bluuebunny/crossref_metadata_2025 huggingface dataset:
A Unified Pipeline for FISH Spatial Transcriptomics
Authors: Cisar Cecilia , Keener Nicholas , Ruffalo Mathew , Paten Benedict
Published: February 2023

In recent years, high-throughput spatial transcriptomics has emerged as a powerful tool for investigating the spatial distribution of mRNA expression and the effects it may have on cellular function. There is a lack of standardized tools for analyzing spatial transcriptomics data, leading many groups to write their own in-house tools that are often poorly documented and not generalizable to other datasets. Currently, the only publicly available tools for extracting annotated transcript locations from raw multiplexed fluorescentin situhybridization (FISH) images are starfish, which is lacking in key areas, and MERlin, which is restricted to only MERFISH data. To address this, we have expanded and improved the starfish library and used those tools to create PIPEFISH, a semi-automated and generalizable pipeline that performs transcript annotation for FISH-based spatial transcriptomics. PIPEFISH has options for image processing, decoding, and cell segmentation, and calculates quality control metrics on the output to allow the user to assess the pipeline’s performance on their data. We used this pipeline to annotate transcript locations from three real datasets from three different common types of FISH image-based experiments: MERFISH, seqFISH, and targetedin situsequencing (ISS), and verified that the results were high quality using the internal quality metrics of the pipeline and also a comparison to a orthogonal method of measuring RNA expression in a similar tissue sample. We have made PIPEFISH publicly available through Github for anyone interested in analyzing data from FISH-based spatial transcriptomic assays.
Effect of growing regions on morphological characteristics, protein nutrition, rumen degradation and molecular structures of various whole-plant silage corn cultivars
Authors: Zhang Xinyue , Khan Nazir Ahmad , Yao Enyue , Kong Fanlin , Chen Ming , Khan Rifat Ullah , Liu Xin , Zhang Yonggen , Xin Hangshu ,   with the Lorem Ipsum Consortium
Published: February 2023

Little information exists on the variation of morphological characteristics, nutritional value, ruminal degradability, and molecular structural makeup of diverse whole-plant silage corn (WPSC) cultivars among different growing regions. This study investigated the between-regions discrepancies in five widely used WPSC cultivars in China (FKBN, YQ889, YQ23, DK301 and ZD958) in terms of 1) morphological characteristics; 2) crude protein (CP) chemical profile; 3) Cornell Net Carbohydrate and Protein System (CNCPS) CP subfractions; 4)in situCP degradation kinetics; and 5) CP molecular structures. Our results revealed that significant difference were observed on growing region and WPSC cultivar interaction for all estimated morphological characteristics (P< 0.001), CP chemical profile (P< 0.001), CNCPS subfractions (P< 0.001) and CP molecular structural features (P< 0.05). Except ear weight (P= 0.18), all measured morphological characteristics varied among different growing regions (P< 0.001). Besides, WPSC cultivars planted in different areas had remarkably different (P< 0.01) CP chemical profiles and CNCPS subfractions. All spectral parameters of protein primary structure of WPSC differed (P< 0.05) due to the various growing regions, except amide II area (P= 0.28). Finally, the area ratio of amide I to II was negatively correlated with the contents of soluble CP (δ= -0.66;P= 0.002), CP (δ= - 0.61;P= 0.006), non-protein N (δ= -0.56;P= 0.004) and acid detergent insoluble CP (δ= - 0.43;P= 0.008), in conjunction with positively correlated with moderately degradable CP (PB1;δ= 0.58;P= 0.01). In conclusion, the current study suggested that even for the same WPSC cultivar, the morphological characteristics, protein nutritional values and rumen degradability significantly varied among different grown regions due to distinguished molecular structures.

Author summary

As the major roughage source, whole plant silage corn plays an essential role in ruminant feed industry. The quality and quantity of it largely influenced by environmental and climate conditions except genetic factors. However, there was limited information to systematically analyze whole plant silage corn from morphological characteristics, nutritional components, rumen degradation to its inherent molecular structures. Thus, this study was conducted to investigate the discrepancies of various silage-corn cultivars grown in different regions from internal structure to phenotype based novel technology - fourier transform infrared spectroscopy.
Solid Phase Synthesis of Fluorosulfate Containing Macrocycles for Chemoproteomic Workflows
Authors: Faucher Franco F. , Abegg Daniel , Ipock Phillip , Adibekian Alexander , Lovell Scott , Bogyo Matthew
Published: February 2023

Macrocyclic peptides are attractive for chemoproteomic applications due to their modular synthesis and potential for high target selectivity. We describe a solid phase synthesis method for the efficient generation of libraries of small macrocycles that contain an electrophile and alkyne handle. The modular synthesis produces libraries that can be directly screened using simple SDS-PAGE readouts and then optimal lead molecules applied to proteomic analysis. We generated a library of 480 macrocyclic peptides containing the weakly reactive fluorosulfate (OSF) electrophile. Initial screening of a subset of the library containing each of the various diversity elements identified initial molecules of interest. The corresponding positional and confirmational isomers were then screened to select molecules that showed specific protein labeling patterns that were dependent on the probe structure. The most promising hits were applied to standard chemoproteomic workflows to identify protein targets. Our results demonstrate the feasibility of rapid, on-resin synthesis of diverse macrocyclic electrophiles to generate new classes of covalent ligands.
Tracking and curating putative SARS-CoV-2 recombinants with RIVET
Authors: Smith Kyle , Ye Cheng , Turakhia Yatish
Published: February 2023

Identifying and tracking recombinant strains of SARS-CoV-2 is critical to understanding the evolution of the virus and controlling its spread. But confidently identifying SARS-CoV-2 recombinants from thousands of new genome sequences that are being shared online every day is quite challenging, causing many recombinants to be missed or suffer from weeks of delay in being formally identified while undergoing expert curation. We present RIVET – a software pipeline and visual platform that takes advantage of recent algorithmic advances in recombination inference to comprehensively and sensitively search for potential SARS-CoV-2 recombinants, and organizes the relevant information in a web interface that would help greatly accelerate the process identifying and tracking recombinants.

Availability and Implementation

RIVET-based web interface displaying the most updated analysis of potential SARS-CoV-2 recombinants is available athttps://rivet.ucsd.edu/. RIVET’s frontend and backend code is freely available under MIT license athttps://github.com/TurakhiaLab/rivet. All inputs necessary for running the RIVET’s backend workflow for SARS-CoV-2 are available through a public database maintained by UCSC (https://hgdownload.soe.ucsc.edu/goldenPath/wuhCor1/UShER_SARS-CoV-2/).

Contact

yturakhia@ucsd.edu
Barriers to access to antiretroviral therapy by people living with HIV in Indonesia during the COVID-19 pandemic: A qualitative study
Authors: Fauk Nelsensius Klau , Gesesew Hailay Abhra , Seran Alfonsa Liquory , Ward Paul Russell
Published: February 2023

Background

The coronavirus disease (COVID-19) pandemic has a significant influence on access to healthcare services. This study aimed to understand the views and experiences of people living with HIV (PLHIV) about barriers to their access to antiretroviral therapy (ART) service in Belu district, Indonesia, during the COVID-19 pandemic.

Methods

This qualitative inquiry employed in-depth interviews to collect data from 21 participants who were recruited using a snowball sampling technique. Data analysis was guided by a thematic framework analysis.

Results

The findings showed that fear of contracting COVID-19 was a barrier that impeded participants’ access to ART service. Such fear was influenced by their awareness of their vulnerability to the infection, the possibility of unavoidable physical contact in public transport during a travelling to HIV clinic and the widespread COVID-19 infection in healthcare facilities. Lockdowns, COVID-19 restrictions and lack of information about the provision of ART service during the pandemic were also barriers that impeded their access to the service. Other barriers included the mandatory regulation for travellers to provide their COVID-19 vaccine certificate, financial difficulty, long-distance travel to the HIV clinic and a lack of public transport.

Conclusions

The findings indicate the need for dissemination of information about the provision of ART service during the pandemic and the benefits of COVID-19 vaccination for the health of PLHIV. The findings also indicate the need for new strategies to bring ART service closer to PLHIV during the pandemic such as a community-based delivery system. Future large-scale studies exploring views and experiences of PLHIV about barriers to their access to ART service during the COVID-19 pandemic and new intervention strategies are recommended.
Child Support Grant expansion and cognitive function among women in rural South Africa: findings from a natural experiment in HAALSI cohort
Authors: Chakraborty Rishika , Kobayashi Lindsay C. , Jock Janet , Wing Coady , Chen Xiwei , Phillips Meredith , Berkman Lisa , Kahn Kathleen , Kabudula Chodziwadziwa Whiteson , Rosenberg Molly
Published: February 2023

Cash transfers are a promising but understudied intervention that may protect cognitive function in adults by promoting their cognitive reserve. South Africa has a rapidly ageing population, however, less is known about the nature of association between cash transfers and cognitive function in this setting. We leveraged natural experiments from Child Support Grant (CSG) age-eligibility expansions to investigate the association between duration of CSG eligibility and cognitive function among biological mothers of child beneficiaries in South Africa. We analysed 2014/2015 baseline data from 944 women, aged 40 - 59 years with at least one CSG-eligible child, enrolled in the HAALSI cohort in Agincourt, South Africa. Duration of CSG eligibility for each mother was calculated based on the birth dates of all their children and the CSG age eligibility expansion years. Cognitive function was measured using a cognitive battery administered to the mothers at baseline interview. Linear regression was used to estimate the association between duration of CSG eligibility, dichotomized as low (≤10 years) and high (>10 years) eligibility, and cognitive function z-scores of the mothers. Our study finds that high duration of CSG eligibility, compared to low, was associated with higher cognitive function z-scores in the full sample [β: 0.15 SD; 95% CI: 0.04, 0.26; p-value = 0.01]. In mothers with one to four lifetime children, but not five or more, high duration of CSG eligibility, compared to low, was associated with higher cognitive function z-scores [β: 0.19 SD; 95% CI: 0.05, 0.34, p-value = 0.02]. Government cash transfers given to support raising children may confer substantial protective effect on cognitive function of mothers in their mid-life. Further studies are needed to understand how parity may influence this relationship. Our findings bring evidence to policymakers for designing income supplementation programmes to promote healthy cognitive ageing in low-income settings.
Sodium and Potassium Consumption in Jamaica: National Estimates and Associated Factors from the Jamaica Health and Lifestyle Survey 2016-2017
Authors: Ferguson Trevor S , Younger-Coleman Novie Om , Webster-Kerr Karen , Tulloch-Reid Marshall K. , Bennett Nadia R , Davidson Tamu , Grant Andriene S , Gordon-Johnson Kelly-Ann M. , Govia Ishtar , Soares-Wynter Suzanne , Mckenzie Joette A , Walker Evelyn , Cunningham-Myrie Colette A , Anderson Simon G , Blake Alphanso L , Ho James , Stephenson Robyn , Edwards Sharmaine E , Mcfarlane Shelly R , Spence Simone , Wilks Rainford J
Published: February 2023

Objective

To estimate dietary sodium and potassium consumption among Jamaicans and evaluate associations with sociodemographic and clinical characteristics.

Methods

We conducted a cross-sectional analysis of data from the Jamaica Health and Lifestyle Survey 2016-2017. Participants were non-institutionalized Jamaicans, ≥15 years. Trained staff collected sociodemographic and health data via interviewer administered questionnaires and collected spot urine samples. The Pan American Health Organization Formulae were used to estimate 24-hour urine sodium and potassium excretion. High sodium was defined as ≥2000 mg/day and low potassium as <3510 mg/day (World Health Organization criteria). Associations of these outcomes with sociodemographic and clinical characteristics were explored in sex specific multivariable ANOVA models.

Results

Analyses included 1009 participants (368 males, 641 females; mean age 48.5 years). Mean sodium excretion was 3582 mg/day (males 3943 mg/day, females 3245 mg/day, p<0.001). Mean potassium excretion was 2052 mg/day (males 2210 mg/day, females 1904 mg/day, p=0.001). The prevalence of high sodium consumption was 66.6% (males 72.8%, female 60.7%, p<0.001) and low potassium intake was 88.8% (85.1% males, 92.3% females, p<0.001). Among males, sodium consumption was inversely associated with older age and prehypertension, but directly associated with current smoking and obesity. Among females, sodium consumption was inversely associated with hypertension, impaired fasting glucose, low GFR and high physical activity, but was directly associated with obesity.

Conclusion

Most Jamaican adults have diets high in sodium and low in potassium. Sodium consumption was directly associated with obesity in both men and women. Population based strategies are therefore required to address these cardiovascular risk factors.
Comparative Effectiveness of BNT162b2 and NVX-CoV2373 Vaccines in Korean Adults
Authors: Park Seon Kyeong , Choe Young June , Choe Seung Ah , Cowling Benjamin John , Hwang Ji Hae , Lee Ju Hee , Lee Kil Hun , Yi Seonju , Lee Sang Won , Kwon Geun-Yong , Jang Eun Jung , Kim Ryu Kyung , Park Young-Joon
Published: February 2023

Background

Various types of vaccines against SARS-CoV-2 have reduced the burden of coronavirus diseases 2019 (COVID-19) across the world. We conducted an observational study to evaluate the effectiveness of NVX-CoV2373 and BNT162b2 in providing protection in Korean adults.

Methods

This study was a retrospective matched cohort study to emulate a target trial of three doses of NVX-CoV2373 (N-N-N) versus three doses of BNT162b2 (B-B-B) vaccines in presumed immune-naive adults. We used data from the Korea COVID-19 Vaccine Effectiveness (K-COVE) cohort, combining all COVID-19 laboratory-confirmed cases and all COVID-19 immunization registry, between February and November 2022. We calculated 40-week risk differences and risk ratios between the two vaccines.

Results

A total of 3,019 recipients of NVX-CoV2373 vaccine and 3,027 recipients of BNT162b2 vaccine were eligible for the study. The 40-week risk ratios for recipients of the NVX-CoV2373 vaccine as compared with recipients of the BNT162b2 vaccine were 1.169 (95% CI, 1.015 to 1.347) for laboratory-confirmed SARS-CoV-2 infection, and 0.504 (95% CI, 0.126 to 2.014) for severe SARS-CoV-2 infection. Estimated risk of severe infection was 0.001 events per 1000 persons (95% CI, 0 to 0.003) for the NVX-CoV2373 vaccine and 0.002 events per 1000 persons (95% CI, 0.001 to 0.006) for BNT162b2 vaccine.

Conclusion

This study identifies reduced risk of SARS-CoV-2 infection and severe infection after receipt of three doses of either NVX-CoV2373 or BNT162b2 vaccines in Korean adults. Direct, vaccine-conferred protection may be of importance among high risk persons to mitigate from serious clinical outcome from COVID-19.
Quantification of all 12 canonical ribonucleotides by real-time fluorogenicin vitrotranscription
Authors: Purhonen Janne , Kallijärvi Jukka
Published: February 2023

Enzymatic methods to quantify deoxyribonucleoside triphosphates have existed for decades. In contrast, no general enzymatic method to quantify ribonucleoside triphosphates (rNTPs), which drive almost all cellular processes and serve as precursors of RNA, exists to date. ATP can be measured with an enzymatic luminometric method employing the firefly luciferase, but the quantification of the other ribonucleoside mono-, di-, and triphosphates is still a challenge for a non-specialized laboratory and practically impossible without chromatography equipment. To allow feasible quantification of ribonucleoside phosphates in any laboratory with typical molecular biology and biochemistry tools, we developed a robust microplate assay based on real-time detection of the Broccoli aptamer duringin vitrotranscription. The assay employs the bacteriophage T7 and SP6 RNA polymerases, two oligonucleotide templates encoding the 49-nucleotide Broccoli aptamer, and a high-affinity fluorogenic aptamer-binding dye to quantify each of the four canonical rNTPs. The inclusion of nucleoside mono- and diphosphate kinases in the assay reactions enabled the quantification of the mono- and diphosphate counterparts. The assay is inherently specific and tolerates concentrated tissue and cell extracts. In summary, we describe the first chromatography-free method to quantify ATP, ADP, AMP, GTP, GDP, GMP, UTP, UDP, UMP, CTP, CDP, and CMP in biological samples.
Massive Multiplexing of Spatially Resolved Single Neuron Projections with Axonal BARseq
Authors: Yuan Li , Chen Xiaoyin , Zhan Huiqing , Gilbert Henry L. , Zador Anthony M.
Published: February 2023

Neurons in the cortex are heterogenous, sending diverse axonal projections to multiple brain regions. Unraveling the logic of these projections requires single-neuron resolution. Although a growing number of techniques have enabled high-throughput reconstruction, these techniques are typically limited to dozens or at most hundreds of neurons per brain, requiring that statistical analyses combine data from different specimens. Here we present axonal BARseq, a high-throughput approach based on reading out nucleic acid barcodes usingin situRNA sequencing, which enables analysis of even densely labeled neurons. As a proof of principle, we have mapped the long-range projections of >8000 mouse primary auditory cortex neurons from a single brain. We identified major cell types based on projection targets and axonal trajectory. The large sample size enabled us to systematically quantify the projections of intratelencephalic (IT) neurons, and revealed that individual IT neurons project to different layers in an area-dependent fashion. Axonal BARseq is a powerful technique for studying the heterogeneity of single neuronal projections at high throughput within individual brains.
Novel Evoked Synaptic Activity Potentials (ESAPs) elicited by Spinal Cord Stimulation
Authors: Sharma Mahima , Bhaskar Vividha , Yang Lillian , FallahRad Mohamad , Gebodh Nigel , Zhang Tianhe , Esteller Rosana , Martin John , Bikson Marom
Published: February 2023

Spinal cord stimulation (SCS) evokes fast epidural Evoked Compound Action Potential (ECAPs) that represent activity of dorsal column axons, but not necessarily a spinal circuit response. Using a multimodal approach, we identified and characterized a delayed and slower potential evoked by SCS that reflects synaptic activity within the spinal cord. Anesthetized female Sprague Dawley rats were implanted with an epidural SCS lead, epidural motor cortex stimulation electrodes, an epidural spinal cord recoding lead, an intraspinal penetrating recording electrode array, and intramuscular electromyography (EMG) electrodes in the hindlimb and back. We stimulated the motor cortex or the epidural spinal cord and recorded epidural, intraspinal, and EMG responses. SCS pulses produced characteristic propagating ECAPs (composed of P1, N1, and P2 waves with latencies <2 ms) and an additional wave (“S1”) starting after the N2. We verified the S1-wave was not a stimulation artifact and was not a reflection of hindlimb/back EMG. The S1-wave has a distinct stimulation-intensity dose response and spatial profile compared to ECAPs. CNQX (a selective competitive antagonist of AMPA receptors) significantly diminished the S1-wave, but not ECAPs. Furthermore, cortical stimulation, which did not evoke ECAPs, produced epidurally detectable and CNQX-sensitive responses at the same spinal sites, confirming epidural recording of an evoked synaptic response. Finally, applying 50 Hz SCS resulted in dampening of ESAPs, but not ECAPs. Therefore, we hypothesize that the S1-wave is synaptic in origin, and we term the S1-wave type responses: Evoked Synaptic Activity Potentials (ESAPs). The identification and characterization of epidurally recorded ESAPs from the dorsal horn may elucidate SCS mechanisms.

Significance Statement

Spinal cord stimulation (SCS) is an established treatment for chronic pain and has applications to other disorders and neurorehabilitation. Notwithstanding decades of trials and research, questions remain about SCS mechanisms of action - and indicators thereof. Recent technological developments have enabled the detection of Evoked Compound Action Potential (ECAPs) – reflecting synchronous activity of the dorsal column axons activated by SCS. However, ECAP is not a direct measure of sensory processing in the dorsal horn. Here, we identify and characterize a novel electrophysiological signal that is evoked and detectable by epidural SCS electrodes and reflects spinal synaptic currents. This new signal, termed an Evoked Synaptic Activity Potential (ESAP), is thus a novel means with which to interrogate spinal gray matter circuits during SCS.
Diameter Dependence of Transport through Nuclear Pore Complex Mimics Studied Using Optical Nanopores
Authors: Klughammer Nils , Barth Anders , Dekker Maurice , Fragasso Alessio , Onck Patrick R. , Dekker Cees
Published: February 2023

The nuclear pore complex (NPC) regulates the selective transport of large biomolecules through the nuclear envelope. As a model system for nuclear transport, we construct NPC mimics by functionalizing the pore walls of freestanding palladium zero-mode waveguides with the FG-nucleoporin Nsp1. This approach enables the measurement of single-molecule translocations through individual pores using optical detection. We probe the selectivity of Nsp1-coated pores by quantitatively comparing the translocation rates of the nuclear transport receptor Kap95 to the inert probe BSA over a wide range of pore sizes from 35 nm to 160 nm. Pores below 55 ± 5 nm show significant selectivity that gradually decreases for larger pores. This finding is corroborated by coarse-grained molecular-dynamics simulations of the Nsp1 mesh within the pore, which suggest that leakage of BSA occurs by diffusion through transient openings within the dynamic mesh. Furthermore, we experimentally observe a modulation of the BSA permeation when varying the concentration of Kap95. The results demonstrate the potential of single-molecule fluorescence measurements on biomimetic NPCs to elucidate the principles of nuclear transport.
Matreex: compact and interactive visualisation for scalable studies of large gene families
Authors: Rossier Victor , Train Clement , Nevers Yannis , Robinson-Rechavi Marc , Dessimoz Christophe
Published: February 2023

Studying gene family evolution strongly benefits from insightful visualisations. However, the evergrowing number of sequenced genomes is leading to increasingly larger gene families, which challenges existing gene tree visualisations. Indeed, most of them present users with a dilemma: display complete but intractable gene trees, or collapse subtrees, thereby hiding their children’s information. Here, we introduce Matreex, a new dynamic tool to scale-up the visualisation of gene families. Matreex’s key idea is to use “phylogenetic” profiles, which are dense representations of gene repertoires, to minimise the information loss when collapsing subtrees. We illustrate Matreex usefulness with three biological applications. First, we demonstrate on the MutS family the power of combining gene trees and phylogenetic profiles to delve into precise evolutionary analyses of large multi-copy gene families. Secondly, by displaying 22 intraflagellar transport gene families across 622 species cumulating 5’500 representatives, we show how Matreex can be used to automate large-scale analyses of gene presence-absence. Notably, we report for the first time the complete loss of intraflagellar transport in the myxozoanThelohanellus kitauei. Finally, using the textbook example of visual opsins, we show Matreex’s potential to create easily interpretable figures for teaching and outreach. Matreex is available from the Python Package Index (pip install matreex) with the source code and documentation available athttps://github.com/DessimozLab/matreex.
Bacterial responses to complex mixtures of chemical pollutants
Authors: Smith Thomas P. , Clegg Tom , Ransome Emma , Martin-Lilley Thomas , Rosindell James , Woodward Guy , Pawar Samraat , Bell Thomas
Published: February 2023

Our understanding of how microbes respond to pollutants is almost wholly based on single-species responses to individual chemicals. However, in natural environments, microbes experience the effects of multiple pollutants simultaneously, and their responses to these mixtures of chemicals may not be readily predictable based on their responses to each pollutant in isolation. Here we extended the scope and complexity of previous multi-stressor experiments by assaying the growth of model and non-model strains of bacteria in all 255 combinations of 8 chemical stressors. This approach allowed us to identify fitness effects arising from potential high-order interactions among stressor responses. We found that the bacterial strains responded in different ways to stressor mixtures, which could not be predicted simply from their phylogenetic relatedness. Responses to increasingly complex chemical mixtures were more likely to show a significant deviation from a null model based on the responses to each chemical alone. However, these net responses were mainly driven by lower-order interactions among a small number of chemicals, suggesting a limited role for complex high-order interactions. These results simplify the predictability of microbial populations and communities responding to multiple stressors, paving the way for the development of efficient next-generation eco-toxicological assays.
Serotonin modulates social responses to stressed conspecifics via insular 5-HT2Creceptors in rat
Authors: Ng Alexandra J. , Vincelette Lindsay K. , Li Jiayi , Brady Bridget H. , Christianson John P.
Published: February 2023

Social interaction allows for the transfer of affective states among individuals, and the behaviors and expressions associated with pain and fear can evoke anxiety-like states in observers which shape subsequent social interactions. We hypothesized that social reactions to stressed individuals engage the serotonergic dorsal raphe nucleus (DRN) which promotes anxiety-like behavior via postsynaptic action of serotonin at serotonin 2C (5-HT2C) receptors in the forebrain. First, we inhibited the DRN by administering an agonist (8-OH-DPAT, 1µg in 0.5µL) for the inhibitory 5-HT1Aautoreceptors which silences 5-HT neuronal activity via G-protein coupled inward rectifying potassium channels. 8-OH-DPAT prevented the approach and avoidance, respectively, of stressed juvenile (PN30) or stressed adult (PN60) conspecifics in the social affective preference (SAP) test in rats. Similarly, systemic administration of a 5-HT2Creceptor antagonist (SB242084, 1mg/kg, i.p.) prevented approach and avoidance of stressed juvenile or adult conspecifics, respectively. Seeking a locus of 5-HT2Caction, we considered the posterior insular cortex which is critical for social affective behaviors and rich with 5-HT2Creceptors. SB242084 administered directly into the insular cortex (5µM in 0.5µL bilaterally)interfered with the typical approach and avoidance behaviors observed in the SAP test. Finally, using fluorescentin situhybridization, we found that 5-HT2Creceptor mRNA (htr2c)is primarily colocalized with mRNA associated with excitatory glutamatergic neurons (vglut1) in the posterior insula. Importantly, the results of these treatments were the same in male and female rats. These data suggest that interactions with stressed others require the serotonergic DRN and that serotonin modulates social affective decision-making via action at insular 5-HT2Creceptors.
A metal ion-dependent mechanism of RAD51 nucleoprotein filament disassembly
Authors: Appleby Robert , Bollschweiler Daniel , Chirgadze Dimitri Y. , Joudeh Luay , Pellegrini Luca
Published: February 2023

The RAD51 ATPase polymerises on single-stranded DNA to form nucleoprotein filaments (NPFs) that are critical intermediates in the DNA strand-exchange reactions of Homologous Recombination (HR). ATP binding is important to maintain the NPF in a competent conformation for strand pairing and exchange. Once strand exchange is completed, ATP hydrolysis licenses the filament for disassembly. Here we show using high-resolution cryoEM that the ATP-binding site of the RAD51 NPF contains a second metal ion. In the presence of ATP, the metal ion promotes the local folding of RAD51 into the conformation required for DNA binding. The metal ion is absent in the structure of an ADP-bound RAD51 filament, that rearranges in a conformation incompatible with DNA binding. The presence of the second metal ion explains how RAD51 couples the nucleotide state of the filament to DNA binding. We propose that loss of the second metal ion upon ATP hydrolysis drives RAD51 dissociation from the DNA and weakens filament stability, thus contributing to NPF disassembly, a critical step in the completion of HR.
mRNA interactions with disordered regions control protein activity
Authors: Luo Yang , Pratihar Supriya , Horste Ellen H. , Mitschka Sibylle , Mey Antonia S. J. S. , Al-Hashimi Hashim M. , Mayr Christine
Published: February 2023

The cytoplasm is compartmentalized into different translation environments. mRNAs use their 3′UTRs to localize to distinct cytoplasmic compartments, including TIS granules (TGs). Many transcription factors, including MYC, are translated in TGs. It was shown that translation of proteins in TGs enables the formation of protein complexes that cannot be established when these proteins are translated in the cytosol, but the mechanism is poorly understood. Here we show that MYC protein complexes that involve binding to the intrinsically disordered region (IDR) of MYC are only formed when MYC is translated in TGs. TG-dependent protein complexes require TG-enriched mRNAs for assembly. These mRNAs bind to a new and widespread RNA-binding domain in neutral or negatively charged IDRs in several transcription factors, including MYC. RNA-IDR interaction changes the conformational ensemble of the IDR, enabling the formation of MYC protein complexes that act in the nucleus and control functions that cannot be accomplished by cytosolically-translated MYC. We propose that certain mRNAs have IDR chaperone activity as they control IDR conformations. In addition to post-translational modifications, we found a novel mode of protein activity regulation. Since RNA-IDR interactions are prevalent, we suggest that mRNA-dependent control of protein functional states is widespread.
LRG1 is a novel HER3 ligand to promote growth in colorectal cancer
Authors: Rathore Moeez , Wright Michel’le , Martin Daniel , Huang Wei , Taylor Derek , Miyagi Masaru , Feng Hao , Li Yamu , Wang Zhenghe , Elis Lee M , Winter Jordan , Moss Stephen , Greenwood John , Wang Rui
Published: February 2023

Therapy failure for patients with metastatic colorectal cancer (mCRC) remains an overarching challenge in the clinic. We find that liver endothelial cells secrete soluble factor(s) to promote mCRC growth in vitro and in vivo. We identify LRG1 in ECs secretome, which promotes growth in tumor cells through binding and activation of HER3. Pharmacological blocking of the LRG1/HER3 axis using LRG1 antibody 15C4 completely attenuated LRG1-induced HER3 activation and in vitro and in vivo growth of the tumor. Moreover, LRG1-/- mice with CRC allografts in the liver had 2 times longer overall survival than tumor-bearing LRG1+/+ mice. Lastly, unbiased -omics analysis and target-specific inhibitors identified eIF4-protein synthesis is significantly activated by the LRG1/HER3/RSK1/2 axis. This work reveals a paracrine mechanism of mCRC growth in liver microenvironment and highlighted the potential of blocking LRG1-HER3 and involved downstream pathways for treating patients with mCRC.

Abstract Figure
A quantitative PCR assay for detection of the mycotoxigenic plant pathogen and food spoiling moldPaecilomyces niveusin fruit, food, and soil
Authors: Wang Tristan W. , Strickland David A. , Haredy Yasmin , Cox Kerik D. , Hodge Kathie T.
Published: February 2023

The postharvest fruit pathogenPaecilomyces niveusproduces ascospores that can survive some pasteurization temperatures, spoil fruit products, and contaminate them with patulin, an FDA-regulated mycotoxin. PreventingP. niveusfrom entering food systems requires a robust detection method to effectively determine sources ofP. niveusspoilage and disease inoculum. We designed a new robust and culture-independent detection method using species-specific primers (PnPATf/r) based on the patK gene, encoding a 6-methylsalicylic acid synthase, inP. niveus, for use in a rapid qPCR assay. Primer specificity was validated using 24 differentP. niveusisolates and 16 other important food spoilage and fruit pathogenic fungi. The threshold for detection of qPCR was 18 genome equivalents. To further validate our new detection method, we demonstrate its use in detectingP. niveusin infected fruits, infested soils and ciders, and in fruit arising from apple blossoms sprayed with aP. niveusspore suspension. Results from this study may help fruit producers address spoilage and patulin contamination by this food spoiling fungus.

Highlights

New primers specific toPaecilomyces niveus(PnPATf/r) were developed based on the patK gene

A qPCR assay to detectP. niveuswas validated, and shown to be able to detect quantities ofP. niveusDNA as low as 18 genome equivalents

The new qPCR assay was used to investigate the ability ofP. niveusascospores to infect strawberry fruits and enter apple fruits through apple blossom infestation
Is resting state fMRI better than individual characteristics at predicting cognition?
Authors: Omidvarnia Amir , Sasse Leonard , Larabi Daouia I. , Raimondo Federico , Hoffstaedter Felix , Kasper Jan , Dukart Juergen , Petersen Marvin , Cheng Bastian , Thomalla Götz , Eickhoff Simon B. , Patil Kaustubh R.
Published: February 2023

Changes in spontaneous brain activity at rest provide rich information about behavior and cognition. The mathematical properties of resting-state functional magnetic resonance imaging (rsfMRI) are a depiction of brain function and are frequently used to predict cognitive phenotypes. Individual characteristics such as age, gender, and total intracranial volume (TIV) play an important role in predictive modeling of rsfMRI (for example, as “confounders” in many cases). It is unclear, however, to what extent rsfMRI carries independent information from the individual characteristics that is able to predict cognitive phenotypes. Here, we used predictive modeling to thoroughly examine the predictability of four cognitive phenotypes in 20,000 healthy UK Biobank subjects. We extracted common rsfMRI features of functional brain connectivity (FC) and temporal complexity (TC). We assessed the ability of these features to predict outcomes in the presence and absence of age, gender, and TIV. Additionally, we assessed the predictiveness of age, gender, and TIV only. We find TC and FC features to perform comparably with regard to predicting cognitive phenotypes. As compared to rsfMRI features, individual characteristics provide systematically better predictions with smaller sample sizes and, to some extent, in larger cohorts. It is also consistent across different levels of inherent temporal noise in rsfMRI. Our results suggest that when the objective is to perform cognitive predictions as opposed to understanding the relationship between brain and behavior, individual characteristics are more applicable than rsfMRI features.
Cortical activity emerges in region-specific patterns during early brain development
Authors: Suárez Rodrigo , Bluett Tobias , McCullough Michael H. , Avitan Lilach , Black Dylan A. , Paolino Annalisa , Fenlon Laura R. , Goodhill Geoffrey J. , Richards Linda J.
Published: February 2023

The development of precise neural circuits in the brain requires spontaneous patterns of neural activity prior to functional maturation. In the rodent cerebral cortex patchwork and wave patterns of activity develop in somatosensory and visual regions, respectively, and are present at birth. However, whether such activity patterns occur in non-eutherian mammals, as well as when and how they arise during development remain open questions relevant to understand brain formation in health and disease. Since the onset of patterned cortical activity is challenging to study prenatally in eutherians, here we offer a new approach in a minimally invasive manner using marsupial dunnarts, whose cortex forms postnatally. We discovered similar patchwork and travelling waves in the dunnart somatosensory and visual cortices at stage 27 (equivalent to newborn mice), and examined progressively earlier stages of development to determine their onset and how they first emerge. We observed that these patterns of activity emerge in a region-specific and sequential manner, becoming evident as early as stage 24 in somatosensory and stage 25 in visual cortices (equivalent to embryonic day 16 and 17, respectively, in mice), as cortical layers establish and thalamic axons innervate the cortex. In addition to sculpting synaptic connections of existing circuits, evolutionarily conserved patterns of neural activity could therefore help regulate early events in cortical development.

Significance Statement

Region-specific patterns of neural activity are present at birth in rodents and are thought to refine synaptic connections during critical periods of cerebral cortex development. Marsupials are born much more immature than rodents, allowing the investigation of how these patterns arise in vivo. We discovered that cortical activity patterns are remarkably similar in marsupial dunnarts and rodents, and that they emerge very early, before cortical neurogenesis is complete. Moreover, they arise from the outset in different patterns specific to somatosensory and visual areas (i.e., patchworks and waves) indicating they may also play evolutionarily conserved roles in cortical regionalization during development.
The Relationship between Alcohol- and Sleep-related Traits: Results from Polygenic Risk Score Analyses and Mendelian Randomization Studies
Authors: Chakravorty Subhajit , Kember Rachel L. , Mazzotti Diego R. , Dashti Hassan S. , Toikumo Sylvanus , Gehrman Philip R. , Kranzler Henry R.
Published: February 2023

Background

Epidemiologic studies have shown an association between sleep abnormalities and alcohol-related traits. Recent genome-wide association studies (GWAS) have identified genetic variants associated with sleep-related traits, including insomnia and sleep duration, and with alcohol-related phenotypes, including alcohol use disorder (AUD) and level of alcohol consumption.

Objectives

We investigated whether genetic risk for insomnia and sleep duration abnormalities are associated with AUD and alcohol consumption. We also evaluated the causal relationships between sleep- and alcohol-related traits.

Methods

Individual level phenotype and genotype data from the Million Veteran Program was used. Polygenic risk scores (PRS) were computed using summary statistics from two recent discovery GWAS of insomnia (N=453,379 European-ancestry (EA) individuals) and sleep duration (N=446,118 EAs) and tested for association with lifetime AUD diagnosis (cases, N=34,658 EAs) and past-year Alcohol Use Disorders Identification Test-Consumption scale scores (AUDIT-C, N=200,680 EAs). Bi-directional two-sample Mendelian Randomization (MR) analyses assessed causal associations between the two sleep traits and the two alcohol-related traits.

Results

Insomnia PRS was positively associated with AUD at 2/9 PRS thresholds, with p<0.01 being the most significant (OR = 1.02, p = 3.48 × 10−5). Conversely, insomnia PRS was negatively associated with AUDIT-C at 6/9 PRS thresholds (most significant threshold being p=0.001 (β = - 0.02, p = 5.6 × 10−8). Sleep duration PRS was not associated with AUD, but was positively associated with AUDIT-C at 2/9 PRS thresholds, with the most significant threshold being p = 1 × 10−6(β = 0.01, p = 0.0009). MR analyses supported a significant positive causal effect of insomnia on AUD (14 SNPs; beta = 104.14; SE = 16.19; p = 2.22 × 10−5), although with significant heterogeneity. MR analyses also provided nominal evidence of a causal effect of AUD on insomnia (10 SNPs; beta = 0.01; SE = 0.007; p = 0.01). Finally, MR analyses showed that decreased sleep duration had a causal effect on the risk of AUD (27 SNPs; beta = -63.05; SE = 3.54; p = 4.55 × 10−16) and was robust to sensitivity analyses.

Conclusion

The genetic risk for insomnia shows pleiotropy with AUD, and sleep continuity abnormalities have a causal influence on the development of AUD.
Tau expression and phosphorylation in enteroendocrine cells
Authors: Chapelet Guillaume , Béguin Nora , Castellano Blandine , Grit Isabelle , Oullier Thibauld , Neunlist Michel , Blottière Hervé , Rolli-Derkinderen Malvyne , Dréan Gwenola Le , Derkinderen Pascal
Published: February 2023

Background and objective

There is mounting evidence to suggest that the gut-brain axis is involved in the development of Parkinson’s disease (PD). In this regard, the enteroendocrine cells (EEC), which faces the gut lumen and are connected with both enteric neurons and glial cells have received growing attention. The recent observation showing that these cells express alpha-synuclein, a presynaptic neuronal protein genetically and neuropathologically linked to PD came to reinforce the assumption that EEC might be a key component of the neural circuit between the gut lumen and the brain for the bottom-up propagation of PD pathology. Besides alpha-synuclein, tau is another key protein involved in neurodegeneration and converging evidences indicate that there is an interplay between these two proteins at both molecular and pathological levels. There are no existing studies on tau in EEC and therefore we set out to examine the isoform profile and phosphorylation state of tau in these cells.

Methods

Surgical specimens of human colon from control subjects were analyzed by immunohistochemistry using a panel of anti-tau antibodies together with chromogranin A and Glucagon-like peptide-1 (two EEC markers) antibodies. To investigate tau phosphorylation and expression further, two EEC lines, namely GLUTag and NCI-H716 were analyzed by western blot after dephosphorylation with pan-tau and tau isoform specific antibodies. Eventually, GLUTag were treated with propionate and butyrate, two short chain fatty acids known to sense EEC, and analyzed at different time points by western blot with an antibody specific for tau phosphorylated at Thr205.

Results

We found that tau is expressed and phosphorylated in EEC in adult human colon and that both EEC lines mainly express two tau isoforms that are phosphorylated under basal condition. Both propionate and butyrate regulated tau phosphorylation state by decreasing its phosphorylation at Thr205.

Conclusion and inference

Our study is the first to characterize tau in human EEC and in EEC lines. As a whole, our findings provide a basis to unravel the functions of tau in EEC and to further investigate the possibility of pathological changes in tauopathies and synucleinopathies.
Reorganization of corticospinal projections after prominent recovery of finger dexterity from partial spinal cord injury in macaque monkeys
Authors: Sawada Masahiro , Yoshino-Saito Kimika , Ninomiya Taihei , Oishi Takao , Yamashita Toshihide , Onoe Hirotaka , Takada Masahiko , Nishimura Yukio , Isa Tadashi
Published: February 2023

We investigated morphological changes in the corticospinal tract (CST) to understand the mechanism underlying recovery of hand function after lesion of the CST at the C4/C5 border in 7 macaque monkeys. All monkeys exhibited complete recovery of precision grip success ratio within a few months. The trajectories and terminals of CST from the contralesional (n = 4) and ipsilesional (n = 3) hand area of primary motor cortex (M1) were investigated at 5-29 months after the injury using an anterograde neural tracer, biotinylated dextran amine (BDA). Reorganization of the CST was assessed by counting the number of BDA-labeled axons and button-like swellings in the gray and white matters. Rostral to the lesion (at C3), the number of axon collaterals of the descending axons from both contralesional and ipsilesional M1 entering the ipsilesional and contralesional gray matter, respectively, were increased. Caudal to the lesion (at C8), axons originating from the contralesional M1, descending in the preserved gray matter around the lesion, and terminating in ipsilesional laminae VI/VII and IX were observed. In addition, axons and terminals from the ipsilesional M1 increased in the ipsilesional laminae VI/VII and IX after recrossing the midline, which were not observed in intact monkeys. Conversely, axons originating from the ipsilesional M1 and directed toward the contralesional laminae VI/VII and IX decreased. These results suggest that multiple reorganizations of the corticospinal projections to spinal segments both rostral and caudal to the lesion originating from bilateral M1 underlie a prominent recovery in long-term after spinal cord injury.

SIGNIFICANCE STATEMENT

Previous studies have shown that dexterous finger movements recover prominently after lesion of the corticospinal tract (CST) at the mid-cervical segments through rehabilitative training in macaque monkeys. Here, we show reorganization of the CST including sprouting of axons originating from the contralesional and ipsilesional motor cortex in the gray matter both caudal and rostral to the lesion, including a re-direction of the CST to hand motoneurons in the monkeys 5-29 months after the lesion. Thus, multiple mechanisms of reorganization of CST axons underlie the recovery of impaired cortico-motoneuronal pathways for the long-term recovery of finger dexterity.