bluuebunny/crossref_metadata_2025 huggingface dataset:
Temperature and depth dependence of the spatial distribution of snow crab
Authors: Choi Jae S. , Cameron Brent , Christie Kate , Glass Amy , MacEachern Ellen
Published: December 2022

The cascading effects of rapid climate change is a reality with which all biota are challenged. In this context, we examine the spatiotemporal probability of occurrence of snow crab as a means to express viable habitat. This is attempted for three demographic components, morphometrically mature males and females and immature adolescent crab in the Scotian Shelf region of the northwest Atlantic, Canada. We use a robust approach, known as Conditional AutoRegressive models, to define viable habitat. Further, we focus upon viable habitat, conditioned on the marginal influence of temperature and depth as they are known to be important constraints on snow crab. We observe some niche partitioning in terms of depth and temperature. We also note declines in viable habitat marginal to depth and temperature since 2010 for all demographic groups. This population representing the southern-most distribution of snow crab in the northwest Atlantic are vulnerable to degradation of viable habitat attributable to rapid climate change.

One-Sentence Summary

Rapid climate change and a decadal scale change in the viable habitat of snow crab of the Scotian Shelf ecosystem.
High-throughput functional characterization of combinations of transcriptional activators and repressors
Authors: Mukund Adi X. , Tycko Josh , Allen Sage J. , Robinson Stephanie A. , Andrews Cecelia , Ludwig Connor H. , Spees Kaitlyn , Bassik Michael C. , Bintu Lacramioara
Published: December 2022

Despite growing knowledge of the functions of individual human transcriptional effector domains, much less is understood about how multiple effector domains within the same protein combine to regulate gene expression. Here, we measure transcriptional activity for 8,400 effector domain combinations by recruiting them to reporter genes in human cells. In our assay, weak and moderate activation domains synergize to drive strong gene expression, while combining strong activators often results in weaker activation. In contrast, repressors combine linearly and produce full gene silencing, and repressor domains often overpower activation domains. We use this information to build a synthetic transcription factor whose function can be tuned between repression and activation independent of recruitment to target genes by using a small molecule drug. Altogether, we outline the basic principles of how effector domains combine to regulate gene expression and demonstrate their value in building precise and flexible synthetic biology tools.
Distributing Aminophospholipids Asymmetrically Across Leaflets Causes Anomalous Membrane Stiffening
Authors: Frewein Moritz PK , Piller Paulina , Semeraro Enrico Federico , Czakkel Orsolya , Gerelli Yuri , Porcar Lionel , Pabst Georg
Published: December 2022

We studied the mechanical leaflet coupling of prototypic mammalian plasma membranes using neutron spin-echo spectroscopy. In particular, we examined a series of asymmetric phospholipid vesicles with phosphatidylcholine and sphingomyelin enriched in the outer leaflet and inner leaflets composed of phosphatidylethanolamine / phosphatidylserine mixtures. The bending rigidities of most asymmetric membranes were anomalously high, exceeding even those of symmetric membranes formed from their cognate leaflets. Only asymmetric vesicles with outer leaflets enriched in sphingolipid displayed bending rigidities in conformity with these symmetric controls. We performed complementary small-angle neutron and X-ray experiments on the same vesicles to examine possible links to structural coupling mechanisms, which would show up in corresponding changes in membrane thickness. Additionally, we estimated differential stress between leaflets originating either from a mismatch of their lateral areas or spontaneous curvatures. However, no correlation with asymmetry-induced membrane stiffening was observed. To reconcile our findings, we speculate that an asymmetric distribution charged or H-bond forming lipids may induce an intraleaflet coupling which increases the weight of hard undulatory modes of membrane fluctuations and hence the overall membrane stiffness.
Likelihood-based signal and noise analysis for docking of models into cryo-EM maps
Authors: Read Randy J. , Millán Claudia , McCoy Airlie J. , Terwilliger Thomas C.
Published: December 2022

Fast, reliable docking of models into cryo-EM maps requires understanding of the errors in the maps and the models. Likelihood-based approaches to errors have proven to be powerful and adaptable in experimental structural biology, finding applications in both crystallography and cryo-EM. Indeed, previous crystallographic work on the errors in structural models is directly applicable to likelihood targets in cryo-EM. Likelihood targets in Fourier space are derived here to characterise, based on the comparison of half-maps, the direction- and resolution-dependent variation in the strength of both signal and noise in the data. Because the signal depends on local features, the signal and noise are analysed in local regions of the cryo-EM reconstruction. The likelihood analysis extends to prediction of the signal that will be achieved in any docking calculation for a model of specified quality and completeness. A related calculation generalises a previous measure of the information gained by making the cryo-EM reconstruction.
A Jacob/nsmf gene knockout does not protect against hypoxia- and NMDA-induced neuronal cell death
Authors: Gomes Guilherme M. , Bär Julia , Karpova Anna , Kreutz Michael R.
Published: December 2022

Jacob is a synapto-nuclear messenger protein that encodes and transduces the origin of synaptic and extrasynaptic NMDA receptor signals to the nucleus. The protein assembles a signalosome that differs in case of synaptic or extrasynaptic NMDAR activation. Following nuclear import Jacob docks these signalosomes to the transcription factor CREB. We have recently shown that amyloid-beta and extrasynaptic NMDAR activation triggers the translocation of a Jacob signalosome that results in inactivation of the transcription factor CREB, a phenomenon termed Jacob-induced CREB shut-off (JaCS). JaCS contributes to early Alzheimer’s disease pathology and a gene knockout of nsmf, the gene encoding Jacob, protects against amyloid pathology. Given that extrasynaptic activity is also involved in acute excitotoxicity, like in stroke, we asked whether nsmf gene knockout will also protect against acute insults, like oxygen and glucose deprivation and excitotoxic NMDA stimulation. Here we show that organotypic hippocampal slices from wild-type and nsmf-/-mice display similar degrees of degeneration when exposed to either oxygen glucose deprivation or 50 µM NMDA incubation. This lack of neuroprotection indicates that JaCS is mainly relevant in conditions of low level chronic extrasynaptic NMDAR activation that results in cellular degeneration induced by alterations in gene transcription.
Myristoyl’s dual role in allosterically regulating and localizing Abl kinase
Authors: de Buhr Svenja , Gräter Frauke
Published: December 2022

c-Abl kinase, a key signalling hub in many biological processes ranging from cell development to proliferation, is tightly regulated by two inhibitory Src homology domains. An N-terminal myristoyl-modification can bind to a hydrophobic pocket in the kinase C-lobe, which stabilizes the auto-inhibitory assembly. Activation is triggered by myristoyl release. We used molecular dynamics simulations to show how both myristoyl and the Src homology domains are required to impose the full inhibitory effect on the kinase domain, and reveal the allosteric transmission pathway at residue-level resolution. Importantly, we find myristoyl insertion into a membrane to thermodynamically compete with binding to c-Abl. Myristoyl thus not only localizes the protein to the cellular membrane, but membrane attachment at the same time enhances activation of c-Abl by stabilizing its pre-activated state. Our data put forward a model in which lipidation tightly couples kinase localization and regulation, a scheme that currently appears to be unique for this non-receptor tyrosine kinase.
Identification of quiescent FOXC2+spermatogonial stem cells in adult mammals
Authors: Wang Zhipeng , Jin Cheng , Li Pengyu , Li Yiran , Tang Jielin , Yu Zhixin , Jiao Tao , Ou Jinhuan , Wang Han , Zou Dingfeng , Li Mengzhen , Mang Xinyu , Liu Jun , Lu Yan , Li Kai , Zhang Ning , Yu Jia , Miao Shiying , Wang Linfang , Song Wei
Published: December 2022

In adult mammals, spermatogenesis embodies the complex developmental process from spermatogonial stem cells (SSCs) to spermatozoa. At the top of this developmental hierarchy lie a series of SSC subpopulations. Their individual identities as well as the relationships with each other, however, remain largely elusive. Using single-cell analysis and lineage tracing, we discovered both in mice and humans the quiescent adult SSC subpopulation marked specifically by forkhead box protein C2 (FOXC2). All spermatogenic progenies can be derived from FOXC2+SSCs and the ablation of FOXC2+SSCs led to the depletion of the undifferentiated spermatogonia pool. During germline regeneration, FOXC2+SSCs were activated and able to completely restore the process. Germ cell specificFoxc2knockout resulted in an accelerated exhaustion of SSCs and eventually led to male infertility. Furthermore, FOXC2 prompts the expressions of negative regulators of cell cycle thereby ensures the SSCs reside in quiescence. Thus, this work proposes that the quiescent FOXC2+SSCs are essential for maintaining the homeostasis and regeneration of spermatogenesis in adult mammals.
Abundant pleiotropy across neuroimaging modalities identified through a multivariate genome-wide association study
Authors: Tissink E.P. , Shadrin A.A. , van der Meer D. , Parker N. , Hindley G. , Roelfs D. , Frei O. , Fan C.C. , Nagel M. , Nærland T. , Budisteanu M. , Djurovic S. , Westlye L. T. , van den Heuvel M.P. , Posthuma D. , Kaufmann T. , Dale A.M. , Andreassen O.A.
Published: December 2022

Genetic pleiotropy is abundant across spatially distributed brain characteristics derived from one neuroimaging modality (e.g. structural, functional or diffusion MRI). A better understanding of pleiotropy across modalities could inform us on the integration of brain function, micro- and macrostructure. Here we show extensive genetic overlap across neuroimaging modalities at a locus and gene level in the UK Biobank (N=34,029) and ABCD Study (N=8,607). When jointly analysing phenotypes derived from structural, functional and diffusion MRI with the Multivariate Omnibus Statistical Test (MOSTest), we boost the discovery of loci and genes beyond previously identified effects for each modality individually. Cross-modality genes are involved in fundamental biological processes and predominantly expressed during prenatal brain development. We additionally boost prediction of psychiatric disorders by conditioning independent GWAS on our multimodal multivariate GWAS. These findings shed light on the shared genetic mechanisms underlying variation in brain morphology, functional connectivity, and tissue composition.

Graphical abstract
Likelihood-based docking of models into cryo-EM maps
Authors: Millán Claudia , McCoy Airlie J. , Terwilliger Thomas C. , Read Randy J.
Published: December 2022

Optimized docking of models into cryo-EM maps requires exploiting an understanding of the signal expected in the data to minimize the calculation time while maintaining sufficient signal. The likelihood-based rotation function used in crystallography can be employed to establish plausible orientations in a docking search. A phased likelihood translation function yields scores for the placement and rigid-body refinement of oriented models. Optimised strategies for choices of the resolution of data from the cryo-EM maps to use in the calculations and the size of search volumes are based on expected log-likelihood-gain scores, computed in advance of the search calculation. Tests demonstrate that the new procedure is fast, robust and effective at placing models into even challenging cryo-EM maps.

Synopsis

Exploiting analogies to crystallographic molecular replacement, a strategy for docking into cryo-EM maps is informed by calculations of expected log-likelihood-gain scores.
Anatomy of the complete mouse eye vasculature in development and pathology explored by light-sheet fluorescence microscopy
Authors: Krimpenfort Luc , Garcia-Collado Maria , van Leeuwen Tom , Locri Filippo , Luik Anna-Liisa , Queiro-Palou Antonio , Kanatani Shigeaki , André Helder , Uhlén Per , Jakobsson Lars
Published: December 2022

Eye development and function rely on precise establishment, regression and maintenance of its many sub-vasculatures. These crucial vascular properties have been extensively investigated in eye development and disease utilizing genetic and experimental mouse models. However, due to technical limitations, individual studies have often restricted their focus to one specific sub-vasculature. Here, we apply a workflow that allows for visualisation of complete vasculatures of mouse eyes of various developmental stages. Through tissue depigmentation, immunostaining, clearing and light-sheet fluorescence microscopy (LSFM) entire vasculatures of the retina, vitreous (hyaloids) and uvea were simultaneously imaged at high resolution. In silico dissection provided detailed information on their 3D architecture and interconnections. By this method we describe remodelling of the postnatal iris vasculature following its disconnection to the feeding hyaloid vasculature. In addition, we demonstrate examples of conventional and LSFM-mediated analysis of choroidal neovascularisation after laser-induced wounding, showing added value of the presented workflow in analysis of modelled eye disease. These advancements in visualisation and analysis of the respective eye vasculatures in development and complex eye disease open for novel observations of their functional interplay at a whole-organ level.
SAFB associates with nascent RNAs to promote gene expression in mouse embryonic stem cells
Authors: Cherney Rachel E. , Eberhard Quinn E. , Mills Christine A. , Porrello Alessandro , Zhang Zhiyue , White David , Herring Laura E. , Calabrese J. Mauro
Published: December 2022

Scaffold Attachment Factor B (SAFB) is a conserved RNA Binding Protein (RBP) that is essential for early mammalian development. However, the RNAs that associate with SAFB in mouse embryonic stem cells have not been characterized. Here, we addressed this unknown using RNA-seq and SAFB RNA immunoprecipitation followed by RNA-seq (RIP-seq) in wild-type ESCs and in ESCs in which SAFB and SAFB2 were knocked out. SAFB predominantly associated with introns of protein-coding genes through purine-rich motifs. The transcript most enriched in SAFB association was the lncRNAMalat1, which also contains a purine-rich region in its 5′end. Knockout of SAFB/2 led to down- and upregulation of approximately 1,000 genes associated with multiple biological processes, including genes that are regulated by Polycomb and genes involved in apoptosis, cell division, and cell migration. The spliced and nascent transcripts of many downregulated genes associated with high levels of SAFB in wild-type cells, implying that SAFB binding promotes their expression. Reintroduction of SAFB into double-knockout cells restored gene expression towards wild-type levels, an effect that was again observable at the level of spliced and nascent transcripts. Proteomics analysis revealed a significant enrichment of nuclear speckle-associated and RS-domain containing proteins among SAFB interactors. Our findings suggest that among other potential functions in mouse embryonic stem cells, SAFB promotes the expression of a subset of genes through its ability to bind purine regions in nascent RNA.
Contribution of Notch/Wnt signaling modulation in reactive astrocyte reparative response after brain injury
Authors: Delgado-Garcia Lina Maria , Benincasa Julia C. , Courbassier Natália Rodrigues , Ribeiro Tais Novaki , Porcionatto Marimélia
Published: December 2022

After a Traumatic Brain Injury (TBI), the neural network activates a reparative response seeking to restore homeostasis. Astrocyte reactivation is an essential component of this response. The injury creates a temporal microenvironment where neurogenic signaling molecules regulate cell fate decisions of neocortical neural progenitors. Likewise, astrocyte reactivation triggers a transcriptional-proliferative program where neurogenic signaling molecules play crucial roles. However, precise molecular mechanisms are context-specific and are not fully understood. Here we studied cellular and molecular aspects of reactive astrocytes response after Notch-Wnt neurogenic signaling modulation. Our results provide new evidence of cortical Notch-Wnt signaling activation after TBI. Reactive astrocytes in the core of Notch signaling showed a differential aggregated distribution.In vitro, Notch inhibition promoted a neural precursor profile and might increase the number of cells committed in a proliferative response. Finally, we found an indirect co-regulation of Wnt-Shh signaling in BHLH-Notch target genes and a Notch-supportive effect in Wnt-Shh signaling activation.
Identification of S1PR4 as an immune modulator for favourable prognosis in HNSCC through unbiased machine learning
Authors: Huang Chenshen , Zhu Fengshuo , Wang Ning , Huang Qi
Published: December 2022

As the largest family of membrane proteins, G protein-coupled receptors (GPCRs) are the most prominent family of pharmacological targets. However, only a few GPCRs have been well-defined in terms of their physiological and pathological functions. Thus, an efficient way to identify key GPCRs involved in tumour formation is urgently needed. In this study, patients with head and neck squamous cell carcinoma (HNSCC) were classified into two different subtypes based on the characteristics of GPCRs using an unbiased machine learning method. Notably, these two subtypes showed significant differences in prognosis, gene expression, and immune microenvironment, especially in the infiltration of CD8+T cells. Based on these differences, we screened three potential key regulators (S1PR4, S1PR5, and GPR87) from all GPCRs and constructed a prognostic nomogram for patients with HNSCC. We identified S1PR4 as the key GPCR in determining the two subtypes for positive correlation with the proportion and cytotoxicity of CD8+T cells in HNSCC and was mainly expressed in a subset of CX3CR1+CD8+T cells. We also demonstrated that S1PR4 is an immune modulator for the favourable prognosis of HNSCC patients. We found that S1PR4 was highly expressed in CD8+T cells from the tumours of HNSCC patients, which was significantly associated with better prognosis, and S1PR4 expression was accompanied by higher T cell cytotoxic marker expression (IFNG and GZMB). Notably, S1PR4 co-localised with CX3CR1, which has been identified as the most cytotoxic marker of CD8+T cells. Furthermore, S1PR4 upregulation could significantly increase T cell function in CAR-T cell therapy, indicating its great potential in cancer immunotherapy. Therefore, these results identified S1PR4 as a key indicator of cytotoxicity and the proportion of tumour-infiltrating CD8+T cells and confirmed the prognostic value of S1PR4 in HNSCC. Our findings contribute to the knowledge of S1PR4 in anti-tumour immunity, providing a potential GPCR-targeted therapeutic option for future HNSCC treatment.
AIRRSHIP: simulating human B cell receptor repertoire sequences
Authors: Sutherland Catherine , Cowan Graeme J M
Published: December 2022

Adaptive Immune Receptor Repertoire Sequencing is a rapidly developing field that has advanced understanding of the role of the adaptive immune system in health and disease. Numerous tools have been developed to analyse the complex data produced by this technique but work to compare their accuracy and reliability has been limited. Thorough, systematic assessment of their performance is dependent on the ability to produce high quality simulated datasets with known ground truth. We have developed AIRRSHIP, a flexible and fast Python package that produces synthetic human B cell receptor sequences. AIRRSHIP uses a comprehensive set of reference data to replicate key mechanisms in the immunoglobulin recombination process, with a particular focus on junctional complexity. Repertoires generated by AIRRSHIP are highly similar to published data and all steps in the sequence generation process are recorded. These data can be used to not only determine the accuracy of repertoire analysis tools but can also, by tuning of the large number of user-controllable parameters, give insight into factors that contribute to inaccuracies in results.

Availability and Implementation

AIRRSHIP is implemented in Python. It is available viahttps://github.com/Cowanlab/airrshipand on PyPI athttps://pypi.org/project/airrship/. Documentation can be found athttps://airrship.readthedocs.io.

Contact

graeme.cowan@ed.ac.uk
Network-Guided Sparse Subspace Clustering on Single-Cell Data
Authors: Yuan Chenyang , Jiang Shunzhou
Published: December 2022

With the rapid development of single-cell RNA sequencing (scRNA-seq) technology, people are able to investigate gene expression at the individual cell level. Identification of cell types via unsupervised clustering is one of the fundamental issues in analyzing single-cell data. However, due to the high dimensionality of expression profiles, traditional clustering methods are difficult to generate satisfactory results. To address this problem, we designed NetworkSSC, a network-guided sparse subspace clustering (SSC) approach. NetworkSSC is based on a similar assumption in SSC that the expression of cells within the same type lies in the same subspace. Moreover, it integrates an additional regularization term to include the gene network’s Laplacian matrix, so as to utilize the network information. The comparison results of 5 scRNA-seq data sets show that NetworkSSC outperforms ordinary SSC and other clustering methods in most cases.
TheFLOWERING LOCUS T LIKE 2-1gene ofChenopodiumtriggers precocious flowering in Arabidopsis seedlings
Authors: Abeyawardana Oushadee A. J. , Moravec Tomáš , Krüger Manuela , Belz Claudia , Gutierrez-Larruscain David , Vondráková Zuzana , Eliášová Kateřina , Štorchová Helena
Published: December 2022

TheFLOWERING LOCUS T(FT)gene is the essential integrator of flowering regulatory pathways in angiosperms. The paralogs of theFTgene may perform antagonistic functions, as exemplified byBvFT1, that suppresses flowering inBeta vulgaris, unlike the paralogous activatorBvFT2. The roles ofFTgenes in other amaranths were less investigated. Here, we transformedArabidopsis thalianawith theFLOWERING LOCUS T like(FTL) genes ofChenopodiumand found, that bothFTL1andFTL2-1accelerated flowering, despite having been the homologs of theBeta vulgarisfloral promoter and suppressor, respectively. The floral promotive effect ofFTL2-1was so strong that it caused lethality when overexpressed under the35Spromoter.FTL2-1placed in inducible cassette accelerated flowering after the induction with methoxyphenozide. The occasional expression ofFTL2-1led to precocious flowering in some primary transformants even without chemical induction. After theFTLgene duplication in Amaranthaceae, theFTL1copy maintained the role of floral activator. The second copyFTL2underwent subsequent duplication and functional diversification, which enabled to control the onset of flowering in amaranths to adapt to variable environments.

HIGHLIGHT

TheFLOWERING LOCUS T like 2-1(FTL 2-1) gene ofChenopodiumacts as a strong activator of flowering in Arabidopsis, despite being a homolog of floral repressorBvFT1.
CAbiNet: Joint visualization of cells and genes based on a gene-cell graph
Authors: Zhao Yan , Kohl Clemens , Rosebrock Daniel , Hu Qinan , Hu Yuhui , Vingron Martin
Published: December 2022

In routine single-cell RNA-sequencing (scRNA-seq) analysis workflows, cells are commonly visualized in 2D to show the patterns in the data. However, these visualization approaches do not give any information about the genes that define the cell groups or clusters. It is therefore desirable to display cells and genes simultaneously such that by their relative position to each other information about the genes’ expression in a cluster can be obtained. Here we propose “Correspondence Analysis based Biclustering on Networks” (CAbiNet) as a novel approach to jointly visualize cells and genes by a non-linear embedding approach, called biMAP. The biMAP allows for easy and interactive exploration of cells and their corresponding marker genes in a single plot. CabiNet additionally offers an intuitive way to perform biclustering jointly on cells and genes, providing a simplified workflow to annotate cell types on the biMAP. CAbiNet is accessible through GitHub as an R package.
Nature Notes: Spatiotemporal variation in the competitive environment, with implications for how climate change may affect a species with parental care
Authors: Potticary Ahva L. , Otto Hans W. , McHugh Joseph V. , Moore Allen J.
Published: December 2022

Burying beetles of the genusNicrophorushave become a model for studying the evolution of complex parental care in a laboratory.Nicrophorusspecies depend on small vertebrate carcasses to breed, which they process and provision to their begging offspring. However, vertebrate carcasses are highly sought after by a wide variety of species and so competition is expected to be critical to the evolution of parental care. Despite this, the competitive environment forNicrophorusis rarely characterized in the wild and remains a missing factor in laboratory studies. Here, we performed a systematic sampling ofNicrophorus orbicollisliving near the southern extent of their range at Whitehall Forest in Clarke County, Georgia, USA. We determined the density ofN. orbicollisand other necrophilous species that may affect the availability of this breeding resource through interference or exploitation competition. In addition, we characterize body size, a key trait involved in competitive ability, for allNicrophorusspecies at Whitehall Forest throughout the season. Finally, we compare our findings to other published natural history data for Nicrophorines. We document a significantly longer active season than was observed twenty years previously at Whitehall Forest for bothN. orbicollisandNicrophorus tomentosus, potentially due to climate change. As expected, the adult body size ofN. orbicolliswas larger thanN. tomentosus, the only otherNicrophorusspecies that was captured in 2022 at Whitehall Forest. The other most prevalent interspecific insects captured included species in the families Staphylinidae, Histeridae, Scarabaeidae, and Elateridae, which may act as competitors or predators ofNicrophoruseggs and larvae. Together, our results indicate significant variation in intra- and interspecific competition relative to populations within theN. orbicollisrange. These findings suggest that the competitive environment varies extensively over space and time, which help to inform the role of ecology in the evolution of parental care in this species.
Alcohol and Cannabinoid Binges and Daily Exposure to Nicotine in Adolescent/Young Adult Rats induce Sex-Dependent Long-Term Learning and Motivation Alterations
Authors: Abela Norbert , Haywood Katie , Di Giovanni Giuseppe
Published: December 2022

Adolescence is a critical developmental period, concerning anatomical, neurochemical and behavioral changes. Moreover, adolescents are more sensitive to the long-term deleterious effects of drug abuse. Binge-like consumption of alcohol and marijuana, along with tobacco smoking, is a dangerous pattern often observed in adolescents during weekends. Nevertheless, the long-term effect of their adolescent co-exposure has not been experimentally investigated yet.

Long-Evans adolescent male (n = 20) and female (n = 20) rats from postnatal day 30 (P30) until P60 were daily treated with nicotine (0.3 mg/kg, i.p.), and, on two consecutive ‘binging days’ per week (for a total of eight times), received an intragastric ethanol solution (3 g/kg) and an intraperitoneal (i.p.) dose of cannabinoid 1/2 receptor agonist WIN55,212-2 (1.2 mg/kg). These rats were tested after treatment discontinuation at >P90 for associative food-rewarded operant learning in the two-lever conditioning chambers for six consecutive days on a fixed ratio 1 (FR1) schedule followed by another six days of daily FR2 schedule testing, after 45 days rest. We found the main effects of sex x treatment interactions in FR1 but not in FR2 experiments. Treated females show attenuated operant responses for food pellets during all FR1 and the FR2 schedule, whilst the treated males show an impairment in FR2 but not in the FR1 schedule. Moreover, the treated females’ percentage of learners was significantly lower than female controls in FR1 while treated males and females were lower than controls in FR2.

Our findings suggest that intermittent adolescent abuse of common drugs, such as alcohol and marijuana, and chronic tobacco exposure can cause significant long-term effects on motivation for natural reinforcers later in adulthood in both sexes. Females appear to be more sensitive to the deleterious effects of adolescent polydrug abuse with both sexes having an increased likelihood of developing lifelong brain alterations.
Higher hyperpolarization activated current (Ih) in a subpopulation of interneurons in stratum oriens of area CA1 in the hippocampus of Fragile X mice
Authors: Hewitt Lauren T. , Brager Darrin H.
Published: December 2022

Fragile X syndrome is the most common inherited form of intellectual disability and the leading monogenetic cause of autism. Studies in mouse models of autism spectrum disorders, including the Fmr1 knockout (FX) mouse, suggest that abnormal inhibition in hippocampal circuits contributes to behavioral phenotypes. We and others previously identified changes in multiple voltage-gated ion channels in hippocampal excitatory pyramidal neurons in FX mice. Whether the intrinsic properties of hippocampal inhibitory interneurons are altered in FX remains largely unknown. We made whole-cell current clamp recordings from three types of interneurons in stratum oriens of the hippocampus: fast-spiking (FS) cells and two classes of low threshold spiking cells, oriens-lacunosum moleculare (OLM) and low-threshold high Ih(LTH) neurons. We found that in FX mice, input resistance and action potential firing frequency were lower in LTH, but not FS or OLM, interneurons compared to wild type. Bath application of the h-channel blocker ZD7288 had a larger effect on input resistance in FX LTH cells and normalized input resistance between wild type and FX LTH cells, suggesting a greater contribution of Ihin FX LTH cells. In agreement, voltage clamp recordings showed that Ihwas higher in FX LTH cells compared to wild type. Our results suggest that the intrinsic excitability of LTH inhibitory interneurons may contribute to altered inhibition in the hippocampus of FX mice.

Significance statement

Changes in the balance between excitation and inhibition underlie many neurodevelopmental disorders. Changes in several voltage-gated ion channels, which contribute to altered intrinsic excitability, were previously identified in excitatory hippocampal neurons in the Fmr1 mouse model of Fragile X syndrome. In this paper we use physiological and biochemical approaches to investigate the intrinsic excitability of inhibitory interneurons in hippocampal area CA1 of the Fragile X mouse. We found that higher Ihlowers the intrinsic excitability of one specific type of interneuron. This study highlights how changes to voltage-gated ion channels in specific neuronal populations may contribute to the altered excitatory/inhibitory balance in Fragile X syndrome.
EPEK: creation and analysis of an Ectopic Pregnancy Expression Knowledgebase
Authors: Natarajan Ananya , Chivukula Nikhil , Dhanakoti Gokul Balaji , Sahoo Ajaya Kumar , Ravichandran Janani , Samal Areejit
Published: December 2022

Ectopic pregnancy (EP) is one of the leading causes of maternal mortality, where the fertilized embryo grows outside of the uterus. Recent experiments on mice have uncovered the importance of genetic factors in the transport of embryos inside the uterus. In the past, efforts have been made to identify possible gene or protein markers in EP in humans through multiple expression studies. Although there exist comprehensive gene resources for other maternal health disorders, there is no specific resource that compiles the genes associated with EP from such expression studies. Here, we address that knowledge gap by creating a computational resource, Ectopic Pregnancy Expression Knowledgebase (EPEK), that involves manual compilation and curation of expression profiles of EP in humans from published articles. In EPEK, we compiled information on 314 differentially expressed genes, 17 metabolites, and 3 SNPs associated with EP. Computational analyses on the gene set from EPEK showed the implication of cellular signaling processes in EP. We also identified possible exosome markers that could be clinically relevant in the diagnosis of EP. In a nutshell, EPEK is the first and only dedicated resource on the expression profile of EP in humans. EPEK is accessible athttps://cb.imsc.res.in/epek.
Switching between external and internal attention in hippocampal networks
Authors: Poskanzer Craig , Aly Mariam
Published: December 2022

Everyday experience requires processing external signals from the world around us and internal information retrieved from memory. To do both, the brain must fluctuate between states that are optimized for external vs. internal attention. Here, we focus on the hippocampus as a region that may serve at the interface between these forms of attention, and ask how it switches between prioritizing sensory signals from the external world vs. internal signals related to memories and thoughts. Pharmacological, computational, and animal studies have identified input from the cholinergic basal forebrain as important for biasing the hippocampus towards processing external information, whereas complementary research suggests the dorsal attention network (DAN) may aid in allocating attentional resources towards accessing internal information. We therefore tested the hypothesis that the basal forebrain and DAN drive the hippocampus towards external and internal attention, respectively. We used data from 29 human participants (17 female) who completed 2 attention tasks during fMRI. One task (“memory-guided”) required proportionally more internal attention, and proportionally less external attention, than the other (“explicitly instructed”). We discovered that background functional connectivity between the basal forebrain and hippocampus was stronger during the explicitly instructed vs. memory-guided task. In contrast, DAN-hippocampus background connectivity was stronger during the memory-guided vs. explicitly instructed task. Finally, the strength of DAN-hippocampus background connectivity was correlated with performance on the memory-guided but not explicitly instructed task. Together, these results provide evidence that the basal forebrain and DAN may modulate the hippocampus to switch between external and internal attention.

Significance Statement

How does the brain balance the need to pay attention to internal thoughts and external sensations? We focused on the human hippocampus, a region that may serve at the interface between internal and external attention, and asked how its functional connectivity varies based on attentional states. The hippocampus was more strongly coupled with the cholinergic basal forebrain when attentional states were guided by the external world rather than retrieved memories. This pattern flipped for functional connectivity between the hippocampus and dorsal attention network, which was higher for attention tasks that were guided by memory rather than external cues. Together, these findings show that distinct networks in the brain may modulate the hippocampus to switch between external and internal attention.
Designing epitope-focused vaccinesviaantigen reorientation
Authors: Xu Duo , Li Chunfeng , Utz Ashley , Weidenbacher Payton A.B. , Tang Shaogeng , Sanyal Mrinmoy , Pulendran Bali , Kim Peter S.
Published: December 2022

A major challenge in vaccine development, especially against rapidly evolving viruses, is the ability to focus the immune response toward evolutionarily conserved antigenic regions to confer broad protection. For example, while many broadly neutralizing antibodies against influenza have been found to target the highly conserved stem region of hemagglutinin (HA-stem), the immune response to seasonal influenza vaccines is predominantly directed to the immunodominant but variable head region (HA-head), leading to narrow-spectrum efficacy. Here, we first introduce an approach to controlling antigen orientation based on the site-specific insertion of short stretches of aspartate residues (oligoD) that facilitates antigen-binding to alum adjuvants. We demonstrate the generalizability of this approach to antigens from the Ebola virus, SARS-CoV-2, and influenza and observe enhanced antibody responses following immunization in all cases. Next, we use this approach to reorient HA in an “upside down” configuration, which we envision increases HA-stem exposure, therefore also improving its immunogenicity compared to HA-head. When applied to HA of H2N2 A/Japan/305/1957, the reoriented H2 HA (reoH2HA) on alum induced a stem-directed antibody response that cross-reacted with both group 1 and 2 influenza A HAs. Our results demonstrate the possibility and benefits of antigen reorientationviaoligoD insertion, which represents a generalizable immunofocusing approach readily applicable for designing epitope-focused vaccine candidates.

GRAPHICAL ABSTRACT

Seasonal influenza vaccines induce a biased antibody response against the variable head of hemagglutinin, whereas conserved epitopes on the stem are a target for universal vaccines. Here we show that reorienting HA in an “upside-down” configuration sterically occludes the head and redirects the antibody response to the more exposed stem, thereby inducing broad cross-reactivity against hemagglutinins from diverse influenza strains.
Bovine blastocyst like structures derived from stem cell cultures
Authors: Pinzón-Arteaga Carlos A. , Wang Yinjuan , Wei Yulei , Li Leijie , Ribeiro Orsi Ana Elisa , Scatolin Giovanna , Liu Lizhong , Sakurai Masahiro , Ye Jianfeng , Yu Leqian , Li Bo , Jiang Zongliang , Wu Jun
Published: December 2022

Understanding blastocyst formation and implantation is critical for improving farm animal reproduction but is hampered by a limited supply of embryos. We developed an efficient method to generate bovine blastocyst-like structures (termed blastoids) via the assembly of trophoblast stem cells and expanded potential stem cells. Bovine blastoids resemble blastocysts in morphology, cell composition, single-cell transcriptomes, and represent an accessible in vitro model for studying bovine embryogenesis.
Scoring thermal limits in small insects using open-source, computer assisted motion detection
Authors: Perez-Galvez Fernan R , Wilson Annabelle C , Zhou Sophia , Awde David N , Teets Nicholas M
Published: December 2022

Scoring large amounts of thermal tolerance traits live or with recorded video can be time consuming and susceptible to investigator bias, and as with many physiological measurements, there can be trade-offs between accuracy and throughput. Recent studies show that particle tracking is a viable alternative to manually scoring videos, although it may not detect subtle movements, and many of the software options are proprietary and costly. In this study, we present a novel strategy for automated scoring of thermal tolerance videos by inferring motor activity with motion detection using an open-source Python command line application called DIME (Detector of Insect Motion Endpoint). We apply our strategy to both dynamic and static thermal tolerance assays, and our results indicate that DIME can accurately measure thermal acclimation responses, generally agrees with visual estimates of thermal limits, and can significantly increase the throughput over manual methods.

Summary statement

Motion detection algorithm for reliable, automatic scoring of thermal limits in insects with open-source tool
Thermal cycling-hyperthermia down-regulates liposaccharide-induced inflammation in human blood and helps with clearance of herpes simplex virus type 1
Authors: Kuo Yu-Yi , Lin Guan-Bo , Chen Wei-Ting , Chen You-Ming , Liu Hsu-Hsiang , Chao Chih-Yu
Published: December 2022

Infection would lead to temperature increase in the affected region or entire human body, in order to weaken the pathogens, such as virus, or activate the immune system. As an alternative therapy with extensive application for various diseases, hyperthermia (HT) can regulate the release of pro-inflammatory cytokines and the antiviral activity of immune system. However, existing studies have found that overheating impairs healthy tissues and immune cells. The study puts forth a modified HT treatment, thermal cycling-hyperthermia (TC-HT), looking into its effect on immunomodulation and cellular viabilities. It shows that TC-HT can reduce the secretion of pro-inflammatory cytokines, induced by lipopolysaccharide (LPS) bothex vivoandin vitro, and elevate the efficacy of U-937 macrophages in clearing herpes simplex virus type 1 (HSV-1)in vitro. Furthermore, via optimizing its parameters, TC-HT can boost the efficacy of U-937 macrophage in clearing HSV-1, which may be attributed to the enhancement of actin polymerization and phagocytosis activity via TC-HT. In sum, TC-HT outperforms HT in safety and therapeutic effect in immunomodulation, shedding light on its potential in the treatment of immunological diseases.
Benchmark of force fields to characterize the intrinsically disordered R2-FUS-LC region
Authors: Chan-Yao-Chong Maud , Chan Justin , Kono Hidetoshi
Published: December 2022

Amyloid fibrils formations are involved in many neurodegenerative diseases such as Alzheimer’s disease, Parkinson disease, Amyotrophic Lateral Sclerosis (ALS) and others. The proteins associated with the formation of amyloid fibrils are Intrinsically Disordered Proteins (IDP) in the unbound state. Nevertheless, this type of proteins can self-aggregate and form cross-β amyloid fibrils structures at physiological condition.

Due to the flexibility of these IDPs, no single experimental approach could completely characterize this system, especially in the unbound state. All-atom molecular dynamics (MD) simulations could be used to study the conformational ensemble of IDPs. Unfortunately, force fields (FF) and water models (WM) were developed to simulate one structure of folded proteins. Recently, several FF/WM were improved to properly generate conformational ensembles of IDP. However, it is unknown if the force fields (FF) can properly reproduce the behavior of IDP and also self-aggregate in cross-β amyloid fibrils structures.

In this paper, we will focus of the R2 region of the FUS-LC domain (R2-FUS-LC region) which is an Intrinsically Disordered Region (IDR) of 16 residues in the unbound state but forms cross-β fibrils in the bound state. For the R2-FUS-LC region, we benchmarked thirteen commonly used FFs for studying IDPs. We show that CHARMM36m (updated in 2021) with mTIP3P water model performs the best to generate extended structures and cross-β amyloid fibril.
The SOCS1 KIR and SH2 domain are both required for suppression of cytokine signalingin vivo
Authors: Doggett Karen , Keating Narelle , Dehkhoda Farhad , Bidgood Grace M. , Leong Evelyn , Kueh Andrew , Nicola Nicos A. , Kershaw Nadia J. , Babon Jeffrey J. , Alexander Warren S. , Nicholson Sandra E.
Published: December 2022

Suppressor Of Cytokine Signaling (SOCS) 1 is a critical negative regulator of cytokine signaling and required to protect against an excessive inflammatory response. Genetic deletion ofSocs1results in unrestrained cytokine signaling and neonatal lethality, characterised by an inflammatory immune infiltrate in multiple organs. Overexpression and structural studies have suggested that the SOCS1 kinase inhibitory region (KIR) and Src homology 2 (SH2) domain are important for interaction with and inhibition of the receptor-associated JAK1, JAK2 and Tyk2 tyrosine kinases, which initiate downstream signaling. To investigate the role of the KIR and SH2 domain in SOCS1 function, we independently mutated key conserved residues in each domain and analysed the impact on cytokine signaling, and thein vivoimpact on SOCS1 function. Mutation of the SOCS1-KIR or SH2 domain had no impact on the integrity of the SOCS box complex, however, mutation within the phosphotyrosine binding pocket of the SOCS1-SH2 domain specifically disrupted SOCS1 interaction with phosphorylated JAK1. In contrast, mutation of the KIR did not affect the interaction with JAK1, but did prevent SOCS1 inhibition of JAK1 autophosphorylation. In human and mouse cell lines, both mutants impacted the ability of SOCS1 to restrain cytokine signaling, and crucially,Socs1-R105AandSocs1-F59Amice displayed a neonatal lethality and excessive inflammatory phenotype similar to SOCS1 null mice. This study defines a critical and non-redundant role for both the KIR and SH2 domain in endogenous SOCS1 function.
A small excitation window allows long-duration single-molecule imaging, with reduced background autofluorescence, inC. elegansneurons
Authors: Mitra Aniruddha , Loseva Elizaveta , Haasnoot Guus H. , Peterman Erwin J.G.
Published: December 2022

Single-particle imaging using laser-illuminated widefield epi-fluorescence microscopy is a powerful tool to investigate molecular processesin vivo. Performing high-quality single-molecule imaging in such biological systems, however, remains a challenge due to difficulties in controlling the number of fluorescing molecules, photobleaching, and the autofluorescence background. Here, we show that by exciting only a small, 5-15 µm wide region in chemosensory neurons in liveC. elegans, we can significantly improve the duration and quality of single-molecule imaging. Small-window illumination microscopy (SWIM) allows long-duration single-particle imaging since fluorescently labelled proteins are only excited upon entering the small excited area, limiting their photobleaching. Remarkably, we also find that using a small excitation window significantly improves the signal-to-background ratio of individual particles. With the help of theoretical calculations, we explain that the improved signal-to-background ratio is due to reduced background, mostly caused by out-of-focus autofluorescence. We demonstrate the potential of this approach by studying the dendritic transport of a ciliary calcium channel protein, OCR-2, in the chemosensory neurons ofC. elegans. We reveal that OCR-2-associated vesicles are continuously transported back and forth along the length of the dendrite and can switch between directed and diffusive states. Furthermore, we perform single-particle tracking of OCR-2-associated vesicles to quantitatively characterize the transport dynamics. SWIM can be readily applied to otherin vivosystems where intracellular transport or cytoskeletal dynamics occur in elongated protrusions, such as axons, dendrites, cilia, microvilli and extensions of fibroblasts.