Frontiers in glycomics; bioinformatics and biomarkers in disease. September 11-13, 2006 Natcher Conference Center, NIH Campus, Bethesda, MD, USA

This is a short summary of a meeting entitled "The Frontiers in Glycomics; Bioinformatics and Biomarkers in Disease" which was jointly organized by the NIH Consortium for Functional Glycomics (CFG), Human Disease Glycomics/Proteome Initiative (HGPI), National Cancer Institute, National Institute of General Medical Sciences, Japan Society for the Promotion of Science and National Center for Research Resources held at the NIH Campus, Bethesda, MD, Natcher Conference Center in September 11-13, 2006.     

Functional characterization of the phosphorelay protein Mpr1p from Schizosaccharomyces pombe

Histidine-containing phosphotransfer (HPt) proteins play an essential role in multistep histidine-aspartate phosphorelay signal transduction systems in prokaryotes and eukaryotes. The putative HPt protein in Schizosaccharomyces pombe, Mpr1p (also known as Spy1p), is a 295 amino acid protein that appears to be composed of more than one functional domain. The amino acid sequence of the N-terminal region of Mpr1p lacks homology to other known proteins, whereas the C-terminal domain is predicted to have structural similarity to the Ypd1p HPt protein from Saccharomyces cerevisiae. This study provides both in vitro and in vivo evidence that the C-terminal domain of Mpr1p indeed functions as an HPt protein in shuttling phosphoryl groups from one response regulator domain to another. Furthermore, we find that various deletions of the N-terminal region diminish both the phosphotransfer activity of Mpr1p and its affinity for response regulator domains, suggesting a possible role for the N-terminal domain in HPt-response regulator domain interactions.     

Caspases in yeast apoptosis-like death: facts and artefacts

Various findings suggest that programmed cell death (PCD) is induced in yeast as a response to the impact of a deleterious environment and/or an intracellular defect. Moreover, the specifically localized PCD within multicellular colonies seems to be important for the safe degradation of cell subpopulations to simple compounds that can be used as nutrients by healthy survivors occurring in propitious colony areas, being thus important for proper development and survival of the yeast population. In spite of this, the question remains whether yeast dies by real apoptosis, i.e. death involving caspases, or by other kinds of PCD. A large group of mammalian caspases includes those that are responsible for monitoring of the stimulus and initiating the dying process, as well as those involved in the execution of death. Additionally, paracaspases and metacaspases, that share some homology with real caspases, but possibly differ in substrate specificity, have been identified in plants, fungi, Dictyostelium and metazoa. In yeast, one homologue of caspases, metacaspase Mca1p/Yca1p, has been identified so far, although there are several indications of the presence of other caspase-like activities in yeast. In this minireview, we summarize various data on the possible involvement of Mca1p and other caspase-like activities in yeast PCD.     

Thrombin inhibitors with novel P1 binding pocket functionality: free energy of binding analysis

The high incidence of thrombembolic diseases justifies the development of new antithrombotics. The search for a direct inhibitor has resulted in the synthesis of a considerable number of low molecular weight molecules that inhibit human α-thrombin potently. However, efforts to develop an orally active drug remain in progress as the most active inhibitors with a highly basic P1 moiety exhibit an unsatisfactory bioavailability profile. In our previous work we solved several X-ray structures of human α-thrombin in complexes with (1) novel bicyclic arginine mimetics attached to the glycylproline amide and pyridinone acetamide scaffold and (2) inhibitors with a novel aza scaffold and with charged or neutral P1 moieties. In the present contribution, we correlate the structures of the complex between these inhibitors and the protein with the calculated free energy of binding. The energy of solvation was calculated using the Poisson–Boltzmann approach. In particular, the requirements for successful recognition of an inhibitor at the protein’s active site pocket S1 are discussed. Figure We report here on free energy of binding analysis of thrombin inhibitors with novel aza scaffold and novel bicyclic arginine mimetics in S1 pocket of thrombin     

The impact of daylight on suicide rates

Since Durkheim and Morselli found a spring peak in suicides in the late 19th century, researchers have presented possible explanations, including daylight variation, for this seasonal pattern. Our identification strategy exploits the idiosyncratic variation in daylight within Norwegian regions, arising from the country’s substantial latitudinal range. We use full population data for a period of 45 years in a pre-registered research design. We find a small and non-significant relationship: One extra hour of daylight increases the suicide rate by merely 0.75 % (95 % CI: −0.4 % to 1.9 %).     

耳穴埋豆联合针刺对脑梗死患者睡眠质量及吞咽功能的影响

摘要 目的：探讨耳穴埋豆联合针刺对脑梗死患者睡眠质量及吞咽功能的影响。方法：选取2016年3月2日至2021年3月2日于我院进行脑梗死治疗的80例患者,将其随机分为观察组（n=40）和对照组（n=40）,观察组采用耳穴埋豆联合针刺治疗干预,对照组采用常规治疗,对比两组患者匹兹堡睡眠质量指数问卷（Pitsburgh sleep quality index,PSQI）评分和睡眠状况自评量表（Self-Rating Scale of Sleep,SRSS）评分、渗透-误吸量表（Penetration-aspiration scale,PAS）评分、吞咽功能治疗有效率、治疗满意度。结果：治疗干预后,观察组患者的PSQI评分及SRSS评分明显优于对照组,差异有统计学意义（P<0.05）;治疗前,比较两组患者3种食团PAS评分,差异均无统计学意义（P>0.05）。治疗后,比较两组患者3种食团PAS评分,均较治疗前明显下降,差异有统计学意义（P<0.05）。观察组5 mL水、10 mL水PAS评分明显低于对照组（P<0.05）,而比较两组患者5 mL布丁样食物PSA评分,差异无统计学意义（P>0.05）;观察组患者吞咽障碍经治疗后总有效率为90 %;对照组患者吞咽障碍经治疗后总有效率为70 %。差异有统计学意义（P<0.05）;观察组满意度明显高于对照组（P<0.05）。结论：耳穴埋豆联合针刺治疗方法应用于脑梗死患者,可有效改善睡眠质量,提升患者吞咽功能,提高吞咽障碍治疗率,患者满意度提高,可应用于临床。     

Improvement of glycine biosynthesis from one-carbon compounds and ammonia catalyzed by the glycine cleavage system in vitro

Glycine cleavage system (GCS) plays a central role in one-carbon (C1) metabolism and receives increasing interest as a core part of the recently proposed reductive glycine pathway (rGlyP) for assimilation of CO₂ and formate. Despite decades of research, GCS has not yet been well understood and kinetic data are barely available. This is to a large degree because of the complexity of GCS, which is composed of four proteins (H, T, P, and L) and catalyzes reactions involving different substrates and cofactors. In vitro kinetics of reconstructed microbial multi-enzyme glycine cleavage/synthase system is desired to better implement rGlyP in microorganisms like Escherichia coli for the use of C1 resources. Here, we examined in vitro several factors that may affect the rate of glycine synthesis via the reverse GCS reaction. We found that the ratio of GCS component proteins has a direct influence on the rate of glycine synthesis, namely higher ratios of P protein and especially H protein to T and L proteins are favorable, and the carboxylation reaction catalyzed by P protein is a key step determining the glycine synthesis rate, whereas increasing the ratio of L protein to other GCS proteins does not have significant effect and the ratio of T protein to other GCS proteins should be kept low. The effect of substrate concentrations on glycine synthesis is quite complex, showing interdependence with the ratios of GCS component proteins. Furthermore, adding the reducing agent dithiothreitol to the reaction mixture not only results in great tolerance to high concentration of formaldehyde, but also increases the rate of glycine synthesis, probably due to its functions in activating P protein and taking up the role of L protein in the non-enzymatic reduction of H_ox to H_red. Moreover, the presence of some monovalent and divalent metal ions can have either positive or negative effect on the rate of glycine synthesis, depending on their type and their concentration.     

Current capacity,bottlenecks, and future projections for offsetting habitat loss using Mitigation and Conservation banking in the United States

Habitat banking in its many iterations is an established and popular mechanism to deliver environmental offsets. The United States can look back at over 30 years of banking experience with the underlying framework and policies being consistently updated and improved. Given the increased demand in habitat banking, we provide insights into how bank area capacity is distributed across the United States for four different bank targets (wetlands, streams, multiple ecosystems, species) based on information extracted from the Regulatory In-lieu Fee and Bank Information Tracking System, as well as, estimating future capacities and area reserves through a predictive modeling approach based on data from the past 26 years. Future predictions indicate a decrease in available reserves for banks targeting wetlands or multiple ecosystems, with potential bottlenecks relating to large reserves being limited to the southeast and release schedules not catching up to the current and anticipated demand. Banks targeting species or streams are predicted to meet future demand, with species banks (conservation banks) following a different legislative and operational approach based on the listing of endangered species and pro-active approaches with anticipated future demand. Most current reserves for all four bank types are restricted to very few service areas with around one-third of all bank areas still awaiting release, limiting their availability on a broader scale. Strategic planning networks are necessary to meet future demand on a national scale and to identify areas suitable for banking or likely to experience future environmental or developmental stress.