bluuebunny/crossref_metadata_2025 huggingface dataset:
Meta-Apo improves accuracy of 16S-amplicon-based prediction of microbiome function
Authors: Jing Gongchao , Zhang Yufeng , Cui Wenzhi , Liu Lu , Xu Jian , Su Xiaoquan
Published: January 2021

Background

Due to their much lower costs in experiment and computation than metagenomic whole-genome sequencing (WGS), 16S rRNA gene amplicons have been widely used for predicting the functional profiles of microbiome, via software tools such as PICRUSt 2. However, due to the potential PCR bias and gene profile variation among phylogenetically related genomes, functional profiles predicted from 16S amplicons may deviate from WGS-derived ones, resulting in misleading results.

Results

Here we present Meta-Apo, which greatly reduces or even eliminates such deviation, thus deduces much more consistent diversity patterns between the two approaches. Tests of Meta-Apo on > 5000 16S-rRNA amplicon human microbiome samples from 4 body sites showed the deviation between the two strategies is significantly reduced by using only 15 WGS-amplicon training sample pairs. Moreover, Meta-Apo enables cross-platform functional comparison between WGS and amplicon samples, thus greatly improve 16S-based microbiome diagnosis, e.g. accuracy of gingivitis diagnosis via 16S-derived functional profiles was elevated from 65 to 95% by WGS-based classification. Therefore, with the low cost of 16S-amplicon sequencing, Meta-Apo can produce a reliable, high-resolution view of microbiome function equivalent to that offered by shotgun WGS.

Conclusions

This suggests that large-scale, function-oriented microbiome sequencing projects can probably benefit from the lower cost of 16S-amplicon strategy, without sacrificing the precision in functional reconstruction that otherwise requires WGS. An optimized C++ implementation of Meta-Apo is available on GitHub (https://github.com/qibebt-bioinfo/meta-apo) under a GNU GPL license. It takes the functional profiles of a few paired WGS:16S-amplicon samples as training, and outputs the calibrated functional profiles for the much larger number of 16S-amplicon samples.
Comparative Analysis of Genome of Ehrlichia sp. HF, a Model Bacterium to Study Fatal Human Ehrlichiosis
Authors: Lin Mingqun , Xiong Qingming , Chung Matthew , Daugherty Sean C. , Nagaraj Sushma , Sengamalay Naomi , Ott Sandra , Godinez Al , Tallon Luke J. , Sadzewicz Lisa , Fraser Claire , Dunning Hotopp Julie C. , Rikihisa Yasuko
Published: January 2021

Background

The genusEhrlichiaconsists of tick-borne obligatory intracellular bacteria that can cause deadly diseases of medical and agricultural importance.Ehrlichiasp. HF, isolated fromIxodes ovatusticks in Japan [also referred to asI. ovatus Ehrlichia(IOE) agent], causes acute fatal infection in laboratory mice that resembles acute fatal human monocytic ehrlichiosis caused byEhrlichia chaffeensis. As there is no small laboratory animal model to study fatal human ehrlichiosis,Ehrlichiasp. HF provides a needed disease model. However, the inability to cultureEhrlichiasp. HF and the lack of genomic information have been a barrier to advance this animal model. In addition,Ehrlichiasp. HF has several designations in the literature as it lacks a taxonomically recognized name.

Results

We stably culturedEhrlichiasp. HF in canine histiocytic leukemia DH82 cells from the HF strain-infected mice, and determined its complete genome sequence.Ehrlichiasp. HF has a single double-stranded circular chromosome of 1,148,904 bp, which encodes 866 proteins with a similar metabolic potential asE. chaffeensis.Ehrlichiasp. HF encodes homologs of all virulence factors identified inE. chaffeensis, including 23 paralogs of P28/OMP-1 family outer membrane proteins, type IV secretion system apparatus and effector proteins, two-component systems, ankyrin-repeat proteins, and tandem repeat proteins.Ehrlichiasp. HF is a novel species in the genusEhrlichia, as demonstrated through whole genome comparisons with six representativeEhrlichiaspecies, subspecies, and strains, using average nucleotide identity, digital DNA-DNA hybridization, and core genome alignment sequence identity.

Conclusions

The genome ofEhrlichiasp. HF encodes all known virulence factors found inE. chaffeensis, substantiating it as a modelEhrlichiaspecies to study fatal human ehrlichiosis. Comparisons betweenEhrlichiasp. HF andE. chaffeensiswill enable identification ofin vivovirulence factors that are related to host specificity, disease severity, and host inflammatory responses. We propose to nameEhrlichiasp. HF asEhrlichia japonicasp. nov. (type strain HF), to denote the geographic region where this bacterium was initially isolated.
Unbiased RNA-Seq-driven identification and validation of reference genes for quantitative RT-PCR analyses of pooled cancer exosomes
Authors: Dai Yao , Cao Yumeng , Köhler Jens , Lu Aiping , Xu Shaohua , Wang Haiyun
Published: January 2021

Background

Exosomes are extracellular vesicles (EVs) derived from endocytic compartments of eukaryotic cells which contain various biomolecules like mRNAs or miRNAs. Exosomes influence the biologic behaviour and progression of malignancies and are promising candidates as non-invasive diagnostic biomarkers or as targets for therapeutic interventions. Usually, quantitative real-time polymerase chain reaction (qRT-PCR) is used to assess gene expression in cancer exosomes, however, the ideal reference genes for normalization yet remain to be identified.

Results

In this study, we performed an unbiased analysis of high-throughput mRNA and miRNA-sequencing data from exosomes of patients with various cancer types and identify candidate reference genes and miRNAs in cancer exosomes. The expression stability of these candidate reference genes was evaluated by the coefficient of variation “CV” and the average expression stability value “M”. We subsequently validated these candidate reference genes in exosomes from an independent cohort of ovarian cancer patients and healthy control individuals by qRT-PCR.

Conclusions

Our study identifies OAZ1 and hsa-miR-6835-3p as the most reliable individual reference genes for mRNA and miRNA quantification, respectively. For superior accuracy, we recommend the use of a combination of reference genes - OAZ1/SERF2/MPP1 for mRNA and hsa-miR-6835-3p/hsa-miR-4468-3p for miRNA analyses.
Physical mapping and InDel marker development for the restorer gene Rf2 in cytoplasmic male sterile CMS-D8 cotton
Authors: Feng Juanjuan , Zhang Xuexian , Zhang Meng , Guo Liping , Qi Tingxiang , Tang Huini , Zhu Haiyong , Wang Hailin , Qiao Xiuqin , Xing Chaozhu , Wu Jianyong
Published: January 2021

Background

Cytoplasmic male sterile (CMS) with cytoplasm from Gossypium Trilobum (D8) fails to produce functional pollen. It is useful for commercial hybrid cotton seed production. The restore line of CMS-D8 containing Rf2 gene can restore the fertility of the corresponding sterile line. This study combined the whole genome resequencing bulked segregant analysis (BSA) with high-throughput SNP genotyping to accelerate the physical mapping of Rf2 locus in CMS-D8 cotton.

Methods

The fertility of backcross population ((sterile line×restorer line)×maintainer line) comprising of 1623 individuals was investigated in the field. The fertile pool (100 plants with fertile phenotypes, F-pool) and the sterile pool (100 plants with sterile phenotypes, S-pool) were constructed for BSA resequencing. The selection of 24 single nucleotide polymorphisms (SNP) through high-throughput genotyping and the development insertion and deletion (InDel) markers were conducted to narrow down the candidate interval. The pentapeptide repeat (PPR) family genes and upregulated genes in restore line in the candidate interval were analysed by qRT-PCR.

Results

The fertility investigation results showed that fertile and sterile separation ratio was consistent with 1:1. BSA resequencing technology, high-throughput SNP genotyping, and InDel markers were used to identify Rf2 locus on candidate interval of 1.48 Mb on chromosome D05. Furthermore, it was quantified in this experiment that InDel markers co-segregated with Rf2 enhanced the selection of the restorer line. The qRT-PCR analysis revealed PPR family gene Gh_D05G3391 located in candidate interval had significantly lower expression than sterile and maintainer lines. In addition, utilization of anther RNA-Seq data of CMS-D8 identified that the expression level of Gh_D05G3374 encoding NB-ARC domain-containing disease resistance protein in restorer lines was significantly higher than that in sterile and maintainer lines.

Conclusions

This study not only enabled us to precisely locate the restore gene Rf2 but also evaluated the utilization of InDel markers for marker assisted selection in the CMS-D8 Rf2 cotton breeding line. The results of this study provide an important foundation for further studies on the mapping and cloning of restorer genes.
Utility of basophil activation test for predicting the outcome of wheezing in children: a pilot study
Authors: Li Jingyang , Wu Jinhong , Liu Haipei , Hua Li , Liu Quanhua , Fang Dingzhu , Chen Yi , Ji Ruoxu , Zhang Jianhua , Zhong Wenwei
Published: January 2021

Background

No reliable biological marker for the diagnosis of asthma in younger children is currently available. In this study, we analyzed the differences in basophil activation test (BAT) results among children with recurrent wheezing episodes who had different asthma outcomes.

Results

A prospective cohort study was conducted in children aged under 5 years who visited our pediatric respiratory clinic and ward for wheezing. After enrollment, the participants provided samples for a CD63-based BAT performed using an inhalant allergen mixture as a stimulant. Histories of personal allergic diseases and family allergic diseases were evaluated by using a questionnaire. All participants were followed up for 2 years, and their asthma outcomes were evaluated at the end of the follow-up period. The correlation between the BAT results and asthma outcomes was analyzed. Of the 45 originally enrolled children, 38 completed both the follow-up and a BAT. After stimulation with the inhalant mixture, the CD63 expression on basophils and the rate of positive CD63-based BAT results in children diagnosed with asthma were both significantly higher than those in children who were not diagnosed with asthma (p < 0.05 and p < 0.01, respectively). For the prediction of asthma, the positive predictive value and negative predictive value of CD63-based BAT was 71.8 and 69.2%, respectively. The positive likelihood ratio and negative likelihood ratio of CD63-based BAT were 1.70 and 0.3, respectively.

Conclusions

Our pilot study indicates that CD63-based BAT has potential clinical value for predicting asthma outcome in young children with wheezing episodes.
Alterations in the intestinal microbiome and mental health status of workers in an underground tunnel environment
Authors: Lu Zhen-Hua , Liu Yi-Wen , Ji Zhao-Hua , Fu Ting , Yan Min , Shao Zhong-jun , Long Yong
Published: January 2021

Background

Working in an underground tunnel environment is unavoidable in professions such as miners and tunnel workers, and there is a concern about the health of these workers. Few studies have addressed alterations in the intestinal microbiome of workers within that environment.

Results

Fecal samples were collected from the workers before they entered the tunnel (baseline status, BS) and after they left the tunnel (exposed status, ES), respectively (a time period of 3 weeks between them). We analyzed 16S rRNA sequencing to show the changes in microbial composition and self-evaluation of mental health questionnaire was also performed. The results showed that Shannon and Simpson indices decreased significantly from BS to ES. A higher abundance was found in the phylumActinobacteria, classesActinobacteriaandDeltaproteobacteria, ordersBifidobacteriales,Coriobacteriales, andDesulfovibrionales, familiesBifidobacteriaceae,Peptostreptococcaceae,Coriobacteriaceae,Clostridiaceae_1,Desulfovibrionaceae, Pseudomonadaceae, and Microbacteriaceae, and generaBifidobacterium,Romboutsia,Clostridiumsensu stricto, andLeucobacterin ES, while BS showed greater levels of generaFaecalibacteriumandRoseburia. The self-evaluation showed that at least one-half of the tunnel workers experienced one or more symptoms of mental distress (inattention, sleeplessness, loss of appetite, headache or dizziness, irritability) after working in the underground tunnel environment.

Conclusions

Collectively, the underground tunnel environment led to alterations in the intestinal microbiome, which might be relevant to symptoms of mental distress in underground-tunnel workers.
Differential production and secretion of potentially toxigenic extracellular proteins from hypervirulent Aeromonas hydrophila under biofilm and planktonic culture
Authors: Barger Priscilla C. , Liles Mark R. , Beck Benjamin H. , Newton Joseph C.
Published: January 2021

Background

Hypervirulent Aeromonas hydrophila (vAh) is an emerging pathogen in freshwater aquaculture that results in the loss of over 3 million pounds of marketable channel catfish, Ictalurus punctatus, and channel catfish hybrids (I. punctatus, ♀ x blue catfish, I. furcatus, ♂) each year from freshwater catfish production systems in Alabama, U.S.A. vAh isolates are clonal in nature and are genetically unique from, and significantly more virulent than, traditional A. hydrophila isolates from fish. Even with the increased virulence, natural infections cannot be reproduced in aquaria challenges making it difficult to determine modes of infection and the pathophysiology behind the devastating mortalities that are commonly observed. Despite the intimate connection between environmental adaptation and plastic response, the role of environmental adaption on vAh pathogenicity and virulence has not been previously explored. In this study, secreted proteins of vAh cultured as free-living planktonic cells and within a biofilm were compared to elucidate the role of biofilm growth on virulence.

Results

Functional proteolytic assays found significantly increased degradative activity in biofilm secretomes; in contrast, planktonic secretomes had significantly increased hemolytic activity, suggesting higher toxigenic potential. Intramuscular injection challenges in a channel catfish model showed that in vitro degradative activity translated into in vivo tissue destruction. Identification of secreted proteins by HPLC-MS/MS revealed the presence of many putative virulence proteins under both growth conditions. Biofilm grown vAh produced higher levels of proteolytic enzymes and adhesins, whereas planktonically grown cells secreted higher levels of toxins, porins, and fimbrial proteins.

Conclusions

This study is the first comparison of the secreted proteomes of vAh when grown in two distinct ecological niches. These data on the adaptive physiological response of vAh based on growth condition increase our understanding of how environmental niche partitioning could affect vAh pathogenicity and virulence. Increased secretion of colonization factors and degradative enzymes during biofilm growth and residency may increase bacterial attachment and host invasiveness, while increased secretion of hemolysins, porins, and other potential toxins under planktonic growth (or after host invasion) could result in increased host mortality. The results of this research underscore the need to use culture methods that more closely mimic natural ecological habitat growth to improve our understanding of vAh pathogenesis.
The type VI secretion system of Xanthomonas phaseoli pv. manihotis is involved in virulence and in vitro motility
Authors: Montenegro Benavides Nathaly Andrea , Alvarez B. Alejandro , Arrieta-Ortiz Mario L. , Rodriguez-R Luis Miguel , Botero David , Tabima Javier Felipe , Castiblanco Luisa , Trujillo Cesar , Restrepo Silvia , Bernal Adriana
Published: January 2021

Background

The type VI protein secretion system (T6SS) is important in diverse cellular processes in Gram-negative bacteria, including interactions with other bacteria and with eukaryotic hosts. In this study we analyze the evolution of the T6SS in the genusXanthomonasand evaluate its importance of the T6SS for virulence and in vitro motility inXanthomonas phaseolipv.manihotis(Xpm), the causal agent of bacterial blight in cassava (Manihot esculenta). We delineate the organization of the T6SS gene clusters inXanthomonasand then characterize proteins of this secretion system inXpmstrain CIO151.

Results

We describe the presence of three different clusters in the genusXanthomonasthat vary in their organization and degree of synteny between species. Using a gene knockout strategy, we also found thatvgrGandhcpare required for maximal aggressiveness ofXpmon cassava plants whileclpVis important for both motility and maximal aggressiveness.

Conclusion

We characterized the T6SS in 15 different strains inXanthomonasand our phylogenetic analyses suggest that the T6SS might have been acquired by a very ancient event of horizontal gene transfer and maintained through evolution, hinting at their importance for the adaptation ofXanthomonasto their hosts. Finally, we demonstrated that the T6SS ofXpmis functional, and significantly contributes to virulence and motility. This is the first experimental study that demonstrates the role of the T6SS in theXpm-cassava interaction and the T6SS organization in the genusXanthomonas.
Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals
Authors: Xie Yirui , Sun Jia , Wei Li , Jiang Haiyin , Hu Caiqin , Yang Jiezuan , Huang Ying , Ruan Bing , Zhu Biao
Published: January 2021

Background

Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly active antiretroviral therapy (HAART) is still not well understood. Gut microbiota and immune activation were studied in 36 non-HIV-infected subjects (healthy controls) and 58 HIV-infected individuals, including 28 immunological responders (IR) and 30 immunological non-responders (INR) (≥500 and < 200 CD4+ T-cell counts/μl after 2 years of HIV-1 viral suppression respectively) without comorbidities.

Results

Metagenome sequencing revealed that HIV-infected immunological responders and immunological non-responders could not recover completely from the gut microbiota dysbiosis. At a 97% similarity level, the relative abundances ofFusobacterium, Ruminococcus gnavusandMegamonaswere greater, whereasFaecalibacterium, Alistipes, Bifidobacterium, Eubacterium rectaleandRoseburiawere more depleted in the IR and INR groups than those in the healthy controls.RuminococcaceaeandAlistipeswere positively correlated with nadir and current CD4+ T-cell counts, but negatively correlated with CD8 + CD57+ T-cell counts.Inflammation markers and translocation biomarkers (LPS) levels were positively correlated with the abundances of generaRuminococcusandFusobacteriumbut were negatively correlated with the genusFaecalibacterium. The relative abundances ofEscherichia-ShigellaandBlautiawere significantly higher in the IR than those in the INR group.Escherichia-Shigellawere negatively correlated with the CD4/CD8 ratio but positively correlated with the amount ofCD8 + CD57+ T-cells.RoseburiaandBlautiawere negatively associated with nadir CD4+ T-cell and positively associated with CD8 + CD57+ T-cell counts.

Conclusions

Gut microbiota dysbiosis may be one of the factors contributing to different immune responses and treatment outcomes to HAART.
Metabolic acclimation supports higher aluminium-induced secretion of citrate and malate in an aluminium-tolerant hybrid clone of Eucalyptus
Authors: Li Wannian , Finnegan Patrick M. , Dai Qin , Guo Dongqiang , Yang Mei
Published: January 2021

Background

Eucalyptus is the main plantation wood species, mostly grown in aluminized acid soils. To understand the response of Eucalyptus clones to aluminum (Al) toxicity, the Al-tolerant Eucalyptus grandis × E. urophylla clone GL-9 (designated “G9”) and the Al-sensitive E. urophylla clone GL-4 (designated “W4”) were employed to investigate the production and secretion of citrate and malate by roots.

Results

Eucalyptus seedlings in hydroponics were exposed to the presence or absence of 4.4 mM Al at pH 4.0 for 24 h. The protein synthesis inhibitor cycloheximide (CHM) and anion channel blocker phenylglyoxal (PG) were applied to explore possible pathways involved in organic acid secretion. The secretion of malate and citrate was earlier and greater in G9 than in W4, corresponding to less Al accumulation in G9. The concentration of Al in G9 roots peaked after 1 h and decreased afterwards, corresponding with a rapid induction of malate secretion. A time-lag of about 6 h in citrate efflux in G9 was followed by robust secretion to support continuous Al-detoxification. Malate secretion alone may alleviate Al toxicity because the peaks of Al accumulation and malate secretion were simultaneous in W4, which did not secrete appreciable citrate. Enhanced activities of citrate synthase (CS) and phosphoenolpyruvate carboxylase (PEPC), and reduced activities of isocitrate dehydrogenase (IDH), aconitase (ACO) and malic enzyme (ME) were closely associated with the greater secretion of citrate in G9. PG effectively inhibited citrate and malate secretion in both Eucalyptus clones. CHM also inhibited malate and citrate secretion in G9, and citrate secretion in W4, but notably did not affect malate secretion in W4.

Conclusions

G9 immediately secrete malate from roots, which had an initial effect on Al-detoxification, followed by time-delayed citrate secretion. Pre-existing anion channel protein first contributed to malate secretion, while synthesis of carrier protein appeared to be needed for citrate excretion. The changes of organic acid concentrations in response to Al can be achieved by enhanced CS and PEPC activities, but was supported by changes in the activities of other enzymes involved in organic acid metabolism. The above information may help to further explore genes related to Al-tolerance in Eucalyptus.
The development of SSR markers based on RNA-sequencing and its validation between and within Carex L. species
Authors: Liu Lingyun , Fan Xifeng , Tan Penghui , Wu Juying , Zhang Hui , Han Chao , Chen Chao , Xun Lulu , Guo Weier , Chang Zhihui , Teng Ke
Published: January 2021

Background

CarexL. is one of the largest genera in the Cyperaceae family and an important vascular plant in the ecosystem. However, the genetic background ofCarexis complex and the classification is not clear. In order to investigate the gene function annotation ofCarex, RNA-sequencing analysis was performed. Simple sequence repeats (SSRs) were generated based on the Illumina data and then were utilized to investigate the genetic characteristics of the 79Carexgermplasms.

Results

In this study, 36,403 unigenes with a total length of 41,724,615 bp were obtained and annotated based on GO, KOG, KEGG, NR databases. The results provide a theoretical basis for gene function exploration. Out of 8776 SSRs, 96 pairs of primers were randomly selected. One hundred eighty polymorphic bands were amplified with a polymorphism rate of 100% based on 42 pairs of primers with higher polymorphism levels. The average band number was 4.3 per primer, the average distance value was 0.548, and the polymorphic information content was ranged from 0.133 to 0.494. The number of observed alleles (Na), effective alleles (Ne), Nei’s (1973) gene diversity (H), and the Shannon information index (I) were 2.000, 1.376, 0.243, and 0.391, respectively. NJ clustering divided into three groups and the accessions from New Zealand showed a similar genetic attribute and clustered into one group. UPGMA and PCoA analysis also revealed the same result. The analysis of molecular variance (AMOVA) revealed a superior genetic diversity within accessions than between accessions based on geographic origin cluster and NJ cluster. What’s more, the fingerprints of 79Carexspecies are established in this study. Different combinations of primer pairs can be used to identify multipleCarexat one time, which overcomes the difficulties of traditional identification methods.

Conclusions

The transcriptomic analysis shed new light on the function categories from the annotated genes and will facilitate future gene functional studies. The genetic characteristics analysis indicated that gene flow was extensive among 79Carexspecies. These markers can be used to investigate the evolutionary history ofCarexand related species, as well as to serve as a guide in future breeding projects.
Characterization of type-2 diacylglycerol acyltransferases in Haematococcus lacustris reveals their functions and engineering potential in triacylglycerol biosynthesis
Authors: Cui Hongli , Zhao Chunchao , Xu Wenxin , Zhang Hongjiang , Hang Wei , Zhu Xiaoli , Ji Chunli , Xue Jinai , Zhang Chunhui , Li Runzhi
Published: January 2021

Background

Haematococcus lacustris is an ideal source of astaxanthin (AST), which is stored in oil bodies containing esterified AST (EAST) and triacylglycerol (TAG). Diacylglycerol acyltransferases (DGATs) catalyze the last step of acyl-CoA-dependent TAG biosynthesis and are also considered as crucial enzymes involved in EAST biosynthesis in H. lacustris. Previous studies have identified four putative DGAT2-encoding genes in H. lacustris, and only HpDGAT2D allowed the recovery of TAG biosynthesis, but the engineering potential of HpDGAT2s in TAG biosynthesis remains ambiguous.

Results

Five putative DGAT2 genes (HpDGAT2A, HpDGAT2B, HpDGAT2C, HpDGAT2D, and HpDGAT2E) were identified in H. lacustris. Transcription analysis showed that the expression levels of the HpDGAT2A, HpDGAT2D, and HpDGAT2E genes markedly increased under high light and nitrogen deficient conditions with distinct patterns, which led to significant TAG and EAST accumulation. Functional complementation demonstrated that HpDGAT2A, HpDGAT2B, HpDGAT2D, and HpDGAT2E had the capacity to restore TAG synthesis in a TAG-deficient yeast strain (H1246) showing a large difference in enzymatic activity. Fatty acid (FA) profile assays revealed that HpDGAT2A, HpDGAT2D, and HpDGAT2E, but not HpDGAT2B, preferred monounsaturated fatty acyl-CoAs (MUFAs) for TAG synthesis in yeast cells, and showed a preference for polyunsaturated fatty acyl-CoAs (PUFAs) based on their feeding strategy. The heterologous expression of HpDGAT2D in Arabidopsis thaliana and Chlamydomonas reinhardtii significantly increased the TAG content and obviously promoted the MUFAs and PUFAs contents.

Conclusions

Our study represents systematic work on the characterization of HpDGAT2s by integrating expression patterns, AST/TAG accumulation, functional complementation, and heterologous expression in yeast, plants, and algae. These results (1) update the gene models of HpDGAT2s, (2) prove the TAG biosynthesis capacity of HpDGAT2s, (3) show the strong preference for MUFAs and PUFAs, and (4) offer target genes to modulate TAG biosynthesis by using genetic engineering methods.
Integrated analysis of DNA methylome and transcriptome reveals epigenetic regulation of CAM photosynthesis in pineapple
Authors: Shi Yan , Zhang Xingtan , Chang Xiaojun , Yan Maokai , Zhao Heming , Qin Yuan , Wang Haifeng
Published: January 2021

Background

Crassulacean acid metabolism (CAM) photosynthesis is an important carbon fixation pathway especially in arid environments because it leads to higher water-use efficiency compared to C3 and C4 plants. However, the role of DNA methylation in regulation CAM photosynthesis is not fully understood.

Results

Here, we performed temporal DNA methylome and transcriptome analysis of non-photosynthetic (white base) and photosynthetic (green tip) tissues of pineapple leaf. The DNA methylation patterns and levels in these two tissues were generally similar for the CG and CHG cytosine sequence contexts. However, CHH methylation was reduced in white base leaf tissue compared with green tip tissue across diel time course in both gene and transposon regions. We identified thousands of local differentially methylated regions (DMRs) between green tip and white base at different diel periods. We also showed that thousands of genes that overlapped with DMRs were differentially expressed between white base and green tip leaf tissue across diel time course, including several important CAM pathway-related genes, such as beta-CA, PEPC, PPCK, and MDH.

Conclusions

Together, these detailed DNA methylome and transcriptome maps provide insight into DNA methylation changes and enhance our understanding of the relationships between DNA methylation and CAM photosynthesis.
Effects of intravenous lidocaine, dexmedetomidine, and their combination on IL-1, IL-6 and TNF-α in patients undergoing laparoscopic hysterectomy: a prospective, randomized controlled trial
Authors: Xu Siqi , Hu Shenghong , Ju Xia , Li Yuanhai , Li Qing , Wang Shengbin
Published: January 2021

Background

Surgical-related inflammatory responses have negative effects on postoperative recovery. Intravenous (IV) lidocaine and dexmedetomidine inhibits the inflammatory response. We investigated whether the co-administration of lidocaine and dexmedetomidine could further alleviate inflammatory responses compared with lidocaine or dexmedetomidine alone during laparoscopic hysterectomy.

Methods

A total of 160 patients were randomly allocated into four groups following laparoscopic hysterectomy: the control group (group C) received normal saline, the lidocaine group (group L) received lidocaine (bolus infusion of 1.5 mg/kg over 10 min, 1.5 mg/kg/h continuous infusion), the dexmedetomidine group (group D) received dexmedetomidine (bolus infusion of 0.5 μg/kg over 10 min, 0.4 μg/kg/h continuous infusion), and the lidocaine plus dexmedetomidine group (group LD) received a combination of lidocaine (bolus infusion of 1.5 mg/kg over 10 min, 1.5 mg/kg/h continuous infusion) and dexmedetomidine (bolus infusion of 0.5 μg/kg over 10 min, 0.4 μg/kg/h continuous infusion). The levels of plasma interleukin-1 (IL-1), interleukin-6 (IL-6), and tumor necrosis factor-α (TNF-α) at different time points were the primary outcomes. Secondary outcomes included hemodynamic variables, postoperative visual analogue scale (VAS) scores, time to first flatus, and incidence of nausea and vomiting after surgery.

Results

The levels of plasma IL-1, IL-6, and TNF-α were lower in groups D and LD than in group C and were lowest in group LD at the end of the procedure and 2 h after the operation (P < 0.05). The VAS scores were decreased in groups D and LD compared with group C (P < 0.05). The heart rate (HR) was decreased at the end of the procedure and 2 h after the operation in groups D and LD compared to groups C and L (P < 0.001). The mean blood pressure (MBP) was lower at 2 h after the operation in groups L, D, and LD than in group C (P < 0.001). There was a lower incidence of postoperative nausea and vomiting (PONV) in group LD than in group C (P < 0.05).

Conclusions

The combination of lidocaine and dexmedetomidine significantly alleviated the inflammatory responses, decreased postoperative pain, and led to fewer PONV in patients undergoing laparoscopic hysterectomy.

Trial registration

ClinicalTrials.gov (NCT03276533), registered on August 23, 2017.
Arterial duct stent versus surgical shunt for patients with duct-dependent pulmonary circulation: a meta-analysis
Authors: Li Dongxu , Zhou Xu , Li Mengsi
Published: January 2021

Background

Both systemic-pulmonary shunt and arterial duct stent could be the palliation of duct-dependent pulmonary circulation. We aimed to compare the safety and efficacy of the two approaches.

Methods

The PubMed, EMBASE, and Cochrane Library databases were searched through December 2019 for studies comparing stent implantation and surgical shunt in duct-dependent pulmonary circulation. The baseline characteristics included ventricle physiology and cardiac anomaly. The main outcomes were hospital stay and total mortality. Additional outcomes included procedural complications, intensive care unit (ICU) stay, pulmonary artery growth at follow-up, and other indexes. A random- or fixed-effects model was used to summarize the estimates of the mean difference (MD)/risk ratio (RR) with 95% confidence intervals (CIs).

Results

In total, 757 patients with duct-dependent pulmonary circulation from six studies were included. Pooled estimates of hospital stay (MD, − 4.83; 95% CI − 7.92 to − 1.74; p < 0.05), total mortality (RR 0.44; 95% CI 0.28–0.70; p < 0.05), complications (RR 0.49; 95% CI 0.30–0.81; p < 0.05) and ICU stay (MD, − 4.00; 95% CI − 5.96 to − 2.04; p < 0.05) favored the stent group. Significant differences were found in the proportions of patients with a single ventricle (RR 0.82; 95% CI 0.68–0.98; p < 0.05) or a double ventricle (RR 1.23; 95% CI 1.07–1.41; p < 0.05) between the stent and shunt groups. Additionally, pulmonary artery growth showed no significant differences between the two groups.

Conclusion

Arterial duct stent appears to have not inferior outcomes of procedural complications, mortality, hospital and ICU stay, and pulmonary artery growth in selected patients compared with a surgical shunt.

Trial registration

CRD42019147672.
Non-celiac wheat sensitivity: rationality and irrationality of a gluten-free diet in individuals affected with non-celiac disease: a review
Authors: Sergi Consolato , Villanacci Vincenzo , Carroccio Antonio
Published: January 2021

Non-celiac gluten or wheat sensitivity (NCWS) is a “clinical entity induced by the ingestion of wheat leading to intestinal and/or extraintestinal symptoms that improve once the wheat-containing foodstuff is removed from the diet, and celiac disease and wheat allergy have been excluded”. This mostly accepted definition raises several points that remain controversial on this condition. In the present review, the authors summarize the most recent advances in the clinic and research on NCWS through an accurate analysis of different studies. We screened PubMed, Medline, Embase, and Scopus using the keywords “non-celiac gluten sensitivity”, “non-celiac wheat sensitivity”, and “diagnosis”. We would like to emphasize two main points, including (A) the controversial clinical and etiological aspects in different trials and experiences with particular attention to the Salerno criteria for the diagnosis of NCWS and (B) the histological aspects. The etiology of NCWS remains controversial, and the relationship with irritable bowel syndrome is obscure. Histologically, the duodenal mucosa may show a variable pattern from unremarkable to a slight increase in the number of T lymphocytes in the superficial epithelium of villi. The endorsement of this disease is based on a positive response to a gluten-free diet for a limited period, followed by the reappearance of symptoms after gluten challenge. The Salerno expert criteria may help to diagnose NCWS accurately. Social media and inaccurate interpretation of websites may jeopardize the diagnostic process if individuals self-label as gluten intolerant.
The clinical features of chronic intestinal schistosomiasis-related intestinal lesions
Authors: Qin Xian , Liu Cai-Yuan , Xiong Yi-Lin , Bai Tao , Zhang Lei , Hou Xiao-Hua , Song Jun
Published: January 2021

Background

Chronic intestinal schistosomiasis has been reported to be associated with colonic polyps, colorectal cancer and ulcerative colitis. We aim to investigate the clinical characteristics of intestinal-related lesions caused by chronic intestinal schistosomiasis japonicum.

Methods

Patients with and without chronic intestinal schistosomiasis were retrospectively enrolled from the endoscopy center of Wuhan Union Hospital from September 1, 2014, to June 30, 2019 with a ratio of 4:1. The characteristics of infected intestinal segments were analyzed in patients with chronic intestinal schistosomiasis. We also compared the characteristics of intestinal-related lesions, including colorectal polyps, colorectal cancer (CRC), ulceration or erosion of the intestinal mucosa and hemorrhoids, between the two groups.

Results

A total of 248 patients with chronic intestinal schistosomiasis and 992 patients without chronic intestinal schistosomiasis were analyzed. The most common sites of chronic intestinal schistosomiasis were the sigmoid colon (79.0%) and rectum (84.7%). The frequency of intestinal polyps (64.5% vs. 42.8%, p < 0.001), especially rectal polyps (62.5% vs. 45.0%, p = 0.002), in the intestinal schistosomiasis group was significantly higher than that in the control group. Morphologically, type IIa polyps were more common in the schistosomiasis enteropathy group (68.5% vs. 60.7%, p = 0.001). Female patients with intestinal schistosomiasis had a higher detection rate of CRC than women in the control group (13.8% vs. 5.4%, p = 0.017). There was no significant difference in the incidence of ulcerative colitis between the two groups (0.8% vs. 0.6%, p = 0.664). In addition, the schistosomiasis enteropathy patients had a higher detection rate of internal hemorrhoids (58.9% vs. 51.0%, p = 0.027).

Conclusions

Chronic intestinal schistosomiasis mainly involved the rectum and sigmoid colon and was more likely to induce intestinal polyps, especially rectal polyps and internal hemorrhoids. Women with chronic schistosomiasis have a higher risk of colorectal cancer.
Pulmonary nocardiosis in a patient with pemphigus foliaceus: case report and literature review
Authors: Luo Ning , Tan Shifan , Li Xiaocai , Liu Si , Singh Shivank , Chen Mafeng , Yang Weiye , He Yanhong , Chen Chunna , Liang Min
Published: January 2021

Background

Nocardiosis is an uncommon opportunistic infection seen in immunocompromised patients or those with a dysfunctional immune system. Nocardia asteroides infection in patients with Pemphigus foliaceus (PF) has never been reported.

Case presentation

We report an interesting case of nocardiosis-characterized by pulmonary intra-cavitary infection, in a 54-year-old man with PF and diabetes mellitus. The man finally recovered from the infection.

Conclusions

This is the first case reporting pulmonary nocardiosis in a patient with PF. We recommend that physicians be aware of nocardiosis in patients with pemphigus as a possible cause of underlying infectious disease to avoid misdiagnoses and mismanagement.
Enteric pathogen infection and consequences for child growth in young Aboriginal Australian children: a cross-sectional study
Authors:   on behalf of the Child Health and Nutrition Study team, Hanieh Sarah , Mahanty Siddhartha , Gurruwiwi George , Kearns Therese , Dhurrkay Roslyn , Gondarra Veronica , Shield Jenny , Ryan Norbert , Azzato Francesca , Ballard Susan A. , Orlando Nicole , Nicholson Sullen , Gibney Katherine , Brimblecombe Julie , Page Wendy , Harrison Leonard C. , Biggs Beverley-Ann
Published: January 2021

Background

To determine the prevalence of enteric infections in Aboriginal children aged 0–2 years using conventional and molecular diagnostic techniques and to explore associations between the presence of pathogens and child growth.

Methods

Cross-sectional analysis of Aboriginal children (n = 62) residing in a remote community in Northern Australia, conducted from July 24th - October 30th 2017. Stool samples were analysed for organisms by microscopy (directly in the field and following fixation and storage in sodium-acetate formalin), and by qualitative PCR for viruses, bacteria and parasites and serology for Strongyloides-specific IgG. Child growth (height and weight) was measured and z scores calculated according to WHO growth standards.

Results

Nearly 60% of children had evidence for at least one enteric pathogen in their stool (37/62). The highest burden of infection was with adenovirus/sapovirus (22.9%), followed by astrovirus (9.8%) and Cryptosporidium hominis/parvum (8.2%). Non-pathogenic organisms were detected in 22.5% of children. Ten percent of children had diarrhea at the time of stool collection. Infection with two or more pathogens was negatively associated with height for age z scores (− 1.34, 95% CI − 2.61 to − 0.07), as was carriage of the non-pathogen Blastocystis hominis (− 2.05, 95% CI - 3.55 to − 0.54).

Conclusions

Infants and toddlers living in this remote Northern Australian Aboriginal community had a high burden of enteric pathogens and non-pathogens. The association between carriage of pathogens/non-pathogens with impaired child growth in the critical first 1000 days of life has implications for healthy child growth and development and warrants further investigation. These findings have relevance for many other First Nations Communities that face many of the same challenges with regard to poverty, infections, and malnutrition.
Morphological study of the vastus medialis oblique in recurrent patellar dislocation based on magnetic resonance images
Authors: Shu Lei , Yang Xu , He Hangyuan , Chen Biao , Chen Liaobin , Ni Qubo
Published: January 2021

Background

To investigate the morphological parameters of the vastus medialis obliquus (VMO) muscle and delineate its importance in the maintenance of patellofemoral joint stability.

Methods

The magnetic resonance imaging data of seventy-five knees (fifty-four patients) with recurrent lateral patella dislocation (LPD) and seventy-five knees (seventy patients) without recurrent LPD were retrospectively analysed. Five morphological parameters related to the VMO (elevation in the sagittal plane and coronal plane, craniocaudal extent, muscle-fibre angulation, cross-sectional area ratio) and two patella tilt parameters (patella tilt angle, bisect offset ratio) were measured in MR images. The independent-samples t test or chi-square test was used for statistical comparisons.

Results

The mean ages of the patients in the recurrent LPD group and control group were 22.1 ± 9.9 years and 24.0 ± 6.5 years, respectively. Eighteen out of seventy-five (24%) patients MRI showed VMO injuries. Compared with the control group, the patients with recurrent LPD showed significantly higher sagittal VMO elevation (10.4 ± 2.3 mm vs. 4.1 ± 1.9 mm), coronal VMO elevation (15.9 ± 5.7 mm vs. 3.9 ± 3.7 mm), muscle-fibre angulation (35.4 ± 8.0° vs. 27.9 ± 6.3°), patella tilt angle (25.9 ± 10.7° vs. 9.1 ± 5.2°), and bisect offset ratio values (0.9 ± 0.3 vs. 0.5 ± 0.1) and significantly lower craniocaudal extent (13.7 ± 5.3 mm vs. 16.7 ± 5.1 mm) and cross-sectional area ratio values (0.05 ± 0.02 vs. 0.07 ± 0.02).

Conclusions

The results showed that abnormalities in the VMO and patella tilt were clearly present in recurrent LPD patients compared with normal people.
Myeloma cast nephropathy with diffuse amyloid casts without systemic amyloidosis: two cases report
Authors: Yong Zi-hao , Yu Xiao-juan , Lin Zi-shan , Zhou Fu-de , Cen Xi-nan , Wang Su-xia , Zhao Ming-hui
Published: January 2021

Background

Multiple myeloma (MM) is a plasma-cell derived hematologic malignant disease. The malignant proliferating plasma cells secrete massive monoclonal immunoglobulins which lead to various pathologic types of renal injury. Myeloma cast nephropathy (MCN) is the most common histopathologic lesion with the worst renal prognosis. Rarely, the free light chains in the protein casts can form amyloid fibrils. Here, we reported two rare cases of MCN with diffuse amyloid casts.

Case presentation

Case 1: A 54-year-old Chinese man presented with a 4-year history of multiple myeloma, proteinuria and hematuria. He had monoclonal IgAλ plus free λ spike in both serum and urine. He had been on chemotherapy for 4 years and maintained normal serum creatinine until 11 months ago. Then, his renal function deteriorated and he went on hemodialysis 4 months before admission. Renal biopsy showed diffuse amyloid casts in the tubular lumens, without any obvious amyloid deposits in other kidney compartments or signs of extra-renal amyloidosis. The amyloid fibrils formed around mononuclear cells which were CD68 negative. According to the morphology and location, these mononuclear cells were considered as tubular epithelial cells. The patient was maintained on chemotherapy and hemodialysis. He died 8 months after renal biopsy.

Case 2: A 58-year-old Chinese man presented with a one-and-a-half-year history of proteinuria and slowly rising serum creatinine. He had monoclonal IgDλ spike in both serum and urine. Amyloid casts were observed in the tubular lumens and mononuclear cells could be identified in the center of some casts. There were no amyloid deposits in other kidney compartments and no sign of systemic amyloidosis. The patient also had fine granular deposits along the tubular basement membrane with λ linear staining along tubular basement membrane suggesting light chain deposition disease. He was treated with bortezomib-based chemotherapy followed by lenalidomide-based chemotherapy and achieved very good partial remission (VGPR). After 27 months of follow-up, the patient still showed no signs of systemic amyloidosis.

Conclusions

These 2 cases of MCN with diffuse amyloid casts have different histopathologic characteristics from the usual myeloma casts and tubular epithelial cells might play important roles in the pathogenesis.
The association between retinal vessel abnormalities and H-type hypertension
Authors: Huang Kuankuan , Zhang Zhixiang , Huang Shan , Jia Yanwen , Zhang Min , Yun Wenwei
Published: January 2021

Background

This study aimed to investigate the relationship between H-type hypertension and retinal vessel abnormalities.

Methods

Hypertensive patients were retrospectively enrolled in this study. According to plasma homocysteine (HCY), patients were divided into isolated hypertension and H-type hypertension groups. The diameter of retinal vessels and retinopathy were evaluated by retinal fundus photography. The differences of retinal vessel abnormalities between H-type hypertension and isolated hypertension were investigated by univariate and multivariate regression.

Results

A total of 191 hypertensive patients were included, of which 86 were with isolated hypertension and 105 with H-type hypertension. The H-type hypertension group had a higher ratio of retinopathy(P = 0.004) and higher degree of retinal arteriosclerosis (P = 0.005) than the isolated hypertension group. CRAE (107.47 ± 13.99µ m vs. 113.49 ± 11.72µ m, P = 0.002) and AVR (0.55 ± 0.06 vs. 0.58 ± 0.06, P = 0.001) were smaller in H-type hypertension group than those in isolated hypertension group. Multivariate analysis showed that after adjusting for age, sex, course of hypertension and diabetes, H-type hypertension was an independent risk factor of retinopathy (OR, 2.259; 95%CI, 1.165—4.378; P = 0.016), CRAE (β=-5.669; 95%CI, -9.452—-1.886; P = 0.004), and AVR (β=-0.023; 95%CI, -0.039—-0.007; P = 0.005).

Conclusions

H-type hypertension is closely related to more retinal vessel abnormalities than isolated hypertension. Controlling H-type hypertension may reduce the risk of small vascular damage.