Homogenisation of water and sediment bacterial communities in a shallow lake (lake Balihe,China)

1. Planktonic and benthic bacterial communities hold central roles in the functioning of freshwater ecosystems and mediate key ecosystem services such as primary production and nutrient remineralisation. Although it is clear that such communities vary in composition both within and between lakes, the environmental factors and processes shaping the diversity and composition of freshwater bacteria are still not fully understood.
2. In order to assess seasonal and spatial variability in lake bacterial communities and identify environmental factors underpinning biogeographical patterns, we performed a large-scale sampling campaign with paired water and sediment sample collection at 18 locations during four seasons in Lake Balihe, a subtropical shallow fish-farming lake in mid-eastern China.
3. Pelagic and benthic bacterial communities were distinctly different in terms of diversity, taxonomic composition and community structure, with Actinobacteria, Bacteroidetes, Cyanobacteria and Alphaproteobacteria dominating lake water, and Acidobacteria, Bacteroidetes, Chloroflexi, Gammaproteobacteria and Deltaproteobacteria dominating sediment. Nevertheless, these two communities had stronger spatial concordance and overlap in taxa during spring and autumn seasons. Together, the main drivers of both the spatial and temporal variations in Lake Balihe bacterial communities were identified as water temperature, turbidity, nitrogen and phosphorus availability, and thermal stratification controlled by wind-mixing and activity of the dense farmed fish populations. Notably, populations affiliated with Firmicutes, known to be abundant in fish gut microbiome, were especially abundant in the summer season and locations where high fish biomass was found, suggesting a potential link between fish gut microbiome and the pelagic bacterial communities.
4. Our findings demonstrated seasonal homogenisation of pelagic and benthic bacterial communities linked to marked shifts in a set of seasonally-driven environmental variables including water temperature and nutrient availability.

     

Unusual Diheme Conformation of the Heme-Degrading Protein from Mycobacterium tuberculosis

Heme degradation plays a pivotal role in the availability of the essential nutrient, iron, in pathogenic bacteria. A previously unannotated protein from Mycobacterium tuberculosis, Rv3592, which shares homology to heme-degrading enzymes, has been identified. Biochemical analyses confirm that Rv3592, which we have termed MhuD (mycobacterial heme utilization, degrader), is able to bind and degrade heme. Interestingly, contrary to previously reported stoichiometry for the Staphylococcus aureus heme degraders, iron-regulated surface determinant (Isd)G and IsdI, MhuD has the ability to bind heme in a 1:2 protein-to-heme ratio, although the MhuD-diheme complex is inactive. Furthermore, the 1.75-Å crystal structure of the MhuD-diheme complex reveals two stacked hemes forming extensive contacts with residues in the active site. In particular, the solvent-exposed heme is axially liganded by His75 and is stacked planar upon the solvent-protected heme. The solvent-protected heme is coordinated by a chloride ion, which is, in turn, stabilized by Asn7. Structural comparison between MhuD-diheme and inactive IsdG and IsdI bound to only one highly distorted metalloporphyrin ring reveals that several residues located in α-helix 2 and the subsequent loop appear to be responsible for heme stoichiometric differences and suggest open and closed conformations for substrate entry and product exit.     

A nonheme iron(II) complex that models the redox cycle of lipoxygenase

The air-stable complex [Fe(6-Me3-TPA) (O2CAr)]+ [1; 6-Me3-TPA = tris(6-methyl-2-pyridylmethyl)amine] has been synthesized as a model for the iron(II) site of lipoxygenase. This iron(II) complex reacts with 0.5 equiv ROOH to form a yellow species, which has been formulated as [FeIII(OH)(6-Me3-TPA) (O2CAr)]+ (2) by electrospray mass spectrometry. Addition of more ROOH converts 2 into a purple species, which is characterized by electrospray ionization mass spectrometry and resonance Raman spectroscopy as [FeIII(OOR)(6-Me3-TPA)(O2CAr)]+. The purple species is metastable and decomposes via Fe-O bond homolysis to regenerate the starting iron(II) complex. These metal-centered transformations parallel the changes observed for lipoxygenase in its reaction with its product hydroperoxide.     

Distribution of integron-associated trimethoprim–sulfamethoxazole resistance determinants among Escherichia coli from humans and food-producing animals

Aims: To compare the distribution of integrons and trimethoprim–sulfamethoxazole resistance genes among Escherichia coli isolates from humans and food‐producing animals. Methods and Results: A collection of 174 multidrug‐resistant E. coli isolates obtained from faecal samples of food‐producing animals (n = 64) and humans (n = 59), and patients with urinary tract infections (n = 51) in Hong Kong during 2002–2004 were studied. The strains were analysed for their phylogenetic groups, the presence of sul genes (sul1 and sul2), integrons (intl1 and intl2) and class 1 integron‐associated dfr cassette genes by PCR, restriction enzyme analysis and sequencing. Integrons were identified in 110 (63·2%) isolates. The prevalence of integrons was significantly different according to the specimen sources (animal faecal 84·4%, human faecal 67·8% and human urinary 31·4%) and phylogenetic groups (B1 80·8%, A 77·6%, D 54·1% and B2 11·5%). Faecal isolates (both human and animal) are more likely to belong to group A and B1. In contrast, most urinary isolates were either groups B2 and D. Among dfr containing isolates, dfrA1 and dfrA12 were almost exclusively found in strains of phylogenetic groups A and B1; and were present in animal and human faecal isolates. In contrast, dfrA17 was found in both faecal and urinary isolates and comprised strains from all phylogenetic groups. The sul1 and sul2 genes were equally prevalent among the isolates irrespective of the specimen source and phylogenetic group status. Pulsed‐field gel electrophoresis analysis of isolates with identical cassette genes showed that they were genetically diverse. Conclusions: More animal faecal isolates carry class 1 integrons than human faecal and human urinary isolates, and the distribution of phylogenetic groups is common across animal and human faecal isolates but different from human urinary isolates. Significance and Impact of the Study: Commensal isolates from food‐producing animals are an important reservoir for integrons carrying antibiotic resistance genes.     

Sterol carrier protein-x gene and effects of sterol carrier protein-2 inhibitors on lipid uptake in <Emphasis Type="Italic">Manduca sexta</Emphasis>

Background  

Cholesterol uptake and transportation during the feeding larval stages are critical processes in insects because they are auxotrophic for exogenous (dietary) cholesterol. The midgut is the main site for cholesterol uptake in many insects. However, the molecular mechanism by which dietary cholesterol is digested and absorbed within the midgut and then released into the hemolymph for transportation to utilization or storage sites is poorly understood. Sterol carrier proteins (SCP), non-specific lipid transfer proteins, have been speculated to be involved in intracellular cholesterol transfer and metabolism in vertebrates. Based on the high degree of homology in the conserved sterol transfer domain to rat and human SCP-2, it is supposed that insect SCP-2 has a parallel function to vertebrate SCP-2.     

Active biocatalysts based on Candida rugosa lipase immobilized in vesicular silica

Vesicular silica (VS) with hierarchical structure was prepared by utilizing cationic surfactant cetyltrimethylammonium bromide (CTAB) and anionic surfactant sodium dodecyl sulfate (SDS) as the structure directing agents, and 1,3,5-triisopropylbenzene (TIPB) as the micelle expander. The resulting unilamellar and multilamellar VS with interlamellar mean mesopore size of 15–20 nm and shell thickness of 5–15 nm were used as supports for immobilization of Candida rugosa lipase (CRL) through physical adsorption. Possible mechanisms for the formation of VS and the immobilization of CRL on VS are proposed. N₂ adsorption-desorption experiments and Fourier transform infrared spectroscopy (FT-IR) measurements demonstrated that CRL was adsorbed into the curved channels of the VS. The catalytic activity, thermal stability, and reusability of VS immobilized CRL were assayed in phosphate buffer medium by hydrolysis of triacetin. The effects of pH and temperature on enzyme activity were also investigated. We report that VS immobilized CRL exhibited outstanding adaptability at higher pH and temperature, and excellent thermal stability and reusability compared with free CRL.     

Generation and basic characterization of a gene-trap knockout mouse model of Scn2a with a substantial reduction of voltage-gated sodium channel Nav1.2 expression

Large-scale genetic studies revealed SCN2A as one of the most frequently mutated genes in patients with neurodevelopmental disorders. SCN2A encodes for the voltage-gated sodium channel isoform 1.2 (Na_v1.2) expressed in the neurons of the central nervous system. Homozygous knockout (null) of Scn2a in mice is perinatal lethal, whereas heterozygous knockout of Scn2a (Scn2a^+/−) results in mild behavior abnormalities. The Na_v1.2 expression level in Scn2a^+/− mice is reported to be around 50–60% of the wild-type (WT) level, which indicates that a close to 50% reduction of Na_v1.2 expression may not be sufficient to lead to major behavioral phenotypes in mice. To overcome this barrier, we characterized a novel mouse model of severe Scn2a deficiency using a targeted gene-trap knockout (gtKO) strategy. This approach produces viable homozygous mice (Scn2a^gtKO/gtKO) that can survive to adulthood, with about a quarter of Na_v1.2 expression compared to WT mice. Innate behaviors like nesting and mating were profoundly disrupted in Scn2a^gtKO/gtKO mice. Notably, Scn2a^gtKO/gtKO mice have a significantly decreased center duration compared to WT in the open field test, suggesting anxiety-like behaviors in a novel, open space. These mice also have decreased thermal and cold tolerance. Additionally, Scn2a^gtKO/gtKO mice have increased fix-pattern exploration in the novel object exploration test and a slight increase in grooming, indicating a detectable level of repetitive behaviors. They bury little to no marbles and have decreased interaction with novel objects. These Scn2a gene-trap knockout mice thus provide a unique model to study pathophysiology associated with severe Scn2a deficiency.     

NK4 inhibits the proliferation and induces apoptosis of human rheumatoid arthritis synovial cells

Rheumatoid arthritis (RA) is a chronic inflammatory disease characterized by proliferation and insufficient apoptosis of synovial cells. NK4 is a hepatocyte growth factor antagonist and is implicated in cell proliferation, viability, and apoptosis of many tumour cells. This study aimed to investigate the role of NK4 in the regulation of human RA synovial cell proliferation and apoptosis. Fibroblast‐like synoviocytes (FLSs) isolated from RA patients and MH7A synovial cells were subjected to MTT, flow cytometry, and Western blot analysis. We found that NK4 suppressed cell proliferation through cell cycle arrest at the G0/G1 phase and induced apoptosis in RA synovial cells. Furthermore, NK4 altered the expression of cell cycle and apoptosis‐related proteins such as cyclin D1, cyclin B1, PCNA, p21, p53, Bcl‐2, Bax, cleaved caspase‐9, and cleaved caspase‐3. Additionally, NK4 reduced the phosphorylation level of NF‐κB p65 and upregulated the expression of sirt1, but did not change the levels of p38 and p‐p38 in RA‐FLS and MH7A cells. In conclusion, NK4 inhibits the proliferation and induces apoptosis of human RA synovial cells. NK4 is a promising therapeutic target for RA. We demonstrated that NK4 inhibited cell proliferation by inducing apoptosis and arresting cell cycle in RA‐FLS and MH7A cells. The apoptotic effects of NK4 may be mediated in part by decreasing Bcl‐2 protein level, increasing Bax and caspase 3 protein levels, and inhibiting NF‐κB signalling in RA‐FLS and MH7A cells. These findings reveal potential mechanism underlying the role of NK4 in RA synovial cells and suggest that NK4 is a promising agent for RA treatment.