bluuebunny/crossref_metadata_2025 huggingface dataset:
Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize
Authors: Zhou Peng , Enders Tara A. , Myers Zachary A. , Magnusson Erika , Crisp Peter A , Noshay Jaclyn , Gomez-Cano Fabio , Liang Zhikai , Grotewold Erich , Greenham Kathleen , Springer Nathan
Published: January 2021

Changes in gene expression are important for response to abiotic stress. Transcriptome profiling performed on maize inbred and hybrid genotypes subjected to heat or cold stress identifies many transcript abundance changes in response to these environmental conditions. Motifs that are enriched near differentially expressed genes were used to develop machine learning models to predict gene expression responses to heat or cold. The best performing models utilize the sequences both upstream and downstream of the transcription start site. Prediction accuracies could be improved using models developed for specific co-expression clusters compared to using all up- or down-regulated genes or by only using motifs within unmethylated regions. Comparisons of expression responses in multiple genotypes were used to identify genes with variable response and to identifycis-ortrans-regulatory variation. Models trained on B73 data have lower performance when applied to Mo17 or W22, this could be improved by using models trained on data from all genotypes. However, the models have low accuracy for correctly predicting genes with variable responses to abiotic stress. This study provides insights intocis-regulatory motifs for heat- and cold-responsive gene expression and provides a framework for developing models to predict expression response to abiotic stress across multiple genotypes.

One sentence summary

Transcriptome profiling of maize inbred and hybrid seedlings subjected to heat or cold stress was used to identify key cis-regulatory elements and develop models to predict gene expression responses.
SCFFbxw5targets MCAK in G2/M to facilitate ciliogenesis in the following cell cycle
Authors: Schweiggert Jörg , Habeck Gregor , Hess Sandra , Mikus Felix , Meese Klaus , Hata Shoji , Knobeloch Klaus-Peter , Melchior Frauke
Published: January 2021

The microtubule depolymerase Kif2C/MCAK plays important roles in various cellular processes and is frequently overexpressed in different cancer types. Despite the importance of its correct abundance, remarkably little is known about how MCAK levels are regulated in cells.

Using comprehensive screening on protein microarrays, we identified 161 candidate substrates of the multi-subunit ubiquitin E3 ligase SCFFbxw5, including MCAK.In vitroreconstitution assays demonstrate that MCAK and its closely related orthologs Kif2A and Kif2B become efficiently polyubiquitylated by neddylated SCFFbxw5and Cdc34, without requiring preceding modifications. In cells, SCFFbxw5targets MCAK for proteasomal degradation specifically during G2/M. While this seems largely dispensable for mitotic progression, loss of Fbxw5 leads to increased MCAK levels at basal bodies, which impair formation of primary cilia in the following G1. We have thus identified a novel regulatory event of ciliogenesis that occurs already within the G2/M phase of the preceding cell cycle.
Endothelial NRP2 influences angiogenesis by regulating actin pattern development and α5-integrin-p-FAK complex recruitment to assembling adhesion sites
Authors: Benwell Christopher J , Taylor James AGE , Robinson Stephen D
Published: January 2021

The ability to form a variety of cell-matrix connections is crucial for angiogenesis to take place. Without stable anchorage to the extracellular matrix (ECM), endothelial cells (ECs) are unable to sense, integrate and disseminate growth factor stimulated responses that drive growth of a vascular bed. Neuropilin-2 (NRP2) is a widely expressed membrane-bound multifunctional non-tyrosine kinase receptor, that has previously been implicated in influencing cell adhesion and migration by interacting with α5-integrin and regulating adhesion turnover. α5-integrin, and its ECM ligand fibronectin (FN) are both known to be upregulated during the formation of neo-vasculature. Despite being descriptively annotated as a candidate biomarker for aggressive cancer phenotypes, the EC-specific roles for NRP2 during developmental and pathological angiogenesis remain unexplored. The data reported here support a model whereby NRP2 actively promotes EC adhesion and migration by regulating dynamic cytoskeletal remodelling and by stimulating Rab11-dependent recycling of α5-integrin-p-FAK complexes to newly assembling adhesion sites. Furthermore, temporal depletion of EC-NRP2in vivoimpairs primary tumour growth by disrupting vessel formation. We also demonstrate that EC-NRP2 is required for normal postnatal retinal vascular development, specifically by regulating cell-matrix adhesion. Upon loss of endothelial NRP2, vascular outgrowth from the optic nerve during superficial plexus formation is disrupted, likely due to reduced FAK phosphorylation within sprouting tip cells.
A gelation transition enables the self-organization of bipolar metaphase spindles
Authors: Dalton Benjamin A. , Oriola David , Decker Franziska , Jülicher Frank , Brugués Jan
Published: January 2021

The mitotic spindle is a highly dynamic bipolar structure that emerges from the self-organization of microtubules, molecular motors, and other proteins. Sustained motor-driven poleward flows of short dynamic microtubules play a key role in the bipolar organization of spindles. However, it is not understood how the local activity of motor proteins generates these large-scale coherent poleward flows. Here, we combine experiments and simulations to show that a gelation transition enables long-ranged microtubule transport causing spindles to self-organize into two oppositely polarized microtubule gels. Laser ablation experiments reveal that local active stresses generated at the spindle midplane propagate through the structure thereby driving global coherent microtubule flows. Simulations show that microtubule gels undergoing rapid turnover can exhibit long stress relaxation times, in agreement with the long-ranged flows observed in experiments. Finally, we show that either disrupting such flows or decreasing the network connectivity can lead to a microtubule polarity reversal in spindles both in the simulations and in the experiments. Thus, we uncover an unexpected connection between spindle rheology and architecture in spindle self-organization.
Activated PI3Kδ syndrome, an immunodeficiency disorder, leads to sensorimotor deficits recapitulated in a murine model
Authors: Serra Ines , Manusama Olivia R. , Kaiser Fabian M. P. , Floriano Izi Izumi , Wahl Lucas , van der Zalm Christian , IJspeert Hanna , van Hagen P. Martin , van Beveren Nico J.M. , Arend Sandra M. , Okkenhaug Klaus , Pel Johan J.M. , Dalm Virgil A.S.H. , Badura Aleksandra
Published: January 2021

The phosphoinositide-3-kinase (PI3K) family plays a major role in cell signalling and is predominant in leukocytes. Gain-of-function (GOF) mutations in thePIK3CDgene lead to the development of activated PI3Kδ syndrome (APDS), a rare primary immunodeficiency disorder. A subset of APDS patients also displays neurodevelopmental delay symptoms, suggesting a potential role ofPIK3CDin cognitive and behavioural function. However, the extent and nature of the neurodevelopmental deficits has not been previously quantified. Here, we assessed the cognitive functions of two APDS patients, and investigated the causal role of thePIK3CDGOF mutation in neurological deficits using a murine model of this disease. We used E1020K knock-in mice, harbouring the most common APDS mutation in patients. We found that APDS patients present with visuomotor deficits, exacerbated by autism spectrum disorder comorbidity, whereas p110δE1020Kmice exhibited impairments in motor behaviour, learning and repetitive behaviour patterning. Our data indicate thatPIK3CDGOF mutations increase the risk for neurodevelopmental deficits, supporting previous findings on the interplay between the nervous and the immune system. Further, our results validate the knock-in mouse model, and offer an objective assessment tool for patients that could be incorporated in diagnosis and in the evaluation of treatments.
Using zebrafish to elucidate glial-vascular interactions during CNS development
Authors: Umans Robyn A. , Pollock Carolyn , Mills William A. , Sontheimer Harald
Published: January 2021

An emerging area of interest in Neuroscience is the cellular relationship between glia and blood vessels, as many of the presumptive support roles of glia require an association with the vasculature. These interactions are best studiedin vivoand great strides have been made using mice to longitudinally image glial-vascular interactions. However, these methods are cumbersome for developmental studies, which could benefit from a more accessible system. Zebrafish (Danio rerio) are genetically tractable vertebrates, and given their translucency, are readily amenable for daily live imaging studies. We set out to examine whether zebrafish glia have conserved traits with mammalian glia regarding their ability to interact with and maintain the developing brain vasculature. We utilized transgenic zebrafish strains in whicholigodendrocyte transcription factor 2(olig2) andglial fibrillary acidic protein(gfap) identify different glial populations in the zebrafish brain and document their corresponding relationship with brain blood vessels. Our results demonstrate thatolig2andgfapzebrafish glia have distinct lineages and each interact with brain vessels as previously observed in mouse brain. Additionally, we manipulated these relationships through pharmacological and genetic approaches to distinguish the roles of these cell types during blood vessel development.olig2glia use blood vessels as a pathway during their migration and Wnt signaling inhibition decreases their single-cell vessel co-option. By contrast, the ablation ofgfapglia at the beginning of CNS angiogenesis impairs vessel development through a reduction in Vascular endothelial growth factor (Vegf), supporting a role forgfapglia during new brain vessel formation in zebrafish. This data suggests that zebrafish glia, akin to mammalian glia, have different lineages that show diverse interactions with blood vessels, and are a suitable model for elucidating glial-vascular relationships during vertebrate brain development.
Meiosis-specific ZFP541 repressor complex promotes meiotic prophase exit during spermatogenesis
Authors: Horisawa-Takada Yuki , Kodera Chisato , Takemoto Kazumasa , Sakashita Akihiko , Horisawa Kenichi , Maeda Ryo , Usuki Shingo , Fujimura Sayoko , Tani Naoki , Matsuura Kumi , Shimada Ryuki , Akiyama Tomohiko , Suzuki Atsushi , Niwa Hitoshi , Tachibana Makoto , Ohba Takashi , Katabuchi Hidetaka , Namekawa Satoshi H. , Araki Kimi , Ishiguro Kei-ichiro
Published: January 2021

During spermatogenesis, meiosis is accompanied by robust alteration in gene expression and chromatin status. However, it remained elusive how meiotic transcriptional program is established to ensure completion of meiotic prophase. Here, we identified a novel protein complex consisting of germ-cell-specific zinc-finger protein ZFP541 and its interactor KCTD19 as the key transcriptional regulator for meiotic prophase exit. Our genetic study showed that ZFP541 and KCTD19 are co-expressed from pachytene onward and play an essential role in the completion of meiotic prophase program in the testis. Furthermore, our ChIP-seq and transcriptome analyses revealed that ZFP541 binds to and suppresses a broad range of genes whose function is associated with biological processes of transcriptional regulation and covalent chromatin modification. The present study demonstrated that germ-cell specific ZFP541-KCTD19 containing complex promotes meiotic prophase exit in males, and triggers reconstruction of the transcription network and chromatin organization leading to post-meiotic development.
Mechanisms Driving Genome Reduction of a NovelRoseobacterLineage Showing Vitamin B12Auxotrophy
Authors: Feng Xiaoyuan , Chu Xiao , Qian Yang , Henson Michael W. , Celeste Lanclos V. , Qin Fang , Zhao Yanlin , Thrash J. Cameron , Luo Haiwei
Published: January 2021

Members of the marineRoseobactergroup are key players in the global carbon and sulfur cycles. While over 300 species have been described, only 2% possess reduced genomes (mostly 3-3.5 Mbp) compared to an average roseobacter (>4 Mbp). These taxonomic minorities are phylogenetically diverse but form a PelagicRoseobacterCluster (PRC) at the genome content level. Here, we cultivated eight isolates constituting a novelRoseobacterlineage which we named ‘CHUG’. Metagenomic and metatranscriptomic read recruitment analyses showed that CHUG members were globally distributed and active in marine environments. CHUG members possess some of the smallest genomes (~2.52 Mb) among all known roseobacters, but they do not exhibit canonical features of genome streamlining like higher coding density or fewer paralogues and pseudogenes compared to their sister lineages. While CHUG members are clustered with traditional PRC members at the genome content level, they show important differences. Unlike other PRC members, neither the relative abundances of CHUG members nor their gene expression levels are correlated with chlorophyll a concentration across the global samples. Moreover, CHUG members cannot synthesize vitamin B12, a key metabolite made by most roseobacters but not by many phytoplankton species and thus thought to mediate the roseobacter-phytoplankton interactions. This combination of features is evidence for the hypothesis that CHUG members may have evolved a free-living lifestyle decoupled from phytoplankton. This ecological transition was accompanied by the loss of signature genes involved in roseobacter-phytoplankton symbiosis, suggesting that relaxation of purifying selection is likely an important driver of genome reduction in CHUG.
Learning from unexpected events in the neocortical microcircuit
Authors: Gillon Colleen J. , Pina Jason E. , Lecoq Jérôme A. , Ahmed Ruweida , Billeh Yazan N. , Caldejon Shiella , Groblewski Peter , Henley Timothy M. , Kato India , Lee Eric , Luviano Jennifer , Mace Kyla , Nayan Chelsea , Nguyen Thuyanh V. , North Kat , Perkins Jed , Seid Sam , Valley Matthew T. , Williford Ali , Bengio Yoshua , Lillicrap Timothy P. , Richards Blake A. , Zylberberg Joel
Published: January 2021

Scientists have long conjectured that the neocortex learns the structure of the environment in a predictive, hierarchical manner. According to this conjecture, expected, predictable features are differentiated from unexpected ones by comparing bottom-up and top-down streams of information. It is theorized that the neocortex then changes the representation of incoming stimuli, guided by differences in the responses to expected and unexpected events. In line with this conjecture, different responses to expected and unexpected sensory features have been observed in spiking and somatic calcium events. However, it remains unknown whether these unexpected event signals occur in the distal apical dendrites where many top-down signals are received, and whether these signals govern subsequent changes in the brain’s stimulus representations. Here, we show that both somata and distal apical dendrites of cortical pyramidal neurons exhibit distinct unexpected event signals that systematically change over days. These findings were obtained by tracking the responses of individual somata and dendritic branches of layer 2/3 and layer 5 pyramidal neurons over multiple days in primary visual cortex of awake, behaving mice using two-photon calcium imaging. Many neurons in both layers 2/3 and 5 showed large differences between their responses to expected and unexpected events. Interestingly, these responses evolved in opposite directions in the somata and distal apical dendrites. These differences between the somata and distal apical dendrites may be important for hierarchical computation, given that these two compartments tend to receive bottom-up and top-down information, respectively.
Reduction in transfer of micro-organisms between patients and staff using short-sleeved gowns and hand/arm hygiene in Intensive Care during the Covid pandemic: a simulation-based randomised trial
Authors: Vincent Laura , Ibrahim Mudathir , Kitchin Joanne , Pickering Claire , Wilson Jennie , Sorrentino Enrico , Salvagno Claudia , Earl Laurie , Ma Louise , Simpson Kathryn , Baker Rose , McCulloch Peter
Published: January 2021

Background

Current PPE practices in UK intensive care units involve “sessional” gown use. This protects staff, but puts patients at risk of nosocomial infection via PPE gowns. Anecdotal reports of such infections in ITUs during Covid are frequent. We therefore explored the use of short-sleeved gowns with hand and arm hygiene as an alternative to sessional gowns.

Methods

ITU Staff were invited for simulation suite training in Covid intubation and proning. They were trained in a specific hand and arm washing technique before performing simulated tasks using both standard and modified (short sleeved) PPE. Fluorescent powder was used to simulate micro-organisms, and detected using standardised photos under U/V light. Teams of staff were randomised to use standard or modified PPE first. Individuals were questioned about their feeling of personal safety, comfort and the patient’s safety at 4 intervals.

Results

68 staff and 17 proning volunteers were studied in 17 sessions. Modified PPE completely prevented staff contamination during Covid intubation, which occurred in 30/67 staff wearing standard PPE (p = 0.0029, McNemar). Conversely, proning volunteers were contaminated by staff in 15/17 sessions with standard PPE and in 1/17 with modified PPE (P = 0.0227 McNemar). Impressions of staff comfort were superior with modified PPE (p< 0.001, t-test); personal safety scored higher with standard PPE, but the difference decreased during the session (p<0.001 start, 0.068 end). Impressions of patient safety were initially similar (p=0.87) but finished strongly in favour of modified PPE (p<0.001).

Conclusions

Modified PPE using short sleeves and hand/arm cleansing appears superior to standard PPE with sessional gowns in preventing transfer of contamination between staff and patients. A clinical trial of this strategy is merited.
Maternal prenatal anxiety and depression and trajectories of cardiometabolic risk factors across childhood and adolescence: a prospective cohort study
Authors: Matvienko-Sikar Karen , O’ Neill Kate N , Fraser Abigail , Hayes Catherine , Howe Laura D , Huizink Anja C , Kearney Patricia M , Khashan Ali , Redsell Sarah , O’Keeffe Linda M
Published: January 2021

Background

Quantifying long-term offspring cardiometabolic health risks associated with maternal prenatal anxiety and depression can guide cardiometabolic risk prevention. This study examines associations between maternal prenatal anxiety and depression, and offspring cardiometabolic risk from birth to 18 years.

Methods

Participants were 526-8,606 mother-offspring pairs from the Avon Longitudinal Study of Parents and Children (ALSPAC). Exposures were anxiety (Crown-Crisp Inventory score) and depression (Edinburgh Postnatal Depression Scale score) measured at 18 and 32 weeks gestation. Outcomes were trajectories of offspring body mass index; fat mass; lean mass; pulse rate; glucose, diastolic and systolic blood pressure; triglycerides, high-density lipoprotein cholesterol and non-high-density lipoprotein cholesterol, and insulin from birth/early childhood to 18 years. Exposures were analysed categorically using clinically relevant, cut-offs and continuously to examine associations across the distribution of prenatal anxiety and depression.

Results

We found no strong evidence of associations between maternal anxiety and depression, and offspring trajectories of any cardiometabolic risk factors, except for small, inconsistent associations with fat mass trajectories that attenuated upon confounder adjustment. For instance, in unadjusted analyses, anxiety at both 18 and 32 weeks was associated with a 1.8% (95% Confidence Interval (CI), 0.29,3.33) higher mean BMI, which spanned the null (difference (95% CI): 0.7% (−0.76,2.13) after adjustment for confounders.

Conclusions

This is the first examination of maternal prenatal anxiety and depression and trajectories of offspring cardiometabolic risk. Our findings suggest that prevention of maternal prenatal anxiety and depression may have limited impact on offspring cardiometabolic health across the first two decades of life.
Nationwide large-scale data of acute lower gastrointestinal bleeding in Japan uncover detailed etiologies and relevant outcomes: CODE BLUE J-Study
Authors: Nagata Naoyoshi , Kobayashi Katsumasa , Yamauchi Atsushi , Yamada Atsuo , Omori Jun , Ikeya Takashi , Aoyama Taiki , Tominaga Naoyuki , Sato Yoshinori , Kishino Takaaki , Ishii Naoki , Sawada Tsunaki , Murata Masaki , Takao Akinari , Mizukami Kazuhiro , Kinjo Ken , Fujimori Shunji , Uotani Takahiro , Fujita Minoru , Sato Hiroki , Suzuki Sho , Narasaka Toshiaki , Hayasaka Junnosuke , Funabiki Tomohiro , Kinjo Yuzuru , Mizuki Akira , Kiyotoki Shu , Mikami Tatsuya , Gushima Ryosuke , Fujii Hiroyuki , Fuyuno Yuta , Gunji Naohiko , Toya Yosuke , Narimatsu Kazuyuki , Manabe Noriaki , Nagaike Koji , Kinjo Tetsu , Sumida Yorinobu , Funakoshi Sadahiro , Kawagishi Kana , Matsuhashi Tamotsu , Komaki Yuga , Miki Kuniko , Watanabe Kazuhiro , Fukuzawa Masakatsu , Itoi Takao , Uemura Naomi , Kawai Takashi , Kaise Mitsuru
Published: January 2021

Background

The value of endoscopy for acute lower GI bleeding (ALGIB) remains unclear, given few large cohort studies. We aim to provide detailed clinical data for ALGIB management and to identify patients at risk for adverse outcomes based on endoscopic diagnosis.

Methods

We conducted a multicenter, retrospective cohort study, named CODE BLUE J-Study, in 49 hospitals throughout Japan and studied 10,342 cases admitted for outpatient-onset of acute hematochezia.

Results

Cases were mostly elderly, with 29.5% hemodynamic instability and 60.1% comorbidity. 69.1% and 87.7 % of cases underwent CT and colonoscopy, respectively. Diagnostic yield of colonoscopy reached 94.9%, revealing 48 etiologies, most frequently diverticular bleeding. During hospitalization, the endoscopic therapy rate was 32.7%, mostly using clipping and band ligation. IVR and surgery were infrequently performed, for 2.1% and 1.4%. In-hospital rebleeding and death occurred in 15.2% and 0.9%. Diverticular bleeding cases had higher rates of hemodynamic instability, rebleeding, endoscopic therapy, IVR, and transfusion, but lower rates of death and surgery than other etiologies. Small bowel bleeding cases had significantly higher rates of surgery, IVR, and transfusion than other etiologies. Malignancy or upper GIB cases had significantly higher rates of thromboembolism and death than other etiologies. Etiologies that have favorable outcomes were ischemic colitis, infectious colitis, and post-endoscopy bleeding.

Conclusions

Large-scale data of patients with acute hematochezia revealed high proportions of colonoscopy and CT, resulting in high endoscopic therapy rates. We highlight the importance of colonoscopy in detecting accurate bleeding etiologies that stratify patients at high or low risk of adverse outcomes.
Brassinosteroid signaling component SlBES1 promotes tomato fruit softening through transcriptional repression ofPMEU1
Authors: Liu Haoran , Liu Lihong , Liang Dongyi , Zhang Min , Jia Chengguo , Qi Mingfang , Liu Yuanyuan , Shao Zhiyong , Meng Fanliang , Hu Songshen , Li Chuanyou , Wang Qiaomei
Published: January 2021

Firmness is one of the most important factors that affect postharvest properties of tomato fruit. However, the regulatory mechanism underlying firmness formation in tomato fruit is poorly understood. Here, we report a novel role of SlBES1, a transcriptional factor (TF) mediating brassinosteroid (BR) signaling, in tomato fruit softening. We first found that SlBES1 promotes fruit softening during tomato fruit ripening and postharvest storage. RNA-seq analysis suggested thatPMEU1, which encodes a pectin de-methylesterification protein, might participate in SlBES1-mediated fruit softening. Biochemical and immunofluorescence assays inSlBES1transgenic fruits indicated that SlBES1 inhibitedPMEU1-related pectin de-methylesterification. Further molecular and genetic evidence verified that SlBES1 directly binds to the E-box in the promoter ofPMEU1to repress its expression, leading to the softening of the tomato fruits. Loss-of-functionSlBES1mutant generated by CRISPR/cas9 showed firmer fruits and longer shelf life during postharvest storage without the color, size and nutritional quality alteration. Collectively, our results indicated the potential of manipulatingSlBES1to regulate fruit firmness via transcriptional inhibition ofPMEU1without negative consequence on visual and nutrition quality.
Chromatin dynamics controls epigenetic domain formation
Authors: Katava Marina , Shi Guang , Thirumalai D.
Published: January 2021

In multicellular organisms, nucleosomes carry epigenetic information that defines distinct patterns of gene expression, which are inherited over multiple generations. The enhanced capacity for information storage arises by nucleosome modifications, triggered by enzymes. Modified nucleosomes can transfer the mark to others that are in proximity by a positive feedback (modification begets modification) mechanism. We created a polymer model in which each bead, representing a nucleosome, stochastically switches between unmodified (U) and modified (M) states depending on the states of the neighbors. Spreading is initiated at a specific nucleation site (NS) that is permanently in theMstate. Modifications spread among the non-nucleation loci probabilistically. If the spreading rate is higher than the chromatin relaxation rate, domains containing the modified nucleosomes form without bound. In the opposite biologically relevant limit, finite-sized domains form, driven by contacts between nucleosomes through a three-dimensional looping mechanism, with chromatin remaining in an expanded state, as is appropriate for fission yeast. Surprisingly, finite bounded domains arisewithoutthe need for any boundary elements as long as the spreading is slow. Maintenance of spatially and temporally stable domains require the presence of the NS whose removal eliminates finite-sized modified domains. By varying the solvent quality we show that finite heterochromatin domains form as long as initially chromatin is not fully condensed. The predictions compare well with experimental data for H3K9me3 spreading in Mouse Embryonic Stem cell.
Loss of Cysteine Rich domain was critical for evolution of heterodimerization in Toll proteins
Authors: Ranga Poonam , Sawanth Suresh Kumar , Mrinal Nirotpal
Published: January 2021

Toll proteins play roles in immunity/development which have largely remained conserved. However, there are differences in Toll biology as mammalian TLRs recognise pathogen associated molecular patterns (PAMPs) but not their invertebrate homologues. The reason for the same is not known. One critical molecular difference is absence of Cysteine Rich Domain (CRD) in vertebrate Tolls and their presence in invertebrates. Interestingly, in Drosophila, all Toll proteins have CRD except Toll9. This provided us the appropriate model to investigate significance of loss of CRD in Toll evolution. CRDs nudge protein dimerization by forming disulphide bonds hence we asked if they did same in Drosophila Toll-proteins. We tested if, Toll-1(which forms homodimer) can heterodimerize with Toll-9. We found that wildtype Toll-1 didn’t interact with Toll9 however; when CRD of Toll1 was deleted/mutated it formed heterodimer with Toll9. This indicates that presence of CRD limits Toll proteins to form homodimer and thus its loss was a critical event which pushed Toll proteins towards heterodimerization. We further show that Drosophila Toll9 can directly bind dsRNA, a PAMP. Interestingly, dsRNA affinity for toll-9 monomer was twice as that for the dimer, which can be attributed to CRD loss. Thus, we show that loss of CRD was a major step in Toll evolution as it resulted in functional diversity and was a first step towards heterodimer formation. Therefore, we propose that CRD loss was under positive selection and also that heterodimerization of Toll-proteins is an evolved property.

One line summary

Loss of Cysteine Rich Domain in Drosophila Toll9 and recognition of dsRNA.
Immunoengineered Nanobead System for the Isolation and Detection of Circulating Tumor Cells
Authors: Zhang Pengfei , Draz Mohamed S. , Xiong Anwen , Yan Wannian , Han Huanxing , Chen Wansheng
Published: January 2021

Highly efficient capture and detection of circulating tumor cells (CTCs) remain elusive mainly because of their extremely low concentration in the peripheral blood of patients. Herein, we present an approach for the simultaneous capturing, isolation, and detection of CTCs using an immuno-fluorescent magnetic nanobead system (iFMNS) coated with a monoclonal anti-EpCAM antibody. The developed antibody nanobead system allows magnetic isolation and fluorescent-based quantification of CTCs. The expression of EpCAM on the surface of captured CTCs could be directly visualized without additional immune-fluorescent labeling. Our approach is shown to result in a 70 - 95% capture efficiency of CTCs, and 95% of the captured cells remain viable. Using our approach, the isolated cells could be directly used for culture, reverse transcription-polymerase chain reaction (RT-PCR), and immunocytochemistry (ICC) identification. We applied iFMNS for testing CTCs in peripheral blood samples from a lung cancer patient, which suggested that this approach would be a promising tool for CTCs enrichment and detection in one step.
Evaluation of the effects of SARS-CoV-2 genetic mutations on diagnostic RT-PCR assays
Authors: Nakabayashi Takeru , Kawasaki Yuki , Murashima Koichiro , Omi Kazuya , Yuhara Satoshi
Published: January 2021

Several mutant strains of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are emerging. Mismatch(es) in primer/probe binding regions would decrease the detection sensitivity of the PCR test, thereby affecting the results of clinical testing. In this study, we conducted an in silico survey on SARS-CoV-2 sequence variability within the binding regions of primer/probe published by the Japan National Institute of Infectious Diseases (NIID) and Centers for Disease Control and Prevention (CDC). In silico analysis revealed the presence of mutations in the primer/probe binding regions. We performed RT-PCR assays using synthetic RNAs containing the mutations and showed that some mutations significantly decreased the detection sensitivity of the RT-PCR assays.

Our results highlight the importance of genomic monitoring of SARS-CoV-2 and evaluating the effects of mismatches on PCR testing sensitivity.
Individuality, as well as genotype, affects characteristics and temporal consistency of courtship songs in male mice
Authors: Melotti Luca , Siestrup Sophie , Peng Maja , Vitali Valerio , Dowling Daniel , Sachser Norbert , Kaiser Sylvia , Richter S. Helene
Published: January 2021

Courtship songs in mice have been investigated to understand the mechanisms and ecological relevance of vocal communication. There is evidence that courtship song characteristics vary between different genotypes, but little is known on whether individuals, even within the same genotype, differ from each other in the composition, complexity, and temporal consistency of their songs. In a first study, we aimed to systematically identify song features typical of different genotypes, by assessing the composition and complexity (i.e., entropy) of the syllabic sequences of male laboratory mice from four different strains(Mus musculusf.domestica:C57BL/6J, BALB/c, DBA/2 and B6D2F1). Mice were individually presented with a swab containing fresh female urine for 5 minutes to elicit courtship songs. The four strains differed not only in the composition but also in the complexity of their syllabic sequences. In a second study, we investigated within-strain individual differences in temporal consistency and recurring motifs (i.e., identical sets of syllables that are repeated within a song), using BALB/c and DBA/2 mice. The same procedure as in the first study was followed, but in addition testing was repeated weekly over three weeks. Both strains showed some level of individual temporal consistency; BALB/c in the overall amount of emitted vocalisations and DBA/2 in the expression of specific syllable types. However, hierarchical cluster analysis revealed remarkable individual variability in how consistent song characteristics were over time. Furthermore, recurring motifs were expressed at varying levels depending on the individual. Taken together, not only genotype but also individuality can affect variability in courtship songs in mice, suggesting the existence of different courtship strategies (e.g., higher song consistency to facilitate individual identification) related to varying levels of behavioural plasticity.

HIGHLIGHTS

Courtship songs in mice can serve as a model to study vocal communication

We explore how genotype and individuality affect courtship songs’ characteristics

Genotypes differ in composition and also in complexity of syllabic sequences

We find remarkable individual variability in how consistent songs are over time

Results suggest the existence of variation in male courting behaviour
Evolution of phenotypic variance in response to a novel hot environment
Authors: Lai Wei-Yun , Schlötterer Christian
Published: January 2021

Shifts in trait means are widely considered as evidence for adaptive responses, but the impact on phenotypic variance remains largely unexplored. Classic quantitative genetics provides a theoretical framework to predict how selection on phenotypic mean affects the variance. In addition to this indirect effect, it is also possible that the variance of the trait is the direct target of selection, but experimentally characterized cases are rare. Here, we studied gene expression variance ofDrosophila simulansmales before and after 100 generations of adaptation to a novel hot laboratory environment. In each of the two independently evolved populations, the variance of 125 and 97 genes was significantly reduced. We propose that the drastic loss in environmental complexity from nature to the lab may have triggered selection for reduced variance. Our observation that selection could drive changes in the variance of gene expression could have important implications for studies of adaptation processes in natural and experimental populations.
SARS-CoV-2 infection of circulating immune cells is not responsible for virus dissemination in severe COVID-19 patients
Authors: Rosin Nicole L. , Jaffer Arzina , Sinha Sarthak , Mulloy Rory P. , Robinson Carolyn , Labit Elodie , Almeida Luiz G. , Dufour Antoine , Corcoran Jennifer A. , Yipp Bryan , Biernaskie Jeff
Published: January 2021

In late 2019 a novel coronavirus (SARS-CoV-2) emerged, and has since caused a global pandemic. Understanding the pathogenesis of COVID-19 disease is necessary to inform development of therapeutics, and management of infected patients. Using scRNAseq of blood drawn from SARS-CoV-2 patients, we asked whether SARS-CoV-2 may exploit immune cells as a ‘Trojan Horse’ to disseminate and access multiple organ systems. Our data suggests that circulating cells are not actively infected with SARS-CoV-2, and do not appear to be a source of viral dissemination.
Protein-coding repeat polymorphisms strongly shape diverse human phenotypes
Authors: Mukamel Ronen E. , Handsaker Robert E. , Sherman Maxwell A. , Barton Alison R. , Zheng Yiming , McCarroll Steven A. , Loh Po-Ru
Published: January 2021

Hundreds of the proteins encoded in human genomes contain domains that vary in size or copy number due to variable numbers of tandem repeats (VNTRs) in proteincoding exons. VNTRs have eluded analysis by the molecular methods—SNP arrays and high-throughput sequencing—used in large-scale human genetic studies to date; thus, the relationships of VNTRs to most human phenotypes are unknown. We developed ways to estimate VNTR lengths from whole-exome sequencing data, identify the SNP haplotypes on which VNTR alleles reside, and use imputation to project these haplotypes into abundant SNP data. We analyzed 118 protein-altering VNTRs in 415,280 UK Biobank participants for association with 791 phenotypes. Analysis revealed some of the strongest associations of common variants with human phenotypes including height, hair morphology, and biomarkers of human health; for example, a VNTR encoding 13-44 copies of a 19-amino-acid repeat in the chondroitin sulfate domain of aggrecan (ACAN) associated with height variation of 3.4 centimeters (s.e. 0.3 cm). Incorporating large-effect VNTRs into analysis also made it possible to map many additional effects at the same loci: for the blood biomarker lipoprotein(a), for example, analysis of the kringle IV-2 VNTR within theLPAgene revealed that 18 coding SNPs and the VNTR inLPAexplained 90% of lipoprotein(a) heritability in Europeans, enabling insights about population differences and epidemiological significance of this clinical biomarker. These results point to strong, cryptic effects of highly polymorphic common structural variants that have largely eluded molecular analyses to date.
NF-kB c-Rel is dispensable for the development but is required for the cytotoxic function of NK cells
Authors: Vicioso Y , Zhang K , Ramakrishnan Parameswaran , Parameswaran Reshmi
Published: January 2021

Natural Killer (NK) cells are cytotoxic lymphocytes critical to the innate immune system. We found that germline deficiency of NF-kB c-Rel results in a marked decrease in cytotoxic function of NK cells, both in vitro and in vivo, with no significant differences in the stages of NK cell development. We found that c-Rel binds to the promoters of perforin and granzyme B, two key proteins required for NK cytotoxicity, and controls their transactivation. We generated a NK cell specific c-Rel conditional knockout to study NK cell intrinsic role of c-Rel and found that both global and conditional c-Rel deficiency leads to decreased perforin and granzyme B expression and thereby cytotoxic function. We also confirmed the role of c-Rel in perforin and granzyme B expression in human NK cells. c-Rel reconstitution rescued perforin and granzyme B expressions in c-Rel deficient NK cells and restored their cytotoxic function. Our results show a previously unknown role of c-Rel in transcriptional regulation of perforin and granzyme B expressions and control of NK cell cytotoxic function.
Dihydroartemisinin attenuated the symptoms of mice model of systemic lupus erythematosus by restoring the Treg/Th17 balance
Authors: Chen Yan , Tao Tingjun , Wang Weiliang , Yang Botao , Cha Xushan
Published: January 2021

The Treg/Th17 imbalance is associated with the development of systemic lupus erythematosus (SLE). Dihydroartemisinin (DHA), a semi‐synthetic derivative of artemisinin, is isolated from the traditional Chinese herb Artemisia annuaArtemisia annua L. This study aims to evaluate the effects of DHA alone or in combination with prednisone in immunodeficiency of SLE. In vivo, the therapeutical effect of DHA alone or in combination with prednisone was assessed in the pristane‐induced SLE mouse model. Then, the level of serum antibodies, creatinine (Cre), blood urea nitrogen (BUN), urine protein, kidney histopathology, interleukin (IL)‐17, IL‐6, transforming growth factor (TGF)‐β, the expression of RORγt and Foxp3, the percentages of Treg and Th17 in peripheral blood and spleen were assayed. In vitro, the mouse spleen lymphocytes were separated and treated with DHA alone or DHA in combination with prednisone. Then the percentages of Treg and Th17, the concentration of IL‐17, IL‐6, TGF‐β, and the expression of RORγt and Foxp3 were assayed. It was shown that DHA alone or in combination with prednisone treatment significantly alleviated the manifestations of pristane‐induced SLE mice, suppressed inflammation and restored the Treg/Th17 balance. DHA alone or in combination with prednisone significantly inhibited Th17 cell differentiation while induced Treg cell differentiation in vitro. DHA alone or in combination with prednisone also reduced the transcription of RORγt and increased Foxp3 in lymphocytes, as well as IL‐17 and TGF‐β levels. Our data indicated that DHA can produce synergistic effect with prednisone to attenuate the symptoms of SLE by restoring Treg/Th17 balance.
Embedding Impact in Research: Addressing the Interactional Production of Workplace Activities
Authors: vom Lehn Dirk , Heath Christian
Published: January 2021

As scholars both in the UK and we discuss a distinctive approach to developing impact that rests upon close cooperation between academics and practitioners from the outset of a particular project. The approach draws upon ethnomethodology and conversation analysis and addresses the social and interactional foundations of work and organization, an approach that increasingly uses video‐recordings of everyday activities augmented by field studies. We discuss examples drawn from our own research, projects concerned with such matters as eye tests, auctions of fine art and urban transport, and seek to show that developing impact in cooperation with practitioners does not necessitate compromising the academic contribution of research.
Policy Approaches Addressing the Ongoing Humanitarian and Environmental Consequences of Nuclear Weapons: A Commentary
Authors: Van Duzer Nate , Sanders‐Zakre Alicia
Published: January 2021

The 2017 Treaty on the Prohibition of Nuclear Weapons (TPNW) not only bans nuclear weapons, it obligates its states parties to engage in assisting victims and remediating contaminated environments (Articles 6 and 7). As states and civil society consider the best methods to implement these provisions, it is important to take stock and review existing policy approaches addressing the ongoing humanitarian and environmental consequences of nuclear weapons. This practitioner commentary, written by members of the International Campaign to Abolish Nuclear Weapons (ICAN), which was awarded the 2017 Nobel Peace Prize for its advocacy for the TPNW, reviews existing programs of victim assistance and environmental remediation. It highlights key considerations for policy makers seeking to improve on the existing mechanisms.
Commentary on Addressing the Legacies of Nuclear Weapons Use and Testing: Perspectives from Survivors
Authors: Minor Elizabeth , Umezawa Hana , Tanaka Terumi , Kido Sueichi , Vesselov Dmitriy
Published: January 2021

To develop an effective and responsive global policy framework for addressing the humanitarian and environmental consequences of nuclear weapons, survivors and communities affected by nuclear weapons use and testing, and their perspectives and expertise on what is needed, must be included. Testimony from survivors was crucial to the global effort for the Treaty on the Prohibition of Nuclear Weapons (TPNW). Articles 6 and 7 will require states joining the TPNW to provide assistance (such as medical and psychological support, and social and economic inclusion) to the victims of nuclear weapons use and testing, and to take measures towards remediating environments that are still affected (See Bolton & Minor and Docherty’s contributions in this Special Section for further details). Going forward, policy development on the implementation of Articles 6 and 7 of the TPNW should be guided by the priorities that affected communities identify.
Fertility in men with hypospadias: A nationwide register‐based study using dizygotic twinning rates as an indicator of semen quality
Authors: Phillips Lottie , Lundholm Cecilia , Örtqvist Lisa , Almqvist Catarina , Nordenskjöld Agneta , Skarin Nordenvall Anna
Published: January 2021

Background

It is not known if impaired fertility in men with hypospadias is caused by decreased semen quality or other factors. Semen quality in men born with hypospadias may be impaired due to effects of androgens or testicular dysgenesis but has been very little studied.

Objectives

To study semen quality in men with hypospadias using dizygotic twinning rates as an epidemiological indicator. We further aimed to study men treated for cryptorchidism, given a hypothesized mutual etiology for decreased semen quality.

Materials and methods

We conducted a population‐based study using national Swedish registers. A total of 4,363,165 births between 1964 and 2013 were included. The association between hypospadias and cryptorchidism, and fathering dizygotic multiple births was estimated using logistic regression and presented as odds ratios. The main analyses excluded births conceived using assisted reproductive technology (ART).

Results

We identified a total of 5317 births with fathers with hypospadias, including 26 dizygotic births conceived unassisted. No significant association was found between hypospadias and dizygotic twinning (OR 1.10, 0.75–1.61). We estimated a significantly increased odds for dizygotic multiple births in men treated for cryptorchidism (OR 1.35, 1.01–1.81) which was decreased after exclusion of ART, but the estimate was not significant (OR 0.75, 0.48–1.18).

Discussion

Using dizygotic twinning rates as an indicator of semen quality, we did not find any difference between fathers with hypospadias and controls. Due to sample size, we could not analyze phenotypes separately and can therefore not exclude impaired semen quality in severe hypospadias. We could not demonstrate any association between dizygotic twinning and cryptorchidism. Men treated for cryptorchidism were more likely than controls to use ART to conceive.

Conclusion

Men with hypospadias who conceived without ART were not shown to have impaired semen quality using dizygotic twinning as an epidemiological indicator.
Dietary supplementation of essential oils and lysozyme reduces mortality and improves intestinal integrity of broiler chickens with necrotic enteritis
Authors: Du Encun , Guo Yuming
Published: January 2021

The objective of this study was to investigate the individual and combined effects of essential oils (EO; comprised of thymol and carvacrol) and lysozyme on experimental NE in broiler chickens. A total of 320 1‐day‐old chicks were randomly assigned to five treatment groups: no‐challenge control (NC), NC + C. perfringens challenge (CC), CC + 120 mg/kg of EO, CC + 100 mg/kg of lysozyme, and CC + 120 mg/kg of EO + 100 mg/kg of lysozyme. The results showed that EO or lysozyme decreased the mortality, alleviated the gut lesions, inhibited the liver Enterobacteriaceae carriage, and increased the villus height of the ileum compared with CC (p < .05), although the proliferation of C. perfringens in the ileum was not inhibited (p > .05). Moreover, EO or lysozyme was found to decrease the ileal concentration of sialic acid and the Mucin2 mRNA expression (p < .05). However, the blend of EO and lysozyme did not display significant effect on the NE‐associated mortality or gut damage in contrast with CC (p > .05). In conclusion, these findings suggest the similar protective effects of EO and lysozyme in NE‐associated mortality and intestinal impairment, but their blend did not exhibit ameliorative effect.