Streptococcus mutans Displays Altered Stress Responses While Enhancing Biofilm Formation by Lactobacillus casei in Mixed-Species Consortium.

Like Streptococcus mutans, lactobacilli are commonly isolated from carious sites, although their exact role in caries development remains unclear. This study used mixed-species models to analyze biofilm formation by major groups of oral lactobacilli, including L. casei, L. fermentum, L. rhamnosus, L. salivarius ssp. salivarius, and L. gasseri. The results showed that lactobacilli did not form good biofilms when grown alone, although differences existed between different species. When grown together with S. mutans, biofilm formation by L. gasseri and L. rhamnosus was increased by 2-log (P < 0.001), while biofilms by L. fermentum reduced by >1-log (P < 0.001). L. casei enhanced biofilm formation by ~2-log when grown with S. mutans wild-type, but no such effects were observed with S. mutans deficient of glucosyltransferase GtfB and adhesin P1. Both S. mutans and L. casei in dual-species enhanced resistance to acid killing with increases of survival rate by >1-log (P < 0.001), but drastically reduced the survival rates following exposure to hydrogen peroxide (P < 0.001), as compared to the respective mono-species cultures. When analyzed by RNA-seq, more than 134 genes were identified in S. mutans in dual-species with L. casei as either up- or down-regulated when compared to those grown alone. The up-regulated genes include those for superoxide dismutase, NADH oxidase, and members of the mutanobactin biosynthesis cluster. Among the down-regulated genes were those for GtfB and alternative sigma factor SigX. These results further suggest that interactions between S. mutans and oral lactobacilli are species-specific and may have significant impact on cariogenic potential of the community.

Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform.

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools in pre-configured workflows. These workflows, coupled with the ease of use of the environment, provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications for microbial research.

Integrated sequence and immunology filovirus database at Los Alamos.

The Ebola outbreak of 2013-15 infected more than 28 000 people and claimed more lives than all previous filovirus outbreaks combined. Governmental agencies, clinical teams, and the world scientific community pulled together in a multifaceted response ranging from prevention and disease control, to evaluating vaccines and therapeutics in human trials. As this epidemic is finally coming to a close, refocusing on long-term prevention strategies becomes paramount. Given the very real threat of future filovirus outbreaks, and the inherent uncertainty of the next outbreak virus and geographic location, it is prudent to consider the extent and implications of known natural diversity in advancing vaccines and therapeutic approaches. To facilitate such consideration, we have updated and enhanced the content of the filovirus portion of Los Alamos Hemorrhagic Fever Viruses Database. We have integrated and performed baseline analysis of all family ITALIC! Filoviridaesequences deposited into GenBank, with associated immune response data, and metadata, and we have added new computational tools with web-interfaces to assist users with analysis. Here, we (i) describe the main features of updated database, (ii) provide integrated views and some basic analyses summarizing evolutionary patterns as they relate to geo-temporal data captured in the database and (iii) highlight the most conserved regions in the proteome that may be useful for a T cell vaccine strategy.Database URL:www.hfv.lanl.gov.

ADEPT, a dynamic next generation sequencing data error-detection program with trimming.

BACKGROUND: Illumina is the most widely used next generation sequencing technology and produces millions of short reads that contain errors. These sequencing errors constitute a major problem in applications such as de novo genome assembly, metagenomics analysis and single nucleotide polymorphism discovery. RESULTS: In this study, we present ADEPT, a dynamic error detection method, based on the quality scores of each nucleotide and its neighboring nucleotides, together with their positions within the read and compares this to the position-specific quality score distribution of all bases within the sequencing run. This method greatly improves upon other available methods in terms of the true positive rate of error discovery without affecting the false positive rate, particularly within the middle of reads. CONCLUSIONS: ADEPT is the only tool to date that dynamically assesses errors within reads by comparing position-specific and neighboring base quality scores with the distribution of quality scores for the dataset being analyzed. The result is a method that is less prone to position-dependent under-prediction, which is one of the most prominent issues in error prediction. The outcome is that ADEPT improves upon prior efforts in identifying true errors, primarily within the middle of reads, while reducing the false positive rate.

Protective Effects of Hydrogen-Rich Saline on Rats with Smoke Inhalation Injury.

OBJECTIVE: To explore the protective effects of hydrogen-rich saline on rats with smoke inhalation injury. METHODS: 36 healthy male Sprague-Dawley rats were randomly divided into 3 groups (n = 12 per group): sham group (S), inhalation injury plus normal saline treatment group (I+NS), and inhalation injury plus hydrogen-rich saline treatment group (I+HS). 30 min after injury, normal saline and hydrogen-rich saline were injected intraperitoneally (5 mL/kg) in I+NS group and I+HS group, respectively. All rats were euthanized and blood and organ specimens were collected for determination 24 h after inhalation injury. RESULTS: Tumor necrosis factor-alpha (TNF-α) levels, malondialdehyde (MDA) concentrations, nuclear factor kappa B (NF-κB) p65 expression, and apoptosis index (AI) in I+HS group were significantly decreased (P < 0.05), while superoxide dismutase (SOD) activities were increased compared with those in I+NS group; and a marked improvement in alveolar structure was also found after hydrogen-rich saline treatment. CONCLUSIONS: Hydrogen-rich saline treatment exerts protective effects in acute lung injury induced by inhalation injury, at least in part through the activation of anti-inflammatory and antioxidant pathways and inhibition of apoptosis.

[Clinical observation on the treatment of phenol burn patients complicated by acute kidney injury with early blood purification].

OBJECTIVE: To observe the clinical effects of early blood purification in the treatment of phenol burn patients complicated by acute kidney injury (AKI). METHODS: Five phenol burn patients complicated by AKI, matched with the inclusion criteria, were hospitalized from January 2010 to July 2014. Within post injury hour 24, patients received rapid liquid support, positive wound management, and hemoperfusion (HP) combined with continuous veno-venous hemofiltration (CVVH) for 2 to 3 hours, then HP was stopped and CVVH was continued for 16 to 21 hours. HP combined with CVVH was performed for 2 to 3 times, then HP was stopped and CVVH was continued for 12 to 22 days. On post injury day (PID) 1, 3, 5, 7, 14, and 21, urea nitrogen, creatinine, ALT, AST, total bilirubin (TBIL), direct bilirubin (DBIL) in serum were determined, and the volume of liquid intake, urine, ultrafiltration, and liquid output were recorded, and the concentrations of IL-6, IL-10 and TNF-α in serum were determined by ELISA. General conditions of patients were recorded. Data were processed with one-way analysis of variance and LSD- t test. RESULTS: (1) On PID 1, the levels of urea nitrogen and creatinine were (9.0 ± 3.2) mmol/L and (115 ± 24) µmol/L respectively, which were obviously higher than normal values (with the values of 2.9-8.2 mmol/L and 45-104 µmol/L respectively). On PID 3, 5, 7 and 21, the levels of urea nitrogen were (12.5 ± 4.1), (11.2 ± 5.6), (8.7 ± 2.3) and (6.4 ± 3.9) mmol/L respectively, which were similar with the value of DID 1 (with t values 1.53, 0.76, 0.17 and 1.17 respectively, P values above 0.05). On PID 14, the level of urea nitrogen was (15.8 ± 3.3) mmol/L, which was obviously higher than the value of PID 1 (t =3 .29, P = 0.023). On PID 3, 5, 7 and 14, the levels of creatinine were (248 ± 67), (224 ± 87), (276 ± 59) and (307 ± 77) µmol/L respectively, which were obviously higher than the value of PID 1 (with t values 4.17, 2.70, 5.65 and 5.32 respectively, P values below 0.01). On PID 21, the level of creatinine was (78 ± 28) µmol/L, which was obviously lower than the value of PID 1 (t = 2.23, P = 0.041). The levels of ALT, AST, TBIL, and DBIL were higher than normal values from PID 1, and the levels were higher than normal values on PID 3, 5, 7, and 14, and they were similar with the normal values on PID 21. (2) On PID 1, 3, 5, 7, 14, and 21, the volume ratio of liquid intake to liquid output maintained from1:1 to 2:1. On PID 1, 3, 5, 7, and 14, although the volume of urine fluctuated, they were still less than 400 mL/d, and the volume for ultrafiltration showed a tendency from declining at first to a rise later. On PID 21, the volume of urine increased, and the volume for ultrafiltration decreased. (3) On PID 1, the serum concentrations of TNF-α and IL-6 increased, and the serum concentration of IL-10 decreased. On PID 3, 5, and 7, the serum concentrations of TNF-α and IL-6 decreased, and the serum concentration of IL-10 increased. On PID 14, the serum concentrations of TNF-α and IL-6 were elevated again but without a high peak value, and the serum concentration of IL-10 decreased but still higher than the value of PID 1. On PID 21, the serum concentrations of TNF-α and IL-6 obviously decreased, and the serum concentration of IL-10 obviously elevated. (4) Primary healing of the wound was achieved on PID 21 to 28. Patients were all cured and left hospital on PID 28 to 45. All the patients were followed up for 6 months to 3 years. At the last follow up, patients had no symptoms of chronic poisoning and the functions of liver and kidney were normal. CONCLUSIONS: Early blood purification treatment is effective for phenol patients phenol burn patients complicated by AKI, and wound healing and kidney function recovery were assured.

Facile, high quality sequencing of bacterial genomes from small amounts of DNA.

Sequencing bacterial genomes has traditionally required large amounts of genomic DNA (~1 µg). There have been few studies to determine the effects of the input DNA amount or library preparation method on the quality of sequencing data. Several new commercially available library preparation methods enable shotgun sequencing from as little as 1 ng of input DNA. In this study, we evaluated the NEBNext Ultra library preparation reagents for sequencing bacterial genomes. We have evaluated the utility of NEBNext Ultra for resequencing and de novo assembly of four bacterial genomes and compared its performance with the TruSeq library preparation kit. The NEBNext Ultra reagents enable high quality resequencing and de novo assembly of a variety of bacterial genomes when using 100 ng of input genomic DNA. For the two most challenging genomes (Burkholderia spp.), which have the highest GC content and are the longest, we also show that the quality of both resequencing and de novo assembly is not decreased when only 10 ng of input genomic DNA is used.

Fitness costs of rifampicin resistance in Mycobacterium tuberculosis are amplified under conditions of nutrient starvation and compensated by mutation in the ß' subunit of RNA polymerase.

Rifampicin resistance, a defining attribute of multidrug-resistant tuberculosis, is conferred by mutations in the ß subunit of RNA polymerase. Sequencing of rifampicin-resistant (RIF-R) clinical isolates of Mycobacterium tuberculosis revealed, in addition to RIF-R mutations, enrichment of potential compensatory mutations around the double-psi ß-barrel domain of the ß' subunit comprising the catalytic site and the exit tunnel for newly synthesized RNA. Sequential introduction of the resistance allele followed by the compensatory allele in isogenic Mycobacterium smegmatis showed that these mutations respectively caused and compensated a starvation enhanced growth defect by altering RNA polymerase activity. While specific combinations of resistance and compensatory alleles converged in divergent lineages, other combinations recurred among related isolates suggesting transmission of compensated RIF-R strains. These findings suggest nutrient poor growth conditions impose larger selective pressure on RIF-R organisms that results in the selection of compensatory mutations in a domain involved in catalysis and starvation control of RNA polymerase transcription.

Mycobacterium tuberculosis--heterogeneity revealed through whole genome sequencing.

The emergence of whole genome sequencing (WGS) technologies as primary research tools has allowed for the detection of genetic diversity in Mycobacterium tuberculosis (Mtb) with unprecedented resolution. WGS has been used to address a broad range of topics, including the dynamics of evolution, transmission and treatment. Here, we have analyzed 55 publically available genomes to reconstruct the phylogeny of Mtb, and we have addressed complications that arise during the analysis of publically available WGS data. Additionally, we have reviewed the application of WGS to the study of Mtb and discuss those areas still to be addressed, moving from global (phylogeography), to local (transmission chains and circulating strain diversity), to the single patient (clonal heterogeneity) and to the bacterium itself (evolutionary studies). Finally, we discuss the current WGS approaches, their strengths and limitations.

Near-contact interactions between a sphere and a plane.

The hydrodynamic behavior observed for a sphere released under gravity in a Newtonian liquid is not consistent with that predicted by classical continuum theory when the sphere is near a solid wall. An irreversibility arises in the velocity of the sphere as it approaches and recedes from the plane that cannot be accounted for using continuum hydrodynamic equations alone. Earlier experiments on spheres falling from a plane were conducted under conditions such that this irreversibility could be attributed to the surface roughness of the spheres. In this investigation, we extend these studies to situations where the pressure field between the receding sphere and the plane drops to the vapor pressure of the fluid and cavitation occurs. Experimental data supports the theoretical prediction for a sphere's motion based on the irreversible effect of cavitation.

[Repair of finger deep burn with the island skin flap nourished by the cutaneous nerve nutrient vessel of the dorsum of hand].

OBJECTIVE: To investigate the reverse island skin flap nourished by the cutaneous nerve nutrient vessel of the dorsum of hand in the repair of the finger deep burn. METHODS: Fifteen reverse island skin flaps nourished by the cutaneous nerve nutrient vessel of the dorsum of hand were used to repair finger deep burn in 15 patients. The size of the reverse island skin flap ranged from 5 cm x 3 cm to 3 x 2 cm. RESULTS: All the flaps survived. Postoperative follow-up showed satisfactory results in appearance, function and aesthesia. CONCLUSIONS: The reverse island skin flap nourished by the cutaneous nerve nutrient vessel of the dorsum of hand has reliable blood supply, without damage of a known vessel, can meet the demands of fingertip reconstruction. The flap also has the advantages of minor injury of the donor site, easy manipulation and popularization.