Dibenzocyclooctadiene lignans from Kadsura philippinensis

Lignans with the dibenzocyclooctadiene skeleton, kadsuphilols I-L, and one C₁₉-homolignan, kadsuphilol M, were isolated by chromatographic fractionation of an ethyl acetate extract of the aerial parts of Kadsura philippinensis. Their structures were elucidated through extensive spectroscopic methods, including HRESIMS and 2D NMR experiments (HMQC, COSY and HMBC). The stereochemistry at the chiral centers and the biphenyl moist, were determined using NOESY, as well as analysis of CD spectra, respectively. The relative configuration of heteroclitin J was confirmed by single crystal X-ray crystallographic analysis. The in vitro radical-scavenging activities of these compounds by using DPPH were evaluated.     

Enhanced levan production using chitin-binding domain fused levansucrase immobilized on chitin beads

Levan is a homopolymer of fructose which can be produced by the transfructosylation reaction of levansucrase (EC 2.4.1.10) from sucrose. In particular, levan synthesized by Zymomonas mobilis has found a wide and potential application in the food and pharmaceutical industry. In this study, the immobilization of Z. mobilis levansucrae (encoded by levU) was attempted for repeated production of levan. By fusion levU with the chitin-binding domain (ChBD), the hybrid protein was overproduced in a soluble form in Escherichia coli. After direct absorption of the protein mixture from E. coli onto chitin beads, levansucrase tagged with ChBD was found to specifically attach to the affinity matrix. Subsequent analysis indicated that the linkage between the enzyme and chitin beads was substantially stable. Furthermore, with 20% sucrose, the production of levan was enhanced by 60% to reach 83 g/l using the immobilized levansucrase as compared to that by the free counterpart. This production yield accounts for 41.5% conversion yield (g/g) on the basis of sucrose. After all, a total production of levan with 480 g/l was obtained by recycling of the immobilized enzyme for seven times. It is apparent that this approach offers a promising way for levan production by Z. mobilis levansucrase immobilized on chitin beads.     

Target selection and annotation for the structural genomics of the amidohydrolase and enolase superfamilies

To study the substrate specificity of enzymes, we use the amidohydrolase and enolase superfamilies as model systems; members of these superfamilies share a common TIM barrel fold and catalyze a wide range of chemical reactions. Here, we describe a collaboration between the Enzyme Specificity Consortium (ENSPEC) and the New York SGX Research Center for Structural Genomics (NYSGXRC) that aims to maximize the structural coverage of the amidohydrolase and enolase superfamilies. Using sequence- and structure-based protein comparisons, we first selected 535 target proteins from a variety of genomes for high-throughput structure determination by X-ray crystallography; 63 of these targets were not previously annotated as superfamily members. To date, 20 unique amidohydrolase and 41 unique enolase structures have been determined, increasing the fraction of sequences in the two superfamilies that can be modeled based on at least 30% sequence identity from 45% to 73%. We present case studies of proteins related to uronate isomerase (an amidohydrolase superfamily member) and mandelate racemase (an enolase superfamily member), to illustrate how this structure-focused approach can be used to generate hypotheses about sequence–structure–function relationships. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Rethinking ‘style’ for historians and philosophers of science: converging lessons from sexuality, translation, and East Asian studies

Historians and philosophers of science have furnished a wide array of theoretical-historiographical terms to emphasize the discontinuities among different systems of knowledge. Some of the most famous include Thomas Kuhn’s “paradigm”, Michel Foucault’s “episteme”, and the notion of “styles of reasoning” more recently developed by Ian Hacking and Arnold Davidson. This paper takes up this theoretical-historiographical thread by assessing the values and limitations of the notion of “style” for the historical and philosophical study of science. Specifically, reflecting on various methodological and theoretical concerns prompted by sexuality, translation, and East Asian studies, this paper argues that the heretofore ways in which historians and philosophers of science have used the notion of “style” are severely restricted in terms of its mere applicability to the intellectual history of Western science. The particular example of the translation of “homosexuality” into Chinese during the May Fourth era reveals that the notion of “style” has the potential of carrying a much more dynamic conceptual weight, as when used in “styles of argumentation”. The paper also engages briefly with the historiography of scientific “national styles” and ends with some concluding remarks on the limitations of “social histories from below” and the under appreciated importance of “epistemological histories of possibilities”.     

Polymorphism and selection of rpoS in pathogenic Escherichia coli

Background  

Though RpoS is important for survival of pathogenic Escherichia coli in natural environments, polymorphism in the rpoS gene is common. However, the causes of this polymorphism and consequential physiological effects on gene expression in pathogenic strains are not fully understood.     

Age-related plumage differences of Dunlins along the East Asian-Australasian Flyway

ABSTRACT.   For some populations of Dunlins ( Calidris alpina ), determining the age of individuals on the nonbreeding grounds can be difficult. This difficulty arises in part because some populations undergo their primary molt during the boreal summer, leaving adult and first-year Dunlins with similar amounts of abrasion on their primaries. Ageing Dunlins is further complicated by the presence of adults with buff-fringed, inner median coverts in some populations, a feature often used to age juvenile Dunlins. We examined a number of characteristics helpful in the ageing Dunlins at nonbreeding areas along the East Asian-Australasian Flyway, including: (1) the pattern of white fringes on the inner primary coverts, (2) the color of fringes on the inner median wing coverts, (3) the color of the tip on the carpal covert, (4) the presence or absence of a dark subterminal band on tertial or tertial coverts, and (5) remnants of alternate or juvenile plumage on the belly. Our results demonstrate that the pattern of white fringes on the inner primary coverts is an important character for ageing Dunlin along the East Asian-Australasian Flyway. In addition, we found that all characteristics used for ageing fade with time, and that breeding adults along the East Asian-Australasian Flyway are more difficult to age than adults elsewhere, in part due to the presence of "adult buff" coverts (ABCs) and in part because of the early timing of primary molt. Finally, we suggest that the presence of ABCs might be useful for differentiating the two Dunlin subspecies ( C. a. arcticola and C. a. pacifica ) occurring in Alaska.     

Specific variants in the MLH1 gene region may drive DNA methylation, loss of protein expression, and MSI-H colorectal cancer

Background

We previously identified an association between a mismatch repair gene, MLH1, promoter SNP (rs1800734) and microsatellite unstable (MSI-H) colorectal cancers (CRCs) in two samples. The current study expanded on this finding as we explored the genetic basis of DNA methylation in this region of chromosome 3. We hypothesized that specific polymorphisms in the MLH1 gene region predispose it to DNA methylation, resulting in the loss of MLH1 gene expression, mismatch-repair function, and consequently to genome-wide microsatellite instability.

Methodology/Principal Findings

We first tested our hypothesis in one sample from Ontario (901 cases, 1,097 controls) and replicated major findings in two additional samples from Newfoundland and Labrador (479 cases, 336 controls) and from Seattle (591 cases, 629 controls). Logistic regression was used to test for association between SNPs in the region of MLH1 and CRC, MSI-H CRC, MLH1 gene expression in CRC, and DNA methylation in CRC. The association between rs1800734 and MSI-H CRCs, previously reported in Ontario and Newfoundland, was replicated in the Seattle sample. Two additional SNPs, in strong linkage disequilibrium with rs1800734, showed strong associations with MLH1 promoter methylation, loss of MLH1 protein, and MSI-H CRC in all three samples. The logistic regression model of MSI-H CRC that included MLH1-promoter-methylation status and MLH1 immunohisotchemistry status fit most parsimoniously in all three samples combined. When rs1800734 was added to this model, its effect was not statistically significant (P-value  = 0.72 vs. 2.3×10⁻⁴ when the SNP was examined alone).

Conclusions/Significance

The observed association of rs1800734 with MSI-H CRC occurs through its effect on the MLH1 promoter methylation, MLH1 IHC deficiency, or both.     

Establishment of Protein Delivery Systems Targeting Podocytes

Background

Podocytes are uniquely structured cells that are critical to the kidney filtration barrier. Their anatomic location on the outer side of the glomerular capillaries expose podocytes to large quantities of both plasma and urinary components and thus are reachable for drug delivery. Recent years have made clear that interference with podocyte-specific disease pathways can modulate glomerular function and influence severity and progression of glomerular disease.

Methodology/Principal Findings

Here, we describe studies that show efficient transport of proteins into the mammalian cells mouse 3T3 fibroblasts and podocytes, utilizing an approach termed profection. We are using synthetic lipid structures that allow the safe packing of proteins or antibodies resulting in the subsequent delivery of protein into the cell. The uptake of lipid coated protein is facilitated by the intrinsic characteristic of cells such as podocytes to engulf particles that are physiologically retained in the extracellular matrix. Profection of the restriction enzyme MunI in 3T3 mouse fibroblasts caused an increase in DNA degradation. Moreover, purified proteins such as β-galactosidase and the large GTPase dynamin could be profected into podocytes using two different profection reagents with the success rate of 95–100%. The delivered β-galactosidase enzyme was properly folded and able to cleave its substrate X-gal in podocytes. Diseased podocytes are also potential recipients of protein cargo as we also delivered fluorophore labeled IgG into puromycin treated podocytes. We are currently optimizing our protocol for in vivo profection.

Conclusions

Protein transfer is developing as an exciting tool to study and target highly differentiated cells such as podocytes.     

Life cycle of the aquatic firefly Luciola ficta (Coleoptera: Lampyridae)

This research is the first to record the complete life history of the aquatic firefly Luciola ficta (Olivier) using a unique individual rearing method. Transparent containers (250 ml; height: 6 cm; bottom diameter: 8 cm; mouth diameter: 9.5 cm) were used to rear individuals from egg to adult in the laboratory, so that they could be observed throughout the whole life cycle. Larvae were fed on the meat of the water snail Cipangopaludina chinensis (Gray). Temperature ranged from 18 °C to 30 °C, relative humidity (RH) was 80 ± 5%, and the light:dark (L:D) ratio was 10:14. Of 80 eggs, 35 individuals completed their life cycle under these laboratory conditions in Jiji, Nantou County, Taiwan. The external morphological characteristics of each growing stage were described. Egg hatching rate was 95%. On average, one generation spanned 388.2 ± 25.7 days. The durations of egg, larva, climbing larva, cocoon, and adult stages were 19.1 ± 1.5 days, 328.9 ± 33.2 days, 10.9 ± 7.8 days, 14.7 ± 5.3 days, and 15.7 ± 5.2 days, respectively. The number of larval instars ranged from five to seven, with a modal value of six instars for males and seven instars for females. Female larval duration averaged 337.1 ± 31.2 days, which was higher than the 307.6 ± 34.1 days of the males. From January to December 2002, adult emergence peaked twice, with the main high peak appearing in April and the second peak occurring in August. The results of indoor rearing and of field investigations in Jiji, Nantou County, suggested that L. ficta is univoltine. Adult body length is negatively correlated with larval duration (P < 0.01). The life history traits of L. ficta show plasticity in adult occurrence, egg size, egg duration, larval duration, larval instars, and adult body length. Some variations were discussed in the context of survivorship in field habitats.