Proteomic characterization of human milk whey proteins during a twelve-month lactation period

Human milk is a rich source of bioactive proteins that support the early growth and development of the newborn. Although the major components of the protein fraction in human milk have been studied, the expression and relative abundance of minor components have received limited attention. We examined the expression of low-abundance proteins in the whey fraction of human milk and their dynamic changes over a twelve-month lactation period. The low-abundance proteins were enriched by ProteoMiner beads, and protein identification was performed by liquid chromatography tandem mass spectrometry. One hundred and fifteen proteins were identified, thirty-eight of which have not been previously reported in human colostrum or milk. We also for the first time described differences in protein patterns among the low-abundance proteins during lactation. These results enhance our knowledge about the complexity of the human milk proteome, which constitutes part of the advantages to the breast-fed infant.     

Functional Roles of the Non-Catalytic Calcium-Binding Sites in the N-Terminal Domain of Human Peptidylarginine Deiminase 4

This study investigated the functional roles of the N-terminal Ca²⁺ ion-binding sites, in terms of enzyme catalysis and stability, of peptidylarginine deiminase 4 (PAD4). Amino acid residues located in the N-terminal Ca²⁺-binding site of PAD4 were mutated to disrupt the binding of Ca²⁺ ions. Kinetic data suggest that Asp155, Asp157 and Asp179, which directly coordinate Ca3 and Ca4, are essential for catalysis in PAD4. For D155A, D157A and D179A, the k _cat/K _m,BAEE values were 0.02, 0.63 and 0.01 s⁻¹mM⁻¹ (20.8 s⁻¹mM⁻¹ for WT), respectively. Asn153 and Asp176 are directly coordinated with Ca3 and indirectly coordinated with Ca5 via a water molecule. However, N153A displayed low enzymatic activity with a k _cat value of 0.3 s⁻¹ (13.3 s⁻¹ for wild-type), whereas D176A retained some catalytic power with a k _cat of 9.7 s⁻¹. Asp168 is the direct ligand for Ca5, and Ca5 coordination by Glu252 is mediated by two water molecules. However, mutation of these two residues to Ala did not cause a reduction in the k _cat/K _m,BAEE values, which indicates that the binding of Ca5 may not be required for PAD4 enzymatic activity. The possible conformational changes of these PAD4 mutants were examined. Thermal stability analysis of the PAD4 mutants in the absence or presence of Ca²⁺ indicated that the conformational stability of the enzyme is highly dependent on Ca²⁺ ions. In addition, the results of urea-induced denaturation for the N153, D155, D157 and D179 series mutants further suggest that the binding of Ca²⁺ ions in the N-terminal Ca²⁺-binding site stabilizes the overall conformational stability of PAD4. Therefore, our data strongly suggest that the N-terminal Ca²⁺ ions play critical roles in the full activation of the PAD4 enzyme.     

Spectroscopic characterization and molecular weight distribution of dissolved organic matter in sediment porewaters from Lake Erhai, Southwest China

Dissolved organic matter (DOM) in sediment porewaters from Lake Erhai, Southwest China was investigated using dissolved organic carbon (DOC) concentration, UV absorbance, fluorescence and molecular weight distribution. DOC exhibited a high concentration at the sediment–water interface with a rapid decrease to the oxic–anoxic interface at approximately 7 cm, and then increased with depth. Similar trends were also found for the UV absorption coefficients at 254 and 280 nm in the porewaters. DNA in the sediment was also measured, which confirmed the high abundance of aerobic bacteria in the upper layer of the sediment. Both humic-like (peaks A and C) and protein-like (peaks B and D) fluorescence were observed in the porewater DOM, and their fluorescence intensities exhibited a similar porewater profile as DOC concentration. A strong correlation was found between the peak fluorescence intensity ratio r(A, C) and r(D, B). Both the fluorescence index and UV absorption coefficient at 254 nm suggested a dramatic increase in aromaticity of porewater DOM across the oxic–anoxic interface. Porewater DOM exhibited a multimodal distribution of molecular weight with a relatively low polydispersity. The results of this study offer significant insight into the nature and properties of DOM in freshwater ecosystems.     

Biochemical evidence for the presence of mixed membrane topologies of the severe acute respiratory syndrome coronavirus envelope protein expressed in mammalian cells

Coronavirus envelope (E) protein is a small integral membrane protein with multi-functions in virion assembly, morphogenesis and virus-host interaction. Different coronavirus E proteins share striking similarities in biochemical properties and biological functions, but seem to adopt distinct membrane topology. In this report, we study the membrane topology of the SARS-CoV E protein by immunofluorescent staining of cells differentially permeabilized with detergents and proteinase K protection assay. It was revealed that both the N- and C-termini of the SARS-CoV E protein are exposed to the cytoplasmic side of the membranes (N(cyto)C(cyto)). In contrast, parallel experiments showed that the E protein from infectious bronchitis virus (IBV) spanned the membranes once, with the N-terminus exposed luminally and the C-terminus exposed cytoplasmically (N(exo(lum)-)C(cyto)). Intriguingly, a minor proportion of the SARS-CoV E protein was found to be modified by N-linked glycosylation on Asn 66 and inserted into the membranes once with the C-terminus exposed to the luminal side. The presence of two distinct membrane topologies of the SARS-CoV E protein may provide a useful clue to the pathogenesis of SARS-CoV.     

Species composition and diversity of soil animals in the oil shale dump in Maoming, Guangdong Province, China

Pollution from the oil shale dump in Maoming, Guangdong Province, China, was a major social problem due to the great amount of environmental damage it caused. Therefore, a great deal of attention needed to be paid for the ecological restoration and reconstruction. The objective of this study was to investigate the species composition of soil fauna and its diversity in oil shale dumps after the application of different ecological restoration schemes in order to understand the impact they had on ecological restoration. Three plots were selected on an oil shale dump near the city of Maoming. The “north plot” was a newly-planted young forest mixed with various tree species, while the “south plot” was a 20-year-old Acacia auriculaeformis forest, and the “control plot” was a 20-year-old naturally-recovering grassland. Soil animals, mainly including macro-meso groups, were collected by hand-sorting and Tullgren funnel extraction. They were then identified to family or genus level with only a small portion to order (e.g. Chllopoda) or species (e.g. Isopoda) level. The specimens obtained in the present study was 11164 individuals, belonging to 27 orders and 110 families or genera. The Shannon index (H′), DG_s (based on species) and DG_g (based on groups) were used to analyze the diversity of soil animals between different plots. The major results were as follows: A total of 33 families or genera belonging to nine orders were found in the “north plot”. The main group was Caritermes, accounting for 63.4% of the total, followed by Tetramorium with 21.3%. Hymenoptera, mainly Formicidae, had more genera than others, accounting for 80% of the total genera in this group. The diversity of soil animals in this plot was very low because the H′ index was only 1.2, while the DG_s index was 4.0 and the DG_g index was 1.3. A total of 61 families or genera belonging to 23 orders were found in the “south plot”. Malmcoangelia and Tetramorium were the main groups, which accounted for 60.3% and 10.2%, respectively. Two genera of Annelda and two genera of Isopoda only accounted for 2.6% and 1.9%, respectively, but they were considered to be major groups due to their large body sizes and the distinct characteristics of their habitat. Acarina had a greater number of individuals and families or genera with its individual number accounting for 67.5% of the total, and the number of families or genera of this group account for 70% in this plot. The diversity indexes (H′, DG_s and DG_g) in this plot were significantly higher than those in the “north plot”, and were 1.65, 16.7 and 7.75, respectively. In the “control plot”, there were 67 families or genera of soil animals belonging to 23 orders. The main groups were Tetramorium (20%), Lasius (17.1%), Bothriomymex of Formicidae (13.8%), and Malmcoangelia of oribatid mites (14.5%). Formicidae of Hymenoptera was the group with the maximum number of individuals, accounting for 51.0%, while Diplopoda had the most families or genera. The H′ and DG_s indexes, being 2.54 and 17.7, were higher than those in the “south plot”, while the DG_g index of 7.20 was lower than that in the “south plot”. The results showed that the species composition and diversity indexes were higher in the “south plot” than in the “north plot” and the “control plot”, which demonstrated that using Acacia auriculaeformis forest to restore the oil shale dump was an effective approach in terms of soil biodiversity.     

Structure-based design and structure-activity relationships of 1,2,3,4-tetrahydroisoquinoline derivatives as potential PDE4 inhibitors

This paper describes our medicinal chemistry efforts on 7-(cyclopentyloxy)-6-methoxy1,2,3,4-tetrahydroisoquinoline scaffold: design, synthesis and biological evaluation using conformational restriction approach and bioisosteric replacement strategy. Biological data revealed that the majority of the synthesized compounds of this series displayed moderate to potent inhibitory activity against PDE4B and strong inhibition of LPS-induced TNFα release. Among them, compound 19 exhibited the strongest inhibition against PDE4B with an IC₅₀ of 0.88?µM and 21 times more potent selectivity toward PDE4B over PDE4D when compared to rolipram. A primary structure-activity relationship study showed that the attachment of CH₃O group or CF₃O group to the phenyl ring at the para-position was helpful to enhance the inhibitory activity against PDE4B. Moreover, sulfonamide group played a key role in improving the inhibitory activity against PDE4B and subtype selectivity. In addition, the attachment of the additional rigid substituents at the C-3 position of 1,2,3,4-tetrahydroisoquinoline ring was favored to subtype selectivity, which was consistent well with the observed docking simulation.     

A case study of a shared/buy-in computing ecosystem

Many research institutions are deploying computing clusters based on a shared/buy-in paradigm. Such clusters combine shared computers, which are free to be used by all users, and buy-in computers, which are computers purchased by users for semi-exclusive use. The purpose of this paper is to characterize the typical behavior and performance of a shared/buy-in computing cluster, using data traces from the Shared Computing Cluster (SCC) at Boston University that runs under this paradigm as a case study. Among our main findings, we show that the semi-exclusive policy, which allows any SCC user to use idle buy-in resources for a limited time, increases the utilization of buy-in resources by 17.4%, thus significantly improving the performance of the system as a whole. We find that jobs allowed to run on idle buy-in resources arrive more frequently and run for a shorter time than other jobs. Finally, we identify the run time limit (i.e., the maximum time during which a job is allowed to use resources) and the type of parallel environment as two factors that have a significant impact on the different performance experienced by shared and buy-in jobs.     

双依他尼酸乙醇胺对谷胱甘肽S-转硫酶mu的选择性抑制作用

谷胱甘肽S-转移酶(GST)的同工酶mu(GSTM)高表达与卵巢癌顺铂耐药有关.以GST非选择性抑制剂依他尼酸设计二价潜抑制剂双依他尼酸乙醇胺(aminoethanol di-ethacrynic acid,ADEA),测定ADEA及其与还原型谷胱甘肽(glutathione,GSH)加合物对GST同工酶亚型A1、P1...     

肺动脉内皮细胞与肺动脉平滑肌细胞增殖的相互调节

血管内皮细胞和血管平滑肌细胞在结构和功能上关系密切,二者的相互关系在血管舒缩和血管壁结构的调节中起重要作用。本文观察了培养的小牛肺动脉内皮细胞（ＰＡＥＣ）和肺动脉平滑肌细胞（ＰＡＳＭ）在细胞增殖方面的相互调节作用。混合培养的ＰＡＥＣ和ＰＡＳＭ细胞的３Ｈ－ＴｄＲ参入明显降低（Ｐ＜０．００１,与对照组相比）。无论向培养的ＰＡＥＣ和ＰＡＳＭ中分别加入ＰＡＳＭ和ＰＡＥＣ的条件培养基还是二者共培养时,均发现ＰＡＥＣ的３Ｈ－ＴｄＲ参入明显降低,而ＰＡＳＭ的３Ｈ－ＴｄＲ明显升高（Ｐ＜０．０５,与对照组相比）。流式细胞测定也发现共培养时ＰＡＥＣ的Ｇ１期细胞增多,Ｇ２／Ｍ期细胞减少;而ＰＡＳＭ的Ｇ１期细胞减少,Ｇ２／Ｍ期细胞增多。共培养的ＰＡＳＭ细胞内ｃＡＭＰ增加,ｃＧＭＰ含量降低;而ＰＡＥＣ细胞的ｃＡＭＰ和ｃＧＭＰ含量均降低（Ｐ＜０．０１,与对照组相比）。上述结果提示,ＰＡＥＣ和ＰＡＳＭ相互作用可能通过第二信使而调节它们本身的增殖