The complete chloroplast genome sequence and phylogenetic analysis of the Bichetii grass Chlorophytum laxum (Asparagaceae).

Chlorophytum laxum of Asparagaceae is a valuable ornamental plant native to the tropical regions of Asia, Africa, and Australia. The plant also has medicinal properties and is used as source for folk medicine. Despite being commercially important, genetic studies of C. laxum are still limited. To expand the genomic information of this plant species, we sequenced, assembled, and characterized its complete chloroplast genome. The chloroplast genome was 153,678 bp in length, with a large single-copy region (83,225 bp) and a small single-copy region (18,031 bp) separated by a pair of inverted repeat regions (26,211 bp each). A total of 127 genes were predicted, including 81 protein-coding, 38 tRNA, and eight rRNA genes. The overall GC content was 37.3%. Based on current sampling size, phylogenetic analysis using the maximum likelihood based on the complete chloroplast genome sequence revealed that the relationship in Chlorophytum is well resolved; C. laxum was closely related to C. rhizopendulum.

Mechanical Resistance of the Largest Denticle on the Movable Claw of the Mud Crab.

Decapod crustaceans have tooth-like white denticles that are present only on the pinching side of the claws. In the mud crab, Scylla serrata, a huge denticle exists on the movable finger of the dominant claw. This is mainly used to crush the shells of the crab's staple food. The local mechanical properties, hardness (HIT) and elastic modulus (Er), of the peak and valley areas of the largest denticle were examined via a nanoindentation test. The microstructure and elemental composition were characterized using a scanning electron microscope and energy-dispersive X-ray spectroscopy. The striation patterns originating from a twisted plywood structure parallel to the surface were visible over the entire denticle. Most of the largest denticle was occupied by a hard area without phosphorus, and there was a soft layer corresponding to the endocuticle with phosphorus in the innermost part. The HIT of the denticle valley was about 40% lower than that of the denticle peak, and the thickness of the soft endocuticle of the denticle valley was five times thicker than that of the denticle peak. The HIT-Er map showed that the abrasion resistance of the denticle surface was vastly superior and was in the top class among organisms. The claw denticles were designed with the necessary characteristics in the necessary places, as related to the ecology of the mud crab.

Mechanical Resistance and Tissue Structure of Claw Denticles of Various Sizes in the Mud Crab, Scylla serrata.

Decapod crustaceans have tooth-like denticles on their claw fingers, which come into direct contact with predators and prey. Since the denticles are subject to more frequent and intense stress than other parts of the exoskeleton, they must be especially resistant to wear and abrasion. We clarified the mechanical resistance and tissue structure of the denticles arranged in a line on the fixed finger of the mud crab, which has huge claws. The denticles of the mud crab are small at the fingertip and become larger closer to the palm. The denticles have a twisted-plywood-pattern structure stacked parallel to the surface regardless of size, but the abrasion resistance strongly depends on the size of the denticles. Due to the dense tissue structure and calcification, the abrasion resistance increases as the denticle size increases, reaching its maximum at the denticle surface. The denticles of the mud crab have a tissue structure that prevents them from breaking when pinched. The high abrasion resistance of the large denticle surface is an essential feature for the frequent crushing of shellfish, which is the mud crab's staple food. The characteristics and tissue structure of the claw denticles on the mud crab may provide ideas for developing stronger, tougher materials.

Differentiation of Salmonella vaccinated and infected animals by serological detection of antibody to T3SS effector SsaK in an indirect ELISA.

The differentiation of animals that are vaccinated and those that are naturally infected with Salmonella is difficult by conventional serological tests. We have shown here an indirect Enzyme-linked immunosorbent assay for detection of Salmonella infection based on the presence of a Type III secretory effector SsaK in the sera.

Transcriptional landscape of Burkholderia pseudomallei cultured under environmental and clinical conditions.

Burkholderia pseudomallei, a Gram-negative pathogen, is the causative agent of melioidosis in humans. This bacterium can be isolated from the soil, stagnant and salt-water bodies, and human and animal clinical specimens. While extensive studies have contributed to our understanding of B. pseudomallei pathogenesis, little is known about how a harmless soil bacterium adapts when it shifts to a human host and exhibits its virulence. The bacterium's large genome encodes an array of factors that support the pathogen's ability to survive under stressful conditions, including the host's internal milieu. In this study, we performed comparative transcriptome analysis of B. pseudomallei cultured in human plasma versus soil extract media to provide insights into B. pseudomallei gene expression that governs bacterial adaptation and infectivity in the host. A total of 455 genes were differentially regulated; genes upregulated in B. pseudomallei grown in human plasma are involved in energy metabolism and cellular processes, whilst the downregulated genes mostly include fatty acid and phospholipid metabolism, amino acid biosynthesis and regulatory function proteins. Further analysis identified a significant upregulation of biofilm-related genes in plasma, which was validated using the biofilm-forming assay and scanning electron microscopy. In addition, genes encoding known virulence factors such as capsular polysaccharide and flagella were also overexpressed, suggesting an overall enhancement of B. pseudomallei virulence potential when present in human plasma. This ex vivo gene expression profile provides comprehensive information on B. pseudomallei's adaptation when shifted from the environment to the host. The induction of biofilm formation under host conditions may explain the difficulty in treating septic melioidosis.

Superconducting Joining Concept for Internal Magnesium Diffusion-Processed Magnesium Diboride Wires.

A superconducting joint of unreacted monofilament internal magnesium diffusion-processed magnesium diboride (MgB2) wires was fabricated by exploiting the phenomenon of magnesium diffusion into the boron layer inside the superconducting joint. Unprecedentedly, the joint was able to carry an almost identical transport current compared to the bare wire in a 2-7 T magnetic field at 20 K. The joint also exhibited very low joint resistance of 2.01 × 10-13 Ω in self-field at 20 K. Among commercially available superconductors, this work is the first to successfully realize a superconducting joint that is capable of transferring current from one conductor to another without any notable degradation under strong magnetic fields. This work demonstrates great potential to apply MgB2 in a range of practical applications, where superconducting joints are essential.

Quality evaluation of Pinellia tuber by LC-TOF/MS targeted to ephedrine.

Pinellia tuber (PTE, , , , , , , , ) is derived from the tuber of Pinellia ternata Breitenbach (Araceae), which is a crude drug used in traditional Japanese Kampo medicine for the purpose of antiemesis and expectoration. Since the separation of ephedrine from PTE in 1978, it has been listed as a PTE component in textbooks and internet information. Therefore, there are harmful effects on appropriate use in clinical practice because PTE is dealt with as a crude drug for doping target, and traditional Japanese Kampo medicine containing PTE must be carefully administered to the elderly. However, since the 1978 published report, there has not been any report on the isolation of ephedrine from PTE and the interpretation of biosynthesis remains questionable. In the present study, we analyzed the PTE samples in market distribution products by LC-TOF/MS. From the analysis of the result of ephedrine's m/z 148.113 [M + H-H2O]+, PTE was not detected (n = 55, detection limit: 0.5 ppb). Additionally, the tuber of P. tripartite (PTR, ), the tuber of P. pedatisecta (PPE, ), Arisaema Tuber (ART, ), and the tuber of Typhonium flagelliforme (TFI, ) that have a similar description to PTE were also not detected. Moreover, the genetic analysis of experimental samples showed that PTE is derived from P. ternata. Furthermore, our attempt to isolate ephedrine from PTE based on the past literature was unsuccessful. These results suggest that PTE in market distribution products may not contain ephedrine as a component.

Development of repeatable arrays of proteins using immobilized DNA microplate (RAPID-M) technology.

BACKGROUND: Protein microarrays have enormous potential as in vitro diagnostic tools stemming from the ability to miniaturize whilst generating maximum evaluation of diagnostically relevant information from minute amounts of sample. In this report, we present a method known as repeatable arrays of proteins using immobilized DNA microplates (RAPID-M) for high-throughput in situ protein microarray fabrication. The RAPID-M technology comprises of cell-free expression using immobilized DNA templates and in situ protein purification onto standard microarray slides. RESULTS: To demonstrate proof-of-concept, the repeatable protein arrays developed using our RAPID-M technology utilized green fluorescent protein (GFP) and a bacterial outer membrane protein (OmpA) as the proteins of interest for microarray fabrication. Cell-free expression of OmpA and GFP proteins using beads-immobilized DNA yielded protein bands with the expected molecular sizes of 27 and 30 kDa, respectively. We demonstrate that the beads-immobilized DNA remained stable for at least four cycles of cell-free expression. The OmpA and GFP proteins were still functional after in situ purification on the Ni-NTA microarray slide. CONCLUSION: The RAPID-M platform for protein microarray fabrication of two different representative proteins was successfully developed.

Global transcriptional analysis of Burkholderia pseudomallei high and low biofilm producers reveals insights into biofilm production and virulence.

BACKGROUND: Chronic bacterial infections occur as a result of the infecting pathogen's ability to live within a biofilm, hence escaping the detrimental effects of antibiotics and the immune defense system. Burkholderia pseudomallei, a gram-negative facultative pathogen, is distinctive in its ability to survive within phagocytic and non-phagocytic cells, to persist in vivo for many years and subsequently leading to relapse as well as the development of chronic disease. The capacity to persist has been attributed to the pathogen's ability to form biofilm. However, the underlying biology of B. pseudomallei biofilm development remains unresolved. RESULTS: We utilised RNA-Sequencing to identify genes that contribute to B. pseudomallei biofilm phenotype. Transcriptome analysis of a high and low biofilm producer identified 563 differentially regulated genes, implying that expression of ~9.5% of the total B. pseudomallei gene content was altered during biofilm formation. Genes involved in surface-associated motility, surface composition and cell wall biogenesis were over-expressed and probably play a role in the initial attachment of biofilms. Up-regulation of genes related to two component signal transduction systems and a denitrification enzyme pathway suggest that the B. pseudomallei high biofilm producer is able to sense the surrounding environmental conditions and regulate the production of extracellular polymeric substance matrix, a hallmark of microbial biofilm formation. CONCLUSIONS: The transcriptome profile described here provides the first comprehensive view of genes that contribute to the biofilm phenotype in B. pseudomallei.

High prevalence of hepatitis E virus in wild boar (Sus scrofa) in Yamaguchi Prefecture, Japan.

Hepatitis E virus (HEV) causes a food- and water-borne disease in humans, and Japanese wild boar (Sus scrofa leucomystax) meat is one of the most important sources of infection in Japan. We tested 113 serum samples from wild boar captured in Shimonoseki City, Yamaguchi Prefecture, Japan from 2010 to 2012. Serum samples were tested by enzyme-linked immunosorbent assay (ELISA) using virus-like particles as antigen and nested reverse-transcription PCR (RT-PCR). Anti-HEV IgG antibodies were detected in 47 of the 113 wild boar serum samples (42%), and HEV RNA was detected in five samples (4%). Sequence analysis showed that the five HEV isolates belonged to genotype 4, forming a cluster with a previous isolate from a human hepatitis E case in this region in 2011. These results indicate that wild boar in this region are infected with potentially pathogenic HEV at a high prevalence.

Observation of the magnetic skyrmion lattice in a MnSi nanowire by Lorentz TEM.

We report here the real-space observation of skyrmions and helical magnetic domains in a MnSi nanowire (NW) using Lorentz transmission electron microscopy (LTEM). The MnSi NW was thinned to a rectangular cross-section by focused-ion beam milling to reduce obstructive Fresnel fringes. Helimagnetic domains, imaged as alternating bright and dark contrast stripes with an 18 nm period, were observed to be the spontaneous magnetic ground state at 6 K, while the hexagonal skyrmion lattice (SkX) with a domain diameter of 18 nm was observed under a normal magnetic field of 210 mT. Temperature-dependent measurements reveal that the SkX is stable over a larger range in this NW system (6-35 K) compared to the narrow temperature regime of skyrmion phase in bulk MnSi (26-30 K) and thin films of MnSi (5-23 K).

Multiple-antigen ELISA for melioidosis--a novel approach to the improved serodiagnosis of melioidosis.

BACKGROUND: Burkholderia pseudomallei, the causative agent of melioidosis, is endemic to Southeast Asia and northern Australia. Clinical manifestations of disease are diverse, ranging from chronic infection to acute septicaemia. The current gold standard of diagnosis involves bacterial culture and identification which is time consuming and often too late for early medical intervention. Hence, rapid diagnosis of melioidosis is crucial for the successful management of melioidosis. METHODS: The study evaluated 4 purified B. pseudomallei recombinant proteins (TssD-5, Omp3, smBpF4 and Omp85) as potential diagnostic agents for melioidosis. A total of 68 sera samples from Malaysian melioidosis patients were screened for the presence of specific antibodies towards these proteins using enzyme-linked immunosorbent assay (ELISA). Sera from patients with various bacterial and viral infections but negative for B. pseudomallei, as well as sera from healthy individuals, were also included as non-melioidosis controls. The Mann Whitney test was performed to compare the statistical differences between melioidosis patients and the non-melioidosis controls. RESULTS: TssD-5 demonstrated the highest sensitivity of 71% followed by Omp3 (59%), smBpF4 (41%) and Omp85 (19%). All 4 antigens showed equally high specificity (89-96%). A cocktail of all 4 antigens resulted in slightly reduced sensitivity of 65% but improved specificity (99%). Multiple-antigen ELISA provided improved sensitivity of 88.2% whilst retaining good specificity (96%). There was minimal reactivity with sera from healthy individuals proposing the utility of these antigens to demarcate diseased from non-symptomatic individuals in an endemic country. CONCLUSIONS: TssD-5 demonstrated high detection sensitivity and specificity and the results were obtained within a few hours compared to time consuming culture and IFAT methods commonly used in a clinical setting. The use of multiple-antigens resulted in improved sensitivity (88.2%) whilst maintaining superior specificity. These data highlight the use of TssD-5 and other recombinant antigens tested in this study as potential serodiagnostic agents for melioidosis.

Function of feline signaling lymphocyte activation molecule as a receptor of canine distemper virus.

Morbilliviruses use signaling lymphocyte activation molecule (SLAM) as a receptor for their entry to cells. In this study, a complete gene encoding SLAM of a domestic cat was identified. The identity of feline SLAM with canine one was 73%, and feline SLAM formed the same cluster with those of carnivores. Furthermore, feline cell expressing feline SLAM supported growth of canine distemper virus (CDV) as well as that expressing canine one. These results indicated that feline SLAM can function as a receptor for morbilliviruses, and our established feline cells that express feline SLAM might be useful for analysis of morbilliviruses originated from felids.

Immunogenic Burkholderia pseudomallei outer membrane proteins as potential candidate vaccine targets.

BACKGROUND: Burkholderia pseudomallei is the causative agent of melioidosis, a disease of significant morbidity and mortality in both human and animals in endemic areas. There is no vaccine towards the bacterium available in the market, and the efficacy of many of the bacterium's surface and secreted proteins are currently being evaluated as vaccine candidates. METHODOLOGY/PRINCIPAL FINDINGS: With the availability of the B. pseudomallei whole genome sequence, we undertook to identify genes encoding the known immunogenic outer membrane protein A (OmpA). Twelve OmpA domains were identified and ORFs containing these domains were fully annotated. Of the 12 ORFs, two of these OmpAs, Omp3 and Omp7, were successfully cloned, expressed as soluble protein and purified. Both proteins were recognised by antibodies in melioidosis patients' sera by Western blot analysis. Purified soluble fractions of Omp3 and Omp7 were assessed for their ability to protect BALB/c mice against B. pseudomallei infection. Mice were immunised with either Omp3 or Omp7, subsequently challenged with 1x10(6) colony forming units (cfu) of B. pseudomallei via the intraperitoneal route, and examined daily for 21 days post-challenge. This pilot study has demonstrated that whilst all control unimmunised mice died by day 9 post-challenge, two mice (out of 4) from both immunised groups survived beyond 21 days post-infection. CONCLUSIONS/SIGNIFICANCE: We have demonstrated that B. pseudomallei OmpA proteins are immunogenic in mice as well as melioidosis patients and should be further assessed as potential vaccine candidates against B. pseudomallei infection.