Characterization of heparin oligosaccharides binding specifically to antithrombin III using mass spectrometry

Heparan sulfate (HS) is a sulfated glycosaminoglycan attached to a core protein on the cell surface. Protein binding to cell surface HS is a key regulatory event for many cellular processes such as blood coagulation, cell proliferation, and migration. The concept whereby protein binding to HS is not random but requires a limited number of sulfation patterns is becoming clear. Here we describe a hydrophobic trapping assay for screening a library of heparin hexasaccharides for binders to antithrombin III (ATIII). The hexasaccharide compositions are defined with their building block content in the following format: (DeltaHexA:HexA:GlcN:SO 3:Ac). Of five initial compositions present in the library, (1:2:3:6:1), (1:2:3:7:1), (1:2:3:7:0), (1:2:3:8:0), and (1:2:3:9:0), only two are shown to bind ATIII, namely, (1:2:3:8:0) and (1:2:3:9:0). The use of amide hydrophilic interaction (HILIC) liquid chromatography-mass spectrometry permitted reproducible quantitative analysis of the composition of the initial library as well as that of the binding fraction. The specificity of the hexasaccharides binding ATIII was confirmed by assaying their ability to enhance ATIII-mediated inhibition of Factor Xa in vitro.     

Bio-samtools: Ruby bindings for SAMtools, a library for accessing BAM files containing high-throughput sequence alignments

ABSTRACT: BACKGROUND: The SAMtools utilities comprise a very useful and widely used suite of software for manipulating files and alignments in the SAM and BAM format, used in a wide range of genetic analyses. The SAMtools utilities are implemented in C and provide an API for programmatic access, to help make this functionality available to programmers wishing to develop in the high level Ruby language we have developed bio-samtools, a Ruby binding to the SAMtools library. RESULTS: The utility of SAMtools is encapsulated in 3 main classes, Bio::DB::Sam, representing the alignment files and providing access to the data in them, Bio::DB::Alignment, representing the individual read alignments inside the files and Bio::DB::Pileup, representing the summarised nucleotides of reads over a single point in the nucleotide sequence to which the reads are aligned. CONCLUSIONS: bio-samtools is a flexible and easy to use interface that programmers of many levels of experience can use to access the information in the popular and common SAM/BAM format.     

荒漠草原不同雨量带土壤-植物-微生物C、N、P及其化学计量特征

降水作为关键性驱动因子深刻影响着荒漠草原生态系统养分循环过程。采用生态化学计量学方法,调查了荒漠草原不同雨量带土壤-植物-微生物C、N、P及其生态化学计量特征对降水格局的适应性规律。研究区不同雨量带土壤C、N、P随降水梯度的递减亦呈现递减趋势。平均土壤C∶N∶P比例为28.9∶2.7∶1,主要受到P元素控制。不同雨量带平均土壤MBC∶MBN∶MBP比例为108.6∶5.6∶1,表现出明显的C富集现象。不同雨量带平均植物C∶N∶P比例为117.4∶6.7∶1,表现为明显的C、N缺乏或P富集。降水为主的气候原因造成了研究区环境中P含量相对较高,并直接反映在了植物化学计量特征上。研究区土壤C和N之间具有极显著的正相关关系(P0.01),相关系数高达0.98。植物N和P之间具有显著的正相关关系(P0.05),相关系数为0.90。土壤N与植物C、P分别呈显著正相关和显著负相关(P0.05),相关系数分别为0.84和-0.82。降水在塑造荒漠草原生态格局以及驱动生态系统养分循环过程中发挥了关键性作用。     

Gastric Potential Difference in Fasted Rats: Circadian Studies

The pathophysiology of gastroduodenal ulcer disease remains the subject of intense research and controversy. One model of gastric ulcerogenesis implicates a disruption of complementary circadian rhythms between protective and destructive factors. Parallel circadian rhythms have been reported between acid secretion and gastric potential difference (PD) in in vitro models. The purpose of this study was to investigate the circadian measurements of PD, a parameter of intact gastric mucosal function and thus a putative parameter of gastric protection, in intact, fasted, anesthetized rats. Sixty-four male Sprague-Dawley rats were acclimatized in sound-attenuating, lightproof chambers for 3 weeks on a 12:12-h light-dark schedule. Eight rats were fasted 18 h before being sampled at each of eight times on the circadian clock (01:00, 04:00, 07:00, 10:00, 13:00, 16:00, 19:00. and 22:00 hours after lights on) (HALO). In each rat, after anesthesia (ketamine/ acepromazine) and laparotomy, the tip of a catheter (pre-filled with KC1 agar) was passed into the gastric corpus through the duodenum. The tip of a second KC1-agar catheter was placed within the peritoneal cavity. The position of the intragas-tric catheter was gently adjusted for obtaining the highest stable PD reading. The data showed significantly higher values at 07:00 and 10:00 HALO. The lowest value was at 13:00 HALO. The difference between high (10:00 HALO) and low (13:00 HALO) values was 4.5 mV or 13% of the mean. This difference was highly significant (p = 0.003) Analysis of variance showed that the values at 07:00 and 10:00 HALO were significantly higher than the values at 01:00, 13:00, and 16:00 HALO. Thus, the existence of a circadian rhythm in gastric PD is supported.     

Kinetic studies of chicken and turkey liver mitochondrial aspartate aminotransferase.

The kinetic behaviour of chicken liver and turkey liver aspartate aminotransferases (L-aspartate:2-oxoglutarate aminotransferase, EC 2.6.1.1) was studied. Steady-state data were obtained from a wide range of concentrations of substrates and product L-glutamate. The data were fitted by rational functions of degree 1:1, 1:2 and 2:2 with respect to substrates and 0:1, 1:1, 0:2 and 1:2 with regard to product (L-glutamate), by using a non-linear regression program that guarantees the fit. The goodness of fit was improved by the use of a computer program that combines model discrimination parameter refinement and sequential experimental design. It was concluded that aspartate aminotransferase requires a minimum velocity equation of degree 2:2 for L-aspartate, 2:2 for 2-oxoglutarate and 1:2 for L-glutamate. Finally, a plausible kinetic mechanism that justifies these experimental results is proposed.     

Association of DNA quadruplexes through G:C:G:C tetrads. Solution structure of d(GCGGTGGAT)

The structure formed by the DNA sequence d(GCGGTGGAT) in a 100 mM Na(+) solution has been determined using molecular dynamics calculations constrained by distance and dihedral restraints derived from NMR experiments performed at isotopic natural abundance. The sequence folds into a dimer of dimers. Each symmetry-related half contains two parallel stranded G:G:G:G tetrads flanked by an A:A mismatch and by four-stranded G:C:G:C tetrads. Each of the two juxtaposed G:C:G:C tetrads is composed of alternating antiparallel strands from the two halves of the dimer. For each single strand, a thymine intersperses a double chain reversal connecting the juxtaposed G:G:G:G tetrads. This architecture has potential implications in genetic recombination. It suggests a pathway for oligomerization involving association of quadruplex entities through GpC steps.     

Biphasic Liberation of Arachidonic and Stearic Acids During Cerebral Ischemia

The mode of free fatty acid (FFA) liberation from the mouse brain during ischemia was investigated at various times after decapitation and under nizofenone treatment. Normal nonischemic brain FFAs consist mainly of palmitic acid (16:0), stearic acid (18:0), and oleic acid (18:1) with smaller amounts of arachidonic acid (20:4), docosahexaenoic acid (22:6), and others. Postdecapitative ischemia induced a rapid, biphasic release of 20:4 after a short lag of less than 30 s. The first phase showed a rapid 6.4-fold increase within 1 min of decapitation, followed by the second phase involving a slow release at less than one-fifth the rate of the first phase and lasting for at least 10 min. A similar, but not so marked, biphasic liberation was observed with 18:0. However, all of the other fatty acids (16:0, 18:1, 22:6, and others) were released only in a single phase at a slow rate. The time course for the rapid and specific liberation of 20:4 coincided with the time course for the decrease in brain ATP concentration during ischemia. Pretreatment of the animals with nizofenone resulted in a marked suppression of both FFA liberation and ATP depletion during ischemia. This suppression was particularly noteworthy with 20:4 and 18:0. The present study indicates that there is a specific and rapid liberation of 20:4 and 18:0 in a very early stage of ischemia and that this liberation seems to depend on availability of ATP in the brain. The physiological role of this transient 20:4 liberation during ischemia is discussed.     

Brucella abortus 16S rRNA and lipid A reveal a phylogenetic relationship with members of the alpha-2 subdivision of the class Proteobacteria

On the basis of ribosomal 16S sequence comparison, Brucella abortus has been found to be a member of the alpha-2 subdivision of the class Proteobacteria (formerly named purple photosynthetic bacteria and their nonphototrophic relatives). Within the alpha-2 subgroup, brucellae are specifically related to rickettsiae, agrobacteria, and rhizobiae, organisms that also have the faculty or the obligation of living in close association to eucaryotic cells. The composition of Brucella lipid A suggests a close phylogenetical relationship with members of the alpha-2 group. The chemical analysis of the lipid A fraction revealed that Brucella species contain both glucosamine and diaminoglucose, thus suggesting the presence of a so-called mixed lipid A type. The serological analysis with polyclonal and monoclonal antibodies is in agreement with the existence of mixed lipid A type in B. abortus. The amide-linked fatty acid present as acyl-oxyacyl residues were 3-O-C(16:0)12:0, 3-O-C(16:0)13:0, 3-O-C(16:0)14:0, and 3-O-C(18:0)14:0. The only amide-linked unsubstituted fatty acid detected was 3-OH-C16:0. The ester-linked fatty acids are 3-OH-C16:0, 3-OH-C18:0, C16:0, C17:0, and C18:0. Significant amounts of the large-chain 27-OH-C28:0 were detected together with traces of 25-OH-C26:0 and 29-OH-C30:0. Comparison of the Brucella lipid composition with that of the other Proteobacteria also suggests a close phylogenetical relationship with members of the alpha-2 subdivision. The genealogical grouping of Brucella species with pericellular and intracellular plant and animal pathogens as well as with intracellular plant symbionts suggests a possible evolution of Brucella species from plant-arthropod-associated bacteria.     

A phylogenetic analysis of Prunus and the Amygdaloideae (Rosaceae) using ITS sequences of nuclear ribosomal DNA

The economically important plum or cherry genus (PRUNUS:) and the subfamily Amygdaloideae of the Rosaceae have a controversial taxonomic history due to the lack of a phylogenetic framework. Phylogenetic analysis using the ITS sequences of nuclear ribosomal DNA (nrDNA) was conducted to construct the evolutionary history and evaluate the historical classifications of PRUNUS: and the Amygdaloideae. The analyses suggest two major groups within the Amygdaloideae: (1) PRUNUS: s.l. (sensu lato) and MADDENIA:, and (2) EXOCHORDA:, Oemleria, and PRINSEPIA: The ITS phylogeny supports the recent treatment of including EXOCHORDA: (formerly in the Spiraeoideae) in the Amygdaloideae. MADDENIA: is found to be nested within PRUNUS: s.l. in the parsimony and distance analyses, but basal to PRUNUS: s.l. in the maximum likelihood analysis. Within PRUNUS:, two major groups are recognizable: (1) the AMYGDALUS:-PRUNUS: group, and (2) the CERASUS:-LAUROCERASUS:-PADUS: group. The clades in the ITS phylogeny are not congruent with most subgeneric groups in the widely used classification of PRUNUS: by Rehder. A broadly defined PRUNUS: is supported.     

Interactions of proteins with ganglioside-enriched microdomains on the membrane: the lateral phase separation of molecular species of GD1a ganglioside, having homogeneous long-chain base composition, is recognized by Vibrio cholerae sialidase

The thermotropic behavior (studied by high-sensitivity differential scanning calorimetry) and susceptibility to Vibrio cholerae sialidase hydrolysis of large unilamellar vesicles of dipalmitoyl-phosphatidylcholine, containing native GD1a ganglioside or the molecular species of GD1a containing C18:1 or C20:1 long-chain base (C18:1 GD1a; C20:1 GD1a), were studied. Vesicles containing ganglioside (10% in molar terms) showed the presence in the heat capacity function of a second minor peak besides the phospholipid main transition peak. The presence of a second peak is much more evident with C20:1 GD1a than with C18:1 GD1a, the difference being potentiated by Ca2+ and indicating a different tendency of the CD1a molecular species to undergo lateral phase separation. The scans of vesicles containing native GD1a showed the features of those obtained with C18:1 GD1a and C20:1 GD1a, indicating that the main components of native GD1a, C18:1 GD1a and C20:1 GD1a, maintain their individual aggregative properties. V. cholerae sialidase affects vesicle-bound GD1a at a much higher rate (17-25-fold) than it does micellar GD1a, the activation by Ca2+ being 3- and 2-fold, respectively. The Vmax values were identical on C18:1 GD1a and C20:1 GD1a in micellar dispersions, whereas they were markedly higher (from 20 to 50%) on C18:1 GD1a than on C20:1 GD1a in vesicular dispersions. Exhaustive sialidase hydrolysis of vesicles carrying native GD1a produced C18:1 GM1 and C20:1 GM1 in the same proportion as the C18:1 and C20:1 species present in native GD1a (53.9% and 46.1%).(ABSTRACT TRUNCATED AT 250 WORDS)     

The anaerobic degradability of thermoplastic starch: polyvinyl alcohol blends: potential biodegradable food packaging materials

A systematic study on the anaerobic degradability of a series of starch:polyvinyl alcohol (TPS:PVOH) blends was performed to determine their fate upon disposal in either anaerobic digesters or bioreactor landfills. The aims of the study were to measure the rate and extent of solubilisation of the plastics. The extent of substrate solubilisation on a COD basis reached 60% for a 90:10 (w/w) blend of TPS:PVOH, 40% for 75:25, 30% for 50:50 and 15% for PVOH only. The rate of substrate solubilisation was most rapid for the 90:10 blend (0.041 h(-1)) and decreased with the amount of starch in the blend in the following order 0.034 h(-1)(75:25); 0.023 h(-1)(50:50). The total solids that remained after 900 h were 10 wt.% (90:10); 23 wt.% (75:25); 55 wt.% (50:50); 90 wt.% (0:100). Starch containing substrates produced a higher concentration of volatile fatty acids (VFAs) and biogas, compared to the 0:100 substrate. The major outcome was that PVOH inhibited the degradation of the starch from the blend.     

Distribution of the four flagellar (H) antigenic subserotypes of Bacillus thuringiensis H serotype 3 in Japan

A total of 302 strains of Bacillus thuringiensis flagellar (H) serotype 3, collected from sericultural environments and soils of the three main islands (Honshu, Shikoku and Kyushu) of Japan, were examined for their H antigenic subserotypes. Of these strains, 259 (85.8%) were identified as the H subserotype 3a : 3c (subsp. alesti ), 16 (5.3%) were referable to the subserotype 3a : 3b : 3c (subsp. kurstaki ), 26 (8.6%) belonged to the subserotype 3a : 3d : 3e (subsp. fukuokaensis ) and one strain (0.3%) was the subserotype 3a : 3d (subsp. sumiyoshiensis ). The subserotypes 3a : 3c and 3a : 3b : 3c were present in sericultural environments only; the former was distributed in Honshu and Shikoku Islands but not in Kyushu Island, and the latter was distributed in Honshu and Kyushu Islands but not in Shikoku Island. The subserotype 3a : 3d : 3e, mainly found in soils but occasionally in sericultural environments, was distributed in the three main islands. It also appeared that the subserotype 3a : 3d : 3e, a recently described subserotype, was distributed in Japan more widely than the globally disseminated subserotype 3a : 3b : 3c. The results clearly showed geographical and ecological differences in the distribution of subserotypes.     

Occurrence of a monophasic strain of Salmonella group B isolated from cetaceans in England and Wales between 1990 and 2002

Between September 1990 and December 2002, 511 cetacean carcasses stranded or caught in commercial fisheries in England and Wales were examined post mortem . Salmonella group B was isolated from 60 of 279 (21.51%) harbour porpoises ( Phocoena phocoena ), predominantly from lung tissue. Forty-three of the Salmonella group B isolates were subsequently serotyped and all found to have the antigenic structure O4,12:a:-. The annual proportion of harbour porpoises testing positive for Salmonella O4,12:a:- increased significantly from 6% in the early 1990s to 27% after 1999. The cause(s) of the increasing prevalence of Salmonella O4,12:a:- are not known, but may reflect natural variation in the epidemiological cycle of Salmonella O4,12:a:- in harbour porpoises. The probability of isolating Salmonella O4,12:a:- from harbour porpoises increased with age, suggesting that the mode of transmission is principally horizontal. There appeared to be a weak degree of seasonality in the probability of isolating Salmonella O4,12:a:- with a low proportion of cases in the months of April and May. Based on pathological findings from infected carcasses, Salmonella O4,12:a:- may be part of the normal commensal flora of the lungs of cetaceans with the potential to act as an opportunistic pathogen.     

pMAA-Red: a new pPZP-derived vector for fast visual screening of transgenic Arabidopsis plants at the seed stage

ABSTRACT: BACKGROUND: The production of transgenic plants, either for the overproduction of the protein of interest, for promoter::reporter lines, or for the downregulation of genes is an important prerequisite in modern plant research but is also very time-consuming. RESULTS: We have produced additions to the pPZP family of vectors. Vector pPZP500 (derived from pPZP200) is devoid of NotI sites and vector pPZP600 (derived from pPZP500) contains a bacterial kanamycin resistance gene. Vector pMAA-Red contains a Pdf2.1::DsRed marker and a CaMV::GUS cassette within the T-DNA and is useful for the production of promoter::GUS lines and overexpression lines. The Pdf2.1 promoter is expressed in seeds and syncytia induced by the beet cyst nematode Heterodera schachti in Arabidopsis roots. Transgenic seeds show red fluorescence which can be used for selection and the fluorescence level is indicative of the expression level of the transgene. The advantage is that plants can be grown on soil and that expression of the marker can be directly screened at the seed stage which saves time and resources. Due to the expression of the Pdf2.1::DsRed marker in syncytia, the vector is especially useful for the expression of a gene of interest in syncytia. CONCLUSIONS: The vector pMAA-Red allows for fast and easy production of transgenic Arabidopsis plants with a strong expression level of the gene of interest.     

Dissection of the Yersinia enterocolitica virulence plasmid pYVO8 into an operating unit and virulence gene modules

Abstract Mesophilic Aeromonas hydrophila from serotypes O:11 and O:34 grown in a glucose-rich medium produce a capsule that can be seen under light and electron microscopy. The purified capsular polysaccharide has a composition qualitatively similar for strains O:11 and O:34, but quantitatively different. The capsular polysaccharides were immunogenic in rabbits, and did not cross-react with specific antibodies against either purified lipopolysaccharide from strains O:34 or O:11 or against the S-layer characteristic of strains from serotype O:11.     

A preliminary assessment of intra-oral lubricating systems for dry mouth patients

Objective: To provide extended intra-oral delivery of a saliva substitute. Intervention: Three different types of prostheses containing saliva substitute were designed and assessed: a two-part device resembling a mandibular complete denture sealed by cobalt-samerium magnets, a one-part clear resin device for the edentate patients and a flexible mouth guard type of appliance containing a lubricant releasing bubble for the dentate patients. Setting: A teaching hospital Oral Medicine and Rheumatology Clinic. Subjects: 8 edentate and 3 dentate Sjogren Syndrome sufferers. Outcome measures: Subjective dryness after a week of wearing the lubricating appliance. Results: The majority of the subjects wore the appliances for 6–12 hours during each 24 hours. The initial dryness severity diminished after wearing the lubricating prosthesis. The patients preferred to wear the appliance at night. Conclusion: All criteria were fulfilled on designing a saliva substitute lubricating appliance and some of the subjects have worn this prosthesis successfully for up to 3 years. Particular benefit was obtained by night-time wear.     

中缅树鼩体温、代谢率和蒸发失水日节律

为研究中缅树鼩(Tupaia belangeri)体温、代谢率和蒸发失水的日节律变化,采用植入式体温计测定了中缅树鼩24 h的体温,以及24 h中4个时间段(05:00～07:00时、11:00～13:00时、17:00～19:00时和23:00～01:00时)热中性区(30℃)的静止代谢率(RMR)、非颤抖性产热(NST)和蒸发失水(EWL)。结果显示,中缅树鼩的体温具有日节律变化,最高值和最低值分别出现在11:00时和03:00时,各为(39.45±0.26)℃和(36.34±0.24)℃;静止代谢率、非颤抖性产热和蒸发失水在4个时间段都有显著差异,表现出显著的日节律变化,代谢率在23:00～01:00时最大,O2含量为(2.58±0.04)ml/(g.h),在11:00～13:00时最小,O2含量为(2.28±0.09)ml/(g.h);非颤抖性产热在05:00～07:00时最大,O2含量为(3.08±0.14)ml/(g.h),在11:00～13:00最小,O2含量为(2.69±0.63)ml/(g.h);蒸发失水在17:00～19:00时最大,失水量为(3.60±0.31)mg/(g.h)。结果表明,体温的日节律变化主要与环境温度的日节律变化和下午出窝取食活动性增强有关;当夜晚环境温度相对较低的时候,通过增强静止代谢率和非颤抖性产热来增加产热,而白天环境温度相对较高的时候,通过增强蒸发失水散热来调节体温。     

Polyunsaturated fatty acid biosynthesis from [1-14C]20:3 n-6 acid in rat cultured Sertoli cells. Linoleic acid effect

Primary culture is a suitable system to study lipid metabolism and polyunsaturated fatty acid biosynthesis. Sertoli cell-enriched preparations were used to determine the fatty acid composition after 5 and 7 days in culture (serum free) as well as the uptake and metabolism of [1-14C]eicosa-8,11,14-trienoic acid. The addition of unlabeled linoleic acid (0.2 and 2.0 microg/ml) was also evaluated. Fatty acid methyl esters derived from cellular lipids were analyzed by gas liquid chromatography and radiochromatography. After 5 days in culture, cells had significantly less 18:2, 20:4, 22:5 and 24:5 and more 18:3, 20:3, 22:4 and 24:4 n-6 fatty acids than non-cultured cells. On day 7, an additional increment in 22:4 n-6 and a decrease in linoleic, gamma-linoleic and 24:4 n-6 fatty acids were observed. The presence of linoleic acid (low dose) produced a significant decrease in saturated and monounsaturated acids and an increase in 18:2, 20:4 and 22:5 n-6 fatty acids. At a high concentration almost all fatty acids belonging to 18:2 n-6 increased significantly. The drop in 20:4 n-6/20:3 n-6 ratio was considered as an indirect evidence of a Delta 5 desaturase activity depression. This assumption was corroborated by studying the transformation of [1-14C]eicosa-8,11,14-trienoic acid into 20:4, 22:4, 22:5, 24:4 and 24:5 n-6 fatty acids. We conclude that Sertoli cells after 7 days in culture evidenced changes in the fatty acid profile similar to those described under fat deprivation. The addition of linoleic acid reverted this pattern and indicated that the Delta 5 desaturase activity is a limiting step in the polyunsaturated fatty acid biosynthesis.