bluuebunny/crossref_metadata_2025 huggingface dataset:
Trends Related to Evidence-Based Dietetic Practice Among Dietitians With Varying Levels of Education and Experience
Authors: Van Horn Leslie Thompson , Wright Lauri
Published: March 2022

This qualitative study evaluates registered dietitian nutritionists' (RDNs) use of evidence-based dietetic practices (EBDPs) by education level and years of experience. Interviews were conducted with bachelor's and master's-trained RDNs (n = 9). The following themes regarding EBDP were identified: (1) resources utilized, (2) personal utilization and perceptions, (3) barriers and areas for improvement, and (4) collaboration. It was noted that master's-trained RDNs were more knowledgeable regarding EBDP resources. While it was reported that EBDP had improved with experience, those further from their didactic training had less awareness of EBDP resources. Continuing education should aim to bridge this gap in knowledge among RDNs.
Utility of Functional MRI and Magnetoencephalography in the Diagnosis of Infantile Spasms and Hypsarrhythmia
Authors: Coan Ana Carolina , Cavalcante Charlington M. , Burgess Richard C.
Published: March 2022

Neuroimaging and neurophysiology techniques can add a significant contribution to the comprehension of infantile spasms (IS) and hypsarrhythmia. Functional MRI and magnetoencephalography (MEG) are two noninvasive tools that can be used in young children with IS. In the past two decades, interesting data about IS have emerged from functional MRI and MEG studies. Regarding their clinical utility, MEG has supported the concept that epileptic spasms can have a focal origin. Moreover, MEG might contribute to the localization of the epileptogenic zone in children with IS under investigation for epilepsy surgery. Functional MRI data have contributed to improve the knowledge about the physiopathology of IS and hypsarrhythmia. It has demonstrated abnormal brainstem involvement during the high-amplitude slow waves of hypsarrhythmia and cortical involvement during the epileptiform discharges. Since the feasibility of these techniques has been demonstrated in infants, it is possible that, in the future, larger functional MRI and MEG studies might contribute to the treatment and the definition of the long-term prognosis of children with IS.
LncRNA Malat1 represses Th17 effector program by maintaining a critical bivalent super-enhancer and promotes intestinal inflammation
Authors: Ma Shengyun , Zhou Bing , Abe Yohei , Chen Nicholas , Luo Claire , Zheng Anna , Li Yuxin , Patel Parth R. , Patel Shefali A. , Hao Yajing , Chang John T. , Fu Xiang-Dong , Huang Wendy Jia Men
Published: March 2022

Interleukin IL-17 cytokines are central regulators of mucosal homeostasis and disease. In mouse models of colonic tissue injury, IL-17A promotes epithelial barrier functions and restricts local inflammation. Here, we report that IL-17A production by the diverse T lymphocyte subsets is dynamically regulated at different stages of colitis pathogenesis. During the onset and peak of the disease, Tγδ17 cells are the major IL-17A producers, while Th17 activity is temporally restricted by long non-coding RNA (lncRNA) Malat1. In response to IL-6 and TGFβ signaling, Malat1 is recruited to the Th17-specific cis-regulatory elements, CNS3 and CNS4, of the Il17a locus to fine-tune bivalent super-enhancer activities and repress local transcription. During the resolution phase of inflammation, Malat1 expression is down-regulated to enhance Th17 activities, allowing Th17 cells to emerge as the main producers of IL-17A in the colonic lamina propria. Genetic ablation of Malat1 potentiates IL-17A production in Th17 cells and improves disease outcomes in mouse models of colitis. These findings uncover a surprising role of a chromatin-associated lncRNA in regulating colonic Th17-specific responses to control the timing of inflammation resolution.

Significance Statement

T cells are critical modulators of mucosal barrier function and inflammation. The function of long-noncoding RNAs (lncRNAs) in T cells and their role in mucosal inflammation remain elusive. Here, we identify an essential role of the lncRNA Malat1 restricting transcription of the Il17a locus in Th17 cells encoding a cytokine implicated in epithelial barrier function post-injury. By controlling the activity of the bivalent super-enhancer at the Il17a locus, Malat1 regulates the timing of inflammation resolution in the intestine. The Malat1-Il17a pathway reveals new targets for combating mucosal diseases.

Graphic Abstract
REVERSE: A user-friendly web server for analyzing next-generation sequencing data from in vitro selection/evolution experiments
Authors: Weiss Zoe , DasGupta Saurja
Published: March 2022

Next-generation sequencing (NGS) enables the identification of functional nucleic acid sequences from in vitro selection/evolution experiments and illuminates the evolutionary process at single nucleotide resolution. However, analyzing the vast output from NGS can be daunting, especially with limited programming skills. No single platform exists that performs all the steps necessary to generate publishable results starting with raw sequence data. We developed REVERSE (Rapid EValuation of Experimental RNA Selection/Evolution) (https://www.reverseserver.org/), a web server that incorporates an integrated computational pipeline through a graphical user interface, which performs both pre-processing and sequence level analyses within minutes. FASTQ files from multiple rounds are quality filtered, dereplicated, and trimmed before being analyzed by two pipelines. The first pipeline counts, sorts, and tracks enrichment of unique sequences and tracks the enrichment of sequence motifs. It also identifies mutational intermediates present in the sequence data that connect two input sequences. The second pipeline sorts similar sequences into clusters and tracks enrichment of peak sequences. It also performs nucleotide conservation analysis on the cluster of choice. Both pipelines generate downloadable high-resolution figures. Collectively, REVERSE is a one stop-solution for the rapid analysis of NGS data obtained from in vitro selection/evolution experiments that obviates the need for computational expertise.
Neuronal temperature perception induces specific defenses that enable C. elegans to cope with the enhanced reactivity of hydrogen peroxide at high temperature
Authors: Servello Francesco A. , Fernandes Rute , Eder Matthias , Harris Nathan , Martin Olivier M. F. , Oswal Natasha , Lindberg Anders , Derosiers Nohelly , Sengupta Piali , Stroustrup Nicholas , Apfeld Javier
Published: March 2022

Hydrogen peroxide is the most common reactive chemical that organisms face on the microbial battlefield. The rate with which hydrogen peroxide damages biomolecules required for life increases with temperature, yet little is known about how organisms cope with this temperature-dependent threat. Here, we show that Caenorhabditis elegans nematodes use temperature information perceived by sensory neurons to cope with the temperature-dependent threat of hydrogen peroxide produced by the pathogenic bacterium Enterococcus faecium. These nematodes preemptively induce the expression of specific hydrogen peroxide defenses in response to perception of high temperature by a pair of sensory neurons. These neurons communicate temperature information to target tissues expressing those defenses via an insulin/IGF1 hormone. This strategy, which we call “enhancer sensing,” is the first example of a multicellular organism inducing their defenses to a chemical when they sense an inherent enhancer of the reactivity of that chemical.
Multi-finger Receptive Field Properties in Primary Somatosensory Cortex: A Revised Account of the Spatio-Temporal Integration Functions of Area 3b
Authors: Trzcinski Natalie K. , Hsiao S.S. , Connor Charles E. , Gomez-Ramirez Manuel
Published: March 2022

Abstract

The leading view in the somatosensory system indicates that area 3b serves as a cortical relay site that encodes cutaneous (tactile) features limited to individual digits. Our recent work argues against this model by showing that cells in area 3b integrate information from cutaneous and proprioceptive modalities. Here, we further test this model, by studying the multi-finger neural integration properties of area 3b. In contrast to the prevailing view, we found that most cells in area 3b have a receptive field (RF) that extends to multiple digits. Responses to tactile stimulation emerged earlier in cells with a multi-digit (MD) vs. single-digit (SD) RF. We also found that the RF size of MD cells (the number of responsive digits) increased across time, and the orientation preference across digits was highly correlated. Taken together, these data provide strong evidence that area 3b plays a larger role in generating neural representations of tactile objects, as opposed to just being a ‘feature detector’ relay site.
DCATS: differential composition analysis for complex single-cell experimental designs
Authors: Lin Xinyi , Chau Chuen , Huang Yuanhua , Ho Joshua W.K.
Published: March 2022

Differential composition analysis – the identification of cell types that have statistically significantly change in abundance between multiple experimental conditions – is one of the most common tasks in single cell omic data analysis. However, it remains challenging to perform differential composition analysis in the presence of complex experimental designs and uncertainty in cell type assignment. Here, we introduce a statistical model and an open source R package, DCATS, for differential composition analysis based on a beta-binomial regression framework that addresses these challenges. Our empirical evaluation shows that DCATS consistently maintain high sensitively and specificity compared to state-of-the-art methods.
Persistence of rareSalmonellaTyphi genotypes susceptible to first-line antibiotics in the remote islands of Samoa
Authors: Sikorski Michael J. , Hazen Tracy H. , Desai Sachin N. , Nimarota-Brown Susana , Tupua Siaosi , Sialeipata Michelle , Rambocus Savitra , Ingle Danielle J. , Duchene Sebastian , Ballard Susan A. , Valcanis Mary , Zufan Sara , Ma Jianguo , Sahl Jason W. , Maes Mailis , Dougan Gordon , Thomsen Robert E. , Robins-Browne Roy M. , Howden Benjamin P. , Naseri Take K. , Levine Myron M. , Rasko David A.
Published: March 2022

For decades, the remote island nation of Samoa (pop. ~200,000) has faced endemic typhoid fever despite improvements in water quality, sanitation, and economic development. We recently described the epidemiology of typhoid fever in Samoa from 2008-2019 by person, place, and time; however, the localSalmonella entericaserovar Typhi (S.Typhi) population structure, evolutionary origins, and genomic features remained unknown. Herein, we report whole genome sequence analyses of 306S.Typhi isolates from Samoa collected between 1983 and 2020. Phylogenetics revealed a dominant population of rare genotypes 3.5.4 and 3.5.3, together comprising 292/306 (95.4%) of Samoan versus 2/4934 (0.04%) globalS.Typhi isolates. Three distinct 3.5.4 genomic sub-lineages were identified and their defining polymorphisms were determined. These dominant Samoan genotypes, which likely emerged in the 1970s, share ancestry with other clade 3.5 isolates from South America, Southeast Asia, and Oceania. Additionally, a 106-kb pHCM2 phenotypically-cryptic plasmid, detected earliest in a 1992 SamoanS.Typhi isolate, was identified in 106/306 (34.6%) of Samoan isolates; this is more than double the observed proportion of pHCM2-containing isolates in the global collection. In stark contrast with globalS.Typhi trends, resistance-conferring polymorphisms were detected in only 15/306 (4.9%) of SamoanS.Typhi, indicating overwhelming susceptibility to antibiotics that are no longer effective in most of South and Southeast Asia. This country-level genomic framework can help local health authorities in their ongoing typhoid surveillance and control efforts, as well as to fill a critical knowledge gap inS.Typhi genomic data from Oceania.

IMPORTANCE

In this study we used whole genome sequencing and comparative genomics analyses to characterize the population structure, evolutionary origins, and genomic features ofS.Typhi associated with decades of endemic typhoid fever in Samoa. Our analyses of Samoan isolates from 1983 to 2020 identified a rareS.Typhi population in Samoa that likely emerged around the early 1970s and evolved into sub-lineages that presently dominate. The dominance and persistence of these endemic genotypes in Samoa are not readily explained by any apparent genomic competitive advantage or widespread acquisition of antimicrobial resistance. These data establish the necessary framework for future genomic surveillance ofS.Typhi in Samoa for public health benefit.
Ventricular and Atrial Pressure-Volume Loops: Analysis of the Effects Induced by Right Centrifugal Pump Assistance
Authors: De Lazzari Beatrice , Iacovoni Attilio , Capoccia Massimo , Papa Silvia , Badagliacca Roberto , Vizza Carmine Dario , De Lazzari Claudio
Published: March 2022

Background and Objective

The main indications for right ventricular assist device (RVAD) support are right heart failure after implantation of a left ventricular assist device (LVAD) or early graft failure following heart transplantation. About 30-40% of patients will need RVAD support after LVAD implantation. Pulmonary hypertension is also an indication for right heart assistance. Several types of RVAD generating pulsatile or continuous flow are available on the market. These assist devices can be connected to the cardiovascular system in different ways. We sought to analyse the effects induced by different RVAD connections when right ventricular elastance is modified using a numerical simulator. The analysis was based on the behaviour of both left and right ventricular and atrial loops in the pressure-volume plane.

Methods

New modules of the cardiovascular network and a right ventricular centrifugal pump were implemented in CARDIOSIM© software simulator platform. The numerical pump model generated continuous flow when connected in series or parallel to the right ventricle. When the RVAD was connected in series (parallel), the pump removed blood from the right ventricle (atrium) and ejected it into the pulmonary artery. In our study, we analysed the effects induced by RVAD support on left/right ventricular/atrial loops when right ventricular elastance slope (EesRIGHT) changed from 0.3 to 0.8 mmHg/ml with the pump connected either in series or parallel. The effect of low and high rotational pump speed was also addressed.

Results

Percentage changes up to 60% were observed for left ventricular pressure-volume area and external work during in-parallel RVAD support at 4000 rpm with EesRIGHT = 0.3mmHg/ml. The same pump setting and connection type led to percentage variation up to 20% for left ventricular ESV and up to 25% for left ventricular EDV with EesRIGHT = 0.3mmHg/ml. Again the same pump setting and connection generated up to 50% change in left atrial pressure-volume loop area (PVLAL-A) and only 3% change in right atrial pressure-volume loop area (PVLAR-A) when EesRIGHT = 0.3mmHg/ml. Percentage variation was lower when EesRIGHT was increased up to 0.8 mmHg/ml.

Conclusion

Early recognition of right ventricular failure followed by aggressive treatment is desirable to achieve a more favourable outcome. RVAD support remains an option for advanced right ventricular failure although onset of major adverse events may preclude its use.
Single cell Transcriptome and T cell Repertoire Mapping of the Mechanistic Signatures and T cell Trajectories Contributing to Vascular and Dermal Manifestations of Behcet’s Disease
Authors: Chang Ling , Zheng Zihan , Zou Qinghua , Zhong Bing , Chen Chengshun , Cheng Xian , Ni Qingshan , Che Tiantian , Zhao Zhihua , Cao Chunhao , Zhou Yiwen , Tang Xiangyu , Zhai Zhifang , Zhao Jing , Zhang Junying , Wang Liting , Wan Ying , Chen Guangxing , Li Jingyi , Zou Liyun , Wu Yuzhang
Published: March 2022

Behcet’s disease (BD) is a form of vasculitis characterized by complex multi-organ manifestations that may frequently recur and induce major tissue damage. Although genetic association studies have identified a number of risk factors, the etiology of BD and its tissue manifestations remains unknown, and the landscape of immune responses in BD is opaque, particularly in terms of inflammatory recurrence. In this study, we mapped the transcriptomes of the immune cell compartment in BD at single-cell resolution, sampling both circulation and affected skin in order to chart the immune interplay driving pathogenesis. Through comprehensive expression and communication analysis of the twenty major cell types identified, we observe striking mechanistic differences in immune response between BD skin lesions and peripheral circulation involving TNF signaling and T cell migration. Through integrated TCR sequencing, we further discover a pattern of clonal sharing between circulating and skin CD8+T cell populations along a trajectory defined by the acquisition of tissue-residential properties. In addition, we also identify a population of expanded CD4+ Tregs with the propensity to produce IL-32. Instead of suppressing effector T cell proliferation and function, IL-32 triggers increased expression of CD97, and may thus encourage prolonged local T cell activity in the skin. Collectively, our data serve to advance understandings of contributions of varying immune cell types to BD pathogenesis in the vasculature and skin, as well as the lifecycle patterns of T cells clones in this context. These data may also assist in further investigations of the mechanisms contributing to Treg dysfunction in systemic autoimmunity, while generating a conceptual model of T cell function contributing to BD recurrence.
scMAGS: Marker gene selection from scRNA-seq data for spatial transcriptomics studies
Authors: Baran Yusuf , Doğan Berat
Published: March 2022

Single-Cell RNA sequencing (scRNA-seq) has provided unprecedented opportunities for exploring gene expression and thus uncovering regulatory relationships between genes at the single cell level. However, scRNA-seq relies on isolating cells from tissues. Thus, the spatial context of the regulatory processes is lost. A recent technological innovation, spatial transcriptomics, allows to measure gene expression while preserving spatial information. A first step in the spatial transcriptomic analysis is to identify the cell type which requires a careful selection of cell-specific marker genes. For this purpose, currently scRNA-seq data is used to select limited number of marker genes from among all genes that distinguish cell types from each other. This study proposes scMAGS (single-cell MArker Gene Selection), a new approach for marker gene selection from scRNA-seq data for spatial transcriptomics studies. scMAGS uses a filtering step in which the candidate genes are extracted prior to the marker gene selection step. For the selection of marker genes, cluster validity indices, Silhouette index or Calinski-Harabasz index (for large datasets) are utilized. Experimental results showed that, in comparison to the existing methods, scMAGS is scalable, fast and accurate. Even for the large datasets with millions of cells, scMAGS could find the required number of marker genes in a reasonable amount of time with less memory requirements.
Density-dependent attributes of schooling in small pelagic fishes
Authors: Furuichi Sho , Kamimura Yasuhiro , Suzuki Masahiro , Yukami Ryuji
Published: March 2022

Many small pelagic fishes obligately form schools; some of these schools attain a remarkable size. Although the school is a fundamental and important ecological unit and is the site of biological interactions such as competition and predation, information on schooling processes in the field remains scarce. Here, we examined the quantitative relationships between population density and school size, the number of schools, and other school characteristics (i.e., packing density, volume, and cross-sectional area) in three species of small pelagic fishes: Japanese anchovyEngraulis japonicus, Japanese sardineSardinops melanostictus, and chub mackerelScomber japonicus. We found that school size increased almost linearly with population density, whereas the number of schools and other characteristics increased non-linearly with population density, whereby the rate of increase slowed radically as population density increased. These results indicate that, at low population densities, an increase in density causes an increase in both school size and the number of schools, whereas at higher population densities, an increase in density triggers the formation of larger schools rather than more schools. Furthermore, we found that the shapes of the relationships of all school characteristics with population density differed among species. Our results indicate that the schooling behaviour of small pelagic fishes is density-dependent, and responses to changes in density are species-specific. Our results provide insight into how biological interactions such as intra- and inter-specific competition and predator-prey interactions mediate the density-dependent processes that underlie the population dynamics and community structure of small pelagic fishes in marine ecosystems.
Occurrence and quantities of DNA modifications across the tree of life
Authors: Varma Sreejith Jayasree , Calvani Enrica , Grüning Nana-Maria , Messner Christoph , Grayson Nicholas , Capuano Floriana , Mülleder Michael , Ralser Markus
Published: March 2022

Enzymatic DNA modifications like methylcytosine (5mdC), methyladenine (N6mdA), or hydroxymethylcytosine (5hmdC) are key for chromatin function, gene expression regulation, and antiviral defense, but they remain understudied in non-model organisms. We established a mass spectrometric method for the sensitive and accurate quantification of enzymatic DNA modifications, and analyzed 85 bacterial genomes, 19 plant samples, 41 tissues from 12 animal species, 6 yeast species, and two archaeal species. We report no or only very low concentrations of DNA modifications in yeast and insects, but find DNA modifications universal to both bacteria and higher eukaryotes. Specifically for prokaryotes, our dataset indicates that evolutionary relationships and host–pathogen interactions, but not the ecological niche in general, select for a similar degree of DNA modification. In higher eukaryotes, largest concentration differences between tissues are detected for 5hmdC. Our dataset further reveals unique biological cases that warrant attention in the study of DNA modifications. For instance, while our data shows that most species contain just one dominating DNA modification, we detect all dominianting DNA modifications (5mdC, N6mdA, and 5hmdC) to exist in parallel in Raphanus sativus. Other plant species, like onion, sunflower, or the grass big bluestem, can have more than 35% of cytosines methylated. Finally, 5hmdC, so far mostly studied in the vertebrate central nervous system, was identified to reach a concentration of up to 8% of all cytosines in the Oman garra brain, and was also detected in several plants, like Lepidium sativum. The present study underscores the exploitation of biological diversity for studying DNA modifications.
Strain design optimization using reinforcement learning
Authors: Sabzevari Maryam , Szedmak Sandor , Penttilä Merja , Jouhten Paula , Rousu Juho
Published: March 2022

Engineered microbial cells present a sustainable alternative to fossil-based synthesis of chemicals and fuels. Cellular synthesis routes are readily assembled and introduced into microbial strains using state-of-the-art synthetic biology tools. However, the optimization of the strains required to reach industrially feasible production levels is far less efficient. It typically relies on trial-and-error leading into high uncertainty in total duration and cost. New techniques that can cope with the complexity and limited mechanistic knowledge of the cellular regulation are called for guiding the strain optimization.

In this paper, we put forward a multi-agent reinforcement learning (MARL) approach that learns from experiments to tune the metabolic enzyme levels so that the production is improved. Our method is model-free and does not assume prior knowledge of the microbe’s metabolic network or its regulation. The multi-agent approach is well-suited to make use of parallel experiments such as multi-well plates commonly used for screening microbial strains.

We demonstrate the method’s capabilities using the genome-scale kinetic model of Escherichia coli, k-ecoli457, as a surrogate for an in vivo cell behaviour in cultivation experiments. We investigate the method’s performance relevant for practical applicability in strain engineering i.e. the speed of convergence towards the optimum response, noise tolerance, and the statistical stability of the solutions found. We further evaluate the proposed MARL approach in improving L-tryptophan production by yeast Saccharomyces cerevisiae, using publicly available experimental data on the performance of a combinatorial strain library.

Overall, our results show that multi-agent reinforcement learning is a promising approach for guiding the strain optimization beyond mechanistic knowledge, with the goal of faster and more reliably obtaining industrially attractive production levels.

Author summary

Engineered microbial cells offer a sustainable alternative solution to chemical production from fossil resources. However, to make the chemical production using microbial cells economically feasible, they need to be substantially optimized. Due to the biological complexity, this optimization to reach sufficiently high production is typically a costly trial and error process.

This paper presents an Artificial Intelligence (AI) approach to guide this task. Our tool learns a model from previous experiments and uses the model to suggest improvements to the engineering design, until a satisfactory production performance is reached. This paper evaluates the behaviour of the proposed AI method from several angles, including the amount of experiments needed, the tolerance to noise as well as the stability of the proposed designs.
Phenology of plant reproduction, foliar infection, and herbivory change along an urbanization gradient
Authors: Fox Quinn N. , Bugay Mahal J. , Grant Eleanor , Shaw Olivia , Farah Keiko , Penczykowski Rachel M.
Published: March 2022

Urbanization involves numerous environmental changes that may affect the timing of plant reproduction and foliar damage by pathogens, herbivores, and human activities. Yet such relationships have not been examined simultaneously in plant populations across levels of urbanization.

We conducted monthly surveys of 22 populations ofPlantago lanceolataandP. rugeliiin parks spanning an urbanization gradient. We quantified plant reproductive development and prevalence of powdery mildew infection, insect herbivory, and mowing damage. Additionally, we placed potted “sentinel” plants into field populations to directly measure infection and herbivory rates.

Urbanization was associated with earlier flowering and more seed production forP. rugelii, but less seed maturation forP. lanceolata. Mildew epidemics onP. rugeliistarted earlier and achieved greater prevalence in more urban sites. Correspondingly, sentinels only became infected in suburban and urban sites. There was less infection onP. lanceolata, including sentinels, suggesting low availability of pathogen genotypes able to infect this species. Early-summer herbivory on both plant species was accelerated in urban sites.

Urbanization has species-specific associations with reproductive phenology and is associated with increased early-summer herbivory, larger epidemics of a foliar pathogen, and more mowing damage on two weedy herbs
Modulation of the DA1 pathway in maize shows that translatability of information from Arabidopsis to crops is complex
Authors: Gong Pan , Demuynck Kirin , De Block Jolien , Aesaert Stijn , Coussens Griet , Pauwels Laurens , Inzé Dirk , Nelissen Hilde
Published: March 2022

Modern agriculture is struggling to meet the increasing food, silage and raw material demands due to the rapid growth of population and climate change. In Arabidopsis, DA1 and DAR1 are proteases that negatively regulate cell proliferation and control organ size. DA1 and DAR1 are activated by ubiquitination catalyzed by the E3 ligase BIG BROTHER (BB). Here, we characterized the DA1, DAR 1 and BB gene families in maize and analyzed whether perturbation of these genes regulates organ size similar to what was observed in Arabidopsis. We generated da1_dar1a_dar1b triple CRISPR maize mutants and bb1_bb2 double mutants. Detailed phenotypic analysis showed that the size of leaf, stem, cob, and seed was not consistently enlarged in these mutants. Also overexpression of a dominant-negative DA1R333K allele, resembling the da1-1 allele of Arabidopsis which has larger leaves and seeds, did not alter the maize phenotype. The mild negative effects on plant height of the DA1R333K_bb1_bb2 mutant indicate that the genes in the DA1 pathway may control organ size in maize, albeit less obvious than in Arabidopsis.
An Orobanche cernua x Orobanche cumana segregating population provides insight into the regulation of germination specificity in a parasitic plant
Authors: Larose Hailey , Plakhine Dina , Wycoff Nathan , Zhang Na , Conn Caitlin , Nelson David C. , Eizenberg Hanan , Joel Daniel M. , Tadmor Yaakov , Westwood James H.
Published: March 2022

Germination of seeds of Orobanche species requires specific chemicals exuded by host roots. A family of “divergent” KARRIKIN INSENSITIVE2 (KAI2d) genes encode proteins that recognize strigolactone (SL) class germination simulants. We explored specificity of germination stimulant detection by analyzing interspecific segregants of a cross between Orobanche cernua and O. cumana, closely related species that differ in stimulant response. O. cernua parasitizes tomato and germinates in response to the SL orobanchol, while O. cumana parasitizes sunflower and responds to dehydrocostus lactone (DCL). KAI2d genes were catalogued in parents and in segregants that showed stimulant specificity. KAI2d genes were also functionally assayed in the Arabidopsis kai2 mutant background. We identified five full-length KAI2d genes in O. cernua and eight in O. cumana. The O. cernua KAI2d2, as well as its ortholog in O. cumana, are associated with SL perception. A cluster of O. cumana KAI2d genes was genetically linked to DCL perception, although no specific receptor gene was identified by heterologous complementation. These findings support the KAI2d-mediated perception of SLs, but fall short of explaining how O. cumana perceives DCL. The ability of some O. cumana KAI2d genes to detect SLs points to the involvement of additional factors in regulating stimulant specificity.
Recovering false negatives in CRISPR fitness screens with JLOE
Authors: Dede Merve , Hart Traver
Published: March 2022

It is widely accepted that pooled library CRISPR knockout screens offer greater sensitivity and specificity than prior technologies in detecting genes whose disruption leads to fitness defects, a critical step in identifying candidate cancer targets. However, the assumption that CRISPR screens are saturating has been largely untested. Through integrated analysis of screen data in cancer cell lines generated by the Cancer Dependency Map, we show that a typical CRISPR screen has a ∼20% false negative rate, in addition to library-specific false negatives. Replicability falls sharply as gene expression decreases, while cancer subtype-specific genes within a tissue show distinct profiles compared to false negatives. Cumulative analyses across tissues improves our understanding of core essential genes and suggest only a small number of lineage-specific essential genes, enriched for transcription factors that define pathways of tissue differentiation. To recover false negatives, we introduce a method, Joint Log Odds of Essentiality (JLOE), which builds on our prior work with BAGEL to selectively rescue the false negatives without an increased false discovery rate.
Dampened inflammatory signalling and myeloid-derived suppressor-like cell accumulation reduces circulating monocytic HLA-DR density and associates with malignancy risk in long-term renal transplant recipients
Authors: Bottomley Matthew J , Harden Paul N , Wood Kathryn J , Hester Joanna , Issa Fadi
Published: March 2022

Background

Malignancy is a major cause of morbidity and mortality in transplant recipients. Identification of those at highest risk could facilitate pre-emptive intervention such as reduction of immunosuppression. Reduced circulating monocytic HLA-DR density is a marker of immune depression in the general population and associates with poorer outcome in critical illness. It has recently been used as a safety marker in adoptive cell therapy trials in renal transplantation. Despite its potential as a marker of dampened immune responses, factors that impact upon monocytic HLA-DR density and the long-term clinical sequelae of this have not been assessed in transplant recipients.

Methods

A cohort study of stable long-term renal transplant recipients was undertaken. Serial circulating monocytic HLA-DR density and other leucocyte populations were quantified by flow cytometry. Gene expression of monocytes was performed using the Nanostring nCounter platform, and 13-plex cytokine bead array used to quantify serum concentrations. The primary outcome was malignancy development during one-year follow-up. Risk of malignancy was calculated by univariate and multivariate proportionate hazards modelling with and without adjustment for competing risks.

Results

Monocytic HLA-DR density was stable in long-term renal transplant recipients (n=135) and similar to non-immunosuppressed controls (n=29), though was suppressed in recipients receiving prednisolone. Decreased mHLA-DRd was associated with accumulation of CD14+CD11b+CD33+HLA-DRlo monocytic myeloid-derived suppressor-like cells. Pathway analysis revealed downregulation of pathways relating to cytokine and chemokine signalling in monocytes with low HLA-DR density; however serum concentrations of major cytokines did not differ between these groups. There was an independent increase in malignancy risk during follow-up with decreased HLA-DR density.

Conclusions

Dampened chemokine and cytokine signalling drives a stable reduction in monocytic HLA-DR density in long-term transplant recipients and associates with subsequent malignancy risk. This may function as a novel marker of excess immunosuppression. Further study is needed to understand the mechanism behind this association.
Elevated T-cell exhaustion and urinary tumor DNA levels are associated with BCG failure in patients with non-muscle invasive bladder cancer
Authors: Strandgaard Trine , Lindskrog Sia Viborg , Nordentoft Iver , Christensen Emil , Birkenkamp-Demtröder Karin , Andreasen Tine Ginnerup , Lamy Philippe , Kjær Asbjørn , Ranti Daniel , Wang Yuan-Sho , Bieber Christine , Prip Frederik , Rasmussen Julie , Steiniche Torben , Birkbak Nicolai , Sfakianos John , Horowitz Amir , Jensen Jørgen Bjerggaard , Dyrskjøt Lars
Published: March 2022

Background

The functional status of immune cells within the tumor microenvironment and tumor characteristics may explain Bacillus Calmette-Guérin (BCG)-failure in high-risk non-muscle invasive bladder cancer (NMIBC).

Objective

To characterize molecular correlates of BCG-failure using a multiomics approach.

Design, Setting, and Participants

BCG-treated NMIBC patients (n=156) were included. Metachronous tumors were analyzed using RNA-sequencing (n=170) and whole exome sequencing (n=198). Urine samples were analyzed for immune-oncology related proteins (n=190), and tumor-derived DNA (tdDNA; n=192).

Outcome Measurement and Statistical Analysis

Primary endpoint was BCG-failure. Cox regression, Wilcoxon Rank Sum test, t-test or Fisher’s exact test were used.

Results and Limitations

BCG caused activation of the immune system regardless of clinical response; however, immune-inhibitory proteins were observed in the urine of BCG-unresponsive patients post-treatment (CD70, PD1, CD5). BCG-failure was associated with post-BCG T-cell exhaustion (p=0.0021). Pre-BCG tumors from patients with post-BCG T-cell exhaustion were characterized by high expression of cell division and immune-related genes. A high post-BCG exhaustion prediction score in pre-BCG tumors was associated with worse post-BCG high-grade recurrence free survival (HGRFS), reflecting BCG-failure (p=0.0084). Pre-BCG tumors of class 2a and 2b were likewise associated with worse post-BCG HGRFS(p=0.0023). Post-BCG exhaustion was observed in patients with high pre-BCG neoantigen load (p=0.023) and mutations in MUC4 (p=0.0007). Finally, absence of post-BCG tdDNA clearance identified patients at high risk of recurrence (p=0.028). The retrospective design, lack of maintenance BCG, and partial overlap in analyses are limitations to the study.

Conclusions

BCG failure may be caused by T-cell exhaustion. Tumor subtype and Pre-BCG tumor characteristics may identify patients at high risk of BCG-failure prior to treatment. Urinary measurements have the potential to be used as a real-time assessment of treatment response.

Patient Summary

A dysfunctional immune response to BCG therapy may explain lack of response to the treatment.
Proof-of-concept: SCENTinel 1.1 rapidly discriminates COVID-19 related olfactory disorders
Authors: Hunter Stephanie R. , Hannum Mackenzie E. , Pellegrino Robert , O’Leary Maureen A. , Rawson Nancy E. , Reed Danielle R. , Dalton Pamela H. , Parma Valentina
Published: March 2022

It is estimated that 20-67% of those with COVID-19 develop olfactory disorders, depending on the SARS-CoV-2 variant. However, there is an absence of quick, population-wide olfactory tests to screen for olfactory disorders. The purpose of this study was to provide a proof-of-concept that SCENTinel 1.1, a rapid, inexpensive, population-wide olfactory test, can discriminate between anosmia (total smell loss), hyposmia (reduced sense of smell), parosmia (distorted odor perception), and phantosmia (odor sensation without a source). Participants were mailed a SCENTinel 1.1 test, which measures odor detection, intensity, identification, and pleasantness, using one of four possible odors. Those who completed the test (N = 381) were divided into groups based on their self-reported olfactory function: quantitative olfactory disorder (anosmia or hyposmia, N = 135), qualitative olfactory disorder (parosmia and/or phantosmia; N = 86), and normosmia (normal sense of smell; N = 66). SCENTinel 1.1 accurately discriminates quantitative olfactory disorders, qualitative olfactory disorders, and normosmia groups. When olfactory disorders were assessed individually, SCENTinel 1.1 discriminates between hyposmia, parosmia and anosmia. Participants with parosmia rated common odors less pleasant than those without parosmia. We provide proof-of-concept that SCENTinel 1.1, a rapid smell test, can discriminate quantitative and qualitative olfactory disorders, and is the only direct test to rapidly discriminate parosmia.
Association of COVID-19 with risks of hospitalization and mortality from other disorders post-infection: A study of the UK Biobank
Authors: Xiang Yong , Zhang Ruoyu , Qiu Jinghong , So Hon-Cheong
Published: March 2022

Objective

To study whether COVID-19 infection may be associated with increased hospitalization and mortality from other diseases.

Design

Cohort study.

Setting

The UK Biobank.

Participants

All subjects in the UK Biobank with available hospitalization records and alive as of 31-Jan-2020 (N= 412,096; age 50-87).

Main outcome measures

We investigated associations of COVID-19 with hospitalization and mortality due to different diseases post-infection. We conducted a comprehensive survey on disorders from all systems (up to 135 disease categories). Multivariable Cox and Poisson regression was conducted controlling for main confounders. For sensitivity analysis, we also conducted separate analysis for new-onset and recurrent cases, and other analysis such as the prior event rate adjustment(PERR) approach to minimize effects of unmeasured confounders. We also performed association analyses stratified by vaccination status. Time-dependent effects on subsequent hospitalization and mortality were also tested.

Results

Compared to individuals with no known history of COVID-19, those with severe COVID-19 (requiring hospitalization) exhibited higher hazards of hospitalization and/or mortality due to multiple disorders (median follow-up=608 days), including disorders of respiratory, cardiovascular, neurological, gastrointestinal, genitourinary and musculoskeletal systems. Increased hazards of hospitalizations and/or mortality were also observed for injuries due to fractures, various infections and other non-specific symptoms. These results remained largely consistent after sensitivity analyses. Severe COVID-19 was also associated with increased all-cause mortality (HR=14.700, 95% CI: 13.835-15.619).

Mild (non-hospitalized) COVID-19 was associated with modestly increased risk of all-cause mortality (HR=1.237, 95% CI 1.037-1.476) and mortality from neurocognitive disorders, as well as hospital admission from a few disorders such as aspiration pneumonitis, musculoskeletal pain and other general signs/symptoms.

All-cause mortalities and hospitalizations from other disorders post-infection were generally higher in the pre-vaccination era. The deleterious effect of COVID-19 was observed to wane over time, with maximum HR in the initial phase.

Conclusions

In conclusion, this study revealed increased risk of hospitalization and mortality from a wide variety of pulmonary and extra-pulmonary diseases after COVID-19, especially for severe infections. Mild disease was also associated with increased all-cause mortality. Causality however cannot be established due to observational nature of the study. Further studies are required to replicate our findings.
Vaccine Equity in Low and Middle Income Countries: A Systematic Review and Meta-analysis
Authors: Ali Huda , Hartner Anna-Maria , Echeverria-Londono Susy , Roth Jeremy , Li Xiang , Abbas Kaja , Portnoy Allison , Vynnycky Emilia , Woodruff Kim , Ferguson Neil M , Toor Jaspreet , Gaythorpe Katy AM
Published: March 2022

Background

Evidence to date has shown that inequality in health, and vaccine coverage in particular, can have ramifications to wider society. However, whilst individual studies have sought to characterise these heterogeneities in immunisation coverage at national level, few have taken a broad and quantitative view of the contributing factors to heterogeneity in vaccine coverage and impact. This systematic review aims to highlight these geographic, demographic, and sociodemographic characteristics through a qualitative and quantitative approach, vital to prioritise and optimise vaccination policies.

Methods

A systematic review of two databases (PubMed and Web of Science) was undertaken using Medical Subject Headings (MeSH) and keywords to identify studies examining factors on vaccine inequality and heterogeneity in vaccine coverage. Inclusion criteria were applied independently by two researchers. Studies including data on key characteristics of interest were further analysed through a meta-analysis to produce a pooled estimate of the risk ratio using a random effects model for that characteristic.

Results

One hundred and eight studies were included in this review. We found that inequalities in wealth, education, and geographic access can affect vaccine impact and vaccine dropout. We estimated those living in rural areas were not significantly different in terms of full vaccination status compared to urban areas but noted considerable heterogeneity between countries. We found that females were 3% (95%CI[1%, 5%]) less likely to be fully vaccinated than males. Additionally, we estimated that children whose mothers had no formal education were 28% (95%CI[18%,47%]) less likely to be fully vaccinated than those whose mother had primary level, or above, education. Finally, we found that individuals in the poorest wealth quintile were 27% (95%CI [16%,37%]) less likely to be fully vaccinated than those in the richest.

Conclusions

We found a nuanced picture of inequality in vaccine coverage and access with wealth disparity dominating, and likely driving, other disparities. This review highlights the complex landscape of inequity and further need to design vaccination strategies targeting missed subgroups to improve and recover vaccination coverage following the COVID-19 pandemic.

Registration

Prospero CRD42021261927
True-to-scale DNA-density maps correlate with major accessibility differences between active and inactive chromatin
Authors: Gelléri Márton , Chen Shih-Ya , Szczurek Aleksander , Hübner Barbara , Sterr Michael , Neumann Jan , Kröger Ole , Sadlo Filip , Imhoff Jorg , Markaki Yolanda , Hendzel Michael J. , Cremer Marion , Cremer Thomas , Strickfaden Hilmar , Cremer Christoph
Published: March 2022

Chromatin compaction differences may have a strong impact on accessibility of individual macromolecules and macromolecular assemblies to their DNA target sites. Estimates based on fluorescence microscopy with conventional resolution, however, suggested only modest compaction differences (∼2-10x) between active and inactive nuclear compartments (ANC and INC). Here, we present maps of nuclear landscapes with true-to-scale DNA-densities, ranging from <5 Mbp/µm3 to >300 Mbp/µm3. Maps were generated from individual human and mouse cell nuclei with single-molecule localization microscopy at ∼20 nm lateral and ∼100 nm axial resolution and supplemented by electron spectroscopic imaging. Microinjection of fluorescent nanobeads with sizes corresponding to macromolecular assemblies for transcription and replication into nuclei of living cells, demonstrated their localization and movements within the ANC and exclusion from the INC.
Cryo-EM structures of human zinc transporter ZnT7 reveal the mechanism of Zn2+uptake into the Golgi apparatus
Authors: Han Bui Ba , Watanabe Satoshi , Nomura Norimichi , Liu Kehong , Uemura Tomoko , Inoue Michio , Tsutsumi Akihisa , Fujita Hiroyuki , Kinoshita Kengo , Iwata So , Kikkawa Masahide , Inaba Kenji
Published: March 2022

Zinc ions (Zn2+) are vital to most cells, with the intracellular concentrations of Zn2+being tightly regulated by multiple zinc transporters located at the plasma and organelle membranes. We herein present the 2.8-2.9 Å-resolution cryo-EM structures of a Golgi-localized human Zn2+/H+antiporter ZnT7 (hZnT7) in its outward- and inward-facing forms. Cryo-EM analyses showed that hZnT7 exists as a homodimer via tight interactions in both the cytosolic and transmembrane (TM) regions of two protomers, each of which contains a single Zn2+-binding site in its TM domain. hZnT7 undergoes a TM-helix rearrangement to create a negatively charged cytosolic cavity for Zn2+entry in the inward-facing form and a widened luminal cavity for Zn2+release in the outward-facing form. An exceptionally long cytosolic histidine-rich loop characteristic of hZnT7 can bind at least two Zn2+ions, likely facilitating Zn2+recruitment from the cytosol. Unique mechanisms of hZnT7-mediated Zn2+uptake into the Golgi are proposed.