bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis provides insights into copper toxicology in piebald naked carp (Gymnocypris eckloni)
Authors: Jin Wenjie , Li Zixuan , Ran Fengxia , Huang Shen , Huo Kefan , Li Jianjuan , Han Qingshuo , Wang Guojie , Wang Zhenji , Jian Shenlong , Li Kemao , Li Changzhong 
Published: June 2021

Abstract
Background
Copper was used for many years in aquaculture operations as an effective algaecide or a parasite treatment of fish. It is an essential nutrient with numerous functions in organisms, but is toxic at high concentrations. However, the toxicity of copper to fish remains unclear. In this study, we used the piebald naked carp, Gymnocypris eckloni, as a model. RNA-seq data from different tissues, including gills, kidney, and liver, were used to investigate the underlying mechanism of copper toxicology in G. eckloni.

Results
We compared the transcriptomes from different tissues with different time durations of copper ion treatment. After 72 h copper ion treatment, the number of genes with different expression in gills and liver changed dramatically, but not in kidneys. In KEGG functional enrichment, the pattern of differentially expressed genes (DEGs) was also similar in the gills and liver. The most enriched pathway of DEGs was “Ribosome” in both tissues. Furthermore, we analyzed the expression levels of genes involved in oxidative stress response and protein synthesis using qPCR and RNA-seq data. Our results showed that several genes involved in oxidative stress response were up-regulated both in gills and liver. Up-regulation of these genes indicated that copper treatment caused oxidative stress, which is likely to result in ribosome damage. In addition, our results showed that the expression of Eef1b2, a transcription elongation factor, was decreased in the liver under oxidative stress, and the expression of translation initiation factors Eif4ebp1 and eIF2α, and elongation factor eEF2 was up-regulated. These results supported the idea that oxidative stress inhibits protein synthesis in cells.

Conclusions
Our results indicate that copper exposure caused different responses in different tissues, since the gene expression patterns changed substantially either in the gills or liver, while the effect on the kidney was relatively weak. Furthermore, our results indicated that the expression pattern of the genes involved in the ribosome, which is a complex molecular machine orchestrating protein synthesis in the cell, together with translation initiation factor and elongation factors, were affected by copper exposure both in the gills and liver of piebald naked carp. This result leads us to speculate that the downregulation of global protein synthesis is an acute response strategy of fish to metal-induced oxidative stress. Moreover, we speculate that this strategy not only exists in the selective translation of proteins but also exists in the specific translation of functional proteins in tissues and cells.
TMT-based quantitative proteomics analysis reveals the key proteins related with the differentiation process of goat intramuscular adipocytes
Authors: Du Yu , Wang Yong , Xu Qing , Zhu Jiangjiang , Lin Yaqiu 
Published: June 2021

Abstract
Background
Intramuscular adipocytes differentiation is a complex process, which is regulated by various transcription factor, protein factor regulators and signal transduction pathways. However, the proteins and signal pathways that regulates goat intramuscular adipocytes differentiation remains unclear.

Result
In this study, based on nanoscale liquid chromatography mass spectrometry analysis (LC-MS/MS), the tandem mass tag (TMT) labeling analysis was used to investigate the differentially abundant proteins (DAPs) related with the differentiation process of goat intramuscular adipocytes. Gene Ontology, Kyoto Encyclopedia of Genes and Genomes enrichment and protein-protein interaction network analyses were performed for the characterization of the identified DAPs. The candidate proteins were verified by parallel reaction monitoring analysis. As a result, a total of 123 proteins, 70 upregulation proteins and 53 downregulation proteins, were identified as DAPs which may be related with the differentiation process of goat intramuscular adipocytes. Furthermore, the cholesterol metabolism pathway, glucagon signaling pathway and glycolysis / gluconeogenesis pathway were noticed that may be the important signal pathways for goat Intramuscular adipocytes differentiation.

Conclusions
By proteomic comparison between goat intramuscular preadipocytes (P_IMA) and intramuscular adipocytes (IMA), we identified a series protein that might play important role in the goat intramuscular fat differentiation, such as SRSF10, CSRP3, APOH, PPP3R1, CRTC2, FOS, SERPINE1 and AIF1L, could serve as candidates for further elucidate the molecular mechanism of IMF differentiation in goats.
Genome-wide association studies reveal candidate genes associated to bacteraemia caused by ST93-IV CA-MRSA
Authors: Pang Stanley , Daley Denise A , Sahibzada Shafi , Mowlaboccus Shakeel , Stegger Marc , Coombs Geoffrey W 
Published: June 2021

Abstract
Background
The global emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has seen the dominance of specific clones in different regions around the world with the PVL-positive ST93-IV as the predominant CA-MRSA clone in Australia. In this study we applied a genome-wide association study (GWAS) approach on a collection of Australian ST93-IV MRSA genomes to screen for genetic traits that might have assisted the ongoing transmission of ST93-IV in Australia. We also compared the genomes of ST93-IV bacteraemia and non-bacteraemia isolates to search for potential virulence genes associated with bacteraemia.

Results
Based on single nucleotide polymorphism phylogenetics we revealed two distinct ST93-IV clades circulating concurrently in Australia. One of the clades contained isolates primarily isolated in the northern regions of Australia whilst isolates in the second clade were distributed across the country. Analyses of the ST93-IV genome plasticity over a 15-year period (2002–2017) revealed an observed gain in accessory genes amongst the clone’s population. GWAS analysis on the bacteraemia isolates identified two gene candidates that have previously been associated to this kind of infection.

Conclusions
Although this hypothesis was not tested here, it is possible that the emergence of a ST93-IV clade containing additional virulence genes might be related to the high prevalence of ST93-IV infections amongst the indigenous population living in the northern regions of Australia. More importantly, our data also demonstrated that GWAS can reveal candidate genes for further investigations on the pathogenesis and evolution of MRSA strains within a same lineage.
Uphyloplot2: visualizing phylogenetic trees from single-cell RNA-seq data
Authors: Kurtenbach Stefan , Cruz Anthony M. , Rodriguez Daniel A. , Durante Michael A. , Harbour J. William 
Published: June 2021

Abstract
Background
Recent advances in single cell sequencing technologies allow for greater resolution in assessing tumor clonality using chromosome copy number variations (CNVs). While single cell DNA sequencing technologies are ideal to identify tumor sub-clones, they remain expensive and in contrast to single cell RNA-seq (scRNA-seq) methods are more limited in the data they generate. However, CNV data can be inferred from scRNA-seq and bulk RNA-seq, for which several tools have been developed, including inferCNV, CaSpER, and HoneyBADGER. Inferences regarding tumor clonality from CNV data (and other sources) are frequently visualized using phylogenetic plots, which previously required time-consuming and error-prone, manual analysis.

Results
Here, we present Uphyloplot2, a python script that generates phylogenetic plots directly from inferred RNA-seq data, or any Newick formatted dendrogram file. The tool is publicly available at https://github.com/harbourlab/UPhyloplot2/.

Conclusions
Uphyloplot2 is an easy-to-use tool to generate phylogenetic plots to depict tumor clonality from scRNA-seq data and other sources.
The effect of methanol fixation on single-cell RNA sequencing data
Authors: Wang Xinlei , Yu Lei , Wu Angela Ruohao 
Published: June 2021

AbstractBackgroundSingle-cell RNA sequencing (scRNA-seq) has led to remarkable progress in our understanding of tissue heterogeneity in health and disease. Recently, the need for scRNA-seq sample fixation has emerged in many scenarios, such as when samples need long-term transportation, or when experiments need to be temporally synchronized. Methanol fixation is a simple and gentle method that has been routinely applied in scRNA-sEq. Yet, concerns remain that fixation may result in biases which may change the RNA-seq outcome.ResultsWe adapted an existing methanol fixation protocol and performed scRNA-seq on both live and methanol fixed cells. Analyses of the results show methanol fixation can faithfully preserve biological related signals, while the discrepancy caused by fixation is subtle and relevant to library construction methods. By grouping transcripts based on their lengths and GC content, we find that transcripts with different features are affected by fixation to different degrees in full-length sequencing data, while the effect is alleviated in Drop-seq result.ConclusionsOur deep analysis reveals the effects of methanol fixation on sample RNA integrity and elucidates the potential consequences of using fixation in various scRNA-seq experiment designs.
SnoRNA copy regulation affects family size, genomic location and family abundance levels
Authors: Bergeron Danny , Laforest Cédric , Carpentier Stacey , Calvé Annabelle , Fafard-Couture Étienne , Deschamps-Francoeur Gabrielle , Scott Michelle S. 
Published: June 2021

Abstract
Background
Small nucleolar RNAs (snoRNAs) are an abundant class of noncoding RNAs present in all eukaryotes and best known for their involvement in ribosome biogenesis. In mammalian genomes, many snoRNAs exist in multiple copies, resulting from recombination and retrotransposition from an ancestral snoRNA. To gain insight into snoRNA copy regulation, we used Rfam classification and normal human tissue expression datasets generated using low structure bias RNA-seq to characterize snoRNA families.

Results
We found that although box H/ACA families are on average larger than box C/D families, the number of expressed members is similar for both types. Family members can cover a wide range of average abundance values, but importantly, expression variability of individual members of a family is preferred over the total variability of the family, especially for box H/ACA snoRNAs, suggesting that while members are likely differentially regulated, mechanisms exist to ensure uniformity of the total family abundance across tissues. Box C/D snoRNA family members are mostly embedded in the same host gene while box H/ACA family members tend to be encoded in more than one different host, supporting a model in which box C/D snoRNA duplication occurred mostly by cis recombination while box H/ACA snoRNA families have gained copy members through retrotransposition. And unexpectedly, snoRNAs encoded in the same host gene can be regulated independently, as some snoRNAs within the same family vary in abundance in a divergent way between tissues.

Conclusions
SnoRNA copy regulation affects family sizes, genomic location of the members and controls simultaneously member and total family abundance to respond to the needs of individual tissues.
A high-throughput screening assay based on automated microscopy for monitoring antibiotic susceptibility of Mycobacterium tuberculosis phenotypes
Authors: Kalsum Sadaf , Andersson Blanka , Das Jyotirmoy , Schön Thomas , Lerm Maria 
Published: June 2021

Abstract
Background
Efficient high-throughput drug screening assays are necessary to enable the discovery of new anti-mycobacterial drugs. The purpose of our work was to develop and validate an assay based on live-cell imaging which can monitor the growth of two distinct phenotypes of Mycobacterium tuberculosis and to test their susceptibility to commonly used TB drugs.

Results
Both planktonic and cording phenotypes were successfully monitored as fluorescent objects using the live-cell imaging system IncuCyte S3, allowing collection of data describing distinct characteristics of aggregate size and growth. The quantification of changes in total area of aggregates was used to define IC50 and MIC values of selected TB drugs which revealed that the cording phenotype grew more rapidly and displayed a higher susceptibility to rifampicin. In checkerboard approach, testing pair-wise combinations of sub-inhibitory concentrations of drugs, rifampicin, linezolid and pretomanid demonstrated superior growth inhibition of cording phenotype.

Conclusions
Our results emphasize the efficiency of using automated live-cell imaging and its potential in high-throughput whole-cell screening to evaluate existing and search for novel antimycobacterial drugs.
Differential transcription pathways associated with rootstock-induced dwarfing in breadfruit (Artocarpus altilis) scions
Authors: Zhou Yuchan , Underhill Steven J. R. 
Published: June 2021

AbstractBackgroundBreadfruit (Artocarpus altilis) is a traditional staple tree crop throughout the tropics. Through interspecific grafting, a dwarf phenotype with over 50% reduction in plant height was identified when marang (Artocarpus odoratissimus) rootstocks were used. However, the molecular mechanism underlying the rootstock-induced breadfruit dwarfing is poorly understood.ResultsAn RNA-sequencing study of breadfruit scions at 22 months after grafting identified 5409 differentially expressed genes (DEGs) of which 2069 were upregulated and 3339 were downregulated in scion stems on marang rootstocks compared to those on self-graft. The DEGs were predominantly enriched for biological processes involved in carbon metabolism, cell wall organization, plant hormone signal transduction and redox homeostasis. The down-regulation of genes encoding vacuolar acid invertases and alkaline/neutral invertases, was consistent with the decreased activity of both enzymes, accompanying with a higher sucrose but lower glucose and fructose levels in the tissues. Key genes of biosynthetic pathways for amino acids, lipids and cell wall were down regulated, reflecting reduction of sucrose utilisation for stem growth on dwarfing rootstocks. Genes encoding sugar transporters, amino acid transporters, choline transporters, along with large number of potassium channels and aquaporin family members were down-regulated in scion stems on marang rootstocks. Lower activity of plasma membrane H+-ATPase, together with the predominance of genes encoding expansins, wall-associated receptor kinases and key enzymes for biosynthesis and re-modelling of cellulose, xyloglucans and pectins in down-regulated DGEs suggested impairment of cell expansion. Signalling pathways of auxin and gibberellin, along with strigolacton and brassinosteroid biosynthetic genes dominated the down-regulated DEGs. Phenylpropanoid pathway was enriched, with key lignin biosynthetic genes down-regulated, and flavonoid biosynthetic genes upregulated in scions on marang rootstocks. Signalling pathways of salicylic acid, jasmonic acid, ethylene and MAPK cascade were significantly enriched in the upregulated DEGs.ConclusionsRootstock-induced disruption in pathways regulating nutrient transport, sucrose utilisation, cell wall biosynthesis and networks of hormone transduction are proposed to impair cell expansion and stem elongation, leading to dwarf phenotype in breadfruit scions. The information provides opportunity to develop screening strategy for rootstock breeding and selection for breadfruit dwarfing.
Effect of graphene / metal nanocomposites on the key genes involved in rosmarinic acid biosynthesis pathway and its accumulation in Melissa officinalis
Authors: Soraki Roya Karimi , Gerami Mahyar , Ramezani Moazzameh 
Published: June 2021

Abstract
Background
Recently, numerous investigations have been done to study graphene and silver nanoparticle in the fields of agriculture and medicine. In the present study, the green synthesis of nanoparticles with two concentrations (0, 40, 60 mM) and their effect on the molecular and biochemical biosynthesis pathway of rosmarinic acid in a new method, low cost, and safe for the environment has been investigated. The transcript levels of key genes in the rosmarinic acid biosynthesis pathway (Tyrosine aminotransferase, rosmarinic acid synthase, and phenylalanine-ammonia lyase) were studied using real-time quantitative polymerase chain reaction. Then, the rosmarinic acid content was evaluated using HPLC.

Results
The results showed that a concentration-dependent manner was observed in treated plants. At the biochemical level, the use of nanocomposites at concentration of 40 mM showed higher soluble carbohydrate (37%), flavonoids (21%), total phenol (35%) as well as total protein (47%) compared to the control plants. HPLC results showed that rosmarinic acid content in the treated plants with a low concentration of nanocomposite (40 mM) was more affected than plants treated with a high concentration of nanocomposite (60 mM) (26%) and also compared to other treatments. At the molecular level, the result showed that Tyrosine aminotransferase and rosmarinic acid synthase gene expression was positively correlated with both silver nanoparticle concentrations and nanocomposite treatments, but phenylalanine-ammonia lyase gene expression was positively correlated only with nanocomposite at 40 mM concentration.

Conclude
It can conclude that the nanocomposite at low concentration is more likely to induce molecular and biochemical parameters. And also, in the rosmarinic acid biosynthesis pathway, the Tyrosine aminotransferase -derived pathway is more efficient than the phenylalanine-ammonia lyase -derived pathway by causing a nano-elicitor. Therefore, it was concluded that studied elicitor at low concentration, can create plants with higher production capacity.
Different body parts’ fat mass and corrected QT interval on the electrocardiogram: The Fasa PERSIAN Cohort Study
Authors: Yazdanpanah Mohammad Hosein , Bahramali Ehsan , Naghizadeh Mohammad Mehdi , Farjam Mojtaba , Mobasheri Maryam , Dadvand Shiva 
Published: June 2021

Abstract
Background
Previous studies suggested that obesity and fat mass are associated with QT interval prolongation, but the role of different body parts' fat mass is unclear. The associations between total and regional fat mass (FM) and corrected QT interval (QTc) were investigated for the first time in this study.

Methods
In this sub-analysis of Fasa PERSIAN cohort Study data, 3217 subjects aged 35–70 entered our study. Body fat mass was assessed by bioelectrical impedance analysis and QTc interval calculated by the QT interval measured by Cardiax® software from ECGs and Bazett’s formula. Uni- and multi-variable linear and logistic regression was performed in IBM SPSS Statistics v23.

Results
In males, the fat mass to fat-free mass (FM/FFM) ratio in the trunk, arms, total body, and legs were significantly higher in the prolonged QTc group (QTc > 450 ms). Trunk (B = 0.148), total (B = 0.137), arms (B = 0.124), legs (B = 0.107) fat mass index (FMI) showed significant positive relationship with continuous QTc (P-value < 0.001). Also, just the fat-free mass index of legs had significant positive associations with QTc interval (P-value < 0.05). Surprisingly, in females, the mean of FM/FFM ratio in trunk and legs in the normal QTc group had higher values than the prolonged QTc group (QTc > 470 ms). Also, none of the body composition variables had a significant correlation with continuous QTc.

Conclusion
Our study suggested that FMI ratios in the trunk, total body, arms, and legs were positively associated with QTc interval in males, respectively, from a higher to a lower beta-coefficient. Such associations were not seen in females. Our study implies that body fat mass may be an independent risk factor for higher QTc interval and, consequently, more cardiovascular events that should be investigated.
Instruments used to assess quality of life of older adults in African countries: a scoping review
Authors: Attafuah Priscilla Y. A. , Everink Irma H. J. , Halfens Ruud J. G. , Lohrmann Christa , Abuosi Aaron , Schols Jos M. G. A. 
Published: June 2021

Abstract
Background
Over 60% of the population in sub-Saharan Africa, live in informal settlements (slums) with little or no resources. To be prepared to meet the needs of older people living in slums, it is necessary to know more about their quality of life (QoL). The objective of this review is to identify instruments, which can be used by researchers to assess the QoL of older adults living in African countries, especially those dwelling in slums.

Methods
A scoping review was performed using the databases Scopus, PubMed, and ISI Web of Science to retrieve studies published from January 2008 – September 2020. Studies were included if they reported generic QoL instruments, focused on adults with a mean age ≥ 50 and were conducted in African countries.

Results
In total, 18 studies were included using 7 unique instruments to measure QoL (EUROHIS-QOL-8, SWLS, WHOQOL-OLD, the WHOQOL-BREF, SF-36, SF-12 and RAND-38). All instruments could be interviewer-administered and had 5–36 items. However, little is known about their psychometric properties (validity and reliability), time-investment and cultural sensitivity of the domains included in the instruments.

Conclusions
Even though this review retrieved instruments used to assess QoL of older adults in African countries, there is a need for further research on adjustment and validation of currently existing QoL instruments. In addition, the development and validation of a new instrument which can be used in (illiterate) older populations, living in slums in Africa should be considered.