SNPer: An R Library for Quantitative Variant Analysis on Single Nucleotide Polymorphisms among Influenza Virus Populations

Influenza virus (IFV) can evolve rapidly leading to genetic drifts and shifts resulting in human and animal influenza epidemics and pandemics. The genetic shift that gave rise to the 2009 influenza A/H1N1 pandemic originated from a triple gene reassortment of avian, swine and human IFVs. More minor genetic alterations in genetic drift can lead to influenza drug resistance such as the H274Y mutation associated with oseltamivir resistance. Hence, a rapid tool to detect IFV mutations and the potential emergence of new virulent strains can better prepare us for seasonal influenza outbreaks as well as potential pandemics. Furthermore, identification of specific mutations by closely examining single nucleotide polymorphisms (SNPs) in IFV sequences is essential to classify potential genetic markers associated with potentially dangerous IFV phenotypes. In this study, we developed a novel R library called “SNPer” to analyze quantitative variants in SNPs among IFV subpopulations. The computational SNPer program was applied to three different subpopulations of published IFV genomic information. SNPer queried SNPs data and grouped the SNPs into (1) universal SNPs, (2) likely common SNPs, and (3) unique SNPs. SNPer outperformed manual visualization in terms of time and labor. SNPer took only three seconds with no errors in SNP comparison events compared with 40 hours with errors using manual visualization. The SNPer tool can accelerate the capacity to capture new and potentially dangerous IFV strains to mitigate future influenza outbreaks.     

Characterization and comparative genomic analysis of gamma-aminobutyric acid (GABA)-producing lactic acid bacteria from Thai fermented foods

Objectives

This study aimed to screen, characterize, and annotate the genome along with the comparison of GABA synthesis genes presented in lactic acid bacteria (LAB).

Results

Thirty-five LAB isolates from fermented foods were screened for GABA production using thin-layer chromatography (TLC). Fifteen isolates produced GABA ranging from 0.07 to 22.94 g/L. Based on their GTG₅ profiles, phenotypic, and genotypic characteristics, isolates LSI1-1, LSI1-5, LSI2-1, LSI2-2, LSI2-3, LSI2-5, and LSM3-1-4 were identified as Lactobacillus plantarum subsp. plantarum; isolate LSM1-4 was Lactobacillus argentoratensis; isolates CAB1-2, CAB1-5, CAB1-7, and LSI1-4 were Lactobacillus pentosus; and CAB1-1, LSM3-1-1 and LSM3-2-3 were Lactobacillus fermentum. Strains LSI2-1 and CAB1-7 from pickled vegetables were selected for genome analysis. The gadA gene (1410 bp, 470aa) was encountered in GABA production of both strains and no other glutamate decarboxylase (GAD) genes were found in the genomes when compared with other LAB strains. The presence of gadA is evidence for GABA production. Strains LSI2-1 and CAB1-7 produced 22.94 g/L and 11.59 g/L of GABA in GYP broth supplemented with 3% (w/v) MSG at 30 °C for 72 h, respectively.

Conclusions

Our report highlights the characterization of LAB and GABA production of L. plantarum LSI2-1 strain with its GABA synthesis gene.

Graphic abstract

GABA production of strains LSI2-1 and CAB1-7 in GYP broth with 3% (w/v) MSG and comparative GAD genes

     

Enhanced production of pharmaceutically important isoflavones from hairy root rhizoclones of <Emphasis Type="Italic">Trifolium pratense</Emphasis> L.

These studies report the development of an efficient technique for large-scale cultivation of fast-growing hairy root culture systems for production of bioactive isoflavones. Trifolium pratense L. is an important source of pharmaceutically important isoflavones with immense health care applications. Trifolium pratense was transformed using different strains of Agrobacterium rhizogenes for hairy root induction and establishment of hairy root rhizoclones. Selected fast-growing rhizoclones of T. pratense were evaluated for their growth and isoflavone production. This study is the first report of stable production of isoflavones through successive culture passages from transformed hairy-root rhizoclones of T. pratense. One of the fast-growing hairy-root rhizoclones 2364A displayed significantly higher accumulation of all four pharmaceutically important isoflavones, 8.56 mg (gdw)^?1 of daidzein, 2.45 mg (gdw)^?1 of genistein, 15.23 mg (gdw)^?1 of formononetin, and 1.10 mg (gdw)^?1 of biochanin A, compared to other rhizoclones.     

Microwave synthesis, spectroscopy, thermal analysis and crystal structure of an one-dimensional polymeric {[Cu(4,4′-bipy)(H2O)3(SO4)] · 2H2O}n complex

A metal organic-inorganic coordination framework formulated as {[Cu(4,4′-bipy)(H₂O)₃(SO₄)] · 2H₂O}_n (1) (where 4,4′-bipy = 4,4′-bipyridine) has been successfully prepared by microwave synthesis. The title complex has been characterized by single crystal X-ray crystallography, FT-IR spectroscopy and thermal analysis. Complex (1) is an one-dimensional (1D) polymer in which 4,4′-bipy acts as a bridging ligand supporting the formation of infinite [Cu(4,4′-bipy)(H₂O)₃(SO₄)] chains. The packing diagram shows that a 3D network is formed via hydrogen bonds. The infrared spectra and thermographic data are consistent with the chemical formula.     

Fucosylation enhances colonization of ticks by Anaplasma phagocytophilum

Fucosylated structures participate in a wide range of pathological processes in eukaryotes and prokaryotes. The impact of fucose on microbial pathogenesis, however, has been less appreciated in arthropods of medical relevance. Thus, we used the tick‐borne bacterium Anaplasma phagocytophilum– the agent of human granulocytic anaplasmosis to understand these processes. Here we show that A. phagocytophilum uses α1,3‐fucose to colonize ticks. We demonstrate that A. phagocytophilum modulates the expression of α1,3‐fucosyltransferases and gene silencing significantly reduces colonization of tick cells. Acquisition but not transmission of A. phagocytophilum was affected when α1,3‐fucosyltransferases were silenced during tick feeding. Our results uncover a novel mechanism of pathogen colonization in arthropods. Decoding mechanisms of pathogen invasion in ticks might expedite the development of new strategies to interfere with the life cycle of A. phagocytophilum.     

Heavy metal accumulation in rice (Oryza sativa) near electronic waste dumps and related human health risk assessment

This research was conducted to assess heavy metal contamination in the environment and within Oryza sativa. The translocation factors (TFs) and bioaccumulation factors (BAFs) for heavy metals in O. sativa and estimated daily intake (EDI) and health risk index (HRI) were measured. The samples were analyzed for heavy metals using inductively coupled plasma optical emission spectrometry (ICP-OES). Pb and Cr concentrations in water samples within and near the electronic-waste dumping area exceeded water quality standards for surface water sources from the Pollution Control Department in the Ministry of Natural Resources and Environment of Thailand (PCD). The Pb concentration in soil samples within the area also exceeded soil quality standards for habitat and agriculture from PCD. Most of the metals were highly concentrated in roots, except for Mn which has the highest concentration in leaves. Pb concentrations in rice grains exceeded the FAO/WHO standard (0.2 mg/kg). The average TF values for heavy metals from the soil to roots, roots to stems, stems to leaves, and stems to grains were Mn > Pb > Ni > Cr, Mn > Cr > Ni > Pb, Ni > Pb > Mn > Cr, and Pb > Ni > Cr > Mn, respectively. The average BAF values in O. sativa were Mn > Ni > Pb > Cr. The EDI for Cr, Pb, Mn, and Ni via O. sativa consumption were 6.19, 6.02, 370.57, and 3.80 µg/kg/day, respectively. The HRI for Cr, Pb, Mn, and Ni via O. sativa consumption were 0.30, 1.50, 2.60, and 0.002, respectively.     

Altered chemokine production and accumulation of regulatory T cells in intestinal adenomas of APCMin/+ mice

Tumor progression in the colon moves from aberrant crypt foci to adenomatous polyps to invasive carcinomas. The composition of the tumor-infiltrating leukocyte population affects the ability of the immune system to fight the tumor. T cell infiltration into colorectal adenocarcinomas, particularly T helper 1 (Th1) type T cells as well as increased regulatory T cell (Treg) frequencies, is correlated with improved prognosis. However, whether Th1 cells and Tregs are already present at the adenoma stage is not known. In this study, the APC^Min/+ mouse model of intestinal adenomatous polyposis was used to investigate tumor-associated lymphocyte subsets and the mechanisms of their accumulation into gastrointestinal adenomas. Compared to unaffected tissue, adenomas accumulated CD4⁺FoxP3⁺ putative Treg in parallel with lower frequencies of conventional T cells and B cells. The accumulation of Treg was also observed in human adenomatous polyps. Despite high Treg numbers, the function of conventional T cells present in the APC^Min/+ adenomas was not different from those in the unaffected tissue. Adenomas displayed an altered chemokine balance, with higher CCL17 and lower CXCL11 and CCL25 expression than in the unaffected tissue. In parallel, CXCR3⁺ Tregs were largely absent from adenomas. The data indicate that already in early stages of tumor development, the balance of lymphocyte-recruiting chemokines is altered possibly contributing to the observed shift toward higher frequencies of Treg.     

Is Your Ethics Committee Efficient? Using “IRB Metrics” as a Self-Assessment Tool for Continuous Improvement at the Faculty of Tropical Medicine,Mahidol University,Thailand

Tensions between researchers and ethics committees have been reported in several institutions. Some reports suggest researchers lack confidence in the quality of institutional review board (IRB) reviews, and that emphasis on strict procedural compliance and ethical issues raised by the IRB might unintentionally lead to delays in correspondence between researchers and ethics committees, and/or even encourage prevarication/equivocation, if researchers perceive committee concerns and criticisms unjust. This study systematically analyzed the efficiency of different IRB functions, and the relationship between efficiency and perceived quality of the decision-making process. The major purposes of this study were thus (1) to use the IRB Metrics developed by the Faculty of Tropical Medicine, Mahidol University, Thailand (FTM-EC) to assess the operational efficiency and perceived effectiveness of its ethics committees, and (2) to determine ethical issues that may cause the duration of approval process to be above the target limit of 60 days. Based on a literature review of definitions and methods used and proposed for use, in assessing aspects of IRB quality, an “IRB Metrics” was developed to assess IRB processes using a structure-process-outcome measurement model. To observe trends in the indicators evaluated, data related to all protocols submitted to the two panels of the FTM-EC (clinical and non-clinical), between January 2010–September 2013, were extracted and analyzed. Quantitative information based on IRB Metrics structure-process-outcome illuminates different areas for internal-process improvement. Ethical issues raised with researchers by the IRB, which were associated with the duration of the approval process in protocol review, could be considered root causes of tensions between the parties. The assessment of IRB structure-process-outcome thus provides a valuable opportunity to strengthen relationships and reduce conflicts between IRBs and researchers, with positive outcomes for all parties involved in the conduct of human-subject research.