Comparison of Gold and Silver/Gold Bimetallic Surface for Highly Sensitive Near-infrared SPR Sensor at 1550 nm

A large majority of surface plasmon resonance (SPR) sensors reported in the literature are designed to operate in the visible electromagnetic spectrum. However, the near-infrared, particularly at the telecommunications wavelength of 1550 nm, is also especially attractive for SPR sensing applications. In fact, SPR sensors operating in this region benefit from narrower resonance and deeper field penetration. In this paper, we report a theoretical and experimental study of an SPR sensor operating at a fixed wavelength of 1550 nm. The influence of the choice of metals and the interrogation methods on the sensitivity of the resulting SPR sensor is investigated. Two types of sensor chips (simple gold (Au) and bimetallic silver/Au structure) and three interrogation methods (monitoring of the position of the reflectivity minimum, the position of the centroid, and the intensity evolution of the reflectivity) are examined. We show that a refractive index resolution of 2.7?×?10^?6 refractive index unit can be easily obtained, and with further optimization of the measurement system, the ultimate limit of detection is expected to be even lowered. Therefore, the approach discussed here already shows a promising potential for highly sensitive SPR sensors.     

Pathology Associated with AAV Mediated Expression of Beta Amyloid or C100 in Adult Mouse Hippocampus and Cerebellum

Accumulation of beta amyloid (Aβ) in the brain is a primary feature of Alzheimer’s disease (AD) but the exact molecular mechanisms by which Aβ exerts its toxic actions are not yet entirely clear. We documented pathological changes 3 and 6 months after localised injection of recombinant, bi-cistronic adeno-associated viral vectors (rAAV2) expressing human Aβ40-GFP, Aβ42-GFP, C100-GFP or C100^V717F-GFP into the hippocampus and cerebellum of 8 week old male mice. Injection of all rAAV2 vectors resulted in wide-spread transduction within the hippocampus and cerebellum, as shown by expression of transgene mRNA and GFP protein. Despite the lack of accumulation of Aβ protein after injection with AAV vectors, injection of rAAV2-Aβ42-GFP and rAAV2- C100^V717F-GFP into the hippocampus resulted in significantly increased microgliosis and altered permeability of the blood brain barrier, the latter revealed by high levels of immunoglobulin G (IgG) around the injection site and the presence of IgG positive cells. In comparison, injection of rAAV2-Aβ40-GFP and rAAV2-C100-GFP into the hippocampus resulted in substantially less neuropathology. Injection of rAAV2 vectors into the cerebellum resulted in similar types of pathological changes, but to a lesser degree. The use of viral vectors to express different types of Aβ and C100 is a powerful technique with which to examine the direct in vivo consequences of Aβ expression in different regions of the mature nervous system and will allow experimentation and analysis of pathological AD-like changes in a broader range of species other than mouse.     

Thermochemical transformation of sulfur compounds in Japanese domestic Allium, Allium victorialis L

Sulfur compounds contributed to the health promotion in Allium species are produced via enzymic and thermal reactions. Potent antithrombotic agents which have been identified as allyl trisulfides, dithiins, and ajoene in garlic (A. sativum) and caucas (A. victorialis) are thermochemically transformed from allicin (allyl 2-propenethiosulfinate). The leaves and stems of Japanese domestic Allium plant, A. victorialis L. which is widely distributed in the northern part of Japan, under the name "Gyoja-ninniku" is a nutritious vegetable. The significant flavor compounds of caucas are methyl allyl disulfide (Chinese chive odor), diallyl disulfide (garlic-like odor), and dimethyl disulfide and methyl allyl trisulfide (pickles-like odor) among more than 85 peaks on the gas chromatogram. 2-Vinyl-4H-1,3-dithiin and 3,4-dihydro-3-vinyl-1,2-dithiin as platelet aggregation inhibitors were found eliminated in dichloromethane extract of caucas. The significant health promoting factors, allyl trisulfides and dithiins were relatively increased when caucas was cooked on a frying pan.     

Dependence of alignment direction on magnitude of strain in esophageal smooth muscle cells

The response of cells in vitro to mechanical forces has been the subject of much research using devices to exert controlled mechanical stimulation on cultured cells or isolated tissue. In this study, esophageal smooth muscle cells were seeded on flexible polyurethane membranes to form a confluent cell layer. The cells were then subjected to uniform cyclic stretch of varying magnitudes at a frequency of approximately five cycles per minute in a custom made mechatronic bioreactor, providing similar strains experienced in the in vivo mechanical environment of the esophagus. The results show that the orientation response is dependent on the magnitude of cyclic stretch applied. Smooth muscle cells showed parallel alignment to the force direction at low cyclic strains (2%) compared to the hill‐valley morphology of static controls. At higher strains (5% and 10% magnitude), the cells exhibited a consistent alignment perpendicular to the strain. To our knowledge, this is the first time that the alignment direction's dependence on strain magnitude has been demonstrated. MTS analysis indicated that cell metabolism was reduced when mechanical strain was applied, and proliferation was inhibited by mechanical strain. Protein expression indicates a decrease in smooth muscle α‐actin, indicative of changes in cell phenotype, an increase in vimentin, which is associated with increased cell motility, and an increase in desmin, indicating differentiation in stimulated cells. Biotechnol. Bioeng. 2009;102: 1703–1711. © 2008 Wiley Periodicals, Inc.     

Probabilistic alignments with quality scores: an application to short-read mapping toward accurate SNP/indel detection

MOTIVATION: Recent studies have revealed the importance of considering quality scores of reads generated by next-generation sequence (NGS) platforms in various downstream analyses. It is also known that probabilistic alignments based on marginal probabilities (e.g. aligned-column and/or gap probabilities) provide more accurate alignment than conventional maximum score-based alignment. There exists, however, no study about probabilistic alignment that considers quality scores explicitly, although the method is expected to be useful in SNP/indel callers and bisulfite mapping, because accurate estimation of aligned columns or gaps is important in those analyses. RESULTS: In this study, we propose methods of probabilistic alignment that consider quality scores of (one of) the sequences as well as a usual score matrix. The method is based on posterior decoding techniques in which various marginal probabilities are computed from a probabilistic model of alignments with quality scores, and can arbitrarily trade-off sensitivity and positive predictive value (PPV) of prediction (aligned columns and gaps). The method is directly applicable to read mapping (alignment) toward accurate detection of SNPs and indels. Several computational experiments indicated that probabilistic alignments can estimate aligned columns and gaps accurately, compared with other mapping algorithms e.g. SHRiMP2, Stampy, BWA and Novoalign. The study also suggested that our approach yields favorable precision for SNP/indel calling.     

Unzipping the cuticle of the human hair shaft to obtain micron/nano keratin filaments

An attempt has been made to obtain intact individual keratin filaments of various levels from micron cortical, micron macrofibril to nano intermediate filament and polypeptide alpha-helix from the human hair shaft. The feasibility of this initiative has been largely demonstrated by finding that there is a longitudinal seam/zipper on the cuticle of the human hair shaft, which can be unzipped by certain solvents such as performic acid and urea, allowing one to use an anatomical approach to separate intact individual micron/nano filaments. Micron cortical and macrofibril filaments have been obtained. It is also found that the cortical filaments are twisted together to form a yarn, giving rise to the strength for the hair shaft; and that individual cortical filaments are often 2-2 paired in a similar structure to the double helix.     

Acoustic structure of male loud-calls support molecular phylogeny of Sumatran and Javanese leaf monkeys (genus <Emphasis Type="Italic">Presbytis</Emphasis>)

Background  

The degree to which loud-calls in nonhuman primates can be used as a reliable taxonomic tool is the subject of ongoing debate. A recent study on crested gibbons showed that these species can be well distinguished by their songs; even at the population level the authors found reliable differences. Although there are some further studies on geographic and phylogenetic differences in loud-calls of nonhuman primate species, it is unclear to what extent loud-calls of other species have a similar close relation between acoustic structure, phylogenetic relatedness and geographic distance. We therefore conducted a field survey in 19 locations on Sumatra, Java and the Mentawai islands to record male loud-calls of wild surilis (Presbytis), a genus of Asian leaf monkeys (Colobinae) with disputed taxanomy, and compared the structure of their loud-calls with a molecular genetic analysis.     

Comparison of l‐tyrosine containing dipeptides reveals maximum ATP availability for l‐prolyl‐l‐tyrosine in CHO cells

Increasing markets for biopharmaceuticals, including monoclonal antibodies, have triggered a permanent need for bioprocess optimization. Biochemical engineering approaches often include the optimization of basal and feed media to improve productivities of Chinese hamster ovary (CHO) cell cultures. Often, l ‐tyrosine is added as dipeptide to deal with its poor solubility at neutral pH. Showcasing IgG1 production with CHO cells, we investigated the supplementation of three l ‐tyrosine (TYR, Y) containing dipeptides: glycyl‐l ‐tyrosine (GY), l ‐tyrosyl‐l ‐valine (YV), and l ‐prolyl‐l ‐tyrosine (PY). While GY and YV led to almost no phenotypic and metabolic differences compared to reference samples, PY significantly amplified TYR uptake thus maximizing related catabolic activity. Consequently, ATP formation was roughly four times higher upon PY application than in reference samples.