bluuebunny/crossref_metadata_2025 huggingface dataset:
Repeated exposure to high-THCCannabissmoke during gestation alters sex ratio, behavior, and amygdala gene expression of Sprague Dawley rat offspring
Authors: Sandini Thaisa M. , Onofrychuk Timothy J. , Roebuck Andrew J. , Hammond Austin , Udenze Daniel , Hayat Shahina , Herdzik Melissa A. , McElroy Dan L. , Orvold Spencer N. , Greba Quentin , Laprairie Robert B. , Howland John G
Published: March 2023

Due to the recent legalization ofCannabisin many jurisdictions and the consistent trend of increasing THC content inCannabisproducts, there is an urgent need to understand the impact ofCannabisuse during pregnancy on fetal neurodevelopment and behavior. To this end, we repeatedly exposed female Sprague-Dawley rats toCannabissmoke from gestational days 6 to 20 (n=12; Aphria Mohawk; 19.51% THC, <0.07% cannabidiol) or room-air as a control (n=10) using a commercially available system. Maternal reproductive parameters, behavior of the adult offspring, and gene expression in the offspring amygdala were assessed. Body temperature was decreased in dams following smoke exposure and more fecal boli were observed in the chambers before and after smoke exposure in those dams exposed to smoke. Maternal weight gain, food intake, gestational length, litter number, and litter weight were not altered by exposure toCannabissmoke. A significant increase in the male-to-female ratio was noted in theCannabis-exposed litters. In adulthood, both male and femaleCannabissmoke-exposed offspring explored the inner zone of an open field significantly less than control offspring. GestationalCannabissmoke exposure did not affect behavior on the elevated plus maze test or social interaction test in the offspring.Cannabisoffspring were better at visual pairwise discrimination and reversal learning tasks conducted in touchscreen-equipped operant conditioning chambers. Analysis of gene expression in the adult amygdala using RNAseq revealed subtle changes in genes related to development, cellular function, and nervous system disease in a subset of the male offspring. These results demonstrate that repeated exposure to high-THCCannabissmoke during gestation alters maternal physiological parameters, sex ratio, and anxiety-like behaviors in the adulthood offspring.

Significance statement

Cannabisuse by pregnant women has increased alongside increased THC content in recent years. As smokingCannabisis the most common method of use, we used a validated model ofCannabissmoke exposure to repeatedly expose pregnant rats to combusted high-THCCannabissmoke. Our results show alterations in litter sex ratio, anxiety-like behavior, and decision making in the offspring which may relate to subtle changes in expression of amygdala genes related to development, cellular function, and nervous system disease. Thus, we believe this gestationalCannabisexposure model may be useful in delineating long-term effects on the offspring.
Interactions of the Protein Tyrosine Phosphatase PTPN3 with Viral and Cellular Partners through its PDZ Domain: Insights into Structural Determinants and Phosphatase Activity
Authors: Genera Mariano , Colcombet-Cazenave Baptiste , Croitoru Anastasia , Raynal Bertrand , Mechaly Ariel , Caillet Joël , Haouz Ahmed , Wolff Nicolas , Caillet-Saguy Célia
Published: March 2023

The human protein tyrosine phosphatase non-receptor type 3 (PTPN3) is a phosphatase containing a PDZ (PSD-95/Dlg/ZO-1) domain that has been found to play both tumor-suppressive and tumor-promoting roles in various cancers, despite limited knowledge of its cellular partners and signaling functions. Notably, the high-risk genital human papillomavirus (HPV) types 16 and 18 and the hepatitis B virus (HBV) target the PDZ domain of PTPN3 through PDZ-binding motifs (PBMs) in their E6 and HBc proteins respectively.

This study focuses on the interactions between the PTPN3 PDZ domain (PTPN3-PDZ) and PBMs of viral and cellular protein partners. The solved X-ray structures of complexes between PTPN3-PDZ and PBMs of E6 of HPV18 and the tumor necrosis factor-alpha converting enzyme (TACE) reveal two novel interactions. We provide new insights into key structural determinants of PBM recognition by PTPN3 by screening the selectivity of PTPN3-PDZ recognition of PBMs, and by comparing the PDZome binding profiles of PTPN3-recognized PBMs and the interactome of PTPN3-PDZ.

The PDZ domain of PTPN3 was known to auto-inhibit the protein’s phosphatase activity. We discovered that the linker connecting the PDZ and phosphatase domains is involved in this inhibition, and that the binding of PBMs does not impact this catalytic regulation.

Overall, the study sheds light on the interactions and structural determinants of PTPN3 with its cellular and viral partners, as well as on the inhibitory role of its PDZ domain on its phosphatase activity.
Trait repetitive negative thinking in depression is associated with functional connectivity in negative thinking state rather than resting state
Authors: Misaki Masaya , Tsuchiyagaito Aki , Guinjoan Salvador M. , Rohan Michael L. , Paulus Martin P.
Published: March 2023

Resting-state functional connectivity (RSFC) has been proposed as a potential indicator of repetitive negative thinking (RNT) in depression. However, identifying the specific functional process associated with RSFC alterations is challenging, and it remains unclear whether alterations in RSFC for depressed individuals are directly related to the RNT process or to individual characteristics distinct from the negative thinking process per se. To investigate the relationship between RSFC alterations and the RNT process in individuals with major depressive disorder (MDD), we compared RSFC with functional connectivity during an induced negative-thinking state (NTFC) in terms of their predictability of RNT traits and associated whole-brain connectivity patterns using connectome-based predictive modeling (CPM) and connectome-wide association (CWA) analyses. Thirty-six MDD participants and twenty-six healthy control participants underwent both resting state and induced negative thinking state fMRI scans. Both RSFC and NTFC distinguished between healthy and depressed individuals with CPM. However, trait RNT in depressed individuals, as measured by the Ruminative Responses Scale-Brooding subscale, was only predictable from NTFC, not from RSFC. CWA analysis revealed that negative thinking in depression was associated with higher functional connectivity between the default mode and executive control regions, which was not observed in RSFC. These findings suggest that RNT in depression involves an active mental process encompassing multiple brain regions across functional networks, which is not represented in the resting state. Although RSFC indicates brain functional alterations in MDD, they may not directly reflect the negative thinking process.
Virtual screening of antimicrobial plant extracts by machine-learning classification of chemical compounds in semantic space
Authors: Yabuuchi Hiroaki , Hayashi Kazuhito , Shigemoto Akihiko , Fujiwara Makiko , Nomura Yuhei , Nakashima Mayumi , Ogusu Takeshi , Mori Megumi , Tokumoto Shin-ichi , Miyai Kazuyuki
Published: March 2023

Plant extract is a mixture of diverse phytochemicals, and considered as an important resource for drug discovery. However, large-scale exploration of the bioactive extracts has been hindered by various obstacles until now. In this research, we have introduced and evaluated a new computational screening strategy that classifies bioactive compounds and plants in semantic space generated by word embedding algorithm. The classifier showed good performance in binary (presence/absence of bioactivity) classification for both compounds and plant genera. Furthermore, the strategy led to the discovery of antimicrobial activity of essential oils fromLindera trilobaandCinnamomum sieboldiiagainstStaphylococcus aureus. The results of this study indicate that machine-learning classification in semantic space can be a highly efficient approach for exploring bioactive plant extracts.
Spinal sensorimotor circuits play a prominent role in hindlimb locomotor recovery after staggered thoracic lateral hemisections but cannot restore posture and interlimb coordination during quadrupedal locomotion in adult cats
Authors: Audet Johannie , Yassine Sirine , Lecomte Charly G , Mari Stephen , Félix Soucy , Caroline Morency , Merlet Angèle N , Harnie Jonathan , Beaulieu Claudie , Gendron Louis , Rybak Ilya A. , Prilutsky Boris I. , Frigon Alain
Published: March 2023

Spinal sensorimotor circuits interact with supraspinal and peripheral inputs to generate quadrupedal locomotion. Ascending and descending spinal pathways ensure coordination between the fore-and hindlimbs. Spinal cord injury disrupts these pathways. To investigate the control of interlimb coordination and hindlimb locomotor recovery, we performed two lateral thoracic hemisections placed on opposite sides of the cord (right T5-T6 and left T10-T11) at an interval of approximately two months in eight adult cats. In three cats, we then made a complete spinal transection caudal to the second hemisection at T12-T13. We collected electromyography and kinematic data during quadrupedal and hindlimb-only locomotion before and after spinal lesions. We show that 1) cats spontaneously recover quadrupedal locomotion following staggered hemisections but require balance assistance after the second one, 2) coordination between the fore-and hindlimbs displays 2:1 patterns and becomes weaker and more variable after both hemisections, 3) left-right asymmetries in hindlimb stance and swing durations appear after the first hemisection and reverse after the second, and 4) support periods reorganize after staggered hemisections to favor support involving both forelimbs and diagonal limbs. Cats expressed hindlimb locomotion the day following spinal transection, indicating that lumbar sensorimotor circuits play a prominent role in hindlimb locomotor recovery after staggered hemisections. These results reflect a series of changes in spinal sensorimotor circuits that allow cats to maintain and recover some level of quadrupedal locomotor functionality with diminished motor commands from the brain and cervical cord, although the control of posture and interlimb coordination remains impaired.

Significance Statement

Coordinating the limbs during locomotion depends on pathways in the spinal cord. We used a spinal cord injury model that disrupts communication between the brain and spinal cord by sectioning half of the spinal cord on one side and then about two months later, half the spinal cord on the other side at different levels of the thoracic cord in cats. We show that despite a strong contribution from neural circuits located below the second spinal cord injury in the recovery of hindlimb locomotion, the coordination between the forelimbs and hindlimbs weakens and postural control is impaired. We can use our model to test approaches to restore the control of interlimb coordination and posture during locomotion after spinal cord injury.
From Microstates to Macrostates in the Conformational Dynamics of GroEL: a Single-Molecule FRET Study
Authors: Liebermann Demian G. , Jungwirth Jakub , Riven Inbal , Barak Yoav , Levy Dorit , Horovitz Amnon , Haran Gilad
Published: March 2023

The chaperonin GroEL is a multi-subunit molecular machine that assists in protein folding in theE. colicytosol. Past studies have shown that GroEL undergoes large allosteric conformational changes during its reaction cycle. However, a measurement of subunit dynamics and their relation to the allosteric cycle of GroEL has been missing. Here, we report single-molecule FRET measurements that directly probe the conformational transitions of one subunit within GroEL and its single-ring variant under equilibrium conditions. We find that four microstates span the conformational manifold of the protein and interconvert on the submillisecond time scale. A unique set of relative populations of these microstates, termed a macrostate, is obtained by varying solution conditions, e.g., adding different nucleotides or the co-chaperone GroES. Strikingly, ATP titration studies demonstrate that the partition between the apo and ATP-liganded conformational macrostates traces a sigmoidal response with a Hill coefficient similar to that obtained in bulk experiments of ATP hydrolysis, confirming the essential role of the observed dynamics in the function of GroEL.

Significance Statement

GroEL is a large protein-folding machine whose activity is accompanied by considerable conformational motions. Here, we use single-molecule FRET spectroscopy in combination with photon-by-photon statistical analysis to characterize the motions of a single GroEL subunit in real time and in the presence of ADP, ATP, and the co-chaperone GroES. Our results reveal transitions between four conformations on a timescale much faster than the functional cycle. We show that the motions of an individual subunit are directly coupled to the concerted allosteric mechanism of GroEL. This work, therefore, further demonstrates the impact of fast conformational dynamics on the biochemical function of molecular machines.
Thalamic regulation of ocular dominance plasticity in adult visual cortex
Authors: Qin Yi , Ahmadlou Mehran , Suhai Samuel , Neering Paul , de Kraker Leander , Heimel J. Alexander , Levelt Christiaan N.
Published: March 2023

Experience-dependent plasticity in the adult visual system is generally thought of as a cortical process. However, several recent studies have shown that perceptual learning or monocular deprivation can also induce plasticity in the adult dorsolateral geniculate nucleus (dLGN) of the thalamus. How plasticity in the thalamus and cortex interact in the adult visual system is ill understood. To assess the influence of thalamic plasticity on plasticity in primary visual cortex (V1), we made use of our previous finding that during the critical period, ocular dominance (OD) plasticity occurs in dLGN and requires thalamic synaptic inhibition. Using multielectrode recordings we find that this is also true in adult mice, and that in the absence of thalamic inhibition and plasticity, OD plasticity in adult V1 is absent. To study the influence of V1 on thalamic plasticity we silenced V1 and show that during the critical period, but not in adulthood, the OD shift in dLGN is partially caused by feedback from V1. We conclude that during adulthood, the thalamus plays an unexpectedly dominant role in experience-dependent plasticity in V1. Our findings highlight the importance of considering the thalamus as a potential source of plasticity in learning events that are typically thought of as cortical processes.
Modelling Emergence ofWolbachiaToxin-Antidote Protein Functions with an Evolutionary Algorithm
Authors: Beckmann John , Gillespie Joe , Tauritz Daniel
Published: March 2023

Evolutionary algorithms (EAs) simulate Darwinian evolution and adeptly mimic natural evolution. Most EA applications in biology encode high levels of abstraction in top-down ecological population models. In contrast, our research merges protein alignment algorithms from bioinformatics into codon based EAs that simulate molecular protein string evolution from the bottom up. We apply our EA to reconcile a problem in the field ofWolbachiainduced cytoplasmic incompatibility (CI).Wolbachiais a microbial endosymbiont that lives inside insect cells. CI is conditional insect sterility that operates as a toxin antidote (TA) system. Although, CI exhibits complex phenotypes not fully explained under a single discrete model. We instantiate in-silico genes that control CI, CI factors (cifs), as strings within the EA chromosome. We monitor the evolution of their enzymatic activity, binding, and cellular localization by applying selective pressure on their primary amino acid strings. Our model helps rationalize why two distinct mechanisms of CI induction might coexist in nature. We find that nuclear localization signals (NLS) and Type IV secretion system signals (T4SS) are of low complexity and evolve fast, whereas binding interactions have intermediate complexity, and enzymatic activity is the most complex. Our model predicts that as ancestral TA systems evolve into eukaryotic CI systems, the placement of NLS or T4SS signals can stochastically vary, imparting effects that might impact CI induction mechanics. Our model highlights how preconditions, genetic diversity, and sequence length can bias evolution ofcifstowards one mechanism or another.
Video-rate three-photon imaging in deepDrosophilabrain based on a single Cr:forsterite oscillator
Authors: Chou Lu-Ting , Wu Shao-Hsuan , Hung Hao-Hsuan , Jang Je-Chi , Chen Chung-Ming , Chang Ting-Chen , Lin Wei-Zhong , Chu Li-An , Sun Chi-Kuang , Kärtner Franz X. , Ivanov Anatoly A. , Chu Shi-Wei , Chia Shih-Hsuan
Published: March 2023

We have demonstrated 30-Hz three-photon imaging using a single 24-MHz mode-locked Cr:forsterite oscillator with a center wavelength at 1260 nm. By managing the dispersion distribution in the resonator using double-chirped mirrors, we have produced 32-fs pulses with 22-nJ pulse energy. Using the oscillator as a driving source, we have realized multi-color three-photon images using a GFP-labeledDrosophilabrain and an AF647-labeled mouse brain. To demonstrate the capability of deep-tissue imaging, we have obtained a 10-times higher SBR from the three-photon images than the two-photon results at different depths in a GFP-labeledDrosophilabrain dissection. Furthermore, we have shown the impact of excitation pulse width on three-photon deep-tissue imaging. Our results indicate the superiority of using shorter pulses for deeper-tissue imaging, especially in theDrosophilabrain. In addition, we have recorded the three-photon calcium imagingin vivofrom theDrosophilamushroom body in response to external electric shocks. We believe our demonstration provides a robust approach for high-speed three-photon microscopy applications, especially for intravital investigations in theDrosophilabrain.
High-altitude hypoxia exposure inhibits erythrophagocytosis by inducing macrophage ferroptosis in the spleen
Authors: Yang Wan-ping , Li Mei-qi , Ding Jie , Li Jia-yan , Wu Gang , Liu Bao , Gao Yu-qi , Wang Guo-hua , Luo Qian-qian
Published: March 2023

High-altitude polycythemia (HAPC) is a chronic condition prevalent in individuals residing at high altitudes (HA), characterized by an augmented production of red blood cells (RBCs) due to hypoxic conditions. Despite its prevalence, the pathophysiological basis and molecular mechanisms driving HAPC remain largely unelucidated. In our study, we utilized a mouse model exposed to hypobaric hypoxia (HH), replicating the environmental conditions experienced at 6000 m above sea level, coupled within vitroanalysis of primary splenic macrophages under 1% O2to investigate these mechanisms. Our findings revealed that HH exposure significantly stimulates erythropoiesis, leading to erythrocytosis. This was accompanied by a notable sequence of splenic changes, initially characterized by splenic contraction, which subsequently progressed to splenomegaly over 14 days. A key observation was the impairment on the capacity of spleen to process RBCs, primarily attributed to a reduction in splenic macrophages located in the red pulp. Extended HH treatment over 7 and 14 days precipitated increased iron mobilization and the onset of ferroptosis within the spleen. This was evidenced by altered expression levels of iron metabolism and ferroptosis-related proteins, paralleling gene expression patterns observed in human peripheral blood mononuclear cells. Single-cell sequencing of splenic tissue post-HH exposure demonstrated a marked decrease in macrophage populations after 7 days. Our study further disclosed a significant increase in RBCs retention in the spleen following HH exposure, likely a consequence of diminished red pulp macrophages (RPMs) and erythrophagocytosis. This hypothesis was corroborated through comprehensive analyses involving flow cytometry, histological staining, and immunostaining, which collectively provided a detailed understanding of RBCs dynamics under HH conditions.In vitroanalyses substantiated the decline in primary splenic macrophages and induction of ferroptosis under hypoxic treatment, effects that were relieved by pre-treatment with the ferroptosis inhibitor ferrostatin-1. Collectively, our data suggest that HH exposure initiates splenic ferroptosis, leading primarily to a decrease in RPMs. This decrease potentially impacts erythrophagocytosis, contributing to increased RBCs retention and subsequent splenomegaly. Such changes could potentially foster continuous RBCs production and accelerate the progress of HAPC. In conclusion, our study highlights the important role of the spleen and splenic macrophages in the pathogenesis of HAPC, providing crucial insights into the disease progression and potential therapeutic targets.
Conditionalin vivodeletion of LYN kinase has little effect on aBRCA1loss-of-function-associated mammary tumour model
Authors: Tornillo Giusy , Warrington Lauren , Kendrick Howard , Higgins Adam T. , Hay Trevor , Beck Sam , Smalley Matthew J.
Published: March 2023

LYN kinase is expressed in BRCA1 loss-of-function-dependent mouse mammary tumours, in the cells of origin of such tumours, and in human breast cancer. Suppressing LYN kinase activity in BRCA1-defective cell lines, as well as inin vitrocultures ofBrca1-null mouse mammary tumours, is deleterious to their growth. Here, we have examined the interaction between LYN kinase and BRCA1 loss-of-function in anin vivomouse mammary tumour model, using conditional knockoutBrca1andLynalleles. Comparison ofBrca1tumour cohorts showed little difference in mammary tumour formation between animals that were wild type, heterozygous or homozygous for the conditionalLynallele, although this was confounded by factors including incompleteLynrecombination in some tumours. RNAseq analysis demonstrated that tumours with high levels ofLyngene expression had a slower doubling time, but this was not correlated with levels of LYN staining in tumour cells themselves. Rather, highLynexpression and slower tumour growth were likely a result of B-cell infiltration. The multifaceted role of LYN means it is likely to present difficulties as a therapeutic target in breast cancer.
Analysis of evolutionary dynamics and clonal architecture in prostate cancer
Authors: Conway Jake R. , Tewari Alok K. , Camp Sabrina Y. , Han Seunghun , Crowdis Jett , He Meng Xiao , Nyame Yaw A. , AlDubayan Saud H. , Schultz Nikolaus , Szallasi Zoltan , Pomerantz Mark M. , Freedman Matthew L. , Fong Lawrence , Nelson Peter S. , Brown Myles , Salari Keyan , Allen Eliezer Van
Published: March 2023

The extent to which clinical and genomic characteristics associate with prostate cancer clonal architecture, tumor evolution, and therapeutic response remains unclear. Here, we reconstructed the clonal architecture and evolutionary trajectories of 845 prostate cancer tumors with harmonized clinical and molecular data. We observed that tumors from patients who self-reported as Black had more linear and monoclonal architectures, despite these men having higher rates of biochemical recurrence. This finding contrasts with prior observations relating polyclonal architecture to adverse clinical outcomes. Additionally, we utilized a novel approach to mutational signature analysis that leverages clonal architecture to uncover additional cases of homologous recombination and mismatch repair deficiency in primary and metastatic tumors and link the origin of mutational signatures to specific subclones. Broadly, prostate cancer clonal architecture analysis reveals novel biological insights that may be immediately clinically actionable and provide multiple opportunities for subsequent investigation.

Statement of significance

Tumors from patients who self-reported as Black demonstrate linear and monoclonal evolutionary trajectories yet experience higher rates of biochemical recurrence. In addition, analysis of clonal and subclonal mutational signatures identifies additional tumors with potentially actionable alterations such as deficiencies in mismatch repair and homologous recombination.
SMASH: Scalable Method for Analyzing Spatial Heterogeneity of genes in spatial transcriptomics data
Authors: Seal Souvik , Bitler Benjamin G. , Ghosh Debashis
Published: March 2023

In high-throughput spatial transcriptomics (ST) studies, it is of great interest to identify the genes whose level of expression in a tissue covaries with the spatial location of cells/spots. Such genes, also known as spatially variable genes (SVGs), can be crucial to the biological understanding of both structural and functional characteristics of complex tissues. Existing methods for detecting SVGs either suffer from huge computational demand or significantly lack statistical power. We propose a non-parametric method termed SMASH that achieves a balance between the above two problems. We compare SMASH with other existing methods in varying simulation scenarios demonstrating its superior statistical power and robustness. We apply the method to four ST datasets from different platforms revealing interesting biological insights.
On the limits to invasion prediction using coexistence outcomes
Authors: Deng Jie , Taylor Washington , Levin Simon A. , Saavedra Serguei
Published: March 2023

The dynamics of ecological communities in nature are typically characterized by probabilistic processes involving invasion dynamics. Because of technical challenges, however, the majority of theoretical and experimental studies have focused on coexistence dynamics. Therefore, it has become central to understand the extent to which coexistence outcomes can be used to predict analogous invasion outcomes relevant to systems in nature. Here, we study the limits to this predictability under a geometric and probabilistic Lotka-Volterra framework. We show that while survival probability in coexistence dynamics can be fairly closely translated into colonization probability in invasion dynamics, the translation is less precise between community persistence and community augmentation, and worse between exclusion probability and replacement probability. These results provide a guiding and testable theoretical framework regarding the translatability of outcomes between coexistence and invasion outcomes when communities are represented by Lotka-Volterra dynamics under environmental uncertainty.
A Single-Nucleus Atlas of Seed-to-Seed Development in Arabidopsis
Authors: Lee Travis A. , Nobori Tatsuya , Illouz-Eliaz Natanella , Xu Jiaying , Jow Bruce , Nery Joseph R. , Ecker Joseph R.
Published: March 2023

Extensive studies of the reference plant Arabidopsis have enabled a deep understanding of tissues throughout development, yet a census of cell types and states throughout development is lacking. Here, we present a single-nucleus transcriptome atlas of seed-to-seed development employing over 800,000 nuclei, encompassing a diverse set of tissues across ten developmental stages, with spatial transcriptomic validation of the dynamic seed and silique. Cross-organ analyses revealed transcriptional conservation of cell types throughout development and heterogeneity within individual cell types influenced by organ-of-origin and developmental timing, including groups of transcription factors, suggesting gatekeeping by transcription factor activation. This atlas provides a resource for the study of cell type specification throughout the development continuum and a reference for stimulus-response and genetic perturbations at the single-cell resolution.
Mapping the neutralizing specificity of human anti-HIV serum by deep mutational scanning
Authors: Radford Caelan E. , Schommers Philipp , Gieselmann Lutz , Crawford Katharine H. D. , Dadonaite Bernadeta , Yu Timothy C. , Dingens Adam S. , Overbaugh Julie , Klein Florian , Bloom Jesse D.
Published: March 2023

Understanding the specificities of human serum antibodies that broadly neutralize HIV can inform prevention and treatment strategies. Here we describe a deep mutational scanning system that can measure the effects of combinations of mutations to HIV envelope (Env) on neutralization by antibodies and polyclonal serum. We first show that this system can accurately map how all functionally tolerated mutations to Env affect neutralization by monoclonal antibodies. We then comprehensively map Env mutations that affect neutralization by a set of human polyclonal sera known to target the CD4-binding site that neutralize diverse strains of HIV. The neutralizing activities of these sera target different epitopes, with most sera having specificities reminiscent of individual characterized monoclonal antibodies, but one sera targeting two epitopes within the CD4 binding site. Mapping the specificity of the neutralizing activity in polyclonal human serum will aid in assessing anti-HIV immune responses to inform prevention strategies.
Stereotypical hippocampal clustering predicts navigational success in virtualized real-world environments
Authors: Ozubko Jason D. , Campbell Madelyn , Verhayden Abigail , Demetri Brooke , Brady Molly , Brunec Iva
Published: March 2023

Structural differences along the long-axis of the hippocampus have long been believed to underlie meaningful functional differences, such as the granularity of information processing. Recent findings show that data-driven parcellations of the hippocampus sub-divide the hippocampus into a 10-cluster map with anterior-medial, anterior-lateral, and posteroanterior-lateral, middle, and posterior components. We tested whether task and experience could modulate this clustering using a spatial learning experiment where subjects were trained to virtually navigate a novel neighborhood in a Google Street View-like environment over a two-week period. Subjects were scanned while navigating routes early in training and at the end of their two-week training. Using the 10-cluster map as the ideal template, we find that subjects who eventually learn the neighborhood well have hippocampal cluster-maps consistent with the ideal—even on their second day of learning—and their cluster mappings do not change over the two week training period. However, subjects who eventually learn the neighborhood poorly begin with hippocampal cluster-maps inconsistent with the ideal, though their cluster mappings become more stereotypical by the end of the two week training. Interestingly this improvement seems to be route specific as even after some early improvement, when a new route is navigated participants’ hippocampal maps revert back to less stereotypical organization. We conclude that hippocampal clustering is not dependent solely on anatomical structure, and instead is driven by a combination of anatomy, task, and importantly, experience. Nonetheless, while hippocampal clustering can change with experience, efficient navigation depends on functional hippocampal activity clustering in a stereotypical manner, highlighting optimal divisions of processing along the hippocampal anterior-posterior and medial-lateral-axes.
MIDASim: a fast and simple simulator for realistic microbiome data
Authors: He Mengyu , Zhao Ni , Satten Glen A.
Published: March 2023

Background

Advances in sequencing technology has led to the discovery of associations between the human microbiota and many diseases, conditions, and traits. With the increasing availability of microbiome data, many statistical methods have been developed for studying these associations. The growing number of newly developed methods highlights the need for simple, rapid, and reliable methods to simulate realistic microbiome data, which is essential for validating and evaluating the performance of these methods. However, generating realistic microbiome data is challenging due to the complex nature of microbiome data, which feature correlation between taxa, sparsity, overdispersion, and compositionality. Current methods for simulating microbiome data are deficient in their ability to capture these important features of microbiome data, or can require exorbitant computational time.

Methods

We develop MIDASim (MIcrobiomeDAtaSimulator), a fast and simple approach for simulating realistic microbiome data that reproduces the distributional and correlation structure of a template microbiome dataset. MIDASim is a two-step approach. The first step generates correlated binary indicators that represent the presence-absence status of all taxa, and the second step generates relative abundances and counts for the taxa that are considered to be present in step 1, utilizing a Gaussian copula to account for the taxon-taxon correlations. In the second step, MIDASim can operate in both a nonparametric and parametric mode. In the nonparametric mode, the Gaussian copula uses the empirical distribution of relative abundances for the marginal distributions. In the parametric mode, an inverse generalized gamma distribution is used in place of the empirical distribution.

Results

We demonstrate improved performance of MIDASim relative to other existing methods using gut and vaginal data. MIDASim showed superior performance by PER-MANOVA and in terms of alpha diversity and beta dispersion in either parametric or nonparametric mode. We also show how MIDASim in parametric mode can be used to assess the performance of methods for finding differentially abundant taxa in a compositional model.

Conclusions

MIDASim is easy to implement, flexible and suitable for most microbiome data simulation situations. MIDASim has three major advantages. First, MIDASim performs better in reproducing the distributional features of real data compared to other methods at both presence-absence level and relative-abundance level. MIDASim-simulated data are more similar to the template data than competing methods, as quantified using a variety of measures. Second, MIDASim makes few distributional assumptions for the relative abundances, and thus can easily accommodate complex distributional features in real data. Third, MIDASim is computationally efficient and can be used to simulate large microbiome datasets.
Quadratic trends: a morphometric tool both old and new
Authors: Bookstein Fred L.
Published: March 2023

The original exposition of the method of “Cartesian transformations” in D’Arcy Thompson’s great essayOn Growth and Formof 1917 is still its most cited. But generations of theoretical biologists have struggled ever since to invent a biometric method aligning that approach with the comparative anatomist’s ultimate goal of inferring bio-logically meaningful hypotheses from empirical geometric patterns. Thirty years ago our community converged on a common data resource, samples of landmark configurations, and a currently popular biometric toolkit for this purpose, the “morphometric synthesis,” that combines Procrustes shape coordinates with thin-plate spline renderings of their various multivariate statistical comparisons. But because both tools algebraically disarticulate the landmarks in the course of a linear multivariate analysis, they have no access to the actual anatomical information conveyed by the arrangements and adjacencies of these locations as they combine in pairs or higher numbers into substructures. This paper explores a geometric approach circumventing these fundamental difficulties: an explicit statistical methodology for the simplest nonlinear patterning of these comparisons at their largest scale, their fits by what Sneath (1967) called quadratic trend surfaces. After an initial quadratic regression of target configurations on a template, the proposed method ignores individual shape coordinates completely, replacing them by a close reading of the regression coefficients accompanied by several new diagrams, notably the exhaustive summary of each regression by an unfamiliar biometric ellipse, its circuit of second-order directional derivatives. These novel trend coordinates, directly visualizable in their own coordinate plane, do not reduce to any of the usual Procrustes or thin-plate summaries. The geometry and algebra of these second-derivative ellipses seem a serviceable first approximation for applications in evo-devo studies and elsewhere. Two examples are offered, one the classic growth data set of Vilmann neurocranial octagons and the other the Marcus group’s data set of midsagittal cranial landmarks over most of the orders of the mammals. Each analysis yields startling new findings inaccessible to the current GMM toolkit. A closing discussion suggests a variety of ways by which innovations in this spirit might burst the current strait-jacket of Procrustes coordinates and thin-plate splines that together so severely constrain the conversion of landmark locations into understanding across our science.
Understanding Complex Trait Susceptibilities and Ethnical Diversity in a Sample of 4,145 Russians Through Analysis of Clinical and Genetic Data
Authors: Usoltsev Dmitrii , Kolosov Nikita , Rotar Oxana , Loboda Alexander , Boyarinova Maria , Moguchaya Ekaterina , Kolesova Ekaterina , Erina Anastasia , Tolkunova Kristina , Rezapova Valeriia , Melnik Olesya , Freylikhman Olga , Paskar Nadezhda , Alieva Asiiat , Baranova Elena , Bazhenova Elena , Beliaeva Olga , Vasilyeva Elena , Kibkalo Sofia , Skitchenko Rostislav , Babenko Alina , Sergushichev Alexey , Dushina Alena , Lopina Ekaterina , Basyrova Irina , Libis Roman , Duplyakov Dmitrii , Cherepanova Natalya , Donner Kati , Laiho Paivi , Kostareva Anna , Konradi Alexandra , Shlyakhto Evgeny , Palotie Aarno , Daly Mark J. , Artomov Mykyta
Published: March 2023

The population of Russia consists of more than 150 local ethnicities. The ethnic diversity and geographic origins, which extend from eastern Europe to Asia, make the population uniquely positioned to investigate the shared properties of inherited disease risks between European and Asian ethnicities.

We present the analysis of genetic and phenotypic data from a cohort of 4,145 individuals collected in three metro areas in western Russia. We show the presence of multiple admixed ancestry clusters spanning from primarily European to Asian and high identity-by-descent sharing with the Finnish population. As a result, there was notable enrichment of Finnish-specific variants in Russia. We illustrate the utility of Russian-descent cohorts for discovery of novel population-specific genetic associations, as well as replication of previously identified associations that were thought to be population-specific in other cohorts.

Finally, we provide access to a database of GWAS results for 465 unique phenotypes and allele frequencies.
A regimen compression strategy for commercial vaccines leveraging an injectable hydrogel depot technology for sustained vaccine exposure
Authors: Yan Jerry , Ou Ben S. , Saouaf Olivia M. , Meany Emily L. , Eckman Noah , Appel Eric A.
Published: March 2023

Equitable global access to vaccines requires we overcome challenges associated with complex immunization schedules and their associated economic burdens that hinder delivery in under resourced environments. The rabies vaccine, for example, requires multiple immunizations for effective protection and each dose is cost prohibitive, and therefore inaccessibility disproportionately impacts low- and middle-income countries. In this work we developed an injectable hydrogel depot technology for sustained delivery of commercial inactivated rabies virus vaccines. In a mouse model, we showed that a single immunization of a hydrogel-based rabies vaccine elicited comparable antibody titers to a standard prime-boost bolus regimen of a commercial rabies vaccine, despite these hydrogel vaccines comprising only half of the total dose delivered in the bolus control. Moreover, these hydrogel-based vaccines elicited similar antigen-specific T-cell responses and neutralizing antibody responses compared to the bolus vaccine. Notably, we demonstrated that while addition of a potent clinical TLR4 agonist adjuvant to the gels slightly improved binding antibody responses, inclusion of this adjuvant to the inactivated virion vaccine was detrimental to neutralizing responses. Taken together, these results suggest that these hydrogels can enable an effective regimen compression and dosesparing strategy for improving global access to vaccines.
Endothelial Cell SMAD6 Balances ACVRL1/Alk1 Function to Regulate Adherens Junctions and Hepatic Vascular Development
Authors: Kulikauskas Molly R , Oatley Morgan , Yu Tianji , Liu Ziqing , Matsumura Lauren , Kidder Elise , Ruter Dana , Bautch Victoria L
Published: March 2023

BMP signaling is critical to blood vessel formation and function, but how pathway components regulate vascular development is not well-understood. Here we find that inhibitory SMAD6 functions in endothelial cells to negatively regulate ALK1/ACVRL1-mediated responses, and it is required to prevent vessel dysmorphogenesis and hemorrhage in the embryonic liver vasculature. ReducedAlk1gene dosage rescued embryonic hepatic hemorrhage and microvascular capillarization induced bySmad6deletion in endothelial cellsin vivo. At the cellular level, co-depletion of Smad6 and Alk1 rescued the destabilized junctions and impaired barrier function of endothelial cells depleted for SMAD6 alone. At the mechanistic level, blockade of actomyosin contractility or increased PI3K signaling rescued endothelial junction defects induced by SMAD6 loss. Thus, SMAD6 normally modulates ALK1 function in endothelial cells to regulate PI3K signaling and contractility, and SMAD6 loss increases signaling through ALK1 that disrupts endothelial junctions. ALK1 loss-of-function also disrupts vascular development and function, indicating that balanced ALK1 signaling is crucial for proper vascular development and identifying ALK1 as a “Goldilocks” pathway in vascular biology regulated by SMAD6.
Somatic small-variant calling methods in Illumina DRAGEN™ Secondary Analysis
Authors: Scheffler Konrad , Catreux Severine , O’Connell Taylor , Jo Heejoon , Jain Varun , Heyns Theo , Yuan Jeffrey , Murray Lisa , Han James , Mehio Rami
Published: March 2023

We present the DRAGEN™ somatic pipeline for calling small somatic variants from tumor samples, with or without paired normal samples. The DRAGEN somatic variant caller offers 1) a flexible architecture that can be used on a wide array of somatic use cases; 2) built-in noise models enabling robustness against various sources of noise artifacts (mapping, genome context, or sample specific); 3) performance of joint analysis of tumor and normal samples in the case of a tumor-normal workflow yielding improved accuracy; 4) benefits from FPGA acceleration for efficient run time. We demonstrate the speed and accuracy of the DRAGEN tumor-normal pipeline across a range of whole genome sequencing (WGS) datasets and compare against third party tools such as Mutect2/GATK4 [1] and Strelka2 [2]. DRAGEN secondary analysis outperforms all other tools with its ability to complete a 110x/40x T/N whole-genome analysis in less than two hours. It offers exceptional accuracy, with higher sensitivity and precision than third party tools. We also show that the DRAGEN T/N workflow supports analysis of liquid and late-stage solid tumors by tolerating tumor-in-normal (TiN) contamination.
FRS2-independent GRB2 interaction with FGFR2 is not required for embryonic development
Authors: Clark James F , Soriano Philippe
Published: March 2023

FGF activation is known to engage canonical signals, including ERK/MAPK and PI3K/AKT, through various effectors including FRS2 and GRB2.Fgfr2FCPG/FCPGmutants that abrogate canonical intracellular signaling exhibit a range of mild phenotypes but are viable in contrast to embryonic lethalFgfr2-/-mutants. GRB2 has been reported to interact with FGFR2 through a non-traditional mechanism, by binding to the C-terminus of FGFR2 independently of FRS2 recruitment. To investigate if this interaction provides functionality beyond canonical signaling, we generated mutant mice harboring a C-terminal truncation (T). We found thatFgfr2T/Tmice are viable and have no distinguishable phenotype, indicating that GRB2 binding to the C-terminal end of FGFR2 is not required for development or adult homeostasis. We further introduced theTmutation on the sensitizedFCPGbackground but found thatFgfr2FCPGT/FCPGTmutants did not exhibit significantly more severe phenotypes. We therefore conclude that, while GRB2 can bind to FGFR2 independently of FRS2, this binding does not have a critical role in development or homeostasis.
Deficits in mitochondrial function and glucose metabolism seen in sporadic and familial Alzheimer’s disease derived Astrocytes are ameliorated by increasing hexokinase 1 expression
Authors: Bell Simon M , Wareing Hollie , Hamshaw Alexander , De Suman , New Elizabeth , Shaw Pamela J , De Marco Matteo , Venneri Annalena , Blackburn Daniel J , Ferraiuolo Laura , Mortiboys Heather
Published: March 2023

Background

Astrocytes have multiple roles including providing neurons with metabolic substrates and maintaining neurotransmitter synaptic homeostasis. Astrocyte glucose metabolism plays a key role in learning and memory with astrocytic glycogen a key substrate supporting memory encoding. The neuronal support provided by astrocytes has a high metabolic demand. Deficits in astrocytic mitochondrial metabolic functioning and glycolysis could impair neuronal function. Changes to cellular metabolism are seen early in Alzheimer’s disease (AD). Understanding cellular metabolism changes in AD astrocytes could be exploited as a new biomarker or synergistic therapeutic agent when combined with anti-amyloid treatments in AD.

Methods

In this project, we characterised mitochondrial and glycolytic function in astrocytes derived from patients with sporadic (n=6) and familial (PSEN1, n=3) forms of AD. Astrocytes were derived using direct reprogramming methods. Astrocyte metabolic outputs: ATP, and extracellular lactate levels were measured using luminescent and fluorescent protocols. Mitochondrial respiration and glycolytic function were measured using a Seahorse XF Analyzer. Hexokinase deficits identified where corrected by transfecting astrocytes with an adenovirus viral vector containing the hexokinase 1 gene.

Results

There was a reduction of total cellular ATP of 20% (p=0.05 in sAD astrocytes) and of 48% (p<0.01) in fAD. A 44% reduction (p<0.05), and 80% reduction in mitochondrial spare capacity was seen in sAD and fAD astrocytes respectively. Reactive oxygen species (ROS) were increased in both AD astrocyte types (p=0.05). Mitochondrial complex I and II was significantly increased in sAD (p<0.05) but not in fAD. Astrocyte glycolytic reserve and extracellular lactate was significantly reduced when compared to controls in both sAD and fAD (p<0.05). We identified a deficit in the glycolytic pathway enzyme hexokinase, and correcting this deficit restored most of the metabolic phenotype in sAD but not fAD astrocytes.

Conclusion

AD astrocytes have abnormalities in functional capacity of mitochondria and the process of glycolysis. These functional deficits can be improved by correcting hexokinase expression deficits with adenoviral vectors. This suggests that hexokinase 1 deficiency could potentially be exploited as a new therapeutic target for AD.