Characterization of horse spleen apoferritin reactive lysines by MALDI-TOF mass spectrometry combined with enzymatic digestion

Ferritins are a class of iron storage protein spheres found mainly in the liver and spleen, which have attracted many research interests due to their unique structural features and biological properties. Recently, ferritin and apoferritin (ferritin devoid of the iron core), have been employed as chemically addressable nanoscale building blocks for functional materials development. However, the reactive residues of apoferritin or ferritin have never been specified and it is still unclear about the chemoselectivity of apoferritin towards different kinds of bioconjugation reagents. In this work, matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry combined with enzymatic digestion analysis was used to identify the reactive lysine residues of horse spleen apoferritin when conjugated with N-hydroxysuccinimide reagents. The result demonstrated that among all the lysine residues, K97, K83, K104, K67 and K143 are the reactive ones that can be addressed.     

Recognition of aminoacyl-tRNA: a common molecular mechanism revealed by cryo-EM

The accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by EF-Tu, which forms a ternary complex with aminoacyl(aa)-tRNA. To study the binding modes of different aa-tRNAs, we compared cryo-EM maps of the kirromycin-stalled ribosome bound with ternary complexes containing Phe-tRNA^Phe, Trp-tRNA^Trp, or Leu-tRNA^LeuI. The three maps suggest a common binding manner of cognate aa-tRNAs in their specific binding with both the ribosome and EF-Tu. All three aa-tRNAs have the same ‘loaded spring' conformation with a kink and twist between the D-stem and anticodon stem. The three complexes are similarly integrated in an interaction network, extending from the anticodon loop through h44 and protein S12 to the EF-Tu-binding CCA end of aa-tRNA, proposed to signal cognate codon–anticodon interaction to the GTPase centre and tune the accuracy of aa-tRNA selection.     

Assignment of MS-based metabolomic datasets via compound interaction pair mapping

Assignment of physical meaning to mass spectrometry (MS) data peaks is an important scientific challenge for metabolomics investigators. Improvements in instrumental mass accuracy reduce the number of spurious database matches, however, this alone is insufficient for accurate, unique high-throughput assignment. We present a method for clustering MS instrumental artifacts and a stochastic local search algorithm for the automated assignment of large, complex MS-based metabolomic datasets. Artifact peaks and their associated source peaks are grouped into “instrumental clusters.” Instrumental clusters, peaks grouped together by shared peak shape in the temporal domain, serve as a guide for the number of assignments necessary to completely explain a given dataset. We refine mass only assignments through the intersection of peak correlation pairs with a database of biochemically relevant interaction pairs. Further refinement is achieved through a stochastic local search optimization algorithm that selects individual assignments for each instrumental cluster. The algorithm works by choosing the peak assignment that maximally explains the connectivity of a given cluster. We demonstrate that this methodology provides a significant advantage over standard methods for the assignment of metabolites in a UPLC-MS diabetes dataset. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Weight regain and health-related quality of life in postmenopausal women

Weight loss improves health-related quality of life (HRQoL). However, regain after loss is common; little is known about the impact of weight regain on HRQoL in postmenopausal women. Woman on the Move through Activity and Nutrition (WOMAN) is a randomized lifestyle intervention trial of diet, physical activity, and weight loss in 508 postmenopausal women aged 52-62 years. This analysis focused on the women who lost > or =5 lb during the initial phase of the study, baseline to 6 months (n = 248). This cohort was divided into three groups based on subsequent weight change between 6 and 18 months: weight loss (WL; > or =5 lb loss), weight stable (WS; <+/-5 lb change), and weight regain (WR; > or =5 lb gain). HRQoL was measured at baseline, 6, and 18 months using the Short Form-36. Of the 248 women studied, 51 (21%) continued to lose weight after initial weight loss, while 127 (51%) maintained a stable weight, and 70 (28%) regained weight. Between baseline and 6 months, women in WR group had decreased mental health and social-functioning scores, while the WL and WS groups improved in these subscales. Between baseline and 18 months, energy improved most significantly in those with continued weight loss (P = 0.0003). Weight loss was correlated with a small to moderate improvement in perceived general health and energy, which was reversed by weight gain. Further study is needed to investigate the impact of a decline in mental health and social functioning on future weight regain.     

Survival of eastern oysters Crassostrea virginica from three lines following experimental challenge with bacterial pathogens

Shellfish production is often affected by bacterial pathogens that cause high losses in hatcheries and nurseries. We evaluated the relative survival of larvae and juveniles of 3 Crassostrea virginica oyster lines: (1) GHP, a Rhode Island line; (2) NEHY, a line resistant to dermo and multinucleated sphere X diseases; and (3) FLOWERS, a line resistant to Roseovarius oyster disease, experimental challenge with Vibrio spp. isolates RE22 and RE101, causative agents of bacillary necrosis in Pacific oyster larvae, and the type strain of Roseovarius crassostreae, causative agent of Roseovarius oyster disease. All of the isolates were able to induce significant mortalities in oyster larvae and juveniles. Susceptibility to bacterial challenge in larvae was significantly higher at 25 degrees C than at 20 degrees C. Susceptibility decreased with oyster age; mean survival time ranged from 24 h in oyster larvae to more than 6 wk in juveniles. Significant differences in susceptibility to bacterial challenge were observed between oyster lines; NEHY was the most resistant line overall. Extracellular products (ECPs) from Vibrio sp. RE22 and R. crassostreae, as well as viable bacteria, were toxic to hemocytes from the 3 oyster lines, suggesting that ECPs are involved in pathogenesis and that external and mucosal barriers to infection are major contributors to resistance to bacterial challenge. These protocols will be useful in the elucidation of mechanisms of bacterial pathogenesis and resistance to infection in oysters.     

Neurocognitive processing of esophageal central sensitization in the insula and cingulate gyrus

The cingulate and insular cortices are parts of the limbic system that process and modulate gastrointestinal sensory signals. We hypothesized that sensitization of these two limbic area may operate in esophageal sensitization. Thus the objective of the study was to elucidate the neurocognitive processing in the cingulate and insular cortices to mechanical stimulation of the proximal esophagus following infusion of acid or phosphate buffer solution (PBS) into the esophagus. Twenty-six studies (14 to acid and 12 to PBS infusion) were performed in 20 healthy subjects (18-35 yr) using high-resolution (2.5 x 2.5 x 2.5 mm(3) voxel size) functional MRI (fMRI). Paradigm-driven, 2-min fMRI scans were performed during randomly timed 15-s intervals of proximal esophageal barostatically controlled distentions and rest, before and after 30-min of distal esophageal acid or PBS perfusion (0.1 N HCl or 0.1 M PBS at 1 ml/min). Following distal esophageal acid infusion, at subliminal and liminal levels of proximal esophageal distentions, the number of activated voxels in both cingulate and insular cortices showed a significant increase compared with before acid infusion (P < 0.05). No statistically significant change in cortical activity was noted following PBS infusion. We conclude that 1) acid stimulation of the esophagus results in sensitization of the cingulate and insular cortices to subliminal and liminal nonpainful mechanical stimulations, and 2) these findings can have ramifications with regard to the mechanisms of some esophageal symptoms attributed to reflux disease.     

Headspace sorptive extraction and GC-TOFMS for the identification of volatile fungal metabolites

Volatiles from fungi cultivated in Petri dishes were collected by a simple headspace polydimethylsiloxane (PDMS) sorptive extraction technique (HSSE), thermally desorbed into a gas chromatographic capillary column and detected and identified by gas chromatography-time-of-flight mass spectrometry (GC-TOFMS). The method was used to compare metabolite profiles of seven species of fungi grown on two types of sterile agars - potato dextrose and Sabouraud dextrose. Three species from the genus Penicillium (P. italicum, P. camemberti, and P. roqueforti) and four outgroups, each from a different phylum (Saprolegnia sp.; Sordaria fimicola, wild-type; Coprinus cinereus; and Rhizopus stolonifer) were grown on the two types of agars and analyzed. Multivariate analysis (PCA) was used to determine whether separate classes of fungi can be distinguished from one another based on their metabolite profiles. PCA showed clear class separation between the three Penicillium samples and the outgroups. Slight differences were observed in metabolite profiles as a function of growth medium. HSSE/GC-TOFMS appears to be a relatively simple and accurate technique for classification of fungi based on their volatile metabolite profiles. The volatiles sampling technique reported here is non-destructive, so it can be applied with traditional methods for studying fungal growth and metabolism.     

Pattern of settlement and natural chimerism in the colonial urochordate Botryllus schlosseri

Colonies of the cosmopolitan urochordate Botryllus schlosseri that share one or both alleles at a single allorecognition locus (Fu/HC) and come into tissue contacts, may fuse and form a mixed entity, a chimera. Botryllus populations worldwide exhibit unprecedented extensive polymorphism at this locus, a result that restricts fusions to kin encounters. This study aims to compare spatiotemporal configurations in source and introduced B. schlosseri populations, residing on natural and man-made substrata, respectively. By using four microsatellite loci, we tested genetic consanguinity of colonies settled naturally along spatial vectors on both, natural (native populations) and man-made (introduced) substrates. Four populations were studied. Results revealed that B. schlosseri colonies, on both substrate types, assemble in groups of relatives that share similar microsatellite profiles. We suggest that this pattern of settlement promotes the formation of chimeras, which evoke conflicting interactions: cooperation between different somatic cell lines that constitute the colonial soma and competition between germ cells that inhabit the chimera gonads. Under natural conditions, the chimera may allow genetic flexibility that depends on joint genomic fitness of its partners. This is probably one of the life history characteristics that led to the worldwide distribution success of this species.     

Towards toxicity detection using a lab-on-chip based on the integration of MOEMS and whole-cell sensors

A lab-on-chip consisting of a unique integration of whole-cell sensors, a MOEMS (Micro-Opto-Electro-Mechanical-System) modulator, and solid-state photo-detectors was implemented for the first time. Whole-cell sensors were genetically engineered to express a bioluminescent reporter (lux) as a function of the lac promoter. The MOEMS modulator was designed to overcome the inherent low frequency noise of solid-state photo-detectors by means of a previously reported modulation technique, named IHOS (Integrated Heterodyne Optical System). The bio-reporter signals were modulated prior to photo-detection, increasing the SNR of solid-state photo-detectors at least by three orders of magnitude. Experiments were performed using isopropyl-beta-d-thiogalactopyranoside (IPTG) as a preliminary step towards testing environmental toxicity. The inducer was used to trigger the expression response of the whole-cell sensors testing the sensitivity of the lab-on-chip. Low intensity bio-reporter optical signals were measured after the whole-cell sensors were exposed to IPTG concentrations of 0.1, 0.05, and 0.02 mM. The experimental results reveal the potential of this technology for future implementation as an inexpensive massive method for rapid environmental toxicity detection.