SciCombinator

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139

Decaisnea insignis is a wild resource plant and is used as an ornamental, medicinal, and fruit plant. High-throughput sequencing of chloroplast genomes has provided insight into the overall evolutionary dynamics of chloroplast genomes and has enhanced our understanding of the evolutionary relationships within plant families. In the present study, we sequenced the complete chloroplast genome of D. insignis and used the data to assess its genomic resources. The D. insignis chloroplast genome is 158,683 bp in length and includes a pair of inverted repeats of 26,167 bp that are separated by small and large single copy regions of 19,162 bp and 87,187 bp, respectively. We identified 83 simple sequence repeats and 18 pairs of large repeats. Most simple-sequence repeats were located in the noncoding sections of the large single-copy/small single-copy region and exhibited a high A/T content. The D. insignis chloroplast genome bias was skewed towards A/T on the basis of codon usage. A phylogenetic tree based on 82 protein-coding genes of 33 angiosperms showed that D. insignis was clustered with Akebia in Lardizabalaceae. Overall, the results of this study will contribute to better understanding the evolution, molecular biology and genetic improvement of D. insignis.

Concepts: DNA, Gene, Genetics, Evolution, Molecular biology, Biology, Organism, Genome

139

Few studies addressed trans-regional differences in allergen sensitization between areas within a similar latitudinal range but with distinct geomorphological features. We investigated specific IgE (sIgE) positivity to common allergens in populations from two southern China provinces. Using a uniformed protocol, serum samples were collected from 2778 subjects with suspected atopy in coastal Guangdong and inland Yunnan. The overall prevalence of sIgE positivity were 57.8% (95% CI: 56.0%, 59.6%) from Guangdong vs 60.9% (95% CI: 59.1%, 62.7%) from Yunnan. House dust mite (d1) was the most common allergen in both regions. Among d1-sensitized subjects, only 35.7% (208/583) in Guangdong and 22.9% (147/642) in Yunnan tested positive for d1 alone. Among those poly-sensitized d1-positive subjects, cockroach was the most common co-sensitizing aeroallergen. 41.9% of the d1-sensitized Guangdong subjects showed high-class sIgE reactivity (≥class 4), in contrast to a very low percentage of such reactivity in Yunnan. However, 36.3% of d1-sensitized subjects in Yunnan were concomitantly positive for tree pollen mix. Surprisingly, Yunnan subjects showed high prevalence of sIgE positivity for crabs and shrimps, either by overall or by age-group analysis, compared with their Guangdong counterparts (both P < 0.05). These findings may add to data about local allergies in China and worldwide.

Concepts: Asthma, Allergy, Atopy, Allergen, People's Republic of China, Arachnid, Mite, House dust mite

139

The gastrointestinal (GI) tract, including the rumen and the other intestinal segments of cattle, harbors a diverse, complex, and dynamic microbiome that drives feed digestion and fermentation in cattle, determining feed efficiency and output of pollutants. This microbiome also plays an important role in affecting host health. Research has been conducted for more than a century to understand the microbiome and its relationship to feed efficiency and host health. The traditional cultivation-based research elucidated some of the major metabolism, but studies using molecular biology techniques conducted from late 1980’s to the late early 2000’s greatly expanded our view of the diversity of the rumen and intestinal microbiome of cattle. Recently, metagenomics has been the primary technology to characterize the GI microbiome and its relationship with host nutrition and health. This review addresses the main methods/techniques in current use, the knowledge gained, and some of the challenges that remain. Most of the primers used in qPCR quantification and diversity analysis using metagenomics of ruminal bacteria, archaea, fungi, and protozoa were also compiled.

Concepts: Bacteria, Evolution, Molecular biology, Metabolism, Nutrition, Microbiology, Digestive system, Digestion

139

The Atacama Desert is the most extreme non-polar biome on Earth, the core region of which is considered to represent the dry limit for life and to be an analogue for Martian soils. This study focused on actinobacteria because they are keystone species in terrestrial ecosystems and are acknowledged as an unrivalled source of bioactive compounds. Metagenomic analyses of hyper-arid and extreme hyper-arid soils in this desert revealed a remarkable degree of actinobacterial ‘dark matter’, evidenced by a detected increase of 34% in families against those that are validly published. Rank-abundance analyses indicated that these soils were high-diversity habitats and that the great majority of designated ‘rare’ genera (up to 60% of all phylotypes) were always rare. These studies have enabled a core actinobacterial microbiome common to both habitats to be defined. The great majority of detected taxa have not been recovered by culture dependent methods, neither, with very few exceptions, has their functional ecology been explored. A microbial seed bank of this magnitude has significance not just for Atacama soil ecosystem resilience but represents an enormous untapped resource for biotechnology discovery programmes in an era where resistance to existing antibiotics is rapidly becoming a major threat to global health.

Concepts: Biodiversity, Ecosystem, Chile, Dark matter, Atacama Desert, Desert, Rain shadow, Biosphere

26

We performed integrative network analyses to identify targets that can be used for effectively treating liver diseases with minimal side effects. We first generated co-expression networks (CNs) for 46 human tissues and liver cancer to explore the functional relationships between genes and examined the overlap between functional and physical interactions. Since increased de novo lipogenesis is a characteristic of nonalcoholic fatty liver disease (NAFLD) and hepatocellular carcinoma (HCC), we investigated the liver-specific genes co-expressed with fatty acid synthase (FASN). CN analyses predicted that inhibition of these liver-specific genes decreases FASN expression. Experiments in human cancer cell lines, mouse liver samples, and primary human hepatocytes validated our predictions by demonstrating functional relationships between these liver genes, and showing that their inhibition decreases cell growth and liver fat content. In conclusion, we identified liver-specific genes linked to NAFLD pathogenesis, such as pyruvate kinase liver and red blood cell (PKLR), or to HCC pathogenesis, such as PKLR, patatin-like phospholipase domain containing 3 (PNPLA3), and proprotein convertase subtilisin/kexin type 9 (PCSK9), all of which are potential targets for drug development.

Concepts: Cancer, Fatty acid, Obesity, Cirrhosis, Liver, Non-alcoholic fatty liver disease, Fatty liver, Fatty acid synthase

24

Treatment for tobacco use is efficacious and beneficial to health. Although guidelines recommend that all patients who use tobacco are offered treatment as a part of their clinical care, implementing treatment has proven challenging. In the case of surgical patients, this lack of treatment is particularly unfortunate, as the benefits of abstinence from tobacco are immediate in terms of reducing the risk of surgical complications, including cardiovascular, respiratory, and wound related complications. Surgery also presents an opportunity for patients to quit for good and reduce the long term health risk. This review examines the principles of tobacco use treatment, the rationale for tobacco use treatment in the perioperative period, and how treatment can be incorporated into the routine care of surgical patients. The discipline of implementation science helps to frame these efforts by seeking to better understand how changes in clinical practice occur, and it has the potential to guide an evidence based approach to embedding tobacco treatment into the routine clinical care of surgical patients. This review uses the consolidated framework for implementation research, which includes five major domains, as a representative conceptual framework. A basic understanding of factors potentially important to successful implementation can help to guide clinicians who accept the challenge of implementing tobacco use treatment in surgical care.

Concepts: Health care, Medicine, Clinical trial, Understanding, Hospital, Term, Abstraction, Potential

23

It is challenging to hierarchically pattern high-aspect-ratio nanostructures on microstructures using conventional lithographic techniques, where photoresist film is not able to uniformly cover on the microstructures as the aspect ratio increases. Such non-uniformity causes poor definition of nanopatterns over the microstructures. Nanostencil lithography can provide an alternative means to hierarchically construct nanostructures on microstructures via direct deposition or plasma etching through a free-standing nanoporous membrane. In this work, we demonstrate the hierarchical fabrication of high-aspect-ratio nanostructures on microstructures of silicon using a free-standing nanostencil, which is a nanoporous membrane consisting of metal (Cr), photoresist (PR), and anti-reflective coating (ARC). The nanostencil membrane is used as a deposition mask to define Cr nanodot patterns on the predefined silicon microstructures. Then, deep reactive ion etching (DRIE) is used to hierarchically create nanostructures on the microstructures using the Cr nanodots as an etch mask. With simple modification of the main fabrication processes, high-aspect-ratio nanopillars are selectively defined only on top of the microstructures, on bottom, or on both top and bottom.

Concepts: Definition, Pattern, Semiconductor device fabrication, Etching, Lithography, Reactive-ion etching, Deep reactive-ion etching, Printmaking

23

PurposeWe sought to determine the analytical sensitivity of several extended exome variation analysis approaches in terms of their contribution to diagnostic yield and their clinical feasibility.MethodsWe retrospectively analyzed the results of genetic testing in 1,059 distinct cases referred for exome sequencing to our institution. In these, we routinely employed extended exome analysis approaches in addition to basic variant analysis, including (i) copy-number variation (CNV) detection, (ii) nonconsensus splice defect detection, (ii) genomic breakpoint detection, (iv) homozygosity mapping, and (v) mitochondrial variant analysis.ResultsExtended exome analysis approaches assisted in identification of causative genetic variant in 44 cases, which represented a 4.2% increase in diagnostic yield. The greatest contribution was associated with CNV analysis (1.8%) and splice variant prediction (1.2%), and the remaining approaches contributed an additional 1.2%. Analysis of workload has shown that on average nine additional variants per case had to be interpreted in the extended analysis.ConclusionWe show that extended exome analysis approaches improve the diagnostic yield of heterogeneous genetic disorders and result in considerable increase of diagnostic yield of exome sequencing with a minor increase of interpretative workload.GENETICS in MEDICINE advance online publication, 14 September 2017; doi:10.1038/gim.2017.142.

Concepts: DNA, Gene, Genetics, Cancer, Genetic disorder, Mutation, Copy number variation, Human genome

23

Serum amyloid A protein (SAA) is known as an inflammatory factor and an apolipoprotein that can replace apolipoprotein A-I/II components as the major apolipoprotein of high-density lipoprotein (HDL), which is related to atherosclerosis. The present study is aimed to evaluate whether the SAA gene polymorphism is involved in ischemic stroke in northern Chinese Han population.

Concepts: Inflammation, Atherosclerosis, Stroke, High-density lipoprotein, China, Han Chinese, Chinese language, Serum amyloid A

23

Objectives To examine the risk of relapse and time to relapse after discontinuation of antidepressants in patients with anxiety disorder who responded to antidepressants, and to explore whether relapse risk is related to type of anxiety disorder, type of antidepressant, mode of discontinuation, duration of treatment and follow-up, comorbidity, and allowance of psychotherapy.Design Systematic review and meta-analyses of relapse prevention trials.Data sources PubMed, Cochrane, Embase, and clinical trial registers (from inception to July 2016).Study selection Eligible studies included patients with anxiety disorder who responded to antidepressants, randomised patients double blind to either continuing antidepressants or switching to placebo, and compared relapse rates or time to relapse.Data extraction Two independent raters selected studies and extracted data. Random effect models were used to estimate odds ratios for relapse, hazard ratios for time to relapse, and relapse prevalence per group. The effect of various categorical and continuous variables was explored with subgroup analyses and meta-regression analyses respectively. Bias was assessed using the Cochrane tool.Results The meta-analysis included 28 studies (n=5233) examining relapse with a maximum follow-up of one year. Across studies, risk of bias was considered low. Discontinuation increased the odds of relapse compared with continuing antidepressants (summary odds ratio 3.11, 95% confidence interval 2.48 to 3.89). Subgroup analyses and meta-regression analyses showed no statistical significance. Time to relapse (n=3002) was shorter when antidepressants were discontinued (summary hazard ratio 3.63, 2.58 to 5.10; n=11 studies). Summary relapse prevalences were 36.4% (30.8% to 42.1%; n=28 studies) for the placebo group and 16.4% (12.6% to 20.1%; n=28 studies) for the antidepressant group, but prevalence varied considerably across studies, most likely owing to differences in the length of follow-up. Dropout was higher in the placebo group (summary odds ratio 1.31, 1.06 to 1.63; n=27 studies).Conclusions Up to one year of follow-up, discontinuation of antidepressant treatment results in higher relapse rates among responders compared with treatment continuation. The lack of evidence after a one year period should not be interpreted as explicit advice to discontinue antidepressants after one year. Given the chronicity of anxiety disorders, treatment should be directed by long term considerations, including relapse prevalence, side effects, and patients' preferences.

Concepts: Epidemiology, Medical statistics, Odds ratio, Effect size, Selective serotonin reuptake inhibitor, Posttraumatic stress disorder, Anxiety disorder, Anxiety disorders