bluuebunny/crossref_metadata_2025 huggingface dataset:
Rapid sequence evolution driven by transposable elements at a virulence locus in a fungal wheat pathogen
Authors: Singh Nikhil Kumar , Badet Thomas , Abraham Leen , Croll Daniel
Published: February 2021

Background: Plant pathogens cause substantial crop losses in agriculture production and threaten food security. Plants evolved the ability to recognize virulence factors and pathogens have repeatedly escaped recognition due rapid evolutionary change at pathogen virulence loci (i.e.effector genes). The presence of transposable elements (TEs) in close physical proximity of effector genes can have important consequences for gene regulation and sequence evolution. Species-wide investigations of effector gene loci remain rare hindering our ability to predict pathogen evolvability.

Results: Here, we performed genome-wide association studies (GWAS) on a highly polymorphic mapping population of 120 isolates ofZymoseptoria tritici, the most damaging pathogen of wheat in Europe. We identified a major locus underlying significant variation in reproductive success of the pathogen and damage caused on the wheat cultivar Claro. The most strongly associated locus is intergenic and flanked by genes encoding a predicted effector and a serine type protease, respectively. The center of the locus contained a highly dynamic region consisting of multiple families of TEs. Based on a large global collection of assembled genomes, we show that the virulence locus has undergone substantial recent sequence evolution. Large insertion and deletion events generated length variation between the flanking genes by a factor of seven (5-35 kb). The locus showed also strong signatures of genomic defenses against TEs (i.e.RIP) contributing to the rapid diversification of the locus.

Conclusions: In conjunction, our work highlights the power of combining GWAS and population-scale genome analyses to investigate major effect loci in pathogens.
Advanced Complexity and Plasticity of Neural Activity in Reciprocally Connected Human Cerebral Organoids
Authors: Osaki Tatsuya , Ikeuchi Yoshiho
Published: February 2021

Macroscopic axonal connections in the human brain distribute information and neuronal activity across the brain. Although brain organoid technologies have recently provided novel avenues to investigate human brain function by replicating small neuronal networks of the brainin vitro, functionality of the macroscopic connections between distant regions has not been investigated with organoids. Here, we describe the neural activity of human cerebral organoids reciprocally connected by a bundle of axons. The connected organoids produced significantly more intense and complex oscillatory activity than conventional cerebral organoids. Optogenetic manipulations revealed that the connected organoids could respond to external stimuli and maintain the elevated frequency of neuronal activity for a short term, indicating that the connected organoids exhibit plasticity as a neuronal network. Our findings highlight functional importance of inter-regional connections and suggest that connected organoids can be used as a powerful tool for investigating the development and functions of macroscopic circuits in the human brain. can allow researchers to develop and test compounds to modulate activity ofin vitroneuronal network models in unprecedented ways.
The role of network connectivity on epileptiform activity
Authors: Giacopelli Giuseppe , Tegolo Domenico , Migliore Michele
Published: February 2021

A number of potentially important mechanisms have been identified as key players to generate epileptiform activity, such as genetic mutations, activity-dependent alteration of synaptic functions, and functional network reorganization at the macroscopic level. Here we study how network connectivity at cellular level can affect the onset of epileptiform activity, using computational model networks with different wiring properties. The model suggests that networks connected as in real brain circuits are more resistant to generate seizure-like activity. The results suggest new experimentally testable predictions on the cellular network connectivity in epileptic individuals, and highlight the importance of using the appropriate network connectivity to investigate epileptiform activity with computational models.
Oxidative stress induced by tBHP in human normal colon cells by label free Raman spectroscopy and imaging. The protective role of natural antioxidants in the form of β-carotene
Authors: Brozek-Pluska B. , Beton K.
Published: February 2021

The present study aimed to investigate the protective effect of β-carotene on the oxidative stress injury of human normal colon cell line CCD-18Co triggered by tert-Butyl hydroperoxide (tBHP). XTT examination was used to determine cell viability after β-carotene supplementation and to determine the optimal concentration of antioxidant in spectroscopic studies. Cell biochemistry for CCD-18Co control group, after tBHP adding and for cells in β-carotene - tBHP model was studied by using label-free Raman microspectroscopy. Results for stress treated CCD-18Co human colon normal cells and human colon cancer cells Caco-2 based on vibration features were also compared. Pretreatment with β-carotene alleviated damages in CCD-18Co human normal colon cells induced by tBHP and showed the preventative effect on cells apoptosis. Treatment with β-carotene altered the level of ROS investigated based on intensities of Raman peaks typical for lipids, proteins and nucleic acids. Presented study confirmed the antioxidant, protective role of β-carotene against ROS by using spectroscopic label-free Raman techniques.
HLA binding of self-peptides is biased towards proteins with specific molecular functions
Authors: Karnaukhov Vadim , Paes Wayne , Woodhouse Isaac B. , Partridge Thomas , Nicastri Annalisa , Brackenridge Simon , Scherbinin Dmitrii , Chudakov Dmitry M. , Zvyagin Ivan V. , Ternette Nicola , Koohy Hashem , Borrow Persephone , Shugay Mikhail
Published: February 2021

Human leukocyte antigen (HLA) is highly polymorphic and plays a key role in guiding adaptive immune responses by presenting foreign and self peptides to T cells. Each HLA variant selects a minor fraction of peptides that match a certain motif required for optimal interaction with the peptide-binding groove. These restriction rules define the landscape of peptides presented to T cells. Given these limitations, one might suggest that the choice of peptides presented by HLA is non-random and there is preferential presentation of an array of peptides that is optimal for distinguishing self and foreign proteins. In this study we explore these preferences with a comparative analysis of self peptides enriched and depleted in HLA ligands. We show that HLAs exhibit preferences towards presenting peptides from certain proteins while disfavoring others with specific functions, and highlight differences between various HLA genes and alleles in those preferences. We link those differences to HLA anchor residue propensities and amino acid composition of preferentially presented proteins. The set of proteins that peptides presented by a given HLA are most likely to be derived from can be used to distinguish between class I and class II HLAs and HLA alleles. Our observations can be extrapolated to explain the protective effect of certain HLA alleles in infectious diseases, and we hypothesize that they can also explain susceptibility to certain autoimmune diseases and cancers. We demonstrate that these differences lead to differential presentation of HIV, influenza virus, SARS-CoV-1 and SARS-CoV-2 proteins by various HLA alleles. Finally, we show that the reported self peptidome preferences of distinct HLA variants can be compensated by combinations of HLA-A/HLA-B and HLA-A/HLA-C alleles in frequent haplotypes.
Size matters: An analytical study on the role of tissue size in spatiotemporal distribution of morphogens unveils a transition between different Reaction-Diffusion regimes
Authors: Ceccarelli Alberto S. , Borges Augusto , Chara Osvaldo
Published: February 2021

The reaction-diffusion model constitutes one of the most influential mathematical models to study distribution of morphogens in tissues. Despite its widespread use, the effect of finite tissue size on model-predicted spatiotemporal morphogen distributions has not been completely elucidated. In this study, we analytically investigated the spatiotemporal distributions of morphogens predicted by a reaction-diffusion model in a finite 1D domain, as a proxy for a biological tissue, and compared it with the solution of the infinite-domain model. We explored the reduced parameter, the tissue length in units of a characteristic reaction-diffusion length, and identified two reaction-diffusion regimes separated by a crossover tissue size estimated in ∼3.3 characteristic reaction-diffusion lengths. While above this crossover the infinite-domain model constitutes a good approximation, it breaks below this crossover, whereas the finite-domain model faithfully describes the entire parameter space. We evaluated whether the infinite-domain model renders accurate estimations of diffusion coefficients when fitted to finite spatial profiles, a procedure typically followed in Fluorescence Recovery After Photobleaching (FRAP) experiments. We found that the infinite-domain model overestimates diffusion coefficients when the domain is smaller than the crossover tissue size. Thus, the crossover tissue size may be instrumental in selecting the suitable reaction-diffusion model to study tissue morphogenesis.
Exceptional origin activation revealed by comparative analysis in two laboratory yeast strains
Authors: Peng Jie , Joshi Ishita , Alvino Gina , Kwan Elizabeth , Feng Wenyi
Published: February 2021

We performed a comparative analysis of replication origin activation by genome-wide single-stranded DNA mapping in two common laboratory strains ofSaccharomyces cerevisiaechallenged by hydroxyurea (HU), an inhibitor of the ribonucleotide reductase. By doing so we gained understanding of the impact on origin activation by three factors: replication checkpoint control, DNA sequence polymorphisms, and relative positioning of origin and transcription unit. Our analysis recapitulated the previous finding that the majority of origins are subject to checkpoint control by the Rad53 kinase when cells were treated with HU. In addition, origins either subject to Rad53 checkpoint control or impervious to it are largely concordant between the two strains. However, these two strains also produced different dynamics of origin activation. First, the W303-RAD53cells showed a significant reduction of fork progression than A364a-RAD53cells. This phenotype was accompanied by an elevated level of Rad53 phosphorylation in W303-RAD53cells. Second, W303-rad53K227Acheckpoint-deficient cells activated a greater number of origins accompanied by global reduction of ssDNA across all origins compared to A364a-rad53K227Acells; and this is correlated with lower expression level of the mutant protein in W303 than in A364a. We also show that sequence polymorphism in the consensus motifs of the replication origins plays a minor role in determining origin usage. Remarkably, eight strain-specific origins lack the canonical 11-bp consensus motif for autonomously replicating sequences in either strain background. Finally, we identified a new class of origins that are only active in checkpoint-proficient cells, which we named “Rad53-dependent origins”. The only discernible feature of these origins is that they tend to overlap with an open reading frame, suggesting previously unexplored connection between transcription and origin activation. Our study presents a comprehensive list of origin usage in two diverse yeast genetic backgrounds, fine-tunes the different categories of origins with respect to checkpoint control, and provokes further exploration of the interplay between origin activation and transcription.

Author Summary

Comparative analysis of origins of replication in two laboratory yeast strains reveals new insights into origin activation, regulation and dependency on the Rad53 checkpoint kinase.
Transfer learning via multi-scale convolutional neural layers for human-virus protein-protein interaction prediction
Authors: Yang Xiaodi , Yang Shiping , Lian Xianyi , Wuchty Stefan , Zhang Ziding
Published: February 2021

To predict interactions between human and viral proteins, we combine evolutionary sequence profile features with a Siamese convolutional neural network (CNN) architecture and a multi-layer perceptron (MLP). Our architecture outperforms various feature encodings-based machine learning and state-of-the-art prediction methods. As our main contribution, we introduce two types of transfer learning methods (i.e., ‘frozen’ type and ‘fine-tuning’ type) that reliably predict interactions in a target human-virus domain based on training in a source human-virus domain, by retraining CNN layers. Our transfer learning strategies can effectively apply prior knowledge transfer from large source dataset/task to small target dataset/task to improve prediction performance. Finally, we utilize the ‘frozen’ type of transfer learning to predict human-SARS-CoV-2 PPIs, indicating that our predictions are topologically and functionally similar to experimentally known interactions. Source code and datasets are available athttps://github.com/XiaodiYangCAU/TransPPI/.
Organic electron donors and terminal electron acceptors structure anaerobic microbial communities and interactions in a permanently stratified sulfidic lake
Authors: Rojas Connie A. , De Santiago Torio Ana , Park Serry , Bosak Tanja , Klepac-Ceraj Vanja
Published: February 2021

The extent to which nutrients structure microbial communities in permanently stratified lakes is not well understood. This study characterized microbial communities from the anoxic layers of the meromictic and sulfidic Fayetteville Green Lake (FGL), NY, and investigated the roles of organic electron donors and terminal electron acceptors in shaping microbial community structure and interactions. Bacterial communities from the permanently stratified layer below the chemocline (monimolimnion) and from enrichment cultures inoculated by lake sediments were analyzed using 16S rRNA gene sequencing. Results showed that anoxygenic phototrophs dominated microbial communities in the upper monimolimnion (21 m), which harbored little diversity, whereas the most diverse communities resided at the bottom of the lake (~52 m). Organic electron donors explained 54% of the variation in the microbial community structure in aphotic cultures enriched on an array of organic electron donors and different inorganic electron acceptors. Electron acceptors only explained 10% of the variation, but were stronger drivers of community assembly in enrichment cultures supplemented with acetate or butyrate compared to the cultures amended by chitin, lignin or cellulose. We identified a range of habitat generalists and habitat specialists in both the water column and enrichment samples using Levin’s index. Network analyses of interactions among microbial groups revealed Chlorobi and sulfate reducers as central to microbial interactions in the upper monimolimnion, while Syntrophaceae and other fermenting organisms were more important in the lower monimolimnion. The presence of photosynthetic microbes and communities that degrade chitin and cellulose much below the chemocline supported the downward transport of microbes, organic matter and oxidants from the surface and the chemocline. Collectively, our data suggest niche partitioning of bacterial communities by interactions that depend on the availability of different organic electron donors and terminal electron acceptors. Thus, light, as well as the diversity and availability of chemical resources drive community structure and function in FGL, and likely in other stratified, meromictic lakes.
Metabolic constraints on nitrogen fixation by rhizobia in legume nodules
Authors: Schulte Carolin C. M. , Borah Khushboo , Wheatley Rachel M. , Terpolilli Jason J. , Saalbach Gerhard , Crang Nick , de Groot Daan H. , Ratcliffe R. George , Kruger Nicholas J. , Papachristodoulou Antonis , Poole Philip S.
Published: February 2021

Rhizobia induce nodule formation on legume roots and differentiate into bacteroids, which use plant-derived dicarboxylates as energy and electron sources for reduction of atmospheric N2into ammonia for secretion to plants. Using heterogeneous genome-scale datasets, we reconstructed a model of bacteroid metabolism to investigate the effects of varying dicarboxylate and oxygen supply on carbon and nitrogen allocation. Modelling and13C metabolic flux analysis in bacteroids indicate that microaerobiosis restricts the decarboxylating arm of the TCA cycle and limits ammonia assimilation into glutamate. Catabolism of dicarboxylates induces a higher oxygen demand but also a higher NADH/NAD+ratio compared to sugars. Carbon polymer synthesis and alanine secretion by bacteroids facilitate redox balance in microaerobic nodules with alanine secretion increasing as oxygen tension decreases. Our results provide a framework for understanding fundamental constraints on rhizobial metabolism during symbiotic nitrogen fixation.
THE COMPLEX HODOLOGICAL ARCHITECTURE OF THE MACAQUE DORSAL INTRAPARIETAL AREAS AS EMERGING FROM NEURAL TRACERS AND DW-MRI TRACTOGRAPHY
Authors: Caminiti Roberto , Girard Gabriel , Battaglia-Mayer Alexandra , Borra Elena , Schito Andrea , Innocenti Giorgio M. , Luppino Giuseppe
Published: February 2021

In macaque monkeys, dorsal intraparietal areas are involved in several daily visuo-motor actions. However, their border and sources of cortical afferents remain loosely defined. Through a retrograde tracer and MRI diffusion-based tractography study here we show a complex organization of the dorsal bank of the IPS, which can be subdivided into a rostral area PEip, projecting to the spinal cord, and a caudal area MIP lacking such projections. Both areas include a rostral and a caudal sector, emerging from their ipsilateral, gradient-like connectivity profiles. As tractography estimations, we used the cross-sectional volume of the white matter bundles connecting each area with other parietal and frontal regions, after selecting ROIs corresponding to the injection sites of retrograde tracers. A quantitative analysis between the proportions of cells projecting to all sectors of PEip and MIP along the continuum of the dorsal bank of the IPS and tractography revealed a significant correlation between the two data sets for most connections. Moreover, tractography revealed “false positive” but plausible streamlines awaiting histological validation.
Col6a1+/CD201+mesenchymal cells regulate intestinal morphogenesis and homeostasis
Authors: Melissari Maria-Theodora , Henriques Ana , Tzaferis Christos , Prados Alejandro , Sarris Michalis E. , Chouvardas Panagiotis , Grammenoudi Sofia , Kollias George , Koliaraki Vasiliki
Published: February 2021

Intestinal mesenchymal cells encompass multiple subsets, whose origins, functions, and pathophysiological importance are still not clear. Here, we used theCol6a1Cremouse, which targets telocytes and perivascular cells that can be further distinguished by the combination of the CD201, PDGFRα and αSMA markers. Developmental studies revealed that theCol6a1Cremouse also targets mesenchymal aggregates that are crucial for intestinal morphogenesis and patterning, suggesting an ontogenic relationship between them and homeostatic telocytes. Cell depletion experiments in adulthood showed that Col6a1+/CD201+mesenchymal cells regulate homeostatic enteroendocrine cell differentiation and epithelial proliferation. During acute colitis, they expressed an inflammatory and extracellular matrix remodeling gene signature, but they also retained their properties and topology. Notably, both in homeostasis and tissue regeneration, they were dispensable for normal organ architecture, while CD34+mesenchymal cells expanded, localised at the top of the crypts and showed increased expression of villous-associated morphogenetic factors, providing thus evidence for the plasticity potential of distinct mesenchymal populations in the intestine. Our results provide a comprehensive analysis of the identities, origin, and functional significance of distinct mesenchymal populations in the intestine.
Cardiac Specific Overexpression of Transcription Factor EB (TFEB) in Normal Hearts Induces Pathologic Cardiac Hypertrophy and Lethal Cardiomyopathy
Authors: Kenny Helena C. , Weatherford Eric T. , Collins Greg V. , Allamargot Chantal , Gesalla Taha , Zimmerman Kathy , Goel Harsh , McLendon Jared M. , Dai Dao-Fu , Romac Theo , Streeter Jennifer , Sharafuddin Jacob , Diwan Abhinav , Pereira Renata , Song Long-Sheng , Abel E. Dale
Published: February 2021

TFEB promotes lysosomal biogenesis, autophagy, and lysosomal exocytosis. The present study characterized the consequence of inducible TFEB overexpression in cardiomyocytes in vivo. We generated cardiomyocyte-specific doxycycline inducible (Tet off) mice to achieve spatial and temporal control of TFEB overexpression, by crossing TFEB transgenic mice with mice harboring the tTA transgene (TFEB/tTA). Two weeks after doxycycline removal, an 8-fold increase in TFEB protein expression was observed in transgenic hearts. Heart weight normalized to tibia length was increased by 2.5-fold following TFEB overexpression (TFEB/tTA), characterized by induction of markers of pathological hypertrophy, such asNppa, NppbandActa1, progressive contractile dysfunction and cardiac dilatation. Overexpression of TFEB resulted in premature death, associated with high degree AV block. Reversal of TFEB overexpression normalized cardiac structure and function. Mitochondrial respiration and ATP levels were preserved after 2-weeks of TFEB induction, despite reduced mitochondrial (OXPHOS) protein expression, mtDNA content, and altered mitochondrial morphology. Signaling through mTOR was induced in TFEB/tTA mice, and when inhibited by rapamycin treatment for 4 weeks, partially offset left ventricular dysfunction. Transcriptome analysis revealed early suppression of mitochondrial metabolic pathways, induction of fibrosis and altered calcium signaling. MCOLN1, a lysosomal calcium release channel, the calcineurin target RCAN1.4, and the mitochondrial calcium uniporter (MCU) were strikingly induced in TFEB/tTA mice. In summary, persistent overexpression of TFEB at high levels (8-fold protein upregulation) in cardiomyocytes promotes pathologic cardiac hypertrophy via suppression of mitochondrial bioenergetic pathways and activation of pro-fibrotic and calcium regulatory pathways.
A unified genealogy of modern and ancient genomes
Authors: Wohns Anthony Wilder , Wong Yan , Jeffery Ben , Akbari Ali , Mallick Swapan , Pinhasi Ron , Patterson Nick , Reich David , Kelleher Jerome , McVean Gil
Published: February 2021

The sequencing of modern and ancient genomes from around the world has revolutionised our understanding of human history and evolution1,2. However, the general problem of how best to characterise the full complexity of ancestral relationships from the totality of human genomic variation remains unsolved. Patterns of variation in each data set are typically analysed independently, and often using parametric models or data reduction techniques that cannot capture the full complexity of human ancestry3,4. Moreover, variation in sequencing technology5,6, data quality7and in silico processing8,9, coupled with complexities of data scale10, limit the ability to integrate data sources. Here, we introduce a non-parametric approach to inferring human genealogical history that overcomes many of these challenges and enables us to build the largest genealogy of both modern and ancient humans yet constructed. The genealogy provides a lossless and compact representation of multiple datasets, addresses the challenges of missing and erroneous data, and benefits from using ancient samples to constrain and date relationships. Using simulations and empirical analyses, we demonstrate the power of the method to recover relationships between individuals and populations, as well as to identify descendants of ancient samples. Finally, we show how applying a simple non-parametric estimator of ancestor geographical location to the inferred genealogy recapitulates key events in human history. Our results demonstrate that whole-genome genealogies are a powerful means of synthesising genetic data and provide rich insights into human evolution.
Shared long-term and short-term memory representational formats in occipital and parietal cortex
Authors: Vo Vy A. , Sutterer David W. , Foster Joshua J. , Sprague Thomas C. , Awh Edward , Serences John T.
Published: February 2021

Current theories propose that the short-term retention of information in working memory (WM) and the recall of information from long-term memory (LTM) are supported by overlapping neural mechanisms in occipital and parietal cortex. Both are thought to rely on reinstating patterns of sensory activity evoked by the perception of the remembered item. However, the extent of the shared representations between WM and LTM are unclear, and it is unknown how WM and LTM representations may differ across cortical regions. We designed a spatial memory task that allowed us to directly compare the representations of remembered spatial information in WM and LTM. Critically, we carefully matched the precision of behavioral responses in these tasks. We used fMRI and multivariate pattern analyses to examine representations in (1) retinotopic cortex and (2) lateral parietal cortex (LPC) regions previously implicated in LTM. We show that visual memories were represented in a sensory-like code in both tasks across retinotopic regions in occipital and parietal cortex. LPC regions also encoded remembered locations in both WM and LTM, but in a format that differed from the sensory-evoked activity. These results suggest a striking correspondence in the format of WM and LTM representations across occipital and parietal cortex. On the other hand, we show that activity patterns in nearly all parietal regions, but not occipital regions, contained information that could discriminate between WM trials and LTM trials. Our data provide new evidence for theories of memory systems and the representation of mnemonic content.
Measurement ofKlebsiellaIntestinal Colonization Density to Assess Infection Risk
Authors: Sun Yuang , Patel Alieysa , SantaLucia John , Roberts Emily , Zhao Lili , Kaye Keith S. , Rao Krishna , Bachman Michael A.
Published: February 2021

Background

Klebsiella pneumoniaeand closely related speciesK. variicolaandK. quasipneumoniaeare common causes of healthcare-associated infections, and patients frequently become infected with their intestinal colonizing strain. To assess the association betweenKlebsiellacolonization density and subsequent infections, a case-control study was performed.

Methods

A multiplex qPCR assay was developed and validated to quantifyKlebsiella (K. pneumoniae, K. variicola, and K. quasipneumoniaecombined) relative to total bacterial DNA copies in rectal swabs. Cases ofKlebsiellainfection were identified based on clinical definitions and having a clinical culture isolate and preceding or co-incident colonization isolate with the samewzicapsular sequence type. Controls were colonized patients without subsequent infection and were matched 2:1 to cases based on age, sex, and rectal swab collection date. Quantitative PCR (qPCR) from rectal swab samples was used to measure the association between relative abundance (RA) ofKlebsiellaand subsequent infections.

Results

KlebsiellaRA by qPCR highly correlated with 16S sequencing (ρ=0.79;P<.001). The medianKlebsiellaRA in the study group was 2.6% (interquartile range (IQR) 0.1-22.5, n=238), and was higher in cases (15.7%, IQR 0.93-52.6%, n=83) than controls (1.01%, IQR 0.02-12.8%; n=155;P<0.0001). After adjusting for multiple clinical covariates using inverse probability of treatment weighting, subjects with aKlebsiellaRA > 22% had a 2.87-fold (1.64-5.03,P=0.0003) increased odds of infection compared to those with lower colonization density levels.

Conclusions

Measurement of colonization density by qPCR could represent a novel approach to identify hospitalized patients at risk forKlebsiellainfection.

Importance

Colonization by bacterial pathogens often precedes infection, and offers a window of opportunity to prevent these infections.Klebsiellacolonization is significantly and reproducibly associated with subsequent infection, however factors that enhance or mitigate this risk in individual patients are unclear. This study developed an assay to measure the density ofKlebsiellacolonization, relative to total fecal bacteria, in rectal swabs from hospitalized patients. Applying this assay to 238 colonized patients, highKlebsielladensity defined as >22% of total bacteria, was significantly associated with subsequent infection. Based on widely available polymerase chain reaction (PCR) technology, this type of assay could be deployed in clinical laboratories to identify patients at increased risk ofKlebsiellainfections. As novel therapeutics are developed to eliminate pathogens from the gut microbiome, a rapidKlebsiellacolonization density assay could identify patients who would benefit from this type of infection prevention interventions.
Tdrd3 regulates the progression of meiosis II through translational control ofEmi2mRNA in mouse oocytes
Authors: Takei Natsumi , Sato Keisuke , Takada Yuki , Iyyappan Rajan , Susor Andrej , Yamamoto Takehiro , Kotani Tomoya
Published: February 2021

After completion of meiosis I, the oocyte immediately enters meiosis II and forms a metaphase II (MII) spindle without an interphase, which is fundamental for generating a haploid gamete. Here, we identify tudor domain-containing protein 3 (Tdrd3) as a novel regulator of oocyte meiosis. Although early mitotic inhibitor 2 (Emi2) protein has been shown to ensure the meiosis I to II transition and the subsequent MII spindle formation by inhibiting the anaphase-promoting complex/cyclosome (APC/C), how it accumulates after meiosis I has remained unresolved. We isolated Tdrd3 as a protein directly binding toEmi2mRNA. In GV-stage mouse oocytes,Emi2mRNA assembled into RNA granules containing Tdrd3, while cyclin B1 mRNA, which was translated in early meiosis I, formed different granules. Knockdown of Tdrd3 attenuated Emi2 synthesis in meiosis II without affecting cyclin B1 synthesis in meiosis I. Moreover, Tdrd3-deficient oocytes entered interphase and failed to form an MII spindle after completion of meiosis I. Taken together, our results indicate the importance of Tdrd3-mediated translational control ofEmi2mRNA, which promotes Emi2 synthesis in meiosis II, for the progression of meiosis.
Metagenome-derived virus-microbe ratios across ecosystems
Authors: López-García Purificación , Gutiérrez-Preciado Ana , Krupovic Mart , Ciobanu Maria , Deschamps Philippe , Jardillier Ludwig , López-Pérez Mario , Rodríguez-Valera Francisco , Moreira David
Published: February 2021

It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ∼13 fold and in plankton from marine and saline waters by ∼2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.
Cerebellar modulation of fear behaviour and memory encoding in the PAG
Authors: Lawrenson CL , Paci E , Pickford J , Drake RAR , Lumb BM , Apps R
Published: February 2021

The pivotal role of the periaqueductal grey (PAG) in fear learning is reinforced by the identification of neurons in rat ventral PAG (vPAG) that encode fear memory through signalling the onset and offset of an auditory conditioned stimulus during presentation of the unreinforced conditioned tone during retrieval. Some units only display CS+ onset or offset responses and the two signals differ in extinction sensitivity, suggesting they are independent of each other. In addition, understanding cerebellar contributions to survival circuits is advanced by the discovery that: (i) reversible inactivation of the medial cerebellar nucleus (MCN) during fear consolidation leads in subsequent retrieval to: (a) disruption of the temporal precision of vPAG offset, but not onset responses to the unreinforced conditioned tone, and (b) an increase in duration of freezing behaviour. And (ii) chemogenetic manipulation of the MCN-vPAG projection during fear acquisition: (a) reduces the occurrence of fear- related ultrasonic vocalisations and (b) during subsequent retrieval, slows the extinction rate of fear- related freezing. These findings show that the cerebellum is part of the survival network that regulates fear memory processes at multiple timescales and in multiple ways; raising the possibility that dysfunctional interactions in the cerebellar-survival network may underlie fear-related disorders and comorbidities.

Impact Statement

Cerebellar-periaqueductal grey interactions contribute to fear conditioned processes and, as such, provide a novel target for treating psychological conditions including post-traumatic stress disorder.
AnHB40-Jungbrunnen1-GA 2-OXIDASEregulatory module for gibberellin homeostasis in Arabidopsis
Authors: Dong Shuchao , Tarkowska Danuse , Sedaghatmehr Mastoureh , Molochko Maryna , Gupta Saurabh , Mueller-Roeber Bernd , Balazadeh Salma
Published: February 2021

The phytohormones gibberellins (GAs) play fundamental roles in almost every aspect of plant growth and development. Although there is good knowledge about GA biosynthetic and signaling pathways, factors contributing to the mechanisms homeostatically controlling GA levels remain largely unclear. Here, we demonstrate that homeobox transcription factor HB40 of the HD-Zip family inArabidopsis thalianaregulates GA content at two additive control levels. We show thatHB40expression is induced by GA and in turn reduces the levels of endogenous bioactive GAs by a simultaneous reduction of GA biosynthesis and increased GA deactivation. Hence,HB40overexpression leads to typical GA-deficiency traits, such as small rosettes, reduced plant height, delayed flowering, and male sterility. In contrast, a loss-of-functionhb40mutation enhances GA-controlled growth. Genome-wide RNA-sequencing combined with molecular-genetic analyses revealed that HB40 directly activates transcription ofJUNGBRUNNEN1(JUB1), a key TF repressing growth by suppressing GA biosynthesis and signaling. HB40 also represses genes encoding GA 2-oxidases (GA2oxs) which are major GA catabolic enzymes. The effect of HB40 is ultimately mediated through induction of nuclear growth-repressing DELLA proteins. Our results thus uncover an important role of the HB40/JUB1/GA2ox/DELLA network in controlling GA homeostasis during plant growth.
A minimally destructive protocol for DNA extraction from ancient teeth
Authors: Harney Éadaoin , Cheronet Olivia , Fernandes Daniel M. , Sirak Kendra , Mah Matthew , Bernardos Rebecca , Adamski Nicole , Broomandkhoshbacht Nasreen , Callan Kimberly , Lawson Ann Marie , Oppenheimer Jonas , Stewardson Kristin , Zalzala Fatma , Anders Alexandra , Candilio Francesca , Constantinescu Mihai , Coppa Alfredo , Ciobanu Ion , Dani János , Gallina Zsolt , Genchi Francesco , Nagy Emese Gyöngyvér , Hajdu Tamás , Hellebrandt Magdolna , Horváth Antónia , Király Ágnes , Kiss Krisztián , Kolozsi Barbara , Kovács Péter , Köhler Kitti , Lucci Michaela , Pap Ildikó , Popovici Sergiu , Raczky Pál , Simalcsik Angela , Szeniczey Tamás , Vasilyev Sergey , Virag Cristian , Rohland Nadin , Reich David , Pinhasi Ron
Published: February 2021

Ancient DNA sampling methods—although optimized for efficient DNA extraction—are destructive, relying on drilling or cutting and powdering (parts of) bones and teeth. As the field of ancient DNA has grown, so have concerns about the impact of destructive sampling of the skeletal remains from which ancient DNA is obtained. Due to a particularly high concentration of endogenous DNA, the cementum of tooth roots is often targeted for ancient DNA sampling, but destructive sampling methods of the cementum often result in the loss of at least one entire root. Here, we present a minimally destructive method for extracting ancient DNA from dental cementum present on the surface of tooth roots. This method does not require destructive drilling or grinding, and, following extraction, the tooth remains safe to handle and suitable for most morphological studies, as well as other biochemical studies, such as radiocarbon dating. We extracted and sequenced ancient DNA from 30 teeth (and nine corresponding petrous bones) using this minimally destructive extraction method in addition to a typical tooth sampling method. We find that the minimally destructive method can provide ancient DNA that is of comparable quality to extracts produced from teeth that have undergone destructive sampling processes. Further, we find that a rigorous cleaning of the tooth surface combining diluted bleach and UV light irradiation seems sufficient to minimize external contaminants usually removed through the physical removal of a superficial layer when sampling through regular powdering methods.
Retrograde enhancement of episodic learning by a postlearning stimulus
Authors: Quintanilla Julian , Cox Brittney M. , Gall Christine M. , Mahler Stephen V. , Lynch Gary
Published: February 2021

Evidence suggests encoding of recent episodic experiences may be enhanced by a subsequent salient event. We tested this hypothesis by giving rats a 3-min unsupervised experience with four odors and measuring retention after different delays. Animals recognized that a novel element had been introduced to the odor set at 24 but not 48 h. However, when odor sampling was followed within 5 min by salient light flashes or bedding odor, the memory lasted a full 2 d. These results describe a retroactive influence of salience to promote storage of episodic information and introduce a unique model for studying underlying plasticity mechanisms.
Macromolecular crystallography using microcrystal electron diffraction
Authors: Clabbers Max T. B. , Xu Hongyi
Published: February 2021

Microcrystal electron diffraction (MicroED) has recently emerged as a promising method for macromolecular structure determination in structural biology. Since the first protein structure was determined in 2013, the method has been evolving rapidly. Several protein structures have been determined and various studies indicate that MicroED is capable of (i) revealing atomic structures with charges, (ii) solving new protein structures by molecular replacement, (iii) visualizing ligand-binding interactions and (iv) determining membrane-protein structures from microcrystals embedded in lipidic mesophases. However, further development and optimization is required to make MicroED experiments more accurate and more accessible to the structural biology community. Here, we provide an overview of the current status of the field, and highlight the ongoing development, to provide an indication of where the field may be going in the coming years. We anticipate that MicroED will become a robust method for macromolecular structure determination, complementing existing methods in structural biology.
Optimization of cloud load balancing using fitness function and duopoly theory
Authors: Resma KS , Sharvani GS , Somula Ramasubbareddy
Published: February 2021

Purpose

Current industrial scenario is largely dependent on cloud computing paradigms. On-demand services provided by cloud data centre are paid as per use. Hence, it is very important to make use of the allocated resources to the maximum. The resource utilization is highly dependent on the allocation of resources to the incoming request. The allocation of requests is done with respect to the physical machines present in the datacenter. While allocating the tasks to these physical machines, it needs to be allocated in such a way that no physical machine is underutilized or over loaded. To make sure of this, optimal load balancing is very important.

Design/methodology/approach

The paper proposes an algorithm which makes use of the fitness functions and duopoly game theory to allocate the tasks to the physical machines which can handle the resource requirement of the incoming tasks. The major focus of the proposed work is to optimize the load balancing in a datacenter. When optimization happens, none of the physical machine is neither overloaded nor under-utilized, hence resulting in efficient utilization of the resources.

Findings

The performance of the proposed algorithm is compared with different existing load balancing algorithms such as round-robin load (RR) ant colony optimization (ACO), artificial bee colony (ABC) with respect to the selected parameters response time, virtual machine migrations, host shut down and energy consumption. All the four parameters gave a positive result when the algorithm is simulated.

Originality/value

The contribution of this paper is towards the domain of cloud load balancing. The paper is proposing a novel approach to optimize the cloud load balancing process. The results obtained show that response time, virtual machine migrations, host shut down and energy consumption are reduced in comparison to few of the existing algorithms selected for the study. The proposed algorithm based on the duopoly function and fitness function brings in an optimized performance compared to the four algorithms analysed.
The impostor syndrome: language barriers in organizational ethnography
Authors: Rosales Virginia
Published: February 2021

Purpose

The use of organizational ethnography has grown significantly during the past decades. While language is an important component of ethnographic research, the challenges associated with language barriers are rarely discussed in the literature. The purpose of this paper is to open up a discussion on language barriers in organizational ethnography.

Design/methodology/approach

The author draws on her experience as a PhD student doing an organizational ethnography of an emergency department in a country where she initially did not speak the local language.

Findings

The paper examines the author's research process, from access negotiation to presentation of findings, illustrating the language barriers encountered doing an ethnography in parallel to learning the local language in Sweden.

Research limitations/implications

This paper calls for awareness of the influence of the ethnographer's language skills and shows the importance of discussing this in relation to how we teach and learn ethnography, research practice and diversity in academia.

Originality/value

The paper makes three contributions to organizational ethnography. First, it contributes to the insider/outsider debate by nuancing the ethnographer's experience. Second, it answers calls for transparency by presenting a personal ethnographic account. Third, it contributes to developing the methodology by offering tips to deal with language barriers in doing ethnography abroad.
Uniportal versus three‐port video‐assisted thoracoscopic surgery for non‐small cell lung cancer: A retrospective study
Authors: Li Tian , Xia Lin , Wang Jun , Xu Shibin , Sun Xiaohui , Xu Meiqing , Xie Mingran
Published: February 2021

Background

To investigate the uniportal video‐assisted thoracoscopic surgery (VATS) technique and safety of non‐small cell lung cancer (NSCLC) patients treated with uniportal and three‐port VATS.

Methods

We retrospectively evaluated 146 consecutive patients with NSCLC who underwent VATS lobectomy between January 2018 and May 2018. The general clinical date, perioperative data and life quality were individually compared and analyzed between the two groups.

Results

Intraoperative blood loss was significantly lower in the uniportal than in the three‐port group (p = 0.035), and significantly shorter chest tube drainage and postoperative hospital stay durations were found in the uniportal than in the three‐port group (p = 0.022 and p = 0.008). The postoperative 24 and 72 h numerical rating scale (NRS) scores were significantly lower in the uniportal group than in the three‐port group (p < 0.001 and p < 0.001). There were no significant differences between the two groups in the number or stations of total lymph node dissected (p = 0.222 and p = 0.159). There were no significant differences between the two groups in the postoperative total or respiratory complications (p = 0.917 and p = 0.930).

Conclusions

Uniportal VATS is a safe and effective alternative for patients with NSCLC. It is a preferable option for appropriate cases as it is conducive to patients’ postoperative recovery and quality of life.
Phosphatidylethanol as Blood Biomarker of Alcohol Consumption in Early Pregnancy: An Observational Study in 4,067 Pregnant Women
Authors: Finanger Trine , Spigset Olav , Gråwe Rolf W. , Andreassen Trine N. , Løkken Trine N. , Aamo Trond O. , Bratt Guro E. , Tømmervik Kristin , Langaas Vibeke S. , Finserås Kristin , Salvesen Kjell Å.B. , Skråstad Ragnhild B.
Published: February 2021

Background

The teratogenic effects of alcohol are well documented, but there is a lack of screening methods to detect alcohol use during pregnancy. Phosphatidylethanol 16:0/18:1 (PEth) is a specific and sensitive biomarker reflecting alcohol intake up to several weeks after consumption. The aim of this study was to investigate the prevalence of positive PEth values as an indicator of early prenatal alcohol exposure in a general population of pregnant women.

Methods

Rhesus typing is routinely performed in Norway in all pregnancies around gestational week 12. Rhesus‐negative women have an additional test taken around week 24. Blood samples submitted to St. Olav University Hospital in Trøndelag, Norway, for Rhesus typing during the period September 2017 to October 2018 were collected. A total of 4,533 whole blood samples from 4,067 women were analyzed for PEth (limit of quantification of 0.003 µM).

Results

Fifty‐eight women had a positive PEth sample. Of these, 50 women were positive around gestational week 12, 3 women were positive around week 24, and in 5 cases, the timing was unknown. There were no significant differences in proportions of women with positive PEth values related to age, or rural versus urban residency.

Conclusion

In an unselected pregnant population in Norway, 1.4% had a positive PEth sample around gestational week 12, whereas 0.4% had a positive sample around week 24. The use of PEth as an alcohol biomarker should be further investigated as a diagnostic tool in the antenatal setting.