bluuebunny/crossref_metadata_2025 huggingface dataset:
The temporal organization of corticostriatal communications
Authors: Korponay Cole , Stein Elliot A , Ross Thomas J
Published: July 2022

The cortex and striatum are linked by hundreds of thousands of structural connections, and the transmission of temporally aligned communications across many of these connections at once is an electrophysiological prerequisite for striatal activation. Despite the importance of communication timing in corticostriatal circuitry, there is little understanding of its system-level organization and properties. To investigate this, we leveraged emerging methods to “temporally unwrap” fMRI data and measure patterns of cortex-striatum node-pair coactivation at frame-wise (i.e., <1 sec) resolution in low head-motion subjects from the Human Connectome Project. First, we identify communities of cortex-striatum node-pairs with preferentially synchronized coactivation patterns. Surprisingly, we find that the map of striatal areas with temporally aligned cortical coactivation patterns does not simply reflect the map of striatal areas with similar cortical connectivity profiles. As a result of the distinct spatial organization of these gradients, striatal nodes connected to similar areas of cortex may nonetheless interact with these cortical areas at different times, and striatal nodes connected to different areas of cortex may nonetheless interact with these areas at similar times. We provide evidence for a possible mechanism driving this divergence: striatal nodes with similar cortical connectivity profiles may have differently timed interactions with cortex if they have different modulatory input profiles (i.e., from the midbrain and thalamus) that differentially gate their responsivity to cortical input. Overall, this blended organization may serve to both increase the repertoire of striatal responses to frontal input and facilitate coordination across functional domains in the temporal dimension. Findings provide a framework to investigate the role of corticostriatal temporal coordination in behavior and disease.

SIGNIFICANCE STATEMENT

We provide the first systems-level account of temporal communication patterns between cortex-striatum node-pairs, mapping communities of node-pairs with synchronized communication patterns using an emerging fMRI temporal-unwrapping technique and providing evidence for the mechanism that dictates the organization of these communities. Findings have broad implications for our understanding of the functional architecture of corticostriatal circuits.
Maast: genotyping thousands of microbial strains efficiently
Authors: Shi Zhou Jason , Nayfach Stephen , Pollard Katherine S.
Published: July 2022

Genotyping single nucleotide polymorphisms (SNPs) of intraspecific genomes is a prerequisite to performing population genetic analysis and microbial epidemiology. However, existing algorithms fail to scale for species with thousands of sequenced strains, nor do they account for the biased sampling of strains that has produced considerable redundancy in genome databases. Here we present Maast, a tool that reduces the computational burden of SNP genotyping by leveraging this genomic redundancy. Maast implements a novel algorithm to dynamically identify a minimum set of phylogenetically diverse conspecific genomes that contains the maximum number of SNPs above a user-specified allele frequency. Then it uses these genomes to construct a SNP panel for each species. A species’ SNP panel enables Maast to rapidly genotype thousands of strains using a hybrid of whole-genome alignment and k-mer exact matching. Maast works with both genome assemblies and unassembled sequencing reads. Compared to existing genotyping methods, Maast is more accurate and up to two orders of magnitude faster. We demonstrate Maast’s utility on species with thousands of genomes by reconstructing the genetic structure of Helicobacter pylori across the globe and tracking SARS-CoV-2 diversification during the COVID-19 outbreak. Maast is a fast, reliable SNP genotyping tool that empowers population genetic meta-analysis of microbes at an unrivaled scale.

Availability

source code of Maast is available at https://github.com/zjshi/Maast.

Contact

kpollard@gladstone.ucsf.edu
The mRNA decapping machinery targetsLBD3/ASL9to mediate apical hook and lateral root development inArabidopsis
Authors: Zuo Zhangli , Roux Milena Edna , Chevalier Jonathan Renaud , Dagdas Yasin F. , Yamashino Takafumi , Højgaard Søren Diers , Knight Emilie , Østergaard Lars , Rodriguez Eleazar , Petersen Morten
Published: July 2022

Multicellular organisms perceive and transduce multiple cues to optimize development. Key transcription factors drive developmental changes, but RNA processing also contributes to tissue development. Here, we report that multiple decapping deficient mutants share developmental defects in apical hook, primary and lateral root growth. More specifically,LATERAL ORGAN BOUNDARIES DOMAIN 3(LBD3)/ASYMMETRIC LEAVES 2-LIKE 9(ASL9) transcripts accumulate in decapping deficient plants and can be found in complexes with decapping components. Accumulation ofASL9inhibits apical hook, primary root growth and lateral root formation. Interestingly, exogenous auxin application restores lateral roots formation in bothASL9over-expressors and mRNA decay-deficient mutants. Likewise, mutations in the cytokinin transcription factors type-B ARABIDOPSIS RESPONSE REGULATORS (B-ARRs)ARR10andARR12restore the developmental defects caused by over-accumulation of cappedASL9transcript uponASL9overexpression. Most importantly, loss-of-function ofasl9partially restores apical hook and lateral root formation in decapping deficient mutants. Thus, the mRNA decay machinery directly targetsASL9transcripts for decay, possibly to interfere with cytokinin/auxin responses, during development.
BysR, a LysR-type Pleiotropic Regulator, Controls Production of Occidiofungin by Activating the LuxR-type transcriptional regulator AmbR1 in Burkholderia sp. JP2-270
Authors: Wu Lijuan , Tang Liqun , He Yuchang , Han Cong , Wang Lei , Zhang Yunzeng , Zhiguo E
Published: July 2022

Occidiofungin is a highly effective antifungal glycopeptide produced by certain Burkholderia strains. The ocf gene cluster directing occidiofungin biosynthesis is regulated by cluster-specific regulators encoded by ambR homolog(s) within the same gene cluster, while it remains unknown to what extent occidiofungin biosynthesis is connected with the core regulation network. Here, we report that a LysR-type regulator BysR acts as a pleotropical regulator, and is essential for occidiofungin biosynthesis by directly activating ambR1 transcription in Burkholderia sp. JP2-270. Deletion of bysR and ocfE both abolished the antifungal activity in JP2-270. This defect of the bysR mutant can be recovered by constitutively expressing bysR or ambR1 but not by ambR2. The EMSA assay collectively showed that BysR regulates ambR1 through direct binding to its promoter region. Taken together, occidiofungin produced by JP2-270 is the main substance inhibiting M. oryzae, and BysR controls occidiofungin production by directly activating the expression of ambR1. Besides, transcriptomic analysis revealed altered expression of 350 genes in response to bysR deletion, and the genes engaged in flagellar assembly and bacterial chemotaxis are the most enriched pathways. Also, 400 putative loci targeted by BysR were identified by DAP-seq in JP2-270. These loci not only include genes engaged in key metabolic pathways but also genes involved in secondary metabolic pathways. Collectively, we proposes that BysR may be a novel pleiotropic regulator, and ambR1 is an important target gene of BysR, which is an intra-cluster transcriptional regulatory gene that further activates the transcription of ocf gene cluster.

IMPORTANCE

This study shows that BysR, a LysR-type transcriptional regulator (LTTR) from Burkholderia sp. JP2-270, activates the expression of ambR1 gene responsible for regulating the synthesis of occidiofungin. BysR also acts as a pleiotropic regulator that controls primary and secondary metabolism, antibiotic resistance, motility, transport and other cellular processes in Burkholderia sp. JP2-270. This study provides insight into the regulatory mechanism of occidiofungin synthesis and enhances our understanding of the regulatory patterns of the LysR-type regulator.
The emergence of new lineages of the Mpox virus could affect the 2022 outbreak
Authors: Abrahim Mayla , Guterres Alexandro , Costa Neves Patrícia Cristina da , Ano Bom Ana Paula Dinis
Published: July 2022

Human Mpox is a highly contagious viral disease caused by Mpox virus, currently causing outbreaks in various regions of the world and considered a global public health problem. Understanding how the virus adapts or transfers to a new host species is crucial for effective prevention and treatment of viral infections. A comprehensive analysis of 1,318 accessible Mpox genomes was conducted to assess potential phenotypic effects, incorporating the examination of pseudogenes, gene duplication and deletion, as well as sequences obtained from the 2022 outbreak. This study we analyzed the genomic sequences of Mpox viruses from different clades and found that only a small percentage of proteins were conserved across the analyzed clades, with many proteins exhibiting various mutations, indicating the potential correlation between lineage or clade and variations in the pathology of human Mpox disease. The study highlights the importance of analyzing aligned regions in viral genomes to understand the evolution of the virus and the impact of structural changes on protein functions. In brief, further investigations are required to establish a correlation between the effects of these genetic modifications and the novel transmission pathways, average age, clinical manifestations, and symptoms observed in the ongoing outbreak.
Timing along the cardiac cycle modulates neural signals of reward-based learning
Authors: Fouragnan Elsa , Hosking Billy , Cheung Yin , Prakash Brooke , Rushworth Matthew , Sel Alejandra
Published: July 2022

Natural fluctuations in cardiac activity influence brain activity associated with sensory stimuli and affect perceptual decisions about low magnitude, near-threshold stimuli. However, little is known about the impact of fluctuations in heart activity on other internal representations. Here we investigate cardiac influences on learning-related internal representations – absolute and signed prediction errors. By combining machine learning techniques with electroencephalography (EEG) and both simple, direct indices of task performance and computational model-derived indices of learning, we demonstrate that just as people are more sensitive to low magnitude, near threshold sensory stimuli in certain cardiac phases, so are they more sensitive to low magnitude absolute prediction errors in the same cycles. Importantly, however, this occurs even when the low magnitude prediction errors are associated with clearly suprathreshold sensory events. In addition, participants exhibiting stronger difference in their prediction errors representations between cardiac cycles exhibited higher learning rates and greater task accuracy.
Astrocytes regulate locomotion by orchestrating neuronal rhythmicity in the spinal network via potassium clearance
Authors: Barbay Tony , Pecchi Emilie , Ducrocq Myriam , Rouach Nathalie , Brocard Frédéric , Bos Rémi
Published: July 2022

Summary

Neuronal rhythmogenesis in the spinal cord is correlated with variations in extracellular K+ levels ([K+]e). Astrocytes play important role in[K+]e homeostasis and compute neuronal information. Yet it is unclear how neuronal oscillations are regulated by astrocytic K+ homeostasis. Here we identify the astrocytic inward-rectifying K+ channel Kir4.1 (a.k.a. Kcnj10) as a key molecular player for neuronal rhythmicity in the spinal central pattern generator (CPG). By combining two-photon calcium imaging with electrophysiology, immunohistochemistry and genetic tools, we report that astrocytes display Ca2+ transients before and during oscillations of neighbouring neurons. Inhibition of astrocytic Ca2+ transients with BAPTA decreases the barium-sensitive Kir4.1 current responsible of K+ clearance. Finally, we show in mice that Kir4.1 knockdown in astrocytes progressively prevents neuronal oscillations and alters the locomotor pattern resulting in lower motor performances in challenging tasks. These data identify astroglial Kir4.1 channels as key regulators of neuronal rhythmogenesis in the CPG driving locomotion.

Significance statement

Despite decades of research, the cellular mechanisms responsible of the synchronized rhythmic oscillations driving locomotion remain elusive. To gain insight into the function of the spinal locomotor network, numerous studies have characterized diverse classes of locomotor-related neurons to determine their role in generating rhythmic movements during locomotion. In contrast, studies investigating non-neuronal components of the spinal cord are sparse. Our study represents a significant breakthrough by identifying astrocytic K+ uptake as a key regulator of neuronal rhythmicity synchronization and locomotor pattern at the cellular, microcircuit and system levels. These data provide mechanistic insights into the neuroglial dialogue at play during rhythmogenesis and point to a novel astroglial target for restoring normal neuronal network excitability in brain disorders and neurodegenerative diseases.
Biological evaluation of novel side chain containing CQTrICh-analogs as antimalarials and their development as PfCDPK1 kinase inhibitors
Authors: Irfan Iram , Uddin Amad , Jain Ravi , Gupta Aashima , Gupta Sonal , Napoleon John V. , Hussain Afzal , Alajmi Mohamed F. , Joshi Mukesh C. , Hasan Phool , Abid Mohammad , Singh Shailja
Published: July 2022

To combat the emergence of drug resistance against the existing antimalarials, novel side chain containing 7-chloroquinoline-indole-chalcones tethered with a triazole (CQTrICh-analogs 7 (a-s) and 9) were designed and synthesized by reacting substituted 1-phenyl-3-(1-(prop-2-yn-1- yl)-1H-indol-3-yl) prop-2-en-1-one and 1-(prop-2-yn-1-yl)-1H-indole-3-carbaldehyde with 4- azido-7-chloroquinoline, respectively via a ‘click’ reaction. The selected CQTrICh-analogs: 7l and 7r inhibited chloroquine-sensitive (3D7) and resistant (RKL-9) strains of Plasmodium falciparum, with IC50 values of 2.4 µM & 1.8 µM (7l), and 3.5 µM & 2.7 µM (7r), respectively, and showed insignificant hemolysis and cytotoxicity in mammalian cells. Intra-erythrocytic progression studies revealed that the active hybrids: 7l and 7r are effective against the mature stages of the parasite. Given the importance of Calcium-Dependent Protein Kinase 1 (PfCDPK1) in the parasite biology, notably during late schizogony and subsequent invasion of merozoites into host RBCs, we identified this protein as a possible molecular target of these active hybrids. In silico interaction analysis indicated that 7l and 7r stably interact with the catalytically active ATP-binding pocket of PfCDPK1, by the formation of energetically favorable H-bonds. Furthermore, in vitro Microscale Thermophoresis and kinase assays with recombinant PfCDPK1 demonstrated that the active hybrids interact with and inhibit the kinase activity, thus presumably responsible for the parasite growth inhibition. Interestingly, 7l and 7r showed no inhibitory effect on the human kinases, indicating that they are selective for the parasite kinase. Conceivably, we report the antiplasmodial potential of novel kinase targeting bio-conjugates, a step towards developing pan-kinase inhibitors, which is a prerequisite for cross-stage anti-malarial protection.

GRAPHICAL ABSTRACT
The Trouble with Triples: Examining the Impact of Measurement Error in Mediation Analysis
Authors: Gastonguay Madeleine S. , Keele Gregory R. , Churchill Gary A.
Published: July 2022

Mediation analysis is used in genetic mapping studies to identify candidate gene mediators of quantitative trait loci (QTL). We consider genetic mediation analysis of triplets - sets of three variables consisting of a target trait, the genotype at a QTL for the target trait, and a candidate mediator that is the abundance of a transcript or protein whose coding gene co-locates with the QTL. We show that, in the presence of measurement error, mediation analysis can infer partial mediation even in the absence of a causal relationship between the candidate mediator and the target. We describe a measurement error model and a corresponding latent variable model with estimable parameters that are combinations of the causal effects and measurement errors across all three variables. The relative magnitudes of the latent variable correlations determine whether or not mediation analysis will tend to infer the correct causal relationship in large samples. We examine case studies that illustrate the common failure modes of genetic mediation analysis and demonstrate how to evaluate the effects of measurement error. While genetic mediation analysis is a powerful tool for identifying candidate genes, we recommend caution when interpreting mediation analysis findings.
Deep Phosphoproteomic Elucidation of Metformin-Signaling in Heterogenous Colorectal Cancer Cells
Authors: Salovska Barbora , Gao Erli , Müller-Dott Sophia , Li Wenxue , Dugourd Aurelien , Rosenberger George , Saez-Rodriguez Julio , Liu Yansheng
Published: July 2022

The biguanide drug metformin is a safe and widely prescribed drug for type 2 diabetes. Interestingly, hundreds of clinical trials were set to evaluate the potential role of metformin in the prevention and treatment of cancer including colorectal cancer (CRC). To interrogate cell signaling events and networks in CRC and explore the druggability of the metformin-rewired phosphorylation network, we performed a proteomic and phosphoproteomic analysis on a panel of 12 molecularly heterogeneous CRC cell lines. Using in-depth data-independent analysis mass spectrometry (DIA-MS), we profiled a total of 10,142 proteins and 56,080 phosphosites (P-sites) in CRC cells treated with metformin for 30 minutes and 24 hours. Our results indicate that metformin does not directly trigger or inhibit any immediate phosphorylation events. Instead, it primarily remodels cell signaling in the long-term. Strikingly, the phosphorylation response to metformin was highly heterogeneous in the CRC panel, uncovering four groups of metformin responsivity. We further performed a network analysis to systematically estimate kinase/phosphatase activities and reconstruct signaling cascades in each cell line. We created a “MetScore” which catalogs the most consistently perturbed P-sites among CRC cells for future studies. Finally, we leveraged the metformin P-site signature to identify pharmacodynamic interactions revealing a number of candidate metformin-interacting drugs. Together, we provide a data resource using state-of-the-art phosphoproteomics to understand the metformin-induced cell signaling for potential cancer therapeutics.
Evaluating the efficacy of prototype antiseizure drugs using a preclinical pharmacokinetic approach
Authors: Mensah Jeffrey A. , Johnson Kristina , Reilly Christopher A. , Wilcox Karen S. , Rower Joseph E. , Metcalf Cameron S.
Published: July 2022

Objective

Pharmacokinetics (PK) of a drug drive its exposure, efficacy, and tolerability. A thorough preclinical PK assessment of antiseizure medications (ASMs) is therefore essential to evaluate the clinical potential. We tested protection against evoked seizures of prototype ASMs in conjunction with analysis of plasma and brain PK as a proof-of-principle study to enhance our understanding of drug efficacy and duration of action using rodent seizure models.

Methods

In vivo seizure protection assays were performed in adult male CF-1 mice and Sprague-Dawley rats. Clobazam (CLB), N-desmethylclobzam (NCLB), carbamazepine (CBZ), carbamazepine-10,11-epoxide (CBZE), valproic acid (VPA), and levetiracetam (LEV) concentrations were quantified in plasma and brain using liquid chromatography-tandem mass spectrometry. Mean concentrations of each analyte were calculated and used to determine PK parameters via non-compartmental analysis in Phoenix WinNonLin.

Results

NCLB concentrations were approximately 10-fold greater than CLB in mice. The antiseizure profile of CLB was partially sustained by NCLB in mice. CLB concentrations were lower in rats than in mice. CBZE plasma exposures were approximately 70% of CBZ in both mice and rats, likely contributing to the antiseizure effect of CBZ. VPA showed a relatively short half-life in both mice and rats, which correlated with a sharp decline in efficacy. LEV had a prolonged brain and plasma half-life, associated with a prolonged duration of action in mice.

Significance

The study demonstrates the utility of PK analyses for understanding the seizure protection time-course in mice and rats. The data indicate that distinct PK profiles of ASMs between mice and rats likely drive differences in drug efficacy between rodent models.

Key Points

There exist potential contributions of active metabolites to the efficacy of some ASMs.

The utility of preclinical PK assessment of ASM is critical to guide our insight into a drug efficacy profile and provide a framework for subchronic dosing strategies.

Species-specific variations in PK profiles of ASMs in rodent models of epilepsy may underpin the differences in antiseizure effect in these models.

Pre-clinical drug screening of ASMs should include a (sub)chronic dosing paradigm to better mimic the dosing regimen in the clinic.
A novel RHH family transcription factor aCcr1 and its viral homologs dictate cell cycle progression in archaea
Authors: Yang Yunfeng , Liu Junfeng , Fu Xiaofei , Zhou Fan , Zhang Shuo , Zhang Xuemei , Huang Qihong , Krupovic Mart , She Qunxin , Ni Jinfeng , Shen Yulong
Published: July 2022

Cell cycle regulation is of paramount importance for all forms of life. Here we report that a conserved and essential cell cycle-specific transcription factor (designated as aCcr1) and its viral homologs control cell division in Sulfolobales. We show that the transcription level ofaccr1reaches peak during active cell division (D-phase) subsequent to the expression of CdvA, an archaea-specific cell division protein. Cells over-expressing the 58-aa-long RHH (ribbon-helix-helix) family cellular transcription factor as well as the homologs encoded by large spindle-shaped virusesAcidianustwo-tailed virus (ATV) andSulfolobusmonocaudavirus 3 (SMV3) display significant growth retardation and cell division failure, manifested as enlarged cells with multiple chromosomes. aCcr1 over-expression results in downregulation of 17 genes (>4-folds) includingcdvA. A conserved motif, aCcr1-box, located between the TATA-binding box and the translation initiation site in the promoters of 13 out of the 17 highly repressed genes, is critical for aCcr1 binding. The aCcr1-box is present in the promoters ofcdvAgenes across Sulfolobales, suggesting that aCcr1-mediatedcdvArepression is an evolutionarily conserved mechanism by which archaeal cells dictate cytokinesis progression, whereas their viruses take advantage of this mechanism to manipulate the host cell cycle.
Porechop_ABI: discovering unknown adapters in ONT sequencing reads for downstream trimming
Authors: Bonenfant Quentin , Noé Laurent , Touzet Hélène
Published: July 2022

Motivation

Oxford Nanopore Technologies (ONT) sequencing has become very popular over the past few years and offers a cost-effective solution for many genomic and transcriptomic projects. One distinctive feature of the technology is that the protocol includes ligation of adapters to both ends of each fragment. Those adapters should then be removed before downstream analyses, either during the basecalling step or by explicit trimming. This basic task may be tricky when the definition of the adapter sequence is not well-documented.

Results

We have developed a new method to scan a set of ONT reads to see if it contains adapters, without any prior knowledge on the sequence of the potential adapters, and then trim out those adapters. The algorithm is based on approximate k-mers and is able to discover adapter sequences based on their frequency alone. The method was successfully tested on a variety of ONT datasets with different flowcells, sequencing kits and basecallers.

Availability

The resulting software, named Porechop_ABI, is open-source and is available at https://github.com/bonsai-team/Porechop_ABI.
Transcellular progression of infection threads in Medicago truncatula roots is controlled by locally confined cell wall modifications
Authors: Su Chao , Zhang Guofeng , Rodriguez-Franco Marta , Wietschorke Jenny , Liang Pengbo , Yang Wei , Uhler Leonard , Li Xia , Ott Thomas
Published: July 2022

The root nodule symbiosis with its global impact on nitrogen fertilization of soils is characterized by an intracellular colonization of legume roots by rhizo-bacteria. While the symbionts are initially taken up by morphologically adapted root hairs, rhizobia persistently progress within a membrane-confined infection thread through several root cortical and later nodular cell layers. Throughout this transcellular passaging, rhizobia have to repeatedly pass host plasma membranes and cell walls. Here, we genetically dissected this essential process and describe the concerted action of the symbiosis-specific pectin methyl esterase SyPME and the pectate lyase NPL at the infection thread and transcellular passage sites. Their coordinated function mediates spatially confined pectin alterations in the cell-cell interface that result in the establishment of an apoplastic compartment where bacteria are temporarily released into and taken up from the subjacent cell. This process allows successful intracellular progression of infection threads through the entire root cortical tissue.
Transmembrane 163 (TMEM163) protein interacts with specific mammalian SLC30 zinc efflux transporter family members
Authors: Escobar Adrian , Styrpejko Daniel J. , Ali Saima , Cuajungco Math P.
Published: July 2022

Recently, we reported that TMEM163 is a zinc efflux transporter that likely belongs to the mammalian solute carrier 30 (Slc30/ZnT) subfamily of the cation diffusion facilitator (CDF) protein superfamily. We hypothesized that human TMEM163 forms functional heterodimers with ZNT proteins based on their subcellular localization overlapping with TMEM163 and previous reports that certain ZNT monomers interact with each other. In this study, we heterologously expressed individual constructs with a unique peptide tag containing TMEM163, ZNT1, ZNT2, ZNT3, and ZNT4 (negative control) or co-expressed TMEM163 with each ZNT in HEK-293 cells for co-immunoprecipitation (co-IP) experiments. We also co-expressed TMEM163 with two different peptide tags as a positive co-IP control. Western blot analyses revealed that TMEM163 dimerizes with itself but that it also heterodimerizes with ZNT1, ZNT2, ZNT3, and ZNT4 proteins. Native co-IP using mouse tissues confirmed the interactions while confocal microscopy revealed that TMEM163 and ZNT proteins partially co-localize in cells, suggesting that they exist as homodimers and heterodimers in their respective subcellular sites. Functional zinc flux assays using Fluozin-3 and Newport Green dyes show that cells expressing TMEM163 homodimers extruded zinc slightly less efficiently than cells expressing TMEM163/ZNT heterodimers. Cell surface biotinylation revealed a subtle change in the plasma membrane localization of TMEM163 upon co-expression with certain ZNT proteins, which possibly explains why zinc efflux is marginally different for TMEM163 homodimers than TMEM163/ZNT heterodimers. Overall, our results show that the interaction between TMEM163 and distinct ZNT proteins is functionally relevant and that their heterodimerization may serve to influence their zinc efflux activity within specific tissues or cell types.

Research Highlights

TMEM163 protein heterodimerizes with mammalian ZNT1, ZNT2, ZNT3 and ZNT4 zinc efflux transporters.

TMEM163 and ZNT proteins partially co-localize in their respective plasma membrane or subcellular compartments, suggesting distinct cellular roles as homodimers and heterodimers.

The zinc efflux activity of TMEM163 or ZNT protein homodimers did not markedly differ from their TMEM163/ZNT heterodimer counterparts.

Functional TMEM163/ZNT heterodimers give further credence to the role of TMEM163 as a bona fide member of the SLC30 protein family
An ERP investigation of accented isolated single word processing
Authors: Thomas Trisha , Caffarra Sendy , Martin Clara
Published: July 2022

Previous studies show that there are differences in native and non-native speech processing (Lev-Ari, 2018). However, less is known about the differences between processing native and dialectal accents. Is dialectal processing more similar to foreign or native speech? To address this, two theories have been proposed. The Perceptual Distance Hypothesis states that the mechanisms underlying dialectal accent processing are attenuated versions of those of foreign (Clarke & Garrett, 2004). Conversely, the Different Processes Hypothesis argues that the mechanisms of foreign and dialectal accent processing are qualitatively different (Floccia et al, 2009). The present study addresses these hypotheses. Electroencephalographic data was recorded from 25 participants who listened to 40 isolated words in different accents. Event-Related Potential mean amplitudes were extracted: P2 [150-250 ms], PMN [250-400 ms] and N400 [400-600 ms]. Support for the Different Processes Hypothesis was found in different time windows. Results show that early processing mechanisms distinguish only between native and non-native speech, with a reduced P2 amplitude for foreign accent processing, supporting the Different Processes Hypothesis. Furthermore, later processing mechanisms show a similar binary difference in the processing of the accents, with a larger PMN negativity elicited in the foreign accent than the others, further supporting the Different Processes Hypothesis. Results contribute to the understanding of single word processing, in which it is uniquely difficult to extract acoustic characteristics from foreign accent, and in which foreign accented speech is associated with the largest cost, as compared to native and dialectal speech, of phonological matching between representations and acoustic input.

Highlights

Accent affects early speech processing mechanisms at the level of the isolated word

Acoustic characteristic extraction is more difficult for foreign-accented speech

Phonological normalization of foreign-accented speech is uniquely difficult

Accent no longer affects later speech processing mechanisms at the isolated word
Posterodorsal medial amygdala urocortin-3, GABA and glutamate mediate suppression of LH pulsatility in female mice
Authors: Ivanova Deyana , Li Xiao-Feng , McIntyre Caitlin , O’Byrne Kevin T
Published: July 2022

The posterodorsal subnucleus of the medial amygdala (MePD) is an upstream modulator of the hypothalamic-pituitary-gonadal (HPG) and hypothalamic-pituitary-adrenal (HPA) axes. Inhibition of MePD urocortin-3 (Ucn3) neurons prevents psychological stress-induced suppression of LH pulsatility while blocking the stress-induced elevations in corticosterone (CORT) secretion in female mice. We explore the neurotransmission and neural circuitry suppressing the GnRH pulse generator by MePD Ucn3 neurons and we further investigate whether MePD Ucn3 efferent projections to the PVN control CORT secretion and LH pulsatility. Ucn3-cre-tdTomato female ovariectomised (OVX) mice were unilaterally injected with AAV-ChR2 and implanted with optofluid cannulae targeting the MePD. We optically activated Ucn3 neurons in the MePD with blue light at 10Hz and monitored the effect on LH pulses. Next, we combined optogenetic stimulation of MePD Ucn3 neurons with pharmacological antagonism of GABAA or GABAB receptors with bicuculline or CGP, respectively, as well as a combination of NMDA and AMPA receptor antagonists, AP5 and CNQX respectively, and observed the effect on pulsatile LH secretion. A separate group of Ucn3-cre-tdTomato OVX mice with 17ß-estradiol (E2) replacement were unilaterally injected with AAV-ChR2 in the MePD and implanted with fibreoptic cannulae targeting the PVN. We optically stimulated the MePD Ucn3 efferent projections in the PVN with blue light at 20Hz and monitored the effect on CORT secretion and LH pulses. We reveal for the first time that activation of Ucn3 neurons in the MePD inhibits GnRH pulse generator frequency via GABA and glutamate signalling within the MePD, while MePD Ucn3 projections to the PVN modulate the HPG and HPA axes.
Single-cell reference mapping to construct and extend cell-type hierarchies
Authors: Michielsen Lieke , Lotfollahi Mohammad , Strobl Daniel , Sikkema Lisa , Reinders Marcel J.T. , Theis Fabian J. , Mahfouz Ahmed
Published: July 2022

Single-cell genomics is now producing an ever-increasing amount of datasets that, when integrated, could provide large-scale reference atlases of tissue in health and disease. Such atlases increase the scale and generalizability of analyses and enable combining knowledge generated by individual studies. Specifically, individual studies often differ regarding cell annotation terminology and depth, with different groups often using distinct terminology. Understanding how annotations are related and complement each other would mark a major step towards a consensus-based cell-type annotation reflecting the latest knowledge. Whereas recent computational techniques, referred to as “reference mapping” methods, facilitate the usage and expansion of existing reference atlases by mapping new datasets (i.e., queries) onto an atlas; a systematic approach towards harmonizing dataset-specific cell-type terminology and annotation depth is still lacking. Here, we present “treeArches”, a framework to automatically build and extend reference atlases while enriching them with an updatable hierarchy of cell-type annotations across different datasets. We demonstrate various use cases, from automatically resolving relations between reference and query cell types to identifying unseen cell types absent in the reference, such as disease-associated cell states. We envision treeArches enabling data-driven construction of consensus atlas-level cell-type hierarchies and facilitating efficient usage of reference atlases.
Prox2+ and Runx3+ neurons regulate esophageal motility
Authors: Lowenstein Elijah D. , Ruffault Pierre-Louis , Misios Aristotelis , Osman Kate L. , Li Huimin , Thompson Rebecca , Song Kun , Dietrich Stephan , Li Xun , Vladimirov Nikita , Brunet Jean-François , Woehler Andrew , Zampieri Niccolò , Kühn Ralf , Jia Shiqi , Lewin Gary R. , Rajewsky Nikolaus , Lever Teresa E. , Birchmeier Carmen
Published: July 2022

Sensory neurons of the vagus nerve monitor distention and stretch in the gastrointestinal tract. Major efforts are underway to assign physiological functions to the many distinct subtypes of vagal sensory neurons. Here, we used genetically guided anatomical tracing, optogenetics and electrophysiology to identify and characterize three vagal sensory neuronal subtypes expressing Prox2 and Runx3. We show that these neuronal subtypes innervate the esophagus and stomach where they display regionalized innervation patterns. Their electrophysiological analysis showed that they are all low threshold mechanoreceptors, but possess different adaptation properties. Lastly, genetic ablation of Prox2+ and Runx3+ neurons demonstrated their essential roles for esophageal peristalsis and swallowing in freely behaving animals. Our work reveals the identity and function of the vagal neurons that provide mechanosensory feedback from the esophagus to the brain, and could lead to better understanding and treatment of esophageal motility disorders.
Cyclic AMP is a critical mediator of intrinsic drug resistance and fatty acid metabolism in M. tuberculosis
Authors: Wong Andrew I. , Beites Tiago , Planck Kyle A. , Li Shuqi , Poulton Nicholas C. , Rhee Kyu , Schnappinger Dirk , Ehrt Sabine , Rock Jeremy
Published: July 2022

Cyclic AMP (cAMP) is a ubiquitous second messenger that transduces signals from cellular receptors to downstream effectors. Mycobacterium tuberculosis (Mtb), the etiological agent of tuberculosis, devotes a considerable amount of coding capacity to produce, sense, and degrade cAMP. Despite this fact, our understanding of how cAMP regulates Mtb physiology remains limited. Here, we took a genetic approach to investigate the function of the sole essential adenylate cyclase in Mtb H37Rv, Rv3645. We found that lack of rv3645 resulted in increased sensitivity to numerous antibiotics by a mechanism independent of substantial increases in envelope permeability. We made the unexpected observation that rv3645 is conditionally essential for Mtb growth only in the presence of long-chain fatty acids, a host-relevant carbon source. A suppressor screen further identified mutations in the atypical cAMP phosphodiesterase rv1339 that suppress both fatty-acid and drug sensitivity phenotypes in strains lacking rv3645. Using mass spectrometry, we found that Rv3645 is the dominant source of cAMP under standard laboratory growth conditions, that cAMP production is the essential function of Rv3645 in the presence of long-chain fatty acids, and that reduced levels of cAMP result in increased antibiotic susceptibility. Our work defines rv3645 and cAMP as central mediators of intrinsic multidrug resistance and fatty acid metabolism in Mtb and highlights the potential utility of small molecule modulators of cAMP signaling.
SLIDE-VIP: a comprehensive, cell line- and patient-based framework for synthetic lethality prediction in DNA damage repair, chromatin remodeling and cell cycle
Authors: Markowska Magda , Budzinska Magdalena A , Coenen-Stass Anna , Kang Senbai , Kizling Ewa , Kolmus Krzysztof , Koras Krzysztof , Staub Eike , Szczurek Ewa
Published: July 2022

Discovering synthetic lethal (SL) gene partners of cancer genes is an important step in developing cancer therapies. However, identification of SL interactions is challenging, due to a large number of possible gene pairs, inherent noise and confounding factors in the observed signal. To discover robust SL interactions, we devised SLIDE-VIP, a novel framework combining eight statistical tests, including a new patient data-based test iSurvLRT. SLIDE-VIP leverages multi-omics data from four different sources: gene inactivation cell line screens, cancer patient data, drug screens and gene pathways. We applied SLIDE-VIP to discover SL interactions between genes involved in DNA damage repair, chromatin remodeling and cell cycle, and their potentially druggable partners. The top 883 ranking SL candidates had strong evidence in cell line and patient data, 250-fold reducing the initial space of 200K pairs. Drug screen and pathway tests provided additional corroboration and insights into these interactions. We rediscovered well-known SL pairs such as RB1 and E2F3 or PRKDC and ATM, and in addition, proposed strong novel SL candidates such as PTEN and PIK3CB. In summary, SLIDE-VIP opens the door to the discovery of SL interactions with clinical potential. All analysis and visualizations are available via the online SLIDE-VIP WebApp.
Detecting aquatic pathogens with field-compatible dried qPCR assays
Authors: Rieder Jessica , Martin-Sanchez Pedro M. , Osman Omneya A. , Adrian-Kalchhauser Irene , Eiler Alexander
Published: July 2022

Field-ready qPCR assays with a long shelf-life support monitoring programs for emerging aquatic pathogens and enable quick conservation and management decisions. Here, we develop, validate, and test the shelf-life of qPCR assays targetingGyrodactylus salarisandAphanomyces astaciwith lyophilization and air-drying.
Individual differences in experiential diversity shape event segmentation granularity
Authors: Hodgetts Carl J. , Berry Samuel C. , Postans Mark , Williams Angharad N.
Published: July 2022

Parsing experience into meaningful events or units, known as event segmentation, may be critical for structuring episodic memory, planning, and navigating the spatial and social world. However, little is known about what factors shape inter-individual differences in event segmentation. Here, we show that individuals with greater variation in their daily social and spatial lives (experiential diversity) displayed more fine-grained event segmentation during a movie-viewing task. Further analyses revealed that this relationship held after considering potential confounds, such as anxiety and loneliness, and was primarily driven by variation in social experiential diversity. These results support the view that event segmentation can occur proactively based on social and spatial environmental dynamics learned ‘in the wild’ and provide a potential cognitive pathway through which isolation impacts cognitive health.
Canada goose fecal microbiota correlate with geography more than host-associated co-factors
Authors: Gil Joshua C. , Cuellar Celeste , Hird Sarah M.
Published: July 2022

The gut microbiota has many positive effects on the host, but how the microbiota is shaped and influenced can vary greatly. These factors affect the composition, diversity, and function of host-associated microbiota; however, these factors vary greatly from organism to organism and clade to clade. The avian microbiota often correlates more with the sampling locations rather than host-associated co-factors. These correlations between location and microbiota often only include a few sampling locations within the species’ range. To better understand the connection between geographic distance and the microbiota, were collected from non-migratory Canada geese across the United States. We expected host-associated factors to have minimal effect on the microbiota and geese microbiota will be strongly correlated to geography. We hypothesized more proximal geese will be exposed to more similar environmental microbes and will have more similar microbiota. Canada geese microbiota are largely similar across the entire sampling range. Several bacterial taxa were shared by more than half of the geese. Four phyla were found in the majority of the samples: Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Three genera were also present in the majority of the samples: Helicobacter, Subdoligranulum, and Faecalibacterium. There were minimal differences in alpha diversity with respect to age, sex, and flyway. There were significant correlations between geography and beta diversity. Supervised machine learning models were able to predict the location of a fecal sample based on taxonomic data alone. Distance decay analysis show a positive relationship between geographic distance and beta diversity. Our work provides novel insights into the microbiota of the ubiquitous Canada goose and further supports the claim that the avian microbiota is largely dominated by the host’s environment. This work also suggests that there is a minimum distance that must be reached before significant differences in the microbiota between two individuals can be observed.
Using colony size to measure fitness in Saccharomyces cerevisiae
Authors: Miller James H. , Fasanello Vincent J. , Liu Ping , Longan Emery R. , Botero Carlos A. , Fay Justin C.
Published: July 2022

Competitive fitness assays in liquid culture have been a mainstay for characterizing experimental evolution of microbial populations. Growth of microbial strains has also been extensively characterized by colony size and could serve as a useful alternative if translated to per generation measurements of relative fitness. To examine fitness based on colony size, we established a relationship between cell number and colony size for strains of Saccharomyces cerevisiae robotically pinned onto solid agar plates in a high-density format. This was used to measure growth rates and estimate relative fitness differences between evolved strains and their ancestors. After controlling for edge effects through both normalization and agar-trimming, we found that fitness based on colony size is as sensitive as competitive fitness assays grown in liquid medium. While fitnesses determined from liquid and solid mediums were not equivalent, our results demonstrate that colony size provides a sensitive means of measuring fitness that is particularly well suited to measurements across many environments.
Regulation of TRIB1 abundance in hepatoma models
Authors: Soubeyrand Sébastien , Lau Paulina , McPherson Ruth
Published: July 2022

Tribbles related homolog 1 (TRIB1) contributes to lipid and glucose homeostasis by facilitating the degradation of cognate cargos by the proteasome. We previously reported that TRIB1 was unstable in non-hepatic cellular models. Moreover, inclusion of proteasome inhibitors failed to prevent TRIB1 loss, consistent with the involvement of proteasome independent degradative processes. In view of the key role of TRIB1 in liver function, we continue our exploration of TRIB1 regulation pathways in two commonly used human hepatocyte models, HuH-7 and HepG2 cells. Proteasome inhibitors potently upregulated both endogenous and recombinant TRIB1 mRNA and protein levels. Increased transcript abundance was independent of MAPK activation while ER stress was a relatively mild inducer. Despite increasing TRIB1 protein abundance and stabilizing bulk ubiquitination, proteasome inhibition failed to stabilize TRIB1, pointing to the predominance of proteasome independent protein degradation processes controlling TRIB1 protein abundance in hepatomas. Proteasome inhibition via downregulation of its PSMB3 regulatory subunit, in contrast to its chemical inhibition, had minimal impact on TRIB1 levels. Moreover, immunoprecipitation experiments showed no evidence of TRIB1 ubiquitination. Cytoplasmic retained TRIB1 was unstable, indicating that TRIB1 lability is regulated prior to its nuclear import. Substitution of the TRIB1 PEST-like region with a GST helical region or N-terminal deletions failed to fully stabilize TRIB1. Finally, inclusion of protease or autophagy inhibitors in vivo did not rescue TRIB1 stability. This work excludes proteasome-mediated degradation as a significant contributor to TRIB1 instability and identifies transcriptional regulation as a prominent mechanism regulating TRIB1 abundance in liver models in response to proteasome inhibition.
A multi-pronged human microglia response to Alzheimer’s disease Aβ pathology
Authors: Mancuso Renzo , Fattorelli Nicola , Martinez-Muriana Anna , Davis Emma , Wolfs Leen , Van Den Daele Johanna , Geric Ivana , Preman Pranav , Serneels Lutgarde , Poovathingal Suresh , Balusu Sriram , Verfaille Catherine , Fiers Mark , De Strooper Bart
Published: July 2022

Microglial activation and neuroinflammation are initial steps in the pathogenesis of Alzheimer’s disease (AD). However, studies in mouse models and human postmortem samples have yielded divergent results regarding microglia cell states relevant to AD. Here, we investigate 127,000 single cell expression profiles of human microglia isolated freshly from a xenotransplantation model for early AD. While human microglia adopt a disease-associated (DAM) profile, they display a much more pronounced HLA-cell state related to antigen presentation in response to amyloid plaques. In parallel, a distinctive pro-inflammatory cytokine and chemokine CRM response is mounted against oligomeric amyloid-β. TREM2 and, to a lesser extent, APOE polymorphisms, modulate the response of microglia to amyloid-β plaques, in contrast with the response to oligomeric Aβ. Specific polygenic risk genes are enriched in each branch of these multi-pronged response of human microglia to amyloid pathology (ARM). ARM responses can be captured in post-mortem studies when reanalyzed in light of this novel, comprehensive data set. In conclusion, therapeutic strategies targeting microglia in AD need to carefully assess how they affect the different cell states, as the overall balance between distinct microglial profiles might determine a protective or damaging outcome.