CGAL: computing genome assembly likelihoods

Assembly algorithms have been extensively benchmarked using simulated data so that results can be compared to ground truth. However, in de novo assembly, only crude metrics such as contig number and size are typically used to evaluate assembly quality. We present CGAL, a novel likelihood-based approach to assembly assessment in the absence of a ground truth. We show that likelihood is more accurate than other metrics currently used for evaluating assemblies, and describe its application to the optimization and comparison of assembly algorithms. Our methods are implemented in software that is freely available at http://bio.math.berkeley.edu/cgal/.     

Regulation of Human T-Lymphotropic Virus Type I Latency and Reactivation by HBZ and Rex

Human T lymphotropic virus type I (HTLV-I) infection is largely latent in infected persons. How HTLV-1 establishes latency and reactivates is unclear. Here we show that most HTLV-1-infected HeLa cells become senescent. By contrast, when NF-κB activity is blocked, senescence is averted, and infected cells continue to divide and chronically produce viral proteins. A small population of infected NF-κB-normal HeLa cells expresses low but detectable levels of Tax and Rex, albeit not Gag or Env. In these “latently” infected cells, HTLV-1 LTR trans-activation by Tax persists, but NF-κB trans-activation is attenuated due to inhibition by HBZ, the HTLV-1 antisense protein. Furthermore, Gag-Pol mRNA localizes primarily in the nuclei of these cells. Importantly, HBZ was found to inhibit Rex-mediated export of intron-containing mRNAs. Over-expression of Rex or shRNA-mediated silencing of HBZ led to viral reactivation. Importantly, strong NF-κB inhibition also reactivates HTLV-1. Hence, during HTLV-1 infection, when Tax/Rex expression is robust and dominant over HBZ, productive infection ensues with expression of structural proteins and NF-κB hyper-activation, which induces senescence. When Tax/Rex expression is muted and HBZ is dominant, latent infection is established with expression of regulatory (Tax/Rex/HBZ) but not structural proteins. HBZ maintains viral latency by down-regulating Tax-induced NF-κB activation and senescence, and by inhibiting Rex-mediated expression of viral structural proteins.     

In vitro auxin treatment promotes cell division and delays endoreduplication in developing seeds of the model legume species Medicago truncatula

The role of auxins in the morphogenesis of immature seeds of Medicago truncatula was studied, focusing on the transition from the embryo cell division phase to seed maturation. We analyzed seed development in vitro, by flow cytometry, and through the determination of the kinetics of seed fresh weight and size. Thus, seeds were harvested at 8, 10 and 12 days after pollination and cultured in vitro on a medium either without auxin or supplemented with indole‐3‐butyric acid (IBA) or naphthalene acetic acid (NAA) at 1 mg l^?1. All parameters studied were determined every 2 days from the start of in vitro culture. The results showed that both auxins increased the weight and size of seeds with NAA having a stronger effect than IBA. We further demonstrated that the auxin treatments modulate the transition between mitotic cycles and endocycles in M. truncatula developing seed by favoring sustained cell divisions while simultaneously prolonging endoreduplication, which is known to be the cytogenetical imprint of the transition from the cell division phase to the storage protein accumulation phase during seed development.     

HTLV-1 Tax Stimulates Ubiquitin E3 Ligase,Ring Finger Protein 8, to Assemble Lysine 63-Linked Polyubiquitin Chains for TAK1 and IKK Activation

Human T lymphotropic virus type 1 (HTLV-1) trans-activator/oncoprotein, Tax, impacts a multitude of cellular processes, including I-κB kinase (IKK)/NF-κB signaling, DNA damage repair, and mitosis. These activities of Tax have been implicated in the development of adult T-cell leukemia (ATL) in HTLV-1-infected individuals, but the underlying mechanisms remain obscure. IKK and its upstream kinase, TGFβ-activated kinase 1 (TAK1), contain ubiquitin-binding subunits, NEMO and TAB2/3 respectively, which interact with K63-linked polyubiquitin (K63-pUb) chains. Recruitment to K63-pUb allows cross auto-phosphorylation and activation of TAK1 to occur, followed by TAK1-catalyzed IKK phosphorylation and activation. Using cytosolic extracts of HeLa and Jurkat T cells supplemented with purified proteins we have identified ubiquitin E3 ligase, ring finger protein 8 (RNF8), and E2 conjugating enzymes, Ubc13:Uev1A and Ubc13:Uev2, to be the cellular factors utilized by Tax for TAK1 and IKK activation. In vitro, the combination of Tax and RNF8 greatly stimulated TAK1, IKK, IκBα and JNK phosphorylation. In vivo, RNF8 over-expression augmented while RNF8 ablation drastically reduced canonical NF-κB activation by Tax. Activation of the non-canonical NF-κB pathway by Tax, however, is unaffected by the loss of RNF8. Using purified components, we further demonstrated biochemically that Tax greatly stimulated RNF8 and Ubc13:Uev1A/Uev2 to assemble long K63-pUb chains. Finally, co-transfection of Tax with increasing amounts of RNF8 greatly induced K63-pUb assembly in a dose-dependent manner. Thus, Tax targets RNF8 and Ubc13:Uev1A/Uev2 to promote the assembly of K63-pUb chains, which signal the activation of TAK1 and multiple downstream kinases including IKK and JNK. Because of the roles RNF8 and K63-pUb chains play in DNA damage repair and cytokinesis, this mechanism may also explain the genomic instability of HTLV-1-transformed T cells and ATL cells.     

Comparative analysis of IgM sub-variants in salmonid fish and identification of a residue in μ3 which is essential for MAb4C10 reactivity

In rainbow trout (Onchorhynchus mykiss) it has been shown that high affinity IgM antibodies have a higher degree of disulfide polymerization and a longer half life time. In the present study, distinct IgM sub-variants related to ancestral tetraploidy in salmonid fish were analyzed to reveal possible characteristic differences between these. A monoclonal antibody (MAb4C10) which distinguishes between IgM-A and IgM-B in Atlantic salmon (Salmo salar) and brown trout (Salmo trutta) was further characterized. It was shown that substitution of a proline located in the loop between the B and C beta strands of the third constant domain (μ3) of salmon μA eliminated MAb4C10 reactivity. Accordingly, the reverse substitution in salmon μB restored MAb4C10 reactivity. Molecular cloning of μ cDNA from arctic char (Salvelinus alpinus) revealed two sub-variants (μA-1 and μA-2), i.e. a similar situation as in Atlantic salmon and brown trout. However, arctic char IgM eluted in one peak by anion exchange chromatography, in contrast to salmon and brown trout IgM that are eluted in two peaks. The only characteristic residue of salmon and brown trout μB is an additional cysteine in the C-terminal part of μ4. Most likely, this cysteine is involved in inter-chain disulfide bonding and influences the elution profiles of IgM-A and IgM-B on anion exchange chromatography. Neither of the μ sub-variants in arctic char have the additional cysteine, and char IgM, as well as salmon and brown trout IgM-A, showed a lower degree of inter-chain disulfide bonding than IgM-B when subjected to denaturation and gel electrophoresis under non-reducing conditions. Hybrids of char/salmon expressed μA-1, μA-2, μA and μB, indicating that there are two paralogous Ig heavy chain gene complexes in the haploid genome of char, like in Atlantic salmon. A comparison of salmonid μ sequences is presented, including representatives of Salmoninae (trout, salmon and char), Thymallinae (grayling) and Coregoninae (whitefish).     

Protease inhibitors: A panacea?

With the increasing evidence of protease involvement in several diseases, novel strategies for drug development involve the use of protease inhibitors (PIs). The local balance between protease inhibitors and proteases is an important determinant of the occurrence and progression of a particular disease. Hence, enzymes and their cognate inhibitors are finding their applications as diagnostic and prognostic markers. PIs are widely implicated for their use in host defense against infection, tissue repair and matrix production, blood coagulation, cancer, and they are, therefore, the current focus as therapeutic alternatives for major diseases such as AIDS and Alzheimer's diseases. This review is a brief summary of the varied role of protein protease inhibitors in controlling the activity of aberrant enzymes in several diseases afflicting mankind today. © 2010 Wiley Periodicals, Inc. J Biochem Mol Toxicol 24:270–277, 2010; View this article online at wileyonlinelibrary.com . DOI 10.1002/jbt.20335     

Effects of different phytosterol analogs on colonic mucosal cell proliferation in hamsters

OBJECTIVE: The aim of this study was to investigate the effects of different phytosterols and their analogs on colonic mucosal cell proliferation in hamsters. METHOD: Hamsters (n=70) were randomly assigned to seven groups after a 2-week acclimation and fed the experimental diet for 5 weeks. Diets included (i) the semipurified diet with no cholesterol (Con), (ii) the Con diet plus 0.25% cholesterol (Ch-con), or the Ch-con diet with (iii) 1% phytosterols (Ste), (iv) 1% phytostanols (Sta), (v) 1.76% sterol esters (esterified to fish oil, SteF), (vi) 0.71% stanol esters (esterified to ascorbic acid [disodium ascorbyl phytostanol phosphate, FM-VP4], 0.7% StaA) and (vii) 1.43% stanol esters (1.4% StaA), respectively. After 5 weeks on experimental diet, hamsters were sacrificed, and colons were collected. Colonic mucosal cell proliferation was measured by immunohistochemistry using monoclonal antibodies against antigen Ki-67. RESULTS: Colonic mucosal cell proliferation was 21.4% (P<.01) lower in the 0.7%, but not 1.4%, StaA relative to the Ch-con group. In addition, a lower (-13.9%) cell proliferation was observed in the SteF group in comparison to the Ch-con group; however, this difference achieved only a borderline level of statistical significance (P=.069). No differences were observed between Con and Ch-con, as well as among Ste, Sta, 1.4% StaA and Ch-con treatments. CONCLUSION: Plant stanols esterified to ascorbic acid may possess anticarcinogenic properties in the colon by suppressing colonic mucosa cell proliferation; however, this effect was not observed with free plant sterols or stanols.     

Determinants of infant and young child feeding practices by mothers in two rural districts of Sindh,Pakistan: a cross-sectional survey

Background

Infant and young child feeding (IYCF) practices during the first two years of life are important for the growth and development of a child. The aim of this study was to assess IYCF practices and its associated factors in two rural districts of Pakistan.

Methods

A cross-sectional study was conducted in two rural districts of Sindh province, Pakistan as part of a stunting prevention project between May and August 2014. A standard questionnaire on IYCF practices recommended by World Health Organization was used to collect information from 2013 mothers who had a child aged between 0 and 23 months.

Results

Only 49% of mothers initiated breastfeeding within one hour of birth. Thirty-seven percent of mothers exclusively breastfed their infants for six months. Seventy-percent mothers introduced complementary feeding at 6–8 months of age. Eighty-two percent of mothers continued breastfeeding for at least one year and 75% for at least two years of age. IYCF practices were not significantly different for boys and girls in the study area. Being an employed mother (AOR 2.14; 95% CI 1.02, 4.51) was positively associated with the early initiation of breastfeeding. Children who were born at a health facility (AOR 0.65; 95% CI 0.50, 0.84) and were aged six to eleven months (AOR 0.70; 95% CI 0.54, 0.90) were less likely to be have an early initiation of breastfeeding. Mothers aged 25 to 29 years (AOR 1.83; 95% CI 1.05, 3.18), being literate (AOR 1.79; 95% CI 1.15, 2.78), and higher income (AOR 10.6; 95% CI 4.40, 25.30) were more likely to have an improved dietary diversity. Being an employed mother (AOR 2.18; 95% CI 1.77, 4.03) and higher income were more likely to have minimum acceptable diet (AOR 9.7; 95% CI 4.33, 21.71).

Conclusion

IYCF practices were below the acceptable level and associated with maternal age, maternal illiteracy, unemployment, and poor household wealth status. Emphasis should be given to improve maternal literacy and reduction in poverty to improve IYCF practices.

     

Effect of Rheology and Poloxamers Properties on Release of Drugs from Silicon Dioxide Gel-Filled Hard Gelatin Capsules—A Further Enhancement of Viability of Liquid Semisolid Matrix Technology

The liquid and semisolid matrix technology, filling liquids, semi-solids and gels in hard gelatin capsule are promising, thus, there is a need of enhanced research interest in the technology. Therefore, the present study was aimed to investigate isoniazid (freely soluble) and metronidazole (slightly soluble) gels filled in hard gelatin capsules for the effect of poloxamers of different viscosities on release of the drugs. Gel of each drug (10% w/w, particle size 180–250 μm), prepared by mixing poloxamer and 8% w/w hydrophilic silicon dioxide (Aerosil® A200), was assessed for rheology, dispersion stability and release profile. Both the drugs remained dispersed in majority of gels for more than 30 days, and dispersions were depended on gels’ viscosity, which was further depended on viscosity of poloxamers. A small change in viscosity was noted in gels on storage. FTIR spectra indicated no interactions between components of the gels. The gels exhibited thixotropic and shear-thinning behaviour, which were suitable for filling in hard gelatin capsules without any leakage from the capsules. The release of both drugs from the phase-stable gels for 30 days followed first-order kinetics and was found to be correlated to drugs’ solubility, poloxamers’ viscosity, polyoxyethylene contents and proportion of block copolymer (poloxamers) in the gels. The findings of the present study indicated that release of drugs of different solubilities (isoniazid and metronidazole) might be modified from gels using different poloxamers and Aerosil® A200.