Impact of post-collection freezing delay on the reliability of serum metabolomics in samples reflecting the California mid-term pregnancy biobank

Background

Population-based biorepositories are important resources, but sample handling can affect data quality.

Objective

Identify metabolites of value for clinical investigations despite extended postcollection freezing delays, using protocols representing a California mid-term pregnancy biobank.

Methods

Blood collected from non-pregnant healthy female volunteers (n?=?20) underwent three handling protocols after 30 min clotting at room temperature: (1) ideal—samples frozen (??80 °C) within 2 h of collection; (2) delayed freezing—samples held at room temperature for 3 days, then 4 °C for 9 days, the median times for biobank samples, and then frozen; (3) delayed freezing with freeze–thaw—the delayed freezing protocol with a freeze–thaw cycle simulating retrieved sample sub-aliquoting. Mass spectrometry-based untargeted metabolomic analyses of primary metabolism and complex lipids and targeted profiling of oxylipins, endocannabinoids, ceramides/sphingoid-bases, and bile acids were performed. Metabolite concentrations and intraclass correlation coefficients (ICC) were compared, with the ideal protocol as the reference.

Results

Sixty-two percent of 428 identified compounds had good to excellent ICCs, a metric of concordance between measurements of samples handled with the different protocols. Sphingomyelins, phosphatidylcholines, cholesteryl esters, triacylglycerols, bile acids and fatty acid diols were the least affected by non-ideal handling, while sugars, organic acids, amino acids, monoacylglycerols, lysophospholipids, N-acylethanolamides, polyunsaturated fatty acids, and numerous oxylipins were altered by delayed freezing. Freeze–thaw effects were assay-specific with lipids being most stable.

Conclusions

Despite extended post-collection freezing delays characteristic of some biobanks of opportunistically collected clinical samples, numerous metabolomic compounds had both stable levels and good concordance.

     

Genomic changes underlying host specialization in the bee gut symbiont Lactobacillus Firm5

Bacteria that engage in long‐standing associations with particular hosts are expected to evolve host‐specific adaptations that limit their capacity to thrive in other environments. Consistent with this, many gut symbionts seem to have a limited host range, based on community profiling and phylogenomics. However, few studies have experimentally investigated host specialization of gut symbionts and the underlying mechanisms have largely remained elusive. Here, we studied host specialization of a dominant gut symbiont of social bees, Lactobacillus Firm5. We show that Firm5 strains isolated from honey bees and bumble bees separate into deep‐branching host‐specific phylogenetic lineages. Despite their divergent evolution, colonization experiments show that bumble bee strains are capable of colonizing the honey bee gut. However, they were less successful than honey bee strains, and competition with honey bee strains completely abolished their colonization. In contrast, honey bee strains of divergent phylogenetic lineages were able to coexist within individual bees. This suggests that both host selection and interbacterial competition play important roles in host specialization. Using comparative genomics of 27 Firm5 isolates, we found that the genomes of honey bee strains harbour more carbohydrate‐related functions than bumble bee strains, possibly providing a competitive advantage in the honey bee gut. Remarkably, most of the genes encoding carbohydrate‐related functions were not conserved among the honey bee strains, which suggests that honey bees can support a metabolically more diverse community of Firm5 strains than bumble bees. These findings advance our understanding of the genomic changes underlying host specialization.     

In Silico Design of Multimeric HN-F Antigen as a Highly Immunogenic Peptide Vaccine Against Newcastle Disease Virus

Application of molecular biology techniques to the production of new vaccines against different strains of the Newcastle disease virus (NDV) has been the subject of recent research reports. Development of improved techniques for genome sequencing has led to the recognition of protective mechanisms and the identification of possible candidate antigens. Such procedures could generate meaningful results regarding the virulence determinants of NDV. This study proposed an in silico approach by assembling potential and conserved epitopic regions of hemagglutinin–neuraminidase (HN) and fusion (F) glycoproteins of NDV to induce multiepitopic responses against the virus. Epitope predictions showed that the hypothetical synthetic construct could induce immature B and T cell epitopes that expect a high immune response because of their location in four distinct parts of the construct, namely the head, stalk and the heptad repeated regions known as the HRA and HRB domains. Most regions of the chimeric construct were found to have high antigenic propensity and surface accessibility, which further confirmed the strategy for selection of precise continuous and discontinuous epitopes of HN and F antigens. Thermodynamic folding of mRNA structures revealed correct folding of the RNA construct, indicating good stability of the mRNA to increase the efficiency of translation in the target host. The three-dimensional structure of the native HN-F chimeric protein was successfully generated and validated as a proper model which may define reliability, structural quality and conformation.     

Niche Conservatism and Future Changes in the Potential Area Coverage of Arundina graminifolia,an Invasive Orchid Species from Southeast Asia

The Asian orchid, Arundina graminifolia, has been introduced to many locations over the last 50 yr, predominantly in South and Central America. A list of localities of A. graminifolia was compiled and used to model potential climatic niches based on the maximum entropy method. The differences are presented between niches occupied by native and invasive populations of A. graminifolia, and possible changes in the potential range of the species are discussed on the basis of various climate change scenarios. The coverage of habitats suitable for A. graminifolia will be reduced under future climate changes scenarios. The created niche distribution models indicated a more significant reduction in the potential ecological niches of the studied species in its invasive range. Nevertheless, areas with potentially suitable bioclimatic conditions for A. graminifolia should be monitored to prevent future uncontrolled invasion of the orchid into new habitats and to study its impact on the local ecosystems, as vast areas of its potential niche in the Americas are still unoccupied.     

The Na transport in gram-positive bacteria defect in the Mrp antiporter complex measured with Na nuclear magnetic resonance

²³Na nuclear magnetic resonance (NMR) has previously been used to monitor Na⁺ translocation across membranes in gram-negative bacteria and in various other organelles and liposomes using a membrane-impermeable shift reagent to resolve the signals resulting from internal and external Na⁺. In this work, the ²³Na NMR method was adapted for measurements of internal Na⁺ concentration in the gram-positive bacterium Bacillus subtilis, with the aim of assessing the Na⁺ translocation activity of the Mrp (multiple resistance and pH) antiporter complex, a member of the cation proton antiporter-3 (CPA-3) family. The sodium-sensitive growth phenotype observed in a B. subtilis strain with the gene encoding MrpA deleted could indeed be correlated to the inability of this strain to maintain a lower internal Na⁺ concentration than an external one.     

Incidence and Characteristics of Injuries during the 2010 FELDA/FAM National Futsal League in Malaysia

Objective

In Malaysia, futsal is a popular sport played by individuals across all ages and genders. Despite its popularity, information on futsal related injury in Malaysia is not available. The purpose of this study is to examine the injury incidence and injury patterns among amateur men and women futsal players in Malaysia.

Methods

Players reported injury to the tournament medical team during the FELDA/FAM National Futsal League 2010 were interviewed and assessed by a Sports Medicine registrar. Player''s socio-demographic profiles and information about the injury were documented in the injury report form adapted from medical report form used by FIFA: Medical Assessment and Research Centre (F-Marc).

Results

A total of 86 injuries were reported from 141 matches, equivalent to an incidence of 91.5 injuries per 1000 player hours (95% CI 72.2 to 110.8), or 61.0 injuries per 1000 player matches (95% CI 48.1 to 73.9). Most were minor injuries resulted from contact with another player. Injuries often involved the lower extremity (44%) followed by the trunk (14%) and the upper limb (13%). Ankle (n = 7; 39%) and knee (n = 6; 33%) sprains were the most prevalent diagnoses of time-loss injuries. A significant association between time-loss and type of injury was found χ ² (1,N = 86) = 3.99, p = 0.04. In addition, time-loss injury was significantly associated with playing surface χ ² (1,N = 86) = 10.11, p = 0.018.

Conclusion

The injury rate during the FELDA/FAM National Amateur Futsal Men''s League in Malaysia was lower compared with previous Futsal World Cups competition. Most injuries resulted from contact with another player were minor and did not lead to time-loss from participation. Time-loss injury was significantly associated with type of injury and playing surface.     

Vesicular trafficking–related proteins as the potential therapeutic target for breast cancer

Protoplasma - Vesicular trafficking between endoplasmic reticulum and Golgi plays a major role in the growth and proliferation of breast cancer cells. Various proteins regulate this ER-Golgi...