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Coverage evaluation of universal bacterial primers using the metagenomic datasets

BMC MICROBIOLOGY 2012年第1期12卷 66-66页

作者： Mao, Dan-Ping Zhou, Quan Chen, Chong-Yu Quan, Zhe-Xue Fudan Univ Sch Life Sci Dept Microbiol & Microbial Engn Shanghai 200433 Peoples R China

Background: The coverage of universal primers for the bacterial 16S rRNA gene plays a crucial role in the correct understanding of microbial community structure. However, existing studies on primer coverage are limited by the lack of appropriate databases and are restricted to the domain level. Additionally, most studies do not account for the positional effect of single primer-template mismatches. In this study, we used 7 metagenomic datasets as well as the Ribosomal Database Project (RDP) to assess the coverage of 8 widely used bacterial primers. Results: The coverage rates for bacterial primers were found to be overestimated by previous studies that only investigated the RDP because of PCR amplification bias in the sequence composition of the dataset. In the RDP, the non-coverage rates for all primers except 27F were <6%, while in the metagenomic datasets, most were >10%. If one considers that a single mismatch near the 3' end of the primer might greatly reduce PCR efficiency, then some phylum non-coverage rates would change by more than 20%. Primer binding-site sequence variants that could not pair with their corresponding primers are discussed. Conclusions: Our study revealed the potential bias introduced by the use of universal bacterial primers in the assessment of microbial communities. With the development of high-throughput, next-generation sequencing techniques, it will become feasible to sequence more of the hypervariable regions of the bacterial 16S rRNA gene. This, in turn, will lead to the more frequent use of the primers discussed here.

关键词： basic local alignment search tool Ribosomal Database Project Phylum Level Universal Bacterial Primer Metagenomic Dataset

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Annotation, phylogenetics, and expression of the nuclear receptors in Daphnia pulex

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BMC GENOMICS 2009年第1期10卷 500-500页

作者： Thomson, Susanne A. Baldwin, William S. Wang, Ying H. Kwon, Gwijun LeBlanc, Gerald A. N Carolina State Univ Dept Environm & Mol Toxicol Raleigh NC 27695 USA Clemson Univ Dept Biol Sci Pendleton SC USA Clemson Univ Environm Toxicol Program Pendleton SC USA

Background: The nuclear receptor superfamily currently consists of seven gene subfamilies that encompass over 80 distinct receptor proteins. These transcription factors typically share a common five-domain structure with a highly conserved DNA-binding domain. Some nuclear receptors are ubiquitous among the metazoans, while others are unique to specific phylogenetic groups. Crustaceans represent the second largest group of arthropods with insects being the largest. However, relative to insects, little is known about the nuclear receptors of crustaceans. The aim of this study was to identify putative nuclear receptors from the first assembled genome of a crustacean Daphnia pulex http://***. Nuclear receptor expression was evaluated and receptors were subjected to phylogenetic analyses to gain insight into evolution and function. Results: Twenty-five putative nuclear receptors were identified in D. pulex based on the presence of a conserved DNA-binding domain. All of the nuclear receptor protein sequences contain a highly homologous DNA-binding domain and a less conserved ligand-binding domain with the exception of the NR0A group. These receptors lack a ligand-binding domain. Phylogenetic analysis revealed the presence of all seven receptor subfamilies. The D. pulex genome contains several nuclear receptors that have vertebrate orthologs. However, several nuclear receptor members that are represented in vertebrates are absent from D. pulex. Notable absences include receptors of the 1C group (peroxisome proliferators-activated receptors), the 3A group (estrogen receptor), and the 3C group (androgen, progestogen, mineralcorticoid, and glucocorticoid receptors). The D. pulex genome also contains nuclear receptor orthologs that are present in insects and nematodes but not vertebrates, including putative nuclear receptors within the NR0A group. A novel group of receptors, designated HR97, was identified in D. pulex that groups with the HR96/CeNHR8/48/DAF12 clade,

关键词： Nuclear Receptor basic local alignment search tool Receptor Group basic local alignment search tool search Hormone Response Element

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gene cluster analysis for the biosynthesis of elgicins, novel lantibiotics produced by Paenibacillus elgii B69 (vol 12, pg 45, 2012)

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BMC MICROBIOLOGY 2012年第1期12卷 45-45页

作者： Teng, Yi Zhao, Wenpeng Qian, Chaodong Li, Ou Zhu, Liang Wu, Xuechang Zhejiang Univ Coll Life Sci Inst Microbiol Hangzhou 310058 Zhejiang Peoples R China

The recent increase in bacterial resistance to antibiotics has promoted the exploration of novel antibacterial materials. As a result, many researchers are undertaking work to identify new lantibiotics because of their potent antimicrobial activities. The objective of this study was to provide details of a lantibiotic-like gene cluster in Paenibacillus elgii B69 and to produce the antibacterial substances coded by this gene cluster based on culture screening. Analysis of the P. elgii B69 genome sequence revealed the presence of a lantibiotic-like gene cluster composed of five open reading frames (elgT1, elgC, elgT2, elgB, and elgA). Screening of culture extracts for active substances possessing the predicted properties of the encoded product led to the isolation of four novel peptides (elgicins AI, AII, B, and C) with a broad inhibitory spectrum. The molecular weights of these peptides were 4536, 4593, 4706, and 4820 Da, respectively. The N-terminal sequence of elgicin B was Leu-Gly-Asp-Tyr, which corresponded to the partial sequence of the peptide ElgA encoded by elgA. Edman degradation suggested that the product elgicin B is derived from ElgA. By correlating the results of electrospray ionization-mass spectrometry analyses of elgicins AI, AII, and C, these peptides are deduced to have originated from the same precursor, ElgA. A novel lantibiotic-like gene cluster was shown to be present in P. elgii B69. Four new lantibiotics with a broad inhibitory spectrum were isolated, and these appear to be promising antibacterial agents.

关键词： Gene Cluster basic local alignment search tool Leader Peptide MibC Subtilis ATCC

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In Silico cancer cell versus stroma cellularity index computed from species-specific human and mouse transcriptome of xenograft models: towards accurate stroma targeting therapy assessment

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BMC MEDICAL GENOMICS 2014年第1-Sup期7卷 1-13页

作者： Yang, Xinan Huang, Yong Lee, Younghee Gardeux, Vincent Achour, Ikbel Regan, Kelly Rebman, Ellen Li, Haiquan Lussier, Yves A. Univ Chicago Dept Med Ctr Biom Info Med Genet Sect Chicago IL 60637 USA Univ Illinois Inst Translat Hlth Informat Chicago IL 60680 USA EISTI Engn Sch Dept Informat Cergy France Univ Illinois Dept Med Chicago IL 60680 USA Univ Chicago Ctr Comprehens Canc Chicago IL 60637 USA Univ Chicago Ludwig Ctr Metastasis Res Chicago IL 60637 USA Univ Chicago Med Comer Childrens Hosp Dept Pediat Hematol Oncol Sect Chicago IL 60637 USA Univ Illinois Dept Bioengn Chicago IL 60680 USA Univ Illinois Dept Pharmaceut Sci Chicago IL 60680 USA Argonne Natl Lab Comp Inst Argonne IL 60439 USA Argonne Natl Lab Inst Genom & Syst Bio Argonne IL 60439 USA Univ Chicago Chicago IL 60637 USA Univ Illinois Inst Personalized Resp Med Chicago IL 60680 USA Univ Arizona Ctr Canc Inst BIO5 Clin & Translat Sci Inst Tucson AZ 85721 USA

Background: The current state of the art for measuring stromal response to targeted therapy requires burdensome and rate limiting quantitative histology. Transcriptome measures are increasingly affordable and provide an opportunity for developing a stromal versus cancer ratio in xenograft models. In these models, human cancer cells are transplanted into mouse host tissues (stroma) and together coevolve into a tumour microenvironment. However, profiling the mouse or human component separately remains problematic. Indeed, laser capture microdissection is labour intensive. Moreover, gene expression using commercial microarrays introduces significant and underreported cross-species hybridization errors that are commonly overlooked by biologists. Method: We developed a customized dual-species array, H&M array, and performed cross-species and species-specific hybridization measurements. We validated a new methodology for establishing the stroma vs cancer ratio using transcriptomic data. Results: In the biological validation of the H&M array, cross-species hybridization of human and mouse probes was significantly reduced (4.5 and 9.4 fold reduction, respectively;p < 2x10(-16) for both, Mann-Whitney test). We confirmed the capability of the H&M array to determine the stromal to cancer cells ratio based on the estimation of cellularity index of mouse/human mRNA content in vitro. This new metrics enable to investigate more efficiently the stroma-cancer cell interactions (e. g. cellularity) bypassing labour intensive requirement and biases of laser capture microdissection. Conclusion: These results provide the initial evidence of improved and cost-efficient analytics for the investigation of cancer cell microenvironment, using species-specificity arrays specifically designed for xenografts models.

关键词： basic local alignment search tool Laser Capture Microdissection Biological Experiment Cross Species Hybridization Human Array

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Plasmalogens - Ubiquitous molecules occurring widely, from anaerobic bacteria to humans

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PROGRESS IN LIPID REsearch 2021年 83卷 101111-101111页

作者： Vitova, Milada Palyzova, Andrea Rezanka, Tomas Czech Acad Sci Inst Microbiol Lab Cell Cycles Algae Novohradska 237 Trebon 37981 Czech Republic Czech Acad Sci Inst Microbiol Videnska 1083 Prague 14220 Czech Republic

Plasmalogens are a group of lipids mainly found in the cell membranes. They occur in anaerobic bacteria and in some protozoa, invertebrates and vertebrates, including humans. Their occurrence in plants and fungi is controversial. They can protect cells from damage by reactive oxygen species, protect other phospholipids or lipoprotein particles against oxidative stress, and have been implicated as signaling molecules and modulators of membrane dynamics. Biosynthesis in anaerobic and aerobic organisms occurs by different pathways, and the main biosynthetic pathway in anaerobic bacteria was clarified only this year (2021). Many different analytical techniques have been used for plasmalogen analysis, some of which are detailed below. These can be divided into two groups: shotgun lipidomics, or electrospray ionization mass spectrometry in combination with high performance liquid chromatography (LC-MS). The advantages and limitations of both techniques are discussed here, using examples from anaerobic bacteria to specialized mammalian (human) organs.

关键词： ACBD acyl-CoA-binding domain APCI atmospheric pressure chemical ionization A-PE 1-alkyl-2-acyl phosphatidylethanolamine BLAST basic local alignment search tool CL cardiolipin DHAP dihydroxyacetone phosphate DRG diradylglycerol ELSD evaporative light scattering detection ESI electrospray ionization FA fatty acid PUFA polyunsaturated fatty acids FAME fatty acid methyl esters GC gas chromatography HILIC hydrophilic interaction liquid chromatography HPLC High Performance Liquid Chromatography IPTG isopropyl β-d-1-thiogalactopyranoside LC liquid chromatography MALDI matrix-assisted laser desorption ionization MHDRG monohexosyldiradylglycerol MHMAG monohexosyl monoacylglycerol MS mass spectrometry NGF nerve growth factor NPLC normal phase liquid chromatography PA phosphatidic acid P-CL 1-alkenyl-2-acyl cardiolipin PE phosphatidylethanolamine PG phosphatidylglycerol P-PC 1-alkenyl-2-acyl phosphatidylcholine P-PE 1-alkenyl-2-acyl phosphatidylethanolamine P-PS 1-alkenyl-2-acyl phosphatidylserine PS phosphatidylserine PT phosphatidylthreonine TAG triacylglyceride Q-TOF quadrupole time-of-flight RP reverse phase TLC thin layer chromatography UHPLC ultra-high-pressure liquid chromatography VAP vesicle-associated membrane protein

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Generation of wild-type rat Glucocerebrosidase homology modeling: Identification of putative interactions site and mechanism for chaperone using combined in-silico and in-vitro studies

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BIOORGANIC CHEMISTRY 2022年 126卷 105871页

作者： Tripathi, Pratigya Ganeshpurkar, Ankit Singh, Sushil Kumar Krishnamurthy, Sairam Banaras Hindu Univ Indian Inst Technol Dept Pharmaceut Engn & Technol Neurotherapeut Lab Varanasi 221005 Uttar Pradesh India Banaras Hindu Univ Indian Inst Technol Dept Pharmaceut Engn & Technol Pharmaceut Chem Res Lab Varanasi 221005 Uttar Pradesh India

Disease-modifying treatment strategy for Parkinson's disease (PD) by stabilization of Glucocerebrosidase (GCase) enzyme by chaperones is of particular interest. Wild-type rat is a widely used animal model for PD;however, the in-silico model to elucidate the nature of rat GCase (rGCase)-chaperone interactions, mechanisms, and structural stability is still unavailable. Hence, we have developed pH-dependent rGCase homology models, in-silico (docking and molecular dynamics), and in -vitro techniques (enzyme kinetics and thermal stability) to address this gap. The homology modeling results revealed >= 90% rGCase residues were in the favored regions, representing adequate models quality. In-silico studies showed an interaction between chaperone (Ambroxol, AMB) and the active site residues TYR 331, TYR 263, GLN 266, and GLU 358 with the higher affinity at neutral pH than acidic pH. In-vitro studies showed higher inhibitory activity (IC50) and binding affinity (K-i) of AMB at neutral pH (IC50: 8.2 +/- 2.6 mu M and K-i: 4.3 +/- 1.2 mu M) than acidic pH (IC50 and K-i: not identified). AMB improved rGCase thermostability was confirmed by thermal denaturation assay. We have developed the homology model for rGCase, which provides a perspective for designing and screening the chaperones at the initial phases of drug discovery to ameliorate PD.

关键词： rGCase rat Glucocerebrosidase AMB Ambroxol ER Endoplasmic reticulumn IC 50 Half maximal inhibitory concentration K i Inhibitory Constant 6-OHDA 6-hydroxydopamine GH Glycoside hydroxylase MD Molecular dynamics TDC Taurodeoxycholic acid sodium salt 4-MUG 4-methylumbelliferyl-β- d -glucopyranoside, 4-MU, 4-methylumbelliferone BLAST basic local alignment search tool LGA Lamarckian genetic algorithm TIP3P Transferable intermolecular potential with 3 Points UBP Unbound protein BP Bound protein RMSD Root mean square deviation RMSF Root mean square fluctuation R g Radius of gyration SASA Solvent accessible surface area

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Repeated Occupational Exposure to Low-level Blast in the Canadian Armed Forces: Effects on Hearing, Balance, and Ataxia

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MILITARY MEDICINE 2022年第1-2期187卷 E201-E208页

作者： Nakashima, Ann Vartanian, Oshin Rhind, Shawn G. King, Kristen Tenn, Catherine Jetly, Col Rakesh Toronto Res Ctr Def Res & Dev Canada Toronto ON M3K 2C9 Canada Def Res & Dev Canada Suffield Res Ctr Medicine Hat AB T1A 8K5 Canada Canadian Forces Hlth Serv Ottawa ON K1A 0K2 Canada

Introduction: Recently, there has been increasing concern about the adverse health effects of long-term occupational exposure to lowlevel blast in military personnel. Occupational blast exposure occurs routinely in garrison through use of armaments and controlled blast detonations. In the current study, we focused on a population of breaching instructors and range staff. Breaching is a tactical technique that is used to gain entry into closed spaces, often through the use of explosives. Materials and Methods: Initial measurements of blast overpressure collected during breaching courses found that up to 10% of the blasts for range staff and up to 32% of the blasts for instructors exceeded the recommended 3 psi exposure limit. Using a cross-sectional design, we used tests of balance, ataxia, and hearing to compare a sample of breachers (n = 19) to age-and sex-matched military controls (n = 19). Results: There were no significant differences between the two groups on the balance and ataxia tests, although the average scores of both groups were lower than would be expected in a normative population. The prevalence of hearing loss was low in the breacher group (4 of 19), and hearing thresholds were not significantly different from the controls. However, the prevalence of self-reported tinnitus was significantly higher in the breacher group (12 of 19) compared with the controls (4 of 19), and all breachers who were identified as having hearing loss also reported tinnitus. Conclusions: Our results suggest that basic tests of balance, ataxia, and hearing on their own were not sensitive to the effects of long-term occupational exposure to low-level blast. Some of the blast exposure levels exceeded limits, and there was a significant association of exposure with tinnitus. Future studies should supplement with additional information including exposure history and functional hearing assessments. These findings should be considered in the design of future acute and longitudinal

关键词： ataxia military personnel occupational exposure tinnitus hearing loss basic local alignment search tool

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Phylogenetic reconstruction in the Order Nymphaeales: ITS2 secondary structure analysis and in silico testing of maturase k (matK) as a potential marker for DNA bar coding

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BMC BIOINFORMATICS 2012年第17-sup期13卷 S26-S26页

作者： Biswal, Devendra Kumar Debnath, Manish Kumar, Shakti Tandon, Pramod NE Hill Univ Bioinformat Ctr Shillong 793022 Meghalaya India

Background: The Nymphaeales (waterlilly and relatives) lineage has diverged as the second branch of basal angiosperms and comprises of two families: Cabombaceae and Nymphaceae. The classification of Nymphaeales and phylogeny within the flowering plants are quite intriguing as several systems (Thorne system, Dahlgren system, Cronquist system, Takhtajan system and APG III system (Angiosperm Phylogeny Group III system) have attempted to redefine the Nymphaeales taxonomy. There have been also fossil records consisting especially of seeds, pollen, stems, leaves and flowers as early as the lower Cretaceous. Here we present an in silico study of the order Nymphaeales taking maturaseK (matK) and internal transcribed spacer (ITS2) as biomarkers for phylogeny reconstruction (using character-based methods and Bayesian approach) and identification of motifs for DNA barcoding. Results: The Maximum Likelihood (ML) and Bayesian approach yielded congruent fully resolved and well-supported trees using a concatenated (ITS2+ matK) supermatrix aligned dataset. The taxon sampling corroborates the monophyly of Cabombaceae. Nuphar emerges as a monophyletic clade in the family Nymphaeaceae while there are slight discrepancies in the monophyletic nature of the genera Nymphaea owing to Victoria-Euryale and Ondinea grouping in the same node of Nymphaeaceae. ITS2 secondary structures alignment corroborate the primary sequence analysis. Hydatellaceae emerged as a sister clade to Nymphaeaceae and had a basal lineage amongst the water lilly clades. Species from Cycas and Ginkgo were taken as outgroups and were rooted in the overall tree topology from various methods. Conclusions: MatK genes are fast evolving highly variant regions of plant chloroplast DNA that can serve as potential biomarkers for DNA barcoding and also in generating primers for angiosperms with identification of unique motif regions. We have reported unique genus specific motif regions in the Order Nymphaeles from matK dataset w

关键词： basic local alignment search tool Position Specific Scoring Matrix Basal Angiosperm Water Lily Consensus Structure

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Immunogenicity of autoantigens

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BMC GENOMICS 2011年第1期12卷 340-340页

作者： Backes, Christina Ludwig, Nicole Leidinger, Petra Harz, Christian Hoffmann, Jana Keller, Andreas Meese, Eckart Lenhof, Hans-Peter Univ Saarland Ctr Bioinformat D-66041 Saarbrucken Germany Univ Saarland Dept Human Genet D-66421 Homburg Germany

Background: Autoantibodies against self-antigens have been associated not only with autoimmune diseases, but also with cancer and are even found in healthy individuals. The mechanism causing the autoantibody response remains elusive for the majority of the immunogenic antigens. To deepen the understanding of autoantibody responses, we ask whether natural-occurring, autoimmunity-associated and tumor-associated antigens have structural or biological features related to the immune response. To this end, we have carried out the most comprehensive in-silicio study of different groups of autoantigens including large antigen sets identified by our groups combined with publicly available antigen sets. Results: We found evidence for an enrichment of genes with a larger exon length increasing the probability of the occurrence of potential immunogenic features such as mutations, SNPs, immunogenic sequence patterns and structural epitopes, or alternative splicing events. While SNPs seem to play a more central role in autoimmunity, somatic mutations seem to be stronger enriched in tumor-associated antigens. In addition, antigens of autoimmune diseases are different from other antigen sets in that they appear preferentially secreted, have frequently an extracellular location, and they are enriched in pathways associated with the immune system. Furthermore, for autoantibodies in general, we found enrichment of sequence-based properties including coiled-coils motifs, ELR motifs, and Zinc finger DNA-binding motifs. Moreover, we found enrichment of proteins binding to proteins or nucleic acids including RNA and enrichment of proteins that are part of ribosome or spliceosome. Both, homologies to proteins of other species and an enrichment of ancient protein domains indicate that immunogenic proteins are evolutionary conserved and that mimicry might play a central role. Conclusions: Our results provide evidence that proteins which i) are evolutionary conserved, ii) show specific sequen

关键词： Gene Ontology Tumor Antigen basic local alignment search tool Molecular Mimicry Epitope Spreading

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microRNA-93 promotes cell proliferation via targeting of PTEN in Osteosarcoma cells

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JOURNAL OF EXPERIMENTAL & CLINICAL CANCER REsearch 2015年第1期34卷 76-76页

作者： Kawano, Masanori Tanaka, Kazuhiro Itonaga, Ichiro Ikeda, Shinichi Iwasaki, Tatsuya Tsumura, Hiroshi Oita Univ Fac Med Dept Orthopaed Surg Oita 8795593 Japan

Background: Aberrant microRNA (miRNA) expression plays an essential role in osteosarcoma (OS) pathogenesis. Recent studies have shown that dysregulation of miRNA expression is associated with increased tumorigenesis and poor prognosis in several types of cancers, including OS. The aim of this study was to investigate the relevant microRNAs involved in the development of OS. Methods: To explore possible oncogenic factors in OS, we used a microarray-based approach to profile changes in the expression of miRNAs and their target mRNAs in five OS cell lines and human mesenchymal stem cells (hMSCs). An miRNA, miR-93, was significantly up-regulated, whereas phosphatase and tensin homologue (PTEN) expression was significantly down-regulated in all tested OS cells, when compared with hMSCs. Results: When anti-miR-93 was transfected into OS cell lines, PTEN expression was greatly increased, suggesting that PTEN might be a target of miR-93 in ES cells. The expression of phosphorylated Akt protein, which is known to be inversely correlated with that of PTEN, was significantly down-regulated in anti-miR-93-transfected cells. Furthermore, transfection of anti-miR-93 inhibited the proliferation and cell cycle progression of ES cells. In addition, the down-regulation of miR-93 in these cells significantly suppressed tumor growth in vivo. Conclusion: Ectopic expression of miR-93 decreased PTEN protein levels. Furthermore, miR-93 increased proliferation and decreased apoptosis in OS cells, whereas its silencing in these cells inhibited such carcinogenic processes. Taking these observations together, miR-93 can be seen to play a critical role in carcinogenesis through suppression of PTEN, and may serve as a therapeutic target for the treatment of OS.

关键词： basic local alignment search tool PTEN Expression Saos Cell PTEN mRNA Saos Cell Line

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