http://chineseinput.net/에서 pinyin(병음)방식으로 중국어를 변환할 수 있습니다.
변환된 중국어를 복사하여 사용하시면 됩니다.
Identification and Accurate Quantitation of Biological Oligosaccharide Mixtures
Strum, John S.,Kim, Jaehan,Wu, Shuai,De Leoz, Maria Lorna A.,Peacock, Kyle,Grimm, Rudolf,German, J. Bruce,Mills, David A.,Lebrilla, Carlito B. American Chemical Society 2012 ANALYTICAL CHEMISTRY - Vol.84 No.18
<P>Structure-specific characterization and quantitation is often required for effective functional studies of oligosaccharides. Inside the gut, HMOs are preferentially bound and catabolized by the beneficial bacteria. HMO utility by these bacteria employs structure-specific catabolism based on a number of glycosidases. Determining the activity of these enzymes requires accurate quantitation of a large number of structures. In this study, we describe a method for the quantitation of human milk oligosaccharide (HMO) structures employing LC/MS and isotopically labeled internal standards. Data analysis was accomplished with a newly developed software tool, LC/MS Searcher, that employs a reference structure library to process LC/MS data yielding structural identification with accurate quantitation. The method was used to obtain a meta-enzyme analysis of bacteria, the simultaneous characterization of all glycosidases employed by bacteria for the catabolism of milk oligosaccharides. Analysis of consumed HMO structures confirmed the utility of a β-1,3-galactosidase in <I>Bifidobacterium longum subsp. infantis</I> ATCC 15697 (<I>B. infantis</I>). In comparison, <I>Bifidobacterium breve</I> ATCC 15700 showed significantly less HMO catabolic activity compared to <I>B. infantis</I>.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancham/2012/ancham.2012.84.issue-18/ac301128s/production/images/medium/ac-2012-01128s_0002.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ac301128s'>ACS Electronic Supporting Info</A></P>
Next-generation approaches to the microbial ecology of food fermentations
( Nicholas A. Bokulich ),( David A. Mills ) 생화학분자생물학회(구 한국생화학분자생물학회) 2012 BMB Reports Vol.45 No.7
Food fermentations have enhanced human health since the dawn of time and remain a prevalent means of food processing and preservation. Due to their cultural and nutritional importance, many of these foods have been studied in detail using molecular tools, leading to enhancements in quality and safety. Furthermore, recent advances in high-throughput sequencing technology are revolutionizing the study of food microbial ecology, deepening insight into complex fermentation systems. This review provides insight into novel applications of select molecular techniques, particularly next-generation sequencing technology, for analysis of microbial communities in fermented foods. We present a guideline for integrated molecular analysis of food microbial ecology and a starting point for implementing next-generation analysis of food systems. [BMB Reports 2012;45(7): 377-389]
( Kyung Hun Jeong ),( Beenish Israr ),( Sharon P. Shoemaker ),( David A. Mills ),( Jaehan Kim ) 한국미생물 · 생명공학회 2016 Journal of microbiology and biotechnology Vol.26 No.6
Lactobacillus brevis ATCC 14869 exhibited a carbon catabolite derepressed phenotype that has ability to consume fermentable sugars simultaneously with glucose. To evaluate this unusual phenotype under harsh conditions during fermentation, the effects of lactic acid and hydrogen ion concentrations on L. brevis ATCC 14869 were examined. Kinetic equations describing the relationship between specific cell growth rate and lactic acid or hydrogen ion concentration were deduced empirically. The change of substrate utilization and product formation according to lactic acid and hydrogen ion concentration in the media were quantitatively described. Although the simultaneous utilization has been observed regardless of hydrogen ion or lactic acid concentration, the preference of substrates and the formation of two-carbon products were changed significantly. In particular, acetic acid present in the medium as sodium acetate was consumed by L. brevis ATCC 14869 under extreme pH of both acid and alkaline conditions.
Jeong, Kyung Hun,Israr, Beenish,Shoemaker, Sharon P.,Mills, David A.,Kim, Jaehan The Korean Society for Microbiology and Biotechnol 2016 Journal of microbiology and biotechnology Vol.26 No.7
Lactobacillus brevis ATCC 14869 exhibited a carbon catabolite derepressed phenotype that has ability to consume fermentable sugars simultaneously with glucose. To evaluate this unusual phenotype under harsh conditions during fermentation, the effects of lactic acid and hydrogen ion concentrations on L. brevis ATCC 14869 were examined. Kinetic equations describing the relationship between specific cell growth rate and lactic acid or hydrogen ion concentration were deduced empirically. The change of substrate utilization and product formation according to lactic acid and hydrogen ion concentration in the media were quantitatively described. Although the simultaneous utilization has been observed regardless of hydrogen ion or lactic acid concentration, the preference of substrates and the formation of two-carbon products were changed significantly. In particular, acetic acid present in the medium as sodium acetate was consumed by L. brevis ATCC 14869 under extreme pH of both acid and alkaline conditions.
Comparative proteomics: assessment of biological variability and dataset comparability
Kim, Sa Rang,Nguyen, Tuong Vi,Seo, Na Ri,Jung, Seunghup,An, Hyun Joo,Mills, David A,Kim, Jae Han BioMed Central 2015 BMC bioinformatics Vol.16 No.-
<P><B>Background</B></P><P>Comparative proteomics in bacteria are often hampered by the differential nature of dataset quality and/or inherent biological deviations. Although common practice compensates by reproducing and normalizing datasets from a single sample, the degree of certainty is limited in comparison of multiple dataset. To surmount these limitations, we introduce a two-step assessment criterion using: (1) the relative number of total spectra (<I>R</I><SUB><I>TS</I></SUB>) to determine if two LC-MS/MS datasets are comparable and (2) nine glycolytic enzymes as internal standards for a more accurate calculation of relative amount of proteins. <I>Lactococcus lactis</I> HR279 and JHK24 strains expressing high or low levels (respectively) of green fluorescent protein (GFP) were used for the model system. GFP abundance was determined by spectral counting and direct fluorescence measurements. Statistical analysis determined relative GFP quantity obtained from our approach matched values obtained from fluorescence measurements.</P><P><B>Results</B></P><P><I>L. lactis</I> HR279 and JHK24 demonstrates two datasets with an <I>R</I><SUB><I>TS</I></SUB> value less than 1.4 accurately reflects relative differences in GFP levels between high and low expression strains. Without prior consideration of <I>R</I><SUB><I>TS</I></SUB> and the use of internal standards, the relative increase in GFP calculated by spectral counting method was 3.92 ± 1.14 fold, which is not correlated with the value determined by the direct fluorescence measurement (2.86 ± 0.42 fold) with the <I>p</I> = 0.024. In contrast, 2.88 ± 0.92 fold was obtained by our approach showing a statistically insignificant difference (<I>p</I> = 0.95).</P><P><B>Conclusions</B></P><P>Our two-step assessment demonstrates a useful approach to: (1) validate the comparability of two mass spectrometric datasets and (2) accurately calculate the relative amount of proteins between proteomic datasets.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12859-015-0561-9) contains supplementary material, which is available to authorized users.</P>