Optimization of food waste hydrolysis in leach bed coupled with methanogenic reactor: effect of pH and bulking agent

The effects of pH and bulking agents on hydrolysis/acidogenesis of food waste were studied using leach bed reactor (LBR) coupled with methanogenic up-flow anaerobic sludge blanket (UASB) reactor. The hydrolysis rate under regulated pH (6.0) was studied and compared with unregulated one during initial experiment. Then, the efficacies of five different bulking agents, i.e. plastic full particles, plastic hollow sphere, bottom ash, wood chip and saw dust were experimented under the regulated pH condition. Leachate recirculation with 50% water replacement was practiced throughout the experiment. Results proved that the daily leachate recirculation with pH control (6.0) accelerated the hydrolysis rate (59% higher volatile fatty acids) and methane production (up to 88%) compared to that of control without pH control. Furthermore, bottom ash improved the reactor alkalinity, which internally buffered the system that improved the methane production rate (0.182 l CH₄/g VS_added) than other bulking agents.     

Complete genome sequence of the veterinary pathogen Staphylococcus pseudintermedius strain HKU10-03, isolated in a case of canine pyoderma

Staphylococcus pseudintermedius is a member of the coagulase-positive staphylococci and is the commonest cause of canine pyoderma. We report the first genome sequence of S. pseudintermedius, which shows the presence of numerous virulence factors akin to those of the related human pathogen Staphylococcus aureus.     

Roles of microRNAs in mammalian reproduction: from the commitment of germ cells to peri‐implantation embryos

MicroRNAs (miRNAs) are active regulators of numerous biological and physiological processes including most of the events of mammalian reproduction. Understanding the biological functions of miRNAs in the context of mammalian reproduction will allow a better and comparative understanding of fertility and sterility in male and female mammals. Herein, we summarize recent progress in miRNA‐mediated regulation of mammalian reproduction and highlight the significance of miRNAs in different aspects of mammalian reproduction including the biogenesis of germ cells, the functionality of reproductive organs, and the development of early embryos. Furthermore, we focus on the gene expression regulatory feedback loops involving hormones and miRNA expression to increase our understanding of germ cell commitment and the functioning of reproductive organs. Finally, we discuss the influence of miRNAs on male and female reproductive failure, and provide perspectives for future studies on this topic.     

The genetic structure of the A mating-type locus of Lentinula edodes

The Shiitake mushroom, Lentinula edodes (Berk.) Pegler is a tetrapolar basidiomycete with two unlinked mating-type loci, commonly called the A and B loci. Identifying the mating-types in shiitake is important for enhancing the breeding and cultivation of this economically-important edible mushroom. Here, we identified the A mating-type locus from the first draft genome sequence of L. edodes and characterized multiple alleles from different monokaryotic strains. Two intron-length polymorphism markers were developed to facilitate rapid molecular determination of A mating-type. L. edodes sequences were compared with those of known tetrapolar and bipolar basidiomycete species. The A mating-type genes are conserved at the homeodomain region across the order Agaricales. However, we observed unique genomic organization of the locus in L. edodes which exhibits atypical gene order and multiple repetitive elements around its A locus. To our knowledge, this is the first known exception among Homobasidiomycetes, in which the mitochondrial intermediate peptidase (mip) gene is not closely linked to A locus.     

Metformin and low levels of thyroid-stimulating hormone in patients with type 2 diabetes mellitus

Background:

Small cross-sectional studies have suggested that metformin, a first-line oral hypoglycemic agent, may lower thyroid-stimulating hormone (TSH) levels. Our objective was to determine whether the use of metformin monotherapy, when compared with sulfonylurea monotherapy, is associated with an increased risk of low TSH levels (< 0.4 mIU/L) in patients with type 2 diabetes mellitus.

Methods:

Using the Clinical Practice Research Datalink, we identified patients who began receiving metformin or sulfonylurea monotherapy between Jan. 1, 1988, and Dec. 31, 2012. We assembled 2 subcohorts of patients with treated hypothyroidism or euthyroidism, and followed them until Mar. 31, 2013. We used Cox proportional hazards models to evaluate the association of low TSH levels with metformin monotherapy, compared with sulfonylurea monotherapy, in each subcohort.

Results:

A total of 5689 patients with treated hypothyroidism and 59 937 euthyroid patients were included in the subcohorts. Among patients with treated hypothyroidism, 495 events of low TSH levels were observed during follow-up (incidence rate 119.7/1000 person-years). In the euthyroid group, 322 events of low TSH levels were observed (incidence rate 4.5/1000 person-years). Compared with sulfonylurea monotherapy, metformin monotherapy was associated with a 55% increased risk of low TSH levels in patients with treated hypothyroidism (incidence rate 79.5/1000 person-years v. 125.2/1000 person-years, adjusted hazard ratio [HR] 1.55, 95% confidence interval [CI] 1.09–2.20), with the highest risk in the 90–180 days after initiation (adjusted HR 2.30, 95% CI 1.00–5.29). No association was observed in euthyroid patients (adjusted HR 0.97, 95% CI 0.69–1.36).

Interpretation:

In this longitudinal population-based study, metformin use was associated with an increased incidence of low TSH levels in patients with treated hypothyroidism, but not in euthyroid patients. The clinical consequences of this need further investigation.Metformin, a first-line oral hypoglycemic agent for the treatment of type 2 diabetes mellitus, improves hepatic insulin resistance and reduces glucose production.¹ However, despite its excellent safety profile,² studies have suggested that its use may lower thyroid-stimulating hormone (TSH) levels in patients with diabetes and hypothyroidism.^3–9 In some studies, the use of metformin was associated with reductions in TSH levels below the reference range,^4–7 potentially exposing patients to the harmful consequences of subclinical hyperthyroidism (e.g., cardiovascular conditions and fractures¹⁰). In contrast, metformin was not associated with changes to TSH levels in euthyroid patients.¹¹ Given the methodologic shortcomings of the few studies conducted to date (i.e., small samples, cross-sectional designs and no active comparator), it remains uncertain whether the use of metformin is associated with an increased risk of low TSH levels in patients with hypothyroidism or euthyroidism and type 2 diabetes.Given the widespread use of metformin in patients with type 2 diabetes and the potential negative consequences of low TSH levels, there is a need to assess the incidence and magnitude of this biochemical event in the natural setting of clinical practice. Thus, the objective of this large population-based study was to determine whether the use of metformin monotherapy, when compared with sulfonylurea monotherapy, is associated with an increased risk of low TSH levels (< 0.4 mIU/L) in patients with treated hypothyroidism or euthyroidism and type 2 diabetes.     

Exo70E2 is essential for exocyst subunit recruitment and EXPO formation in both plants and animals

In contrast to a single copy of Exo70 in yeast and mammals, the Arabidopsis genome contains 23 paralogues of Exo70 (AtExo70). Using AtExo70E2 and its GFP fusion as probes, we recently identified a novel double-membrane organelle termed exocyst-positive organelle (EXPO) that mediates an unconventional protein secretion in plant cells. Here we further demonstrate that AtExo70E2 is essential for exocyst subunit recruitment and for EXPO formation in both plants and animals. By performing transient expression in Arabidopsis protoplasts, we established that a number of exocyst subunits (especially the members of the Sec family) are unable to be recruited to EXPO in the absence of AtExo70E2. The paralogue AtExo70A1 is unable to substitute for AtExo70E2 in this regard. Fluorescence resonance energy transfer assay and bimolecular fluorescence complementation analyses confirm the interaction between AtExo70E2 and Sec6 and Sec10. AtExo70E2, but not its yeast counterpart, is also capable of inducing EXPO formation in an animal cell line (HEK293A cells). Electron microscopy confirms the presence of double-membraned, EXPO-like structures in HEK293A cells expressing AtExo70E2. Inversely, neither human nor yeast Exo70 homologues cause the formation of EXPO in Arabidopsis protoplasts. These results point to a specific and crucial role for AtExo70E2 in EXPO formation.     

Comparative genomic analysis of clinical and environmental strains provides insight into the pathogenicity and evolution of Vibrio parahaemolyticus

Background

Vibrio parahaemolyticus is a Gram-negative halophilic bacterium. Infections with the bacterium could become systemic and can be life-threatening to immunocompromised individuals. Genome sequences of a few clinical isolates of V. parahaemolyticus are currently available, but the genome dynamics across the species and virulence potential of environmental strains on a genome-scale have not been described before.

Results

Here we present genome sequences of four V. parahaemolyticus clinical strains from stool samples of patients and five environmental strains in Hong Kong. Phylogenomics analysis based on single nucleotide polymorphisms revealed a clear distinction between the clinical and environmental isolates. A new gene cluster belonging to the biofilm associated proteins of V. parahaemolyticus was found in clincial strains. In addition, a novel small genomic island frequently found among clinical isolates was reported. A few environmental strains were found harboring virulence genes and prophage elements, indicating their virulence potential. A unique biphenyl degradation pathway was also reported. A database for V. parahaemolyticus (http://kwanlab.bio.cuhk.edu.hk/vp) was constructed here as a platform to access and analyze genome sequences and annotations of the bacterium.

Conclusions

We have performed a comparative genomics analysis of clinical and environmental strains of V. parahaemolyticus. Our analyses could facilitate understanding of the phylogenetic diversity and niche adaptation of this bacterium.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1135) contains supplementary material, which is available to authorized users.     

Composition of Bacterial Assemblages in Different Components of Reed Warbler Nests and a Possible Role of Egg Incubation in Pathogen Regulation

Bacteria play a central role in animal health. Yet, little is known about the acquisition of bacteria and the extent to which bacteria are acquired from different environmental sources. For example, bird nests host diverse bacteria associated with the eggs, nestlings and nesting material, but previous research has typically focussed on only a limited number of nest components at a time. It therefore remains unknown to what extent bacteria are transmitted between these components. Using both molecular and culture techniques, we characterised nest-associated bacterial assemblages throughout the entire nesting cycle of reed warblers by sampling bacteria on eggs before and during incubation, within nestling faeces, and on the nesting material of post-breeding nests. We found that bacterial assemblages clustered by nest component. Yet some overlap existed between nest components, suggesting that bacterial transmission across components is likely to occur. Eggs and nestlings from the same nest harboured more similar bacteria than expected by chance, suggesting an influence of environment or genetics on bacterial assemblages. Bacterial loads were not lower on incubated eggs. Instead, incubation was associated with a change in the structure of assemblages, including a decrease in potentially-harmful Gram-negative bacteria. In addition we show for the first time, that incubation is associated with the complete extinction of harmful haemolytic bacteria. Overall, our study appears to be the first to demonstrate differences in bacterial assemblages between bird nest components. In addition, we highlight the complexity of nest bacterial assemblages and provide new insights into the benefits of incubation.