bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantification of the escape from X chromosome inactivation with the million cell-scale human single-cell omics datasets reveals heterogeneity of escape across cell types and tissues
Authors: Tomofuji Yoshihiko , Edahiro Ryuya , Shirai Yuya , Kock Kian Hong , Sonehara Kyuto , Wang Qingbo S. , Namba Shinichi , Moody Jonathan , Ando Yoshinari , Suzuki Akari , Yata Tomohiro , Ogawa Kotaro , Namkoong Ho , Lin Quy Xiao Xuan , Buyamin Eliora Violain , Tan Le Min , Sonthalia Radhika , Han Kyung Yeon , Tanaka Hiromu , Lee Ho ,   Asian Immune Diversity Atlas Network,   Japan COVID-19 Task Force,   The BioBank Japan Project, Okuno Tatsusada , Liu Boxiang , Matsuda Koichi , Fukunaga Koichi , Mochizuki Hideki , Park Woong-Yang , Yamamoto Kazuhiko , Hon Chung-Chau , Shin Jay W. , Prabhakar Shyam , Kumanogoh Atsushi , Okada Yukinori
Published: October 2023

One of the two X chromosomes of females is silenced through X chromosome inactivation (XCI) to compensate for the difference in the dosage between sexes. Among the X-linked genes, several genes escape from XCI, which could contribute to the differential gene expression between the sexes. However, the differences in the escape across cell types and tissues are still poorly characterized because no methods could directly evaluate the escape under a physiological condition at the cell-cluster resolution with versatile technology. Here, we developed a method,single-cellLevelinactivatedXchromosome mapping (scLinaX), which directly quantifies relative gene expression from the inactivated X chromosome with droplet-based single-cell RNA-sequencing (scRNA-seq) data. The scLinaX and differentially expressed genes analyses with the scRNA-seq datasets of ∼1,000,000 blood cells consistently identified the relatively strong degree of escape in lymphocytes compared to myeloid cells. An extension ofscLinaXformulti-modal datasets,scLinaX-multi, suggested a stronger degree of escape in lymphocytes than myeloid cells at the chromatin-accessibility level with a 10X multiome dataset. The scLinaX analysis with the human multiple-organ scRNA-seq datasets also identified the relatively strong degree of escape from XCI in lymphoid tissues and lymphocytes. Finally, effect size comparisons of genome-wide association studies between sexes identified the larger effect sizes of thePRKXgene locus-lymphocyte counts association in females than males. This could suggest evidence of the underlying impact of escape on the genotype–phenotype association in humans. Overall, scLinaX and the quantified catalog of escape identified the heterogeneity of escape across cell types and tissues and would contribute to expanding the current understanding of the XCI, escape, and sex differences in gene regulation.
Spatial mapping of acoustic impedance of shrimp scale using multiple overlap discrete wavelet transform (moDWT)
Authors: Ojha Shivam , Agarwal Komal , Khan M Sarim Ameed , Shelke Amit , Habib Anowarul
Published: October 2023

There are lots of challenges associated with conventional optical observation of biological tissues, where specimens are typically sliced and stained for better contrast. In contrast, Scanning Acoustic Microscopy (SAM) is a versatile label-free imaging technology widely applied in various domains, including biomedical imaging, non-destructive testing, and material research. It excels in offering precise visualization of both surface and subsurface structures, providing valuable insights through visual inspection and quantitative analysis. Acknowledging the SAM, this paper presents acoustic impedance microscopy of the shrimp scale in a novel manner. The proposed technique aims to image the local distribution of cross-sectional acoustic impedance in biological tissue, which is a parameter closely related to sound speed and potentially valuable for tissue characterization. The study leverages advanced signal processing techniques, maximal overlap discrete wavelet transform (moDWT), to decompose acoustic responses effectively. The moDWT, with its ability to handle signals of various lengths without constraints, is highlighted as a promising approach. To determine shrimp scale impedance, we first establish the accuracy of the proposed algorithm using PVDF as the target and polyimide as reference material. The results indicate an algorithm accuracy exceeding 90%. An impedance map is generated through Gaussian process regression (GPR), which predicts the impedance over the complete domain, addressing spatial variations in biological specimens. The resulting acoustic impedance maps provide in-depth insights into the functional framework and advance our understanding of shrimp biomechanics.
Inferring state-dependent diversification rates using approximate Bayesian computation (ABC)
Authors: Xie Shu , Valente Luis , Etienne Rampal S.
Published: October 2023

State-dependent speciation and extinction (SSE) models provide a framework for quantifying whether species traits have an impact on evolutionary rates and how this shapes the variation in species richness among clades in a phylogeny. However, SSE models are becoming increasingly complex, limiting the application of likelihood-based inference methods. Approximate Bayesian computation (ABC), a likelihood-free approach, is a potentially powerful alternative for estimating parameters. One of the key challenges in using ABC is the selection of efficient summary statistics, which can greatly affect the accuracy and precision of the parameter estimates. In state-dependent diversification models, summary statistics need to capture the complex relationships between rates of diversification and species traits. Here, we develop an ABC framework to estimate state-dependent speciation, extinction and transition rates in the BiSSE (binary state dependent speciation and extinction) model. Using different sets of candidate summary statistics, we then compare the inference ability of ABC with that of using likelihood-based maximum likelihood (ML) and Markov chain Monte Carlo (MCMC) methods. Our results show the ABC algorithm can accurately estimate state-dependent diversification rates for most of the model parameter sets we explored. The inference error of the parameters associated with the species-poor state is larger with ABC than in the likelihood estimations only when the speciation rate is highly asymmetric between the two states (λ1/λ0= 5). Furthermore, we find that the combination of normalized lineage-through-time (nLTT) statistics and phylogenetic signal in binary traits (Fitz and Purvis’sD) constitute efficient summary statistics for the ABC method. By providing insights into the selection of suitable summary statistics, our work aims to contribute to the use of the ABC approach in the development of complex state-dependent diversification models, for which a likelihood is not available.
Minimally Sufficient Experimental Design using Identifiability Analysis
Authors: Gevertz Jana L. , Kareva Irina
Published: October 2023

Mathematical models are increasingly being developed and calibrated in tandem with data collection, empowering scientists to intervene in real time based on quantitative model predictions. Well-designed experiments can help augment the predictive power of a mathematical model but the question of when to collect data to maximize its utility for a model is non-trivial. Here we define data as model-informative if it results in a unique parametrization, assessed through the lens of practical identifiability. The framework we propose identifies an optimal experimental design (how much data to collect and when to collect it) that ensures parameter identifiability (permitting confidence in model predictions), while minimizing experimental time and costs. We demonstrate the power of the method by applying it to a modified version of a classic site-of-action pharmacokinetic/pharmacodynamic model that describes distribution of a drug into the tumor microenvironment (TME), where its efficacy is dependent on the level of target occupancy in the TME. In this context, we identify a minimal set of time points when data needs to be collected that robustly ensures practical identifiability of model parameters. The proposed methodology can be applied broadly to any mathematical model, allowing for the identification of a minimally sufficient experimental design that collects the most informative data.
Enhanced KNa1.1 Channel Underlies Cortical Hyperexcitability and Seizure Susceptibility after Traumatic Brain Injury
Authors: Liu Ru , Sun Lei , Du Le , Guo Xi , Jia Meng , Wang Qun , Wu Jianping
Published: October 2023

Pathogenic variants of the sodium-activated potassium channel KNa1.1, have been reported in multiple epileptic disorders. However, whether and how KNa1.1 channel is involved in epileptogenesis after traumatic brain injury (TBI) remains unknown. Firstly, we used behavioral monitoring and EEG recording to examine physiological property, spontaneous seizure activity, and seizure susceptibility after TBI. We explored the changes of KNa1.1 channel following TBI, including changes of subcellular distribution and expression pattern. Meanwhile, we performed patch-clamp recording to detect the neuronal excitability. Furthermore, we built TBI model usingkcnt1−/−mice and compared seizure activity with those on wild- type mice. We found severity-dependent seizure susceptibility in different degree of injured mice. Meanwhile, increased neuronal expression of KNa1.1 channel, especially in inhibitory neurons, around the lesion was also observed following TBI with increased neuronal excitability including reduced firing rate of interneurons and imbalanced excitation and inhibition (E/I). Although the maximum frequency of action potential ofkcnt1−/−neurons was increased,kcnt1−/−mice displayed decreased seizure susceptibility to the pentylenetetrazole (PTZ) after TBI. Taken together, this study suggests that pathologically enhanced expression and abnormally distributed KNa1.1 channel after TBI contribute to disputed E/I and seizure susceptibility, which might provide a potential therapeutic target on the epileptogenesis after TBI.
Multi-omics profiling reveals ethylene signalling as a key pathway underlying both genetic and epigenetic responses to low-dose ionizing radiation inArabidopsis
Authors: Newman Jeremy R B , Zhou Mingqi , Pires J. Chris , Bacher Rhonda L , Kladde Michael , Concannon Patrick
Published: October 2023

There is increasing interest in the effects of low-dose ionizing radiation (IR) on plants as might occur during spaceflight, or as a consequence of human activities, such as nuclear power generation, that may result in the release of radioactive materials into the environment. High IR doses have long been used for the induction of mutations in plants with the goal of generating desirable traits for agribusiness. Less is known about the responses of plants to acute low doses of IR exposure. Here, we take a multi-omics approach to characterize the response to low dose IR inArabidopsis thaliana. We adapt the Methyltransferase Accessibility Protocol for individual templates (MAPit) technique for use in plants allowing us to assay the epigenetic response to acute low-dose IR (10 cGy and 100 cGy) 72 hr after exposure, and, in parallel, use RNA sequencing to profile the transcription response at 1, 3, 24 and 72 hr after exposure. IR exposures as low as 10 cGy elicit robust genetic responses inA. thalianadetectable as early as 1 hr after exposure. Further examination revealed dose-dependent changes in gene expression, chromatin accessibility and DNA methylation that implicate the ethylene signalling pathway and abiotic stress response as underlying the transcriptional and epigenetic changes associated with IR. These changes are observable up to 72 hr post-exposure, suggesting that they are maintained well after the initial acute exposure. Our findings indicate thatA. thalianaexecutes a multi-modal response to low-dose IR through induction and regulation of the ethylene response pathway.
Assessing the potential for genome-assisted breeding in red perilla using quantitative trait locus analysis and genomic prediction
Authors: Kinoshita Sei , Sakurai Kengo , Hamazaki Kosuke , Tsusaka Takahiro , Sakurai Miki , Kurosawa Terue , Aoki Youichi , Shirasawa Kenta , Isobe Sachiko , Iwata Hiroyoshi
Published: October 2023

Red perilla is an important medicinal plant used in Kampo medicine, and the development of elite varieties of this species is urgently necessary. Medicinal compounds are generally considered target traits in medicinal plant breeding; however, selection based on the phenotypes of the compounds (i.e., conventional selection) is expensive and time-consuming. Here, we proposed genomic selection (GS) and marker-assisted selection (MAS) as suitable selection methods for medicinal plants, and evaluated the effectiveness of GS and MAS in red perilla breeding. Three breeding populations generated from crosses between one red and three green perilla genotypes were used to elucidate the genetic mechanisms underlying the production of major medicinal compounds using quantitative trait locus analysis and to evaluate the accuracy of genomic prediction (GP). We found that GP had sufficiently high accuracy for all traits, confirming that GS was an effective method for perilla breeding. Moreover, the three populations showed varying degrees of segregation, suggesting that use of these populations in breeding may yield simultaneous enhancements of different target traits. This study can contribute to research on the genetic mechanisms of the major medicinal compounds of red perilla as well as the breeding efficiency of this medicinal plant.
Development of covalent chemogenetic K2Pchannel activators
Authors: Deal Parker E. , Lee Haerim , Mondal Abhisek , Lolicato Marco , de Mendonca Philipe Ribeiro Furtado , Black Holly , El-Hilali Xochina , Bryant Clifford , Isacoff Ehud Y. , Renslo Adam R. , Minor Daniel L.
Published: October 2023

K2Ppotassium channels regulate excitability by affecting cellular resting membrane potential in the brain, cardiovascular system, immune cells, and sensory organs. Despite their important roles in anesthesia, arrhythmia, pain, hypertension, sleep, and migraine, the ability to control K2Pfunction remains limited. Here, we describe a chemogenetic strategy termed CATKLAMP (CovalentActivation ofTREK familyK+channels to cLAmpMembranePotential) that leverages the discovery of a site in the K2Pmodulator pocket that reacts with electrophile-bearing derivatives of a TREK subfamily small molecule activator, ML335, to activate the channel irreversibly. We show that the CATKLAMP strategy can be used to probe fundamental aspects of K2Pfunction, as a switch to silence neuronal firing, and is applicable to all TREK subfamily members. Together, our findings exemplify a new means to alter K2Pchannel activity that should facilitate studies both molecular and systems level studies of K2Pfunction and enable the search for new K2Pmodulators.
Keratinocytes Drive the Epithelial Hyperplasia Key to Sea Lice Resistance in Coho Salmon
Authors: Salisbury S.J. , Daniels R. Ruiz , Monaghan S.J. , Bron J.E. , Villamayor P.R. , Gervais O. , Fast M.D. , Sveen L. , Houston R.D. , Robinson N. , Robledo D.
Published: October 2023

Background

Salmonid species have followed markedly divergent evolutionary trajectories in their interactions with sea lice. While sea lice parasitism poses significant economic, environmental, and animal welfare challenges for Atlantic salmon (Salmo salar) aquaculture, coho salmon (Oncorhynchus kisutch) exhibit near-complete resistance to sea lice, achieved through a potent epithelial hyperplasia response leading to rapid louse detachment. The molecular mechanisms underlying these divergent responses to sea lice are unknown.

Results

We characterised the cellular and molecular responses of Atlantic salmon and coho salmon to sea lice using single-nuclei RNA sequencing. Juvenile fish were exposed to copepodid sea lice (Lepeophtheirus salmonis), and lice-attached pelvic fin and skin samples were collected 12h, 24h, 36h, 48h, and 60h after exposure, along with control samples. Comparative analysis of control and treatment samples revealed an immune and wound-healing response that was common to both species, but attenuated in Atlantic salmon, potentially reflecting greater sea louse immunomodulation. Our results revealed unique but complementary roles of three layers of keratinocytes in the epithelial hyperplasia response leading to rapid sea lice rejection in coho salmon. Our results suggest that basal keratinocytes direct the expansion and mobility of intermediate and, especially, superficial keratinocytes, which eventually encapsulate the parasite.

Conclusion

Our results highlight the key role of keratinocytes to coho salmon’s sea lice resistance, and the diverged biological response of the two salmonid host species when interacting with this parasite. This study has identified key pathways and candidate genes that could be manipulated using various biotechnological solutions to improve Atlantic salmon sea lice resistance.
Chemical proteomics reveals that the anticancer drug everolimus affects ubiquitin-proteasome system
Authors: Lobas Anna A. , Saei Amir Ata , Lyu Hezheng , Zubarev Roman A. , Gorshkov Mikhail V.
Published: October 2023

Rapamycin is a natural antifungal, immunosuppressive, and antiproliferative compound allosterically inhibiting mTOR complex 1. The ubiquitin-proteasome system (UPS) responsible for protein turnover is usually not listed among the pathways affected by mTOR signaling; however, a number of reports indicated the interplay between UPS and mTOR. It is also reported that rapamycin and analogs can allosterically inhibit the proteasome itself. We studied the molecular effect of rapamycin and its analogs (rapalogs), everolimus, and temsirolimus by expression chemical proteomics on A549 cell line. The analysis revealed that the cellular response to everolimus differs dramatically from that of rapamycin and temsirolimus. In cluster analysis the effect of everolimus was similar to that of bortezomib, a well-established proteasome inhibitor. UPS-related pathways were enriched in the cluster of proteins specifically up-regulated upon everolimus and bortezomib treatments, suggesting that both compounds have similar proteasome inhibition effects. In particular, the total amount of ubiquitin was significantly elevated in the samples treated with everolimus and bortezomib, and the analysis of the polyubiquitination patterns revealed elevated intensities of the ubiquitin peptide with a GG modification at K48 residue, consistent with a bottleneck in the proteasomal protein degradation. Moreover, everolimus treatment resulted in both ubiquitin phosphorylation and a significant amount of semi-tryptic peptides illustrating the induction of protease activity. These observations suggest that everolimus affects the ubiquitin-proteasome system in a unique way and its mechanism of action is strikingly different from that of its close chemical analogs, rapamycin and temsirolimus. Data are available via ProteomeXchange with identifier PXD045774.
Multi-omics Identification and Route-Specific Characterization of Metastasis-specific EMT Genes and Their Microenvironmental Interactions
Authors: Kim Ki Tae , Lee Jae Eun , Cheong Jae-Ho , Cho In , Choi Yoon Young
Published: October 2023

Background

Gastric cancer (GC) constitute a significant cause of cancer-related mortality worldwide, with metastatic patterns including hematogenous, peritoneal, and ovarian routes. Although GC gene expression patterns have been extensively researched, the metastasis-specific gene expression landscape remains largely unexplored.

Methods

We undertook a whole transcriptome sequencing analysis of 66 paired primary and metastatic (hematogenous, peritoneal, or ovarian) GC tumors from 14 patients. Public databases including The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) was used for validation. Single-cell RNA sequencing (scRNA-seq) of four ascites from serosa positive GC patients and five primary tumors by layer (superficial and deep) were analyzed.

Results

Through differential expression analysis between paired primary and metastatic tumors by routes identified 122 unique metastasis-specific epithelial-mesenchymal transition (msEMT) genes. These genes demonstrated varying expression patterns depending on the metastatic route, suggesting route-specific molecular mechanisms in GC metastasis. High expression of msEMT genes in primary tumors was associated with more frequentCDH1mutations, the genomically stable subtype, and poor prognosis in TCGA GC cohort. This association was further corroborated by poor prognosis and high predictive performance for peritoneal/ovarian recurrence in two independent cohorts (GSE66229; n=300, GSE84437; n=433). scRNA-seq analysis of five primary tumors (GSE167297) and four independent ascites samples from GC patients revealed that msEMT genes were predominantly expressed in diverse fibroblast sub-populations, rather than cancer cells.

Conclusions

This study illuminates the route-specific mechanisms and underlines the significance of msEMT genes and cancer-associated fibroblasts in peritoneal metastasis of GC.
Methylphenidate modulates motor cortical dynamics and behavior
Authors: Verhein Jessica R. , Vyas Saurabh , Shenoy Krishna V.
Published: October 2023

Methylphenidate (MPH, brand: Ritalin) is a common stimulant used both medically and non-medically. Though typically prescribed for its cognitive effects, MPH also affects movement. While it is known that MPH noncompetitively blocks the reuptake of catecholamines through inhibition of dopamine and norepinephrine transporters, a critical step in exploring how it affects behavior is to understand how MPH directly affects neural activity. This would establish an electrophysiological mechanism of action for MPH. Since we now have biologically-grounded network-level hypotheses regarding how populations of motor cortical neurons plan and execute movements, there is a unique opportunity to make testable predictions regarding how systemic MPH administration – a pharmacological perturbation – might affect neural activity in motor cortex. To that end, we administered clinically-relevant doses of MPH to Rhesus monkeys as they performed an instructed-delay reaching task. Concomitantly, we measured neural activity from dorsal premotor and primary motor cortex. Consistent with our predictions, we found dose-dependent and significant effects on reaction time, trial-by-trial variability, and movement speed. We confirmed our hypotheses that changes in reaction time and variability were accompanied by previously established population-level changes in motor cortical preparatory activity and the condition-independent signal that precedes movements. We expected changes in speed to be a result of changes in the amplitude of motor cortical dynamics and/or a translation of those dynamics in activity space. Instead, our data are consistent with a mechanism whereby the neuromodulatory effect of MPH is to increase the gain and/or the signal-to-noise of motor cortical dynamics during reaching. Continued work in this domain to better understand the brain-wide electrophysiological mechanism of action of MPH and other psychoactive drugs could facilitate more targeted treatments for a host of cognitive-motor disorders.
Spatially Resolved Gene Expression is Not Necessary for Identifying Spatial Domains
Authors: Lin Senlin , Zhao Yi , Yuan Zhiyuan
Published: October 2023

The development of Spatially Resolved Transcriptomics (SRT) technologies has revolutionized the study of tissue organization. We introduce a graph convolutional network with an attention and positive emphasis mechanism, named “BINARY,” relying exclusively on binarized SRT data to delineate spatial domains. BINARY outperforms existing methods across various SRT data types while using significantly less input information. Our study suggests that precise gene expression quantification may not always be essential, inspiring further exploration of the broader applications of spatially resolved binarized gene expression data.
PAK1 and NF2/Merlin jointly drive myelination by remodeling actin cytoskeleton in oligodendrocytes
Authors: Baudouin Lucas , Adès Noémie , Kanté Kadia , Bachelin Corinne , Hmidan Hatem , Deboux Cyrille , Panic Radmila , Messaoud Rémy Ben , Velut Yoan , Hamada Soumia , Pionneau Cédric , Duarte Kévin , Poëa-Guyon Sandrine , Barnier Jean-Vianney , Oumesmar Brahim Nait , Bouslama-Oueghlani Lamia
Published: October 2023

In the central nervous system (CNS), myelin formation by oligodendrocytes (OLs) relies on actin dynamics. Actin polymerization supports the ensheathment step, when the OL process contacts the axon, while a drastic shift to actin depolymerization is required to enable the following step of wrapping and expansion of myelin membranes. The molecular mechanisms triggering this switch, essential for proper myelination, have yet to be elucidated. Here, we identify P21-activated kinase 1 (PAK1) as a major regulator of actin depolymerization in OLs. We show that PAK1 accumulates in OLs in a kinase inhibited form, triggering actin disassembly and, consequently, myelin expansion. Remarkably, we identify NF2/Merlin as an endogenous inhibitor of PAK1 by proteomics analysis of its binding partners. We found thatNf2knockdown in OLs results in PAK1 activation and impairs myelin formation, and that pharmacological inhibition of PAK1 inNf2-knockdown OLs rescues these defects. Moreover, we demonstrate that modulating PAK1 activity in OLs controls myelin expansion and provide compelling evidence indicating that specificPak1loss-of-function in oligodendroglia stimulates the thickening of myelin sheathsin vivo. Overall, our data indicate that PAK1-NF2/Merlin duo plays a key role in actin cytoskeleton remodeling in OLs, required for proper myelin formation. These findings have broad mechanistic and therapeutic implications for demyelinating diseases and neurodevelopmental disorders.

Significance

Remodeling actin cytoskeleton plays a crucial role in myelin formation by oligodendrocytes (OLs). Recent studies have shown that expansion and wrapping of myelin membranes around axons depends on actin depolymerization. However, the molecular mechanisms triggering this key step in myelination are not fully elucidated. Using genetic and pharmacological tools as well as proteomics analyses, we found that PAK1 (P21 Activated Kinase 1) kinase activity is maintained inhibited by NF2/Merlin in OLs to allow actin depolymerization and, consequently, myelin membrane expansion.Pak1loss-of-function in OLs leads to an increase in myelin thickness in the white matter of adult mice, confirming the role of PAK1 inactivation in myelin membrane expansion.
Gastrulation-stage gene expression inNipbl+/-mouse embryos foreshadows the development of syndromic birth defects
Authors: Chea Stephenson , Kreger Jesse , Lopez-Burks Martha E. , MacLean Adam L. , Lander Arthur D. , Calof Anne L.
Published: October 2023

In animal models,Nipbl-deficiency phenocopies gene expression changes and birth defects seen in Cornelia de Lange Syndrome (CdLS), the most common cause of which isNipbl-haploinsufficiency. Previous studies inNipbl+/-mice suggested that heart development is abnormal as soon as cardiogenic tissue is formed. To investigate this, we performed single-cell RNA-sequencing on wildtype (WT) andNipbl+/-mouse embryos at gastrulation and early cardiac crescent stages.Nipbl+/-embryos had fewer mesoderm cells than WT and altered proportions of mesodermal cell subpopulations. These findings were associated with underexpression of genes implicated in driving specific mesodermal lineages. In addition,Nanogwas found to be overexpressed in all germ layers, and many gene expression changes observed inNipbl+/-embryos could be attributed toNanogoverexpression. These findings establish a link betweenNipbl-deficiency,Nanogoverexpression, and gene expression dysregulation/lineage misallocation, which ultimately manifest as birth defects inNipbl+/-animals and CdLS.

Teaser

Gene expression changes during gastrulation ofNipbl-deficient mice shed light on early origins of structural birth defects.
Length measurement of cholinergic innervation in the tunica albuginea of rat testis
Authors: Santamaría Luis , Ingelmo Ildefonso
Published: October 2023

The testicular albuginea is not a simple receptacle that contains the testis parenchyma. It is a biologically active structure involved, among other things, in the progression of sperm from the seminiferous tubules to the rete testis. This function, attributed to the albuginea myofibroblasts’ contractile properties, is mediated by its vegetative innervation. Therefore, the quantification of innervation seems relevant to deepen the knowledge of the testicular envelope’s physiology. The albuginea contains cholinergic nerve fibers that are not very evident and with a marked directional arrangement (anisotropy). These structural characteristics require that the quantification of the fibers’ length be carried out using stereological measurements, which ensure the absence of bias in the process. The authors have developed stereological tools usually carried out on vertical VUR (vertical uniform random) sections in the present work. This approach’s novelty is that the albuginea is treated "in toto" as if it were a thick section (slice) on which a cycloid grid is applied through different optical planes. Thus, on a pilot study of three specimens, cholinergic nerve fibers’ length density was estimated, as well as the estimates of the coefficient of error of measurements and the biological variability of the sample.

Furthermore, after estimating the albuginea volume, the mean of the fibers’ absolute length can be obtained. This stereological approach can be used after visualization of the immunostained nerve fibers for various markers, as long as the reagents’ penetration into the tissue is ensured. Moreover, it can be used in other biological structures, such as the intestine of small animals, which can also be processed as whole mounts and treated as thick VUR sections.
Drosophila Bchsoverexpression recapitulates humanWDFY3neurodevelopmental phenotypes with implications for glial cell involvement in altered head circumference
Authors: Körner Marek B. , Velluva Akhil , Bundalian Linnaeus , Krohn Knut , Schön Kathleen , Schumann Isabell , Kromp Jessica , Thum Andreas S. , Garten Antje , Hentschel Julia , Jamra Rami Abou , Mrestani Achmed , Scholz Nicole , Langenhan Tobias , Le Duc Diana
Published: October 2023

The autophagy adaptorWDFY3is linked to neurodevelopmental delay and altered brain size. Loss-of-function variants are associated with an increased brain size in both humans and mice. We thus, hypothesized that the microcephaly observed in some of the patients may be related to a gain-of-function of theWDFY3gene product. While the role ofWDFY3loss-of-function has been studied extensively in neurons, little is known about the effects ofWDFY3overexpression in different neural cell types. We utilized aDrosophila melanogasteroverexpression model to investigate the effect of theWDFY3orthologBchs(blue cheese) on development, CNS size, and gene expression profiles. Glial and neuronal overexpression ofBchsimpaired CNS development, locomotion and autophagy. Glial overexpression ofBchsalso altered CNS size significantly. We identified 79 genes that were differentially expressed and overlapped in flies that overexpressBchsin glial and neuronal cells, respectively. Additionally, upon neuronalBchsoverexpression differentially expressed genes clustered in gene ontology categories associated with autophagy and mitochondria. Our data indicate thatWDFY3/Bchsoverexpression in both neurons and glial cells results in impaired neural development, which corresponds to symptoms observed inWDFY3-related neurodevelopmental delay.
A control policy can be adapted to task demands during both motor execution and motor planning
Authors: Orban de Xivry Jean-Jacques , Hardwick Robert
Published: October 2023

Movement planning consists of several processes related to the preparation of a movement such as decision making, target selection, application of task demands, action selection and specification of movement kinematics. These numerous processes are reflected in the reaction time, which is the time that it takes to start executing the movement. However, not all the processes that lead to motor planning increase reaction time. In this paper, we wanted to test whether tuning the control policy to task demands contributes to reaction time. Taking into account that the tuning of the control policy differs for narrow and wide targets, we used a timed response paradigm in order to track the amount of time needed to tune the control policy appropriately to task demands. We discovered that it does not take any time during motor planning and even that it can occur indistinguishably during motor planning or during motor execution. That is, the tuning the control policy was equally good when the narrow or wide target was displayed before than when it was displayed after the start of the movement. These results suggest that the frontier between motor planning and execution is not as clear cut as it is often depicted.

New & Noteworthy

Movement preparation consists of different processes such as target selection, and movement parameters selection. We investigate the time that it takes to tune movement parameters to task demands. We found that the brain does this instantaneously and that this can even happen during movement. Therefore, this suggests that there exists an overlap during movement planning and execution.
DEGRADATIVE POTENTIALS OF BACTERIA ISOLATED FROM CRUDE OIL CONTAMINATED SOIL
Authors: Augustine Jennifer Ada
Published: October 2023

Petroleum and its products continue to serve as a principle source of energy for industries and daily life. However, their release into the environment is a worldwide concern since some products are acutely toxic or possess mutagenic, teratogenic and carcinogenic properties. Several oil disposal methods have been applied over time with remediation emerging as the most promising technology. It takes advantage of the versatility of soil microbes to degrade hydrocarbon contaminants. Unlike conventional disposal methods, bioremediation ids an environmentally friendly and cost effective method that stimulate natural processes for complete degradation of hydrocarbons into innocuous compounds. This study focused on isolation, morphological and biochemical characterization of bacteria possessing hydrocarbon degrading properties. The study also aimed at optimizing appropriate culture conditions for the isolates. Isolation of hydrocarbon degrading bacteria from soils polluted with crude oil in Elebel, Emeyal I, Emeyal II in Ogbia, Bayelsa State was carried out using mineral salt medium supplemented with 1% crude oil, and the isolates were screened on their ability to use carbon as their sole source of carbon or alternative pathway. Characterization of the isolates was carried out by performing Gram’s iodine test, catalase, oxidase, indole, citrate, motility, coagulase tests. The degrading potential of the isolates were obtained by subculturing them in mineral salt medium for two weeks at room temperature, organisms that could utilize all crude oil made available to them were considered strong degraders while those that could not utilize all the crude oil made available to them were considered weak degraders. Among 40 microbes isolated, 30 were considered strong degraders while 10 were considered weak degraders and these isolates includedPseudomonasspp,Enterobacterspp,Escherichia coli,Arthrobacterspp,Bacillusspp,Acinetobacterspp,Staphylococcus aureus, coagulase negativeStaphylococcusspp,Klebsiellaspp,Micrococcusspp,Vibriospp. The characterized isolates may constitute potential candidates for biotechnological application in environmental cleanup of petroleum contaminants.
Identification and neuroprotective properties of NA-184, a selective calpain-2 inhibitor
Authors: Baudry Michel , Wang Yubin , Bi Xiaoning , Luo Yun Lyna , Wang Zhijun , Kamal Zeechan , Shirokov Alexander , Sullivan Ed , Lagasca Dennis , Khalil Hany , Lee Gary , Fosnaugh Kathy , Bey Philippe , Medi Shujaath , Coulter Greg
Published: October 2023

Our laboratory has shown that calpain-2 activation in the brain following acute injury is directly related to neuronal damage and the long-term functional consequences of the injury, while calpain-1 activation is generally neuroprotective and calpain-1 deletion exacerbates neuronal injury. We have also shown that a relatively selective calpain-2 inhibitor, referred to as C2I, enhanced long-term potentiation and learning and memory, and provided neuroprotection in the controlled cortical impact (CCI) model of traumatic brain injury (TBI) in mice. Similar results were also obtained in conditional calpain-2 knock-out mice. Using molecular dynamic simulation and Site Identification by Ligand Competitive Saturation (SILCS) software, we report here the discovery of a selective calpain-2 inhibitor NA-184, (S)-2-(3-benzylureido)-N-((R,S)-1-((3-chloro-2-methoxybenzyl)amino)-1,2-dioxopentan-3-yl)-4-methylpentanamide whose properties make it a good clinical candidate for the treatment of TBI.
Sibling chimerism among microglia in marmosets
Authors: Rosario Ricardo C.H. del , Krienen Fenna M. , Zhang Qiangge , Goldman Melissa , Mello Curtis , Lutservitz Alyssa , Ichihara Kiku , Wysoker Alec , Nemesh James , Feng Guoping , McCarroll Steven A.
Published: October 2023

Chimerism happens rarely among most mammals but is common in marmosets and tamarins, a result of fraternal twin or triplet birth patterns in whichin uteroconnected circulatory systems (through which stem cells transit) lead to persistent blood chimerism (12-80%) throughout life. The presence of Y-chromosome DNA sequences in other organs of female marmosets has long suggested that chimerism might also affect these organs. However, a longstanding question is whether this chimerism is driven by blood-derived cells or involves contributions from other cell types. To address this question, we analyzed single-cell RNA-seq data from blood, liver, kidney and multiple brain regions across a number of marmosets, using transcribed single nucleotide polymorphisms (SNPs) to identify cells with the sibling’s genome in various cell types within these tissues. Sibling-derived chimerism in all tissues arose entirely from cells of hematopoietic origin (i.e., myeloid and lymphoid lineages). In brain tissue this was reflected as sibling-derived chimerism among microglia (20-52%) and macrophages (18-64%) but not among other resident cell types (i.e., neurons, glia or ependymal cells). The percentage of microglia that were sibling-derived showed significant variation across brain regions, even within individual animals, likely reflecting distinct responses by siblings’ microglia to local recruitment or proliferation cues or, potentially, distinct clonal expansion histories in different brain areas. In the animals and tissues we analyzed, microglial gene expression profiles bore a much stronger relationship to local/host context than to sibling genetic differences. Naturally occurring marmoset chimerism will provide new ways to understand the effects of genes, mutations and brain contexts on microglial biology and to distinguish between effects of microglia and other cell types on brain phenotypes.
High-throughput single-cell sorting by stimulated Raman-activated cell ejection
Authors: Zhang Jing , Lin Haonan , Xu Jiabao , Zhang Meng , Ge Xiaowei , Zhang Chi , Huang Wei E. , Cheng Ji-Xin
Published: October 2023

Single-cell sorting is essential to explore cellular heterogeneity in biology and medicine. Recently developed Raman-activated cell sorting (RACS) circumvents the limitations of fluorescence-activated cell sorting, such as the cytotoxicity of labels. However, the sorting throughputs of all forms of RACS are limited by the intrinsically small cross-section of spontaneous Raman scattering. Here, we report a stimulated Raman-activated cell ejection (S-RACE) platform that enables high-throughput single-cell sorting based on high-resolution multi-channel stimulated Raman chemical imaging,in situimage decomposition, and laser-induced cell ejection. The performance of this platform was illustrated by sorting a mixture of 1 μm polymer beads, where 95% yield, 98% purity, and 14 events per second throughput were achieved. Notably, our platform allows live cell ejection, allowing for the growth of single colonies of bacteria and fungi after sorting. To further illustrate the chemical selectivity, lipid-richRhodotorula glutiniscells were successfully sorted from a mixture withSaccharomyces cerevisiae, confirmed by downstream quantitative PCR. Furthermore, by integrating a closed-loop feedback control circuit into the system, we realized real-time single-cell imaging and sorting, and applied this method to precisely eject regions of interest from a rat brain tissue section. The reported S-RACE platform opens exciting opportunities for a wide range of single-cell applications in biology and medicine.

Significance statement

Image-guided single-cell sorting is a potent tool in diverse biological applications. Current microfluidic cell sorting methods encounter challenges in handling smaller cells and are not applicable to tissue sections. To address these challenges, we have developed a stimulated Raman-activated cell ejection (S-RACE) platform, which is the first demonstration of single-cell ejection coupled with coherent Raman scattering. S-RACE allows label-free chemical imaging guided cell sorting through multispectral stimulated Raman scattering (SRS) imaging, on-the-fly image analysis, and laser-induced cell ejection. Versatile applications of S-RACE to a wide range of samples, such as polymer particles, single-live bacteria, single-live fungus, and tissue sections, are demonstrated.
Tactile versus Motor Imagery: Differences in Corticospinal Excitability Assessed with single-pulse TMS
Authors: Morozova Marina , Nasibullina Aigul , Yakovlev Lev , Syrov Nikolay , Kaplan Alexander , Lebedev Mikhail
Published: October 2023

Tactile Imagery (TI) remains a fairly understudied phenomenon despite an increased attention to this topic in recent years. Here we investigated the effects of TI on corticospinal excitability by measuring motor evoked potentials (MEPs) induced by single-pulse transcranial magnetic stimulation (TMS). The effects of TI were compared with those of tactile stimulation (TS) and kinesthetic motor imagery (kMI). Twenty-two participants performed three tasks in randomly assigned order: imagine finger tapping (kMI); experience vibratory sensations in the middle finger (TS); and mentally reproduce the sensation of vibration (TI). MEPs increased during both kMI and TI, with a stronger increase for kMI. No statistically significant change in MEP was observed during TS. The demonstrated differential effects of kMI, TI and TS on corticospinal excitability have practical implications for the development of imagery-based and TS-based brain-computer interfaces (BCIs), particularly the ones intended to improve neurorehabilitation by evoking plastic changes in sensorimotor circuitry.

Significance Statement

While it is known that tactile imagery (TI) engages the primary somatosensory cortex similarly to physical tactile perceptions, it is not well understood how TI affects neural processing in the primary motor cortex (M1), the area that controls voluntary movements while receiving somatosensory feedback. This study employed transcranial magnetic stimulation (TMS) to examine the responsiveness of M1 to different types of somatosensory imagery in response to TMS. TI facilitated the responses in the forearm and hand muscles but to a significantly lesser extent compared to kinesthetic motor imagery (kMI). This demonstration of the distinct effects of TI and kMI on corticospinal excitability highlights the importance of selecting an imagery strategy when using imagery to modulate cortical representation of the body. These findings have practical implications for the development of imagery-based brain-computer interfaces (BCIs) intended for rehabilitation of sensorimotor impairments.
Neuropeptide Y neurons of the locus coeruleus inhibit noradrenergic system activity to reduce anxiety
Authors: Riga Danai , Rademakers Kelly , Wolterink-Donselaar Inge G. , Meye Frank J.
Published: October 2023

Abstract / Summary

Adaptive responses to challenging environments depend on optimal function of the locus coeruleus (LC), the brain’s main source of noradrenaline and primary mediator of the initial stress response. Built-in systems that exert regulatory control over the LC are largely unidentified. A good candidate system is neuropeptide Y (NPY), which is traditionally linked to anxiety-relief. Currently, the endogenous source of NPY to the LC, and how NPY-expressing neurons modulate the noradrenergic system to regulate anxiety remain unclear. We here identify, in mice, a novel NPY-expressing neuronal population (peri-LCNPY) neighboring LC noradrenergic neurons that locally innervates the pericoerulean space. Moreover, we demonstrate that stress engages peri-LCNPYneurons, increasing their excitability. Mimicking peri-LCNPYneuronal activation usingex vivochemogenetics suppresses LC noradrenergic neuron activity, via an NPY Y1 receptor-mediated mechanism. Furthermore,in vivochemogenetic stimulation of peri-LCNPYneurons results in Y1R-dependent anxiety-relief. Conversely, inhibiting peri-LCNPYneurons increases anxiety-like behaviors. Together, we establish a causal role for peri-LCNPY-mediated neuromodulation of the LC in the regulation of anxiety, providing novel insights in the endogenous mechanisms underlying adaptive responses to adversity.
Chronic social defeat stress induces a depression-relevant outcome in male prairie voles
Authors: Rodriguez Minerva , Themann Anapaula , Garcia-Carachure Israel , Lira Omar , Robison Alfred J. , Cushing Bruce S. , Iñiguez Sergio D.
Published: October 2023

Background

Stress-induced illnesses, like major depression, are among the leading causes of disability across the world. Consequently, there is a dire need for the validation of translationally-suited animal models incorporating social stress to uncover the etiology of depression. Prairie voles (Microtus ochrogaster) are more translationally relevant than many other rodent models as they display monogamous social and parental behaviors and more primate-like neuroanatomy. Therefore, we evaluated whether a novel social defeat stress (SDS) model in male prairie voles induces depression-relevant behavioral outcomes.

Methods

Adult sexually-naïve male prairie voles experienced SDS bouts from a conspecific pair-bonded male aggressor, 10 min per day for 10 consecutive days. Non-stressed controls (same-sex siblings) were housed in similar conditions but never experienced physical stress. Twenty-four hr later, voles were evaluated in social interaction, sucrose preference, and Morris water maze tests – behavioral endpoints validated to assess social withdrawal, anhedonia-related behavior, and spatial memory performance, respectively.

Results

SDS-exposed voles displayed lower sociability and body weight, decreased preference for a sucrose solution, and impairment of spatial memory retrieval. Importantly, no differences in general locomotor activity were observed as a function of SDS exposure.

Limitations

This study does not include female voles in the experimental design.

Conclusions

We found that repeated SDS exposure, in male prairie voles, results in a depression-relevant phenotype resembling an anhedonia-like outcome (per reductions in sucrose preference) along with social withdrawal and spatial memory impairment – highlighting that the prairie vole is a valuable model with potential to study the neurobiology of social stress-induced depression-related outcomes.