9-Fluorenylmethoxycarbonylpyroglutamate, a side-product of derivatization of glutamate with 9-fluorenylmethyl chloroformate: a warning

9-Fluorenylmethyl chloroformate derivatization is widely used for determinations of amino acids in biological material. The derivatization of glutamate leads to the formation of 9-fluorenylmethoxycarbonylpyroglutamate as a side-product, which is thus a methodological artifact.     

Enabling large-scale feather mite studies: an Illumina DNA metabarcoding pipeline

Feather mites are among the most common and diverse ectosymbionts of birds, yet basic questions such as the nature of their relationship remain largely unanswered. One reason for feather mites being understudied is that their morphological identification is often virtually impossible when using female or young individuals. Even for adult male specimens this task is tedious and requires advanced taxonomic expertise, thus hampering large-scale studies. In addition, molecular-based methods are challenging because the low DNA amounts usually obtained from these tiny mites do not reach the levels required for high-throughput sequencing. This work aims to overcome these issues by using a DNA metabarcoding approach to accurately identify and quantify the feather mite species present in a sample. DNA metabarcoding is a widely used molecular technique that takes advantage of high-throughput sequencing methodologies to assign the taxonomic identity to all the organisms present in a complex sample (i.e., a sample made up of multiple specimens that are hard or impossible to individualise). We present a high-throughput method for feather mite identification using a fragment of the COI gene as marker and Illumina Miseq technology. We tested this method by performing two experiments plus a field test over a total of 11,861 individual mites (5360 of which were also morphologically identified). In the first experiment, we tested the probability of detecting a single feather mite in a heterogeneous pool of non-conspecific individuals. In the second experiment, we made 2?×?2 combinations of species and studied the relationship between the proportion of individuals of a given species in a sample and the proportion of sequences retrieved to test whether DNA metabarcoding can reliably quantify the relative abundance of mites in a sample. Here we also tested the efficacy of degenerate primers (i.e., a mixture of similar primers that differ in one or several bases that are designed to increase the chance of annealing) and investigated the relationship between the number of mismatches and PCR success. Finally, we applied our DNA metabarcoding pipeline to a total of 6501 unidentified and unsorted feather mite individuals sampled from 380 European passerine birds belonging to 10 bird species (field test). Our results show that this proposed pipeline is suitable for correct identification and quantitative estimation of the relative abundance of feather mite species in complex samples, especially when dealing with a moderate number (>?30) of individuals per sample.     

Isolation and characterization of a cellulase-free endo-β-1,4-xylanase produced by an invertebrate-symbiotic bacterium, Cellulosimicrobium sp. HY-13

A xylanolytic bacterium, Cellulosimicrobium sp. HY-13, was isolated from the digestive tract of an earthworm, Eisenia fetida. The purified cellulase-free endo-β-1,4-xylanase (XylK) produced by strain HY-13 was found to contain an N-terminal amino acid sequence of APSTLEAAAE and to have a relative molecular mass of 36 kDa. It was most active at pH 6.0 and 55 °C and had V_max and K_m values toward oat spelt xylan of 4067 IU/mg and 2.78 mg/ml, respectively. XylK primarily degraded xylan to a series of xylooligosaccharides composed of xylobiose to xylotetraose, but it could not further hydrolyze xylobiose to xylose. The results of the present study suggest that the relatively highly active XylK lacking exo-xylanolytic activity is a promising candidate for the efficient production of non-digestible xylooligosaccharides that may have beneficial effects to gastrointestinal health via promotion of the growth of probiotics.     

Risk factors of Streptococcus suis infection in Vietnam. A case-control study

Background

Streptococcus suis infection, an emerging zoonosis, is an increasing public health problem across South East Asia and the most common cause of acute bacterial meningitis in adults in Vietnam. Little is known of the risk factors underlying the disease.

Methods and Findings

A case-control study with appropriate hospital and matched community controls for each patient was conducted between May 2006 and June 2009. Potential risk factors were assessed using a standardized questionnaire and investigation of throat and rectal S. suis carriage in cases, controls and their pigs, using real-time PCR and culture of swab samples. We recruited 101 cases of S. suis meningitis, 303 hospital controls and 300 community controls. By multivariate analysis, risk factors identified for S. suis infection as compared to either control group included eating “high risk” dishes, including such dishes as undercooked pig blood and pig intestine (OR₁ = 2.22; 95%CI = [1.15–4.28] and OR₂ = 4.44; 95%CI = [2.15–9.15]), occupations related to pigs (OR₁ = 3.84; 95%CI = [1.32–11.11] and OR₂ = 5.52; 95%CI = [1.49–20.39]), and exposures to pigs or pork in the presence of skin injuries (OR₁ = 7.48; 95%CI = [1.97–28.44] and OR₂ = 15.96; 95%CI = [2.97–85.72]). S. suis specific DNA was detected in rectal and throat swabs of 6 patients and was cultured from 2 rectal samples, but was not detected in such samples of 1522 healthy individuals or patients without S. suis infection.

Conclusions

This case control study, the largest prospective epidemiological assessment of this disease, has identified the most important risk factors associated with S. suis bacterial meningitis to be eating ‘high risk’ dishes popular in parts of Asia, occupational exposure to pigs and pig products, and preparation of pork in the presence of skin lesions. These risk factors can be addressed in public health campaigns aimed at preventing S. suis infection.     

Assembly of the capsid protein of red-spotted grouper nervous necrosis virus during purification,and role of calcium ions in chromatography

Currently virus-like particles (VLPs) are receiving much attention as platforms for next generation vaccines. However, chromatography-based methods for purifying VLPs remain challenging. Unlike traditional methods using density gradient for purifying VLPs, there have been few advances in explaining how assembled particles can be obtained by chromatography. Nervous necrosis virus (NNV) infects over 30 species of fish and leads to large economic losses in the farmed fish industry. Previously we developed a heparin chromatography-based method for purifying red-spotted grouper NNV (RGNNV) VLPs. However it is unclear how the assembled RGNNV VLPs are obtained by this method. It is known that assembly of NNV capsid proteins depends on calcium ions. In the present study, we found that the yield of purified RGNNV capsid protein in heparin chromatography was enhanced when calcium ions were present during binding. Also, it appears that the capsid protein of RGNNV undergoes partial disassembly and reassembly during sample preparation prior to heparin chromatography and the protein finally undergoes assembly during the chromatography. Therefore, our results indicated that heparin-binding affinity of RGNNV capsid protein is linked to its ability for VLP formation. The assembly of RGNNV capsid proteins recombinantly produced is a good model for explaining VLP formation during chromatography-based purification processes.     

A novel protein, Romo1, induces ROS production in the mitochondria

The majority of endogenous reactive oxygen species (ROS) are produced in the mitochondrial respiratory chain. An imbalance in ROS production alters the intracellular redox homeostasis, triggers DNA damage, and contributes to cancer development and progression. This study identified a novel protein, reactive oxygen species modulator 1 (Romo1), which is localized in the mitochondria. Romo1 was found to increase the level of ROS in the cells. Increased Romo1 expression was observed in various cancer cell lines. This suggests that the increased Romo1 expression during cancer progression may cause persistent oxidative stress to tumor cells, which can increase their malignancy.     

Mechanism of BLyS action in B cell immunity.

The B lymphocyte stimulator (BLyS), also known as BAFF, THANK, TALL-1 and zTNF4, is the most recent addition to the tumor necrosis factor family (TNF) ligands and has a unique role in B cell immunity. Its requirement for the humoral immune response is evident in mice lacking BlyS, which exhibit profound deficiencies in peripheral B cell development and maturation. It regulates the antibody response, as shown in mice overexpressing BLyS, which develop autoimmune manifestations resulting from peripheral B cell expansion and differentiation. Attenuation of apoptosis appears to underlie BLyS action in B cells. However, elucidation of the mechanism of BLyS has proven to be more challenging, because BLyS binds three different TNF receptors (TACI/BCMA/BAFF-R) and shares overlapping functions with a related TNF ligand, APRIL. The unique role of BLyS in B cell development and differentiation and the pathogenesis of autoimmune diseases, systemic lupus erythematosus (SLE) in particular, makes the study of BLyS and its downstream targets attractive in the development of novel therapies.     

Optimal production of 4-deoxy-l-erythro-5-hexoseulose uronic acid from alginate for brown macro algae saccharification by combining endo- and exo-type alginate lyases

Algae are considered as third-generation biomass, and alginate is the main component of brown macroalgae. Alginate can be enzymatically depolymerized by alginate lyases into uronate monomers, such as mannuronic acid and guluronic acid, which are further nonenzymatically converted to 4-deoxy-l-erythro-5-hexoseulose uronic acid (DEH). We have optimized an enzymatic saccharification process using two recombinant alginate lyases, endo-type Alg7D and exo-type Alg17C, for the efficient production of DEH from alginate. When comparing the sequential and simultaneous additions of Alg7D and Alg17C, it was found that the final yield of DEH was significantly higher when the enzymes were added sequentially. The progress of saccharification reactions and production of DEH were verified by thin layer chromatography and gas chromatography–mass spectrometry, respectively. Our results showed that the two recombinant enzymes could be exploited for the efficient production of DEH that is the key substrate for producing biofuels from brown macro algal biomass.