High-Throughput最新文献_第2页

Colonization Resistance in the Infant Gut: The Role of B. infantis in Reducing pH and Preventing Pathogen Growth. 婴儿肠道的定植抗性:婴儿B.在降低pH和防止病原体生长中的作用。

High-Throughput Pub Date : 2020-03-27 DOI: 10.3390/ht9020007

Rebbeca M Duar, David Kyle, Giorgio Casaburi

{"title":"Colonization Resistance in the Infant Gut: The Role of B. infantis in Reducing pH and Preventing Pathogen Growth.","authors":"Rebbeca M Duar, David Kyle, Giorgio Casaburi","doi":"10.3390/ht9020007","DOIUrl":"https://doi.org/10.3390/ht9020007","url":null,"abstract":"Over the past century, there has been a steady increase in the stool pH of infants from industrialized countries. Analysis of historical data revealed a strong association between abundance of Bifidobacterium in the gut microbiome of breasted infants and stool pH, suggesting that this taxon plays a key role in determining the pH in the gut. Bifidobacterium longum subsp. infantis is uniquely equipped to metabolize human milk oligosaccharides (HMO) from breastmilk into acidic end products, mainly lactate and acetate. The presence of these acidic compounds in the infant gut is linked to a lower stool pH. Conversely, infants lacking B. infantis have a significantly higher stool pH, carry a higher abundance of potential pathogens and mucus-eroding bacteria in their gut microbiomes, and have signs of chronic enteric inflammation. This suggests the presence of B. infantis and low intestinal pH may be critical to maintaining a protective environment in the infant gut. Here, we summarize recent studies demonstrating that feeding B. infantis EVC001 to breastfed infants results in significantly lower fecal pH compared to controls and propose that low pH is one critical factor in preventing the invasion and overgrowth of harmful bacteria in the infant gut, a process known as colonization resistance.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"9 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht9020007","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37786404","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 38

Factors Influencing Epigenetic Mechanisms: Is There A Role for Bariatric Surgery? 影响表观遗传机制的因素:减肥手术是否有作用?

High-Throughput Pub Date : 2020-03-20 DOI: 10.3390/ht9010006

Alessio Metere, Claire E Graves

引用次数: 11

Rational Engineering of the Substrate Specificity of a Thermostable D-Hydantoinase (Dihydropyrimidinase). 耐热d -羟酶(二氢嘧啶酶)底物特异性的合理工程研究。

High-Throughput Pub Date : 2020-02-12 DOI: 10.3390/ht9010005

Hovsep Aganyants, Pierre Weigel, Yeranuhi Hovhannisyan, Michèle Lecocq, Haykanush Koloyan, Artur Hambardzumyan, Anichka Hovsepyan, Jean-Noël Hallet, Vehary Sakanyan

{"title":"Rational Engineering of the Substrate Specificity of a Thermostable D-Hydantoinase (Dihydropyrimidinase).","authors":"Hovsep Aganyants, Pierre Weigel, Yeranuhi Hovhannisyan, Michèle Lecocq, Haykanush Koloyan, Artur Hambardzumyan, Anichka Hovsepyan, Jean-Noël Hallet, Vehary Sakanyan","doi":"10.3390/ht9010005","DOIUrl":"https://doi.org/10.3390/ht9010005","url":null,"abstract":"D-hydantoinases catalyze an enantioselective opening of 5- and 6-membered cyclic structures and therefore can be used for the production of optically pure precursors for biomedical applications. The thermostable D-hydantoinase from Geobacillus stearothermophilus ATCC 31783 is a manganese-dependent enzyme and exhibits low activity towards bulky hydantoin derivatives. Homology modeling with a known 3D structure (PDB code: 1K1D) allowed us to identify the amino acids to be mutated at the substrate binding site and in its immediate vicinity to modulate the substrate specificity. Both single and double substituted mutants were generated by site-directed mutagenesis at appropriate sites located inside and outside of the stereochemistry gate loops (SGL) involved in the substrate binding. Substrate specificity and kinetic constant data demonstrate that the replacement of Phe159 and Trp287 with alanine leads to an increase in the enzyme activity towards D,L-5-benzyl and D,L-5-indolylmethyl hydantoins. The length of the side chain and the hydrophobicity of substrates are essential parameters to consider when designing the substrate binding pocket for bulky hydantoins. Our data highlight that D-hydantoinase is the authentic dihydropyrimidinase involved in the pyrimidine reductive catabolic pathway in moderate thermophiles.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht9010005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37645618","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

Comparative Study of NGS Platform Ion Torrent Personal Genome Machine and Therascreen Rotor-Gene Q for the Detection of Somatic Variants in Cancer. NGS平台Ion Torrent个人基因组机与Therascreen Rotor-Gene Q检测癌症体细胞变异的比较研究。

High-Throughput Pub Date : 2020-02-11 DOI: 10.3390/ht9010004

Angela Lombardi, Margherita Russo, Amalia Luce, Floriana Morgillo, Virginia Tirino, Gabriella Misso, Erika Martinelli, Teresa Troiani, Vincenzo Desiderio, Gianpaolo Papaccio, Francesco Iovino, Giuseppe Argenziano, Elvira Moscarella, Pasquale Sperlongano, Gennaro Galizia, Raffaele Addeo, Alois Necas, Andrea Necasova, Fortunato Ciardiello, Andrea Ronchi, Michele Caraglia, Anna Grimaldi

{"title":"Comparative Study of NGS Platform Ion Torrent Personal Genome Machine and Therascreen Rotor-Gene Q for the Detection of Somatic Variants in Cancer.","authors":"Angela Lombardi, Margherita Russo, Amalia Luce, Floriana Morgillo, Virginia Tirino, Gabriella Misso, Erika Martinelli, Teresa Troiani, Vincenzo Desiderio, Gianpaolo Papaccio, Francesco Iovino, Giuseppe Argenziano, Elvira Moscarella, Pasquale Sperlongano, Gennaro Galizia, Raffaele Addeo, Alois Necas, Andrea Necasova, Fortunato Ciardiello, Andrea Ronchi, Michele Caraglia, Anna Grimaldi","doi":"10.3390/ht9010004","DOIUrl":"https://doi.org/10.3390/ht9010004","url":null,"abstract":"Molecular profiling of a tumor allows the opportunity to design specific therapies which are able to interact only with cancer cells characterized by the accumulation of several genomic aberrations. This study investigates the usefulness of next-generation sequencing (NGS) and mutation-specific analysis methods for the detection of target genes for current therapies in non-small-cell lung cancer (NSCLC), metastatic colorectal cancer (mCRC), and melanoma patients. We focused our attention on EGFR, BRAF, KRAS, and BRAF genes for NSCLC, melanoma, and mCRC samples, respectively. Our study demonstrated that in about 2% of analyzed cases, the two techniques did not show the same or overlapping results. Two patients affected by mCRC resulted in wild-type (WT) for BRAF and two cases with NSCLC were WT for EGFR according to PGM analysis. In contrast, these samples were mutated for the evaluated genes using the therascreen test on Rotor-Gene Q. In conclusion, our experience suggests that it would be appropriate to confirm the WT status of the genes of interest with a more sensitive analysis method to avoid the presence of a small neoplastic clone and drive the clinician to correct patient monitoring.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-02-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht9010004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37639959","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Precision Medicine in Non-Communicable Diseases. 非传染性疾病的精准医疗。

High-Throughput Pub Date : 2020-02-07 DOI: 10.3390/ht9010003

Giuseppe Novelli, Michela Biancolella, Andrea Latini, Aldo Spallone, Paola Borgiani, Marisa Papaluca

{"title":"Precision Medicine in Non-Communicable Diseases.","authors":"Giuseppe Novelli, Michela Biancolella, Andrea Latini, Aldo Spallone, Paola Borgiani, Marisa Papaluca","doi":"10.3390/ht9010003","DOIUrl":"https://doi.org/10.3390/ht9010003","url":null,"abstract":"The increase in life expectancy during the 20th century ranks as one of society's greatest achievements, with massive growth in the numbers and proportion of the elderly, virtually occurring in every country of the world. The burden of chronic diseases is one of the main consequences of this phenomenon, severely hampering the quality of life of elderly people and challenging the efficiency and sustainability of healthcare systems. Non-communicable diseases (NCDs) are considered a global emergency responsible for over 70% of deaths worldwide. NCDs are also the basis for complex and multifactorial diseases such as hypertension, diabetes, and obesity. The epidemics of NCDs are a consequence of a complex interaction between health, economic growth, and development. This interaction includes the individual genome, the microbiome, the metabolome, the immune status, and environmental factors such as nutritional and chemical exposure. To counteract NCDs, it is therefore essential to develop an innovative, personalized, preventative, early care model through the integration of different molecular profiles of individuals to identify both the critical biomarkers of NCD susceptibility and to discover novel therapeutic targets.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-02-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht9010003","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37632641","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 13

Acknowledgement to Reviewers of High-Throughput in 2019 2019年高通量评审员致谢

High-Throughput Pub Date : 2020-01-16 DOI: 10.3390/ht9010002

High-Throughput Editorial Office

引用次数: 0

Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer. 下一代测序技术在家族性乳腺癌/卵巢癌分析中的应用

High-Throughput Pub Date : 2020-01-10 DOI: 10.3390/ht9010001

Veronica Zelli, Chiara Compagnoni, Katia Cannita, Roberta Capelli, Carlo Capalbo, Mauro Di Vito Nolfi, Edoardo Alesse, Francesca Zazzeroni, Alessandra Tessitore

{"title":"Applications of Next Generation Sequencing to the Analysis of Familial Breast/Ovarian Cancer.","authors":"Veronica Zelli, Chiara Compagnoni, Katia Cannita, Roberta Capelli, Carlo Capalbo, Mauro Di Vito Nolfi, Edoardo Alesse, Francesca Zazzeroni, Alessandra Tessitore","doi":"10.3390/ht9010001","DOIUrl":"https://doi.org/10.3390/ht9010001","url":null,"abstract":"Next generation sequencing (NGS) provides a powerful tool in the field of medical genetics, allowing one to perform multi-gene analysis and to sequence entire exomes (WES), transcriptomes or genomes (WGS). The generated high-throughput data are particularly suitable for enhancing the understanding of the genetic bases of complex, multi-gene diseases, such as cancer. Among the various types of tumors, those with a familial predisposition are of great interest for the isolation of novel genes or gene variants, detectable at the germline level and involved in cancer pathogenesis. The identification of novel genetic factors would have great translational value, helping clinicians in defining risk and prevention strategies. In this regard, it is known that the majority of breast/ovarian cases with familial predisposition, lacking variants in the highly penetrant BRCA1 and BRCA2 genes (non-BRCA), remains unexplained, although several less penetrant genes (e.g., ATM, PALB2) have been identified. In this scenario, NGS technologies offer a powerful tool for the discovery of novel factors involved in familial breast/ovarian cancer. In this review, we summarize and discuss the state of the art applications of NGS gene panels, WES and WGS in the context of familial breast/ovarian cancer.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2020-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht9010001","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37542238","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 20

Descriptors for High Throughput in Structural Materials Development. 结构材料开发中的高通量描述符

High-Throughput Pub Date : 2019-12-05 DOI: 10.3390/ht8040022

Matthias Steinbacher, Gabriela Alexe, Michael Baune, Ilya Bobrov, Ingmar Bösing, Brigitte Clausen, Tobias Czotscher, Jérémy Epp, Andreas Fischer, Lasse Langstädtler, Daniel Meyer, Sachin Raj Menon, Oltmann Riemer, Heike Sonnenberg, Arne Thomann, Anastasiya Toenjes, Frank Vollertsen, Nicole Wielki, Nils Ellendt

{"title":"Descriptors for High Throughput in Structural Materials Development.","authors":"Matthias Steinbacher, Gabriela Alexe, Michael Baune, Ilya Bobrov, Ingmar Bösing, Brigitte Clausen, Tobias Czotscher, Jérémy Epp, Andreas Fischer, Lasse Langstädtler, Daniel Meyer, Sachin Raj Menon, Oltmann Riemer, Heike Sonnenberg, Arne Thomann, Anastasiya Toenjes, Frank Vollertsen, Nicole Wielki, Nils Ellendt","doi":"10.3390/ht8040022","DOIUrl":"10.3390/ht8040022","url":null,"abstract":"The development of novel structural materials with increasing mechanical requirements is a very resource-intense process if conventional methods are used. While there are high-throughput methods for the development of functional materials, this is not the case for structural materials. Their mechanical properties are determined by their microstructure, so that increased sample volumes are needed. Furthermore, new short-time characterization techniques are required for individual samples which do not necessarily measure the desired material properties, but descriptors which can later be mapped on material properties. While universal micro-hardness testing is being commonly used, it is limited in its capability to measure sample volumes which contain a characteristic microstructure. We propose to use alternative and fast deformation techniques for spherical micro-samples in combination with classical characterization techniques such as XRD, DSC or micro magnetic methods, which deliver descriptors for the microstructural state.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6966690/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43568567","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

From the Laboratory to The Vineyard—Evolution of The Measurement of Grape Composition using NIR Spectroscopy towards High-Throughput Analysis 从实验室到葡萄园——近红外光谱测定葡萄成分向高通量分析的演变

High-Throughput Pub Date : 2019-11-30 DOI: 10.3390/ht8040021

A. Power, V. K. Truong, J. Chapman, D. Cozzolino

引用次数: 17

Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study De Novo转录组在原核生物中组装策略的比较分析——以棒状链霉菌为例

High-Throughput Pub Date : 2019-11-30 DOI: 10.3390/ht8040020

Carlos Caicedo-Montoya, Laura Pinilla, León F. Toro, Jeferyd Yepes-García, Rigoberto Ríos-Estepa

{"title":"Comparative Analysis of Strategies for De Novo Transcriptome Assembly in Prokaryotes: Streptomyces clavuligerus as a Case Study","authors":"Carlos Caicedo-Montoya, Laura Pinilla, León F. Toro, Jeferyd Yepes-García, Rigoberto Ríos-Estepa","doi":"10.3390/ht8040020","DOIUrl":"https://doi.org/10.3390/ht8040020","url":null,"abstract":"The performance of software tools for de novo transcriptome assembly greatly depends on the selection of software parameters. Up to now, the development of de novo transcriptome assembly for prokaryotes has not been as remarkable as that for eukaryotes. In this contribution, Rockhopper2 was used to perform a comparative transcriptome analysis of Streptomyces clavuligerus exposed to diverse environmental conditions. The study focused on assessing the incidence of software parameters on software performance for the identification of differentially expressed genes as a final goal. For this, a statistical optimization was performed using the Transrate Assembly Score (TAS). TAS was also used for evaluating the software performance and for comparing it with related tools, e.g., Trinity. Transcriptome redundancy and completeness were also considered for this analysis. Rockhopper2 and Trinity reached a TAS value of 0.55092 and 0.58337, respectively. Trinity assembles transcriptomes with high redundancy, with 55.6% of transcripts having some duplicates. Additionally, we observed that the total number of differentially expressed genes (DEG) and their annotation greatly depends on the method used for removing redundancy and the tools used for transcript quantification. To our knowledge, this is the first work aimed at assessing de novo assembly software for prokaryotic organisms.","PeriodicalId":53433,"journal":{"name":"High-Throughput","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-11-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/ht8040020","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47870810","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2