Development of a colorimetric assay for rapid quantitative measurement of clavulanic acid in microbial samples

We developed a colorimetric assay to quantify clavulanic acid (CA) in culture broth of Streptomyces clavuligerus, to facilitate screening of a large number of S. clavuligerus mutants. The assay is based on a β-lactamase-catalyzed reaction, in which the yellow substrate nitrocefin (λ _max=390 nm) is converted to a red product (λ _max=486 nm). Since CA can irreversibly inhibit β-lactamase activity, the level of CA in a sample can be measured as a function of the A ₃₉₀/A ₄₈₆ ratio in the assay mixture. The sensitivity and detection window of the assay were determined to be 50 μg L⁻¹ and 50 μg L⁻¹ to 10 mg L⁻¹, respectively. The reliability of the assay was confirmed by comparing assay results with those obtained by HPLC. The assay was used to screen a pool of 65 S. clavuligerus mutants and was reliable for identifying CA over-producing mutants. Therefore, the assay saves time and labor in large-scale mutant screening and evaluation tasks. The detection window and the reliability of this assay are markedly better than those of previously reported CA assays. This assay method is suitable for high throughput screening of microbial samples and allows direct visual observation of CA levels on agar plates.     

Biomechanism of adhesion in gecko setae

The study of the adhesion of millions of setae on the toes of geckos has been advanced in recent years with the emergence of new technology and measurement methods. The theory of the mechanism of adhesion by van der Waals forces is now accepted and broadly understood. However, this paper presents limitations of this theory and gives a new hypothesis of the biomechanism of gecko adhesion. The findings are obtained through measurements of the magnitude of the adhesion of setae under three different conditions, to show the close relationship between adhesion and status of the setae. They are reinforced by demonstrating two setal structures, follicle cells and hair, the former making the setae capable of producing bioelectrical charges, which play an important role in attachment and detachment processes. It is shown that the abundant muscular tissues at the base of the setae cells, which are controlled by peripheral nerves, are instrumental in producing the foot movement involved in attachment and detachment. Our study will further uncover the adhesion mechanism of geckos, and provide new ideas for designing and fabricating synthetic setae.     

Engineering imaging probes and molecular machines for nanomedicine

Nanomedicine is an emerging field that integrates nanotechnology, biomolecular engineering, life sciences and medicine; it is expected to produce major breakthroughs in medical diagnostics and therapeutics. Due to the size-compatibility of nano-scale structures and devices with proteins and nucleic acids, the design, synthesis and application of nanoprobes, nanocarriers and nanomachines provide unprecedented opportunities for achieving a better control of biological processes, and drastic improvements in disease detection, therapy, and prevention. Recent advances in nanomedicine include the development of functional nanoparticle based molecular imaging probes, nano-structured materials as drug/gene carriers for in vivo delivery, and engineered molecular machines for treating single-gene disorders. This review focuses on the development of molecular imaging probes and engineered nucleases for nanomedicine, including quantum dot bioconjugates, quantum dot-fluorescent protein FRET probes, molecular beacons, magnetic and gold nanoparticle based imaging contrast agents, and the design and validation of zinc finger nucleases (ZFNs) and TAL effector nucleases (TALENs) for gene targeting. The challenges in translating nanomedicine approaches to clinical applications are discussed.     

Genetic diversity and phylogeny of rhizobia isolated from Caragana microphylla growing in desert soil in Ningxia, China

Rhizobia are soil bacteria with the capacity to induce nitrogen-fixing nodules on the roots or stems of legume plants. A total of 40 bacterial isolates from the root nodules of Caragana microphylla growing in desert soil in Ningxia, China, were analyzed for genetic diversity and phylogenetic position. These isolates were classified into 7 types of 16S ribosomal DNA (rDNA) using polymerase chain reaction-restriction fragment length polymorphism analysis. They were grouped into 4 clades, Rhizobium-Agrobacterium, Sinorhizobium, Phyllobacterium, and Bradyrhizobium, when the phylogenies of 16S rDNA, recA, and atpD genes were applied. Phylogenetic analysis showed that the tree generated from the 16S rDNA sequencing agreed with that produced from the recA and atpD genes. By analyzing phylogenetic relationship using the 3 loci, the isolates in the branches of Phyllobacterium and Sinorhizobium could be identified as P. brassicacearum and S. meliloti. The isolates in the branch of Rhizobium-Agrobacterium were the most abundant microsymbiont of C. microphylla and were designated R. leguminosarum, R. galegae, R. alamii, and A. tumefaciens. Two isolates with low sequence similarity to the known species of Bradyrhizobium might be novel species in this genus.     

Correlation of Y-chromosome multiple segmental deletions and chromosomal anomalies in non-obstructive azoospermic males from northeastern China

We investigated the frequency and types of Y-chromosome microdeletions and chromosomal anomalies in non-obstructive azoospermic and severely oligozoospermic infertile males in northeastern China. The sample consisted of 519 infertile males (456 azoospermic, 63 severely oligozoospermic). PCR assays for Y-chromosome microdeletions and chromosome analysis were performed on all patients and controls. Array-comparative genomic hybridization was performed for three patients with chromosomal anomalies. Fifty-nine of 519 patients (11.37%) had Y-chromosome microdeletions. Microdeletions were found in 11.18% (51/456) of the non-obstructive azoospermic patients and in 12.7% (8/63) of the severely oligozoospermic patients. Eleven of 51 non-obstructive azoospermic patients with Y-chromosome microdeletions had multiple segmental deletions in the AZFb+c regions; four of these patients had chromosomal anomalies. Our sample from northeastern China had a higher frequency of microdeletions among severely oligozoospermic than among non-obstructive azoospermic males.     

Phylogenetic analysis of Chinese sheeppox and goatpox virus isolates

Background

Sheeppox virus (SPPV) and goatpox virus (GTPV), members of the Capripoxvirus genus of the Poxviridae family are causative agents of sheep pox and goat pox respectively, which are important contagious diseases and endemic in central and northern Africa, the Middle and Far East, and the Indian sub-continent. Both sheep pox and goat pox can cause wool and hide damage, and reduce the production of mutton and milk, which may result in significant economic losses and threaten the stockbreeding. In this study, three SPPVs and two GTPVs were collected from China in 2009 and 2011. We described the sequence features and phylogenetic analysis of the P32 gene, GPCR gene and RPO30 gene of the SPPVs and GTPVs to reveal their genetic relatedness.

Results

Sequence and phylogenetic analysis showed that there was a close relationship among SPPV/GanS/2/2011/China, SPPV/GanS/1/2011/China and SPPV/NingX/2009/China. They were clustered on the same SPPV clade. GTPV/HuB/2009/China and GS-V1 belonged to the GTPV lineage. GS-V1 was closely related to other GTPV vaccine strains. GTPV/HuB/2009/China and GS-V1 were clustered with GTPVs from China and some southern Asian countries.

Conclusion

This study may expand the datum for spread trend research of Chinese SPPVs and GTPVs, meanwhile provide theoretical references to improve the preventive and control strategy.

     

Systems analysis of eleven rodent disease models reveals an inflammatome signature and key drivers

Common inflammatome gene signatures as well as disease‐specific signatures were identified by analyzing 12 expression profiling data sets derived from 9 different tissues isolated from 11 rodent inflammatory disease models. The inflammatome signature significantly overlaps with known drug targets and co‐expressed gene modules linked to metabolic disorders and cancer. A large proportion of genes in this signature are tightly connected in tissue‐specific Bayesian networks (BNs) built from multiple independent mouse and human cohorts. Both the inflammatome signature and the corresponding consensus BNs are highly enriched for immune response‐related genes supported as causal for adiposity, adipokine, diabetes, aortic lesion, bone, muscle, and cholesterol traits, suggesting the causal nature of the inflammatome for a variety of diseases. Integration of this inflammatome signature with the BNs uncovered 151 key drivers that appeared to be more biologically important than the non‐drivers in terms of their impact on disease phenotypes. The identification of this inflammatome signature, its network architecture, and key drivers not only highlights the shared etiology but also pinpoints potential targets for intervention of various common diseases.     

A transient parabiosis skin transplantation model in mice

Parabiosis-conjoined surgery to provide a shared circulation between two mice-has been previously developed to study the hematopoietic system. This protocol describes the use of parabiosis for efficient transplantation of skin from a transgenic to a wild-type mouse. It can be used to study the role of stromal cells in a spontaneous model of distant cancer dissemination (metastasis). We have recently shown that primary tumor-derived stromal cells may facilitate metastasis by providing a provisional stroma at the secondary site. Studying the role of primary tumor-derived stroma cells requires methods for distinguishing and targeting stromal cells originating from the primary tumor versus their counterparts in the metastatic site. Parabiosis may also be used, taking advantage of the shared circulation between the parabiosed mice, to study tumor metastasis from one parabiont to another, or to investigate the role of circulating inflammatory cells or stem cells. Studying the role of stromal cells in metastasis using this model typically takes up to 11 weeks.     

Host tree-recurrence of wood-decaying Dacrymycetes

Host-recurrence of wood-decaying polypores has been substantiated and some species of the class Dacrymycetes, consisting of wood-decaying jelly fungi, occur recurrently on coniferous and broad-leaved tree wood. However, there has been no quantitative analysis for Dacrymycetes. To evaluate their host-recurrence, the fruit body occurrence of Dacrymycetes was investigated at 60 sites, including 13 core sampling sites. A total of 577 samples of 28 species were collected. Principal component analysis revealed characteristic communities on conifers and broad-leaved trees. Binomial tests showed that 12 and four Dacrymycetes species occurred significantly more frequently on conifers and broad-leaved trees, respectively. Of these host-recurrent species, eight and two species exclusively occurred on conifers and broad-leaved trees, respectively, suggesting that some Dacrymycetes species have a strict host-recurrence on these tree groups.