bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chromosome‐levelAmaranthus cruentusgenome assembly highlights gene family evolution and biosynthetic gene clusters that may underpin the nutritional value of this traditional crop
Authors: Ma Xiao , Vaistij Fabián E. , Li Yi , Jansen van Rensburg Willem S. , Harvey Sarah , Bairu Michael W. , Venter Sonja L. , Mavengahama Sydney , Ning Zemin , Graham Ian A. , Van Deynze Allen , Van de Peer Yves , Denby Katherine J. 
Published: May 2021

SummaryTraditional crops have historically provided accessible and affordable nutrition to millions of rural dwellers but have been neglected, with most modern agricultural systems over‐reliant on a small number of internationally traded crops. Traditional crops are typically well‐adapted to local agro‐ecological conditions and many are nutrient‐dense. They can play a vital role in local food systems through enhanced nutrition (particularly where diets are dominated by starch crops), food security and livelihoods for smallholder farmers, and a climate‐resilient and biodiverse agriculture. Using short‐read, long‐read and phased sequencing technologies, we generated a high‐quality chromosome‐level genome assembly forAmaranthuscruentus, an under‐researched crop with micronutrient‐ and protein‐rich leaves and gluten‐free seed, but lacking improved varieties, with respect to productivity and quality traits. The 370.9 Mb genome demonstrates a shared whole genome duplication with a related species,Amaranthushypochondriacus. Comparative genome analysis indicates chromosomal loss and fusion events following genome duplication that are common to both species, as well as fission of chromosome 2 inA. cruentusalone, giving rise to a haploid chromosome number of 17 (versus 16 inA. hypochondriacus). Genomic features potentially underlying the nutritional value of this crop include twoA. cruentus‐specific genes with a likely role in phytic acid synthesis (an anti‐nutrient), expansion of ion transporter gene families, and identification of biosynthetic gene clusters conserved within the amaranth lineage. TheA. cruentusgenome assembly will underpin much‐needed research and global breeding efforts to develop improved varieties for economically viable cultivation and realization of the benefits to global nutrition security and agrobiodiversity.
Boron deficiency‐induced root growth inhibition is mediated by brassinosteroid signalling regulation in Arabidopsis
Authors: Zhang Cheng , He Mingliang , Wang Sheliang , Chu Liuyang , Wang Chuang , Yang Ningmei , Ding Guangda , Cai Hongmei , Shi Lei , Xu Fangsen 
Published: May 2021

SummaryBrassinosteroids (BRs) are pivotal phytohormones involved in the control of root development. Boron (B) is an essential micronutrient for plants, and root growth is rapidly inhibited under B deficiency conditions. However, the mechanisms underlying this inhibition are still unclear. Here, we identified BR‐related processes underlying B deficiency at the physiological, genetic, molecular/cell biological and transcriptomic levels and found strong evidence that B deficiency can affect BR biosynthesis and signalling, thereby altering root growth. RNA sequencing analysis revealed strong co‐regulation between BR‐regulated genes and B deficiency‐responsive genes. We found that the BR receptor mutants bri1‐119 and bri1‐301 were more insensitive to decreased B supply, and the gain‐of‐function mutants bes1‐D and pBZR1‐bzr1‐D exhibited insensitivity to low‐B stress. Under B deficiency conditions, exogenous 24‐epibrassinolide rescued the inhibition of root growth, and application of the BR biosynthesis inhibitor brassinazole exacerbated this inhibitory effect. The nuclear‐localised signal of BES1 was reduced under low‐B conditions compared with B sufficiency conditions. We further found that B deficiency hindered the accumulation of brassinolide to downregulate BR signalling and modulate root elongation, which may occur through a reduction in BR6ox1 and BR6ox2 mRNA levels. Taken together, our results reveal a role of BR signalling in root elongation under B deficiency.
Two loss‐of‐function alleles of the glutathione S‐transferase (GST) gene cause anthocyanin deficiency in flower and fruit skin of peach (Prunus persica)
Authors: Lu Zhenhua , Cao Huihui , Pan Lei , Niu Liang , Wei Bin , Cui GuoChao , Wang Luwei , Yao Jia‐Long , Zeng Wenfang , Wang Zhiqiang 
Published: May 2021

SummaryFlower and fruit colors are important agronomic traits. To date, there is no forward genetic evidence that the glutathione S‐transferase (GST) gene is responsible for the white flower color in peach (Prunus persica). In this study, genetic analysis indicated that the white‐flower trait is monogenetic, is recessive to the non‐white allele, and shows pleiotropic effects with non‐white‐flowered types. The genetic locus underpinning this trait was mapped onto chromosome 3 between 0.421951 and 3.227115 Mb by using bulked segregant analysis in conjunction with whole‐genome sequencing, and was further mapped between 0 and 1.178149 Mb by using the backcross 1 (BC1) population. Finally, the locus was fine‐mapped within 535.974‐ and 552.027‐kb intervals by using 151 F2 individuals and 75 individuals from a BC1 self‐pollinated (BC1S1) population, respectively. Pp3G013600, encoding a GST that is known to transport anthocyanin, was identified within the mapping interval. The analysis of genome sequence data showed Pp3G013600 in white flowers has a 2‐bp insertion or a 5‐bp deletion in the third exon. These variants likely render the GST non‐functional because of early stop codons that reduce the protein length from 215 amino acids to 167 and 175 amino acids, respectively. Genetic markers based on these variants validated a complete correlation between the GST loss‐of‐function alleles and white flower in 128 peach accessions. This correlation was further confirmed by silencing of Pp3G013600 using virus‐induced gene silencing technology, which reduced anthocyanin accumulation in peach fruit. The new knowledge from this study is useful for designing peach breeding programs to generate cultivars with white flower and fruit skin.
Improved genome assembly and pan‐genome provide key insights into eggplant domestication and breeding
Authors: Barchi Lorenzo , Rabanus‐Wallace Mark Timothy , Prohens Jaime , Toppino Laura , Padmarasu Sudharsan , Portis Ezio , Rotino Giuseppe Leonardo , Stein Nils , Lanteri Sergio , Giuliano Giovanni 
Published: May 2021

SummaryEggplant (Solanum melongena L.) is an important horticultural crop and one of the most widely grown vegetables from the Solanaceae family. It was domesticated from a wild, prickly progenitor carrying small, round, non‐anthocyanic fruits. We obtained a novel, highly contiguous genome assembly of the eggplant ‘67/3’ reference line, by Hi‐C retrofitting of a previously released short read‐ and optical mapping‐based assembly. The sizes of the 12 chromosomes and the fraction of anchored genes in the improved assembly were comparable to those of a chromosome‐level assembly. We resequenced 23 accessions of S. melongena representative of the worldwide phenotypic, geographic, and genetic diversity of the species, and one each from the closely related species Solanum insanum and Solanum incanum. The eggplant pan‐genome contained approximately 51.5 additional megabases and 816 additional genes compared with the reference genome, while the pan‐plastome showed little genetic variation. We identified 53 selective sweeps related to fruit color, prickliness, and fruit shape in the nuclear genome, highlighting selection leading to the emergence of present‐day S. melongena cultivars from its wild ancestors. Candidate genes underlying the selective sweeps included a MYBL1 repressor and CHALCONE ISOMERASE (for fruit color), homologs of Arabidopsis GLABRA1 and GLABROUS INFLORESCENCE STEMS2 (for prickliness), and orthologs of tomato FW2.2, OVATE, LOCULE NUMBER/WUSCHEL, SUPPRESSOR OF OVATE, and CELL SIZE REGULATOR (for fruit size/shape), further suggesting that selection for the latter trait relied on a common set of orthologous genes in tomato and eggplant.
Factors affecting the global distribution ofHydrilla verticillata(L. fil.) Royle: A review
Authors: Patrick Anton E. S. , Florentine Singarayer 
Published: May 2021

AbstractHydrilla verticillata(Hydrocharitaceae) is a submerged freshwater flowering plant within the monotypic genus. Over the geological periods, fossils of this family and genus have shown distinct diversifications between warm and cool fluctuations with more adaptations occurring in warmer periods and suppressions during severely cold paleoclimate changes. Recently,H. verticillatahas shown a wide range of adaptive plasticity, allowing successful proliferation into non‐native regions, whilst also undergoing unexplained disappearance from its native localities, and this phenomenon has stimulated this inquiry. Against this somewhat complex background, particular interest for this investigation has been focussed on an understanding of which aspects of climate change have contributed towards global adaptations and distribution patterns ofH.verticillata. Whilst it is recognised that some of these changes are natural, other aggravating impacts are due to anthropogenic influences. Identifying the appropriate combinations of these climatic factors (temperature, rainfall, photoperiod), in concert with environmental (water level, CO2, salinity, eutrophication), geographical (altitude, latitude) and other factors (UV‐B) are necessary precursors for instituting appropriate management strategies. In this respect, control measures are needed in non‐native regions and restoration of this plant in native habitats are essential for its ecologically balanced global distribution.
Insights into the skin microbiome of sickle cell disease leg ulcers
Authors: Byeon Julia , Blizinsky Katherine D. , Persaud Anitra , Findley Keisha , Lee Jung‐Jin , Buscetta Ashley J. , You Shuo , Bittinger Kyle , Minniti Caterina P. , Bonham Vence L. , Grice Elizabeth A. 
Published: May 2021

AbstractLeg ulcers are estimated to occur in 1%–10% of North American patients with sickle cell disease (SCD). Their pathophysiology remains poorly defined, but as with other chronic wounds, it is hypothesised that the microbial milieu, or microbiome, contributes to their healing and clinical outcomes. This study utilises 16S ribosomal RNA (rRNA) gene sequencing to describe, for the first time, the microbiome of the SCD leg ulcer and its association with clinical factors. In a cross‐sectional analysis of 42 ulcers, we recovered microbial profiles similar to other chronic wounds in the predominance of anaerobic bacteria and opportunistic pathogens including Staphylococcus, Corynebacterium, and Finegoldia. Ulcers separated into two clusters: one defined by predominance of Staphylococcus and smaller surface area, and the other displaying a greater diversity of taxa and larger surface area. We also find that the relative abundance of Porphyromonas is negatively associated with haemoglobin levels, a key clinical severity indicator for SCD, and that Finegoldia relative abundance is negatively associated with CD19+ B cell count. Finally, ratios of Corynebacterium:Lactobacillus and Staphylococcus:Lactobacillus are elevated in the intact skin of individuals with a history of SCD leg ulcers, while the ratio of Lactobacillus:Bacillus is elevated in that of individuals without a history of ulcers. Investigations of the skin microbiome in relation to SCD ulcer pathophysiology can inform clinical guidelines for this poorly understood chronic wound, as well as enhance broader understanding about the role of the skin microbiome in delayed wound healing.
Biomimetic analyses of interactions between macrophages and palmar fascia myofibroblasts derived from Dupuytren's disease reveal distinct inflammatory cytokine responses
Authors: Gonga‐Cavé Brianna C. , Pena Diaz Ana Maria , O'Gorman David B. 
Published: May 2021

AbstractDupuytren's disease (DD) is a common and heritable fibrosis of the hand. It is characterized by the shortening and thickening of the palmar fascia into myofibroblastic nodules that can progress to palmar‐digital contractures and permanent loss of dexterity. Molecular analyses of DD tissues and the presence of inflammatory cell infiltrates suggest a pathogenesis initiated by a proinflammatory fascial milieu that promotes myofibroblast activation and palmar fascia contractures. However, the relative contributions of vascular and/or tissue derived immune system cells and cytokine‐sensitive stromal myofibroblasts to the development of this proinflammatory microenvironment are poorly understood. To gain insights into this process, we have developed and tested a collagen‐based 3D tissue biomimetic co‐culture system to assess paracrine interactions between THP‐1‐derived pro‐inflammatory macrophages and primary human palmar fascia myofibroblasts (PFMs). We observed significant and reproducible impacts of collagen‐adherent macrophage and PFM co‐cultures on the cytokine gene expression profiles of these cells compared to their respective monocultures, and significant changes to the resulting cytokine milieu in their shared culture media, notably TNF and IL‐6. Our findings are consistent with central roles for PFMs in cytokine production and immunoregulation of the pro‐inflammatory milieu hypothesized to promote DD development.
Antimicrobial resistance in bacterial isolates from companion animals in Buenos Aires, Argentina: 2011–2017 retrospective study
Authors: Rumi María Valeria , Nuske Ezequiel , Mas Javier , Argüello Andrea , Gutkind Gabriel , Di Conza José 
Published: May 2021

AbstractThe widespread use of antimicrobial therapy in companion animals could lead to increased levels of resistance. Monitoring these levels is critical to understand not only the zoonotic threat of resistant bacteria but also the interspecies transmission of resistance mechanisms. However, data on resistance levels in companion animals of urban areas in Latin America are lacking. In this retrospective study, we analysed 23,922 isolates recovered from clinical samples of dogs and cats between 2011 and 2017. Growing trends of resistance to fluoroquinolones were observed in most bacterial species of veterinary importance with zoonotic potential (Enterobacterales, Pseudomonas and Staphylococcus). Furthermore, an increase of resistance levels to third‐generation cephalosporins was also detected in Enterobacterales. Currently, Pseudomonas aeruginosa, Enterococcus spp. and Streptococcus spp. did not seem to represent a clinical challenge. A high proportion of multidrug‐resistant (MDR) Enterobacterales isolated from urine was reported. It is interesting to outline that resistance to amikacin was exceptional. This study might be considered as a baseline for prospective antimicrobial resistance surveillance in companion animals in our region.
INTRODUCTION TO THE SYMPOSIUM ON EVOLUTION, ORIGINAL SIN, AND THE FALL
Authors: De Cruz Helen , De Smedt Johan 
Published: May 2021

AbstractThis is an introduction to the Symposium on “Evolution, Original Sin, and the Fall,” which has been designed as a thematic section for Zygon: Journal of Religion and Science. The Symposium investigates the enduring question of whether hamartiology (the theological study of sin) is compatible with evolutionary theory. We trace the origins of this question to the debate between Modernists and Traditionalists at the turn of the previous century. Our contributors make headway in these discussions by delving into details, namely, by asking whether the hamartiological views of particular theologians, such as Augustine or Aquinas, can be reconciled with specific aspects of evolutionary theory. They also extend hamartiology in novel directions through the application of critical race theory and literary science to shed new light on the origin and transmission of original sin.
Striated muscle activator of Rho signalling (STARS) overexpression in the mdx mouse enhances muscle functional capacity and regulates the actin cytoskeleton and oxidative phosphorylation pathways
Authors: Sadler Kate J. , Gatta Paul A. Della , Naim Timur , Wallace Marita A. , Lee Albert , Zaw Thiri , Lindsay Angus , Chung Roger S. , Bello Luca , Pegoraro Elena , Lamon Séverine , Lynch Gordon S. , Russell Aaron P. 
Published: May 2021

New Findings
What is the central question of this study?
Striated muscle activator of rho signalling (STARS) is an actin‐binding protein that regulates transcriptional pathways controlling muscle function, growth and myogenesis, processes that are impaired in dystrophic muscle: what is the regulation of the STARS pathway in Duchenne muscular dystrophy (DMD)?
What is the main finding and its importance?
Members of the STARS signalling pathway are reduced in the quadriceps of patients with DMD and in mouse models of muscular dystrophy. Overexpression of STARS in the dystrophic deficient mdx mouse model increased maximal isometric specific force and upregulated members of the actin cytoskeleton and oxidative phosphorylation pathways. Regulating STARS may be a therapeutic approach to enhance muscle health.
AbstractDuchenne muscular dystrophy (DMD) is characterised by impaired cytoskeleton organisation, cytosolic calcium handling, oxidative stress and mitochondrial dysfunction. This results in progressive muscle damage, wasting and weakness and premature death. The striated muscle activator of rho signalling (STARS) is an actin‐binding protein that activates the myocardin‐related transcription factor‐A (MRTFA)/serum response factor (SRF) transcriptional pathway, a pathway regulating cytoskeletal structure and muscle function, growth and repair. We investigated the regulation of the STARS pathway in the quadriceps muscle from patients with DMD and in the tibialis anterior (TA) muscle from the dystrophin‐deficient mdx and dko (utrophin and dystrophin null) mice. Protein levels of STARS, SRF and RHOA were reduced in patients with DMD. STARS, SRF and MRTFA mRNA levels were also decreased in DMD muscle, while Stars mRNA levels were decreased in the mdx mice and Srf and Mrtfa mRNAs decreased in the dko mice. Overexpressing human STARS (hSTARS) in the TA muscles of mdx mice increased maximal isometric specific force by 13% (P < 0.05). This was not associated with changes in muscle mass, fibre cross‐sectional area, fibre type, centralised nuclei or collagen deposition. Proteomics screening followed by pathway enrichment analysis identified that hSTARS overexpression resulted in 31 upregulated and 22 downregulated proteins belonging to the actin cytoskeleton and oxidative phosphorylation pathways. These pathways are impaired in dystrophic muscle and regulate processes that are vital for muscle function. Increasing the STARS protein in dystrophic muscle improves muscle force production, potentially via synergistic regulation of cytoskeletal structure and energy production.
Development of a multiplex assay to determine the expression of mitochondrial genes in human skeletal muscle
Authors: Aird Tom P. , Farquharson Andrew J. , Drew Janice E. , Carson Brian P. 
Published: May 2021

New Findings
What is the central question of this study?
Can a custom‐designed multiplex gene expression assay be used to quantify expression levels of a targeted group of mitochondrial genes in human skeletal muscle?
What is the main finding and its importance?
A custom‐designed GeXP multiplex assay was developed, and the ability to accurately quantify expression of a targeted set of mitochondrial genes in human skeletal muscle was demonstrated. It holds distinct methodological and practical advantages over other commonly used quantification methods.
AbstractSkeletal muscle is an important endocrine tissue demonstrating plasticity in response to external stimuli, including exercise and nutrition. Mitochondrial biogenesis is a common hallmark of adaptations to aerobic exercise training. Furthermore, altered expression of several genes implicated in the regulation of mitochondrial biogenesis, substrate oxidation and nicotinamide adenine dinucleotide (NAD+) biosynthesis following acute exercise underpins longer‐term muscle metabolic adaptations. Gene expression is typically measured using real‐time quantitative PCR platforms. However, interest has developed in the design of multiplex gene expression assays (GeXP) using the GenomeLab GeXP™ genetic analysis system, which can simultaneously quantify gene expression of multiple targets, holding distinct advantages in terms of throughput, limiting technical error, cost effectiveness, and quantifying gene co‐expression. This study describes the development of a custom‐designed GeXP assay incorporating the measurement of proposed regulators of mitochondrial biogenesis, substrate oxidation, and NAD+ biosynthetic capacity in human skeletal muscle and characterises the resting gene expression (overnight fasted and non‐exercised) signature within a group of young, healthy, recreationally active males. The design of GeXP‐based assays provides the capacity to more accurately characterise the regulation of a targeted group of genes with specific regulatory functions, a potentially advantageous development for future investigations of the regulation of muscle metabolism by exercise and/or nutrition.
The molecular mechanism of CFTR‐ and secretin‐dependent renal bicarbonate excretion
Authors: Berg Peder , Svendsen Samuel L. , Sorensen Mads Vaarby , Schreiber Rainer , Kunzelmann Karl , Leipziger Jens 
Published: May 2021

AbstractThis review summarizes the newly discovered molecular mechanism of secretin‐stimulated urine HCO3– excretion and the role of cystic fibrosis transmembrane conductance regulator (CFTR) in renal HCO3– excretion. The secretin receptor is functionally expressed in the basolateral membrane of the HCO3–‐secreting β‐intercalated cells of the collecting duct. Here it activates a fast and efficient secretion of HCO3– into the urine serving to normalize metabolic alkalosis. The ability to acutely increase renal base excretion is entirely dependent on functional pendrin (SLC26A4) and CFTR, and both proteins localize to the apical membrane of the β‐intercalated cells. In cystic fibrosis mice and patients, this function is absent or markedly reduced. We discuss that the alkaline tide, namely the transient urine alkalinity after a meal, has now received a clear physiological explanation.
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Matters Not That Trivial: Damage to the “Safety-Valve” Mechanism in Civil Justice and the Rise of the Boxer Movement in the Late Qing Period
Authors: Qu (渠桂萍) Guiping 
Published: May 2021

Abstract
Litigation in rural China under the Qing involved “trivial matters” 细事 over marriage, land transactions, debt, theft, and so on. “Going to court” 打官司, as a regular means of resolving such disputes, functioned as a “safety valve” in maintaining social order, while the mishandling of civil disputes by local magistrates and prefects often had severe consequences. After 1860, Western missionaries became increasingly active in rural North China under the system of unequal treaties. Their arrogance and interference with lawsuits by providing local converts with judicial protection caused damage to the safety valve and disgruntlement among the victims of their abuses. It was the growing enmity toward the missionaries that led to rampant violence by the Boxers around 1900.