Bacterial community analysis in upflow multilayer anaerobic reactor (UMAR) treating high-solids organic wastes

A novel anaerobic digestion configuration, the upflow multi-layer anaerobic reactor (UMAR), was developed to treat high-solids organic wastes. The UMAR was hypothesized to form multi-layer along depth due to the upflow plug flow; use of a recirculation system and a rotating distributor and baffles aimed to assist treating high-solids influent. The chemical oxygen demand (COD) removal efficiency and methane (CH4) production rate were 89% and 2.10 L CH4/L/day, respectively, at the peak influent COD concentration (110.4 g/L) and organic loading rate (7.5 g COD/L/day). The 454 pyrosequencing results clearly indicated heterogeneous distribution of bacterial communities at different vertical locations (upper, middle, and bottom) of the UMAR. Firmicutes was the dominant (>70%) phylum at the middle and bottom parts, while Deltaproteobacteria and Chloroflexi were only found in the upper part. Potential functions of the bacteria were discussed to speculate on their roles in the anaerobic performance of the UMAR system

A Universal Analysis Pipeline for Hybrid Capture-Based Targeted Sequencing Data with Unique Molecular Indexes

Hybrid capture-based targeted sequencing is being used increasingly for genomic variant profiling in tumor patients. Unique molecular index (UMI) technology has recently been developed and helps to increase the accuracy of variant calling by minimizing polymerase chain reaction biases and sequencing errors. However, UMI-adopted targeted sequencing data analysis is slightly different from the methods for other types of omics data, and its pipeline for variant calling is still being optimized in various study groups for their own purposes. Due to this provincial usage of tools, our group built an analysis pipeline for global application to many studies of targeted sequencing generated with different methods. First, we generated hybrid capture-based data using genomic DNA extracted from tumor tissues of colorectal cancer patients. Sequencing libraries were prepared and pooled together, and an 8-plexed capture library was processed to the enrichment step before 150-bp paired-end sequencing with Illumina HiSeq series. For the analysis, we evaluated several published tools. We focused mainly on the compatibility of the input and output of each tool. Finally, our laboratory built an analysis pipeline specialized for UMI-adopted data. Through this pipeline, we were able to estimate even on-target rates and filtered consensus reads for more accurate variant calling. These results suggest the potential of our analysis pipeline in the precise examination of the quality and efficiency of conducted experiments

Single-step genome-wide association study for social genetic effects and direct genetic effects on growth in Landrace pigs

In livestock social interactions, social genetic effects (SGE) represent associations between phenotype of one individual and genotype of another. Such associations occur when the trait of interest is affected by transmissible phenotypes of social partners. The aim of this study was to estimate SGE and direct genetic effects (DGE, genetic effects of an individual on its own phenotype) on average daily gain (ADG) in Landrace pigs, and to conduct single-step genome-wide association study using SGE and DGE as dependent variables to identify quantitative trait loci (QTLs) and their positional candidate genes. A total of 1,041 Landrace pigs were genotyped using the Porcine SNP 60K BeadChip. Estimates of the two effects were obtained using an extended animal model. The SGE contributed 16% of the total heritable variation of ADG. The total heritability estimated by the extended animal model including both SGE and DGE was 0.52. The single-step genome-wide association study identified a total of 23 QTL windows for the SGE on ADG distributed across three chromosomes (i.e., SSC1, SSC2, and SSC6). Positional candidate genes within these QTL regions included PRDM13, MAP3K7, CNR1, HTR1E, IL4, IL5, IL13, KIF3A, EFHD2, SLC38A7, mTOR, CNOT1, PLCB2, GABRR1, and GABRR2, which have biological roles in neuropsychiatric processes. The results of biological pathway and gene network analyses also support the association of the neuropsychiatric processes with SGE on ADG in pigs. Additionally, a total of 11 QTL windows for DGE on ADG in SSC2, 3, 6, 9, 10, 12, 14, 16, and 17 were detected with positional candidate genes such as ARL15. We found a putative pleotropic QTL for both SGE and DGE on ADG on SSC6. Our results in this study provide important insights that can help facilitate a better understanding of the molecular basis of SGE for socially affected traits.info:eu-repo/semantics/publishedVersio

Letter to the Editor: Detection of EML4-ALK and Other ALK Fusion Genes in Lung Cancer: A Lesson from the Leukemia Fusion Gene Analysis and Future Application

We read with interest the article “EML4-ALK Fusion Gene in Korean Non-Small Cell Lung Cancer ” in a recent issue of the Journal of Korean Medical Science by Jin et al. (1). In this study, EML4-ALK fusion gene was detected in 10 of 167 non-small cell lung cancer (NSCLC) patients by using reverse transcriptase-polymerase chain reaction (RT-PCR) as a basic screening technique instead of fluorescence in situ hybridization (FISH) method. The frequency of EML4-ALK fusion gene in this study (6.0%) was not largely different from a previous study that used the FISH method on Korean NSCLC patients (4.2%) (2), while it did not diverge from the results in previous studies on a general NSCLC patient population that yielded 3%-7 % ratios as well. Based on the experience of detecting leukemia fusion genes with several new molecular methods during the diagnosis of leukemia (3-6), we would like to mention the pros and cons of such methods i

Strong carrier localization and diminished quantum-confined Stark effect in ultra-thin high-indium-content InGaN quantum wells with violet light emission

Here, we report on the optical and structural characteristics of violet-light-emitting, ultra-thin, high-Indium-content (UTHI) InGaN/GaN multiple quantum wells (MQWs), and of conventional low-In-content MQWs, which both emit at similar emission energies though having different well thicknesses and In compositions. The spatial inhomogeneity of In content, and the potential fluctuation in high-efficiency UTHI MQWs were compared to those in the conventional low-In-content MQWs. We conclude that the UTHI InGaN MQWs are a promising structure for achieving better quantum efficiency in the visible and near-ultraviolet spectral range, owing to their strong carrier localization and reduced quantum-confined Stark effect.open0

Melatonin receptor 1 B polymorphisms associated with the risk of gestational diabetes mellitus

<p>Abstract</p> <p>Backgrounds</p> <p>Two SNPs in <it>melatonin receptor 1B </it>gene, <it>rs10830963 </it>and <it>rs1387153 </it>showed significant associations with fasting plasma glucose levels and the risk of Type 2 Diabetes Mellitus (T2DM) in previous studies. Since T2DM and gestational diabetes mellitus (GDM) share similar characteristics, we suspected that the two genetic polymorphisms in <it>MTNR1B </it>may be associated with GDM, and conducted association studies between the polymorphisms and the disease. Furthermore, we also examined genetic effects of the two polymorphisms with various diabetes-related phenotypes.</p> <p>Methods</p> <p>A total of 1,918 subjects (928 GDM patients and 990 controls) were used for the study. Two <it>MTNR1B </it>polymorphisms were genotyped using TaqMan assay. The allele distributions of SNPs were evaluated by <it>x</it>²models calculating odds ratios (ORs), 95% confidence intervals (CIs), and corresponding <it>P </it>values. Multiple regressions were used for association analyses of GDM-related traits. Finally, conditional analyses were also performed.</p> <p>Results</p> <p>We found significant associations between the two genetic variants and GDM, <it>rs10830963</it>, with a corrected <it>P </it>value of 0.0001, and <it>rs1387153</it>, with the corrected <it>P </it>value of 0.0008. In addition, we also found that the two SNPs were associated with various phenotypes such as homeostasis model assessment of beta-cell function and fasting glucose levels. Further conditional analyses results suggested that <it>rs10830963 </it>might be more likely functional in case/control analysis, although not clear in GDM-related phenotype analyses.</p> <p>Conclusion</p> <p>There have been studies that found associations between genetic variants of other genes and GDM, this is the first study that found significant associations between SNPs of <it>MTNR1B </it>and GDM. The genetic effects of two SNPs identified in this study would be helpful in understanding the insight of GDM and other diabetes-related disorders.</p

Manganese based layered oxides with modulated electronic and thermodynamic properties for sodium ion batteries

Manganese based layered oxides have received increasing attention as cathode materials for sodium ion batteries due to their high theoretical capacities and good sodium ion conductivities. However, the Jahn–Teller distortion arising from the manganese (III) centers destabilizes the host structure and deteriorates the cycling life. Herein, we report that zinc-doped Na0.833[Li0.25Mn0.75]O2 can not only suppress the Jahn–Teller effect but also reduce the inherent phase separations. The reduction of manganese (III) amount in the zinc-doped sample, as predicted by first-principles calculations, has been confirmed by its high binding energies and the reduced octahedral structural variations. In the viewpoint of thermodynamics, the zinc-doped sample has lower formation energy, more stable ground states, and fewer spinodal decomposition regions than those of the undoped sample, all of which make it charge or discharge without any phase transition. Hence, the zinc-doped sample shows superior cycling performance, demonstrating that zinc doping is an effective strategy for developing high-performance layered cathode materials