bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-centre derivation and validation of a colitis-associated colorectal cancer risk prediction web-tool
Authors: Curtius Kit , Kabir Misha , Bakir Ibrahim Al , Choi Chang-Ho Ryan , Hartono Juanda , Johnson Michael , East James E ,   Oxford IBD Cohort Study Investigators, Lindsay James O , Vega Roser , Thomas-Gibson Siwan , Wilson Ana , Graham Trevor A , Hart Ailsa
Published: April 2020

Background and Aims

Ulcerative colitis (UC) patients diagnosed with low-grade dysplasia (LGD) have increased risk of developing advanced neoplasia (AN; high-grade dysplasia or colorectal cancer). We aimed to develop and validate a predictor of AN risk in UC patients with LGD and create a visual web-tool to effectively communicate the risk.

Methods

In our retrospective multi-centre validated cohort study, adult UC patients with an index diagnosis of LGD, identified from four UK centres between 2001-2019, were followed until progression to AN. In the discovery cohort (n=248), a multivariate risk prediction model was derived from clinicopathological features using Cox regression. Validation used data from 3 external centres (n=201). The validated model was embedded in a web-based tool to calculate and illustrate patient-specific risk.

Results

Four endoscopic variables were significantly associated with future AN progression in the discovery cohort: endoscopically visible LGD > 1 cm (HR = 2.8; 95% CI 1.3-6.0), incomplete endoscopic resection (HR = 2.9; 95% CI 1.3-6.5), moderate/severe histological inflammation within 5 years of LGD diagnosis (HR = 3.0; 95% CI 1.3- 6.7), and multifocality (HR = 2.8; 95% CI 1.3-6.1). In the validation cohort, this 4-variable model accurately predicted future AN cases with overall calibration Observed/Expected = 1 (95% CI 0.63-1.5), and achieved perfect specificity for the lowest predicted risk group over 13 years of follow-up.

Conclusion

Multi-cohort validation confirms that patients with large, unresected, and multifocal LGD and recent moderate/severe inflammation are at the highest risk of developing AN. Personalised risk prediction provided via the Ulcerative Colitis-Cancer Risk Estimator web-tool (www.UC-CaRE.uk) can be used to support treatment decision-making.
Possibilities of exponential or Sigmoid growth of Covid19 data in different states of India
Authors: Mondal Supriya , Ghosh Sabyasachi
Published: April 2020

We have attempted to understand existing covid19 data of India, where growth of total and new cases with time in different states are kept as focal points. Identifying the last trend of exponential growth, mainly noticed in month of March, we have zoomed in its disaster possibilities by straight forward extrapolation of exponential growth. As a hopeful extrapolation, the existing data might be considered low time-axis values of Sigmoid-type function, whose growth might be saturated to values of 104 or 105. To fulfill this expectation, a turning from increasing to decreasing trend in new case data should be noticed around April-May, which definitely demand extension of present lock-down with additional interventions.
Global COVID-19 transmission rate is influenced by precipitation seasonality and the speed of climate temperature warming
Authors: Chiyomaru Katsumi , Takemoto Kazuhiro
Published: April 2020

The novel coronavirus disease 2019 (COVID-19) became a rapidly spreading worldwide epidemic; thus, it is a global priority to reduce the speed of the epidemic spreading. Several studies predicted that high temperature and humidity could reduce COVID-19 transmission. However, exceptions exist to this observation, further thorough examinations are thus needed for their confirmation. In this study, therefore, we used a global dataset of COVID-19 cases and global climate databases and comprehensively investigated how climate parameters could contribute to the growth rate of COVID-19 cases while statistically controlling for potential confounding effects using spatial analysis. We also confirmed that the growth rate decreased with the temperature; however, the growth rate was affected by precipitation seasonality and warming velocity rather than temperature. In particular, a lower growth rate was observed for a higher precipitation seasonality and lower warming velocity. These effects were independent of population density, human life quality, and travel restrictions. The results indicate that the temperature effect is less important compared to these intrinsic climate characteristics, which might thus be useful for explaining the exceptions. However, the contributions of the climate parameters to the growth rate were moderate; rather, the contribution of travel restrictions in each country was more significant. Although our findings are preliminary owing to data-analysis limitations, they may be helpful when predicting COVID-19 transmission.
Pattern and distribution of cancers in areas of Iraq exposed to Depleted Uranium
Authors: Aldujaily Esraa , Duabil Ali , Abbas Zwain Kussay M. , Fatlawi Hayder K. , Al-Behadili Ali , saabery Emad Al , Alwaaely Yasseen A. , Joboury Sijal Al , Qassid Omar Layth , Kelabi Liwaa Al
Published: April 2020

Introduction

Cancer is one of the major causes of death worldwide. Health systems whether in developed or in developing countries like Iraq are burdened with different programs to control cancer. Our study is intended to provide information about cancer in the region of Middle Euphrates Area (MEA) of Iraq, which is one of the major areas in Iraq that exposed to the depleted Uranium (DU) at different time periods. Therefore, we are aiming to explore more information about the behavior of cancers in this region of Iraq (pattern and distribution).

Aim: our study aims to describe the landscape of cancer with wide focus on the clinicopathological behavior of different types of cancers in MEA of Iraq to determine whether any differences have cropped up over time in Iraqi patients’ presentations.

Patients and methods

This study is a retrospective descriptive study design. Data were collected from a single tertiary cancer care oncology centre for three consecutive years from 2016 up to 2018. This Database covers nearly the entire Middle Euphrates area of Iraq. All statistical tests performed at a 95% level of significance with a two-sided p-value of 0.05 indicating statistical significance.

Results and conclusion

According to this study, the three most common cancers among the entire population were breast, lung, and brain cancers. Females constituted 57.0% of the entire study. Most cancers including breast cancer presented with aggressive clinicopathological behavior. Middle age groups of both sexes are more at risk of developing different cancers. Such findings are important and pave the way for future scientific cancer control programs in Iraq especially for breast cancer. The cancer appears to be flourishing in Iraq, which could be due to multiple factors. Finding a new strategy to predict the treatment response, recurrence or aggressiveness of cancers in Iraq is crucial.

Summary (Strengths and limitations of this study)

Whats new in this study is the wide focus of studying the clinicopathological behavior of all cancers in middle Euphrates area of Iraq to establish a solid base for further future studies that aims at developing the health system and cancer control programs in Iraq and middle east. The area of middle and south of Iraq which is named the middle Euphrates area is an area of major interest for researchers and clinicians as the cancer is flourishing in this area. previous studies excuse this increase of cancer incidence to the exposure to cancerous agents like depleted uranium. This fact inspired us to explore more information about the behavior of cancer in Iraq. The limitations of this study are the lack of therapy and survival data that we hope to include them in future studies.
COVID-19 most vulnerable Mexican cities lack the public health infrastructure to face the pandemic: a new temporally-explicit model
Authors: Dáttilo Wesley , e Silva Alcides Castro , Guevara Roger , Fors Ian MacGregor , Ribeiro Sérvio Pontes
Published: April 2020

Recently, a wide array of epidemiological models have been developed to guide public health actors in containing the rapid dissemination of the new severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), cause of COVID-19. Despite their usefulness, many epidemiological models recently developed to understand the spread of SARS-CoV-2 and infection rates of COVID-19 fall short as they ignore human mobility, limiting our understanding of the spread of the disease, together with the vulnerability of population centers in a broad scale. We developed a new temporally-explicit model and simulated several social distancing scenarios to predict the vulnerability to COVID-19 of 50 Mexican cities that are interconnected by their air transportation network. Additionally, we assessed the sufficiency of the public health infrastructure in the focal cities to face the pandemic over time. Based on our model, we show that the most important cities within the Mexican air transportation network are the most vulnerable to COVID-19, with all assessed public health infrastructure being insufficient to face the modeled scenario for the pandemic after 100 days. Despite these alarming findings, our results show that social distancing could dramatically decrease the total number of infected people (77% drop-off for the 45% distancing scenario when contrasted with no distancing), flattening the growth of infection rate. Thus, we consider that this study provides useful information that may help decision-makers to timely implement health policies to anticipate and lessen the impact of the current pandemic in Mexico.

Significance Statement

We used a new temporally-explicit model focused on air transportation networks to predict the vulnerability of 50 focal Mexican cities to COVID-19. We found that most vulnerable cities lack of the required public health infrastructure (i.e., number of inpatient and intensive care unit beds) to face this new pandemic, overloading in all cases after 100 days. However, our results show that a 45% social distancing scenario can reduce the number of infected people by up to 78.7%, flattening the growth rate of people with COVID-19 before infection rates soar exponentially countrywide.
Genetic timestamping of plasma cellsin vivoreveals homeostatic population turnover
Authors: Xu AQ , Barbosa RR , Calado DP
Published: April 2020

Plasma cells (PC)s are essential for protection from infection, and at the origin of incurable cancers. Current studies do not circumvent limitations of removing PCs from their microenvironment and confound formation and maintenance. This is in part due to the lack of tools to perform specific genetic manipulationin vivo. Also, studies of PC population dynamics have mostly relied on the use of nucleotide analog incorporation that does not label quiescent cells, a property of most PCs. Here we characterize in detail a genetic tool (JchaincreERT2) that permits first-ever specific genetic manipulation in PCin vivo, across immunoglobulin isotypes. Using this tool we found that PC numbers remained constant over-time and that PC decay was compensated by the emergence of new cells, supporting an homeostatic turnover of the population. TheJchaincreERT2genetic tool paves the way for in-depth mechanistic understanding of PC biology and pathologyin vivo, in their microenvironment.

Highlights

Jchainexpression occurs in most plasma cells across immunoglobulin isotypes

JchaincreERT2mediated genetic manipulation is effective only in plasma cells

Genetic timestamping of plasma cells reveals homeostatic regulation
Ahr-bacterial diet interaction modulates aging and associated pathologies inC. elegans
Authors: Brinkmann Vanessa , Schiavi Alfonso , Shaik Anjumara , Puchta Daniel R. , Ventura Natascia
Published: April 2020

Genetic and environmental factors concurrently shape the aging process. The nematodeCaenorhabditis eleganshas been instrumental in the past 30 years to identify most genes and interventions nowadays known to modulate aging (Lopez-Otin et al. 2013, Tigges et al. 2014, Dato et al. 2017). The aryl-hydrocarbon-receptor (AhR) was discovered as a dioxin-binding transcription factor involved in the metabolism of different environmental toxicants and xenobiotics (Poland et al. 1976). Since then, the variety of pathophysiological processes regulated by the AhR has rapidly grown, ranging from the immune response to cell death and metabolic pathways, and we disclosed it promotes aging phenotypes across species (Eckers et al. 2016, Esser et al. 2018). Interestingly, many AhR modulators may impact on aging and age-associated pathologies, but, whether their effects are actually AhR-dependent has never been explored. Here, we show for the first time that lack ofC. elegansAHR-1 affects health and lifespan in a context-dependent manner. Using known mammalian AhR modulators we found that, similar to mammals,ahr-1has protective effects against environmental insults and identified a new role for AhR-bacterial diet interaction in animal lifespan, stress resistance, and age-associated pathologies. We narrowed down the dietary factor involved in the observed AhR-dependent features to a bacterially-extruded metabolite likely involved in tryptophan metabolism. This is the first study clearly establishingC. elegansas a good model organism to investigate evolutionarily conserved functions of AhR-modulators and -regulated processes, indicating it can be exploited to contribute to the discovery of novel information about AhR in mammals.

Significance Statement

The roundwormC. eleganshas been instrumental for the identification of many of the genetic and environmental factors known to concurrently shape the aging process. The aryl-hydrocarbon-receptor (AhR) was originally discovered as a dioxin-binding transcription factor involved in the metabolism of environmental toxicants and, in the past, we found it promotes aging phenotypes across species. Many AhR modulators may impact on aging and age-associated pathologies, but, whether their effects are actually AhR-dependent has never been explored. We show here for the first time thatC. elegansAhR has protective effects against environmental insults such as UVB radiations and the xenobiotic BaP and identified a new critical role for AhR-bacterial diet interaction in animal lifespan, stress resistance, and age-associated pathologies.
SETD2 is an actin lysine methyltransferase
Authors: Seervai Riyad N.H. , Jangid Rahul K. , Karki Menuka , Tripathi Durga Nand , Jung Sung Yun , Kearns Sarah E. , Verhey Kristen J. , Cianfrocco Michael A. , Millis Bryan A. , Tyska Matthew J. , Mason Frank M. , Rathmell W. Kimryn , Park In Young , Dere Ruhee , Walker Cheryl L.
Published: April 2020

SET-domain-containing-2 (SETD2) was identified as the methyltransferase responsible for the histone 3 lysine 36 trimethyl (H3K36me3) mark of the histone code. Most recently, SETD2 has been shown to be a dual-function remodeler that regulates genome stability via methylation of dynamic microtubules during mitosis and cytokinesis. Here we show that actin is abona fidetarget for methylation by SETD2in vitroand in cells. Antibodies against the SETD2 trimethyl lysine epitope recognize methylated actin, with this methyl mark localizing to areas of active actin cytoskeleton reorganization in migrating cells. Disruption of this methylation activity causes defects in actin polymerization and impairs collective cell migration. Together, these data identify SETD2 as a multifunctional cytoskeletal remodeler regulating methylation and polymerization of actin filaments, and provide new avenues for understanding how defects in SETD2 drive disease via aberrant cytoskeletal methylation.
Enhancement of trans-cleavage activity of Cas12a with engineered crRNA enables amplified nucleic acid detection
Authors: Nguyen Long T. , Smith Brianna M. , Jain Piyush K.
Published: April 2020

The CRISPR/Cas12a RNA-guided complexes have a tremendous potential for nucleic acid detection due to its ability to indiscriminately cleave ssDNA once bound to a target DNA. However, the current CRISPR/Cas12a systems are limited to detecting DNA in a picomolar detection limit without an amplification step. Here, we developed a platform with engineered crRNAs and optimized conditions that enabled us to detect DNA, DNA/RNA heteroduplex and methylated DNA with higher sensitivity, achieving a limit of detection of in femtomolar range without any target pre-amplification step. By extending the 3’- or 5’-ends of the crRNA with different lengths of ssDNA, ssRNA, and phosphorothioate ssDNA, we discovered a new self-catalytic behavior and an augmented rate of LbCas12a-mediated collateral cleavage activity as high as 3.5-fold compared to the wild-type crRNA. We applied this sensitive system to detect as low as 25 fM dsDNA from the PCA3 gene, an overexpressed biomarker in prostate cancer patients, in simulated urine over 6 hours. The same platform was used to detect as low as ~700 fM cDNA from HIV, 290 fM RNA from HCV, and 370 fM cDNA from SARS-CoV-2, all within 30 minutes without a need for target amplification. With isothermal amplification of SARS-CoV-2 RNA using RT-LAMP, the modified crRNAs were incorporated in a paper-based lateral flow assay that could detect the target with up to 23-fold higher sensitivity within 40-60 minutes.
Genetic determinants ofEGFR-Driven Lung Cancer Growth and Therapeutic ResponseIn Vivo
Authors: Foggetti Giorgia , Li Chuan , Cai Hongchen , Hellyer Jessica A. , Lin Wen-Yang , Ayeni Deborah , Hastings Katherine , Choi Jungmin , Wurtz Anna , Andrejka Laura , Maghini Dylan , Rashleigh Nicholas , Levy Stellar , Homer Robert , Gettinger Scott , Diehn Maximilian , Wakelee Heather A. , Petrov Dmitri A. , Winslow Monte M. , Politi Katerina
Published: April 2020

Cancer genome sequencing has uncovered substantial complexity in the mutational landscape of tumors. Given this complexity, experimental approaches are necessary to establish the impact of combinations of genetic alterations on tumor biology and to uncover genotype-dependent effects on drug sensitivity. In lung adenocarcinoma,EGFRmutations co-occur with many putative tumor suppressor gene alterations, however the extent to which these alterations contribute to tumor growth and their response to therapyin vivohas not been explored experimentally. By integrating a novel mouse model of oncogenicEGFR-drivenTrp53-deficient lung adenocarcinoma with multiplexed CRISPR–Cas9-mediated genome editing and tumor barcode sequencing, we quantified the effects of inactivation of ten putative tumor suppressor genes. Inactivation ofApc,Rb1, orRbm10most strongly promoted tumor growth. Unexpectedly, inactivation ofLkb1orSetd2 –which are the strongest drivers of tumor growth in an oncogenicKras-driven model – reducedEGFR-driven tumor growth. These results are consistent with the relative frequency of these tumor suppressor gene alterations in humanEGFR-andKRAS-driven lung adenocarcinomas. Furthermore,Keap1inactivation reduces the sensitivity ofEGFR-drivenTrp53-deficient tumors to the EGFR inhibitor osimertinib. Importantly, in humanEGFR/TP53mutant lung adenocarcinomas, mutations in the KEAP1 pathway correlated with decreased time on tyrosine kinase inhibitor treatment. Our study highlights how genetic alterations can have dramatically different biological consequences depending on the oncogenic context and that the fitness landscape can shift upon drug treatment.
Cabozantinib unlocks efficientin vivotargeted delivery of neutrophil-loaded nanoparticles into murine prostate tumors
Authors: Chaudagar Kiranj , Landon-Brace Natalie , Solanki Aniruddh , Hieromnimon Hanna M. , Hegermiller Emma , Li Wen , Shao Yue , Wilkins Devan , Bynoe Kaela , Li Xiang-Ling , Clohessy John , Ullas Soumya , Karp Jeffrey M , Patnaik Akash
Published: April 2020

A major barrier to the successful application of nanotechnology for cancer treatment is the efficient delivery of therapeutic payloads to metastatic tumor deposits. We have previously discovered that cabozantinib, a tyrosine kinase inhibitor, triggers neutrophil-mediated anti-cancer innate immunity, resulting in tumor regression in an aggressive PTEN/p53-deficient genetically engineered murine model of advanced prostate cancer. Here, we specifically investigated the potential of cabozantinib-induced neutrophil activation and recruitment to enhance delivery of bovine serum albumin (BSA)-coated polymeric nanoparticles (NPs) into murine PTEN/p53-deficient prostate tumors. Based on the observation that BSA-coating of NPs enhanced association and internalization by activated neutrophilsin vitro, relative to uncoated NPs, we systemically injected BSA-coated, dye-loaded NPs into prostate-specific PTEN/p53-deficient mice that were pre-treated with cabozantinib. Flow cytometric analysis revealed a 4-fold increase of neutrophil-associated NPs within the tumor microenvironment (TME) of mice pre-treated with cabozantinib relative to untreated controls. At steady-state, following 3 days of cabozantinib/NP administration, 1% of systemically injected dye-loaded NPs selectively accumulated within the TME of mice that were pre-treated with cabozantinib, compared to 0.11% uptake for mice that did not receive cabozantinib pre-treatment. Strikingly, neutrophil depletion with Ly6G antibody abolished NP accumulation in tumors to baseline levels, demonstrating targeted neutrophil-mediated NP delivery to the prostate TME. In summary, we have discovered a novel nano-immunotherapeutic strategy for enhanced intratumoral delivery of injected NPs, which results in significantly higher NP accumulation than reported strategies in the nanotechnology literature to-date.
IRIS: an accurate and efficient barcode calling tool forin situsequencing
Authors: Zhou Yang , Yu Hao , Li Qiye , Ke Rongqin , Zhang Guojie
Published: April 2020

The emergingin situRNA sequencing technologies which can capture and amplify RNA within the original tissues provides efficient solution for producing spatial expression map from dozens to thousands of genes. Most ofin situRNA-seq strategies developed recently infer the expression patterns based on the fluorescence signals from the images taken during sequencing. However, an automate and convenient tool for decoding signals from image information is still absent. Here we present an easy-to-use software named IRIS to efficiently decode image signals fromin situsequencing into nucleotide sequences. This software can record the quality score and the spatial information of the sequencing signals. We also develop an interactive R shiny app named DAIBC for data visualization. IRIS is designed in modules so that it could be easily extended and compatible to new technologies.

Availability and implementation

IRIS and DAIBC are freely available under BSD 3-Clause License at:https://github.com/th00516/ISS_pyIRIS.

Contact

guojie.zhang@bio.ku.dk
Neurophysiological signatures in the retrieval of individual autobiographical memories of real-life episodic events
Authors: Nicolás Berta , Wu Xiongbo , Dimiccolli Mariella , Sierpowska Joanna , Saiz-Masvidal Cristina , Soriano-Mas Carles , Radeva Petia , Fuentemilla Lluís
Published: April 2020

Autobiographical memory (AM) refers to recollected events that belong to an individual’s past. In a classical episodic retrieval experiment in a laboratory, the events to be remembered are words or pictures that have hardly any personal relevance. While such stimuli provide necessary experimental and controlled conditions helping to advance in the understanding of memory, they do not capture the whole complexity of real-world stimuli. Recently, the incorporation of wearable cameras has allowed us to study the cognitive and neural bases of AM retrieval without active participant involvement, and they have been demonstrated to elicit a strong sense of first-person episodic recollection enhancing ecological validity. Here, we provide a new approach to understanding the retrieval of personal events, implementing a convolution network-based algorithm for the selection of the stimuli while monitoring participants’ memory retrieval with scalp EEG recordings over three periods of time after encoding (1 week, 2 weeks, and 6 to 12 months). We also examined an individual with a condition termed Aphantasia that provided more insights into the sensitivity of our protocol in the investigation of individual AM using real-life sequences.
Mindfulness Improves Brain Computer Interface Performance by Increasing Control over Neural Activity in the Alpha Band
Authors: Stieger James R. , Engel Stephen , Jiang Haiteng , Cline Christopher C. , Kreitzer Mary Jo , He Bin
Published: April 2020

Brain-computer interfaces (BCIs) are promising tools for assisting patients with paralysis, but suffer from long training times and variable user proficiency. Mind-body awareness training (MBAT) can improve BCI learning, but how it does so remains unknown. Here we show that MBAT allows participants to learn to volitionally increase alpha band neural activity during BCI tasks that incorporate intentional rest. We trained individuals in mindfulness-based stress reduction (MBSR; a standardized MBAT intervention) and compared performance and brain activity before and after training between randomly assigned trained and untrained control groups. The MBAT group showed reliably faster learning of BCI than the control group throughout training. Alpha-band activity in EEG signals, recorded in the volitional resting state during task performance, showed a parallel increase over sessions, and predicted final BCI performance. The level of alpha-band activity during the intentional resting state correlated reliably with individuals’ mindfulness practice as well as performance on a sustained attention task. Collectively, these results show that MBAT modifies a specific neural signal used by BCI. MBAT, by increasing patients’ control over their brain activity during rest, may increase the effectiveness of BCI in the large population who could benefit from alternatives to direct motor control.
A mathematical model of heat shock response to study the competition between protein folding and aggregation
Authors: Pal Sushmita , Sharma Rati
Published: April 2020

Proteins, under conditions of cellular stress, typically tend to unfold and form lethal aggregates leading to neurological diseases like Parkinson’s and Alzheimer’s. A clear understanding of the conditions that favor dis-aggregation and restore the cell to its healthy state after they have been stressed is therefore important in dealing with these diseases. The heat shock response (HSR) mechanism is a signaling network that deals with these undue protein aggregates and aids in the maintenance of homeostasis within a cell. This framework, on its own, is a mathematically well studied mechanism. However, not much is known about how the various intermediate mis-folded protein states of the aggregation process interact with some of the key components of the HSR pathway such as the Heat Shock Protein (HSP), the Heat Shock transcription Factor (HSF) and the HSP-HSF complex. In this article, using kinetic parameters from the literature, we propose and analyze two mathematical models for HSR that also include explicit reactions for the formation of protein aggregates. Deterministic analysis and stochastic simulations of these models show that the folded proteins and the misfolded aggregates exhibit bistability in a certain region of the parameter space. Further, the models also highlight the role of HSF and the HSF-HSP complex in reducing the time lag of response to stress and in re-folding all the mis-folded proteins back to their native state. These models therefore call attention to the significance of studying related pathways such as the HSR and the protein aggregation and re-folding process in conjunction with each other.
Tissue and regional expression patterns of dicistronic tRNA-mRNA transcripts in grapevine (Vitis vinifera) and their evolutionary co-appearance with vasculature in land plants
Authors: Fabres Pastor Jullian , Anand Lakshay , Sai Na , Pederson Stephen , Zheng Fei , Stewart Alexander A. , Clements Benjamin , Lampugnani Edwin R , Breen James , Gilliham Matthew , Tricker Penny , López Carlos M. Rodríguez , David Rakesh
Published: April 2020

Transfer RNAs (tRNA) are crucial adaptor molecules between messenger RNA (mRNA) and amino acids. Recent evidence in plants suggests that dicistronic tRNA-like structures also act as mobile signals for mRNA transcripts to move between distant tissues. Co-transcription is not a common feature in the plant nuclear genome and, in the few cases where polycistronic transcripts have been found, they include non-coding RNA species such as small nucleolar RNAs and microRNAs. It is not known, however, the extent to which dicistronic transcripts of tRNA and mRNAs are expressed in field-grown plants, or the factors contributing to their expression. We analysed tRNA-mRNA dicistronic transcripts in the major horticultural crop grapevine (Vitis vinifera) using a novel pipeline developed to identify dicistronic transcripts from high-throughput RNA sequencing data. We identified dicistronic tRNA-mRNA in leaf and berry samples from 22 commercial vineyards. Of the 124 tRNA genes that were expressed in both tissues, 18 tRNA were expressed forming part of 19 dicistronic tRNA-mRNAs. The presence and abundance of dicistronic molecules was tissue and geographic sub-region specific. In leaves, the expression patterns of dicistronic tRNA-mRNAs significantly correlated with tRNA expression, suggesting that their transcriptional regulation might be linked. We also found evidence of syntenic genomic arrangements of tRNAs and protein coding genes between grapevine andArabidopsis thaliana, and widespread prevalence of dicistronic tRNA-mRNA transcripts among vascular land plants but no evidence of these transcripts in nonvascular lineages. This suggests that the appearance of plant vasculature and tRNA-mRNA occurred concurrently during the evolution of land plants.
Prefrontal Transcranial Direct Current Stimulation globally improves learning, but does not selectively potentiate the benefits of Targeted Memory Reactivation on awake memory consolidation
Authors: Gilson Médhi , Nitsche Michael A. , Peigneux Philippe
Published: April 2020

Targeted Memory Reactivation (TMR) and transcranial Direct Current Stimulation (tDCS) can enhance memory consolidation. It is currently unknown whether TMR reinforced by simultaneous tDCS has superior efficacy. In this study, we investigated the complementary effect of TMR and bilateral tDCS on the consolidation of emotionally neutral and negative declarative memories. Participants learned neutral and negative word pairs. Each word pair was presented with an emotionally compatible sound. Following learning, participants spent a 20-minutes retention interval awake under 4 possible conditions: (1) TMR alone (i.e. replay of 50% of the associated sounds), (2) TMR combined with anodal stimulation of the left DLPFC, (3) TMR combined with anodal stimulation of the right DLPFC and (4) TMR with sham tDCS. Results evidenced selective memory enhancement for the replayed stimuli in the TMR-only and TMR-sham conditions, which confirms a specific effect of TMR on memory. However, memory was enhanced at higher levels for all learned items (irrespective of TMR) in the TMR-anodal right and TMR-anodal left tDCS conditions, suggesting that the beneficial effects of tDCS overshadow the specific effects of TMR. Emotionally negative memories were not modulated by tDCS hemispheric polarity. We conclude that electrical stimulation of the DLPFC during post-learning period globally benefits memory consolidation, but does not potentiate the specific benefits of TMR.
PLK1- and PLK4-mediated asymmetric mitotic centrosome size and positioning in the early zebrafish embryo
Authors: Rathbun LI , Aljiboury AA , Bai X , Manikas J , Amack JD , Bembenek JN , Hehnly H
Published: April 2020

Factors that regulate mitotic spindle positioning have been elucidatedin vitro, however it remains unclear how a spindle is placed within the confines of extremely large cells. Our studies identified a uniquely large centrosome structure in the early zebrafish embryo (246.44±11.93μm2mitotic centrosome in a 126.86±0.35μm diameter cell), whereasC. eleganscentrosomes are notably smaller (6.75±0.28μm2mitotic centrosome in a 55.83±1.04μm diameter cell). During early embryonic cell divisions, cell size changes rapidly inC. elegansand zebrafish embryos. Notably, mitotic centrosome area scales closely with changing cell size compared to changes in spindle length for both organisms. One interesting difference between the two is that mitotic centrosomes are asymmetric in size across embryonic zebrafish spindles, with the larger mitotic centrosome being 2.14±0.13-fold larger in size than the smaller. The largest mitotic centrosome is placed towards the embryo center in a Polo-Like Kinase (PLK) 1 and PLK4 dependent manner 87.14±4.16% of the time. We propose a model in which uniquely large centrosomes direct spindle placement within the disproportionately large zebrafish embryo cells to orchestrate cell divisions during early embryogenesis.
The Narrowing of Dendrite Branches across Nodes follows a well-defined Scaling Law
Authors: Liao Maijia , Howard Jonathon
Published: April 2020

The systematic variation of diameters in branched networks has tantalized biologists since the discovery of da Vinci’s rule for trees. Da Vinci’s rule can be formulated as a power law with exponent two: the square of the mother branch’s diameter is equal to the sum of the squares of those of the daughters. Power laws, with different exponents, have been proposed for branching in circulatory systems and in neurons. The laws have been derived theoretically, based on optimality arguments, but, for the most part, have not been tested rigorously. In the case of neuronal dendrites, diameter changes across branch points have functional implications for the spread of electrical signals: for example, Rall’s law with an exponent of 3/2 maximizes propagation speeds of action potentials across branch points. Using a super-resolution method to measure the diameters of all dendrites in highly branchedDrosophilaClass IV sensory neurons, we have tested Rall’s law and shown it to be false. In its place, we have discovered a new diameter-scaling law: the cross-sectional area is proportional to the number of dendrite tips supported by the branch plus a constant, corresponding to a minimum dendrite diameter. The law accords with microtubules providing force and transport for dendrite tip growth. That the observed scaling differs from Rall’s law suggests that constraints imposed by cell biological mechanisms may impact electrical signaling in neurons. Our new scaling law generalizes to other branched processes such as the vasculature of plants and the circulatory system of animals.

Significance Statement

To study the systematic variation of dendrite diameters, we have established a super-resolution method that allows us to resolve dendrite diameters inDrosophilaClass IV dendritic arborization neurons, a model cell for studying branching morphogenesis. Interestingly, they do not follow any of the known scaling laws. We propose a new scaling law that follows from two concepts: there is an incremental cross-sectional area needed to support each terminal branch, and there is a minimum branch diameter. The law is consistent with dendrite growing by tip extension and being supported by microtubule-based transport. If the law generalizes to other neurons, it may facilitate segmentation in connectomic studies.
A Live Attenuated Vaccine Model Confers Cross-Protective Immunity Against Different Species ofLeptospiraspp.
Authors: Wunder Elsio A. , Adhikarla Haritha , Hamond Camila , Owers Katharine A. , Liang Li , Rodrigues Camila B. , Bisht Vimla , Nally Jarlath E. , Alt David P. , Reis Mitermayer G. , Diggle Peter J. , Felgner Philip L. , Ko Albert I.
Published: April 2020

Leptospirosis is the leading zoonotic disease in terms of morbidity and mortality worldwide with a great health and economic impact in both humans and animals. Effective prevention is urgently needed as rapid urbanization, climate change and drivers of disease transmission continue to intensify. The key challenge has been developing a widely-applicable vaccine that protects against the 13 different pathogenic species and >300 serovars that can cause leptospirosis, providing a major public health benefit and opportunity to leverage One Health approaches. Live attenuated mutants that can boost immunity and induce protection are enticing vaccine candidates and poorly explored in the field. We evaluated a recently characterized motility-deficient mutant lacking the expression of a flagellar protein, FcpA. Although thefcpA-mutant has lost its ability to penetrate mucous membranes and cause disease, a transient bacteremia prior to clearance by the host immune response was observed. In two animal models, immunization with a single dose of thefcpA-mutant was sufficient to induce robust anti-protein antibodies response that promoted protection against infection with differentLeptospiraspp. species. Furthermore, characterization of the immune response identified a small repertoire of biologically relevant proteins that are highly conserved among pathogenicLeptospiraspecies and potential correlates of cross-protective immunity.
Implementation of single molecule FRET for visualizing intramolecular movement in CRISPR-Cas9
Authors: Narita Haruka , Ebata Hiroshi , Sakai Karibu , Minami Katsuhiko , Uemura Sotaro , Shima Tomohiro
Published: April 2020

SHORT ABSTRACT

This paper summarizes how to visualize the flexible inter-domain movements of CRISPR-associated protein Cas9 using single molecule FRET

LONG ABSTRACT

The CRISPR-associated protein Cas9 is widely used as a genome editing tool because of its ability to be programmed to cleave any DNA sequence that is followed by a protospacer adjacent motif. The continuing expansion of Cas9 technologies has stimulated studies regarding the molecular basis of the Cas9 catalytic process. Here we summarize methods for single molecule FRET (smFRET) to visualize the inter-domain movements of Cas9 protein. Our measurements and analysis demonstrate flexible and reversible movements of the Cas9 domains. Such flexible movements allow Cas9 to adopt transient conformations beyond those solved by crystal structures and play important roles in the Cas9 catalytic process. In addition to the smFRET measurement itself, to obtain precise results, it is necessary to validate Cas9 catalytic activity. Also, fluorescence anisotropy data are required to interpret smFRET data properly. Thus, in this paper, we describe the details of these important additional experiments for smFRET measurements.
The hexosamine biosynthesis pathway is a targetable liability in lung cancers with concurrent KRAS and LKB1 mutations
Authors: Kim Jiyeon , Cai Feng , Ko Bookyung , Yang Chendong , Lee Hyun Min , Muhammad Nefertiti , Li Kailong , Haloul Mohamed , Gu Wen , Faubert Brandon , Kaushik Akash K. , Cai Ling , Kasiri Sahba , Marriam Ummay , Nham Kien , Girard Luc , Wang Hui , Sun Xiankai , Kim James , Minna John D. , Unsal-Kacmaz Keziban , DeBerardinis Ralph J.
Published: April 2020

In non–small cell lung cancer (NSCLC), concurrent mutations in the oncogeneKRASand the tumor suppressorSTK11encoding the kinase LKB1 result in aggressive tumors prone to metastasis but with liabilities arising from reprogrammed metabolism. We previously demonstrated perturbed nitrogen metabolism and addiction to an unconventional pathway of pyrimidine synthesis in KRAS/LKB1 co-mutant (KL) cancer cells. To gain broader insight into metabolic reprogramming in NSCLC, we analyzed tumor metabolomes in a series of genetically engineered mouse models with oncogenic KRAS combined with mutations in LKB1 or p53. Metabolomics and gene expression profiling pointed towards an activation of the hexosamine biosynthesis pathway (HBP), another nitrogen-related metabolic pathway, in both mouse and human KL mutant tumors. KL cells contain high levels of HBP metabolites, higher flux through the HBP pathway and elevated dependence on the HBP enzyme Glutamine-Fructose-6-Phosphate Transaminase 2 (GFPT2). GFPT2 inhibition selectively reduced KL cell growth in culture and xenografts. Our results define a new metabolic vulnerability in KL tumors and provide a rationale for targeting GFPT2 in this aggressive NSCLC subtype.
Distinct CD8+T Cell Programming in the Tumor Microenvironment Contributes to Sex Bias in Bladder Cancer Outcome
Authors: Kwon Hyunwoo , Chung Dongjun , Kaneko Satoshi , Li Anqi , Zhou Lei , Riesenberg Brian , Song No-Joon , Sundi Debasish , Li Xue , Li Zihai
Published: April 2020

Men and women show striking yet unexplained discrepancies in incidence, clinical presentation, and therapeutic response across different types of infectious/autoimmune diseases and malignancies1,2. For instance, bladder cancer shows a 4-fold male-biased incidence that persists after adjustment for known risk factors3,4. Here, we utilize murine bladder cancer models to establish that male-biased tumor burden is driven by sex differences in endogenous T cell immunity. Notably, sex differences exist in early fate decisions by intratumoral CD8+T cells following their activation. While female CD8+T cells retain their effector function, male counterparts readily adopt a Tcf1lowTim3−progenitor state that becomes exhausted over tumor progression. Human cancers show an analogous male-biased frequency of exhausted CD8+T cells. Mechanistically, we describe an opposing interplay between CD8+T cell intrinsic androgen and type I interferon5,6signaling in Tcf1/Tcf7regulation and formation of the progenitor exhausted T cell subset. Consistent with female-biased interferon response7, testosterone-dependent stimulation of Tcf1/Tcf7and resistance to interferon occurs to a greater magnitude in male CD8+T cells. Male-biased predisposition for CD8+T cell exhaustion suggests that spontaneous rejection of early immunogenic bladder tumors is less common in males and carries implications for therapeutic efficacy of immune checkpoint inhibitors8,9.
Insight into biogeochemical models from Scale Transition Theory: A dimensionless, scale-free approach
Authors: Wilson Chris H. , Gerber Stefan
Published: April 2020

Leading an effective response to the accelerating crisis of anthropogenic climate change will require improved understanding of global carbon cycling. A critical source of uncertainty in Earth Systems Models (ESMs) is the role of microbes in mediating both the formation and decomposition of soil organic matter, and hence in determining patterns of CO2 efflux. Traditionally, ESMs model carbon turnover as a first order process impacted primarily by abiotic factors, whereas contemporary biogeochemical models often explicitly represent the microbial biomass and enzyme pools as the active agents of decomposition. However, the combination of non-linear microbial kinetics and ecological heterogeneity across space guarantees that upscaled dyamics will violate mean-field assumptions via Jensen’s Inequality. Violations of mean-field assumptions mean that parameter estimates from models fit to upscaled data (e.g. eddy covariance towers) are likely systematically biased. Here we present a generic mathematical analysis of upscaled michaelis-menten kinetics, grounded in Scale Transition Theory. We advance the framework by providing solutions in dimensionless form, and illustrate how this approach facilitates qualitative insight into the significance of this scale transition, and argue that it will facilitate future cross site intercomparisons of scale transition effects from flux data. We also discuss the critical terms that need to be constrained in order to unbias parameter estimates.
FOXO regulates neuromuscular junction homeostasis duringDrosophilaaging
Authors: Birnbaum Allison , Chang Kai , Bai Hua
Published: April 2020

The transcription factor FOXO is a known regulator of lifespan extension and tissue homeostasis. It has been linked to the maintenance of neuronal processes across many species, and has been shown to promote youthful characteristics by regulating cytoskeletal flexibility and synaptic plasticity at the neuromuscular junction (NMJ). However, the role of FOXO in aging neuromuscular junction function has yet to be determined. We profiled adult Drosophila FOXO-null mutant abdominal ventral longitudinal muscles and found that young mutants exhibited morphological profiles similar to those of aged wild-type flies, such as larger bouton areas and shorter terminal branches. We also observed changes to the axonal cytoskeleton and an accumulation of late endosomes in FOXO null mutants and motor neuron-specific FOXO knockdown flies, similar to those of aged wild-types. Motor neuron-specific overexpression of FOXO can delay age-dependent changes to NMJ morphology, suggesting FOXO is responsible for maintaining NMJ integrity during aging. Through genetic screening, we identify several downstream factors mediated through FOXO-regulated NMJ homeostasis, including genes involved in the p38-MAPK pathway. Interestingly, the phosphorylation of p38 and ERK were increased in the motor neuron-specific FOXO knockdown flies, suggesting FOXO acts as a suppressor of MAPK activation. Our work reveals that FOXO is a key regulator for NMJ homeostasis, and it maintains NMJ integrity by repressing MAPK signaling during aging.
High-frequency phase-switching ofmodBmethylase is associated with phenotypic ceftriaxone susceptibility inNeisseria gonorrhoeae
Authors: Brynildsrud Ola B , Osnes Magnus N , Ma Kevin C , Grad Yonatan H , Koomey Michael , Caugant Dominique A , Eldholm Vegard
Published: April 2020

The gonococcal adenine methylasesmodAandmodB, belonging to separate Type III restriction modification systems, are phase variable and could thus enable rapid adaptation to changing environments. However, the frequency of phase variation across transmission chains and the phenotypic impact of phase variation are largely unknown.

Here we show that the repeat tracts enabling phase variation expand and contract at high rates in bothmodAandmodB. FormodB, multiple ON/OFF transition events were identified over the course of a single outbreak.

A mixed effects model using population samples from Norway and a global meta-analysis collection indicates thatmodBin the OFF state is predictive of moderately decreased ceftriaxone susceptibility. Our findings suggest thatmodBorchestration of genome-wide 6-methyladenine modification controls the expression of genes modulating ceftriaxone susceptibility.

Importance

Despite significant progress, our current understanding of the genetic basis of antibiotic susceptibility remains incomplete. The gonococcal methylasemodBis phase variable, meaning that it can be switched ON or OFF via contraction or expansion of a repeat tract in the gene during replication. We find that transitions between the ON and OFF state occur at high frequency. Furthermore, isolates harbouringmodBin a configuration predicted to be inactive had decreased susceptibility to ceftriaxone, an antibiotic used to treat gonorrhea. This finding improves understanding of the genetic underpinnings of antibiotic resistance, but further work is needed to elucidate the mechanics and broader phenotypic effects of epigenetic modifications and transcription.