bluuebunny/crossref_metadata_2025 huggingface dataset:
A neural mechanism for conserved value computations integrating information and rewards
Authors: Bromberg-Martin Ethan S. , Feng Yang-Yang , Ogasawara Takaya , White J. Kael , Zhang Kaining , Monosov Ilya E.
Published: August 2022

Behavioral and economic theory dictates that we decide between options based on their values. However, humans and animals eagerly seek information about uncertain future rewards, even when this information does not provide any objective value. This implies that decisions can be made by endowing information with subjective value and integrating it with the value of extrinsic rewards, but the mechanism is unknown. Using a novel multi-attribute decision making task we found that human and monkey value judgements are regulated by strikingly conserved computational principles, including how they compute the value of information and scale it with information’s timing and ability to resolve a specific form of uncertainty. We then identified a neural substrate in a highly conserved and ancient structure, the lateral habenula (LHb). LHb neurons signal the subjective value of choice options integrating the value of information with extrinsic rewards, and LHb activity both predicts and causally influences online decisions. Key input regions to LHb provide the necessary ingredients for these computations, but do not themselves signal an integrated value signal to guide multi attribute decisions. Our data thus identifies neural mechanisms of the conserved computations underlying multi-attribute, value-based decisions to seek information about the future.
Toxicity potentials of selected insecticidal plant oils against Anopheles gambiae (Diptera: Culicidae) under laboratory conditions
Authors: Adelaja Olukayode James , Oduola Adedayo Olatubosun , Ande Adeolu Taiwo , Abiodun Oyindamola Olajumoke , Adelaja Abisayo Ruth
Published: August 2022

Despite increasing reports and concerns about resistance development to public-health insecticides in malaria-vectors, significant steps have been put into the quest for novel strategies to disrupt the disease transmission cycle by targeting insect-vectors hence sustaining vector management. This study evaluates the toxicity potential of oils of insecticidal plants shortlisted in an ethnobotanical survey on the larvae and adult stages of Anopheles gambiae. Oils from leaves of Hyptis suaveolens, Ocimum gratissimum, Nicotiana tabacum, Ageratum conyzoides and fruit-peel of Citrus sinensis were extracted by steam-distillation using a Clevenger apparatus. Larvae and female adults of deltamethrin susceptible Anopheles gambiae were gotten from an already established colony in the Entomological Research Laboratory, University of Ilorin. Twenty-five third instar stage larvae were used for larvicidal assays while twenty 2-5 days old adults were used for the adulticidal assays in five replicates. After which, coupled gas chromatography-mass spectrometry analysis (GC-MS) was performed to determine the major chemical-constituents of plant oils. A. gambiae exposed to H. suaveolens and C. sinensis demonstrated significantly higher larval toxicity (94.7-100%) after 24 hours. At 48 hours, the mortality induced by the oils of the four plants peaked at 100%. N. tabacum (0.50 mg/ml) induced the highest percentage adult mortality (100%) on A. gambiae which compared favourably with the positive control Deltamethrin (0.05%). The lowest KdT50 was observed with 0.25 mg/ml of N. tabacum (20.3 minutes) while the lowest KdT95 was observed with 0.10mg/ml of A. conyzoides (35.97 mins) against adult A. gambiae. D-limonene is the key chemical-constituent in oils from C. sinensis and A. conyzoides. The significant larval and adult mortality rates, lower lethal concentration and knockdown times demonstrated by the evaluated plant oils showed promising outcomes that can be further developed for vector control management.

Graphical Abstract
Identification of lactic acid bacteria with reduced inflammatory and enhanced protective properties against influenza virus
Authors: Sugimoto Atsushi , Nakamura Tomoe , Chihama Ryota , Takenaka Yuto , Sato Yuuki
Published: August 2022

Lactic acid bacteria (LAB) exert beneficial effects on health by regulating innate immunity in the intestinal tract. Many LAB that demonstrate anti-viral properties depend on the host’s inflammatory responses; however, a few LAB strains have low inflammatory and anti-viral properties. In this study, the LAB strain D279 (NITE_BP-03645, Latilactobacillus sakei) was isolated from among 741 LAB strains that were analyzed for their ability to induce interleukin 12 (IL-12), and was subsequently characterized. D279 induced the highest levels of IL-12 among the screened LAB. Further, D279 significantly activated anti-viral genes and preferentially induced IFNλ in vitro, which plays a critical role in the epithelial tissue, conferring strong anti-influenza potency without inflammation, whereas IFNα levels were relatively lower. Administration of pasteurized D279 to mice resulted in strong anti-influenza potency, including higher natural killer (NK) cell activity, and a reduced number of viruses in the lung compared to the control. Importantly, no D279-fed mice were sacrificed during the viral infection tests. Taken together, these results suggest that D279 administration confers beneficial effects with reduced inflammation, regulates innate immunity, and may be relevant for commercial use in the future.
Comparing Deep Learning Models for Age Prediction Based on the Resting State fMRI Dataset from the “Brain Dock” Service in Japan
Authors: Minowa Yutaka , Onoda Keiichi , Takamura Masahiro , Yamaguchi Shuhei , Okamoto Naoki , Akama Hiroyuki
Published: August 2022

In Japan, many hospitals provide the unequaled service of medical check-up called the “Brain Dock”; however, there is a paucity of studies aimed at leveraging functional magnetic resonance imaging (fMRI) in hospitals. We obtained the resting-state fMRI (rs-fMRI) scans of about 695 patients who accessed this service for preventive medicine against Alzheimer’s Disease. In this study, we created deep learning models for age prediction with the ultimate aim of arriving at standard protocols for introducing rs-fMRI into clinical settings, particularly in Brain Docks. With that view, an assemblage of modeling conditions was attempted, changing multiple parameter values, features based on data extraction methods (region of interest-wise mean blood-oxygen-level-dependent lump-sum time series models or dynamic functional connectivity models), deep learning algorithms (Transformer, Multi-task Transformer, and unidirectional or bidirectional long short-term memory models), and different atlas-dependent brain region segmentation methods (including the Automated Anatomical Labeling and Harvard-Oxford atlases). As a result, a robust and highly significant correlation was obtained between actual and predicted ages from all types of methodologies. In addition, we determined that some conditions had a relatively large impact on prediction performance based on extended comparisons. The accuracy decreased, particularly according to the choice of atlases but with the same modeling conditions. Notwithstanding, we found that atlases based on intrinsic functional connectivity provided significant prediction accuracy even with a small number of regions to a similar extent as networks lowered spatial granularity. Moreover, we found that multi-task learning with other phenotype data (related to gender differences) was possible, but did not improve the prediction accuracy as much as expected. Despite these limitations, our results could provide a hopeful prospect of introducing fMRI into the field of neuro-clinical practice.

Highlights

Age prediction modeling was performed using the rs-fMRI data of a Japanese “Brain Dock” service targeting mainly elderly people, which made prediction more challenging.

A robust and highly significant correlation was obtained from all types of methodologies changing data extraction methods, deep learning algorithms, and brain atlases.

Age prediction was successful even with a very small number of regions exclusively based on intrinsic functional connectivity networks, although there was a difference in the achievement of modeling.
Accurately modeling biased random walks on weighted networks using node2vec+
Authors: Liu Renming , Hirn Matthew , Krishnan Arjun
Published: August 2022

Motivation

Accurately representing biological networks in a low-dimensional space, also known as network embedding, is a critical step in network-based machine learning and is carried out widely using node2vec, an unsupervised method based on biased random walks. However, while many networks, including functional gene interaction networks, are dense, weighted graphs, node2vec is fundamentally limited in its ability to use edge weights during the biased random walk generation process, thus under-using all the information in the network.

Results

Here, we present node2vec+, a natural extension of node2vec that accounts for edge weights when calculating walk biases and reduces to node2vec in the cases of unweighted graphs or unbiased walks. Using two synthetic datasets, we empirically show that node2vec+ is more robust to additive noise than node2vec in weighted graphs. Then, using genome-scale functional gene networks to solve a wide range of gene function and disease prediction tasks, we demonstrate the superior performance of node2vec+ over node2vec in the case of weighted graphs. Notably, due to the limited amount of training data in the gene classification tasks, graph neural networks such as GCN and GraphSAGE are outperformed by both node2vec and node2vec+

Contact

arjun.krishnan@cuanschutz.edu

Code Availability

https://github.com/krishnanlab/node2vecplus_benchmarks

Supplementary information

Supplementary data are available at Bioinformatics online.
Analysis of the ubiquitin-modified proteome identifies novel host factors in Kaposi’s sarcoma herpesvirus lytic reactivation
Authors: Causey Amerria , Constantine Mathew , Oswald Jessica , Dellomo Anna , Masters Bronwyn , Omorogbe Esosa , Admon Arie , Garzino-Demo Alfredo , Ehrlich Elana
Published: August 2022

Kaposi’s Sarcoma Herpesvirus (KSHV) is the causative agent of Kaposi’s Sarcoma (KS) and is associated with primary effusion lymphoma (PEL), multicentric Castleman’s disease (MCD) and two inflammatory diseases. KSHV-associated cancers are primarily associated with genes expressed during latency, while other pathologies are associated with lytic gene expression. The major lytic switch of the virus, Replication and Transcription Activator (RTA), interacts with cellular machinery to co-opt the host ubiquitin proteasome system to evade the immune response as well as activate the program of lytic replication. Through SILAC labeling, ubiquitin remnant enrichment and mass spectrometry, we have analyzed the RTA dependent ubiquitin-modified proteome. We identified RTA dependent changes in the populations of polyubiquitin chains, as well as changes in ubiquitinated proteins in both cells expressing RTA and naturally infected cells following lytic reactivation. We observed an enrichment of proteins that are also reported to be SUMOylated, suggesting that RTA, a SUMO targeting ubiquitin ligase, may function to alleviate a SUMO dependent block to lytic reactivation. RTA targeted substrates directly through a ubiquitin ligase domain dependent mechanism as well as indirectly through cellular ubiquitin ligase RAUL. Our ubiquitome analysis revealed an RTA dependent mechanism of immune evasion. We provide evidence of inhibition of TAP dependent peptide transport, resulting in decreased HLA complex stability. The results of this analysis increase our understanding of mechanisms governing the latent to lytic transition in addition to the identification of a novel RTA dependent mechanism of immune evasion.

Importance

Kaposi’s sarcoma herpesvirus (KSHV), an AIDS associated pathogen, is associated with multiple cancers and inflammatory syndromes. This virus has a latent and lytic lifecycle, each associated with pathogenesis and oncogenesis. Here we identify proteins that display differential abundance in different phases of the lifecycle. We provide evidence supporting a new model of viral immune evasion. These findings increase our understanding of how the virus manipulates the host cell and provides new targets for intervention.
A microfluidic device for controlled exposure of transgenic Ciona intestinalis larvae to chemical stimuli demonstrates they can respond to carbon dioxide
Authors: Poncelet Guillaume , Parolini Lucia , Shimeld Sebastian M
Published: August 2022

The larva of the ascidian Ciona intestinalis controls a small repertoire of behaviours with a simple nervous system in which each cell is identifiable. As such it offers the prospect of building a cohesive cell-level picture of how a nervous system integrates sensory inputs to produce specific behavioural outcomes. Here, we report the development of a microfluidic chip in which larvae can be immobilised and exposed to chemical stimuli. We generate transgenic larvae in which the calcium ion reporter GCaMP6m is expressed in a defined population of cells, allowing us to record real-time neural activity following stimulation. We then use this to establish that some cell populations can sense dissolved carbon dioxide. We also leverage genome and transcriptome data coupled with molecular evolutionary analysis to identify putative chemoreceptors of the MS4A family in Ciona. Our study demonstrates that Ciona larvae can respond to dissolved carbon dioxide, identifies the cells that are likely responsible for chemosensation, and establishes a chip based imaging platform coupled with transgenic technology that could be adapted to establish where other stimuli are sensed and how such incoming signals are processed in the brain to yield behavioural output.
Cerebrospinal fluid-contacting neuron tracing reveals structural and functional connectivity for locomotion in the mouse spinal cord
Authors: Nakamura Yuka , Kurabe Miyuki , Matsumoto Mami , Sato Tokiharu , Miyashita Satoshi , Hoshina Kana , Kamiya Yoshinori , Tainaka Kazuki , Matsuzawa Hitoshi , Ohno Nobuhiko , Ueno Masaki
Published: August 2022

Cerebrospinal fluid-contacting neurons (CSF-cNs) are enigmatic mechano- or chemosensory cells lying along the central canal of the spinal cord. Recent studies in zebrafish larvae and lampreys have shown that CSF-cNs control postures and movements via spinal connections. However, the structures, connectivity, and functions in mammals remain largely unknown. Here we developed a method to genetically target mouse CSF-cNs that highlighted structural connections and functions. We first found that intracerebroventricular injection of adeno-associated virus with a neuron-specific promoter and Pkd2l1-Cre mice specifically labeled CSF-cNs. Single-cell labeling of 71 CSF-cNs revealed rostral axon extensions of over 1800 μm in unmyelinated bundles in the ventral funiculus and terminated on CSF-cNs to form a recurrent circuitry, which was further determined by serial electron microscopy and electrophysiology. CSF-cNs were also found to connect with axial motor neurons and premotor interneurons around the central canal and within the axon bundles. Chemogenetic CSF-cNs inactivation reduced speed and step frequency during treadmill locomotion. Our data revealed the basic structures and connections of mouse CSF-cNs to control spinal motor circuits for proper locomotion. The versatile methods developed in this study will contribute to further understanding of CSF-cNs functions in mammals.
Development and applications of a CRISPR activation system for facile genetic overexpression in Candida albicans
Authors: Gervais Nicholas C. , La Bella Alyssa A. , Wensing Lauren F. , Sharma Jehoshua , Acquaviva Victoria , Best Madison , Cadena López Ricardo Omar , Fogal Meea , Uthayakumar Deeva , Chavez Alejandro , Santiago-Tirado Felipe , Flores-Mireles Ana L. , Shapiro Rebecca S.
Published: August 2022

For the fungal pathogen Candida albicans, genetic overexpression readily occurs via a diversity of genomic alterations, such as aneuploidy and gain-of-function mutations, with important consequences for host adaptation, virulence, and evolution of antifungal drug resistance. Given the important role of overexpression on C. albicans biology, it is critical to develop and harness tools that enable the analysis of genes expressed at high levels in the fungal cell. Here, we describe the development, optimization, and application of a novel, single-plasmid-based CRISPR activation (CRISPRa) platform for targeted genetic overexpression in C. albicans, which employs a guide RNA to target an activator complex to the promoter region of a gene of interest, thus driving transcriptional expression of that gene. Using this system, we demonstrate the ability of CRISPRa to drive high levels of gene expression in C. albicans, and we assess optimal guide RNA targeting for robust and constitutive overexpression. We further demonstrate the specificity of the system via RNA sequencing. We highlight the application of CRISPRa to overexpress genes involved in pathogenesis and drug resistance and contribute towards the identification of novel phenotypes. Together, this tool will facilitate a broad range of applications for the study of C. albicans genetic overexpression.
Proteome-scale induced proximity screens reveal highly potent protein degraders and stabilizers
Authors: Poirson Juline , Dhillon Akashdeep , Cho Hanna , Lam Mandy Hiu Yi , Alerasool Nader , Lacoste Jessica , Mizan Lamisa , Taipale Mikko
Published: August 2022

Targeted protein degradation and stabilization are promising therapeutic modalities due to their potency and versatility. However, only few E3 ligases and deubiquitinases have been harnessed for this purpose. Moreover, there may be other protein classes that could be exploited for protein stabilization or degradation. Here, we used a proteome-scale platform to identify hundreds of human proteins that can promote the degradation or stabilization of a target protein in a proximity-dependent manner. This allowed us to comprehensively compare the activities of human E3s and deubiquitinases, characterize non-canonical protein degraders and stabilizers, and establish that effectors have vastly different activities against diverse targets. Notably, the top degraders were more potent against multiple therapeutically relevant targets than the currently used E3s CBRN and VHL. Our study provides a functional catalogue of effectors for targeted protein degradation and stabilization and highlights the potential of induced proximity screens for discovery of novel proximity-dependent protein modulators.
Genomics of Natural Populations: Gene Conversion Events Reveal Selected Genes within the Inversions ofDrosophila pseudoobscura
Authors: Schaeffer Stephen W. , Richards Stephen , Fuller Zachary L.
Published: August 2022

When adaptive phenotypic variation or QTLs map within an inverted segment of a chromosome, researchers often despair because it is thought that the suppression of crossing over will prevent the discovery of selective target genes that contribute to the establishment of the rearrangement. If an inversion polymorphism is old enough, then the accumulation of gene conversion tracts offers the promise that QTLs or selected loci within inversions can be mapped. This study uses the inversion polymorphism ofDrosophila pseudoobscuraas a model system to show that gene conversion analysis is a useful tool for mapping selected loci within inversions.D. pseudoobscurahas over 30 different chromosomal arrangements on the third chromosome (Muller C) in natural populations and their frequencies vary with changes in environmental habitats. Statistical tests of fiveD. pseudoobscuragene arrangements identified outlier genes within inverted regions based on local clusters of fixed SNP differences. These outlier genes also had potentially heritable variation, either fixed amino acid differences or differential expression patterns among arrangements. Here, we use genome sequences of the inverted third chromosome (Muller C) to infer 98,443 gene conversion tracts for a total coverage of 142 Mb or 7.2 x coverage of the 19.7 Mb chromosome. We estimated gene conversion tract coverage in the 2,668 genes on Muller C and tested whether the number of genes with significantly low coverage was the same for outlier versus non-outlier loci.. Genes with low gene conversion tract coverage were more frequent in the outlier class than the non-outlier class suggesting that selection removes exchanged DNA from the outlier genes more often than non-outlier genes. These data support the hypothesis that the pattern and organization of genetic diversity on the third chromosome inD. pseudoobscurais consistent with the capture of locally adapted combinations of alleles prior to inversion mutation events.
Açai (Euterpe precatoria Mart. Arecaceae) from the Northern Region of Bolivia is not contaminated with Trypanosoma cruzi
Authors: Rollano-Peñaloza OM , Roque-Marca N , Peñarrieta M , Mollinedo P , Rodriguez C , Larrea-Alcázar D.M.
Published: August 2022

Chagas disease is a very important public health problem in America. It is caused by the protozoan parasite Trypanosoma cruzi and transmitted by vectors such as Triatomine insects. However, oral transmission is generating more T. cruzi infections than vectorial transmission in Brazilian Amazonic regions, probably due to the increased consumption of tropical fruits such as açai. Açai palms have become very popular due to its good nutritional properties. Açai fruits have different sources depending of their geographical origin. Açai palms (Euterpe oleracea) in Brazil are cultivated, while in Bolivia grow in wild populations and belongs to a different species, the solitary açai (Euterpe precatoria). Only açai from Brazil has been involved in T. cruzi oral transmission, while Bolivian açai has been regarded as disease free. In order to verify the absence of T. cruzi on açai products from Bolivia, we developed a method to detect T. cruzi DNA by real-Time PCR with internal controls for solitary açai. In this study we show that açai good manufacturing process did not interfere with the detection of açai or T. cruzi DNA. Finally, we report that freshly collected açai fruits and açai frozen pulps from Bolivia were not contaminated with T. cruzi.
Three R2R3-MYB transcription factors from banana (Musaspp.) activate structural anthocyanin biosynthesis genes as part of an MBW complex
Authors: Busche Mareike , Pucker Boas , Weisshaar Bernd , Stracke Ralf
Published: August 2022

Bananas are among the most popular fruits in the world and provide food security and employment opportunities in several developing countries. An increased anthocyanin content could enhance the health promoting properties of banana fruits. The biosynthesis of anthocyanins is largely regulated at the transcriptional level. However, little is known about transcriptional activation of anthocyanin biosynthesis in banana. We analysed the regulatory activity of threeMusaMYBs predicted by bioinformatic analysis to transcriptionally regulate anthocyanin biosynthesis in banana.MusaMYBA1, MusaMYBA2andMusaMYBPA2did not complement the anthocyanin deficiency phenotype of theA. thaliana pap1/pap2mutant. However, co-transfection experiments inA. thalianaprotoplasts showed thatMusaMYBA1,MusaMYBA2 andMusaMYBPA2 function as components of a transcription factor complex with a bHLH and WD40 protein, called MBW complex, resulting in the activation of theanthocyanin synthaseanddihydroflavonol 4-reductasepromoters fromA. thaliana. The activation potential ofMusaMYBA1,MusaMYBA2 andMusaMYBPA2 increased when combined with the monocot bHLHZmR instead of the dicotAtEGL3. This work paves the path towards decoding the MBW complex-mediated transcriptional activation of anthocyanin biosynthesis in banana. Moreover, it facilitates research towards an elevated anthocyanin content in banana and other monocot crops.
ELI trifocal microscope: A precise cryogenic fabrication system to prepare target cryo-lamellae of cells for in situ cryo-ET study
Authors: Li Shuoguo , Wang Ziyan , Jia Xing , Niu Tongxin , Zhang Jianguo , Yin Guoliang , Zhang Xiaoyun , Zhu Yun , Ji Gang , Sun Fei
Published: August 2022

Cryo-electron tomography (cryo-ET) has become a powerful approach to study the high-resolution structure of cellular macromolecular machines in situ. However, the current correlative cryo-fluorescence and electron microscopy lacks sufficient accuracy and efficiency to precisely prepare cryo-lamellae of target locations for subsequent in situ cryo-ET structural study. Here, we developed a precise cryogenic fabrication system, the ELI trifocal microscope (ELI-TriScope), by setting up an electron (E) beam, a light (L) beam and an ion (I) beam at the same focal point to achieve accurate and efficient preparation of a target cryo-lamella without sacrificing the throughput. ELI-TriScope was developed starting from a commercial dual-beam scanning electron microscope (SEM) by incorporating a cryo-holder-based transfer system and embedding an optical imaging system just underneath the vitrified specimen. Cryo-focused ion beam (FIB) milling can be accurately navigated by monitoring the real-time fluorescence signal of the target molecule. Using ELI-TriScope, we prepared a batch of cryo-lamellae of HeLa cells targeting the centrosome, with an ∼100% success rate, and discovered new in situ structural features of the human centrosome through a subsequent cryo-ET structural study.
DNA methylation age studies of humpback whales
Authors: Horvath Steve , Haghani Amin , Zoller Joseph A. , Fei Zhe , Bérubé Martine , Robbins Jooke
Published: August 2022

Several previous studies have described epigenetic clocks for whale and dolphin species. Here we present a novel and highly robust epigenetic clock for the humpback whale based on methylation levels measured using the Mammalian Methylation Array platform. Skin samples were obtained from 76 individuals that had been studied since their birth year and known to range in age from <1 to 39.5 years. The humpback whale clock provided a highly accurate estimate of chronological age (R=0.96, median error 2.2 years) according to a leave-one-out cross validation analysis. We applied this clock to an independent set of samples from humpback whales of unknown exact age but with sighting histories that were as long as or longer than the upper 20% of the available known-age range. Although there was a strong correlation with minimum age (R=0.89), the clock underestimated age in these older animals by a median error of at least 7.8 years. Finally, we applied the humpback clock to publicly available methylation data from beluga whales. In this data set from a different species, the humpback clock provided an age correlation of R=0.78. While a DNAm age estimator has previously been described for humpback whales, this is the first such clock shown to apply to another cetacean species as well. Our humpback whale clock built from well-studied population lends itself for understanding humpback populations that otherwise lack age data.
Integrative Analysis of Histological Textures and Lymphocyte Infiltration in Renal Cell Carcinoma using Deep Learning
Authors: Brummer Otso , Pölönen Petri , Mustjoki Satu , Brück Oscar
Published: August 2022

Evaluating tissue architecture from routine hematoxylin and eosin-stained (H&E) slides is prone to subjectivity and sampling bias. Here, we extensively annotated ∼40,000 images of five tissue texture types and ∼25,000 images of lymphocyte quantity to train deep learning models. We defined histopathological patterns in over 400 clear-cell renal cell carcinoma H&E-stained slides of The Cancer Genome Atlas (TCGA) and resolved sampling and staining differences by harmonizing textural composition. By integrating multi-omic and imaging data, we profiled their clinical, immunological, genomic, and transcriptomic phenotypes. Histological grade, stage, adaptive immunity, the epithelial-to-mesenchymal transition signature and lower mutation burden were more common in stroma-rich samples. Histological proximity between the malignant and normal renal tissues was associated with poor survival, cellular proliferation, tumor heterogeneity, and wild-type PBRM1. This study highlights textural characterization to standardize sampling differences, quantify lymphocyte infiltration and discover novel histopathological associations both in the intratumoral and peritumoral regions.
Analysis of context-specific KRAS-effectors (sub)complexes in Caco-2 cells
Authors: Ternet Camille , Junk Philipp , Sevrin Thomas , Catozzi Simona , Oliviero Giorgio , Wynne Kieran , Kiel Christina
Published: August 2022

Ras is a key switch controlling cell behavior. In the GTP-bound form, Ras interacts with numerous effectors in a mutually exclusive manner, where individual Ras-effectors are likely part of larger cellular (sub)complexes. The molecular details of these (sub)complexes and their alteration in specific contexts is not understood. Focusing on KRAS, we performed affinity purification (AP)-mass spectrometry (MS) experiments of exogenous expressed FLAG-KRAS WT and three oncogenic mutants (‘genetic contexts’) in the human Caco-2 cell line, each exposed to 11 different culture media (‘culture contexts’) that mimic conditions relevant in the colon and colorectal cancer. We identified four effectors present in complex with KRAS in all genetic and growth contexts (‘context-general effectors’). Seven effectors are found in KRAS complexes in only some contexts (‘context-specific effectors’). Analyzing all interactors in complex with KRAS per condition, we find that the culture contexts had a larger impact on interaction rewiring than genetic contexts. We investigated how changes in the interactome impact functional outcomes and created a shiny app for interactive visualization. We validated some of the functional differences in metabolism and proliferation. Finally, we used networks to evaluate how KRAS effectors are involved in the modulation of functions by random walk analyses of effector-mediated (sub)complexes. Altogether, our work shows the impact of environmental contexts on network rewiring, which provides insights into tissue-specific signaling mechanisms. This may also explain why KRAS oncogenic mutants may be causing cancer only in specific tissues despite KRAS being expressed in most cells and tissues.
ERStruct: A Python Package for Inferring the Number of Top Principal Components from Whole Genome Sequencing Data
Authors: Yang Jinghan , Xu Yuyang , Yao Minhao , Wang Gao , Liu Zhonghua
Published: August 2022

Large-scale multi-ethnic DNA sequencing data is increasingly available owing to decreasing cost of modern sequencing technologies. Inference of the population structure with such sequencing data is fundamentally important. However, the ultra-dimensionality and complicated linkage disequilibrium patterns across the whole genome make it challenging to infer population structure using traditional principal component analysis (PCA) based methods and software. We present the ERStruct Python Package, which enables the inference of population structure using whole-genome sequencing data. By leveraging parallel computing and GPU acceleration, our package achieves significant improvements in the speed of matrix operations for large-scale data. Additionally, our package features adaptive data splitting capabilities to facilitate computation on GPUs with limited memory. Our Python package ERStruct is an efficient and user-friendly tool for estimating the number of top informative PCs that capture population structure from whole genome sequencing data.
Solid/liquid coexistence during aging of FUS condensates
Authors: Shen Yi , Chen Anqi , Wang Wenyun , Shen Yinan , Ruggeri Francesco Simone , Aime Stefano , Wang Zizhao , Qamar Seema , Espinosa Jorge R. , Garaizar Adiran , George-Hyslop Peter St , Collepardo-Guevara Rosana , Weitz David A. , Vigolo Daniele , Knowles Tuomas P. J.
Published: August 2022

A wide range of macromolecules undergo phase separation, forming biomolecular condensates in living cells. These membraneless organelles are typically highly dynamic, formed in a reversible manner, and carry out important functions in biological systems. Crucially, however, a further liquid-to-solid transition of the condensates can lead to irreversible pathological aggregation and cellular dysfunction associated with the onset and development of neurodegenerative diseases. Despite the importance of this liquid-to-solid transition of proteins, the mechanism by which it is initiated in normally functional condensates is unknown. Here we show, by measuring the changes in structure, dynamics and mechanics in time and space, that FUS condensates do not uniformly convert to a solid gel, but rather that liquid and gel phases co-exist simultaneously within the same condensate, resulting in highly inhomogeneous structures. We introduce two new optical techniques, dynamic spatial mapping and reflective confocal dynamic speckle microscopy, and use these to further show that the liquid-to-solid transition is initiated at the interface between the dense phase within condensates and the dilute phase. These results reveal the importance of the spatiotemporal dimension of the liquid-to-solid transition and highlight the interface of biomolecular condensates as a key element in driving pathological protein aggregation.
An exotic allele of barley EARLY FLOWERING 3 contributes to developmental plasticity at elevated temperatures
Authors: Zhu Zihao , Esche Finn , Babben Steve , Trenner Jana , Serfling Albrecht , Pillen Klaus , Maurer Andreas , Quint Marcel
Published: August 2022

Increase in ambient temperatures caused by climate change affects various morphological and developmental traits of plants, threatening crop yield stability. In the model plant Arabidopsis thaliana, EARLY FLOWERING 3 (ELF3) plays prominent roles in temperature sensing and thermomorphogenesis signal transduction. However, how crop species respond to elevated temperatures is poorly understood. Here, we show that the barley ortholog of AtELF3 interacts with high temperature to control growth and development. We used heterogeneous inbred family (HIF) pairs generated from a segregating mapping population and systematically studied the role of exotic ELF3 variants in barley temperature responses. An exotic ELF3 allele from Syrian origin promoted elongation growth in barley at elevated temperatures, whereas plant area and estimated biomass were drastically reduced, resulting in an open canopy architecture. The same allele accelerated inflorescence development at high temperature, which correlated with early transcriptional induction of MADS-box floral identity genes BM3 and BM8. Consequently, barley plants carrying the exotic ELF3 allele displayed stable total grain number and mitigated yield loss at elevated temperatures. Our findings therefore demonstrate that exotic ELF3 variants can contribute to phenotypic and developmental acclimation to elevated temperatures, providing a stimulus for breeding of climate resilient crops.

Highlight

We demonstrate that an exotic allele of EARLY FLOWERING 3 (ELF3) contributes to plant architectural and developmental acclimation, and thereby improves yield stability at high ambient temperatures.
A Novel Framework for In-vivo Diffusion Tensor Distribution MRI of the Human Brain
Authors: Magdoom Kulam Najmudeen , Avram Alexandru V. , Sarlls Joelle E. , Dario Gasbarra , Basser Peter J.
Published: August 2022

Neural tissue microstructure plays an important role in developmental, physiological and pathophysiological processes. Diffusion tensor distribution (DTD) MRI helps probe heterogeneity at the mesoscopic length scale, orders of magnitude smaller than the nominal MRI voxel size, by describing water diffusion within a voxel using an ensemble of non-exchanging compartments characterized by a probability density function of diffusion tensors. In this study, we provide a new framework for acquiring tensor encoded diffusion weighted images (DWIs) and estimating DTD from them for in-vivo human brain imaging. We interfused pulsed field gradients (iPFG) in a single spin echo to generate arbitrary b-tensors of rank one, two, or three without introducing concomitant gradient artifacts. Employing well-defined gradient pulse duration and mixing/diffusion times in our diffusion preparation, we show that iPFG retains salient features of traditional multiple-PFG (mPFG) sequence while overcoming some of its implementation issues thereby extending its applications beyond DTD MRI. We assume DTD is a maximum entropy tensor-variate normal distribution whose tensor random variables are constrained to be positive definite (CNTVD) to ensure their physicality. In each voxel, the second-order mean and fourth-order covariance tensors of the DTD are estimated using a Monte Carlo method that synthesizes micro-diffusion tensors with corresponding size, shape and orientation distributions to best fit the measured DWIs. From these tensors we obtain the mean diffusivity (MD) spectrum, spectrum of diffusion tensor shapes, microscopic orientation distribution function (µODF), and microscopic fractional anisotropy (µFA) which disentangle the underlying heterogeneity within a voxel. Using DTD derived µODF, we introduce a new method to perform fiber tractography capable of resolving complex fiber configurations. The results obtained in the live human brain showed microscopic anisotropy in various gray and white matter regions and skewed MD distribution in cerebellar gray matter not observed previously. DTD MRI tractography captured complex white matter fiber organization consistent with known anatomy. DTD MRI also resolved some degeneracies associated with diffusion tensor imaging (DTI) and identified the source of microscopic anisotropy which may help improve the diagnosis of various neurological diseases and disorders.
Loss of retinogeniculate synaptic function in the DBA/2J mouse model of glaucoma
Authors: Smith Jennie C. , Zhang Kevin Yang , Sladek Asia , Thompson Jennifer , Bierlein Elizabeth R. , Bhandari Ashish , Van Hook Matthew J.
Published: August 2022

Background

Retinal ganglion cell (RGC) axons comprise the optic nerve and carry information to the dorsolateral geniculate nucleus (dLGN) that is relayed to the cortex for conscious vision. Glaucoma is a blinding neurodegenerative disease that commonly results from intraocular pressure (IOP)-associated injury leading to RGC axonal pathology, disruption of RGC outputs to the brain, and eventual apoptotic loss of RGC somata. The consequences of elevated IOP and glaucomatous pathology on RGC signaling to the dLGN are largely unknown and likely to be important contributors to visual system dysfunction in glaucoma. Thus, the goal of this study was to determine how glaucoma affects RGC outputs to the dLGN.

Methods

We used a combination of anatomical and physiological approaches to study the structure and function of retinogeniculate synapses in male and female DBA/2J mice at multiple ages before and after IOP elevation. These included measures of anterograde axonal transport, immunofluorescence staining of RGC axon terminals, patch-clamp recording retinogeniculate (RG) synapses in living brain slices, Sholl analysis of thalamocortical relay neuron dendrites, measurements of RGC somatic density, and treatment with a topical ophthalmic alpha-2 adrenergic agonist (brimonidine).

Results

DBA/2J mice showed progressive loss of anterograde optic tract transport to the dLGN and vGlut2 labeling of RGC axon terminals. Patch-clamp measurements of RG synaptic function showed that the strength of synaptic transmission was lower in 9 and 12-month DBA/2J mice and that this was the result of loss of individual RGC axon contributions. TC neuron dendrites showed a reduction in complexity at 12 months, suggestive of a delayed reorganization following reduced synaptic input. There was no detectable change in RGC soma density in 11-12m DBA/2J retinas indicating that observed effects occurred prior to RGC somatic loss. Finally, treatment with brimonidine eye drops prevented the loss of vGlut2-labeled RGC terminals in the dLGN.

Conclusions

These findings identify glaucoma- and IOP-associated functional deficits in an important subcortical RGC projection target. This sheds light on the processes linking IOP to vision loss and will be critical for informing future diagnostic approaches and vision-restoration therapies.
Minimum effort simulations of split-belt treadmill walking exploit asymmetry to reduce metabolic energy expenditure
Authors: Price Mark , Huber Meghan E. , Hoogkamer Wouter
Published: August 2022

Walking on a split-belt treadmill elicits an adaptation response that changes the baseline step length asymmetry of the walker. The underlying causes of this adaptation, however, are difficult to determine. It has been proposed that effort minimization may drive this adaptation, based on the idea that adopting longer steps on the fast belt, or positive step length asymmetry (SLA), can cause the treadmill to exert net-positive mechanical work on a bipedal walker. However, humans walking on split-belt treadmills have not been observed to reproduce this behavior when allowed to freely adapt. To determine if an energy minimization motor control strategy would result in experimentally observed adaptation patterns, we conducted simulations of walking on different combinations of belt speeds with a human musculoskeletal model which minimized muscle effort. The model adopted increasing amounts of positive step length asymmetry and decreased its net metabolic rate with increasing belt speed asymmetry, up to +25.6% SLA and −14.3% metabolic rate at a 3:1 belt speed ratio, relative to tied-belt walking. These gains were primarily enabled by an increase of braking work and a reduction of propulsion work on the fast belt. The results suggest that a purely energy minimization driven split belt walking strategy would involve substantial positive SLA, and that the lack of this characteristic in human behavior points to additional factors influencing the motor control strategy, such as aversion to excessive joint loads, asymmetry, or instability.

New & Noteworthy

Behavioral observations of split-belt treadmill adaptation have been inconclusive toward its underlying causes. To estimate gait patterns when driven exclusively by one of these possible causes, we simulated split-belt walking with a musculoskeletal model which minimized its energy cost. Our model took significantly longer steps on the fast belt and reduced its metabolic rate below tied-belt walking, unlike experimental observations. This suggests that asymmetry is energetically optimal, but human adaptation involves additional factors.
Phenotype integration improves power and preserves specificity in biobank-based genetic studies of MDD
Authors: Dahl Andrew , Thompson Michael , An Ulzee , Krebs Morten , Appadurai Vivek , Border Richard , Bacanu Silviu-Alin , Werge Thomas , Flint Jonathan , Schork Andrew J. , Sankararaman Sriram , Kendler Kenneth , Cai Na
Published: August 2022

Biobanks often contain several phenotypes relevant to a given disorder, and researchers face complex tradeoffs between shallow phenotypes (high sample size, low specificity and sensitivity) and deep phenotypes (low sample size, high specificity and sensitivity). Here, we study an extreme case: Major Depressive Disorder (MDD) in UK Biobank. Previous studies found that shallow and deep MDD phenotypes have qualitatively distinct genetic architectures, but it remains unclear which are optimal for scientific study or clinical prediction. We propose a new framework to get the best of both worlds by integrating together information across hundreds of MDD-relevant phenotypes. First, we use phenotype imputation to increase sample size for the deepest available MDD phenotype, which dramatically improves GWAS power (increases #loci ~10 fold) and PRS accuracy (increases R2 ~2 fold). Further, we show the genetic architecture of the imputed phenotype remains specific to MDD using genetic correlation, PRS prediction in external clinical cohorts, and a novel PRS-based pleiotropy metric. We also develop a complementary approach to improve specificity of GWAS on shallow MDD phenotypes by adjusting for phenome-wide PCs. Finally, we study phenotype integration at the level of GWAS summary statistics, which can increase GWAS and PRS power but introduces non-MDD-specific signals. Our work provides a simple and scalable recipe to improve genetic studies in large biobanks by combining the sample size of shallow phenotypes with the sensitivity and specificity of deep phenotypes.
Inactivated voltage-gated sodium channels are preferentially targeted in cinacalcet block of mouse neocortical action potentials
Authors: Lindner Jamie S. , Rajayer Salil R. , Smith Stephen M.
Published: August 2022

Voltage-gated sodium channel (VGSC) activation is essential for action potential generation in the brain. Allosteric calcium-sensing receptor (CaSR) agonist, cinacalcet, strongly and ubiquitously inhibits VGSC currents in neocortical neurons via an unidentified, G-protein-dependent blocking molecule. The mechanisms by which VGSC characteristics influence cinacalcet-mediated inhibition are not well understood. Here, using whole-cell patch clamp methods, we investigated the voltage-dependence of cinacalcet-mediated inhibition of VGSCs and the channel state preference of cinacalcet. The rate of inhibition of VGSC currents was accelerated at more depolarized holding potentials. Cinacalcet shifted the voltage-dependence of both fast and slow inactivation of VGSCs in the hyperpolarizing direction. Utilizing a simple model, the voltage-dependence of VGSC current inhibition may be explained if the affinity of the blocking molecule to the channel states follows the sequence: fast-inactivated > slow-inactivated > resting. The state dependence of block contributes to the non-linearity of action potential block by cinacalcet. This dynamic and abundant signaling pathway by which G-proteins regulate VGSC currents provides an important voltage-dependent mechanism for modulating central neuronal excitability.

Key points summary

Voltage-gated sodium channels are essential for the action potential generation and propagation that is central to physiological function in excitable cells. VGSC inhibitors are useful therapies to treat epilepsy, pain, and cardiac arrhythmias.

Cinacalcet inhibits VGSC currents strongly and the underlying G-protein dependent signaling pathway occurs in the vast majority of neocortical and hippocampal neurons.

Here we demonstrate that cinacalcet inhibits the VGSC current by activating a downstream blocking molecule that preferentially binds to the fast-inactivated state, that the blocking molecule stabilizes the inactivated states, and that cinacalcet impacts neuronal excitability in a non-linear manner.

Characterization of the mechanism by which cinacalcet operates will facilitate the determination of its role in regulating neocortical excitability and the identification of new therapeutic targets for epilepsy, pain, and arrythmias.