bluuebunny/crossref_metadata_2025_split huggingface dataset:
Highly efficient generation of sheep with a defined FecBB mutation via adenine base editing
Authors: Zhou Shiwei , Ding Yige , Liu Jiao , Liu Yao , Zhao Xiaoe , Li Guanwei , Zhang Chenguang , Li Chao , Wang Ying , Kalds Peter , Gao Yawei , Zong Bo , Huang Xiaoyu , Huang Shuhong , Yu Honghao , Kou Qifang , Petersen Bjoern , Huang Xingxu , Wang Xiaolong , Ma Baohua , Chen Yulin 
Published: July 2020

AbstractBase editing has the potential to improve important economic traits in agriculture and can precisely convert single nucleotides in DNA or RNA sequences into minimal double-strand DNA breaks (DSB). Adenine base editors (ABE) have recently emerged as a base editing tool for the conversion of targeted A:T to G:C, but have not yet been used in sheep. ABEmax is one of the latest versions of ABE, which consists of a catalytically-impaired nuclease and a laboratory-evolved DNA-adenosine deaminase. The Booroola fecundity (FecBB) mutation (g.A746G, p.Q249R) in the bone morphogenetic protein receptor 1B (BMPR1B) gene influences fecundity in many sheep breeds. In this study, by using ABEmax we successfully obtained lambs with defined point mutations that result in an amino acid substitution (p.Gln249Arg). The efficiency of the defined point mutations was 75% in newborn lambs, since six lambs were heterozygous at the FecBB mutation site (g.A746G, p.Q249R), and two lambs were wild-type. We did not detect off-target mutations in the eight edited lambs. Here, we report the validation of the first gene-edited sheep generated by ABE and highlight its potential to improve economically important traits in livestock.
Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures
Authors: Barroso José Renato M. S. , Mariano Diego , Dias Sandro R. , Rocha Rafael E. O. , Santos Lucianna H. , Nagem Ronaldo A. P. , de Melo-Minardi Raquel C. 
Published: July 2020

Abstract
Background
Protein engineering has many applications for industry, such as the development of new drugs, vaccines, treatment therapies, food, and biofuel production. A common way to engineer a protein is to perform mutations in functionally essential residues to optimize their function. However, the discovery of beneficial mutations for proteins is a complex task, with a time-consuming and high cost for experimental validation. Hence, computational approaches have been used to propose new insights for experiments narrowing the search space and reducing the costs.

Results
In this study, we developed Proteus (an acronym for Protein Engineering Supporter), a new algorithm for proposing mutation pairs in a target 3D structure. These suggestions are based on contacts observed in other known structures from Protein Data Bank (PDB). Proteus’ basic assumption is that if a non-interacting pair of amino acid residues in the target structure is exchanged to an interacting pair, this could enhance protein stability. This trade is only allowed if the main-chain conformation of the residues involved in the contact is conserved. Furthermore, no steric impediment is expected between the proposed mutations and the surrounding protein atoms. To evaluate Proteus, we performed two case studies with proteins of industrial interests. In the first case study, we evaluated if the mutations suggested by Proteus for four protein structures enhance the number of inter-residue contacts. Our results suggest that most mutations proposed by Proteus increase the number of interactions into the protein. In the second case study, we used Proteus to suggest mutations for a lysozyme protein. Then, we compared Proteus’ outcomes to mutations with available experimental evidence reported in the ProTherm database. Four mutations, in which our results agree with the experimental data, were found. This could be initial evidence that changes in the side-chain of some residues do not cause disturbances that harm protein structure stability.

Conclusion
We believe that Proteus could be used combined with other methods to give new insights into the rational development of engineered proteins. Proteus user-friendly web-based tool is available at <http://proteus.dcc.ufmg.br>.
Loqusdb: added value of an observations database of local genomic variation
Authors: Magnusson Måns , Eisfeldt Jesper , Nilsson Daniel , Rosenbaum Adam , Wirta Valtteri , Lindstrand Anna , Wedell Anna , Stranneheim Henrik 
Published: July 2020

Abstract
Background
Exome and genome sequencing is becoming the method of choice for rare disease diagnostics. One of the key challenges remaining is distinguishing the disease causing variants from the benign background variation. After analysis and annotation of the sequencing data there are typically thousands of candidate variants requiring further investigation. One of the most effective and least biased ways to reduce this number is to assess the rarity of a variant in any population. Currently, there are a number of reliable sources of information for major population frequencies when considering single nucleotide variants (SNVs) and small insertion and deletions (INDELs), with gnomAD as the most prominent public resource available. However, local variation or frequencies in sub-populations may be underrepresented in these public resources. In contrast, for structural variation (SV), the background frequency in the general population is more or less unknown mostly due to challenges in calling SVs in a consistent way. Keeping track of local variation is one way to overcome these problems and significantly reduce the number of potential disease causing variants retained for manual inspection, both for SNVs and SVs.

Results
Here, we present loqusdb, a tool to solve the challenge of keeping track of any type of variant observations from genome sequencing data. Loqusdb was designed to handle a large flow of samples and unlike other solutions, samples can be added continuously to the database without rebuilding it, facilitating improvements and additions. We assessed the added value of a local observations database using 98 samples annotated with information from a background of 888 unrelated individuals.

Conclusions
We show both how powerful SV analysis can be when filtering for population frequencies and how the number of apparently rare SNVs/INDELs can be reduced by adding local population information even after annotating the data with other large frequency databases, such as gnomAD. In conclusion, we show that a local frequency database is an attractive, and a necessary addition to the publicly available databases that facilitate the analysis of exome and genome data in a clinical setting.
Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases
Authors: Mariano Diego , Pantuza Naiara , Santos Lucianna H. , Rocha Rafael E. O. , de Lima Leonardo H. F. , Bleicher Lucas , de Melo-Minardi Raquel Cardoso 
Published: July 2020

AbstractΒ-glucosidases are key enzymes used in second-generation biofuel production. They act in the last step of the lignocellulose saccharification, converting cellobiose in glucose. However, most of the β-glucosidases are inhibited by high glucose concentrations, which turns it a limiting step for industrial production. Thus, β-glucosidases have been targeted by several studies aiming to understand the mechanism of glucose tolerance, pH and thermal resistance for constructing more efficient enzymes. In this paper, we present a database of β-glucosidase structures, called Glutantβase. Our database includes 3842 GH1 β-glucosidase sequences collected from UniProt. We modeled the sequences by comparison and predicted important features in the 3D-structure of each enzyme. Glutantβase provides information about catalytic and conserved amino acids, residues of the coevolution network, protein secondary structure, and residues located in the channel that guides to the active site. We also analyzed the impact of beneficial mutations reported in the literature, predicted in analogous positions, for similar enzymes. We suggested these mutations based on six previously described mutants that showed high catalytic activity, glucose tolerance, or thermostability (A404V, E96K, H184F, H228T, L441F, and V174C). Then, we used molecular docking to verify the impact of the suggested mutations in the affinity of protein and ligands (substrate and product). Our results suggest that only mutations based on the H228T mutant can reduce the affinity for glucose (product) and increase affinity for cellobiose (substrate), which indicates an increment in the resistance to product inhibition and agrees with computational and experimental results previously reported in the literature. More resistant β-glucosidases are essential to saccharification in industrial applications. However, thermostable and glucose-tolerant β-glucosidases are rare, and their glucose tolerance mechanisms appear to be related to multiple and complex factors. We gather here, a set of information, and made predictions aiming to provide a tool for supporting the rational design of more efficient β-glucosidases. We hope that Glutantβase can help improve second-generation biofuel production. Glutantβase is available athttp://bioinfo.dcc.ufmg.br/glutantbase.
Desiccation does not drastically increase the accessibility of exogenous DNA to nuclear genomes: evidence from the frequency of endosymbiotic DNA transfer
Authors: Li Xixi , Fang Cheng , Zhao Jun-Peng , Zhou Xiao-Yu , Ni Zhihua , Niu Deng-Ke 
Published: July 2020

Abstract
Background
Although horizontal gene transfer (HGT) is a widely accepted force in the evolution of prokaryotic genomes, its role in the evolution of eukaryotic genomes remains hotly debated. Some bdelloid rotifers that are resistant to extreme desiccation and radiation undergo a very high level of HGT, whereas in another desiccation-resistant invertebrate, the tardigrade, the pattern does not exist. Overall, the DNA double-strand breaks (DSBs) induced by prolonged desiccation have been postulated to open a gateway to the nuclear genome for exogenous DNA integration and thus to facilitate the HGT process, thereby enhancing the rate of endosymbiotic DNA transfer (EDT).

Results
We first surveyed the abundance of nuclear mitochondrial DNAs (NUMTs) and nuclear plastid DNAs (NUPTs) in five eukaryotes that are highly resistant to desiccation: the bdelloid rotifers Adineta vaga and Adineta ricciae, the tardigrade Ramazzottius varieornatus, and the resurrection plants Dorcoceras hygrometricum and Selaginella tamariscina. Excessive NUMTs or NUPTs were not detected. Furthermore, we compared 24 groups of desiccation-tolerant organisms with their relatively less desiccation-tolerant relatives but did not find a significant difference in NUMT/NUPT contents.

Conclusions
Desiccation may induce DSBs, but it is unlikely to dramatically increase the frequency of exogenous sequence integration in most eukaryotes. The capture of exogenous DNA sequences is possible only when DSBs are repaired through a subtype of non-homologous end joining, named alternative end joining (alt-EJ). Due to the deleterious effects of the resulting insertion mutations, alt-EJ is less frequently initiated than other mechanisms.
Fasciclin-like arabinogalactan gene family in Nicotiana benthamiana: genome-wide identification, classification and expression in response to pathogens
Authors: Wu Xinyang , Lai Yuchao , Lv Lanqing , Ji Mengfei , Han Kelei , Yan Dankan , Lu Yuwen , Peng Jiejun , Rao Shaofei , Yan Fei , Zheng Hongying , Chen Jianping 
Published: July 2020

AbstractBackgroundNicotiana benthamianais widely used as a model plant to study plant-pathogen interactions. Fasciclin-like arabinogalactan proteins (FLAs), a subclass of arabinogalactan proteins (AGPs), participate in mediating plant growth, development and response to abiotic stress. However, the members of FLAs inN. benthamianaand their response to plant pathogens are unknown.Results38NbFLAswere identified from a genome-wide study.NbFLAscould be divided into four subclasses, and their gene structure and motif composition were conserved in each subclass.NbFLAsmay be regulated by cis-acting elements such as STRE and MBS, and may be the targets of transcription factors like C2H2. Quantitative real time polymerase chain reaction (RT-qPCR) results showed that selectedNbFLAswere differentially expressed in different tissues. All of the selectedNbFLAswere significantly downregulated following infection by turnip mosaic virus (TuMV) and most of them also byPseudomonas syringae pv tomatostrain DC3000 (PstDC3000), suggesting possible roles in response to pathogenic infection.ConclusionsThis study systematically identifiedFLAsinN. benthamiana, and indicates their potential roles in response to biotic stress. The identification ofNbFLAswill facilitate further studies of their role in plant immunity inN. benthamiana.
Genome-wide identification, characterization and expression profiling of gibberellin metabolism genes in jute
Authors: Honi Ummay , Amin Md. Ruhul , Kabir Shah Md Tamim , Bashar Kazi Khayrul , Moniruzzaman Md. , Jahan Rownak , Jahan Sharmin , Haque Md. Samiul , Islam Shahidul 
Published: July 2020

Abstract
Background
Gibberellin (GA) is one of the most essential phytohormones that modulate plant growth and development. Jute (Corchorus sp.) is the second most important source of bast fiber. Our result has shown that exogenous GA can positively regulate jute height and related characteristics which mean increasing endogenous GA production will help to get a jute variety with improved characteristics. However, genes involved in jute GA biosynthesis have not been analyzed precisely.

Results
Genome-wide analysis identified twenty-two candidate genes involved in jute GA biosynthesis pathway. Among them, four genes- CoCPS, CoKS, CoKO and CoKAO work in early steps. Seven CoGA20oxs, three CoGA3oxs, and eight GA2oxs genes work in the later steps. These genes were characterized through phylogenetic, motif, gene structure, and promoter region analysis along with chromosomal localization. Spatial gene expression analysis revealed that 11 GA oxidases were actively related to jute GA production and four of them were marked as key regulators based on their expression level. All the biosynthesis genes both early and later steps showed tissue specificity. GA oxidase genes were under feedback regulation whereas early steps genes were not subject to such regulation.

Conclusion
Enriched knowledge about jute GA biosynthesis pathway and genes will help to increase endogenous GA production in jute by changing the expression level of key regulator genes. CoGA20ox7, CoGA3ox2, CoGA2ox3, and CoGA2ox5 may be the most important genes for GA production.
Identification of genetic loci associated with forage quality in response to water deficit in autotetraploid alfalfa (Medicago sativa L.)
Authors: Lin Sen , Medina Cesar Augusto , Boge Bill , Hu Jinguo , Fransen Steven , Norberg Steven , Yu Long-Xi 
Published: July 2020

AbstractBackgroundAlfalfa has been cultivated in many regions around the world as an important forage crop due to its nutritive value to livestock and ability to adapt to various environments. However, the genetic basis by which plasticity of quality-relevant traits influence alfalfa adaption to different water conditions remain largely unknown.ResultsIn the present study, 198 accessions of alfalfa of the core collection for drought tolerance were evaluated for 26 forage quality traits in a field trial under an imposed deficit irrigation gradient. Regression analysis between quality traits and water stress revealed that values of fiber-related traits were negatively correlated with values of energy-related traits as water deficit increased. More than one hundred significant markers associated with forage quality under different water treatments were identified using genome-wide association studies with genotyping by sequencing. Among them, 131 markers associated with multiple traits in all the water deficit treatments. Most of the associated markers were dependent to the levels of water deficit, suggesting genetic controls for forage quality traits were dependent to the stress treatment. Twenty-four loci associated with forage quality were annotated to functional genes that may play roles in cell development or in response to water stress.ConclusionsThis study addressed the genetic base of phenotypic variation of forage quality traits under water deficit. The SNP markers identified in this study will be useful in marker-assisted selection for the genetic improvement of alfalfa with enhanced drought tolerance while maintaining forage quality.
Anterior wall myocardial infarction in a 16-year-old man caused by coronary artery aneurysm during the outbreak of COVID-19
Authors: Ma Wenshuai , Li Chunyu , Zhang Wei , Ji Zhaole , Li Yan 
Published: July 2020

Abstract
Background
Coronary artery aneurysm (CAA) is a potential cause of infarction. During the outbreak of coronavirus disease 2019 (COVID-19), home isolation and activity reduction can lead to hypercoagulability. Here, we report a case of sudden acute myocardial infarction caused by large CAA during the home isolation.

Case presentation
During the outbreak of coronavirus disease 2019 (COVID-19),a 16-year-old man with no cardiac history was admitted to CCU of Tang du hospital because of severe chest pain for 8 h. The patient reached the hospital its own, his electrocardiogram showed typical features of anterior wall infarction, echocardiography was performed and revealed local anterior wall dysfunction, but left ventricle ejection fraction was normal, initial high-sensitivity troponin level was 7.51 ng/mL (<1.0 ng/mL). The patient received loading dose of aspirin and clopidogrel bisulfate and a total occlusion of the LAD was observed in the emergency coronary angiography (CAG). After repeated aspiration of the thrombus, TIMI blood flow reached level 3. Coronary artery aneurysm was visualized in the last angiography. No stent was implanted. Intravascular ultrasound (IVUS) was performed and the diagnosis of coronary artery aneurysm was further confirmed. The patient was discharged with a better health condition.

Conclusions
Coronary artery aneurysm is a potential reason of infarction, CAG and IVUS are valuable tools in diagnosis in such cases, during the outbreak of coronavirus disease 2019 (COVID-19), home isolation and activity reduction can lead to hypercoagulability, and activities at home should be increased in the high-risk patients.
Contribution of ESC DAPT guideline-endorsed high thrombotic risk features to long-term clinical outcomes among patients with and without high bleeding risk after PCI
Authors: Wang Hao-Yu , Dou Ke-Fei , Yin Dong , Zhang Dong , Gao Run-Lin , Yang Yue-Jin 
Published: July 2020

Abstract
Background
Whether the underlying risk of high bleeding risk (HBR) influences the relationship of high thrombotic risk (HTR) features with adverse events after drug-eluting stent implantation remains unclear. The purpose of this study was to evaluate (1) the prognostic effect of ESC guideline-endorsed HTR features on long-term clinical outcomes and (2) whether the outcomes of HTR versus non-HTR features vary by HBR status.

Methods
Ten thousand one hundred sixty-seven consecutive patients who underwent percutaneous coronary intervention between January 2013 and December 2013 were prospectively enrolled in Fuwai PCI Registry. Patients who are at HTR were defined as: diffuse multivessel disease in diabetic patients, chronic kidney disease, at least three stents implanted, at least three stents lesions treated, bifurcation with two stents implanted, total stent length > 60 mm, or treatment of chronic total occlusion. The definition of HBR was based on the Academic Research Consortium for HBR criteria. The primary ischemic outcome was major adverse cardiac event (MACE), a composite of cardiac death, myocardial infarction, target vessel revascularization and stent thrombosis. The primary bleeding outcome was clinically relevant bleeding, defined according to Bleeding Academic Research Consortium (BARC) type 2, 3 or 5 bleeding.

Results
With a 2.4-year median follow-up, 4430 patients (43.6%) having HTR experienced a significantly higher risk of MACE (hazard ratio [HR] adjust: 1.56, 95% confidence interval [CI]: 1.34–1.82; P < 0.001) and device-oriented composite endpoint (composite of cardiac death, target-vessel MI, and target lesion revascularization) (HRadjust: 1.52 [1.27–1.83]; P < 0.001), compared to those having non-HTR. The risk of clinically relevant bleeding did not differ between groups (HRadjust: 0.85 [0.66–1.08]; P = 0.174). Associations between HTR and adverse events were similar in HBR and non-HBR groups, without evidence of interaction (all Pinteraction > 0.05); however, adverse event rates were highest among subjects with both HTR and HBR.

Conclusions
ESC guideline-endorsed HTR was associated with significantly increased risk of MACE without any significant differences in clinically relevant bleeding. The presence of HBR does not emerge as a modifier of cardiovascular risk for patients at HTR, suggesting more potent and longer antiplatelet therapy may be beneficial for this patient population.
General practitioner strategies for managing patients with multimorbidity: a systematic review and thematic synthesis of qualitative research
Authors: Damarell Raechel A. , Morgan Deidre D. , Tieman Jennifer J. 
Published: July 2020

AbstractBackgroundGeneral practitioners (GPs) increasingly manage patients with multimorbidity but report challenges in doing so. Patients describe poor experiences with health care systems that treat each of their health conditions separately, resulting in fragmented, uncoordinated care. For GPs to provide the patient-centred, coordinated care patients need and want, research agendas and health system structures and policies will need to adapt to address this epidemiologic transition. This systematic review seeks to understand if and how multimorbidity impacts on the work of GPs, the strategies they employ to manage challenges, and what they believe still needs addressing to ensure quality patient care.MethodsSystematic review and thematic synthesis of qualitative studies reporting GP experiences of managing patients with multimorbidity. The search included nine major databases, grey literature sources, Google and Google Scholar, a hand search ofJournal of Comorbidity, and the reference lists of included studies.ResultsThirty-three studies from fourteen countries were included. Three major challenges were identified: practising without supportive evidence; working within a fragmented health care system whose policies and structures remain organised around single condition care and specialisation; and the clinical uncertainty associated with multimorbidity complexity and general practitioner perceptions of decisional risk. GPs revealed three approaches to mitigating these challenges: prioritising patient-centredness and relational continuity; relying on knowledge of patient preferences and unique circumstances to individualise care; and structuring the consultation to create a sense of time and minimise patient risk.ConclusionsGPs described an ongoing tension between applying single condition guidelines to patients with multimorbidity as security against uncertainty or penalty, and potentially causing patients harm. Above all, they chose to prioritise their long-term relationships for the numerous gains this brought such as mutual trust, deeper insight into a patient’s unique circumstances, and useable knowledge of each individual’s capacity for the work of illness and goals for life. GPs described a need for better multimorbidity management guidance. Perhaps more than this, they require policies and models of practice that provide remunerated time and space for nurturing trustful therapeutic partnerships.