bluuebunny/crossref_metadata_2025_split huggingface dataset:
In silicoProteome analysis of Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)
Authors: Baruah Chittaranjan , Devi Papari , Sharma Dhirendra K. 
Published: May 2020

ABSTRACTSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) (2019-nCoV), is a positive-sense, single-stranded RNA coronavirus. The virus is the causative agent of coronavirus disease 2019 (COVID-19) and is contagious through human-to-human transmission. The present study reports sequence analysis, complete coordinate tertiary structure prediction andin silicosequence-based and structure-based functional characterization of full SARS-CoV-2 proteome based on the NCBI reference sequence NC_045512 (29903 bp ss-RNA) which is identical to GenBank entryMN908947andMT415321. The proteome includes 12 major proteins namely orf1ab polyprotein (includes 15 proteins), surface glycoprotein, ORF3a protein, envelope protein, membrane glycoprotein, ORF6 protein, ORF7a protein, orf7b, ORF8, Nucleocapsid phosphoprotein and ORF10 protein. Each protein of orf1ab polyprotein group has been studied separately. A total of 25 polypeptides have been analyzed out of which 15 proteins are not yet having experimental structures and only 10 are having experimental structures with known PDB IDs. Out of 15 newly predicted structures six (6) were predicted using comparative modeling and nine (09) proteins having no significant similarity with so far available PDB structures were modeled usingab-initiomodeling. Structure verification using recent tools QMEANDisCo 4.0.0 and ProQ3 for global and local (per-residue) quality estimates indicate that the all-atom model of tertiary structure of high quality and may be useful for structure-based drug designing targets. The study has identified nine major targets (spike protein, envelop protein, membrane protein, nucleocapsid protein, 2’-O-ribose methyltransferase, endoRNAse, 3’-to-5’ exonuclease, RNA-dependent RNA polymerase and helicase) for which drug design targets could be considered. There are other 16 nonstructural proteins (NSPs), which may also be percieved from the drug design angle. The protein structures have been deposited to ModelArchive. Tunnel analysis revealed the presence of large number of tunnels in NSP3, ORF 6 protein and membrane glycoprotein indicating a large number of transport pathways for small ligands influencing their reactivity.
Transcriptional re-wiring by mutation of the yeast Hsf1 oligomerization domain
Authors: Morton Elizabeth A. , Dorrity Michael W. , Zhou Wei , Fields Stanley , Queitsch Christine 
Published: May 2020

AbstractResponse to heat stress is mediated by heat shock transcription factors (HSFs), which possess conserved DNA-binding and oligomerization domains. The oligomerization domain is required for HSF1 to transition under heat stress from a monomer to a homotrimer, which alters DNA-binding specificity and affinity. Sequence variation in the oligomerization domain affects HSF1 activity, although this link is poorly understood. We performed a deep mutational scan of >400,000 variants of the oligomerization domain ofSaccharomyces cerevisiaeHsf1 and measured fitness under stress and non-stress conditions. We identify mutations that confer temperature-specific phenotypes; some exceptional Hsf1variants lead to enhanced growth under heat stress and changes toin vivoDNA-binding and transcriptional programs. The link between Hsf1 oligomerization and DNA-binding domain is evolutionarily conserved, with co-evolving residues between these domains found among fungi. Mutation of transcription factor oligomerization domains may represent a path toward re-wiring transcriptional programs without mutation of DNA-binding domains.
SARS-CoV-2 lethality did not change over time in two Italian Provinces
Authors: Flacco Maria Elena , Martellucci Cecilia Acuti , Bravi Francesca , Parruti Giustino , Mascitelli Alfonso , Mantovani Lorenzo , Boccia Stefania , Manzoli Lamberto 
Published: May 2020

AbstractBackgroundSome experts recently reported that SARS-CoV-2 lethality decreased considerably, but no evidence is yet available. This retrospective cohort study aimed to evaluate whether SARS-CoV-2 case-fatality rate decreased with time, adjusting for several potential confounders.MethodsWe included all subjects diagnosed with SARS-CoV-2 infection in Ferrara and Pescara provinces, Italy. Information were collected from local registries, clinical charts, and electronic health records. We compared the case-fatality rate (after ≥28 days of follow-up) of the subjects diagnosed during April and March, 2020. We used Cox proportional hazards analysis and random-effect logistic regression, adjusting for age, gender, hypertension, type II diabetes, major cardiovascular diseases (CVD), chronic obstructive pulmonary diseases (COPD), cancer and renal disease.ResultsThe sample included 2493 subjects (mean age 58.6y; 47.7% males). 258 persons deceased, after a mean of 16.1 days of follow-up. The mean age of those who died substantially increased from March (78.1±11.0y) to April (84.3±10.2y). From March to April, the case-fatality rate did not decrease in the total sample (9.5% versus 12.1%; adjusted hazard ratio 0.93; 95% Confidence Interval: 0.71-1.21; p=0.6), and in any age-class.ConclusionsIn this sample, SARS-CoV-2 case-fatality rate did not decrease over time, in contrast with recent claims of a substantial improvement of SARS-CoV-2 clinical management. The findings require confirmation from larger datasets.Author summaryWhy was this study done?Some experts recently reported that SARS-CoV-2 lethality decreased considerably, but no evidence is yet available.What did the researchers do and find?We carried out a retrospective cohort study on 2493 SARS-CoV-2 infected subjects from two Italian provinces, evaluating the potential variation of the case-fatality rate over time.From March to April, SARS-CoV-2 case-fatality rate did not decrease, overall and in any age-class.What do these findings mean?The therapies and clinical management of SARS-CoV-2 infected subjects did not determine a substantial change of the clinical course of the disease from March to April, 2020.
Structural basis of bile acid receptor activation and Gs coupling
Authors: Yang Fan , Mao Chunyou , Guo Lulu , Lin Jingyu , Ming Qianqian , Xiao Peng , Wu Xiang , Shen Qingya , Guo Shimeng , Shen Dan-Dan , Lu Ruirui , Zhang Linqi , Huang Shenming , Ping Yuqi , Zhang Chenlu , Ma Cheng , Zhang Kai , Liang Xiaoying , Shen Yuemao , Nan Fajun , Yi Fan , Luca Vincent C , Zhou Jiuyao , Jiang Changtao , Sun Jin-Peng , Xie Xin , Yu Xiao , Zhang Yan 
Published: May 2020

AbstractG protein-coupled bile acid receptor (GPBAR) is a membrane receptor that senses bile acids to regulate diverse functions through Gs activation. Here, we report the cryo-EM structures of GPBAR–Gs complexes stabilized by either high-affinity P395 or the semisynthesized bile acid derivative INT-777 at 3-Å resolution. These structures revealed a large oval-shaped ligand pocket with several sporadic polar groups to accommodate the amphipathic cholic core of bile acids. A fingerprint of key residues recognizing diverse bile acids in the orthosteric site, a putative second bile acid binding site with allosteric properties and structural features contributing to bias property were identified through structural analysis and mutagenesis studies. Moreover, structural comparison of GPBAR with other GPCRs uncovered an atypical mode of receptor activation and G-protein– coupling, featuring a different set of key residues connecting the ligand binding pocket to the Gs coupling site, and a specific interaction motif localized in intracellular loop 3. Overall, our study not only provides unique structural features of GPBAR in bile acid recognition, allosteric effects and biased signaling, but also suggests that distinct allosteric connecting mechanisms between the ligand binding pocket and the G protein binding site exist in the GPCR superfamily.
ZDHHC5 targets Protocadherin 7 to the cell surface by a palmitoylation-dependent mechanism to promote successful cytokinesis
Authors: Özkan Küçük Nazlı Ezgi , Yiğit Berfu Nur , Değirmenci Beste Senem , Qureshi Mohammad Haroon , Kamacıoğlu Altuğ , Bavili Nima , Kiraz Alper , Özlü Nurhan 
Published: May 2020

ABSTRACTCell division requires dramatic reorganization of the cell cortex that is primarily driven by the actomyosin network. We previously reported that Protocadherin 7 (PCDH7) enriches at the cell surface during mitosis which is required for building up the full mitotic rounding pressure. Here we showed that PCDH7 gets palmitoylated and interacts with the palmitoyltransferase, ZDHHC5. Both PCDH7 and ZDHHC5 co-localize at the mitotic cell surface, and they translocate to the cleavage furrow during cytokinesis. PCDH7’s localization depends on palmitoylation activity of ZDHHC5. Loss of expression of PCDH7 impairs active RhoA and phospho-myosin levels at the cleavage furrow and increases the rate of multinucleated cells. This work uncovers a palmitoylation-dependent translocation mechanism for PCDH7 and attributes a regulatory role to contributing actomyosin activity during cytokinesis.
A Two-Part Strategy using Genomic Selection in Hybrid Crop Breeding Programs
Authors: Powell Owen , Gaynor R. Chris , Gorjanc Gregor , Werner Christian R. , Hickey John M. 
Published: May 2020

AbstractHybrid crop breeding programs using a two-part strategy produced the most genetic gain, but a maximum avoidance of inbreeding crossing scheme was required to increase long-term genetic gain. The two-part strategy uses outbred parents to complete multiple generations per year to reduce the generation interval of hybrid crop breeding programs. The maximum avoidance of inbreeding crossing scheme manages genetic variance by maintaining uniform contributions and inbreeding coefficients across all crosses. This study performed stochastic simulations to quantify the potential of a two-part strategy in combination with two crossing schemes to increase the rate of genetic gain in hybrid crop breeding programs. The two crossing schemes were: (i) a circular crossing scheme, and (ii) a maximum avoidance of inbreeding crossing scheme. The results from this study show that the implementation of genomic selection increased the rate of genetic gain, and that the two-part hybrid crop breeding program generated the highest genetic gain. This study also shows that the maximum avoidance of inbreeding crossing scheme increased long-term genetic gain in two-part hybrid crop breeding programs completing multiple selection cycles per year, as a result of maintaining higher levels of genetic variance over time. The flexibility of the two-part strategy offers further opportunities to integrate new technologies to further increase genetic gain in hybrid crop breeding programs, such as the use of outbred training populations. However, the practical implementation of the two-part strategy will require the development of bespoke transition strategies to fundamentally change the data, logistics, and infrastructure that underpin hybrid crop breeding programs.Key messageHybrid crop breeding programs using a two-part strategy produced the most genetic gain by using outbred parents to complete multiple generations per year. However, a maximum avoidance of inbreeding crossing scheme was required to manage genetic variance and increase long-term genetic gain.
Daphnia magnamodifies its gene expression extensively in response to caloric restriction revealing a novel effect on haemoglobin isoform preference
Authors: Hearn Jack , Clark Jessica , Wilson Philip J. , Little Tom J. 
Published: May 2020

AbstractCaloric restriction (CR) produces clear phenotypic effects within and between generations of the model crustaceanDaphnia magna. We have previously established that micro RNAs and cytosine methylation change in response to CR in this organism, and we demonstrate here that CR has a dramatic effect on gene expression. Over 6000 genes were differentially expressed between CR and well-fedD. magna, with a bias towards up-regulation of genes under caloric restriction. We identified a highly expressed haemoglobin gene that responds to CR by changing isoform proportions. Specifically, a transcript containing three erythrocruorin domains was strongly down-regulated under CR in favour of transcripts containing fewer or no such domains. This change in the haemoglobin mix is similar to the response to hypoxia inDaphnia,which is mediated through the transcription factor hypoxia-inducible factor 1, and ultimately the mTOR signalling pathway. This is the first report of a role for haemoglobin in the response to CR. We also observed high absolute expression of super-oxide dismutase (SOD) in normally-fed individuals, which contrasts with observations of high SOD levels under in CR in other taxa. However, key differentially expressed genes, like SOD, were not targeted by differentially expressed micro-RNAs. Whether the link between Haemoglobin and CR is the case in other organisms, or is related to the aquatic lifestyle, remains to be tested. It suggests that one response to CR may be to simply transport less oxygen and lower respiration.
Discovery and characterization of a novel family of prokaryotic nanocompartments involved in sulfur metabolism
Authors: Nichols Robert J. , LaFrance Benjamin , Phillips Naiya R. , Oltrogge Luke M. , Valentin-Alvarado Luis E. , Bischoff Amanda J. , Nogales Eva , Savage David F. 
Published: May 2020

AbstractProkaryotic nanocompartments, also known as encapsulins, are a recently discovered proteinaceous organelle in prokaryotes that compartmentalize cargo enzymes. While initial studies have begun to elucidate the structure and physiological roles of encapsulins, bioinformatic evidence suggests that a great diversity of encapsulin nanocompartments remains unexplored. Here, we describe a novel encapsulin in the freshwater cyanobacterium Synechococcus elongatus PCC 7942. This nanocompartment is upregulated upon sulfate starvation and encapsulates a cysteine desulfurase enzyme via an N-terminal targeting sequence. Using cryoelectron microscopy, we have determined the structure of the nanocompartment complex to 2.2 Å resolution. Lastly, biochemical characterization of the complex demonstrated that the activity of the cysteine desulfurase is enhanced upon encapsulation. Taken together, our discovery, structural analysis, and enzymatic characterization of this prokaryotic nanocompartment provide a foundation for future studies seeking to understand the physiological role of this encapsulin in various bacteria.
Draft Genome Sequences of Seven Strains ofDickeya dadantii, a Quick Decline-causing Pathogen in Fruit Trees, Isolated from Japan
Authors: Fujikawa Takashi , Hatomi Hiroe , Ota Nobuyoshi 
Published: May 2020

AbstractPlant pathogenic bacteriumDickeya dadantiicauses quick decline in fruit trees (apple, Japanese pear, and peach). In this study, we report on the draft genome sequences of seven strains ofD. dadantiiisolated from fruit trees with typical quick decline symptoms in Japan.
A proteogenomics workflow to uncover the world of small proteins inStaphylococcus aureus
Authors: Fuchs Stephan , Kucklick Martin , Lehmann Erik , Beckmann Alexander , Wilkens Maya , Kolte Baban , Mustafayeva Ayten , Ludwig Tobias , Diwo Maurice , Wissing Josef , Jänsch Lothar , Ahrens Christian H. , Ignatova Zoya , Engelmann Susanne 
Published: May 2020

AbstractSmall proteins play diverse and essential roles in bacterial physiology and virulence. Despite their importance, automated genome annotation algorithms still cannot accurately annotate all respective small open reading frames (sORFs), as they usually provide insufficient sequence information for domain and homology searches, tend to be species specific and only a few experimentally validated examples are covered in standard proteomics studies. The accuracy and reliability of genome annotations, particularly for sORFs, can be significantly improved by integrating protein evidence from experimental approaches that enrich for small proteins. Here we present a highly optimized and flexible workflow for bacterial proteogenomics, which covers all steps from (i) creation of protein databases, (ii) database searches, (iii) peptide-to-genome mapping to (iv) result interpretation and whose automated execution is supported by two open source tools (SALT&Pepper). We used the workflow to identify high quality peptide spectrum matches (PSMs) for both annotated and unannotated small proteins (≤ 100 aa; SP100) inStaphylococcus aureusNewman. Proteins isolated from cells at the exponential and stationary growth phase were digested with different endopeptidases (trypsin, Lys-C, AspN), the resulting peptides fractionated by gel-based and gel-free methods and measured with highly sensitive mass spectrometers. PSMs or sORF predictions from sORFfinder were stringently filtered allowing us to detect 185 soluble SP100, 69 of which were missing in the used genome annotation. Most interestingly, almost half of the identified SP100 were basic, suggesting a role in binding to more acidic molecules such as nucleic acids or phospholipids. In addition, phage-related functions were proposed for 30 SP100, based on the localization of their coding sequences in the genome.
Cloud computing in SMEs: towards delegation of the CIO role
Authors: Bouaynaya Wafa 
Published: May 2020

Purpose
The purpose of this paper is to contribute to a growing body of research on information systems security, by studying open source alternatives for cloud computing. Several questions have been raised about the reliability of these promising but ambiguous offers, as the adoption of a cloud solution within an enterprise is generally accompanied by a change in the chief information officer (CIOs) role and loss of expertise.

Design/methodology/approach
The research uses a mixed research methodology: a first step is based on a questionnaire survey to investigate the security aspects of open source and understand the role of CIOs in the migration process. The investigation involved nearly 800 companies operating in the cloud computing sector in 16 European countries between November 2015 and January 2016. Then, this paper completes the research with a qualitative study by examining the activity of two sample companies.

Findings
Research confirms that open source cloud solutions offer a higher level of security than proprietary solutions. It is also noted that the role of CIOs is delegated to a third external actor: a transition CIO. Transition CIO is the guarantor of the strategic and security choices of small and medium enterprises.

Research limitations/implications
These findings have important implications and great value to managers and cloud computing providers, in terms of formulating better cloud computing solutions. This study can also assist in increasing their understanding of the new role of CIO in the migration process to cloud computing.

Originality/value
This study contributes to the body of research on cloud computing. It is first of its kind with its focus on open source alternatives. Another novelty of this research is that it suggests a new conception for the CIOs role in the migration to cloud computing. Finally, the findings of this study would serve as a European market study to different companies interested in cloud computing.
The imitation-innovation link, external knowledge search and China's innovation system
Authors: Wu Jie , Zhang Xinhe , Zhuo Shuaihe , Meyer Martin , Li Bin , Yan Haifeng 
Published: May 2020

PurposeThe authors attempt to answer the basic questions: How is imitation tied to innovation? This question is addressed in the context of China's innovation system in the 2000s where Chinese industrial firms simultaneously implement innovation and imitation strategies in their new product developments.Design/methodology/approachThe authors first build on lattice theory and supermodularity theory to provide a rigorous and careful mathematical proof. The authors further conduct the empirical analyses using an original data on Chinese manufacturing firms' innovation and imitation strategies in the development of new products in 2002.FindingsThis article reveals the complementarity relation between imitation and innovation strategies and identifies external knowledge search as the boundary condition that influences the extent to which two strategies reinforce each other.Research limitations/implicationsThe findings of the imitation-innovation complementarity suggest that imitation is not only an indispensable strategy independent of innovation, but also is vital to the effectiveness of innovation itself.Practical implicationsThe imitation-innovation complementarity finding provides some evidence for the contention that Chinese latecomers exploit the synergies of imitation and innovation, transforming themselves from imitators to innovators and vibrant competitors in the global market (Wu et al., 2016) and, as a result, national innovation system has evolved from a state-sponsored imitation program to the imitation-innovation mixture.Originality/valueIn contrast to earlier innovation studies in which innovation and imitation are unrelated, this study reveals that imitation complements innovation, and the extent of Chinese firms' external knowledge search affects the complementary relationship between imitation and innovation. These findings add important insights to the innovation management literature and contribute empirical evidence to the interplay of innovation and imitation enhancing national innovation system.
Evaluation of seven indices of on‐plant seed storage (serotiny) shows that the linear slope is best
Authors: Lamont Byron B. 
Published: May 2020

Abstract

On‐plant storage of seeds (serotiny) is a feature of many fire‐prone dominant trees and shrubs in North America, Mediterranean Basin, South Africa and Australia. Understanding how it has responded to the prevailing fire regime and recruitment/growing conditions, and its genetic basis and adaptive significance, depends on the use of an accurate index of the level of serotiny.

Seven indices, three measuring ‘apparent’ serotiny and four measuring ‘inherent’ serotiny, were evaluated for their ability to reflect the extent to which seeds are stored in the crown for later release. The most widely used indices ignore the temporal aspects of seed attrition and are vulnerable to plant size, age, fecundity and local growing‐condition effects, while age of the oldest crop year with closed cones/fruits depends on the accuracy of a single observation. Presence/absence of serotiny at the individual tree level ignores the effect of plant age on the expression of serotiny.

The slope of the line through the percentage of cones/fruits that still retain their seeds in progressively older crop years, the ‘degree of serotiny’ (100/slope), is shown to be unbiased by annual fluctuations in crop size, differences in plant age or variations in local growing conditions. It also corresponds to a probability, and thus more accurate, estimate of age of the oldest unopened structures. Since seeds have a lower % viability than the % of supporting cones/fruits closed at any age, there is a case for applying the slope method to the fraction of viable seeds retained to arrive at an estimate of the age of the oldest viable seeds on the plant, as the ultimate index of serotiny.

If the level of serotiny is to be related to the fire regime, then care needs to be taken to use records over a sufficiently long time to have had an evolutionary impact, unless this is being used against controls to examine a genetic response to the new fire regime.

Synthesis. Among seven currently available indices of serotiny, the slope measure is shown to be the most accurate for studies that relate the level of serotiny to the fire regime and habitat conditions under which the species evolved, as well as for examining its heritability. Attention needs to shift from just recording cones/fruits closed to include the viability of seeds that remain as a better basis for understanding the role of serotiny in post‐fire recruitment.