Distinct sub-populations of the retinoblastoma protein show a distinct pattern of phosphorylation.

Phosphorylation of the retinoblastoma protein (pRB) is assumed to regulate its growth-controlling function. Moreover, hypophosphorylated and hyperphosphorylated forms of pRB can be distinguished by virtue of the distinct affinities with which they bind to the cell nucleus. This property allows the identification of individual cell nuclei that contain pRB in one or the other form. We show here that after cells emerge from a quiescent (G0) state, conversion of their complement of pRB into a hyperphosphorylated form occurs in late G1, preceding entry into S phase by several hours. Thus, contrary to earlier reports, pRB phosphorylation is not co-ordinated with the G1-S transition and may not directly regulate it. A distinct set of phosphopeptides is found exclusively in those forms of pRB that show the loose nuclear association characteristic of the hyperphosphorylated form of pRB. Another set of phosphopeptides is found with both hypophosphorylated and hyperphosphorylated forms. This suggests the existence of distinct patterns of phosphorylation that are associated with different subsets of pRB molecules. We conclude that substantial phosphorylation of pRB exists in G1 even prior to the hyperphosphorylation point. Cyclin-dependent kinases can cause a liberation of pRB from cell nuclei in vitro. Phosphorylation by members of this kinase family is therefore likely to be directly involved in the change in nuclear affinity in vivo and the associated changes in pRB functioning.     

DNA Binding and Condensation Properties of the Herpes Simplex Virus Type 1 Triplex Protein VP19C

Herpesvirus capsids are regular icosahedrons with a diameter of a 125 nm and are made up of 162 capsomeres arranged on a T = 16 lattice. The capsomeres (VP5) interact with the triplex structure, which is a unique structural feature of herpesvirus capsid shells. The triplex is a heterotrimeric complex; one molecule of VP19C and two of VP23 form a three-pronged structure that acts to stabilize the capsid shell through interactions with adjacent capsomeres. VP19C interacts with VP23 and with the major capsid protein VP5 and is required for the nuclear localization of VP23. Mutation of VP19C results in the abrogation of capsid shell synthesis. Analysis of the sequence of VP19C showed the N-terminus of VP19C is very basic and glycine rich. It was hypothesized that this domain could potentially bind to DNA. In this study an electrophoretic mobility shift assay (EMSA) and a DNA condensation assay were performed to demonstrate that VP19C can bind DNA. Purified VP19C was able to bind to both a DNA fragment of HSV-1 origin as well as a bacterial plasmid sequence indicating that this activity is non-specific. Ultra-structural imaging of the nucleo-protein complexes revealed that VP19C condensed the DNA and forms toroidal DNA structures. Both the DNA binding and condensing properties of VP19C were mapped to the N-terminal 72 amino acids of the protein. Mutational studies revealed that the positively charged arginine residues in this N-terminal domain are required for this binding. This DNA binding activity, which resides in a non-conserved region of the protein could be required for stabilization of HSV-1 DNA association in the capsid shell.     

From genomics to metagenomics

Next-generation sequencing has changed metagenomics. However, sequencing DNA is no longer the bottleneck, rather, the bottleneck is computational analysis and also interpretation. Computational cost is the obvious issue, as is tool limitations, considering most of the tools we routinely use have been built for clonal genomics or are being adapted to microbial communities. The current trend in metagenomics analysis is toward reducing computational costs through improved algorithms and through analysis strategies. Data sharing and interoperability between tools are critical, since computation for metagenomic datasets is very high.     

Dual recombinant Lactococcus lactis for enhanced delivery of DNA vaccine reporter plasmid pPERDBY

Food grade Lactococcus lactis has been widely used as an antigen and DNA delivery vehicle. We have previously reported the use of non‐invasive L. lactis to deliver the newly constructed immunostimulatory DNA vaccine reporter plasmid, pPERDBY. In the present report, construction of dual recombinant L. lactis expressing internalin A of Listeria monocytogenes and harboring pPERDBY (LL InlA + pPERDBY) to enhance the efficiency of delivery of DNA by L. lactis is outlined. After confirmation and validation of LL InlA + pPERDBY, its DNA delivery potential was compared with previously developed non‐invasive r‐ L. lactis::pPERDBY. The use of invasive L. lactis resulted in around threefold increases in the number of enhanced green fluorescent protein‐expressing Caco‐2 cells. These findings reinforce the prospective application of invasive strain of L. lactis for delivery of DNA/RNA and antigens.     

Serum IgG response to an outer membrane porin protein of Burkholderia cepacia in patients with cystic fibrosis

Early and accurate diagnosis of Burkholderia cepacia infection is important, particularly if segregation is to prevent patient-to-patient transmission. We have examined the serum response to a B. cepacia-specific 80-kDa outer membrane protein. 21 patients colonised with B. cepacia and Pseudomonas aeruginosa for 2–51 months (mean 11 months) were age- and sex-matched with 21 patients colonised with P. aeruginosa but not B. cepacia. The 80-kDa protein was recovered by electroelution from outer membrane proteins, separated by SDS-PAGE, coated onto ELISA plates, reacted with patient sera diluted 1:200, protein A-peroxidase and chromogenic substrate. We found that 19/24 patients colonised with B. cepacia and P. aeruginosa had high values, 2/24 patients had intermediate values, and 2/24 patients had a low value. 20/21 patients colonised with P. aeruginosa alone had low values and 1/21 had an intermediate value. We found that in the longitudinal serum samples studied from four patients only one patient developed high values after the first isolation of B. cepacia suggesting that seroconversion does not occur immediately after the first sputum culture of B. cepacia. We conclude that an ELISA test using B. cepacia-specific 80-kDa outer membrane protein can distinguish B. cepacia colonised and non-colonised patients and may be useful in the early diagnosis of B. cepacia infection.     

Assembly of infectious Kaposi’s sarcoma-associated herpesvirus progeny requires formation of a pORF19 pentamer

Herpesviruses cause severe diseases particularly in immunocompromised patients. Both genome packaging and release from the capsid require a unique portal channel occupying one of the 12 capsid vertices. Here, we report the 2.6 Å crystal structure of the pentameric pORF19 of the γ-herpesvirus Kaposi’s sarcoma-associated herpesvirus (KSHV) resembling the portal cap that seals this portal channel. We also present the structure of its β-herpesviral ortholog, revealing a striking structural similarity to its α- and γ-herpesviral counterparts despite apparent differences in capsid association. We demonstrate pORF19 pentamer formation in solution and provide insights into how pentamerization is triggered in infected cells. Mutagenesis in its lateral interfaces blocked pORF19 pentamerization and severely affected KSHV capsid assembly and production of infectious progeny. Our results pave the way to better understand the role of pORF19 in capsid assembly and identify a potential novel drug target for the treatment of herpesvirus-induced diseases.

In herpesviruses, genome packaging and release from the capsid require a unique portal channel. Here, the authors have resolved the crystal structure of a pentameric KSHV pORF19 assembly and find that it resembles the herpesviral portal cap and provides insights how the viral genome is retained within the capsid.     

Bench-Scale Production of Biosurfactants and their Potential in Ex-Situ MEOR Application

The fermentative production of biosurfactants by five Bacillus strains in a bench-scale bioreactor and evaluation of biosurfactant-based enhanced oil recovery using sand pack columns were investigated. Adjusting the initial dissolved oxygen to 100% saturation, without any further control and with collection of foam and recycling of biomass, gave higher biosurfactant production. The microorganisms were able to produce biosurfactants, thus reducing the surface tension and interfacial tension to 28 mN/m and 5.8–0.5 mN/m, respectively, in less than 10 hours. The crude surfactant concentration of 0.08–1.1 g/L, and critical micelle concentration (CMC) values of 19.4–39 mg/L, corresponding to the biosurfactants produced by the different Bacillus strains, were observed. The efficiency of crude biosurfactant preparation obtained from Bacillus strains for enhanced oil recovery, by sand pack column studies, revealed it to vary from 30.22–34.19% of the water flood residual oil saturation. The results are indicative of the potential of the strains for the development of ex-situ, microbial-enhanced, oil recovery processes.     

Integrity of hypothalamic–pituitary‐testicular axis in exceptional longevity

Hypothalamic integrity increasingly is being recognized as a marker of healthy longevity in rodent models. Insight into hypothalamic function in humans with exceptional longevity can be gained via investigation of the hypothalamic–pituitary‐testicular (HPT) axis in men with exceptional longevity. This study aimed to characterize the HPT axis function, defined by levels of testosterone (T) and luteinizing hormone (LH), in 84 Ashkenazi Jewish men aged 90–106 years. We found that 94% of men exhibited preserved hypothalamic–pituitary function, as evidenced by either normal testosterone and LH levels (25%) or an appropriate rise in LH in response to aging‐related primary testicular dysfunction (69%), a hormone pattern mirroring female menopause. Total T level was not associated with metabolic parameters or survival. These results demonstrate a high prevalence of testicular dysfunction with preserved hypothalamic–pituitary function in men with exceptional longevity. Thus, the role of hypothalamic integrity and HPT axis in healthy aging warrants further investigation.     

Aerobic Fitness,Micronutrient Status,and Academic Achievement in Indian School-Aged Children

Aerobic fitness has been shown to have several beneficial effects on child health. However, research on its relationship with academic performance has been limited, particularly in developing countries and among undernourished populations. This study examined the association between aerobic fitness and academic achievement in clinically healthy but nutritionally compromised Indian school-aged children and assessed whether micronutrient status affects this association. 273 participants, aged 7 to 10.5 years, were enrolled from three primary schools in Bangalore, India. Data on participants’ aerobic fitness (20-m shuttle test), demographics, anthropometry, diet, physical activity, and micronutrient status were abstracted. School-wide exam scores in mathematics and Kannada language served as indicators of academic performance and were standardized by grade level. The strength of the fitness/achievement association was analyzed using Spearman’s rank correlation, multiple variable logistic regression, and multi-level models. Significant positive correlations between aerobic capacity (VO2 peak) and academic scores in math and Kannada were observed (P < 0.05). After standardizing scores across grade levels and adjusting for school, gender, socioeconomic status, and weight status (BMI Z-score), children with greater aerobic capacities (mL * kg-1 * min-1) had greater odds of scoring above average on math and Kannada exams (OR=1.08, 95% CI: 1.02 to 1.15 and OR=1.11, 95% CI: 1.04 to 1.18, respectively). This association remained significant after adjusting for micronutrient deficiencies. These findings provide preliminary evidence of a fitness/achievement association in Indian children. While the mechanisms by which aerobic fitness may be linked to academic achievement require further investigation, the results suggest that educators and policymakers should consider the adequacy of opportunities for physical activity and fitness in schools for both their physical and potential academic benefits.     

Human leukemic cells: Cytochemical studies on nuclear proteins

The DNA:histone ratios have been determined by quantitative cytochemical analyses of individual cells in populations of human lymphocytic cells derived in continuous culture from the peripheral blood buffy coats of patients with acute leukemia or infectious mononucleosis. These populations of lymphocytic cells were quite similar with respect to the Feulgen-DNA and protein content per cell. The close association between DNA and histone was reflected in their similar patterns of distribution in fixed and stained cells; and further evidenced by similarities in the DNA: histone ratios characteristic of these different populations of lymphocytic cells. — Chemical acetylation and methylation of nuclear proteins of these cell populations exhibited some quantitative differences. The chemically acetylated histone content was less, and chemically methylated histone content was greater in cells derived from acute leukemia or infectious mononucleosis than in normal human lymphocytes. These quantitative differences in chemical acetylation and methylation may contribute to specific structural alterations in these histones which modify their functional capacity with respect to interactions with DNA. Such alterations may relate to differences in gene expression as reflected, for example, by the biological and biochemical differences among these human lymphocytic cells.These studies were supported in part by research grants C-6516 from the National Cancer Institute and FR-05526 from the Division of Research Facilities and Resources, National Institutes of Health.Holds Research Career Award K6-CA-22,150 from the National Cancer Institute, National Institutes of Health.