A chromosome-scale genome assembly and dense genetic map for Xenopus tropicalis.

The Western clawed frog Xenopus tropicalis is a diploid model system for both frog genetics and developmental biology, complementary to the paleotetraploid X. laevis. Here we report a chromosome-scale assembly of the X. tropicalis genome, improving the previously published draft genome assembly through the use of new assembly algorithms, additional sequence data, and the addition of a dense genetic map. The improved genome enables the mapping of specific traits (e.g., the sex locus or Mendelian mutants) and the characterization of chromosome-scale synteny with other tetrapods. We also report an improved annotation of the genome that integrates deep transcriptome sequence from diverse tissues and stages. The exon-intron structures of these genes are highly conserved relative to both X. laevis and human, as are chromosomal linkages ("synteny") and local gene order. A network analysis of developmental gene expression will aid future studies.

Probing the orientation of inhibitor and epoxy-eicosatrienoic acid binding in the active site of soluble epoxide hydrolase.

Soluble epoxide hydrolase (sEH) is an important therapeutic target of many diseases, such as chronic obstructive pulmonary disease (COPD) and diabetic neuropathic pain. It acts by hydrolyzing and thus regulating specific bioactive long chain polyunsaturated fatty acid epoxides (lcPUFA), like epoxyeicosatrienoic acids (EETs). To better predict which epoxides could be hydrolyzed by sEH, one needs to dissect the important factors and structural requirements that govern the binding of the substrates to sEH. This knowledge allows further exploration of the physiological role played by sEH. Unfortunately, a crystal structure of sEH with a substrate bound has not yet been reported. In this report, new photoaffinity mimics of a sEH inhibitor and EET regioisomers were prepared and used in combination with peptide sequencing and computational modeling, to identify the binding orientation of different regioisomers and enantiomers of EETs into the catalytic cavity of sEH. Results indicate that the stereochemistry of the epoxide plays a crucial role in dictating the binding orientation of the substrate.

Mass spectrometry-based analyses showing the effects of secretor and blood group status on salivary N-glycosylation.

BACKGROUND: The carbohydrate portions of salivary glycoproteins play important roles, including mediating bacterial and leukocyte adhesion. Salivary glycosylation is complex. Many of its glycoproteins present ABO and Lewis blood group determinants. An individual's genetic complement and secretor status govern the expression of blood group antigens. We queried the extent to which salivary glycosylation varies according to blood group and secretor status. First, we screened submandibular/sublingual and parotid salivas collected as ductal secretions for reactivity with a panel of 16 lectins. We selected three lectins that reacted with the largest number of glycoproteins and one that recognized uncommon lactosamine-containing structures. Ductal salivas representing a secretor with complex blood group expression and a nonsecretor with a simple pattern were separated by SDS-PAGE. Gel slices were trypsin digested and the glycopeptides were individually separated on each of the four lectins. The bound fractions were de-N-glycosylated. LC-MS/MS identified the original glycosylation sites, the peptide sequences, and the parent proteins. RESULTS: The results revealed novel salivary N-glycosites and glycoproteins not previously reported. As compared to the secretor, nonsecretor saliva had higher levels of N-glycosylation albeit with simpler structures. CONCLUSIONS: Together, the results suggested a molecular basis for inter-individual variations in salivary protein glycosylation with functional implications for oral health.

A pilot study on the serum pharmacokinetics of nattokinase in humans following a single, oral, daily dose.

CONTEXT: Nattokinase is a serine protease and is derived from natto, a traditional Japanese, fermented, soybean food meal. Multiple authors have described the significant fibrinolytic, antithrombotic, and antihypertensive effects of natto. Nattokinase has been growing in popularity for use as a dietary supplement for the benefit of cardiovascular health. Little is known regarding the pharmacokinetic and pharmacodynamic properties of this enzyme, and the bioavailability of nattokinase is currently unknown. OBJECTIVE: This study intended to (1) detect nattokinase directly and immunologically, (2) show that nattokinase and/or its metabolites were detectable in human blood following ingestion of a commercial preparation, and (3) chart a pharmacokinetic dosing effect for nattokinase. DESIGN: The research team designed the pilot study as an in vivo, human clinical trial. Healthy human subjects responded to an advertisement and were screened. Subjects who satisfied both inclusion and exclusion criteria were enrolled into the study. Subjects were then instructed to orally ingest a single capsule containing a known concentration of nattokinase immediately following a baseline blood draw. Subsequent blood draws occurred over a 24-h period. SETTING: This study was conducted in Oakland, California, at a clinical reference laboratory and was performed with the approval of an institutional review board (IRB) to ensure that appropriate ethical standards were met. PARTICIPANTS: Eleven healthy participants (five male, six female, ages 21-65), who met eligibility criteria, were enrolled. INTERVENTION(S): Administration of nattokinase occurred orally with the ingestion of a single daily dose (2000 FU) of nattokinase. Capsules, each containing approximately 100 mg of nattokinase, in softgel form (NSK-SD, Japan Bio Science Laboratory, Osaka, Japan), were used in the study. OUTCOME MEASURE(S): Baseline blood samples were collected, and participants were observed swallowing a single capsule of the nattokinase supplement before returning at 2, 4, 8, 12, 24, and 48 h post ingestion for subsequent blood draws. The presence of nattokinase in serum was measured by an enzyme-linked immunosorbent assay (ELISA), using a rabbit, polyclonal, antinattokinase-capture antibody. A pharmacokinetic pattern was observed for nattokinase between baseline and 48 h postdose. RESULTS: Peak serum levels of nattokinase were observed at approximately 13.3 h ± 2.5 h (mean ± standard error) postdose. Statistically significant increases in binding were detectable from baseline when comparing averaged data at time points t = 2 h-t = 24 h. CONCLUSIONS: These results provided the first evidence that nattokinase can be measured directly in the blood of humans. The results further suggest that a larger, more extensive, pharmacokinetic study of nattokinase is warranted. Additionally, looking for intact enzyme and bioactive nattokinase peptides should be a consideration for future studies investigating the pharmacokinetic profile of nattokinase.

Towards a North Pacific Ocean long-term monitoring program for plastic pollution: A review and recommendations for plastic ingestion bioindicators.

Marine debris is now a ubiquitous component of the Anthropocene global ocean. Plastic ingestion by marine wildlife was first reported in the 1960s and since that time, roughly one thousand marine species have been reported to consume this debris. This study focuses on plastic ingestion by marine invertebrates and vertebrates in the North Pacific Ocean. Specifically, we reviewed the scientific literature to assess the scope of the problem, identified key bioindicator species, and proposed guidelines for future monitoring of plastic debris in North Pacific marine ecosystems. Our meta-analysis confirmed that the North Pacific is among the most polluted ocean regions globally; roughly half of all fish and seabird specimens and more than three-quarters of sea turtles and bivalve specimens examined in this region had consumed plastic. While there are not enough standardized data to assess if these ingestion rates are changing, sampling standardization and reporting of methods are improving over time. Using a rubric-evaluation approach, we evaluated 352 species for their potential to serve as bioindicators of the prevalence of plastic pollution in the North Pacific. This analysis revealed a suite of 12 bioindicator species candidates which sample a variety of ecosystem components and cover a wide range of plastic size classes. Thus, we contend that these bioindicator candidates provide a key foundation for developing a comprehensive plastic monitoring program in the region. To enhance the utility of these bioindicators, we developed a framework for standardized data collection to minimize methodological variability across different studies and to facilitate the assessment of temporal trends over space and time. Tracking plastic ingestion by these bioindicators will help to assess the effectiveness of mitigation actions in the region, a critical step to evaluate progress towards sustainability and improved ocean health in the 21st century.

Drug-Target Residence Time Affects in Vivo Target Occupancy through Multiple Pathways.

The drug discovery and development process is greatly hampered by difficulties in translating in vitro potency to in vivo efficacy. Recent studies suggest that the long-neglected drug-target residence time parameter complements classical drug affinity parameters (K I, K d, IC50, or EC50) and is a better predictor of in vivo efficacy. Compounds with a long drug-target residence time are often more efficacious in vivo. The impact, however, of the drug-target residence time on in vivo efficacy remains controversial due to difficulties in experimentally determining the in vivo target occupancy during drug treatment. To tackle this problem, an in vivo displacement assay was developed using soluble epoxide hydrolase as a biological model. In this report, we experimentally demonstrated that drug-target residence time affects the duration of in vivo drug-target binding. In addition, the drug-target residence time plays an important role in modulating the rate of drug metabolism which also affects the efficacy of the drug.

Levels of trace elements, methylmercury and polybrominated diphenyl ethers in foraging green turtles in the South China region and their conservation implications.

Sea turtles are globally endangered and face daily anthropogenic threats, including pollution. However, there is a lack of ecotoxicological information on sea turtles, especially in the Asia-Pacific region. This study aims to determine pollutant levels of foraging green turtles (Chelonia mydas) in South China, including Hong Kong, Guangdong and Taiwan, as a basis for their conservation. Scute, liver and muscle tissues of stranded green turtles were analysed for levels of 17 trace elements and methylmercury (MeHg) (n = 86 for scute and n = 14 for liver) and polybrominated diphenyl ethers (PBDEs) (n = 11 for muscle and n = 13 for liver). Ten-fold higher levels of Pb, Ba, V and Tl and 40-fold greater Cd levels were measured in green turtle livers in South China relative to other studies conducted over 10 years ago. Measured PBDE levels were also 27-fold and 50-fold greater than those reported in Australia and Japan. These results warrant further investigation of potential toxicological risks to green turtles in South China and their source rookeries in Malaysia, Micronesia, Indonesia, Marshall Islands, Japan and Taiwan. Research should target monitoring pollutant levels in sea turtles within the West Pacific/Southeast Asia regional management unit spanning East Asia to Southeast Asia to fill in knowledge gaps, in particular in areas such as Thailand, Vietnam, Indonesia, Malaysia and the Philippines where less or no data is available and where foraging grounds of sea turtles have been identified.

TGF-beta-dependent pathogenesis of mitral valve prolapse in a mouse model of Marfan syndrome.

Mitral valve prolapse (MVP) is a common human phenotype, yet little is known about the pathogenesis of this condition. MVP can occur in the context of genetic syndromes, including Marfan syndrome (MFS), an autosomal-dominant connective tissue disorder caused by mutations in fibrillin-1. Fibrillin-1 contributes to the regulated activation of the cytokine TGF-beta, and enhanced signaling is a consequence of fibrillin-1 deficiency. We thus hypothesized that increased TGF-beta signaling may contribute to the multisystem pathogenesis of MFS, including the development of myxomatous changes of the atrioventricular valves. Mitral valves from fibrillin-1-deficient mice exhibited postnatally acquired alterations in architecture that correlated both temporally and spatially with increased cell proliferation, decreased apoptosis, and excess TGF-beta activation and signaling. In addition, TGF-beta antagonism in vivo rescued the valve phenotype, suggesting a cause and effect relationship. Expression analyses identified increased expression of numerous TGF-beta-related genes that regulate cell proliferation and survival and plausibly contribute to myxomatous valve disease. These studies validate a novel, genetically engineered murine model of myxomatous changes of the mitral valve and provide critical insight into the pathogenetic mechanism of such changes in MFS and perhaps more common nonsyndromic variants of mitral valve disease.

Source apportionment of fine particulate matter and risk of term low birth weight in California: Exploring modification by region and maternal characteristics.

Previous studies have demonstrated associations between fine particulate matter (PM2.5) and risk of term low birth weight (TLBW; birth weight<2500g and gestational weeks≥37weeks). However, it remains unclear which PM2.5 sources mainly contribute to these associations, and which subgroups (e.g. by residential region and maternal characteristics) may be more susceptible to these exposures. Using California birth records and PM2.5 data from eight monitoring sites from 2002 to 2009, we examined the relationship between exposures to total PM2.5 and PM2.5 sources and risk of TLBW. Source apportionment was performed for each site using Positive Matrix Factorization, and five PM2.5 sources (i.e., secondary ammonium sulfate, secondary ammonium nitrate, vehicular emissions, biomass burning, and resuspended soil) were included in our analysis. Mean gestational and trimester exposures were calculated for mothers with ZIP codes located within a 20km radius of monitors (N=1,050,330). Logistic regression was conducted and adjusted for maternal age, race/ethnicity, and education, as well as gestational age, year of birth, apparent temperature exposure during gestation, and neighborhood level percentage of households below poverty level. Increased risks of TLBW associated with each interquartile range increase in exposure were 4.9% (95% confidence interval: 2.6, 7.3) for total PM2.5, 7.7% (4.7, 10.7) for secondary ammonium sulfate, 5.6% (3.5, 7.7) for resuspended soil, and 3.1% (1.3, 4.9) for secondary ammonium nitrate. Differences in associations were found between inland and coastal regions, and between northern and southern regions for several sources. Results also showed effect measure modification by maternal race/ethnicity and education, with the lowest risk of TLBW associated with PM2.5 exposures found in mothers with at least a college education and Asian mothers. Some PM2.5 sources may be more harmful than others, and a better understanding of the relative toxicity of PM2.5 from each source could lead to more targeted and cost-effective regulations to protect public health.

Gastroesophageal reflux disease is associated with poor asthma control, quality of life, and psychological status in Chinese asthma patients.

BACKGROUND: Both asthma and gastroesophageal reflux disease (GERD) are common, often coexist, and have significant impact on a patient's quality of life. Our aim was to determine the prevalence of GERD in asthmatic patients at a major hospital in Hong Kong, and to examine the impact of GERD and its association with asthma control. METHODS: Patients with asthma who attended the respiratory clinic at Queen Mary Hospital, Hong Kong, were recruited. Demographic data were collected, and a validated Chinese GERD questionnaire was used. The Medical Outcomes Study 36-item short form (SF-36) was used to assess quality of life, and the Hospital Anxiety and Depression Scale (HADS) was used to assess psychological status. Asthma control was assessed by the asthma control test. RESULTS: A total of 218 patients were recruited; 40.4% of asthmatic patients (88 patients) had GERD, as defined by the GERD questionnaire. Compared with those patients without GERD, those with GERD had significantly worse asthma control (p = 0.022), worse quality of life in all domains of the SF-36 (all p < 0.01), and more anxiety (6.82 vs 4.90, respectively; p < 0.001) and depression (6.09 vs 4.05, respectively; p < 0.001) as reflected by HADSs. CONCLUSIONS: A significant proportion of asthmatic patients in Hong Kong have GERD, and this is associated with poorer asthmatic control, quality of life, and psychological status.

Owenweeksia hongkongensis gen. nov., sp. nov., a novel marine bacterium of the phylum 'Bacteroidetes'.

An aerobic, Gram-negative, non-fermentative, rod-shaped, motile, orange-pigmented bacterium, UST20020801(T), was isolated from sea-water samples collected from Port Shelter, Hong Kong, S.A.R., China, in August 2002. The full 16S rRNA gene sequence of this strain shared only 87.5 % similarity with its nearest relative, Crocinitomix catalasitica, a species of the family Cryomorphaceae. However, strain UST20020801(T) possessed menaquinone-6, a major respiratory quinone of members of the family Flavobacteriaceae. This strain contains unique fatty acids such as i15 : 1G, i17 : 1omega9c, 2-OH 15 : 0, 15 : 1omega6c and three unknown fatty acids of equivalent chain-length of 11.543, 13.565 and 16.582. Further analysis of its ecophysiology and biochemistry suggests that this strain represents a new genus in the phylum 'Bacteroidetes'. The name Owenweeksia hongkongensis gen. nov., sp. nov. is proposed. The type strain is UST20020801(T) (=NRRL B-23963(T) = JCM 12287(T)).