bluuebunny/crossref_metadata_2025 huggingface dataset:
Regulation of prostate androgens by megalin and 25-hydroxyvitamin D status: Mechanism for high prostate androgen in African American men
Authors: Garcia Jason , Krieger Kirsten D. , Loitz Candice , Perez Lillian , Richards Zachary A. , Helou Yves , Kregel Steve , Celada Sasha , Mesaros Clementina A. , Gann Peter H. , Willnow Thomas E. , Griend Donald Vander , Kittles Rick , Prins Gail S. , Penning Trevor , Nonn Larisa
Published: November 2021

Vitamin D deficiency is associated with an increased risk of prostate cancer (PCa) mortality and is hypothesized to contribute to PCa aggressiveness and disparities in African American populations. The prostate epithelium was recently shown to express megalin, an endocytic receptor that internalizes globulin-bound hormones, which suggests regulation of prostate hormone levels, in contrast to the free hormone hypothesis. Here, we demonstrated that megalin imports testosterone bound to sex hormone-binding globulin into prostate cells. Prostatic loss of Lrp2 (megalin) in a mouse model resulted in reduced prostate testosterone and dihydrotestosterone (DHT) levels. Megalin expression was regulated and suppressed by 25-hydroxyvitamin D (25D) in cell lines, patient-derived prostate epithelial cells, and prostate tissue explants, indicating a negative feedback loop. In patent samples, the relationships between hormones support this feedback mechanism, as prostatic DHT levels are higher in African American men and are inversely correlated with serum 25D status. Megalin levels are reduced in localized PCa by the Gleason grade and in patients with future disease recurrence. Our findings suggest that the free hormone hypothesis should be revisited for testosterone and highlight the impact of vitamin D deficiency on prostate androgen levels, which are known drivers of PCa. Thus, we revealed a mechanistic link between vitamin D and PCa disparities observed in African Americans.
Robust and generalizable segmentation of human functional tissue units
Authors: Godwin Leah L. , Ju Yingnan , Sood Naveksha , Jain Yashvardhan , Quardokus Ellen M. , Bueckle Andreas , Longacre Teri , Horning Aaron , Lin Yiing , Esplin Edward D. , Hickey John W. , Snyder Michael P. , Patterson N. Heath , Spraggins Jeffrey M. , Börner Katy
Published: November 2021

The Human BioMolecular Atlas Program aims to compile a reference atlas for the healthy human adult body at the cellular level. Functional tissue units (FTU, e.g., renal glomeruli and colonic crypts) are of pathobiological significance and relevant for modeling and understanding disease progression. Yet, annotation of FTUs is time consuming and expensive when done manually and existing algorithms achieve low accuracy and do not generalize well. This paper compares the five winning algorithms from the “Hacking the Kidney” Kaggle competition to which more than a thousand teams from sixty countries contributed. We compare the accuracy and performance of the algorithms on a large-scale renal glomerulus Periodic acid-Schiff stain dataset and their generalizability to a colonic crypts hematoxylin and eosin stain dataset. Results help to characterize how the number of FTUs per unit area differs in relationship to their position in kidney and colon with respect to age, sex, body mass index (BMI), and other clinical data and are relevant for advancing pathology, anatomy, and surgery.
scHiCSRS: A Self-Representation Smoothing Method with Gaussian Mixture Model for Imputing single cell Hi-C Data
Authors: Xie Qing , Lin Shili
Published: November 2021

Motivation

Single cell Hi-C techniques make it possible to study cell-to-cell variability in genomic features. However, excess zeros are commonly seen in single cell Hi-C (scHi-C) data, making scHi-C matrices extremely sparse and bringing extra difficulties in downstream analysis. The observed zeros are a combination of two events: structural zeros for which the loci never interact due to underlying biological mechanisms, and dropouts or sampling zeros where the two loci interact but are not captured due to insufficient sequencing depth. Although quality improvement approaches have been proposed as an intermediate step for analyzing scHi-C data, little has been done to address these two types of zeros. We believe that differentiating between structural zeros and dropouts would benefit downstream analysis such as clustering.

Results

We propose scHiCSRS, a self-representation smoothing method that improves the data quality, and a Gaussian mixture model that identifies structural zeros among observed zeros. scHiC-SRS not only takes spatial dependencies of a scHi-C 2D data structure into account but also borrows information from similar single cells. Through an extensive set of simulation studies, we demonstrate the ability of scHiCSRS for identifying structural zeros with high sensitivity and for accurate imputation of dropout values in sampling zeros. Downstream analysis for three real datasets show that data improved from scHiCSRS yield more accurate clustering of cells than simply using observed data or improved data from several comparison methods.

Availability and Implementation

The scHiCSRS R package, together with the processed real and simulated data used in this study, are available on Github at https://github.com/sl-lin/scHiCSRS.git.

Contact

shili@stat.osu.edu

Supplementary information

Supplementary data are available online.
Estimating the rates of crossover and gene conversion from individual genomes
Authors: Setter Derek , Ebdon Sam , Jackson Ben , Lohse Konrad
Published: November 2021

Recombination can occur either as a result of crossover or gene conversion events. Population genetic methods for inferring the rate of recombination from patterns of linkage disequilibrium generally assume a simple model of recombination that only involves crossover events and ignore gene conversion. However, distinguishing the two processes is not only necessary for a complete description of recombination, but also essential for understanding the evolutionary consequences of inversions and other genomic partitions in which crossover (but not gene conversion) is reduced. We presentheRho, a simple composite likelihood scheme for co-estimating the rate of crossover and gene conversion from individual diploid genomes. The method is based on analytic results for the distance-dependent probability of heterozygous and homozygous states at two loci. We applyheRhoto simulations and data from the house mouseMus musculus castaneus, a well studied model. Our analyses show i) that the rates of crossover and gene conversion can be accurately co-estimated at the level of individual chromosomes and ii) that previous estimates of the population scaled rate of recombinationunder a pure crossover model are likely biased.
2-Guanidino-quinazoline promotes the readthrough of nonsense mutations underlying human genetic diseases
Authors: Bidou Laure , Bugaud Olivier , Merer Goulven , Coupet Matthieu , Hatin Isabelle , Chirkin Egor , François Pauline , Cintrat Jean-Christophe , Namy Olivier
Published: November 2021

Premature termination codons (PTCs) account for 10% to 20% of genetic diseases in humans. The gene inactivation resulting from PTC can be counteracted by the use of drugs stimulating PTC readthrough, thereby restoring production of the full-length protein. However, a greater chemical variety of readthrough inducers is required to broaden the medical applications of this therapeutic strategy. In this study, we developed a new reporter cell line and performed high-throughput screening (HTS) to identify potential new readthrough inducers. After three successive assays, we isolated 2-guanidino-quinazoline (TLN468). We assessed the clinical potential of this drug as a potent readthrough inducer on the 40 PTCs most frequently responsible for Duchenne muscular dystrophy. We found that TLN468 was more efficient than gentamicin, and acted on a broader range of sequences, without inducing the readthrough of natural stop codons.
REDigest: a Python GUI for In-Silico Restriction Digestion Analysis of Genes or Complete Genome Sequences
Authors: Singh Abhijeet
Published: November 2021

Restriction fragment length polymorphism (RFLP) is a technology for the molecular characterization of DNA and widely used genome mapping, medical genetics, molecular microbiology and forensics etc. Terminal restriction fragment length polymorphism (T-RFLP), a variant of RFLP is extensively used in environmental microbiology for the microbial community profiling based on the restriction digestion profile of marker gene (16S rRNA, FTHFS etc.) amplicons. At present, there is a lack of a tool which can perform in-silico restriction digestion of a large number of sequences at a time, in an interactive way and as an output produce sequences of the restriction fragments and visualization plot. I have developed a graphical user interface based software “REDigest” for the in-silico restriction digestion analysis for gene or genome sequences. The REDigest software program with a graphical user interface is freely available at https://github.com/abhijeetsingh1704/REDigest.
Combining dictionary- and rule-based approximate entity linking with tuned BioBERT
Authors: Mobasher Ghadeer , Mertová Lukrécia , Ghosh Sucheta , Krebs Olga , Heinlein Bettina , Müller Wolfgang
Published: November 2021

Chemical named entity recognition (NER) is a significant step for many downstream applications like entity linking for the chemical text-mining pipeline. However, the identification of chemical entities in a biomedical text is a challenging task due to the diverse morphology of chemical entities and the different types of chemical nomenclature. In this work, we describe our approach that was submitted for BioCreative version 7 challenge Track 2, focusing on the ‘Chemical Identification’ task for identifying chemical entities and entity linking, using MeSH. For this purpose, we have applied a two-stage approach as follows (a) usage of fine-tuned BioBERT for identification of chemical entities (b) semantic approximate search in MeSH and PubChem databases for entity linking. There was some friction between the two approaches, as our rule-based approach did not harmonise optimally with partially recognized words forwarded by the BERT component. For our future work, we aim to resolve the issue of the artefacts arising from BERT tokenizers and develop joint learning of chemical named entity recognition and entity linking using pre-trained transformer-based models and compare their performance with our preliminary approach. Next, we will improve the efficiency of our approximate search in reference databases during entity linking. This task is non-trivial as it entails determining similarity scores of large sets of trees with respect to a query tree. Ideally, this will enable flexible parametrization and rule selection for the entity linking search.
Imaging the extent and location of spatiotemporally distributed epileptiform sources from MEG measurements
Authors: Jiang Xiyuan , Ye Shuai , Sohrabpour Abbas , Bagić Anto , He Bin
Published: November 2021

Non-invasive MEG/EEG source imaging provides valuable information about the epileptogenic brain areas which can be used to aid presurgical planning in focal epilepsy patients suffering from drug-resistant seizures. However, the source extent estimation for electrophysiological source imaging remains to be a challenge and is usually largely dependent on subjective choice. Our recently developed algorithm, fast spatiotemporal iteratively reweighted edge sparsity minimization (FAST-IRES) strategy, has been shown to objectively estimate extended sources from EEG recording, while it has not been applied to MEG recordings. In this work, through extensive numerical experiments and real data analysis in a group of focal drug-resistant epilepsy patients’ interictal spikes, we demonstrated the ability of FAST-IRES algorithm to image the location and extent of underlying epilepsy sources from MEG measurements. Our results indicate the merits of FAST-IRES in imaging the location and extent of epilepsy sources for pre-surgical evaluation from MEG measurements.
Structural Basis for pH-Gating of the K+ Channel TWIK1 at the Selectivity Filter
Authors: Turney Toby S. , Li Vivian , Brohawn Stephen G.
Published: November 2021

TWIK1 is a widely expressed pH-gated two-pore domain K+ channel (K2P) that contributes to cardiac rhythm generation and insulin release from pancreatic beta cells. TWIK1 displays unique properties among K2Ps including low basal activity and inhibition by extracellular protons through incompletely understood mechanisms. Here, we present cryo-EM structures of TWIK1 in lipid nanodiscs at high and low pH that reveal a novel gating mechanism at the K+ selectivity filter. At high pH, TWIK1 adopts an open conformation. At low pH, protonation of an extracellular histidine results in a cascade of conformational changes that close the channel by sealing the top of the selectivity filter, displacing the helical cap to block extracellular ion access pathways, and opening gaps for lipid block of the intracellular cavity. These data provide a mechanistic understanding for extracellular pH-gating of TWIK1 and show how diverse mechanisms have evolved to gate the selectivity filter of K+ channels.
Scalable estimation of microbial co-occurrence networks with Variational Autoencoders
Authors: Morton James T. , Silverman Justin , Tikhonov Gleb , Lähdesmäki Harri , Bonneau Rich
Published: November 2021

Estimating microbe-microbe interactions is critical for understanding the ecological laws governing microbial communities. Rapidly decreasing sequencing costs have promised new opportunities to estimate microbe-microbe interactions across thousands of uncultured, unknown microbes. However, typical microbiome datasets are very high dimensional and accurate estimation of microbial correlations requires tens of thousands of samples, exceeding the computational capabilities of existing methodologies. Furthermore, the vast majority of microbiome studies collect compositional metagenomics data which enforces a negative bias when computing microbe-microbe correlations. The Multinomial Logistic Normal (MLN) distribution has been shown to be effective at inferring microbe-microbe correlations, however scalable Bayesian inference of these distributions has remained elusive. Here, we show that carefully constructed Variational Autoencoders (VAEs) augmented with the Isometric Log-ratio (ILR) transform can estimate low-rank MLN distributions thousands of times faster than existing methods. These VAEs can be trained on tens of thousands of samples, enabling co-occurrence inference across tens of thousands of microbes without regularization. The latent embedding distances computed from these VAEs are competitive with existing beta-diversity methods across a variety of mouse and human microbiome classification and regression tasks, with notable improvements on longitudinal studies.
Zymomonas mobilis ZM4 utilizes an acetaldehyde dehydrogenase to produce acetate
Authors: Felczak Magdalena M. , TerAvest Michaela A.
Published: November 2021

Zymomonas mobilis is a promising bacterial host for biofuel production but further improvement has been hindered because some aspects of its metabolism remain poorly understood. For example, one of the main byproducts generated by Z. mobilis is acetate but the pathway for acetate production is unknown. Acetaldehyde oxidation has been proposed as the major source of acetate and an acetaldehyde dehydrogenase was previously isolated from Z. mobilis via activity guided fractionation, but the corresponding gene has never been identified. We determined that the locus ZMO1754 (also known as ZMO_RS07890) encodes an NADP+-dependent acetaldehyde dehydrogenase that is responsible for acetate production by Z. mobilis. Deletion of this gene from the chromosome resulted in a growth defect in oxic conditions, suggesting that acetaldehyde detoxification is an important role of acetaldehyde dehydrogenase. The deletion strain also exhibited a near complete abolition of acetate production, both in typical laboratory conditions and during lignocellulosic hydrolysate fermentation. Our results show that ZMO1754 encodes the major acetaldehyde dehydrogenase in Z. mobilis and we therefore rename the gene aldB based on functional similarity to the Escherichia coli acetaldehyde dehydrogenase.

Importance

Biofuel production from non-food crops is an important strategy for reducing carbon emissions from the transportation industry but it has not yet become commercially viable. An important avenue to improve biofuel production is to enhance the characteristics of fermentation organisms by genetic engineering. To make genetic modifications successful, we must gain sufficient information about the genome and metabolism of the organism to enable rational design and engineering. Here, we improved understanding of Zymomonas mobilis, a promising biofuel producing bacterium, by identifying a metabolic pathway and associated gene that lead to byproduct formation. This information may be used in the future for genetic engineering to reduce byproduct formation during biofuel production.
SARS-CoV-2 Delta vaccine breakthrough transmissibility in Alachua, Florida
Authors: Magalis Brittany Rife , Rich Shannan , Tagliamonte Massimiliano S , Mavian Carla , Cash Melanie N , Riva Alberto , Marini Simone , Amador David Moraga , Zhang Yanping , Shapiro Jerne , Horine Amelia , Starostik Petr , Pieretti Maura , Vega Samantha , Lacombe Ana Paula , Salinas Jessica , Stevenson Mario , Myers Paul , Morris J. Glenn , Lauzardo Michael , Prosperi Mattia , Salemi Marco
Published: November 2021

Background

SARS-CoV-2 Delta variant has caused a dramatic resurgence in infections in the United Sates, raising questions regarding potential transmissibility among vaccinated individuals.

Methods

Between October 2020 and July 2021, we sequenced 4,439 SARS-CoV-2 full genomes, 23% of all known infections in Alachua County, Florida, including 109 vaccine breakthrough cases. Univariate and multivariate regression analyses were conducted to evaluate associations between viral load (VL) level and patient characteristics. Contact tracing and phylogenetic analysis were used to investigate direct transmissions involving vaccinated individuals.

Results

The majority of breakthrough sequences with lineage assignment were classified as Delta variants (74.6%) and occurred, on average, about three months (104 ± 57.5 days) after full vaccination, at the same time (June-July 2021) of Delta variant exponential spread within the county. Six Delta variant transmission pairs between fully vaccinated individuals were identified through contact tracing, three of which were confirmed by phylogenetic analysis. Delta breakthroughs exhibited broad VL values during acute infection (IQR 1.2 – 8.64 Log copies/ml), on average 38% lower than matched unvaccinated patients (3.29 – 10.81 Log copies/ml, p<0.00001). Nevertheless, 49-50% of all breakthroughs, and 56-60% of Delta-infected breakthroughs exhibited VL above the transmissibility threshold (4 Log copies/ml) irrespective of time post vaccination.

Conclusions

Delta infection transmissibility and general VL patterns in vaccinated individuals suggest limited levels of sterilizing immunity that need to be considered by public health policies. In particular, ongoing evaluation of vaccine boosters should address whether extra vaccine doses might curb breakthrough contribution to epidemic spread.
Could widespread use of antiviral treatment curb the COVID-19 pandemic? A modeling study
Authors: Matrajt Laura , Brown Elizabeth R. , Cohen Myron S. , Dimitrov Dobromir , Janes Holly
Published: November 2021

Despite the development of safe and effective vaccines, effective treatments for COVID-19 disease are still urgently needed. Several antiviral drugs have shown to be effective in reducing progression of COVID-19 disease. In the present work, we use an agent-based mathematical model to assess the potential population impact of the use of antiviral treatments in four countries with different demographic structure and current levels of vaccination coverage: Kenya, Mexico, United States (US) and Belgium. We analyzed antiviral effects on reducing hospitalization and death, and potential antiviral effects on reducing transmission. For each country, we varied daily treatment initiation rate (DTIR) and antiviral effect in reducing transmission (AVT). Irrespective of location and AVT, widespread antiviral treatment of symptomatic adult infections (≥20% DTIR) prevented the majority of COVID-19 deaths, and recruiting 6% of all adult symptomatic infections daily reduced mortality by a third in all countries. Furthermore, our model projected that targeting antiviral treatment to the oldest age group (65 years old and older, DTIR of 20%) can prevent over 47% of deaths. Our results suggest that early antiviral treatment (as soon as possible after inception of infection) is needed to mitigate transmission, preventing 50% more infections compared to late treatment (started 3 to 5 days after symptoms onset). Our results highlight the synergistic effect of vaccination and antiviral treatment: as the vaccination rate increases, antivirals have a larger relative impact on population transmission. These results suggest that antiviral treatments can become a strategic tool that, in combination with vaccination, can significantly reduce COVID-19 hospitalizations and deaths and can help control SARS-CoV-2 transmission.
Nanopore 16S rRNA sequencing reveals alterations in nasopharyngeal microbiome and enrichment ofMycobacteriumandMycoplasmain patients with COVID 19
Authors: Mahapatra Soumendu , Mishra Rasmita , Prasad Punit , Murmu Krushna Chandra , Aggarwal Shifu , Sethi Manisha , Mohapatra Priyanka , Ghosh Arup , Yadav Rina , Dodia Hiren , Ansari Shamima Azma , De Saikat , Singh Deepak , Suryawanshi Amol , Dash Rupesh , Senapati Shantibhushan , Beuria Tushar K. , Chattopadhyay Soma , Syed Gulam Hussain , Swain Rajeeb , Raghav Sunil K. , Parida Ajay
Published: November 2021

The coronavirus disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome corona virus 2 (SARS-CoV-2) is a major global health concern. This virus infects the upper respiratory tract and causes pneumonia-like symptoms. So far, few studies have shown that respiratory infections alter nasopharyngeal (NP) microbiome diversity and enrich opportunistic pathogens. In this study, we have sequenced the 16S rRNA variable regions, V1 through V9, extracted from NP samples of control and COVID-19 (symptomatic and asymptomatic) participants using the Oxford Nanopore™ technology. Comprehensive bioinformatics analysis investigating the alpha/beta diversities, non-metric multidimensional scaling, correlation studies, canonical correspondence analysis, linear discriminate analysis, and dysbiosis index analysis revealed control and COVID-19-specific NP microbiomes. We observed significant dysbiosis in COVID-19 NP microbiome with abundance of opportunistic pathogens such asCutibacterium, Corynebacterium, Oerskovia, andCellulomonasin asymptomatic patients, and ofStreptomycesandMycobacteriaceaefamily in symptomatic patients. Furthermore, we observed sharp rise in enrichment of opportunistic pathogens in symptomatic patients, with abundance ofMycobacteriaandMycoplasma, which strongly correlated with the occurrences of chest pain and fever. Our findings contribute novel insights regarding emergence of opportunistic pathogens in COVID-19 patients and their relationship with symptoms, suggesting their potential role in coinfections.
Understanding national trends in COVID-19 vaccine hesitancy in Canada – April 2020 to March 2021
Authors: Lavoie Kim L. , Gosselin-Boucher Vincent , Stojanovic Jovana , Gupta Samir , Gagne Myriam , Joyal-Desmarais Keven , Seguin Katherine , Sheinfield-Gorin Sherri , Ribeiro Paula , Voisard Brigitte , Vallis Michael , Corace Kim , Presseau Justin , Bacon Simon L. ,   for the iCARE Study Team
Published: November 2021

Objective

Key to reducing COVID-19 morbidity and mortality and reducing the need for further lockdown measures in Canada and worldwide is widespread acceptance of COVID-19 vaccines. Vaccine hesitancy has emerged as a key barrier to achieving optimal vaccination rates, for which there is little data among Canadians. This study examined rates of vaccine hesitancy and their correlates among Canadian adults.

Methods

This study analyzed data from five age, sex and province-weighted population-based samples to describe rates of hesitancy between April 2020 and March 2021 among Canadians who completed online surveys as part of the iCARE Study, and various sociodemographic, clinical and psychological correlates. Vaccine hesitancy was assessed by asking: “If a vaccine for COVID-19 were available today, what is the likelihood that you would get vaccinated?” Responses were dichotomized into ‘very likely’, ‘unlikely’, ‘somewhat unlikely’ (reflecting some degree of vaccine hesitancy) vs ‘extremely likely’ to get the vaccine, which was the comparator.

Results

Overall, 15,019 respondents participated in the study. A total of 42.2% of respondents reported vaccine hesitancy over the course of the study, which was lowest during surveys 1 (April 2020) and 5 (March 2021) and highest during survey 3 (November 2020). Fully adjusted multivariate logistic regression analyses revealed that women, those aged 50 and younger, non-Whites, those with high school education or less, and those with annual household incomes below the poverty line in Canada (i.e., $60,000) were significantly more likely to report being vaccine hesitant over the study period, as were essential and healthcare workers, parents of children under the age of 18, and those who do not get regular flu vaccines. Believing engaging in infection prevention behaviours (like vaccination) is important for reducing virus transmission and high COVID-19 health concerns (being infected and infecting others) were associated with 77% and 54% reduction in vaccine hesitancy, respectively, and having high personal financial concerns (worried about job or income loss) was associated with 1.33 times increased odds of vaccine hesitancy.

Conclusion

Results point to the importance of targeting vaccine efforts to women, younger people and socioeconomically disadvantaged groups, and that vaccine messaging should emphasize the benefits of getting vaccinated, and how the benefits (particularly to health) far outweigh the risks. Future research is needed to monitor ongoing changes in vaccine intentions and behaviour, as well as to better understand motivators and facilitators of vaccine acceptance, particularly among vulnerable groups.
Evaluation of Pre-operational Factors Contributing to a Dorsal Column Stimulator Explantation
Authors: Kinne Maximilian A. , Cowan R. Scott , Knee Alexander
Published: November 2021

Objectives

Implantation of a dorsal column stimulator (DCS) for axial spine and radicular pain is a commonly performed procedure. Despite the benefits of this device to reduce pain and improve quality of life, some patients elect to have the device explanted. The purpose of this study is to describe pre-operational factors among patients who elected to have their DCS explanted and how these factors are associated with reason for explantation.

Materials and Methods

We conducted a retrospective descriptive study using the database of a private outpatient orthopedic clinic. We included all patients who had a DCS explanted between January 1, 2007 and June 19, 2014. Data was collected on patient demographics, past medical and back surgery history, as well as details of implantation, permanent device implantation, and subsequent explantation. Reasons for explantation were categorized as: inadequate pain control using three categories (with no device-related pain/discomfort, with device-related pain/discomfort, or inadequate pain control and patient wants MRI), or pain resolved.

Results

A consecutive sample of 100 subjects who underwent explantation of a DCS was identified for review. Of these 100 subjects, 14 were excluded. Based on our data, we hypothesize that sex (57% female, 43% male) degenerative disc disease (72%), previous back surgery (70%), BMI classified as overweight (subject average = 28.3), history of tobacco usage (57%), and history of narcotic use (80%) may be potential risk factors for explantation.

Conclusions

With respect to clinical evaluation of patients as candidates for spinal cord stimulator implantation, we cannot recommend that any of the evaluated variables be considered a contraindication to proceeding with a trial procedure. Future studies are planned to compare these data to a control group of subjects to establish risk factors predisposing individuals to explantation of a DCS.
Soft, dynamic hydrogel confinement improves kidney organoid lumen morphology and reduces epithelial–mesenchymal transition in culture
Authors: Ruiter Floor A.A. , Morgan Francis L.C. , Roumans Nadia , Schumacher Anika , Slaats Gisela G. , Moroni Lorenzo , LaPointe Vanessa L.S. , Baker Matthew B.
Published: November 2021

Pluripotent stem cell–derived kidney organoids offer a promising solution to renal failure, yet current organoid protocols often lead to off-target cells and phenotypic alterations, preventing maturity. Here, we created various dynamic hydrogel architectures, conferring a controlled and biomimetic environment for organoid encapsulation. We investigated how hydrogel stiffness and stress relaxation affect renal phenotype and undesired fibrotic markers. We observed stiff hydrogel encapsulation led to an absence of certain renal cell types and signs of an epithelial– mesenchymal transition (EMT), whereas encapsulation in soft-stress-relaxing hydrogels led to all major renal segments, fewer fibrosis/EMT associated proteins, apical proximal tubule enrichment, and primary cilia formation, representing a significant improvement over current approaches to culture kidney organoids. Our findings show that engineering hydrogel mechanics and dynamics has a decided benefit for organoid culture. These structure–property– function relationships can enable rational design of materials, bringing us closer to functional engraftments and disease-modelling applications.
Transcriptome innovations in primates revealed by single-molecule long-read sequencing
Authors: Ferrández-Peral Luis , Zhan Xiaoyu , Álvarez-Estapé Marina , Chiva Cristina , Esteller-Cucala Paula , García-Pérez Raquel , Julià Eva , Lizano Esther , Fornas Òscar , Sabidó Eduard , Li Qiye , Marquès-Bonet Tomàs , Juan David , Zhang Guojie
Published: November 2021

Transcriptomic diversity greatly contributes to the fundamentals of disease, lineage-specific biology, and environmental adaptation. However, much of the actual isoform repertoire contributing to shaping primate evolution remains unknown. Here, we combined deep long- and short-read sequencing complemented with mass spectrometry proteomics in a panel of lymphoblastoid cell lines (LCLs) from human, three other great apes, and rhesus macaque, producing the largest full-length isoform catalog in primates to date. Our transcriptomes reveal thousands of novel transcripts, some of them under active translation, expanding and completing the repertoire of primate gene models. Our comparative analyses unveil hundreds of transcriptomic innovations and isoform usage changes related to immune function and immunological disorders. The confluence of these innovations with signals of positive selection and their limited impact in the proteome points to changes in alternative splicing in genes involved in immune response as an important target of recent regulatory divergence in primates.
The genetic diversity of Ethiopian barley genotypes in relation to their geographical origin
Authors: Teklemariam Surafel Shibru , Bayissa Kefyalew Negisho , Matros Andrea , Pillen Klaus , Ordon Frank , Wehner Gwendolin
Published: November 2021

Ethiopia is recognized as a center of diversity for barley, and its landraces are known for the distinct genetic features compared to other barley collections. The genetic diversity of Ethiopian barley likely results from the highly diverse topography, altitude, climate conditions, soil types, and farming systems. To get detailed information on the genetic diversity a panel of 260 accessions, comprising 239 landraces and 21 barley breeding lines, obtained from the Ethiopian biodiversity institute (EBI) and the national barley improvement program, respectively were studied for their genetic diversity using the 50k iSelect single nucleotide polymorphism (SNP) array. A total of 983 highly informative SNP markers were used for structure and diversity analysis. Three genetically distinct clusters were obtained from the structure analysis comprising 80, 71, and 109 accessions, respectively. Analysis of molecular variance (AMOVA) revealed the presence of higher genetic variation (89%) within the clusters than between the clusters (11%), with moderate genetic differentiation (PhiPT=0.11) and adequate gene flow (Nm=2.02). The Mantel test revealed that the genetic distance between accessions is poorly associated with their geographical distance. Despite the observed weak correlation between geographic distance and genetic differentiation, for some regions like Gonder, Jimma, Gamo-Gofa, Shewa, and Welo, more than 50% of the landraces derived from these regions are assigned to one of the three clusters.
tRNA anticodon cleavage by target-activated CRISPR-Cas13a effector
Authors: Jain Ishita , Kolesnik Matvey , Minakhin Leonid , Morozova Natalia , Shiriaeva Anna , Kirillov Alexandr , Medvedeva Sofia , Kuznedelov Konstantin , Borukhov Sergei , Makarova Kira S. , Koonin Eugene V. , Severinov Konstantin , Semenova Ekaterina
Published: November 2021

Type VI CRISPR-Cas systems are the only CRISPR variety that cleaves exclusively RNA1,2. In addition to the CRISPR RNA (crRNA)-guided, sequence-specific binding and cleavage of target RNAs, such as phage transcripts, the type VI effector, Cas13, causes collateral RNA cleavage, which induces bacterial cell dormancy, thus protecting the host population from phage spread3,4. We show here that the principal form of collateral RNA degradation elicited by Cas13a protein from Leptotrichia shahii upon target RNA recognition is the cleavage of anticodons of multiple tRNA species, primarily those with anticodons containing uridines. This tRNA cleavage is necessary and sufficient for bacterial dormancy induction by Cas13a. In addition, Cas13a activates the RNases of bacterial toxin-antitoxin modules, thus indirectly causing mRNA and rRNA cleavage, which could provide a back-up defense mechanism. The identified mode of action of Cas13a resembles that of bacterial anticodon nucleases involved in antiphage defense5, which is compatible with the hypothesis that type VI effectors evolved from an abortive infection module6,7 encompassing an anticodon nuclease.
Experience-Expectant Plasticity in the Mushroom Bodies of the Honeybee
Authors: Fahrbach Susan E. , Moore Darrell , Capaldi Elizabeth A. , Farris Sarah M. , Robinson Gene E.
Published: November 2021

Worker honeybees (Apis mellifera) were reared in social isolation in complete darkness to assess the effects of experience on growth of the neuropil of the mushroom bodies (MBs) during adult life. Comparison of the volume of the MBs of 1-day-old and 7-day-old bees showed that a significant increase in volume in the MB neuropil occurred during the first week of life in bees reared under these highly deprived conditions. All regions of the MB neuropil experienced a significant increase in volume with the exception of the basal ring. Measurement of titers of juvenile hormone (JH) in a subset of bees indicated that, as in previous studies, these rearing conditions induced in some bees the endocrine state of high JH associated with foraging, but there was no correlation between JH titer and volume of MB neuropil. Treatment of another subset of dark-reared bees with the JH analog, methoprene, also had no effect of the growth of the MB neuropil. These results demonstrate that there is a phase of MB neuropil growth early in the adult life of bees that occurs independent of light or any form of social interaction. Together with previous findings showing that an increase in MB neuropil volume begins around the time that orientation flights occur and then continues throughout the phase of life devoted to foraging, these results suggest that growth of the MB neuropil in adult bees may have both experience-expectant and experience-dependent components.
Early Development of Mushroom Bodies in the Brain of the Honeybee Apis mellifera as Revealed by BrdU Incorporation and Ablation Experiments
Authors: Malun Dagmar
Published: November 2021

In the honeybee the mushroom bodies are prominent neuropil structures arranged as pairs in the dorsal protocerebrum of the brain. Each mushroom body is composed of a medial and a lateral subunit. To understand their development, the proliferation pattern of mushroom body intrinsic cells, the Kenyon cells, were examined during larval and pupal stages using the bromodeoxyuridine (BrdU) technique and chemical ablation with hydroxyurea.

By larval stage 1, ∼40 neuroblasts are located in the periphery of the protocerebrum. Many of these stem cells divide asymmetrically to produce a chain of ganglion mother cells. Kenyon cell precursors underly a different proliferation pattern. With the beginning of larval stage 3, they are arranged in two large distinct cell clusters in each side of the brain. BrdU incorporation into newly synthesized DNA and its immunohistochemical detection show high mitotic activity in these cell clusters that lasts until mid-pupal stages. The uniform diameter of cells, the homogeneous distribution of BrdU-labeled nuclei, and the presence of equally dividing cells in these clusters indicate symmetrical cell divisions of Kenyon cell precursors.

Hydroxyurea applied to stage 1 larvae caused the selective ablation of mushroom bodies. Within these animals a variety of defects were observed. In the majority of brains exhibiting mushroom body defects, either one mushroom body subunit on one or on both sides, or three or four subunits (e.g., complete mushroom body ablation) were missing. In contrast, partial ablation of mushroom body subunits resulting in small Kenyon cell clusters and peduncles was observed very rarely. These findings indicate that hydroxyurea applied during larval stage 1 selectively deletes Kenyon stem cells. The results also show that each mushroom body subunit originates from a very small number of stem cells and develops independently of its neighboring subunit.
Food Avoidance Learning in Squirrel Monkeys and Common Marmosets
Authors: Laska Matthias , Metzker Karin
Published: November 2021

Using a conditioned food avoidance learning paradigm, six squirrel monkeys (Saimiri sciureus) and six common marmosets (Callithrix jacchus) were tested for their ability to (1) reliably form associations between visual or olfactory cues of a potential food and its palatability and (2) remember such associations over prolonged periods of time. We found (1) that at the group level both species showed one-trial learning with the visual cues color and shape, whereas only the marmosets were able to do so with the olfactory cue, (2) that all individuals from both species learned to reliably avoid the unpalatable food items within 10 trials, (3) a tendency in both species for quicker acquisition of the association with the visual cues compared with the olfactory cue, (4) a tendency for quicker acquisition and higher reliability of the aversion by the marmosets compared with the squirrel monkeys, and (5) that all individuals from both species were able to reliably remember the significance of the visual cues, color and shape, even after 4 months, whereas only the marmosets showed retention of the significance of the olfactory cues for up to 4 weeks. Furthermore, the results suggest that in both species tested, illness is not a necessary prerequisite for food avoidance learning but that the presumably innate rejection responses toward highly concentrated but nontoxic bitter and sour tastants are sufficient to induce robust learning and retention.
Interactions between Depression and Facilitation within Neural Networks: Updating the Dual-Process Theory of Plasticity
Authors: Prescott Steven A.
Published: November 2021

Repetitive stimulation often results in habituation of the elicited response. However, if the stimulus is sufficiently strong, habituation may be preceded by transient sensitization or even replaced by enduring sensitization. In 1970, Groves and Thompson formulated the dual-process theory of plasticity to explain these characteristic behavioral changes on the basis of competition between decremental plasticity (depression) and incremental plasticity (facilitation) occurring within the neural network. Data from both vertebrate and invertebrate systems are reviewed and indicate that the effects of depression and facilitation are not exclusively additive but, rather, that those processes interact in a complex manner. Serial ordering of induction of learning, in which a depressing locus precedes the modulatory system responsible for inducing facilitation, causes the facilitation to wane. The parallel and/or serial expression of depression and waning facilitation within the stimulus–response pathway culminates in the behavioral changes that characterize dual-process learning. A mathematical model is presented to formally express and extend understanding of the interactions between depression and facilitation.
Conditioning Method Dramatically Alters the Role of Amygdala in Taste Aversion Learning
Authors: Schafe Glenn E. , Thiele Todd E. , Bernstein Ilene L.
Published: November 2021

Although an important role for the amygdala in taste aversion learning has been suggested by work in a number of laboratories, results have been inconsistent and interpretations varied. The present series of studies reevaluated the role of the amygdala in taste aversion learning by examining the extent to which conditioning methods, testing methods and lesioning methods, influence whether amygdala lesions dramatically affect conditioned taste aversion (CTA) learning. Results indicated that when animals are conditioned with an intraoral (I/O) taste presentation, lesions of amygdala eliminate evidence of conditioning whether animals are tested intraorally or with a two-bottle solution presentation. Dramatic effects of amygdala lesions on CTA learning were seen whether lesions were made electrolytically or using an excitotoxin. In contrast, when animals were conditioned using bottle presentation of the taste, electrolytic lesions attenuated CTAs but did not eliminate them, and excitotoxic lesions had no effect. These results are consistent with the hypothesis that neural structures critical for CTA learning may differ depending on the extent to which the method of conditioned stimulus delivery incorporates a response component.
Effects of Age on the Generalization and Incubation of Memory in the F344 Rat
Authors: Houston Frank P. , Stevenson Gail D. , McNaughton Bruce L. , Barnes Carol A.
Published: November 2021

Freezing (immobility) in the presence of aversive stimuli is a species-specific behavior that is used as an operational measure of fear. Conditioning of this response to discrete sensory stimuli and environmental context cues has been used as a tool to study the neuropsychology of memory dynamics and their development over the lifespan. Three age groups of F344 rats (3, 9, and 27 month) received tone–foot shock pairing (or tone only) in a distinctive chamber on two consecutive days. Separate subgroups of rats from each age group were then tested, at retention intervals of 1, 20, 40, or 60 days, for context-mediated fear in the environment in which they were trained, for generalization of the fear response to a novel chamber, and for fear of the tone. Beginning at day 20, the 27-month-old rats exhibited less freezing behavior than did younger rats when tested in the conditioning context. This age difference was a result of freezing behavior becoming progressively stronger with time in the two younger age groups, a phenomenon that has been referred to as memory incubation. Incubation of the contextual fear response was not detected in the old rats. In a novel context, all age groups exhibited significantly more freezing than did control animals. There was also pronounced incubation of this generalized freezing response, and the extent of incubation declined significantly with age. In the novel context, the freezing response to the tone was robust in all age groups and increased over time, in constant proportion to the degree of freezing elicited by the novel context itself, prior to tone onset. The fact that old animals are known to be relatively selectively impaired in forms of memory that depend on a functional hippocampus suggests a possible explanation for the reduced incubation effects seen in old rats; however, whether the increased expression of fear over time is mediated by a hippocampal-dependent memory consolidation process or whether it reflects a generalized increase in the gain of the circuitry mediating the fear response itself, remains to be determined.
Activity-Dependent Activation of TrkB Neurotrophin Receptors in the Adult CNS
Authors: Aloyz Raquel , Fawcett James P. , Kaplan David R. , Murphy Richard A. , Miller Freda D.
Published: November 2021

In this paper we have investigated the hypothesis that neural activity causes rapid activation of TrkB neurotrophin receptors in the adult mammalian CNS. These studies demonstrate that kainic acid-induced seizures led to a rapid and transient activation of TrkB receptors in the cortex. Subcellular fractionation demonstrated that these activated Trk receptors were preferentially enriched in the synaptosomal membrane fraction that also contained postsynaptic glutamate receptors. The fast activation of synaptic TrkB receptors could be duplicated in isolated cortical synaptosomes with KCl, presumably as a consequence of depolarization-induced BDNF release. Importantly, TrkB activation was also observed following pharmacological activation of brain-stem noradrenergic neurons, which synthesize and anterogradely transport BDNF; treatment with yohimbine led to activation of cortical TrkB receptors within 30 min. Pharmacological blockade of the postsynaptic α1-adrenergic receptors with prazosin only partially inhibited this effect, suggesting that the TrkB activation was partially due to a direct effect on postsynaptic cortical neurons. Together, these data support the hypothesis that activity causes release of BDNF from presynaptic terminals, resulting in a rapid activation of postsynaptic TrkB receptors. This activity-dependent TrkB activation could play a major role in morphological growth and remodelling in both the developing and mature nervous systems.