A new collagenase enzyme of the marine sponge pathogen Pseudoalteromonas agarivorans NW4327 is uniquely linked with a TonB dependent receptor.

The primary pathogen of the Great Barrier Reef sponge Rhopaloeides odorabile, recently identified as a novel strain (NW4327) of Pseudoalteromonas agarivorans, produced collagenase which degraded R. odorabile skeletal fibers. We now report the collagenase of P. agarivorans as a metalloprotease which required Ca2+ and Zn2+ as cofactors. The collagenase was a TonB dependent receptor (TBDR) having a carboxypeptidase regulatory like domain (CRLD) in the N-terminal along with an outer membrane (OM) channel superfamily domain. The genes for TBDR sub-components and collagenase formed one unified entity in the genome of P. agarivorans NW4327. This association of a collagenase with a TBDR distinguished it from all known functional collagenases till date and for the first time, established the enzymatic capability of TBDRs. Predicted TBDR model demonstrated only 15% identity with ferripyoverdin receptor and the CRLD displayed merely 24% identity with carboxypeptidase catalytic chain. Presence of signal peptide, lack of transmembrane helices, absence of N-terminal in the cytoplasmic side, extracellular localization and recovery from the culture supernatant implicated that the TBDR was secreted. Stronger binding of the collagenase with marine sponge type IV collagen than type I collagen, revealed through molecular docking, indicated higher specificity of the enzyme towards type IV collagen.

Streptomyces euryhalinus sp. nov., a new actinomycete isolated from a mangrove forest.

A Gram-positive, aerobic, non-motile actinomycete (strain MS 3/20T) was isolated from the sediment of the Sundarbans mangrove forest in India. On International Streptomyces Project (ISP) medium 2, the isolate produced yellowish brown to red aerial hyphae that carried spiny-surfaced spores in a retinaculum-apertum arrangement. Whole-cell hydrolysate of the strain contained LL-diaminopimelic acid and galactose. Predominant menaquinones were MK-9(H8) and MK-9(H6). Diagnostic polar lipids were glycolipid, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylcholine, unidentified phospholipid and unidentified amino lipid. The major fatty acids were anteiso-C15:0 (17.53%), iso-C16:0 (23.89%) and anteiso-C17:0 (10.29%). The strain showed 100% 16S ribosomal RNA (rRNA) gene sequence similarity with Streptomyces variabilis NBRC 12825T, Streptomyces erythrogriseus LMG 19406T, Streptomyces griseoincarnatus LMG 19316T and Streptomyces labedae NBRC 15864T. However, strain MS 3/20T could be distinguished from these and seven other closely related species based on low levels of DNA-DNA relatedness (27.2-53.8%), supported by the unique banding pattern obtained from random amplified polymorphic DNA-PCR amplification and the distinctive matrix-assisted laser desorption/ionization-time-of-flight/mass spectrometry (MALDI-TOF/MS) profile of whole-cell proteins acquired for strain MS 3/20T in comparison with its phylogenetic relatives. Disparate morphological, physiological and chemotaxonomic features, principally growth in NaCl, further corroborated the distinction of strain MS 3/20T from other phylogenetic relatives. Strain MS 3/20T is therefore suggested to be a novel species of the genus Streptomyces, for which the name Streptomyces euryhalinus sp. nov. is proposed. The type strain is MS 3/20T (=CICC 11032T=DSM 103378T).

Predictors of hospital re-admissions among Hispanics with hepatitis C-related cirrhosis.

BACKGROUND: Hospital re-admissions in decompensated cirrhosis are associated with worse patient outcomes. Hispanics have a disproportionately high prevalence of hepatitis C virus (HCV)-related morbidity and mortality. The goal of this study was to evaluate the factors affecting re-admission rates among Hispanics with HCV-related cirrhosis. METHODS: A total of 292 consecutive HCV-related cirrhosis admissions (Hispanics 189, non-Hispanics 103) from January 2009 to December 2012 were retrospectively reviewed; 132 were cirrhosis-related re-admissions. The statistical analysis was performed using STATA version 11.1. Chi-square/Fisher's exact and Student's t-tests were used to compare categorical and continuous variables, respectively. Multivariate logistic regression analysis was performed to identify predictors for hospital readmissions. RESULTS: Among the 132 cirrhosis-related readmissions, 71% were Hispanics while 29% were non-Hispanics (P=0.035). Hepatic encephalopathy (HE) and esophageal variceal hemorrhage were the most frequent causes of the first and subsequent readmissions. Hispanics with readmissions had a higher Child-Turcotte-Pugh (CTP) class (B and C) and higher model for end-stage liver disease (MELD) scores (≥15), as well as a higher incidence of alcohol use, HE, spontaneous bacterial peritonitis, hepatocellular carcinoma, and varices (P<0.05). The majority of the study patients (81%) had MELD scores <15. Multivariate regression analysis identified alcohol use (OR 2.63; 95%CI 1.1-6.4), HE (OR 5.5; 95%CI 2-15.3), varices (OR 3.2; 95%CI 1.3-8.2), and CTP class (OR 3.3; 95%CI 1.4-8.1) as predictors for readmissions among Hispanics. CONCLUSION: CTP classes B and C, among other factors, were the major predictors for hospital readmissions in Hispanics with HCV-related cirrhosis. The majority of these readmissions were due to HE and variceal hemorrhage.

Polymerase chain reaction-based screening method applicable universally to environmental haloarchaea and halobacteria for identifying polyhydroxyalkanoate producers among them.

The existing techniques for detection of polyhydroxyalkanoates (PHA) in halophilic archaea/bacteria are either imprecise or require prior PHA production before screening. The proposed method involves amplification of the approximately 280-300 bp conserved region of Class III PHA synthase (phaC) gene of halophiles using the primers codehopCF and codehopCR (Han et al. Appl Environ Microb 76:7811-7819, 2010). In this study, the best reaction condition was ascertained after repeated trials. This developed method was tested on nine haloarchaeal and halobacterial type strains and 28 environmental halophilic archaea and bacteria isolated from the salt pans of the east and west coasts of India. 29 strains were found to be phaC-positive, while eight were found to be phaC-negative although they appeared PHA positive through conventional Nile Red staining. 16S rRNA-based phylogenetic analysis identified 9 haloarchaeal and 9 halobacterial species as novel PHA producers. Multiple sequence alignment of the phaC gene-derived amino acid sequences showed that only 7 amino acid residues were conserved within all four classes of phaC enzymes, whereas 61 amino acids were identical among the phaC enzyme specific to the haloarchaeal and halobacterial strains presently investigated. All phaC-positive strains produced PHA in standard nutrient deficient medium, whereas the phaC-negative strains did not accumulate any PHA as detected by gas chromatography and nuclear magnetic resonance analyses, thus proving the precision of the developed method and elimination of false positives seen with the traditional Nile Red staining procedure.

The Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile Is a New Strain of Pseudoalteromonas agarivorans Containing Abundant and Diverse Virulence-Related Genes.

Sponge diseases have increased dramatically, yet the causative agents of disease outbreaks have eluded identification. We undertook a polyphasic taxonomic analysis of the only confirmed sponge pathogen and identified it as a novel strain of Pseudoalteromonas agarivorans. 16S ribosomal RNA (rRNA) and gyraseB (gyrB) gene sequences along with phenotypic characteristics demonstrated that strain NW4327 was most closely related to P. agarivorans. DNA-DNA hybridization and in silico genome comparisons established NW4327 as a novel strain of P. agarivorans. Genes associated with type IV pili, mannose-sensitive hemagglutinin pili, and curli formation were identified in NW4327. One gene cluster encoding ATP-binding cassette (ABC) transporter, HlyD and TolC, and two clusters related to the general secretion pathway indicated the presence of type I secretion system (T1SS) and type II secretion system (T2SS), respectively. A contiguous gene cluster of at least 19 genes related to type VI secretion system (T6SS) which included all 13 core genes was found. The absence of T1SS and T6SS in nonpathogenic P. agarivorans S816 established NW4327 as the virulent strain. Serine proteases and metalloproteases of the classes S8, S9, M4, M6, M48, and U32 were identified in NW4327, many of which can degrade collagen. Collagenase activity in NW4327 and its absence in the nonpathogenic P. agarivorans KMM 255(T) reinforced the invasiveness of NW4327. This is the first report unambiguously identifying a sponge pathogen and providing the first insights into the virulence genes present in any pathogenic Pseudoalteromonas genome. The investigation supports a theoretical study predicting high abundance of terrestrial virulence gene homologues in marine bacteria.

Antimicrobial properties of Kalanchoe blossfeldiana: a focus on drug resistance with particular reference to quorum sensing-mediated bacterial biofilm formation.

OBJECTIVES: This study attempts to investigate the antimicrobial properties of Kalanchoe blossfeldiana with a particular reference to quorum sensing (QS)-mediated biofilm formation. METHODS: The methanol extract of K. blossfeldiana leaves (MEKB) was evaluated for antimicrobial properties including QS-controlled production of biofilm (including virulence factor, motility and lactone formation) in Pseudomonas aeruginosa. Methanol extract of K. blossfeldiana was also evaluated for anti-cytokine (tumour necrosis factor-alpha, interleukin-6 and interleukin-1 beta) properties in peripheral blood mononuclear cells (PBMC). KEY FINDINGS: Methanol extract of K. blossfeldiana exhibited antimicrobial effect on clinical isolates, as well as standard reference strains. Pseudomonas aeruginosa exposed to MEKB (subminimum inhibitory concentration (MIC)) displayed reduced biofilm formation, whereas supra-MIC produced destruction of preformed biofilms. Methanol extract of K. blossfeldiana reduced the secretion of virulence factors (protease and pyoverdin) along with generation of acyl homoserine lactone (AHL). Confocal laser scanning microscopy images indicate reduction of biofilm thickness. The extract also reduced cytokine formation in lipopolysaccharide-stimulated PBMC. CONCLUSIONS: Kalanchoe blossfeldiana was found to interfere with AHL production, which in turn may be responsible for downregulating QS-mediated production of biofilm and virulence. This first report on the antibiofilm and anticytokine properties of this plant may open up new vistas for future exploration of this plant for combating biofilm-related resistant infections.

Draft Genome Sequence of Pseudoalteromonas sp. Strain NW 4327 (MTCC 11073, DSM 25418), a Pathogen of the Great Barrier Reef Sponge Rhopaloeides odorabile.

To date, only one marine sponge pathogen (Pseudoalteromonas sp. strain NW 4327) has fulfilled Koch's postulates. We report the 4.48-Mbp draft genome sequence of this strain, which is pathogenic to the Great Barrier Reef sponge Rhopaloeides odorabile. The sequence provides valuable information on sponge-pathogen interactions, including the mode of transmission and associated virulence factors.

Survival of patients with hepatocellular carcinoma in the San Joaquin Valley: a comparison with California Cancer Registry data.

BACKGROUND: Variation in the survival of patients with hepatocellular carcinoma (HCC) is related to racial differences, socioeconomic disparities and treatment options among different populations. METHODS: A retrospective review of the data from medical records of patients diagnosed with HCC were analyzed at an urban tertiary referral teaching hospital and compared to patients in the California Cancer Registry (CCR) - a participant in the Survival Epidemiology and End Results (SEER)program of the National Cancer Institute (NCI). The main outcome measure was overall survival rates. RESULTS: 160 patients with the diagnosis of HCC (M/F=127/33), mean age 59.7±10 years, 32% white, 49% Hispanic, 12% Asian and 6% African American. Multivariate analysis identified tumor size, model for end-stage liver disease (MELD) score, portal vein invasion and treatment offered as the independent predictors of survival (p <0.05). Survival rates across racial groups were not statistically significant. 5.6% received curative treatments (orthotopic liver transplantation, resection, rediofrequency ablation) (median survival 69 months), 34.4% received nonsurgical treatments (trans-arterial chemoembolization, systemic chemotherapy) (median survival 9 months), while 60% received palliative or no treatment (median survival 3 months) (p <0.001). CONCLUSION: There was decreased survival in our patient population with HCC beyond 2 years. 60% of our study population received only palliative or no treatment suggesting a possible lack of awareness of chronic liver disease as well as access to appropriate surveillance modalities. Ethnic disparities such as Hispanic predominance in this study in contrast to the CCR/SEER database may have been a contributing factor for poorer outcome.

Heterotrophic nitrification by Achromobacter xylosoxidans S18 isolated from a small-scale slaughterhouse wastewater.

Heterotrophic carbon utilizing microbes were acclimatized in the laboratory by inoculating sludge collected from the waste discharge pond of a small-scale rural abattoir in India in a nutrient solution intermittently fed with glucose and ammonium chloride. Cultures of 10 well-developed isolates were selected and grown in a basal medium containing glucose and ammonium chloride. Culture supernatants were periodically analyzed for ammonium nitrogen (NH(4)(+)-N) and chemical oxygen demand (COD). Polyphasic taxonomic study of the most active nitrifier (S18) was done. Half saturation concentration (K(s)), maximum rate of substrate utilization (k), yield coefficient (Y) and decay coefficient (K(d)) were determined from the Lineweaver-Burk plot using the modified Monod equation. S18 was able to remove 97 ± 2% of (NH(4)(+)-N) and 88 ± 3% of COD. Molecular phylogenetic study supported by physiological and biochemical characteristics assigned S18 as Achromobacter xylosoxidans. Nitrification activity of A. xylosoxidans was demonstrated for the first time, while interestingly, the distinctive anaerobic denitrification property was preserved in S18. K (s) values were determined as 232.13 ± 1.5 mg/l for COD reduction and 2.131 ± 1.9 mg/l for NH(4)(+)-N utilization. Yield coefficients obtained were 0.4423 ± 0.1134 mg of MLVSS/mg of COD and 0.2461 ± 0.0793 mg of MLVSS/mg of NH(4)(+)-N while the decay coefficients were 0.0627 ± 0.0013 per day and 0.0514 ± 0.0008 per day, respectively. After a contact period of 24 h, 650 ± 5 mg/l solids were produced when the initial concentration of COD and NH(4)(+)-N were 1820 ± 10 mg/l and 120 ± 5.5 mg/l, respectively. This is the first report on the kinetic coefficients for carbon oxidation and nitrification by a single bacterium isolated from slaughterhouse wastewater.

Bedside sublingual video imaging of microcirculation in assessing bacterial infection in cirrhosis.

Bacterial infections are common in cirrhosis and can lead to life-threatening complications. Sidestream dark-field (SDF) imaging has recently emerged as a noninvasive tool for capturing real-time video images of sublingual microcirculation in critically ill patients with sepsis. The objective of this study was to assess the utility of SDF in determining underlying infection in patients with cirrhosis. Sublingual microcirculation was compared among patients with compensated cirrhosis (Group A, n=13), cirrhosis without sepsis (Group B, n=18), cirrhosis with sepsis (Group C, n=14), and sepsis only (Group D, n=10). The blood flow was semi-quantitatively evaluated in four equal quadrants in small (10-25 mm); medium (26-50 mm); and large (51-100 mm) sublingual capillaries. The blood flow was described as no flow (0), intermittent flow (1), sluggish flow (2), and continuous flow (3). The overall flow score or microvascular flow index (MFI) was measured for quantitative assessment of microcirculation and predicting power for concurrent infection in cirrhosis. Marked impairment was observed at all levels of microvasculature in Groups B and C when compared with Group A. This effect was restricted to small vessels only when Group B was compared with Group C. MFI<1.5 was found to have highest sensitivity (100%) and specificity (100%) for infection in decompensated cirrhosis. SDF imaging of sublingual microcirculation can be a useful bedside diagnostic tool to assess bacterial infection in cirrhosis.

A lipidomic analysis of nonalcoholic fatty liver disease.

UNLABELLED: The spectrum of nonalcoholic fatty liver disease (NAFLD) includes a nonalcoholic fatty liver (NAFL) and nonalcoholic steatohepatitis (NASH). The specific types and amounts of lipids that accumulate in NAFLD are not fully defined. The free fatty acid (FFA), diacylglycerol (DAG), triacylglycerol (TAG), free cholesterol (FC), cholesterol ester, and phospholipid contents in normal livers were quantified and compared to those of NAFL and NASH, and the distribution of fatty acids within these classes was compared across these groups. Hepatic lipids were quantified by capillary gas chromatography. The mean (nmol/g of tissue) DAG (normal/NAFL/NASH: 1922 versus 4947 versus 3304) and TAG (13,609 versus 128,585 versus 104,036) increased significantly in NAFLD, but FFA remained unaltered (5533 versus 5929 versus 6115). There was a stepwise increase in the mean TAG/DAG ratio from normal livers to NAFL to NASH (7 versus 26 versus 31, P < 0.001). There was also a similar stepwise increment in hepatic FC (7539 versus 10,383 versus 12,863, P < 0.05 for NASH). The total phosphatidylcholine (PC) decreased in both NAFL and NASH. The FC/PC ratio increased progressively (0.34 versus 0.69 versus 0.71, P < 0.008 for both). Although the levels for linoleic acid (18:2n-6) and alpha-linolenic acid (18:3n-3) remained unaltered, there was a decrease in arachidonic acid (20:4n-6) in FFA, TAG, and PC (P < 0.05 for all) in NASH. Eicosapentanoic acid (20:5n-3) and docosahexanoic acid (22:6n-3) were decreased in TAG in NASH. The n-6:n-3 FFA ratio increased in NASH (P < 0.05). CONCLUSIONS: NAFLD is associated with numerous changes in the lipid composition of the liver. The potential implications are discussed.

Physiologic concentrations of leptin increase collagen production by non-immortalized human hepatic stellate cells.

The effects of leptin, in concentrations seen in obesity, on collagen production and turnover in non-immortalized human hepatic stellate cell (HSC), were unknown. The profibrogenic effects of leptin in these cells were studied. Hepatic stellate cells were obtained from resected livers. Collagen I/III gene expression and protein production were measured by quantitative real-time polymerase chain reaction and sodium dodecyl sulfate-polyacrylamide gel electrophoresis, respectively. The signal transduction pathways involved were evaluated by specific blockers of the phosphatidylinositol 3-kinase (PI3K), mitogen-activated protein kinase kinase (MEK), and Janus kinase 2 (JAK2). The effects on matrix metalloproteinase 1 (MMP-1) and tissue inhibitor of metalloproteinase 1 (TIMP-1) were assessed by their gene transcript levels, collagenolytic activity of cell culture supernatants, and MMP-1 protein levels. At concentrations seen in nonobese individuals ([leptin] < 10 ng/mL), leptin did not affect collagen production. At concentrations seen in obesity (30-50 ng/mL), leptin increased collagen I and III messenger RNA (mRNA) transcript levels by 286% +/- 55% (P < .001) and 167% +/- 62% (P < .007) and protein production by 45.8% +/- .02% and 84.39% +/- .01%, respectively. These effects were blocked by JAK2 inhibition as well as PI3K inhibition. Although MEK inhibition blocked leptin-induced procollagen I and III mRNA levels, there were no significant effects on collagen I and III protein levels. Leptin (10-50 ng/mL) had no significant effects on MMP-1 or TIMP-1 mRNA levels, collagenolytic activity, or MMP-1 protein levels. In conclusion, leptin, at levels seen in obese individuals, produces an increase in collagen production by HSC acting through the JAK and PI3K pathways. At these concentrations, leptin does not affect MMP-1 or TIMP-1 expression or collagenolytic activity of HSC.

Clinical aspects of fatty liver disease.

The global emergence of obesity as an epidemic has made fatty liver disease a public health problem in the Western world. The increased incidence of obesity has been paralleled by an increase in metabolic syndrome in the same cohort of patients. The net consequence of insulin resistance in a large majority of these obese individuals is hepatic steatosis, which over time in a proportion of these patients progresses to steatohepatitis and cirrhosis. Despite the increased awareness among physicians regarding its presence, the diagnostic process has been hampered by the lack of sensitive and specific population-based screening tests. Liver biopsy remains the gold standard for diagnosis as well as for grading and staging of the disease process but its precise role in the diagnostic conundrum continues to be debated.

The histologic spectrum of nonalcoholic fatty liver disease.

Nonalcoholic fatty liver disease (NAFLD) represents a range of histologic lesions in the liver that occur in individuals who do not consume alcohol in quantities that generally are considered to be harmful. The histologic spectrum of NAFLD includes isolated predominantly macrovesicular steatosis alone at one end and steatohepatitis at the other. Nonalcoholic steatohepatitis can progress to cirrhosis and now also is considered to be a precursor of cryptogenic cirrhosis. This article provides an understanding of the histologic features of NAFLD and the potential pitfalls in the histologic assessment of this condition.

Insulin resistance and the pathogenesis of nonalcoholic fatty liver disease.

The prevalence of obesity has reached epidemic proportions in most of the western world. Current estimates suggest that 22.5%of the population of the United States suffers from obesity and is at risk for development of obesity-related complications, including hypertension, coronary artery disease, diabetes, hyperlipidemia,increased predisposition for various cancers, and nonalcoholic fatty liver disease. Fatty liver disease is currently the most common abnormality observed in hepatology practice. Since it was first reported in the 1980s in obese diabetic females, our understanding of nonalcoholic fatty liver (NAFL) and nonalcoholic steatohepatitis (NASH) has undergone significant metamorphosis. It is now universally accepted that insulin resistance and subsequent hyperinsulinemia are key factors that lead to both NAFL and NASH.This article reviews the role of insulin resistance in the genesis of these conditions.

Treatment of Ascites.

Ascites is the most common complication of cirrhosis and occurs in more than half of all patients with cirrhosis. The development of ascites indicates progression of the underlying cirrhosis and is associated with a 50% 2-year survival rate. Conventional therapies used for the treatment of ascites include sodium restriction (<88 mmol/d), diuretics, and large volume paracentesis (LVP) (>5 L). The most effective diuretic combination is that of a potassium-sparing, distal-acting diuretic (eg, spironolactone) with a loop diuretic (eg, furosemide). LVP provides rapid resolution of symptoms with minimal complications and is well tolerated by most patients. Post-paracentesis circulatory dysfunction (PPCD) may occur after LVP and is characterized by hyponatremia, azotemia, and an increase in plasma renin activity. PPCD is associated with an increased mortality and may be prevented by administration of albumin intravenously (6 to 8 g/L of ascites removed) along with LVP. The development of either diuretic-resistant or diuretic-intractable ascites occurs in approximately 5% to 10 % of all cases of ascites. This is a poor prognostic sign, as 50% of such patients die within 6 months of its development. The only definitive therapy for refractory ascites with cirrhosis is orthotopic liver transplantation. The other options that are available include LVP, peritoneovenous shunts, and transjugular intrahepatic portosystemic shunts (TIPS). The TIPS procedure has not been shown to have any influence on survival in patients with cirrhosis and refractory ascites, and TIPS is contraindicated in patients who have advanced liver failure because it can hasten death in such individuals. Peritoneovenous shunts are associated with a high incidence of complications and frequent occlusion. They are, therefore, rarely used for refractory ascites. Spontaneous bacterial peritonitis (SBP) is a common complication of cirrhotic ascites. It may precipitate hepatorenal syndrome. The overall mortality rate from an episode of SBP is approximately 20%. Following an episode of SBP, the 1-year mortality rate approaches 70%. Hospitalized patients should be treated with intravenous third-generation cephalosporins (eg, cefotaxime), and patients at risk should receive prophylaxis with either orally administered quinolones (eg, norfloxacin) or cotrimoxazole.

Skeletal muscle lymphoma.

Lymphoma usually presents with painless lymphadenopathy. However, it can also present at an extranodal site. Presentation with skeletal muscle infiltration is relatively uncommon and can be confused with a wide variety of both inflammatory as well as neoplastic conditions. We report a patient who presented with progressive swelling of the lower extremity resembling inflammatory necrosis on computed tomography scan, but was later diagnosed as skeletal muscle lymphoma on biopsy.