Characterization of transposon-generated protease mutant of xanthomonas campestris pathovar glycine 8ra

Protease negative mutant of Xanthomonas campestris pathovar glycine 8ra (prt-mutant) was constructed by mutagenesis employing artificial transposon Omegon-Km. Transposon delivery was conducted through diparental conjugation using X. campestris pathovar glycine 8ra as recipient and Escherichia coli S17-1 carrying pJFF 3500 plasmid as the donor. The frequency of transconjugation was found 1.9 x 10(-7) per recipient. Enzyme analysis indicated the presence of mutant with lower protease activity than that of the wild-type. Genetic analysis employing pulsed-field gel electrophoresis (PFGE) of the genomic DNA digested with AseI or SpeI restriction endonuclease could significantly differentiate X. campestris pathovar glycine 8ra prt from the wild-type parent. The 9.85 kb pLR omega 6 plasmid was constructed from the genomic DNA of the prt mutant after being digested with KpnI restriction endonuclease and ligated with T4 DNA ligase.     

Relationship of protozoan biomass to phosphate and nitrate removal from activated sludge mixed liquor

The relationship between protozoan biomass concentration and phosphate and nitrate removal was investigated in mixed liquor using three different carbon sources as supplements. The study was carried out using three respective initial biomass concentrations in a shaking flask environment. Samples were taken every 24 h to determine phosphate, nitrate, dissolved oxygen and chemical oxygen demand. The results revealed a direct relationship between decreases in nutrient concentrations and increases in cell densities of the isolates. Between 24 and 96 h, the increases in the protozoan density corresponded to a phosphate decreases from initial ranges of 55.42–57.36 mg/L, 50.27–51.17 mg/L and 50.01–50.83 mg/L to final ranges of 2.46–11.90 mg/L, 0.61–11.80 mg/L and 1.29–13.89 mg/L, in the presence of Aspidisca, Trachelophyllum and Peranema, respectively. Nitrate concentrations were observed to decrease from initial ranges of 23.84–25.90 mg/L, 23.94–25.84 mg/L and 26.12–26.54 mg/L to final ranges of 0.11–6.32 mg/L, 0.16–5.60 mg/L and 0.24–9.04 mg/L, respectively. The study had revealed that an increase in cell density of the test isolates produces a corresponding increase in phosphate and nitrate removal.     

Algae as Reservoirs for Coral Pathogens

Benthic algae are associated with coral death in the form of stress and disease. It''s been proposed that they release exudates, which facilitate invasion of potentially pathogenic microbes at the coral-algal interface, resulting in coral disease. However, the original source of these pathogens remains unknown. This study examined the ability of benthic algae to act as reservoirs of coral pathogens by characterizing surface associated microbes associated with major Caribbean and Indo-Pacific algal species/types and by comparing them to potential pathogens of two dominant coral diseases: White Syndrome (WS) in the Indo-Pacific and Yellow Band Disease (YBD) in the Caribbean. Coral and algal sampling was conducted simultaneously at the same sites to avoid spatial effects. Potential pathogens were defined as those absent or rare in healthy corals, increasing in abundance in healthy tissues adjacent to a disease lesion, and dominant in disease lesions. Potentially pathogenic bacteria were detected in both WS and YBD and were also present within the majority of algal species/types (54 and 100% for WS and YBD respectively). Pathogenic ciliates were associated only with WS and not YBD lesions and these were also present in 36% of the Indo-Pacific algal species. Although potential pathogens were associated with many algal species, their presence was inconsistent among replicate algal samples and detection rates were relatively low, suggestive of low density and occurrence. At the community level, coral-associated microbes irrespective of the health of their host differed from algal-associated microbes, supporting that algae and corals have distinctive microbial communities associated with their tissue. We conclude that benthic algae are common reservoirs for a variety of different potential coral pathogens. However, algal-associated microbes alone are unlikely to cause coral death. Initial damage or stress to the coral via other competitive mechanisms is most likely a prerequisite to potential transmission of these pathogens.     

Circulating plasma serine208‐phosphorylated troponin T levels are indicator of cardiac dysfunction

Heart failure (HF) following myocardial infarction (MI) is characterized by progressive alterations of left ventricular (LV) structure and function, named LV remodelling. Although several risk factors such as infarct size have been identified, HF remains difficult to predict in clinical practice. Recently, using phosphoproteomic technology, we found that serine²⁰⁸‐phosphorylated troponin T (P‐Ser²⁰⁸‐TnT) decreases in LV of HF rats. Our aim was to determine the performance of P‐Ser²⁰⁸‐TnT as plasma biomarker of HF compared to conventional cardiac biomarkers such as B‐type natriuretic peptide (BNP), cardiac troponin I (cTnI), C‐reactive protein (CRP) or tissue inhibitor of metalloproteinase I (TIMP‐1) measured by x‐MAP technology, as well as its capacity to reflect a pharmacological improvement of HF. We observed a significant increase of BNP, TnT and cTnI levels and a significant decrease of P‐Ser²⁰⁸‐TnT and TIMP‐1 in the plasma of 2‐month‐MI rats compared with control rats with no modulation of CRP level. Circulating levels of P‐Ser²⁰⁸‐TnT were shown to be associated with most of the echocardiographic and haemodynamic parameters of cardiac function. We verified that the decrease of P‐Ser²⁰⁸‐TnT was not because of an excess of phosphatase activity in plasma of HF rats. Two‐month‐MI rats treated with the heart rate reducing agent ivabradine had improved LV function and increased plasma levels of P‐Ser²⁰⁸‐TnT. Thus, circulating phosphorylated troponin T is a highly sensitive biological indicator of cardiac dysfunction and has the potentiality of a new biomarker of HF post‐MI, and of a surrogate marker for the efficacy of a successful treatment of HF.     

Identification of additional proteins in differential proteomics using protein interaction networks

In this study, we developed a novel computational approach based on protein–protein interaction networks to identify a list of proteins that might have remained undetected in differential proteomic profiling experiments. We tested our computational approach on two sets of human smooth muscle cell protein extracts that were affected differently by DNase I treatment. Differential proteomic analysis by saturation DIGE resulted in the identification of 41 human proteins. The application of our approach to these 41 input proteins consisted of four steps: (i) Compilation of a human protein–protein interaction network from public databases; (ii) calculation of interaction scores based on functional similarity; (iii) determination of a set of candidate proteins that are needed to efficiently and confidently connect the 41 input proteins; and (iv) ranking of the resulting 25 candidate proteins. Two of the three highest‐ranked proteins, beta‐arrestin 1, and beta‐arrestin 2, were experimentally tested, revealing that their abundance levels in human smooth muscle cell samples were indeed affected by DNase I treatment. These proteins had not been detected during the experimental proteomic analysis. Our study suggests that our computational approach may represent a simple, universal, and cost‐effective means to identify additional proteins that remain elusive for current 2D gel‐based proteomic profiling techniques.     

Classification of Brucella strains isolated from marine mammals by infrequent restriction site-PCR and development of specific PCR identification tests

Brucella strains have been isolated since the 1990s from a wide variety of marine mammals and represent potential zoonotic pathogens. They have distinctive phenotypic and molecular characteristics from the terrestrial mammal Brucella species, and two new species names have been previously proposed based on DNA polymorphism at the omp2 locus and their preferential host, i.e. Brucella cetaceae for cetacean isolates and Brucella pinnipediae for pinniped isolates. The results presented in this study on characterization of these strains by infrequent restriction site-PCR (IRS-PCR), taking into account the higher number of IS711 elements in their genome compared to terrestrial mammal Brucella species, supports this classification. The nucleotide sequences of specific DNA fragments detected by IRS-PCR were determined and used to develop PCR identification tests for either B. cetaceae or B. pinnipediae.     

Antibody prevalence and molecular identification of Babesia spp. In roe deer in France

In a region-wide serologic study carried out in 2004 on free-ranging hunted roe deer in various landscapes, we found that 58% of the animals (237 out of 406) were antibody positive for Babesia divergens antigen. Serologic and infection status was also analyzed for 327 roe deer live-trapped in two fenced forest areas over 5 yr (2004-08). For two consecutive years during this period, 92 and 94% of the deer in these closed populations were antibody-positive for B. divergens. Babesia spp. were isolated in autologous red blood cell culture for 131 of the trapped animals (40%). Molecular typing was done on 76 isolates with polymerase chain reaction (PCR)-restriction fragment length polymorphism methods targeted at the 18S ribosomal subunit gene (18 isolates) and the Bd37 gene coding for a merozo?te surface antigen implicated in a protective response (60 isolates). Results indicated continuous cocirculation of B. capreoli and B. venatorum in both forests and possible coinfection of animals with both species. No infection with B. divergens was detected. Fifteen isolates were confirmed to be B. capreoli by sequencing part of the 18S rRNA gene. Using PCR detection of the Bd37 gene, all nine isolates of B. venatorum in this study were negative, whereas the 15 confirmed and 50 putative B. capreoli isolates showed very variable restriction profiles, distinct from those known for Bd37 in B. divergens. Two isolates showed conflicting results, suggestive of mixed infection.     

Dynamical properties of the loop 320s of substrate-free and substrate-bound muscle creatine kinase by NMR: evidence for independent subunits

Muscle creatine kinase (MCK; EC2.7.3.2) is a 86 kDa homodimer that belongs to the family of guanidino kinases. MCK has been intensively studied for several decades, but it is still not known why it is a dimer because this quaternary structure does not translate into obvious structural or functional advantages over the homologous monomeric arginine kinase. In particular, it remains to be demonstrated whether MCK subunits are independent. Here, we describe NMR chemical-shift perturbation and relaxation experiments designed to study the active site 320s flexible loop of this enzyme. The analysis was performed with the enzyme in its ligand-free and MgADP-complexed forms, as well as with the transition-state analogue abortive complex (MCK-Mg-ADP-creatine-nitrate ion). Our data indicate that each subunit can bind substrates independently.     

40 Years of benthic community change on the Caribbean reefs of Curaçao and Bonaire: the rise of slimy cyanobacterial mats

Over the past decades numerous studies have reported declines in stony corals and, in many cases, phase shifts to fleshy macroalgae. However, long-term studies documenting changes in other benthic reef organisms are scarce. Here, we studied changes in cover of corals, algal turfs, benthic cyanobacterial mats, macroalgae, sponges and crustose coralline algae at four reef sites of the Caribbean islands of Curaçao and Bonaire over a time span of 40 yr. Permanent 9 m² quadrats at 10, 20, 30 and 40 m depth were photographed at 3- to 6-yr intervals from 1973 to 2013. The temporal and spatial dynamics in the six dominant benthic groups were assessed based on image point-analysis. Our results show consistent patterns of benthic community change with a decrease in the cover of calcifying organisms across all sites and depths from 32.6 (1973) to 9.2% (2013) for corals and from 6.4 to 1% for crustose coralline algae. Initially, coral cover was replaced by algal turfs increasing from 24.5 (1973) to 38% around the early 1990s. Fleshy macroalgae, still absent in 1973, also proliferated covering 12% of the substratum approximately 20 yr later. However, these new dominants largely declined in abundance from 2002 to 2013 (11 and 2%, respectively), marking the rise of benthic cyanobacterial mats. Cyanobacterial mats became the most dominant benthic component increasing from a mere 7.1 (2002) to 22.2% (2013). The observed increase was paralleled by a small but significant increase in sponge cover (0.5 to 2.3%). Strikingly, this pattern of degradation and phase change occurred over the reef slope down to mesophotic depths of 40 m. These findings suggest that reefs dominated by algae may be less stable than previously thought and that the next phase may be the dominance of slimy cyanobacterial mats with some sponges.     

Mycobacterium smegmatis produces an HBHA homologue which is not involved in epithelial adherence

Mycobacterium tuberculosis produces heparin-binding hemagglutinin (TB-HBHA), an adhesin involved in binding to non-professional phagocytes and in extrapulmonary dissemination. TB-HBHA binds sulphated glycoconjugates through its C-terminal lysine-rich domain and can be purified by heparin-Sepharose chromatography. Homologues of HBHA are found in other pathogenic mycobacteria, but previous investigations failed to demonstrate them in non-pathogenic Mycobacterium smegmatis. We identified a gene encoding a HBHA-like protein, named MS-HBHA, from the complete M. smegmatis genome. The deduced MS-HBHA amino acid sequence revealed 68% identity with that of TB-HBHA and contains lysine-rich repeats in its C-terminal domain. However, in contrast to TB-HBHA, the lysine-rich domain of MS-HBHA is preceded by a stretch of acidic residues. This difference likely explains the low affinity for heparin displayed by MS-HBHA compared to TB-HBHA. Isolation by heparin-Sepharose chromatography procedure and mass spectrometry analysis indicated that MS-HBHA, similar to TB-HBHA contains several methylated lysine residues in its C-terminal domain. Although MS-HBHA is associated with M. smegmatis cell wall fractions, it does not seem to play a role in epithelial adherence and its function remains unknown. We therefore conclude that TB-HBHA may have evolved as an adhesin in pathogenic mycobacteria from a homolog that serves a different function in a saprophytic mycobacterium.