bluuebunny/crossref_metadata_2025 huggingface dataset:
Separation of multiple motor memories through implicit and explicit processes
Authors: Dawidowicz Gefen , Shaine Yuval , Mawase Firas
Published: May 2021

Acquisition of multiple motor skills without interference is a remarkable ability in sport and daily life. During adaptation to opposing perturbations, a common paradigm to study this ability, each perturbation can be successfully learned when a dynamical contextual cue, such as a follow-through movement, is associated with the direction of the perturbation. It is still unclear, however, to what extent this context-dependent learning engages the cognitive strategy-based explicit process and the implicit process that occurs without conscious awareness. Here, we designed four reaching experiments to untangle the individual contributions of the explicit and implicit components while participants learned opposing visuomotor perturbations, with a second unperturbed follow-through movement that served as a contextual cue. In Exp. 1 we replicated previous adaptation results and showed that follow-through movements also allow learning for opposing visuomotor rotations. For one group of participants in Exp. 2 we isolated strategic explicit learning by inducing a 2-sec time delay between movement and end-point feedback, while for another group we isolated the implicit component using the task-irrelevant error-clamp paradigm, in which participants were firmly instructed to aim their reaches directly to the target. Our data showed that opposing perturbations could be fully learned by explicit strategies; but when strategy was restricted, distinct implicit processes contributed to learning. In Exp.3, we examined whether the learned motor behaviors are influenced by the disparity between the follow-through contexts. We found that the location of follow-through targets had little effect on total learning, yet it led to more instances in which participants failed to learn the task. In Exp. 4, we explored the generalization capability to untrained novel targets. Participants showed near-flat generalization of the implicit and explicit processes to adjacent targets. Overall, our results indicate that follow-through contextual cues influence activity of both implicit and explicit processes during separation of motor memories. Furthermore, the follow-through context might activate, in part, top-down cognitive factors that influence not only the dynamics of the explicit learning but also the implicit process.
Sustained ability of a natural microbial community to remove nitrate from groundwater
Authors: Paradis Charles J. , Miller John I. , Moon Ji-Won , Spencer Sarah J. , Lui Lauren M. , Van Nostrand Joy D. , Ning Daliang , Steen Andrew D. , McKay Larry D. , Arkin Adam P. , Zhou Jizhong , Alm Eric J. , Hazen Terry C.
Published: May 2021

Microbial-mediated nitrate removal from groundwater is widely recognized as the predominant mechanism for nitrate attenuation in contaminated aquifers and is largely dependent on the presence of a carbon-bearing electron donor. The repeated exposure of a natural microbial community to an electron donor can result in the sustained ability of the community to remove nitrate; this phenomenon has been clearly demonstrated at the laboratory scale. However, in situ demonstrations of this ability are lacking. For this study, ethanol (electron donor) was repeatedly injected into a groundwater well (treatment) for six consecutive weeks to establish the sustained ability of a microbial community to remove nitrate. A second well (control) located up-gradient was not injected with ethanol during this time. The treatment well demonstrated strong evidence of sustained ability as evident by concomitant ethanol and nitrate removal and subsequent sulfate removal upon consecutive exposures. Both wells were then monitored for six additional weeks under natural (no injection) conditions. During the final week, ethanol was injected into both treatment and control wells. The treatment well demonstrated sustained ability as evident by concomitant ethanol and nitrate removal whereas the control did not. Surprisingly, the treatment well did not indicate a sustained and selective enrichment of a microbial community. These results suggested that the predominant mechanism(s) of sustained ability likely exist at the enzymatic- and/or genetic-levels. The results of this study demonstrated that the in situ ability of a microbial community to remove nitrate can be sustained in the prolonged absence of an electron donor. Moreover, these results implied that the electron-donor exposure history of nitrate-contaminated groundwater can play an important role nitrate attenuation.

Article Impact Statement

Groundwater microbes sustain ability to remove nitrate in absence of carbon and energy source.
A Universal Approach to Analyzing Transmission Electron Microscopy with ImageJ
Authors: Lam Jacob , Katti Prasanna , Biete Michelle , Mungai Margaret , AshShareef Salma , Neikirk Kit , Garza Lopez Edgar , Vue Zer , Christensen Trace A. , Beasley Heather K. , Rodman Taylor , Salisbury Jeffrey L. , Glancy Brian , Pereira Renata O. , Abel E. Dale , Hinton Antentor
Published: May 2021

2

Transmission electron microscopy (TEM) is a scientific research standard for producing nanometer-resolution ultrastructural images of subcellular components within cells and tissues. Mitochondria, endoplasmic reticulum (ER), lysosomes, and autophagosomes are organelles of particular interest to those investigating metabolic disorders. However, there is no clear consensus amongst regarding the best methods for quantifying the features of organelles in TEM images. In this protocol, we propose a standardized approach to accurately measure the morphology of these important subcellular structures using the free program ImageJ, developed by the National Institutes of Health (NIH). Specifically, we detail procedures for obtaining mitochondrial length, width, area, and circularity, in addition to assessing cristae morphology. We further provide methods for measuring interactions between the mitochondria and ER and measuring the length and width of lysosomes and autophagosomes. This standardized method can be used to quantify key features of organelle morphology, allowing investigators to produce accurate and reproducible measurements of organelle structures in their experimental samples.

1

We discuss a standardized method for measuring and quantifying organelle features using transmission electron microscopy and accessing for interactions between subcellular structures; organelles of focus include mitochondria, endoplasmic reticulum, lysosomes, and autophagosomes.
Perceptual clustering in auditory streaming
Authors: Larigaldie Nathanael , Yates Tim , Beierholm Ulrik R.
Published: May 2021

Perception is dependent on the ability to separate stimuli from different objects and causes in order to perform inference and further processing. We have models of how the human brain can perform such causal inference for simple binary stimuli (e.g., auditory and visual), but the complexity of the models increases dramatically with more than two stimuli. To characterize human perception with more complex stimuli, we developed a Bayesian inference model that takes into account a potentially unlimited number of stimulus sources: it is general enough to factor in any discrete sequential cues from any modality. Because the model employs a non-parametric prior, increased signal complexity does not necessitate the addition of more parameters. The model not only predicts the number of possible sources, but also specifies the source with which each signal is associated. As a test case, we demonstrate that such a model can explain several phenomena in the auditory stream perception literature, that it provides an excellent fit to experimental data, and that it makes novel predictions that we experimentally confirm. These findings have implications not just for human auditory temporal perception, but for a wide range of perceptual phenomena across unisensory and multisensory stimuli.
The Mitochondrial Genome and Epigenome of the Golden Lion Tamarin from Fecal DNA using Nanopore Adaptive Sequencing
Authors: Wanner Nicole , Larsen Peter A. , McLain Adam , Faulk Christopher
Published: May 2021

The golden lion tamarin (Leontopithecus rosalia) is an endangered Platyrrhine primate endemic to the Atlantic coastal forests of Brazil. Despite ongoing conservation efforts, genetic data on this species remains scarce. Complicating factors include limitations on sample collection and a lack of high-quality reference sequences. Here, we used nanopore adaptive sampling to resequence the L. rosalia mitogenome from feces, a sample which can be collected non-invasively. Adaptive sampling doubled the fraction of both host-derived and mitochondrial sequences compared to sequencing without enrichment. 258x coverage of the L. rosalia mitogenome was achieved in a single flow cell by targeting the unfinished genome of the distantly related emperor tamarin (Saguinus imperator) and the mitogenome of the closely related black lion tamarin (Leontopithecus chrysopygus). The L. rosalia mitogenome has a length of 16,597 bp, sharing 99.68% sequence identity with the L. chrysopygus mitogenome. A total of 38 SNPs between them were identified, with the majority being found in the non-coding D-loop region. DNA methylation and hydroxymethylation were directly detected using a neural network model applied to the raw signal from the MinION sequencer. In contrast to prior reports, DNA methylation was negligible in mitochondria in both CpG and non-CpG contexts. Surprisingly, a quarter of the 642 CpG sites exhibited DNA hydroxymethylation greater than 1% and 44 sites were above 5%, with concentration in the 3’ side of several coding regions. Overall, we report a robust new mitogenome assembly for L. rosalia and direct detection of cytosine base modifications in all contexts.
Natural variation at the Drosophila melanogaster Or22 odorant receptor locus is associated with changes in olfactory behaviour
Authors: Shaw Katherine H. , Dent Craig I. , Johnson Travis K. , Anderson Alisha , de Bruyne Marien , Warr Coral G.
Published: May 2021

In insects many critical olfactory behaviours are mediated by the large odorant receptor (Or) gene family, which determine the response properties of different classes of olfactory receptor neurons (ORNs). While ORN responses are generally conserved within and between Drosophila species, variant alleles of the D.melanogaster Or22 locus have previously been shown to the response profiles of an ORN class called ab3A. These alleles show potential clinal variation, suggesting that selection is acting at this locus. Here, we investigated if the changes seen in ab3A responses lead to changes in olfactory-related behaviours. We show that variation at the Or22 locus and in the ab3A neurons are not fully compensated for by other ORNs and lead to overall changes in antennal odorant detection. We further show that this correlates with differences in odorant preference behaviour and with differences in oviposition site preference, with flies that have the chimaeric short allele strongly preferring to oviposit on banana. These findings indicate that variation at the Or22 locus leads to changes in olfactory-driven behaviours that could be under selective pressure, and add support to the idea that the ab3A neurons are of especial importance to the ecology of Drosophila flies.
Revealing conserved mechanisms of neurodegeneration in a colonial chordate
Authors: Anselmi C , Kowarsky MA , Gasparini F , Caicci F , Ishizuka KJ , Palmeri KJ , Sinhar R , Neff N , Quake SR , Weissman IL , Voskoboynik A , Manni L
Published: May 2021

Loss of the brain’s functional ability is a common symptom of aging and neurodegenerative diseases1,2. While the genetic and molecular mechanisms underlying human neurodegeneration are studied in-depth3–6, very little is known about the evolutionary origin of these traits and their involvement in loss of nervous system function in aged invertebrate species. Here we study evolutionarily conserved elements of brain degeneration using the colonial chordate model species Botryllus schlosseri. B. schlosseri reproduces both sexually and asexually7, with adult brains regenerating and degenerating multiple times throughout its adult life. Combining microscopy, transcriptomics and behavioral assays, we characterized adult brains from diverse stages and ages. We found that the number of neurons fluctuates each week, reaching a maximum of ∼1000 cells, and thereafter decreasing while the number of immunocytes increases. Comparing the number of neurons in the adult brains of young and old colonies, we found that older brains are smaller and contain fewer cells. Both during weekly degeneration cycles and overall with age, the decrease in neuron number correlates with reduced response to stimuli and with significant changes in the expression of genes with mammalian homologs associated with neural stem cells and neurodegenerative pathways. These results suggest persistent neural stem cell activity across ages and that cellular and molecular mechanisms of neurodegeneration are evolutionary conserved between tunicates and humans.
Molecular basis for kinin selectivity and activation of the human bradykinin receptors
Authors: Yin Yu-Ling , Ye Chenyu , Zhou Fulai , Wang Jia , Yang Dehua , Yin Wanchao , Wang Ming-Wei , Xu H. Eric , Jiang Yi
Published: May 2021

Bradykinin and kallidin are endogenous kinin peptide hormones that belong to the kallikrein-kinin system and are essential to the regulation of blood pressure, inflammation, coagulation, and pain control. Des-Arg10-kallidin, the carboxy-terminal des-Arg metabolite of kallidin, and bradykinin selectively activate two G protein-coupled receptors, type 1 and type 2 bradykinin receptors (B1R and B2R), respectively. The hyperactivation of bradykinin receptors, termed “bradykinin storm”, is associated with pulmonary edema in COVID-19 patients, suggesting that bradykinin receptors are important targets for COVID-19 intervention. Here we report two G protein complex structures of B1R and B2R bound to des-Arg10-kallidin and bradykinin. Combined with functional analysis, our structures reveal the mechanism of ligand selectivity and specific activation of the bradykinin receptor. These findings also provide a framework for guiding drug design targeting bradykinin receptors for the treatment of inflammation, cardiovascular disorders, and COVID-19.
A homing suppression gene drive with multiplexed gRNAs maintains high drive conversion efficiency and avoids functional resistance alleles
Authors: Yang Emily , Metzloff Matthew , Langmüller Anna M. , Xu Xuejiao , Clark Andrew G. , Messer Philipp W. , Champer Jackson
Published: May 2021

Gene drives are engineered alleles that can bias inheritance in their favor, allowing them to spread throughout a population. They could potentially be used to modify or suppress pest populations, such as mosquitoes that spread diseases. CRISPR/Cas9 homing drives, which copy themselves by homology-directed repair in drive/wild-type heterozygotes, are a powerful form of gene drive, but they are vulnerable to resistance alleles that preserve the function of their target gene. Such resistance alleles can prevent successful population suppression. Here, we constructed a homing suppression drive inDrosophila melanogasterthat utilized multiplexed gRNAs to inhibit the formation of functional resistance alleles in its female fertility target gene. The selected gRNA target sites were close together, preventing reduction in drive conversion efficiency. The construct reached a moderate equilibrium frequency in cage populations without apparent formation of resistance alleles. However, a moderate fitness cost prevented elimination of the cage population, showing the importance of using highly efficient drives in a suppression strategy, even if resistance can be addressed. Nevertheless, our results experimentally demonstrate the viability of the multiplexed gRNAs strategy in homing suppression gene drives.
A cell cycle-dependent GARP-like transcriptional repressor regulates the initiation of differentiation in Giardia lamblia
Authors: Shih Han-Wei , Alas Germain C.M. , Paredez Alexander R.
Published: May 2021

Transcriptional regulation of differentiation is critical for parasitic pathogens to adapt to environmental changes and regulate transmission. In response to encystation stimuli, Giardia lamblia cells shift from G1+S phase of the cell cycle to G2+M. By 2-4 hours, cyst wall proteins are upregulated, indicating that key regulatory steps occur within the first four hours of encystation. However, all characterized transcription factors (TFs) in Giardia have only been investigated at later time points of encystation. How TFs initiate encystation and link it to the cell cycle remains enigmatic. Here, we systematically screened six putative early upregulated TFs for nuclear localization, established their dynamic expression profiles, and determined their functional role in regulating encystation. We found a critical repressor, GLP4 that increases rapidly after 30 min of encystation stimuli and downregulates encystation specific markers, including Cyst Wall Proteins (CWPs) and enzymes in the cyst N-acetyl galactosamine (GalNAc) pathway. Depletion of GLP4 increases cyst production. Importantly, we observe that G2+M cells exhibit higher levels of CWP1 resulting from the activation of MYB2, a TF previously linked to encystation in Giardia. GLP4 upregulation occurs in G1+S cells, suggesting a role in repressing MYB2 and encystation specific genes in the G1+S phase of the cell cycle. Furthermore, we demonstrate that depletion of GLP4 upregulates MYB2 and promotes encystation while overexpression of GLP4 downregulates MYB2 and represses encystation. Together, these results suggest that Giardia employs a dose-dependent transcriptional response that involves the cell cycle regulated repressor GLP4 to orchestrate MYB2 and entry into the encystation pathway.

Importance

Transition between life cycle stages is a common feature among parasitic pathogens and its regulation must be optimized to balance persistence of infection with transmission. The early transcription factors (TFs) regulating commitment to differentiate are totally unknown in Giardia. In this work, we identified GLP4, a previously uncharacterized GARP-like TF, as an early-acting transcriptional repressor that inhibits G1+S cells from entering the encystation pathway. GLP4 is therefore a key regulator controlling the balance between proliferative growth and terminal differentiation into infective cysts.
Loss of N1-Methylation of G37 in tRNA Induces Ribosome Stalling and Reprograms Gene Expression
Authors: Masuda Isao , Hwang Jae-Yeon , Christian Thomas , Maharjan Sunita , Mohammad Fuad , Gamper Howard , Buskirk Allen R. , Hou Ya-Ming
Published: May 2021

N1-methylation of G37 is required for a subset of tRNAs to maintain the translational reading-frame. While loss of m1G37 increases ribosomal +1 frameshifting, whether it incurs additional translational defects is unknown. Here we address this question by applying ribosome profiling to gain a genome-wide view of the effects of m1G37 deficiency on protein synthesis. Using E. coli as a model, we show that m1G37 deficiency induces ribosome stalling at codons that are normally translated by m1G37-containing tRNAs. Stalling occurs during decoding of affected codons at the ribosomal A site, indicating a distinct mechanism than that of +1 frameshifting, which occurs after the A site. Enzyme and cell-based assays show that m1G37 deficiency reduces tRNA aminoacylation and in some cases peptide-bond formation. We observe changes of gene expression in m1G37 deficiency similar to those in the starvation-induced stringent response, consistent with the notion that loss of tRNA aminoacylation activates the response. This work demonstrates a previously unrecognized function of m1G37 that emphasizes its role throughout the entire elongation cycle of protein synthesis, providing new insight into its essentiality for bacterial growth and survival.
Widespread occurrence of hybrid internal-terminal exons in human transcriptomes
Authors: Fiszbein Ana , McGurk Michael , Calvo-Roitberg Ezequiel , Kim GyeungYun , Burge Christopher B. , Pai Athma A.
Published: May 2021

Alternative RNA processing is a major mechanism for diversifying the human transcriptome. Messenger RNA isoform differences are predominantly driven by alternative first exons, cassette internal exons and alternative last exons. Despite the importance of classifying exons to understand isoform structure, there is a lack of tools to look at isoform-specific exon usage using RNA-sequencing data. We recently observed that alternative transcription start sites often arise near annotated internal exons, creating “hybrid” exons that can be used as both first or internal exons. To investigate the creation of hybrid exons, we built the HIT (Hybrid-Internal-Terminal) exon pipeline that systematically classifies exons depending on their isoform-specific usage. Using a combination of junction reads coverage and probabilistic modeling, the HIT index identified thousands of hybrid first-internal and internal-last exons that were previously misclassified. Hybrid exons are enriched in long genes with at least ten internal exons, have longer flanking introns and strong splice sites. The usage of hybrid exons varies considerably across human tissues, but they are predominantly used in brain, testis and colon cells. Notably, genes involved in RNA splicing have the highest fraction of intra-tissue hybrid exons. Further, we found more than 100,000 inter-tissue hybrid exons that changed from internal to terminal exons across tissues. By developing the first method that can classify exons according to their isoform contexts, our findings demonstrate the existence of hybrid exons, expand the repertoire of tissue-specific terminal exons and uncover unexpected complexities of the human transcriptome.
Tightly constrained genome reduction and relaxation of purifying selection during secondary plastid endosymbiosis
Authors: Uthanumallian Kavitha , Iha Cintia , Repetti Sonja I. , Chan Cheong Xin , Bhattacharya Debashish , Duchene Sebastian , Verbruggen Heroen
Published: May 2021

Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids, the light harvesting organelles of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis – the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on the green lineage that has given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes,Lepidodinium). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained as well, with selection relaxed only relative to the background in primary plastids, but purifying selection remaining strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different phases of secondary plastid origin. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, andLepidodiniumdiffer in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection-drift interplay during secondary endosymbiosis, and evolutionary parallels during the process of organelle origination.
ErpY-like lipoprotein of Leptospira outsmart host complement regulation by acquiring complement regulators, activating alternate pathway, and intervening membrane attack complex
Authors: Hota Saswat , Hussain Md Saddam , Kumar Manish
Published: May 2021

The survival of pathogenic Leptospira in the host pivots on its proficiency to circumvent the immune response. These pathogens evade the complement system in serum by enticing and amassing the serum complement regulators onto their surface. ErpY-like lipoprotein, a surface-exposed protein of Leptospira spp., is conserved and exclusively present in the pathogenic spirochete. The recombinant form of this protein is comprehended to interact with multiple extracellular matrix (ECM) components and serum proteins like soluble complement regulators factor H (FH) and factor I (FI). Here, we document that the supplementation of recombinant ErpY-like protein (40 µg/mL) in the host (humans) serum augments the viability of E. coli and saprophytic L. biflexa by more than 2-fold. Pure complement regulators FH and FI, when bound to rErpY-like protein, preserve their respective cofactor and protease activity mandated to cleave the complement component C3b. The supplementation of rErpY-like protein (40 µg/mL) in serum ensued in ∼90 % reduction of membrane attack complex (C5b-9/MAC) deposition through alternate complement pathway (AP) activation. However, rErpY-like protein could moderately reduce (∼16%) MAC deposition in serum through the classical pathway (CP). In addition, the rErpY-like protein solely activated the AP, suggesting its role in the rapid consumption and depletion of the complement components. Blocking the pathogenic L. interrogans surface with anti-rErpY resulted in an increase in MAC formation on the bacterial surface, indicating a specific role of the ErpY-like lipoprotein in complement-mediated immune evasion. This study underscores the role of the ErpY-like lipoprotein of Leptospira in complement evasion.
Vaccine hesitancy and anti-vaccination attitudes during the start of COVID-19 vaccination program: A content analysis on Twitter data
Authors: Küçükali Hüseyin , Ataç Ömer , Palteki Ayşe Seval , Tokaç Ayşe Zülal , Hayran Osman Erol
Published: May 2021

Background

Vaccine hesitation, which is defined as one of the most important global health threats by World Health Organization, maintains its universal importance during the COVID-19 period. Due to the increasing appearance of anti-vaccine arguments on social media, Twitter is a useful resource in detecting these contents. In this study, we aimed to identify the prominent themes about vaccine hesitancy and refusal on social media during the COVID-19 pandemic.

Methods

In this qualitative study we collected Twitter contents which contain a vaccine-related keywords and published publicly between 9/12/2020 and 8/1/2021 (n=551,245). A stratified random sample (n=1041) is selected and analyzed by four researchers with content analysis method.

Results

All tweets included in the study were shared from 1,000 unique accounts of which 2.7% were verified and 11.3% organizational users. 90.5% of the tweets were about vaccines, 22.6% (n=213) of the tweets mentioned at least one COVID-19 vaccine name and the most frequently mentioned COVID-19 vaccine was CorronaVac (51.2%). Yet, it was mostly as “Chinese vaccine” (42.3%). 22.0% (n=207) of the tweets included at least one anti-vaccination theme. Among tweets that included an anti-vaccination theme; poor scientific processes (21.7%), conspiracy theories (16.4%), and suspicions towards manufacturers (15.5%) were the most frequently mentioned themes. The most co-occurred themes were “Poor scientific process” theme come along with “suspicion towards manufacturers” (n=9) and “suspicion towards health authorities” (n=5).

Conclusions

This study may be helpful for health managers to identify the major concerns of the population and organize the preventive measures, through the significant role of social media on early information about vaccine hesitancy and anti-vaccination attitudes.
MATRIX METALLOPROTEINASE 26 (MMP-26) OVEREXPRESSION IN PROSTATIC ADENOCARCINOMA
Authors: da Silva Romildo Luciano , de Lima Ingrid Tavares , Luís Almeida Paes Francisco , Souza da Silva Sandra Maria , Almeida Diniz Gurgel Ana Pavla , Santos Fabiano , da Costa Silva Neto Jacinto
Published: May 2021

Introduction

Matrix metalloproteinases (MMP) have been identified as biomarkers for several diseases, including cancer. MMP-26 is constitutively expressed in some cancer cells of epithelial origin. Despite this, there is a lack of studies regarding the expression of MMP-26 on prostatic carcinoma.

Aim

Here, we investigate the expression of the MMP-26 peptide in benign and malign prostatic tissues.

Patients and Methods

For this, 150 specimens, including atrophy (N = 25), prostatic intraepithelial neoplasia (PIN) (N = 25), benign prostatic hyperplasia (BPH) (N = 50), and prostatic adenocarcinoma (PA) (N = 50), were immunohistochemically (IHC) examined for the expression of MMP-26.

Results

MMP-26 expression was positive in 70 (46.7%) out of the 150 samples, being more prevalent in the PA group (46/50 cases,92%), followed by PIN (22/25 cases, 88%). The BPH group showed only 2/50 (4%) positive cases, and the atrophy group showed no reactivity. ROC curve analysis showed that MMP-26 immunoexpression had a higher area under the curve between PA vs atrophy+PIN+BPH (AUC=0.94; 95% CI 0.9-0.98), PA+PIN vs atrophy+BPH (AUC=0.97; 95% CI 0.94-0.99) and PA vs atrophy+BPH (AUC=0.97; 95% CI 0.95-1.00) groups. In addition, the expression and intensity of the MMP-26 reaction showed a significant association with total PSA values (P=0.001).

Conclusions

Our results showed that MMP-26 immunoexpression was useful to differentiate a group of benign and malignant samples in prostate tumors. This characteristic could assist in the predictive assessment and, consequently, in the development of new strategies for the diagnosis, prognosis, and treatment of prostate cancer.
A genome-wide CRISPR screen identifies regulators of beta cell function involved in type 2 diabetes risk
Authors: Grotz Antje K , Navarro-Guerrero Elena , Bevacqua Romina J , Baronio Roberta , Thomsen Soren K , Nawaz Sameena , Rajesh Varsha , Wesolowska-Andersen Agata , Kim Seung K , Ebner Daniel , Gloyn Anna L
Published: May 2021

Identification of the genes and processes mediating genetic association signals for complex disease represents a major challenge. Since many of the genetic signals for type 2 diabetes exert their effects through pancreatic islet-cell dysfunction, we performed a genome-wide pooled CRISPR loss-of- function screen in human pancreatic beta cells. We focused on the regulation of insulin content as a disease-relevant readout of beta cell function. We identified 580 genes influencing this phenotype: integration with genetic and genomic data provided experimental support for 20 candidate type 2 diabetes effector transcripts including the autophagy receptorCALCOCO2. Our study highlights how cellular screens can augment existing multi-omic efforts to accelerate biological and translational inference at GWAS loci.
Simple and effective serum-free medium for sustained expansion of bovine satellite cells for cell cultured meat
Authors: Stout Andrew J. , Mirliani Addison B. , White Eugene C. , Yuen John S.K. , Kaplan David L.
Published: May 2021

Cell-cultured meat offers the potential for a more sustainable, ethical, resilient, and healthy food system. However, research and development has been hindered by the lack of suitable serum-free media that enable the robust expansion of relevant cells (e.g., muscle satellite cells) over multiple passages. Recently, a low-cost serum-free media (B8) was described for induced pluripotent stem cells. Here, we adapt this media for bovine satellite cells and show that the addition of a single component, recombinant albumin, renders B8 suitable for the long-term expansion of cells without sacrificing myogenicity. We show that this new media (Beefy-9) maintains robust cell growth over the entire culture period tested (seven passages) with an average growth rate of 39 hours per population doubling. Along with demonstrated efficacy for bovine cells, this work provides a promising starting-point for developing serum-free media for cultures from other meat-relevant species. Ultimately, this work offers a promising foundation for escaping the reliance on serum in cultured meat research, thereby accelerating the field.
TALPID3/KIAA0586 regulates multiple aspects of neuromuscular patterning during gastrointestinal development in animal models and human
Authors: Delalande Jean Marie , Nagy Nandor , McCann Conor J. , Natarajan Dipa , Cooper Julie E. , Carreno Gabriela , Dora David , Campbell Alison , Laurent Nicole , Kemos Polychronis , Thomas Sophie , Alby Caroline , Attié-Bitach Tania , Lyonnet Stanislas , Logan Malcolm P. , Goldstein Allan M. , Davey Megan G. , Hofstra Robert M.W. , Thapar Nikhil , Burns Alan J.
Published: May 2021

TALPID3/KIAA0586 is an evolutionary conserved protein, which plays an essential role in protein trafficking. Its role during gastrointestinal (GI) and enteric nervous system (ENS) development has not been studied previously. Here, we analysed chicken, mouse and human embryonic GI tissues with TALPID3 mutations. The GI tract of TALPID3 chicken embryos was shortened and malformed. Histologically, the gut smooth muscle was mispatterned and enteric neural crest cells were scattered throughout the gut wall. Analysis of the Hedgehog pathway and gut extracellular matrix provided causative reasons for these defects. Interestingly, chicken intra-species grafting experiments and a conditional knockout mouse model showed that ENS formation did not require TALPID3, but was dependent on correct environmental cues. Surprisingly, the lack of TALPID3 in enteric neural crest cells (ENCC) affected smooth muscle and epithelial development in a non cell-autonomous manner. Analysis of human gut fetal tissues with aKIAA0586mutation showed strikingly similar findings compared to the animal models demonstrating conservation of TALPID3 and its necessary role in human GI tract development and patterning
Identification of ubiquitin variants that inhibit the E2 ubiquitin conjugating enzyme, Ube2k
Authors: Middleton A.J. , Teyra J. , Zhu J. , Sidhu S.S. , Day C.L.
Published: May 2021

Transfer of ubiquitin to substrate proteins regulates most processes in eukaryotic cells. E2 enzymes are a central component of the ubiquitin machinery, and generally determine the type of ubiquitin signal generated and thus the ultimate fate of substrate proteins. The E2, Ube2k, specifically builds degradative ubiquitin chains on diverse substrates. Here we have identified protein-based reagents, called ubiquitin variants (UbVs), that bind tightly and specifically to Ube2k. Crystal structures reveal that the UbVs bind to the E2 enzyme at a hydrophobic cleft that is distinct from the active site and previously identified ubiquitin binding sites. We demonstrate that the UbVs are potent inhibitors of Ube2k and block both ubiquitin charging of the E2 enzyme, and E3-catalysed ubiquitin transfer. The binding site of the UbVs suggests they directly clash with the ubiquitin activating enzyme, while potentially disrupting interactions with E3 ligases via allosteric effects. Our data reveal the first protein-based inhibitors of Ube2k and unveil a hydrophobic groove that could be an effective target for inhibiting Ube2k and other E2 enzymes.
Triangulation of microbial fingerprinting in anaerobic digestion reveals consistent fingerprinting profiles
Authors: De Vrieze Jo , Heyer Robert , Props Ruben , Van Meulebroek Lieven , Gille Karen , Vanhaecke Lynn , Benndorf Dirk , Boon Nico
Published: May 2021

The anaerobic digestion microbiome has been puzzling us since the dawn of molecular methods for mixed microbial community analysis. Monitoring of the anaerobic digestion microbiome can either take placeviaa non-targeted holistic evaluation of the microbial community through fingerprinting or by targeted monitoring of selected taxa. Here, we compared four different microbial community fingerprinting methods,i.e., amplicon sequencing, metaproteomics, metabolomics and cytomics, in their ability to characterise the full-scale anaerobic digestion microbiome. Cytometric fingerprinting through cytomics reflects a, for anaerobic digestion, novel, single cell-based approach of direct microbial community fingerprinting by flow cytometry. Three different digester types,i.e., sludge digesters, digesters treating agro-industrial waste and dry anaerobic digesters, each reflected different operational parameters. The α-diversity analysis yielded inconsistent results, especially for richness, across the different methods. In contrast, β-diversity analysis resulted in comparable profiles, even when translated into phyla or functions, with clear separation of the three digester types. In-depth analysis of each method’s featuresi.e., operational taxonomic units, metaproteins, metabolites, and cytometric traits, yielded certain similar features, yet, also some clear differences between the different methods, which was related to the complexity of the anaerobic digestion process. In conclusion, cytometric fingerprinting through flow cytometry is a reliable, fast method for holistic monitoring of the anaerobic digestion microbiome, and the complementary identification of key features through other methods could give rise to a direct interpretation of anaerobic digestion process performance.
Long-range organization of primary intestinal fibroblasts guides directed and persistent migration of organoid-derived intestinal epithelia
Authors: Fernández-Majada Vanesa , Comelles Jordi , Abad-Lázaro Aina , Acevedo Verónica , Esteve-Codina Anna , Hernando-Momblona Xavier , Batlle Eduard , Martinez Elena
Published: May 2021

Fibroblasts reside underneath most epithelial tissues. In the intestine, their role has been mostly restricted to a secretory and supportive role. Recent studies have shown that fibroblasts’ migration is key during vilification and wound healing. Yet, whether interactions between epithelial cells with fibroblasts and with the matrix contribute to epithelial movement remains elusive. Here, we show that intestinal fibroblasts enhance the directed and persistent migration of organoid-derived intestinal epithelia. By using a novel gap closurein vitromodel of the intestinal mucosa that includes both the epithelium and the stromal compartments, we demonstrate that the physical presence of fibroblasts in contact with the epithelium plays a crucial role in epithelial restoration by enhancing epithelial tissue integrity. Our results demonstrate that fibroblasts undergo long-range ordering to align perpendicularly to the epithelial migrating front, and deposit protein paths that act as contact guidance features to direct epithelial migration. In turn, only the physical interaction of intestinal fibroblasts with intestinal organoids drives epithelial spreading in three dimensions. Our results demonstrate that fibroblasts actively coordinate to accelerate intestinal epithelial restoration.
Multi-omics analysis of xylem sap uncovers dynamic modulation of poplar defenses by ammonium and nitrate
Authors: Kasper Karl , Abreu Ilka N , Feussner Kirstin , Zienkiewicz Krzysztof , Herrfurth Cornelia , Ischebeck Till , Janz Dennis , Majcherczyk Andrzej , Schmitt Kerstin , Valerius Oliver , Braus Gerhard H. , Feussner Ivo , Polle Andrea
Published: May 2021

Xylem sap is the major transport route for nutrients from roots to shoots. Here, we investigated how variations in nitrogen (N) nutrition affected the metabolome and proteome of xylem sap, growth of the xylem endophyte Brennaria salicis and report transcriptional re-wiring of leaf defenses in poplar (Populus x canescens). We supplied poplars with high, intermediate or low concentrations of ammonium or nitrate. We identified 288 unique proteins in xylem sap. About 85% of the xylem sap proteins were shared among ammonium- and nitrate-supplied plants. The number of proteins increased with increasing N supply but the major functional categories (catabolic processes, cell wall-related enzymes, defense) were unaffected. Ammonium nutrition caused higher abundances of amino acids and carbohydrates, while nitrate caused higher malate levels in xylem sap. Pipecolic acid and N-hydroxy-pipecolic acid increased whereas salicylic acid and jasmonoyl-isoleucine decreased with increasing N nutrition. Untargeted metabolome analyses revealed 2179 features in xylem sap, of which 863 were differentially affected by N treatments. We identified 122 metabolites, mainly from specialized metabolism of the groups of salicinoids, phenylpropanoids, phenolics, flavonoids, and benzoates. Their abundances increased with decreasing N. Endophyte growth was stimulated in xylem sap of high N- and suppressed in that of low N-fed plants. The drastic changes in xylem sap composition caused massive changes in the transcriptional landscape of leaves and recruited defense pathways against leaf feeding insects and biotrophic fungi, mainly under low nitrate. Our study uncovers unexpected complexity and variability of xylem composition with consequences for plant defenses.

Significance statement

This study reports the largest, currently available plant xylem sap proteome and metabolome databases and highlights novel discoveries of specialized metabolites and phytohormones in the xylem sap. This is the first multi-omics study linking differences in nitrogen supply with changes xylem sap composition, endophyte growth and transcriptional defenses in leaves.
PandemicVibrio choleraeAcquired Competitive Traits from an EnvironmentalVibrioSpecies
Authors: Santoriello Francis J. , Kirchberger Paul C. , Boucher Yann , Pukatzki Stefan
Published: May 2021

Background

Vibrio cholerae,the causative agent of cholera, is a human pathogen that thrives in estuarine environments.V. choleraecompetes with neighboring microbes by the contact-dependent translocation of toxic effectors with the type VI secretion system (T6SS). Effector types are highly variable acrossV. choleraestrains, but all pandemic isolates encode the same set of distinct effectors. It is possible that acquisition of these effectors via horizontal gene transfer played a role in the development of pandemicV. cholerae.

Results

We assessed the distribution ofV. choleraeT6SS loci across multipleVibriospecies. We showed that the fish-pathogenV. anguillarumencodes all threeV. choleraecore loci as well as two of the four additional auxiliary clusters. We further demonstrated thatV. anguillarumshares T6SS effectors withV. cholerae,including every pandemic-associatedV. choleraeeffector. We identified a novel T6SS cluster (Accessory Aux1) that is widespread inV. anguillarumand encodes the pandemicV. choleraeeffector TseL. We highlighted potential gene transfer events of Accessory Aux1 fromV. anguillarumtoV. cholerae.Finally, we showed that TseL fromV. choleraecan be neutralized by theV. anguillarumAccessory Aux1 immunity protein and vice versa, indicatingV. anguillarumas the donor oftseLto theV. choleraespecies.

Conclusions

V. anguillarumconstitutes an environmental reservoir of pandemic-associatedV. choleraeT6SS effectors.V. anguillarumandV. choleraelikely share an environmental niche, compete, and exchange T6SS effectors. Further, our findings highlight the fish as a potential reservoir of pandemicV. cholerae.
SARS-CoV-2 transmission via apical syncytia release from primary bronchial epithelia and infectivity restriction in children epithelia
Authors: Beucher Guillaume , Blondot Marie-Lise , Celle Alexis , Pied Noémie , Recordon-Pinson Patricia , Esteves Pauline , Faure Muriel , Métifiot Mathieu , Lacomme Sabrina , Dacheaux Denis , Robinson Derrick , Längst Gernot , Beaufils Fabien , Lafon Marie-Edith , Berger Patrick , Landry Marc , Malvy Denis , Trian Thomas , Andreola Marie-Line , Wodrich Harald
Published: May 2021

The beta-coronavirus SARS-CoV-2 is at the origin of a persistent worldwide pandemic. SARS-CoV-2 infections initiate in the bronchi of the upper respiratory tract and are able to disseminate to the lower respiratory tract eventually causing acute severe respiratory syndrome with a high degree of mortality in the elderly. Here we use reconstituted primary bronchial epithelia from adult and children donors to follow the infection dynamic following infection with SARS-CoV-2. We show that in bronchial epithelia derived from adult donors, infections initiate in multi-ciliated cells. Then, infection rapidly spread within 24-48h throughout the whole epithelia. Within 3-4 days, large apical syncytia form between multi-ciliated cells and basal cells, which dissipate into the apical lumen. We show that these syncytia are a significant source of the released infectious dose. In stark contrast to these findings, bronchial epithelia reconstituted from children donors are intrinsically more resistant to virus infection and show active restriction of virus spread. This restriction is paired with accelerated release of IFN compared to adult donors. Taken together our findings reveal apical syncytia formation as an underappreciated source of infectious virus for either local dissemination or release into the environment. Furthermore, we provide direct evidence that children bronchial epithelia are more resistant to infection with SARS-CoV-2 providing experimental support for epidemiological observations that SARS-CoV-2 cases’ fatality is linked to age.

Significance Statement

Bronchial epithelia are the primary target for SARS-CoV-2 infections. Our work uses reconstituted bronchial epithelia from adults and children. We show that infection of adult epithelia with SARS-CoV-2 is rapid and results in the synchronized release of large clusters of infected cells and syncytia into the apical lumen contributing to the released infectious virus dose. Infection of children derived bronchial epithelia revealed an intrinsic resistance to infection and virus spread, probably as a result of a faster onset of interferon secretion. Thus, our data provide direct evidence for the epidemiological observation that children are less susceptible to SARS-CoV-2.
rPanglaoDB: an R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database
Authors: Osorio Daniel , Kuijjer Marieke L. , Cai James J.
Published: May 2021

Motivation

Characterizing cells with rare molecular phenotypes is one of the promises of high throughput single-cell RNA sequencing (scRNA-seq) techniques. However, collecting enough cells with the desired molecular phenotype in a single experiment is challenging, requiring several samples preprocessing steps to filter and collect the desired cells experimentally before sequencing. Data integration of multiple public single-cell experiments stands as a solution for this problem, allowing the collection of enough cells exhibiting the desired molecular signatures. By increasing the sample size of the desired cell type, this approach enables a robust cell type transcriptome characterization.

Results

Here, we introduce rPanglaoDB, an R package to download and merge the uniformly processed and annotated scRNA-seq data provided by the PanglaoDB database. To show the potential of rPanglaoDB for collecting rare cell types by integrating multiple public datasets, we present a biological application collecting and characterizing a set of 157 fibrocytes. Fibrocytes are a rare monocyte-derived cell type, that exhibits both the inflammatory features of macrophages and the tissue remodeling properties of fibroblasts. This constitutes the first fibrocytes’ unbiased transcriptome profile report. We compared the transcriptomic profile of the fibrocytes against the fibroblasts collected from the same tissue samples and confirm their associated relationship with healing processes in tissue damage and infection through the activation of the prostaglandin biosynthesis and regulation pathway.

Availability and Implementation

rPanglaoDB is implemented as an R package available through the CRAN repositories https://CRAN.R-project.org/package=rPanglaoDB.

Contact

daniecos@uio.no

Supplementary information

Code to replicate the case example and figure 1 is available at https://github.com/dosorio/rPanglaoDB