: October 2021

We aim to broaden the analysis of bone structure by suggesting a new way to incorporate the interactions between behavior, neuromuscular development, and life-history. We examine the associations between these variables and age-related variation in trabecular structure in the calcaneus of Japanese macaques (Macaca fuscata). If skeletal markers linking these variables can be established, our inferences of the biology and behavior of fossil species would be significantly improved. We µCT scanned the calcaneus in a cross-sectional sample of 36 juveniles aged between 0 and 7 years old and 5 adults at the Primate Research Institute, Japan. We calculated whole bone averages of standard trabecular properties and generated whole-bone morphometric maps of bone volume fraction and Young’s modulus. Trabecular structure is increasingly heterogeneous in older individuals. BV/TV decreases during the first month of life and increases afterwards, coinciding with the onset of independent locomotion. At birth, primary Young’s modulus is oriented orthogonal to the ossification center, but after locomotor onset bone structure becomes stiffest in the direction of joint surfaces and muscle attachments. Age-related variation in bone volume fraction is best predicted by an interaction between neuromaturation, body mass, and locomotor independence. Results support the common assumption that trabecular structure dynamically adapts to novel joint loading conditions during ontogeny. The timing of independent locomotion, body size, and neuromuscular development, are all correlated to age-related variation in the trabecular structure of the macaque calcaneus. The causal mechanisms behind the observed patterns cannot be directly inferred from our cross-sectional study. If the model presented in this paper holds up under longitudinal experimental conditions, trabecular structure can be used both to infer behavior from fossil morphology and to serve as a valuable proxy for neuromuscular maturation and life history events like locomotor onset and the achievement of an adult-like gait.
Regulation of Nav1.6-mediated sodium currents underlie the homeostatic control of neuronal intrinsic excitability in the optic tectum of the developingXenopus laevistadpole
Authors: Thompson Adrian C. , Aizenman Carlos D.
Published: October 2021

For individual neurons to function appropriately within a network that is undergoing synaptic reorganization and refinement due to developmental or experience-dependent changes in circuit activity, they must homeostatically adapt their intrinsic excitability to maintain a consistent output despite the changing levels of synaptic input. This homeostatic plasticity of excitability is particularly important for the development of sensory circuits, where subtle deficits in neuronal and circuit function cause developmental disorders including autism spectrum disorder and epilepsy. Despite the critical importance of this process for normal circuit development, the molecular mechanism by which this homeostatic control of intrinsic excitability is regulated is not fully understood. Here, we demonstrate thatXenopusoptic tectal neurons express distinct fast, persistent and resurgent Na+currents. Here, we demonstrate thatXenopusoptic tectal neurons express distinct fast, persistent and resurgent Na+currents. These are regulated with developmental changes in synaptic input, and homeostatically in response to changes in visual input. We show that expression of the voltage-gated Na+channel subtype Nav1.6 is regulated with changes in intrinsic excitability, that blocking Nav1.6 channels is sufficient to decrease intrinsic excitability. Furthermore, that upregulation of Nav1.6 expression is necessary for experience-dependent increases in Na+currents and intrinsic excitability. Finally, by examining behaviors that rely on visual and multisensory integration, we extend these findings to show that tight regulation of Na+channel gene expression during a critical period of tectal circuit development is required for the normal functional development of the tectal circuitry.
Molecular rhythm alterations in prefrontal cortex and nucleus accumbens associated with opioid use disorder
Authors: Xue Xiangning , Zong Wei , Glausier Jill R. , Kim Sam-Moon , Shelton Micah A. , Phan BaDoi N. , Srinivasan Chaitanya , Pfenning Andreas R. , Tseng George C. , Lewis David A. , Seney Marianne L. , Logan Ryan W.
Published: October 2021

Severe and persistent disruptions to sleep and circadian rhythms are common features of people with opioid use disorder (OUD). Preclinical findings suggest altered molecular rhythms in the brain are involved in opioid reward and dependence. However, whether molecular rhythms are disrupted in brains of people with OUD remained an open question, critical to understanding the role of circadian rhythms in opioid addiction. We previously used subjects’ times of death (TOD) as a marker of time of day to investigate transcriptional rhythm alterations in psychiatric disorders. Using TOD and RNA sequencing, we discovered rhythmic transcripts in both the dorsolateral prefrontal cortex (DLPFC) and nucleus accumbens (NAc), key brain areas involved in opioid addiction, were largely distinct between OUD and unaffected comparison subjects. Further, fewer rhythmic transcripts were identified in DLPFC of OUD subjects compared to unaffected subjects, but nearly double the number of rhythmic transcripts were found in the NAc of OUD subjects. In OUD, rhythmic transcripts in the NAc peaked either in the evening or near sunrise, and were associated with dopamine, opioid, and GABAergic neurotransmission. Co-expression network analysis identified several OUD-specific modules in the NAc, enriched for transcripts involved in the modulation of dopamine and GABA synapses, including glutamatergic signaling and extracellular matrices. Integrative analyses with human GWAS revealed that rhythmic transcripts in DLPFC and NAc were enriched for genomic loci associated with sleep duration and insomnia. Overall, our results connect transcriptional rhythm changes in dopamine, opioid, and GABAergic synaptic signaling in human brain to sleep-related phenotypes and OUD.
Single-cell analysis of basal cell carcinoma reveals heat shock proteins promote tumor growth in response to WNT5A-mediated inflammatory signals
Authors: Guerrero-Juarez Christian F. , Lee Gun Ho , Liu Yingzi , Wang Shuxiong , Sha Yutong , Chow Rachel Y. , Nguyen Tuyen T.L. , Aasi Sumaira , Karikomi Matthew , Drummond Michael L. , Nie Qing , Sarin Kavita , Atwood Scott X.
Published: October 2021

How basal cell carcinoma (BCC) interacts with its tumor microenvironment to promote growth is unclear. Here we use singe-cell RNA sequencing to define the human BCC ecosystem and discriminate between normal and malignant epithelial cells. We identify spatial biomarkers of both tumors and their surrounding stroma that reinforce the heterogeneity of each tissue type. Combining pseudotime, RNA velocity, cellular entropy, and regulon analysis in stromal cells reveal a cancer-specific rewiring of fibroblasts where STAT1, TGF-β, and inflammatory signals induce a non-canonical WNT5A program that maintains the stromal inflammatory state. Cell-cell communication modeling suggests that tumors respond to the sudden burst of fibroblast-specific inflammatory signaling pathways by producing heat shock proteins, which we validatedin situ. Finally, dose-dependent treatment with an HSP70 inhibitor suppressesin vitroBCC cell growth and Hedgehog signaling andin vivotumor growth in a BCC mouse model, validating HSP70’s essential role in tumor growth and reinforcing the critical nature of tumor microenvironment crosstalk in BCC progression.
Infection-induced miR-126 suppresses tsc1- and cxcl12a-dependent permissive macrophages during mycobacterial infection
Authors: Wright Kathryn , de Silva Kumudika , Plain Karren M. , Purdie Auriol C. , Britton Warwick J. , Oehlers Stefan H.
Published: October 2021

Regulation of host microRNA (miRNA) expression is a contested node that controls the host immune response to mycobacterial infection. The host must overcome concerted subversive efforts of pathogenic mycobacteria to launch and maintain a protective immune response. Here we examine the role of miR-126 in the zebrafish model of Mycobacterium marinum infection and identify a protective role for this infection-induced miRNA through multiple effector pathways. Specifically, we analyse the impact of the miR-126 knockdown-induced tsc1a and cxcl12a/ccl2/ccr2 signalling axes during early host-M. marinum interactions. We find a strong detrimental effect of tsc1a upregulation that renders zebrafish embryos susceptible to higher bacterial burden and increased cell death despite dramatically higher recruitment of macrophages to the site of infection. We demonstrate that infection-induced miR-126 suppresses tsc1 and cxcl12a expression thus improving macrophage function early in infection, partially through activation of mTOR signalling and strongly through preventing the recruitment of Ccr2+ permissive macrophages, resulting in the recruitment of protective tnfa-expressing macrophages. Together our results demonstrate an important role for infection-induced miR-126 in shaping an effective immune response to M. marinum infection in zebrafish embryos.
VIP interneurons in mouse whisker S1 exhibit sensory and action-related signals during goal-directed behavior
Authors: Ramamurthy Deepa L. , Chen Andrew , Huang Patrick C. , Bharghavan Priyanka , Krishna Gayathri , Casale Kayla , Feldman Daniel E.
Published: October 2021

Vasoactive intestinal peptide-expressing (VIP) interneurons, which constitute 10-15% of the cortical inhibitory neuron population1,2, have emerged as an important cell type for regulating excitatory cell activity based on behavioral state. VIP cells in sensory cortex are potently engaged by neuromodulatory and motor inputs during active exploratory behaviors like locomotion and whisking, which in turn promote pyramidal cell firing via disinhibition3-5. Such state-dependent modulation of activity by VIP cells in sensory cortex has been studied widely in recent years. However, the function of VIP cells during goal-directed behavior is less well understood. It is not clear how task-related events like sensory stimuli, motor actions, or reward activate VIP cells in sensory cortex since there is often temporal overlap in the occurrence of these events. We developed a Go/NoGo whisker touch detection task which incorporates a post-stimulus delay period to separate sensory-driven activity from action- or reward-related activity during behavior. We used 2-photon calcium imaging to measure task-related signals of L2/3 VIP neurons in S1 of behaving mice. We report for the first time that VIP cells in mouse whisker S1 are activated by both whisker stimuli and goal-directed licking. Whisker- and lick-related signals were spatially organized in relation to anatomical columns in S1. Sensory responses of VIP cells were tuned to specific whiskers, whether or not they also displayed lick-related activity.
Gut Bacterial Dysbiosis and Instability is Associated with the Onset of Complications and Mortality in COVID-19
Authors: Schult David , Reitmeier Sandra , Koyumdzhieva Plamena , Lahmer Tobias , Middelhoff Moritz , Erber Johanna , Schneider Jochen , Kager Juliane , Frolova Marina , Horstmann Julia , Fricke Lisa , Steiger Katja , Jesinghaus Moritz , Janssen Klaus-Peter , Protzer Ulrike , Neuhaus Klaus , Schmid Roland M. , Haller Dirk , Quante Michael
Published: October 2021

Objective

There is a growing debate about the involvement of the gut microbiome in COVID-19, although it is not conclusively understood whether the microbiome has an impact on COVID-19, or vice versa, especially as analysis of amplicon data in hospitalized patients requires sophisticated cohort recruitment and integration of clinical parameters. Here, we analyzed fecal and saliva samples from SARS-CoV-2 infected and post COVID-19 patients and controls considering multiple influencing factors during hospitalization.

Design

16S rRNA gene sequencing was performed on fecal and saliva samples from 108 COVID-19 and 22 post COVID-19 patients, 20 pneumonia controls and 26 asymptomatic controls. Patients were recruited over the first and second corona wave in Germany and detailed clinical parameters were considered. Serial samples per individual allowed intra-individual analysis.

Results

We found the gut and oral microbiota to be altered depending on number and type of COVID-19-associated complications and disease severity. The occurrence of individual complications was correlated with low-risk (e.g., Faecalibacterium prausznitzii) and high-risk bacteria (e.g., Parabacteroides). We demonstrated that a stable gut bacterial composition was associated with a favorable disease progression. Based on gut microbial profiles, we identified a model to estimate mortality in COVID-19.

Conclusion

Gut microbiota are associated with the occurrence of complications in COVID-19 and may thereby influencing disease severity. A stable gut microbial composition may contribute to a favorable disease progression and using bacterial signatures to estimate mortality could contribute to diagnostic approaches. Importantly, we highlight challenges in the analysis of microbial data in the context of hospitalization.
A mechanobiological model for tumor spheroids evolution: application to glioblastoma
Authors: Carrasco-Mantis Ana , Castro-Abril Héctor , Randelovic Teodora , Ochoa Ignacio , Doblaré Manuel , Sanz-Herrera José A.
Published: October 2021

Spheroids are in vitro spherical structures of cell aggregates, eventually cultured within a hydrogel matrix, that are used, among other applications, as a technological platform to investigate tumor formation and evolution. Several interesting features can be replicated using this methodology, such as cell communication mechanisms, the effect of gradients of nutrients, or the creation of realistic 3D biological structures. In this paper, we propose a continuum mechanobiological model which accounts for the most relevant phenomena that take place in tumor spheroids evolution under in vitro suspension, namely, nutrients diffusion in the spheroid, kinetics of cellular growth and death, and mechanical interactions among the cells. The model is qualitatively validated, after calibration of the model parameters, versus in vitro experiments of spheroids of different glioblastoma cell lines. This preliminary validation allowed us to conclude that glioblastoma tumor spheroids evolution is mainly driven by mechanical interactions of the cell aggregate and the dynamical evolution of the cell population. In particular, it is concluded that our model is able to explain quite different setups, such as spheroids growth (up to six times the initial configuration for U-87 MG cell line) or shrinking (almost half of the initial configuration for U-251 MG cell line); as the result of the mechanical interplay of cells driven by cellular evolution. Indeed, the main contribution of this work is to link the spheroid evolution with the mechanical activity of cells, coupled with nutrient consumption and the subsequent cell dynamics. All this information can be used to further investigate mechanistic effects in the evolution of tumors and their role in cancer disease.

Author summary

Spheroids structures of cell aggregates are an available experimental platform to analyze the evolution and drug response of solid tumors. In particular, the dynamics of different glioblastoma cell lines have been studied in this work using spheroids. Interestingly, very different behaviors were observed, from a half of the initial configuration shrinking for U-251 MG cell line to six times the initial configuration growth for U-87 MG cell line. These results were replicated by means of a coupled mathematical model which accounts for nutrients diffusion in the spheroid, kinetics of cellular growth and death, and mechanical interactions among the cells. Tumor growth or shrinkage can be explained from a continuum mechanics view driven by cell activity and nutrients availability. This modeling put the focus on mechanistic effects and is aligned with novel experimental techniques to quantify the mechanical microenvironment in tumors. These techniques may be combined with the approach presented in this work to further investigate the role of mechanics in cancer disease.
Polyunsaturated fatty acids inhibit a pentameric ligand-gated ion channel through one of two binding sites
Authors: Dietzen Noah M. , Arcario Mark J. , Chen Lawrence J. , Petroff John T. , Krishnan Kathiresan , Brannigan Grace , Covey Douglas F. , Cheng Wayland W. L.
Published: October 2021

Polyunsaturated fatty acids (PUFAs) inhibit pentameric ligand-gated ion channels (pLGICs) but the mechanism of inhibition is not well understood. The PUFA, docosahexaenoic acid (DHA), inhibits agonist responses of the pLGIC, ELIC, more effectively than palmitic acid, similar to the effects observed in the GABAA receptor and nicotinic acetylcholine receptor. Using photo-affinity labeling and coarse-grained molecular dynamics simulations, we identified two fatty acid binding sites in the outer transmembrane domain (TMD) of ELIC. Fatty acid binding to the photolabeled sites is selective for DHA over palmitic acid, and specific for an agonist-bound state. Hexadecyl-methanethiosulfonate modification of one of the two fatty acid binding sites in the outer TMD recapitulates the inhibitory effect of PUFAs in ELIC. The results demonstrate that DHA selectively binds to multiple sites in the outer TMD of ELIC, but that state-dependent binding to a single intrasubunit site mediates DHA inhibition of ELIC.
High-throughput mutagenesis identifies mutations and RNA-binding proteins controlling CD19 splicing and CART-19 therapy resistance
Authors: Cortés-López Mariela , Schulz Laura , Enculescu Mihaela , Paret Claudia , Spiekermann Bea , Busch Anke , Orekhova Anna , Kielisch Fridolin , Quesnel-Vallières Mathieu , Torres-Diz Manuel , Faber Jörg , Barash Yoseph , Thomas-Tikhonenko Andrei , Zarnack Kathi , Legewie Stefan , König Julian
Published: October 2021

During CART-19 immunotherapy for B-cell acute lymphoblastic leukaemia (B-ALL), many patients relapse due to loss of the cognate CD19 epitope. Since epitope loss can be caused by aberrant CD19 exon 2 processing, we herein investigate the regulatory code that controls CD19 splicing. We combine high-throughput mutagenesis with mathematical modelling to quantitatively disentangle the effects of all mutations in the region comprising CD19 exons 1-3. Thereupon, we identify ~200 single point mutations that alter CD19 splicing and thus could predispose B-ALL patients to CART-19 resistance. Furthermore, we report almost 100 previously unknown splice isoforms that emerge from cryptic splice sites and likely encode non-functional CD19 proteins. We further identify cis-regulatory elements and trans-acting RNA-binding proteins that control CD19 splicing (e.g., PTBP1 and SF3B4) and validate that loss of these factors leads to enhanced CD19 mis-splicing. Our dataset represents a comprehensive resource for potential prognostic factors predicting success of CART-19 therapy.

Highlights

Mutations in relapsed CART-19 patients lead to CD19 mis-splicing

High-throughput mutagenesis uncovers ~200 single point mutations with a potential role in CART-19 therapy resistance

Many mutations generate non-functional CD19 proteins by activating cryptic splice sites

RNA-binding proteins such as PTBP1 are key to the expression of properly spliced, CART-19 immunotherapy-sensitive isoforms