bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

SummaryObjectivePharmacokinetics (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.MethodsIn 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.ResultsNCLB 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.SignificanceThe 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 PointsThere 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

AbstractCell 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

MotivationOxford 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.ResultsWe 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.AvailabilityThe 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

AbstractThe 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

ABSTRACTRecently, 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 HighlightsTMEM163 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

AbstractPrevious 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.HighlightsAccent affects early speech processing mechanisms at the level of the isolated wordAcoustic characteristic extraction is more difficult for foreign-accented speechPhonological normalization of foreign-accented speech is uniquely difficultAccent 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

AbstractThe 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

AbstractSingle-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

SummarySensory 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

ABSTRACTCyclic 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.
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

AbstractField-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.
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

ABSTRACTThe 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

AbstractCompetitive 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.