Institute for Systems Biology

About: Institute for Systems Biology is a nonprofit organization based out in Seattle, Washington, United States. It is known for research contribution in the topics: Population & Proteomics. The organization has 1277 authors who have published 2777 publications receiving 353165 citations.

Proteomic analysis of human prostasomes

Abstract: BACKGROUND Prostasomes are secretory particles in human seminal fluid. Other than a microscopic description of these secretory particles and an incomplete two–dimensional gel electrophoresis (2DE) study, little is known about the composition of proteins in prostasomes. METHODS We employed a direct iterative approach using Gas phase fractionation and microcapillary HPLC-tandem mass spectrometry (μLC-MS/MS) to catalogue the prostasome proteome. RESULTS We identified 139 proteins that can be divided into the following categories: (1) enzymes (33.8% of total), (2) transport/structural (19.4% of total), (3) GTP proteins (14.4% of total), (4) chaperone proteins (5.8% of total), (5) signal transduction proteins (17.3% of total), and (6) unannotated proteins (9.4% of total). A total of 128 of the 139 proteins have not previously been described as prostasomal. CONCLUSIONS The proteins identified can be used as reference dataset in future work comparing prostasome proteins between normal and pathological states such as prostate cancer, benign prostatic hyperplasia, prostatitis, and infertility. Prostate 56: 150–161, 2003. © 2003 Wiley-Liss, Inc.

Bet-hedging during bacterial diauxic shift

Abstract: When bacteria grow in a medium with two sugars, they first use the preferred sugar and only then start metabolizing the second one. After the first exponential growth phase, a short lag phase of nongrowth is observed, a period called the diauxie lag phase. It is commonly seen as a phase in which the bacteria prepare themselves to use the second sugar. Here we reveal that, in contrast to the established concept of metabolic adaptation in the lag phase, two stable cell types with alternative metabolic strategies emerge and coexist in a culture of the bacterium Lactococcus lactis. Only one of them continues to grow. The fraction of each metabolic phenotype depends on the level of catabolite repression and the metabolic state-dependent induction of stringent response, as well as on epigenetic cues. Furthermore, we show that the production of alternative metabolic phenotypes potentially entails a bet-hedging strategy. This study sheds new light on phenotypic heterogeneity during various lag phases occurring in microbiology and biotechnology and adjusts the generally accepted explanation of enzymatic adaptation proposed by Monod and shared by scientists for more than half a century.

Nutritional assessment and therapy in COPD: a European Respiratory Society statement

Abstract: Nutrition and metabolism have been the topic of extensive scientific research in chronic obstructive pulmonary disease (COPD) but clinical awareness of the impact dietary habits, nutritional status and nutritional interventions may have on COPD incidence, progression and outcome is limited. A multidisciplinary Task Force was created by the European Respiratory Society to deliver a summary of the evidence and description of current practice in nutritional assessment and therapy in COPD, and to provide directions for future research. Task Force members conducted focused reviews of the literature on relevant topics, advised by a methodologist. It is well established that nutritional status, and in particular abnormal body composition, is an important independent determinant of COPD outcome. The Task Force identified different metabolic phenotypes of COPD as a basis for nutritional risk profile assessment that is useful in clinical trial design and patient counselling. Nutritional intervention is probably effective in undernourished patients and probably most when combined with an exercise programme. Providing evidence of cost-effectiveness of nutritional intervention is required to support reimbursement and thus increase access to nutritional intervention. Overall, the evidence indicates that a well-balanced diet is beneficial to all COPD patients, not only for its potential pulmonary benefits, but also for its proven benefits in metabolic and cardiovascular risk.

Bcl6 expression specifies the T follicular helper cell program in vivo

Abstract: T follicular helper cells (Tfh cells) play a pivotal role in germinal center reactions, which require B cell lymphoma 6 (Bcl6) transcription factor. To analyze their relationships with other effector T cell lineages and their stability in vivo, we developed and analyzed a new Bcl6 reporter mouse alone or together with other lineage reporter systems. Assisted with genome-wide transcriptome analysis, we show substantial plasticity of T cell differentiation in the early phase of immune response. At this stage, CXCR5 appears to be expressed in a Bcl6-independent manner. Once Bcl6 is highly expressed, Tfh cells can persist in vivo and some of them develop into memory cells. Together, our results indicate Bcl6 as a bona fide marker for Tfh polarized program.