bluuebunny/crossref_metadata_2025 huggingface dataset:
Genotypic sex shapes maternal care in the African pygmy mouse,
Mus minutoides
Authors: Heitzmann Louise D. , Challe Marie , Perez Julie , Castell Laia , Galibert Evelyne , Martin Agnès O. , Valjent Emmanuel , Veyrunes Frédéric
Published: September 2023

Sexually dimorphic behaviours, such as parental care, have long been thought to be mainly driven by gonadal hormones. In the past two decades, a few studies have challenged this view, highlighting the direct influence of the sex chromosome complement (XX versus XY or ZZ versus ZW). The African pygmy mouse,
Mus minutoides
, is a wild mouse species with naturally occurring XY sex reversal induced by a third, feminizing X* chromosome, leading to three female genotypes: XX, XX* and X*Y. Here, we show that sex reversal in X*Y females shapes a divergent maternal care strategy (maternal aggression, pup retrieval and nesting behaviours) from both XX and XX* females. Although neuroanatomical investigations were inconclusive, we show that the dopaminergic system in the anteroventral periventricular nucleus of the hypothalamus is worth investigating further as it may support differences in pup retrieval behaviour between females. Combining behaviours and neurobiology in a rodent subject to natural selection, we evaluate potential candidates for the neural basis of maternal behaviours and strengthen the underestimated role of the sex chromosomes in shaping sex differences in brain and behaviours. All things considered, we further highlight the emergence of a third sexual phenotype, challenging the binary view of phenotypic sexes.
Monitoring and Tracking the Spread of SARS-CoV-2 in Asturias, Spain
Authors: Gonzalez-Alba Jose Maria , Rojo-Alba Susana , Perez-Martinez Zulema , Boga Jose A. , Alvarez-Arguelles Marta Elena , Gomez Juan , Herrero Pablo , Costales Isabel , Alba Luz Maria , Martin-Rodriguez Gabriel , Campo Rainer , Castelló-Abietar Cristian , Sandoval Marta , Abreu-Salinas Fátima , Coto Eliecer , Rodriguez Mercedes , Rubianes Pablo , Sanchez Maria Luisa , Vazquez Fernando , Antuña Luis , Álvarez Victoria , Melón García Santiago
Published: September 2023

Mutational analysis of SARS-CoV-2 can quantify their relative importance over time, enable the dominant mutations to be identified and facilitate near real-time detection, comparison, and tracking of evolving variants. Collected samples in Asturias an autonomous community of Spain with a large aged population, and high levels of migration and tourism was monitored and tracked from its beginning in February 2020 until its decline and stabilization in August 2021, were characterized using whole genomic sequence and single nucleotide polymorphism. Data held in the GISAID database was analyzed to establish patterns in the appearance and persistence of SARS-CoV-2 strains. Only 138 non-synonymous mutations occurring in more than 1% of the population of SARS-CoV-2 were found, identifying 10 major variants worldwide (7 arose before January 2021), 19 regional and 1 local. In Asturias only 17 different variants were found. After vaccination, no further regional majority variants were found. Only half of the defined variants circulated and no new variants were generated, indicating that infection control measures (fast diagnosis, prevention measures and vaccination) were efficient.
Unigems: plasmids and parts to facilitate teaching on assembly, gene expression control and logic in E. coli
Authors: Siddall Alex , Williams Abbie Ann , Sanders Jason , Denton Jai A. , Madden Dean , Schollar John , Bryk Jarosław
Published: September 2023

Synthetic biology enables the creative combination of engineering and molecular biology for exploration of fundamental aspects of biological phenomena. However, there are limited resources available for such applications in the educational context, where straightforward setup, easily measurable phenotypes and extensibility are of particular importance. We developed unigems, a set of ten plasmids that enable classroom-based investigation of gene-expression control and biological logic gates to facilitate teaching synthetic biology and genetic engineering. It is built on a high-copy plasmid backbone and is easily extensible thanks to a common primer set that facilitates Gibson assembly of PCR-generated or synthesized DNA parts into the target vector. It includes two reporter genes with either two constitutive (high- or low-level) or two inducible (lactose- or arabinose-) promoters, as well as a single-plasmid implementation of an AND logic gate. The set can readily be employed in undergraduate teaching settings, during outreach events and for training of iGEM teams. All plasmids have been deposited in Addgene.
Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health
Authors: Chase-Topping Margo , Dallman Timothy J. , Allison Lesley , Lupolova Nadejda , Matthews Louise , Mitchell Sonia , Banks Christopher J. , Prentice Jamie , Brown Helen , Tongue Sue , Henry Madeleine , Evans Judith , Gunn George , Hoyle Deborah , McNeilly Tom N. , Fitzgerald Stephen , Smith-Palmer Alison , Shaaban Sharif , Holmes Anne , Hanson Mary , Woolhouse Mark , Didelot Xavier , Jenkins Claire , Gally David L.
Published: September 2023

For the last two decades, the human infection frequency of

Escherichia coli

O157 (O157) in Scotland has been 2.5-fold higher than in England and Wales. Results from national cattle surveys conducted in Scotland and England and Wales in 2014/2015 were combined with data on reported human clinical cases from the same time frame to determine if strain differences in national populations of O157 in cattle could be associated with higher human infection rates in Scotland. Shiga toxin subtype (Stx) and phage type (PT) were examined within and between host (cattle vs human) and nation (Scotland vs England and Wales). For a subset of the strains, whole genome sequencing (WGS) provided further insights into geographical and host association. All three major O157 lineages (I, II, I/II) and most sub-lineages (Ia, Ib, Ic, IIa, IIb, IIc) were represented in cattle and humans in both nations. While the relative contribution of different reservoir hosts to human infection is unknown, WGS analysis indicated that the majority of O157 diversity in human cases was captured by isolates from cattle. Despite comparable cattle O157 prevalence between nations, strain types were localized. PT21/28 (sub-lineage Ic, Stx2a+) was significantly more prevalent in Scottish cattle [odds ratio (OR) 8.7 (2.3–33.7; P<0.001] and humans [OR 2.2 (1.5–3.2); P<0.001]. In England and Wales, cattle had a significantly higher association with sub-lineage IIa strains [PT54, Stx2c; OR 5.6 (1.27–33.3); P=0.011] while humans were significantly more closely associated with sub-lineage IIb [PT8, Stx1 and Stx2c; OR 29 (4.9–1161); P<0.001]. Therefore, cattle farms in Scotland were more likely to harbour Stx2a+O157 strains compared to farms in E and W (P<0.001). There was evidence of limited cattle strain migration between nations and clinical isolates from one nation were more similar to cattle isolates from the same nation, with sub-lineage Ic (mainly PT21/28) exhibiting clear national association and evidence of local transmission in Scotland. While we propose the higher rate of O157 clinical cases in Scotland, compared to England and Wales, is a consequence of the nationally higher level of Stx2a+O157 strains in Scottish cattle, we discuss the multiple additional factors that may also contribute to the different infection rates between these nations.
The role of sphingosine-1-phosphate receptor 2 in mouse retina light responses
Authors: Shrestha Abhishek P , Stiles Megan , Grambergs Richard C. , Boff Johane M. , Madireddy Saivikram , Mondal Koushik , Rajmanna Rhea , Porter Hunter , Sherry David , Proia Richard L. , Vaithianathan Thirumalini , Mandal Nawajes
Published: September 2023

The bioactive sphingolipid sphingosine-1-phosphate (S1P) acts as a ligand for a family of G protein-coupled S1P receptors (S1PR1-5) to participate in a variety of signaling pathways. However, their specific roles in the neural retina remain unclear. We previously showed that S1P receptor subtype 2 (S1PR2) is expressed in murine retinas, primarily in photoreceptors and bipolar cells, and its expression is altered by retinal stress. This study aims to elucidate the role of S1PR2 in the mouse retina. We examined light responses by electroretinography (ERG), structural differences by optical coherence tomography (OCT), and protein levels by immunohistochemistry (IHC) in wild-type (WT) and S1PR2 knockout (KO) mice at various ages between 3 and 6 months. We found that a- and b-wave responses significantly increased at flash intensities between 400∼2000 and 4∼2,000 cd.s/m2respectively, in S1PR2 KO mice relative to those of WT controls at baseline. S1PR2 KO mice also exhibited significantly increased retinal nerve fiber layer (RNFL) and outer plexiform layer (OPL) thickness by OCT relative to the WT. Finally, in S1PR2 KO mice, we observed differential labeling of synaptic markers by immunohistochemistry (IHC) and quantitative reverse transcription polymerase chain reaction (RT-qPCR). These results suggest a specific involvement of S1PR2 in the structure and synaptic organization of the retina and a potential role in light-mediated functioning of the retina.
Longitudinal Awake Imaging of Mouse Deep Brain Microvasculature with Super-resolution Ultrasound Localization Microscopy
Authors: Wang Yike , Lowerison Matthew R. , Huang Zhe , You Qi , Lin Bing-Ze , Llano Daniel A. , Song Pengfei
Published: September 2023

Ultrasound localization microscopy (ULM) is an emerging imaging modality that resolves microvasculature in deep tissues with high spatial resolution. However, existing preclinical ULM applications are largely constrained to anesthetized animals, introducing confounding vascular effects such as vasodilation and altered hemodynamics. As such, ULM quantifications (e.g., vessel diameter, density, and flow velocity) may be confounded by the use of anesthesia, undermining the usefulness of ULM in practice. Here we introduce a method to address this limitation and achieve ULM imaging in awake mouse brain. Pupillary monitoring was used to support the presence of the awake state during ULM imaging. Vasodilation induced by isoflurane was observed by ULM. Upon recovery to the awake state, reductions in vessel density and flow velocity were observed across different brain regions. In the cortex, the effects induced by isoflurane are more pronounced on venous flow than on arterial flow. In addition, serialin vivoimaging of the same animal brain at weekly intervals demonstrated the highly robust longitudinal imaging capability of the proposed technique. The consistency was further verified through quantitative analysis on individual vessels, cortical regions of arteries and veins, and subcortical regions. This study demonstrates longitudinal ULM imaging in the awake mouse brain, which is crucial for many ULM brain applications that require awake and behaving animals.
The tumor microbiome reacts to hypoxia and can influence response to radiation treatment in colorectal cancer
Authors: Benej Martin , Hoyd Rebecca , Kreamer McKenzie , Wheeler Caroline E. , Grencewicz Dennis J. , Choueiry Fouad , Chan Carlos H.F. , Zakharia Yousef , Ma Qin , Dodd Rebecca D. , Ulrich Cornelia M. , Hardikar Sheetal , Churchman Michelle L. , Tarhini Ahmad A. , Robinson Lary A. , Singer Eric A. , Ikeguchi Alexandra P. , McCarter Martin D. , Tinoco Gabriel , Husain Marium , Jin Ning , Tan Aik Choon , Osman Afaf E.G. , Eljilany Islam , Riedlinger Gregory , Schneider Bryan P. , Benejova Katarina , Kery Martin , Papandreou Ioanna , Zhu Jiangjiang , Denko Nicholas , Spakowicz Daniel
Published: September 2023

Tumor hypoxia has been shown to predict poor patient outcomes in several cancer types, partially because it reduces radiation’s ability to kill cells. We investigated whether some of the clinical effects of hypoxia could also be due to its impact on the tumor microbiome. We examined the RNA-seq data from the Oncology Research Information Exchange Network (ORIEN) database of colorectal cancer (CRC) patients treated with radiotherapy. For each tumor, we identified microbial RNAs and related them to the hypoxic gene expression scores calculated from host mRNA. Our analysis showed that the hypoxia expression score predicted poor patient outcomes and identified tumors enriched with certain microbes such asFusobacterium nucleatum. The presence of other microbes, such asFusobacterium canifelinum,predicted poor patient outcomes, suggesting a potential interaction between hypoxia, the microbiome, and radiation response. To investigate this concept experimentally, we implanted CT26 CRC cells into both immune-competent BALB/c and immune-deficient athymic nude mice. After growth, where tumors passively acquired microbes from the gastrointestinal tract, we harvested tumors, extracted nucleic acids, and sequenced host and microbial RNAs. We stratified tumors based on their hypoxia score and performed metatranscriptomic analysis of microbial gene expression. In addition to hypoxia-trophic and -phobic microbial populations, analysis of microbial gene expression at the strain level showed expression differences based on the hypoxia score. Hypoxia appears to not only associate with different microbial populations but also elicit an adaptive transcriptional response in intratumoral microbes.

SIGNIFICANCE

Tumor hypoxia reduces radiation’s ability to kill cells. We explored whether some of the clinical effects of hypoxia could also be due to interaction with the tumor microbiome. Hypoxic expression scores associated with certain microbes and elicited an adaptive transcriptional response in others.
Autometa 2: A versatile tool for recovering genomes from highly-complex metagenomic communities
Authors: Rees Evan R. , Uppal Siddharth , Clark Chase M. , Lail Andrew J. , Waterworth Samantha C. , Roesemann Shane D. , Wolf Kyle A. , Kwan Jason C.
Published: September 2023

In 2019, we developed Autometa, an automated binning pipeline that is able to effectively recover metagenome-assembled genomes from complex environmental and non-model host-associated microbial communities. Autometa has gained widespread use in a variety of environments and has been applied in multiple research projects. However, the genome-binning workflow was at times overly complex and computationally demanding. As a consequence of Autometa’s diverse application, non-technical and technical researchers alike have noted its burdensome installation and inefficient as well as error-prone processes. Moreover its taxon-binning and genome-binning behaviors have remained obscure. For these reasons we set out to improve its accessibility, efficiency and efficacy to further enable the research community during their exploration of Earth’s environments. The highly augmented Autometa 2 release, which we present here, has vastly simplified installation, a graphical user interface and a refactored workflow for transparency and reproducibility. Furthermore, we conducted a parameter sweep on standardized community datasets to show that it is possible for Autometa to achieve better performance than any other binning pipeline, as judged by Adjusted Rand Index. Improvements in Autometa 2 enhance its accessibility for non-bioinformatic oriented researchers, scalability for large-scale and highly-complex samples and interpretation of recovered microbial communities.

Graphical abstract

Autometa: An automated taxon binning and genome binning workflow for single sample resolution of metagenomic communities.
Crossing host boundaries: the evolutionary drivers and correlates of viral host jumps
Authors: Tan Cedric C.S. , van Dorp Lucy , Balloux Francois
Published: September 2023

Most emerging and re-emerging infectious diseases stem from viruses that naturally circulate in non-human vertebrates. When these viruses cross over into humans, they can cause disease outbreaks and epidemics. While zoonotic host jumps have been extensively studied from an ecological perspective, little attention has gone into characterising the evolutionary drivers and correlates underlying these events. To address this gap, we harnessed the entirety of publicly available viral genomic data, employing a comprehensive suite of network and phylogenetic analyses to investigate the evolutionary mechanisms underpinning recent viral host jumps. Notably, we challenge conventional assumptions about the directionality of host jumps, demonstrating that humans are as much a source as a sink for viral spillover events, insofar we infer more viral host jumps from humans to other animals, than from animals to humans. Moreover, we demonstrate heightened evolution in viral lineages that involve putative host jumps. We further observe that the extent of adaptation associated to a host jump is lower for viruses with broad host ranges. Finally, we show that the genomic targets of natural selection associated to host jumps vary across different viral families with either structural or auxiliary genes being the prime targets of selection. Collectively, our results illuminate some of the evolutionary drivers underlying viral host jumps that may contribute to mitigating viral threats across species boundaries.
Different sensory information is used for state estimation when stationary or moving
Authors: Wong Aaron L , Eyssalenne Alyssa N , Carter Luke , Therrien Amanda S
Published: September 2023

The accurate estimation of limb state is necessary for movement planning and execution. While state estimation requires both feedforward and feedback information, we focus here on the latter. Prior literature has shown that integrating visual and proprioceptive feedback improves estimates of static limb position. However, differences in visual and proprioceptive feedback delays suggest that multisensory integration could be disadvantageous when the limb is moving. We formalized this hypothesis by modeling feedback-based state estimation using the longstanding maximum likelihood estimation model of multisensory integration, which we updated to account for sensory delays. Our model predicted that the benefit of multisensory integration was largely lost when the limb was passively moving. We tested this hypothesis in a series of experiments in human subjects that compared the degree of interference created by discrepant visual or proprioceptive feedback when estimating limb position either statically at the end of the movement or dynamically at movement midpoint. In the static case, we observed significant interference: discrepant feedback in one modality systematically biased sensory estimates based on the other modality. However, no interference was seen in the dynamic case: participants could ignore sensory feedback from one modality and accurately reproduce the motion indicated by the other modality. Together, these findings suggest that the sensory feedback used to compute a state estimate differs depending on whether the limb is stationary or moving. While the former may tend toward multimodal integration, the latter is more likely to be based on feedback from a single sensory modality.

SIGNIFICANCE STATEMENT

The estimation of limb state involves feedforward and feedback information. While estimation based on feedback has been well studied when the limb is stationary, it is unknown if similar sensory processing supports limb position estimates when moving. Using a computational model and behavioral experiments, we show that feedback-based state estimation may involve multisensory integration in the static case, but it is likely based on a single modality when the limb is moving. We suggest that this difference may stem from visual and proprioceptive feedback delays.
Memory encoding and retrieval by retrosplenial parvalbumin interneurons is impaired in Alzheimer’s disease model mice
Authors: Park Kyerl , Kohl Michael M. , Kwag Jeehyun
Published: September 2023

Memory deficits in Alzheimer’s disease (AD) show a strong link with GABAergic interneuron dysfunctions1–7. Ensemble dynamics of GABAergic interneurons are critical in memory encoding and retrieval8–12but how GABAergic interneuron dysfunction affects inhibitory ensemble dynamics in AD is unknown. As retrosplenial cortex (RSC) is a brain area critical for episodic memory13–16and affected by beta-amyloid accumulation in early AD17–21, we address this question by performing Ca2+imaging in RSC parvalbumin-expressing (PV) interneurons during a contextual fear memory (CFM) task in healthy control mice and the 5XFAD mouse model of AD. We found that subpopulations of PV interneurons that were responsive to aversive electric foot shocks during contextual fear conditioning (CFC) in the control mice significantly decreased in the 5XFAD mice, indicating a dysfunction in the recruitment of CFM-encoding PV interneurons. In control mice, CFC-responsive PV interneuron ensemble activities were selectively upregulated during the freezing epoch of the CFM retrieval, manifested by CFC-induced synaptic potentiation of PV interneuron-mediated inhibition. However, CFC-induced changes in PV interneuron ensemble dynamics during CFM retrieval and synaptic plasticity were both absent in the 5XFAD mice. Optogenetic silencing of PV interneurons during CFC in control mice mimicked the CFM deficits in 5XFAD mice, while optogenetic activation of PV interneurons during CFC in the 5XFAD mice restored CFM retrieval. These results demonstrate the necessity and sufficiency of CFC-responsive PV interneurons for CFM retrieval and suggest that synaptic dysfunction in CFM-encoding PV interneurons disrupt the inhibitory ensemble dynamics underlying CFM retrieval, subsequently leading to memory deficits in AD.
Topological evolution of sprouting vascular networks: from day-by-day analysis to general growth rules
Authors: Rojek Katarzyna O. , Wrzos Antoni , Żukowski Stanisław , Bogdan Michał , Lisicki Maciej , Szymczak Piotr , Guzowski Jan
Published: September 2023

Engineering tissues with an embedded vasculature of well-controlled topology remains one of the basic problems in biofabrication. Still, little is known about the evolution of topological characteristics of vascular networks over time. Here, we perform a high-throughput day-by-day analysis of tens of microvasculatures that sprout from endothelial-cell coated micrometric beads embedded in an external fibrin gel. We use the bead-assays to systematically analyze (i) ‘macroscopic’ observables such as the overall length and area of the sprouts, (ii) ‘microscopic’ observables such as the lengths of segments or the branching angles and their distributions, as well as (iii) general measures of network complexity such as the average number of bifurcations per branch. We develop a custom angiogenic image analysis toolkit and track the evolution of the networks for at least 14 days of culture under various conditions, e.g., in the presence of fibroblasts or with added endothelial growth factor (VEGF). We find that the evolution always consists of three stages: (i) an inactive stage in which cells remain bound to the beads, (ii) a sprouting stage in which the sprouts rapidly elongate and bifurcate, and (iii) the maturation stage in which the growth slows down. We show that higher concentrations of VEGF lead to an earlier onset of sprouting and to a higher number of primary branches, yet without significantly affecting the speed of growth of the individual sprouts. We find that the mean branching angle is weakly dependent on VEGF and typically in the range of 60-75 degrees suggesting that, by comparison with the available Laplacian growth models, the sprouts tend to follow local VEGF gradients. Finally, we observe an exponential distribution of segment lengths, which we interpret as a signature of stochastic branching at a constant bifurcation rate (per unit branch length). Our results, due to high statistical relevance, may serve as a benchmark for predictive models and reveal how the external means of control, such as VEGF concentration, could be used to control the morphology of the vascular networks. We provide guidelines for the fabrication of optimized microvasculatures with potential applications in drug testing or regenerative medicine.
evopython: a Python package for feature-focused, comparative genomic data exploration
Authors: Mick Steven T. , Fiszbein Ana
Published: September 2023

Motivation

Software such asLiftOverallows for the intra- and inter-species conversion of genomic coordinates between genome assemblies, but this coordinate-centric workflow is naive to sequence alterations underling the conversion. For instance, it does not clarify the location of any insertions or deletions that might have occurred.

Results

To facilitate inter-species, sequence-based analyses, we developedevopython, a simple, object-oriented Python package that enables the sequence-aware resolution of genomic coordinates directly from pairwise and multiple whole-genome alignment data. The output is a Python dictionary storing all information relevant to the alignment: the participating species’ names, the position of the alignment in each species’ genome assembly, and the aligned sequences.

Availability and implementation

The source code and documentation are available athttps://github.com/fiszbein-lab/evopython.

Contact

anafisz@bu.edu
Assessing the links between pollinators and the genetic and epigenetic features of plant species with contrasting distribution ranges
Authors: Valverde Javier , Medrano Mónica , Herrera Carlos M. , Alonso Conchita
Published: September 2023

In flowering plants, pollinators contribute to gene flow while they also respond to variation in plant traits together determined by genetic, epigenetic and environmental sources of variation. Consequently, a correlation between abundance and diversity of pollinators and the genetic and epigenetic characteristics of plant populations such as diversity or distinctiveness is to be expected, yet no study has explored such long-term dimensions of plant-pollinator interactions. Mediterranean narrow endemics often exhibit unexpectedly high levels of population (epi)genetic diversity. We hypothesize that pollinators may contribute to explain this pattern. Specifically, we expect a stronger association of pollinators with population (epi)genetic variability in narrow endemics than in widely distributed congeners. We studied five pairs of congeneric plant species, consisting of one narrow endemic with a restricted distribution and one widespread congener, found in the Sierra de Cazorla mountains (SE Spain). In up to three populations per species, a comprehensive characterisation of pollinators was carried out to estimate pollinator diversity and visitation rate. Genetic and epigenetic diversity and distinctiveness of each population was calculated using AFLP markers and methylation-sensitive AFLP markers (MSAP) respectively. The relationships with pollinator diversity and visitation rate were assessed. The diversity of pollinators did not vary according to the plant distribution range, whereas visitation rate was higher in widespread species. As predicted, only narrow endemics showed a significant association between pollinators and their population genetic and epigenetic characteristics. Specifically, higher pollinator diversity and visitation rates entailed higher population genetic diversity and lower epigenetic distinctiveness. This work shows the value of exploring the relationships between pollinator abundance and diversity and population (epi)genetics for understanding the evolution of plant rarity.
Magnetic nanocomplexes coupled with an external magnetic field modulate macrophage phenotype – a non-invasive strategy for bone regeneration
Authors: Kumar Harshini Suresh , Yi Zhongchao , Tong Sheng , Annamalai Ramkumar T.
Published: September 2023

Chronic inflammation is a major cause for the pathogenesis of musculoskeletal diseases such as fragility fracture, and nonunion. Studies have shown that modulating the immune phenotype of macrophages from proinflammatory to prohealing mode can heal recalcitrant bone defects. Current therapeutic strategies predominantly apply biochemical cues, which often lack target specificity and controlling their release kineticsin vivois challenging spatially and temporally. We show a magnetic iron-oxide nanocomplexes (MNC)-based strategy to resolve chronic inflammation in the context of promoting fracture healing. MNC internalized pro-inflammatory macrophages, when coupled with an external magnetic field, exert an intracellular magnetic force on the cytoskeleton, which promotes a prohealing phenotype switch. Mechanistically, the intracellular magnetic force perturbs actin polymerization, thereby significantly reducing nuclear to cytoplasm redistribution of MRTF-A and HDAC3, major drivers of inflammatory and osteogenic gene expressions. This significantly reducesNos2gene expression and subsequently downregulates the inflammatory response, as confirmed by quantitative PCR analysis. These findings are a proof of concept to develop MNC-based resolution-centric therapeutic intervention to direct macrophage phenotype and function towards healing and can be translated either to supplement or replace the currently used anti-inflammatory therapies for fracture healing.
Comparative epigenetic and genetic spatial structure in Mediterranean mountain plants: a multispecific comparison
Authors: Valverde Javier , Medrano Mónica , Herrera Carlos M. , Alonso Conchita
Published: September 2023

Abstract

Epigenetic information can be heritable, but also respond to key environmental variables in situ, endowing individuals with an additional capacity to adapt to environmental changes. Thus, it is likely that in sesile organisms such as plants, part of the spatial epigenetic variation found across individuals will reflect the environmental heterogeneity of populations. Analysing the departure of the spatial epigenetic structure from the baseline genetic variation can help in understanding the value of epigenetic regulation in species with different breath of optimal environmental conditions. We performed a multispecies study that considered seven pairs of congeneric plant species, each encompassing a narrow endemic with habitat specialization and a widespread species. In three populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the spatial genetic and epigenetic structures. In contrast to widespread species, narrow endemics showed a significant and generalised lower epigenetic than genetic differentiation across species. Within most populations of narrow species, epigenetic variation was less spatially structured than the genetic variation. This pattern resulted from a lack of correlation between epigenetic and genetic information in populations of narrow endemics. We argue that the differences found between narrow endemics and widespread congeners reflect contrasting breaths of environmental requirements. We pose the hypothesis that in species with a narrow niche breath, epigenetic variation may be more similar across populations and among individuals within a population given the expected higher similarity in environmental requirements.
The simplicity of protein sequence-function relationships
Authors: Park Yeonwoo , Metzger Brian P.H. , Thornton Joseph W.
Published: September 2023

How complicated is the genetic architecture of proteins – the set of causal effects by which sequence determines function? High-order epistatic interactions among residues are thought to be pervasive, making a protein’s function difficult to predict or understand from its sequence. Most studies, however, used methods that overestimate epistasis, because they analyze genetic architecture relative to a designated reference sequence – causing measurement noise and small local idiosyncrasies to propagate into pervasive high-order interactions – or have not effectively accounted for global nonlinearity in the sequence-function relationship. Here we present a new reference-free method that jointly estimates global nonlinearity and specific epistatic interactions across a protein’s entire genotype-phenotype map. This method yields a maximally efficient explanation of a protein’s genetic architecture and is more robust than existing methods to measurement noise, partial sampling, and model misspecification. We reanalyze 20 combinatorial mutagenesis experiments from a diverse set of proteins and find that additive and pairwise effects, along with a simple nonlinearity to account for limited dynamic range, explain a median of 96% of total variance in measured phenotypes (and >92% in every case). Only a tiny fraction of genotypes are strongly affected by third- or higher-order epistasis. Genetic architecture is also sparse: the number of terms required to explain the vast majority of variance is smaller than the number of genotypes by many orders of magnitude. The sequence-function relationship in most proteins is therefore far simpler than previously thought, opening the way for new and tractable approaches to characterize it.
Simultaneous recording of ultrasonic vocalizations and sniffing from socially interacting individual rats using a miniature microphone
Authors: John Shanah Rachel , Tiwari Rishika , Goussha Yizhaq , Amar Rotem , Bizer Alex , Netser Shai , Wagner Shlomo
Published: September 2023

Vocalizations are pivotal in mammalian communication, especially in humans. Rodents accordingly rely on ultrasonic vocalizations (USVs) that reflect their internal state as a primary channel during social interactions. However, attributing vocalizations to specific individuals remains challenging, impeding internal state assessment. Rats emit 50 kHz USVs to indicate positive states and intensify sniffing during alertness and social interactions. Here, we present a method involving a miniature microphone attached to the rat nasal cavity that allows to capture both male and female individual rat vocalizations and sniffing patterns during social interactions. We found that while the emission of 50 kHz USVs increases during close interactions, these signals lack specific behavioral associations. Moreover, a previously unreported low-frequency vocalization type marking rat social interactions was uncovered. Finally, different dynamics of sniffing and vocalization activities point to distinct underlying internal states. Thus, our method facilitates the exploration of internal states concurrent with social behaviors.

Motivation

Here, we sought to solve the problem of identifying the emitter of a specific vocalization during free social interaction of animal models. The use of a miniature microphone carried by the subject and connected to its nasal cavity solved this challenge and allowed for assignment of any vocalization recorded during a social interaction to a specific individual. Moreover, the miniature microphone enabled simultaneous recording of sniffing and vocalization activities of an individual, thus facilitating recognition of the internal states underlying these traits.
Drugs of abuse hijack a mesolimbic pathway that processes homeostatic need
Authors: Tan Bowen , Browne Caleb J. , Nöbauer Tobias , Vaziri Alipasha , Friedman Jeffrey M. , Nestler Eric J.
Published: September 2023

Addiction prioritizes drug use over innate needs by “hijacking” brain circuits that direct motivation, but how this develops remains unclear. Using whole-brain FOS mapping andin vivosingle-neuron calcium imaging, we find that drugs of abuse augment ensemble activity in the nucleus accumbens (NAc) and disorganize overlapping ensemble responses to natural rewards in a cell-type-specific manner. Combining “FOS-Seq”, CRISPR-perturbations, and snRNA-seq, we identifyRhebas a shared molecular substrate that regulates cell-type-specific signal transductions in NAc while enabling drugs to suppress natural reward responses. Retrograde circuit mapping pinpoints orbitofrontal cortex which, upon activation, mirrors drug effects on innate needs. These findings deconstruct the dynamic, molecular, and circuit basis of a common reward circuit, wherein drug value is scaled to promote drug-seeking over other, normative goals.
Gene and protein sequence features augment HLA class I ligand predictions
Authors: Bresser Kaspar , Nicolet Benoit P , Jeko Anita , Wu Wei , Loayza-Puch Fabricio , Agami Reuven , Heck Albert JR , Wolkers Monika C , Schumacher Ton N
Published: September 2023

The sensitivity of malignant tissues to T cell-based cancer immunotherapies is dependent on the presence of targetable HLA class I ligands on the tumor cell surface. Peptide intrinsic factors, such as HLA class I affinity, likelihood of proteasomal processing, and transport into the ER lumen have all been established as determinants of HLA ligand presentation. However, the role of sequence features at the gene and protein level as determinants of epitope presentation has not been systematically evaluated. To address this, we performed HLA ligandome mass spectrometry on patient-derived melanoma lines and used this data-set to evaluate the contribution of 7,124 gene and protein sequence features to HLA sampling. This analysis reveals that a number of predicted modifiers of mRNA and protein abundance and turn-over, including predicted mRNA methylation and protein ubiquitination sites, inform on the presence of HLA ligands. Importantly, integration of gene and protein sequence features into a machine learning approach augments HLA ligand predictions to a comparable degree as predictive models that include experimental measures of gene expression. Our study highlights the value of gene and protein features to HLA ligand predictions.
Sodium channels expressed in nociceptors contribute distinctly to action potential subthreshold phase, upstroke and shoulder
Authors: Köster Phil Alexander , Leipold Enrico , Tigerholm Jenny , Maxion Anna , Namer Barbara , Stiehl Thomas , Lampert Angelika
Published: September 2023

Voltage-gated sodium channels (VGSC) in the peripheral nervous system shape action potentials (AP) and thereby support the detection of sensory stimuli. Most of the nine mammalian VGSC subtypes are expressed in nociceptors, but predominantly, three are linked to several human pain syndromes: while Nav1.7 is suggested to be a (sub-)threshold channel, Nav1.8 is thought to support the fast AP upstroke. Nav1.9, as it produces large persistent currents, is attributed a role in determining the resting membrane potential.

We characterized gating of Nav1.1-Nav1.3 and Nav1.5-Nav1.9 in manual patch clamp with focus on the AP subthreshold depolarization phase. Nav1.9 exhibited the most hyperpolarized activation while its fast inactivation resembled the depolarized inactivation of Nav1.8. For some VGSCs (e.g., Nav1.1 and Nav1.2), a positive correlation between ramp current and window current was detected.

Using a modified Hodgkin-Huxley model which accounts for the time needed for inactivation to occur, we used the acquired data to simulate two nociceptive nerve fiber types (an Aδ-and a mechano-insensitive C-nociceptor) containing VGSC conductances according to published human RNAseq data. Our simulations suggest that Nav1.9 is supporting both the AP upstroke and its shoulder. A reduced threshold for AP generation was induced by enhancing Nav1.7 conductivity or shifting its activation to more hyperpolarized potentials, as observed in Nav1.7-related pain disorders.

Here, we provide a comprehensive, comparative functional characterization of VGSCs relevant in nociception and describe their gating with Hodgkin-Huxley-like models, which can serve as a tool to study their specific contributions to AP shape and sodium channel-related diseases.

Disclaimer

Parts of this study were published as a preprint on bioRxiv: Köster, P.A., T. Stiehl, J. Tigerholm, A. Maxion, B. Namer, and A. Lampert. 2023. Biophysics of sodium channels during subthreshold depolarizationin vitroandin silico. bioRxiv. doi.org/10.1101/2023.09.03.556095 (Preprint posted September 6, 2023)

Subthreshold gating of seven sodium channels (Nav1.1-3, Nav1.5-8) is determined by manual patch clamp and, together with Nav1.9, integrated into a computer model of an Aδ-and a mechano-insensitive nociceptor (CMi). Simulations reveal contribution of Nav1.9 to the action potential upstroke and shoulder and prove useful for Nav1.7-related disease modelling.
Excitotoxic glutamate levels cause the secretion of resident endoplasmic reticulum proteins
Authors: Dossat Amanda M. , Trychta Kathleen A. , Fortuno Lowella V. , Richie Christopher T. , Harvey Brandon K.
Published: September 2023

Dysregulation of synaptic glutamate levels can lead to excitotoxicity such as that observed in stroke, traumatic brain injury, and epilepsy. The role of increased intracellular calcium (Ca2+) in the development of excitotoxicity is well established. However, less is known regarding the impact of glutamate on endoplasmic reticulum (ER)-Ca2+-mediated processes such as proteostasis. To investigate this, we expressed a secreted ER Ca2+modulated protein (SERCaMP) in primary cortical neurons to monitor exodosis, a phenomenon whereby ER calcium depletion causes the secretion of ER resident proteins that perform essential functions to the ER and the cell. Activation of glutamatergic receptors (GluRs) led to an increase in SERCaMP secretion indicating that normally ER resident proteins are being secreted in a manner consistent with ER Ca2+depletion. Antagonism of ER Ca2+channels attenuated the effects of glutamate and GluR agonists on SERCaMP release. We also demonstrate that endogenous proteins containing an ER retention sequence (ERS) are secreted in response to GluR activation supporting that neuronal activation by glutamate promotes ER exodosis. Ectopic expression of KDEL receptors attenuated the secretion of ERS-containing proteins caused by GluR agonists. Taken together, our data indicate that excessive GluR activation causes disruption of neuronal proteostasis by triggering the secretion of ER resident proteins through ER Ca2+depletion and describes a new facet of excitotoxicity.

Significance

During excitotoxicity, the excessive activation of glutamate receptors causes elevated intracellular calcium (Ca2+) that promotes cellular dysfunction and death. While the role of cytosolic Ca2+in excitotoxicity has been well-studied, the consequences of changes in endoplasmic reticulum (ER) Ca2+during excitotoxicity remains unclear. The relatively high concentration of calcium in the ER is necessary for ER resident proteins to function prop out essential functions and maintain cellular proteostasis. We show here that excitotoxic conditions destabilize the ER proteome by triggering ER resident protein secretion. Stabilizing ER Ca2+or overexpressing receptors that interact with ER resident proteins can prevent disruption of proteostasis associated with excitotoxicity. The present study provides a new link between excitotoxicity, ER Ca2+homeostasis, and the ER proteome.
How prior and p-value heuristics are used when interpreting data
Authors: Hermer Ethan , Irwin Ashley A. , Roche Dominique G. , Dakin Roslyn
Published: September 2023

Scientific conclusions are based on the ways that researchers interpret data, a process that is shaped by psychological and cultural factors. When researchers use shortcuts known as heuristics to interpret data, it can sometimes lead to errors. To test the use of heuristics, we surveyed 623 researchers in biology and asked them to interpret scatterplots that showed ambiguous relationships, altering only the labels on the graphs. Our manipulations tested the use of two heuristics based on major statistical frameworks: (1) the strong prior heuristic, where a relationship is viewed as stronger if it is expecteda priori, following Bayesian statistics, and (2) the p-value heuristic, where a relationship is viewed as stronger if it is associated with a small p-value, following null hypothesis statistical testing. Our results show that both the strong prior and p-value heuristics are common. Surprisingly, the strong prior heuristic was more prevalent among inexperienced researchers, whereas its effect was diminished among the most experienced biologists in our survey. By contrast, we find that p-values cause researchers at all levels to report that an ambiguous graph shows a strong result. Together, these results suggest that experience in the sciences may diminish a researcher’s Bayesian intuitions, while reinforcing the use of p-values as a shortcut for effect size. Reform to data science training in STEM could help reduce researchers’ reliance on error-prone heuristics.

Significance Statement

Scientific researchers must interpret data and statistical tests to draw conclusions. When researchers use shortcuts known as heuristics, it can sometimes lead to errors. To test how this occurs, we asked biologists to interpret graphs that showed an ambiguous relationship between two variables, and report whether the relationship was strong, weak, or absent. We altered features of the graph to test whether prior expectations or a statistic called the p-value could influence their interpretations. Our results indicate that both prior expectations and p-values can increase the probability that researchers will report that ambiguous data shows a strong result. These findings suggest that current training and research practices promote the use of error-prone shortcuts in decision-making.
Establishing a comprehensive web-based analysis platform forNicotiana benthamianagenome and transcriptome
Authors: Kurotani Ken-ichi , Hirakawa Hideki , Shirasawa Kenta , Tagiri Koya , Mori Moe , Ichihashi Yasunori , Suzuki Takamasa , Tanizawa Yasuhiro , Nakamura Yasukazu , Isobe Sachiko , Notaguchi Michitaka
Published: September 2023

Nicotiana benthamianahas long served as a crucial plant material extensively used in plant physiology research, particularly in the field of plant pathology, because of its high susceptibility to plant viruses. Additionally, it serves as a production platform to test vaccines and other valuable substances. Among its approximately 3.1 Gb genome, 57,583 genes have been annotated within a 61 Mb region. We created a comprehensive and easy-to-use platform to use transcriptomes for modern annotation. These tools allow to visualize gene expression profiles, draw molecular evolutionary phylogenetic trees of gene families, perform functional enrichment analyses, and facilitate output downloads. To demonstrate their utility, we analyzed the gene expression profiles of enzymes within the nicotine biosynthesis pathway, a secondary metabolic pathway characteristic of theNicotianagenus. Using the developed tool, expression profiles of the nicotine biosynthesis pathway genes were generated. The expression patterns of eight gene groups in the pathway were strongly expressed in the roots and weakly expressed in leaves and flowers ofN. benthamiana. The results were consistent with the established gene expression profiles inNicotiana tabacumand provided insights into gene family composition and expression trends. The compilation of this database tool can facilitate genetic analysis ofN. benthamianain the future.

Significance statement

A tool was developed to visualize gene expression profiles, draw molecular evolutionary phylogenetic trees of gene families, perform functional enrichment analyses, and facilitate output downloads ofNicotiana benthamiana. The database developed using the tool can evolve into a comprehensive all-in-one analysis platform by continuously incorporating transcriptome data released to date, newly released RNA-seq data, and annotations in the future.