Commentary on “Prevalence and evolution of drug resistance HIV-1 vari-ants in Henan, China”

Critical to the implementation and scale-up of successful antiretroviral therapy worldwide is an understanding of theefficacy,toxicities and durability of antiretroviral regimens in the specific populations,which they are utilized.In orderto obtain this i…     

Commentary on “Prevalence and evolution of drug resistance HIV-1 variants in Henan, China”

Critical to the implementation and scale-up of successful antiretroviral therapy worldwide is an understanding of the efficacy, toxicities and durability of antiretroviral regimens in the specific populations, which they are utilized. In order to obtain this information monitoring and evaluation or operational research must be done in each country or population. The article by Li et al in this issue represents an outstanding example of the importance of data obtained in the populations treated . The authors proactively evaluated the outcomes at 3 and 6 months of 118 and 124 HIV infected individuals, respectively, treated with zidovudine, didanosine and nevirapine in one region in China.     

Commentary on “Prevalence and evolution of drug resistance HIV-1 variants in Henan, China“

Critical to the implementation and scale-up of successful antiretroviral therapy worldwide is an understanding of the efficacy, toxicities and durability of antiretroviral regimens in the specific populations, which they are utilized. In order to obtain this information monitoring and evaluation or operational research must be done in each country or population.The article by Li et al in this issue represents an outstanding example of the importance of data obtained in the populations treated [1].……     

Prevalence and Clinical Significance of HIV Drug Resistance Mutations by Ultra-Deep Sequencing in Antiretroviral-Na?ve Subjects in the CASTLE Study

Background

CASTLE compared the efficacy of atazanavir/ritonavir with lopinavir/ritonavir, each in combination with tenofovir-emtricitabine in ARV-naïve subjects from 5 continents.

Objectives

Determine the baseline rate and clinical significance of TDR mutations using ultra-deep sequencing (UDS) in ARV-naïve subjects in CASTLE.

Methods

A case control study was performed on baseline samples for all 53 subjects with virologic failures (VF) at Week 48 and 95 subjects with virologic successes (VS) randomly selected and matched by CD4 count and viral load. UDS was performed using 454 Life Sciences/Roche technology.

Results

Of 148 samples, 141 had successful UDS (86 subtype B, 55 non-B subtypes). Overall, 30.5% of subjects had a TDR mutation at baseline; 15.6% only had TDR(s) at <20% of the viral population. There was no difference in the rate of TDRs by B (30.2%) or non-B subtypes (30.9%). VF (51) and VS (90) had similar rates of any TDRs (25.5% vs. 33.3%), NNRTI TDRs (11.1% vs.11.8%) and NRTI TDRs (24.4% vs. 25.5%). Of 9 (6.4%) subjects with M184V/I (7 at <20% levels), 6 experienced VF. 16 (11.3%) subjects had multiple TAMs, and 7 experienced VF. 3 (2.1%) subjects had both multiple TAMs+M184V, and all experienced VF. Of 14 (9.9%) subjects with PI TDRs (11 at <20% levels): only 1 experienced virologic failure. The majority of PI TDRs were found in isolation (e.g. 46I) at <20% levels, and had low resistance algorithm scores.

Conclusion

Among a representative sample of ARV-naïve subjects in CASTLE, TDR mutations were common (30.5%); B and non-B subtypes had similar rates of TDRs. Subjects with multiple PI TDRs were infrequent. Overall, TDRs did not affect virologic response for subjects on a boosted PI by week 48; however, a small subset of subjects with extensive NRTI backbone TDR patterns experienced virologic failure.     

Are Plasma Biomarkers of Immune Activation Predictive of HIV Progression: A Longitudinal Comparison and Analyses in HIV-1 and HIV-2 Infections?

Background

Chronic immune activation is a hallmark of HIV infection and has been associated with disease progression. Assessment of soluble biomarkers indicating immune activation provide clues into pathogenesis and hold promise for the development of point-of-care monitoring of HIV in resource-poor-settings. Their evaluation in cohort resources is therefore needed to further their development and use in HIV research.

Methodology/Principal Findings

Longitudinal evaluation of βeta-2 microglobulin (β-2 m), neopterin and suPAR soluble urokinase-type plasminogen activator receptor (suPAR) was performed with archived plasma samples to predict disease progression and provided the first direct comparison of levels in HIV-1 and HIV-2 infections. At least 2095 samples from 137 HIV-1 and 198 HIV-2 subjects with starting CD4% of ≥28 and median follow up of 4 years were analysed. All biomarkers were correlated negatively to CD4% and positively to viral load and to each other. Analyses in subjects living for ≥5 years revealed increases in median β-2 m and neopterin and decreases in CD4% over this period and the odds of death within 5 years were positively associated with baseline levels of β-2 m and neopterin. ROC analyses strengthened the evidence of elevation of biomarkers in patients approaching death in both HIV-1 and HIV-2 infections. Regression models showed that rates of biomarker fold change accelerated from 6–8 years before death with no significant differences between biomarker levels in HIV-1 and HIV-2 at equal time points prior to death.An ‘immune activation index’ analysis indicative of biomarker levels at equivalent viral loads also showed no differences between the two infections.

Conclusions/Significance

Our results suggest that β-2 m and neopterin are useful tools for disease monitoring in both HIV-1 and HIV-2 infections, whereas sUPAR performed less well. Levels of immune activation per amount of virus were comparable in HIV-1 and HIV-2 infected subjects.     

Identification and Сharacteristics of Conserved miRNA in Testis Tissue from Chinese Giant Salamander (Andrias davidianus) by Deep Sequencing

Russian Journal of Bioorganic Chemistry - MicroRNAs (miRNAs) are a family of ～22-nucleotide, non-coding, single-stranded RNA molecules, which are considered as key regulators of gene...     

Distinct and Overlapping Roles for AP-1 and GGAs Revealed by the “Knocksideways” System

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Highlights? AP-1 knocksideways depletes ～100 proteins from clathrin-coated vesicles (CCVs) ? GGA2 knocksideways mainly depletes hydrolases and their receptors ? GGA2 depends on AP-1 for incorporation into CCVs ? AP-1 acts as a linchpin for intracellular CCV formation and is bidirectional     

“Remake” by High-Throughput Sequencing of the Microbiota Involved in the Production of Water Buffalo Mozzarella Cheese

Intermediates of production of two batches of traditional mozzarella cheese were analyzed by culture-independent pyrosequencing. The quantitative distribution of taxa within the samples suggested that thermophilic lactic acid bacteria from the natural starter were mainly responsible for the fermentation, while microorganisms found in raw milk did not develop during fermentation.     

Structural Basis for Highly Effective HIV-1 Neutralization by CD4-Mimetic Miniproteins Revealed by 1.5 Å Cocrystal Structure of gp120 and M48U1

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Different Roles of G Protein Subunits β1 and β2 in Neutrophil Function Revealed by Gene Expression Silencing in Primary Mouse Neutrophils

Neutrophils play important roles in host innate immunity and various inflammation-related diseases. In addition, neutrophils represent an excellent system for studying directional cell migration. However, neutrophils are terminally differentiated cells that are short lived and refractory to transfection; thus, they are not amenable for existing gene silencing techniques. Here we describe the development of a method to silence gene expression efficiently in primary mouse neutrophils. A mouse stem cell virus-based retroviral vector was modified to express short hairpin RNAs and fluorescent marker protein at high levels in hematopoietic cells and used to infect mouse bone marrow cells prior to reconstitution of the hematopoietic system in lethally irradiated mice. This method was used successfully to silence the expression of Gβ₁ and/or Gβ₂ in mouse neutrophils. Knockdown of Gβ₂ appeared to affect primarily the directionality of neutrophil chemotaxis rather than motility, whereas knockdown of Gβ₁ had no significant effect. However, knockdown of both Gβ₁ and Gβ₂ led to significant reduction in motility and responsiveness. In addition, knockdown of Gβ₁ but not Gβ₂ inhibited the ability of neutrophils to kill ingested bacteria, and only double knockdown resulted in significant reduction in bacterial phagocytosis. Therefore, we have developed a short hairpin RNA-based method to effectively silence gene expression in mouse neutrophils for the first time, which allowed us to uncover divergent roles of Gβ₁ and Gβ₂ in the regulation of neutrophil functions.     

New Mode of Energy Metabolism in the Seventh Order of Methanogens as Revealed by Comparative Genome Analysis of “Candidatus Methanoplasma termitum”

The recently discovered seventh order of methanogens, the Methanomassiliicoccales (previously referred to as “Methanoplasmatales”), so far consists exclusively of obligately hydrogen-dependent methylotrophs. We sequenced the complete genome of “Candidatus Methanoplasma termitum” from a highly enriched culture obtained from the intestinal tract of termites and compared it with the previously published genomes of three other strains from the human gut, including the first isolate of the order. Like all other strains, “Ca. Methanoplasma termitum” lacks the entire pathway for CO₂ reduction to methyl coenzyme M and produces methane by hydrogen-dependent reduction of methanol or methylamines, which is consistent with additional physiological data. However, the shared absence of cytochromes and an energy-converting hydrogenase for the reoxidation of the ferredoxin produced by the soluble heterodisulfide reductase indicates that Methanomassiliicoccales employ a new mode of energy metabolism, which differs from that proposed for the obligately methylotrophic Methanosphaera stadtmanae. Instead, all strains possess a novel complex that is related to the F₄₂₀:methanophenazine oxidoreductase (Fpo) of Methanosarcinales but lacks an F₄₂₀-oxidizing module, resembling the apparently ferredoxin-dependent Fpo-like homolog in Methanosaeta thermophila. Since all Methanomassiliicoccales also lack the subunit E of the membrane-bound heterodisulfide reductase (HdrDE), we propose that the Fpo-like complex interacts directly with subunit D, forming an energy-converting ferredoxin:heterodisulfide oxidoreductase. The dual function of heterodisulfide in Methanomassiliicoccales, which serves both in electron bifurcation and as terminal acceptor in a membrane-associated redox process, may be a unique characteristic of the novel order.     

Localization of P42 and F1-ATPase α-Subunit Homolog of the Gliding Machinery in Mycoplasma mobile Revealed by Newly Developed Gene Manipulation and Fluorescent Protein Tagging

Mycoplasma mobile has a unique mechanism that enables it to glide on solid surfaces faster than any other gliding mycoplasma. To elucidate the gliding mechanism, we developed a transformation system for M. mobile based on a transposon derived from Tn4001. Modification of the electroporation conditions, outgrowth time, and colony formation from the standard method for Mycoplasma species enabled successful transformation. A fluorescent-protein tagging technique was developed using the enhanced yellow fluorescent protein (EYFP) and applied to two proteins that have been suggested to be involved in the gliding mechanism: P42 (MMOB1050), which is transcribed as continuous mRNA with other proteins essential for gliding, and a homolog of the F₁-ATPase α-subunit (MMOB1660). Analysis of the amino acid sequence of P42 by PSI-BLAST suggested that P42 evolved from a common ancestor with FtsZ, the bacterial tubulin homologue. The roles of P42 and the F₁-ATPase subunit homolog are discussed as part of our proposed gliding mechanism.     

The Effect of “Ferrodex”, Vitamin A and “Rovimix β-Carotene” on the Iron and Copper Levels in Blood Plasma of Calves

In 8 Versuchen wurde der Gärungsverlauf bei der Silierung von nitratarmem Grünfutter von Welschem Weidelgras, Knaulgras und Gras‐Leguminosen‐Gemenge geprüft. Aus den Ergebnissen geht hervor, daß bei Fehlen von Nitrat im Grünfutter bereits zu Gärbeginn Buttersäure entsteht, parallel zur Milchsäuregärung, auch in leicht vergärbarem Grünfutter. Diese frühzeitige Buttersäurebildung ist mit dem Fehlen von Nitrat als natürlicher Clostridieninhibitor zu erklären. Die Clostridienentwicklung verläuft zu Gärbeginn demnach wesentlich schneller als bisher angenommen wurde. Offensichtlich dienen leicht lösliche Kohlenhydrate als Substrat für die Buttersäurebildung. In nitratarmem Grünfutter werden deshalb Clostridien als Nahrungskonkurrenten für die Milchsäurebakterien wirksam. Aminosäuren werden zu Gärbeginn nicht abgebaut. Trotz z.T. hoher Buttersäuregehalte sind die Ammoniakgehalte gering. Höhere Homologe der Buttersäure fehlen. Die Milchsäuregärung erreicht trotz hoher Zuckergehalte im Grünfutter meist nur ein begrenztes Ausmaß. Es werden Unterschiede in der Vergärbarkeit der Kohlen‐hydratfraktion zwischen den Gräsern angenommen.     

Kinetochore-microtubule interactions “in check” by Bub1, Bub3 and BubR1: The dual task of attaching and signalling

The spindle assembly checkpoint (SAC) prevents anaphase onset until all chromosomes accomplish proper bipolar attachments to the mitotic spindle and come under tension, thereby ensuring the fidelity of chromosome segregation. Despite significant advances in our understanding of SAC signalling, a clear link between checkpoint signalling and the molecular mechanisms underlying chromosome attachment to microtubules has not been established so far. However, independent studies from many groups have interestingly found that the bone-a-fide Bub1, BubR1 and Bub3 SAC proteins are themselves required for proper kinetochore-microtubule (K-MT) interactions. Here, we review these findings and discuss the specific contribution of each of these proteins in the regulation of K-MT attachment, taking into consideration their interdependencies for kinetochore localization as well as their relationship with other proteins with a known role in chromosome attachment and congression.     

Inhibition of HIV-1 Infection by Human α-Defensin-5, a Natural Antimicrobial Peptide Expressed in the Genital and Intestinal Mucosae

Background

α-defensin-5 (HD5) is a key effector of the innate immune system with broad anti-bacterial and anti-viral activities. Specialized epithelial cells secrete HD5 in the genital and gastrointestinal mucosae, two anatomical sites that are critically involved in HIV-1 transmission and pathogenesis. We previously found that human neutrophil defensins (HNP)-1 and -2 inhibit HIV-1 entry by specific bilateral interaction both with the viral envelope and with its primary cellular receptor, CD4. Despite low amino acid identity, human defensin-5 (HD5) shares with HNPs a high degree of structural homology.

Methodology/Principal Findings

Here, we demonstrate that HD5 inhibits HIV-1 infection of primary CD4⁺ T lymphocytes at low micromolar concentration under serum-free and low-ionic-strength conditions similar to those occurring in mucosal fluids. Blockade of HIV-1 infection was observed with both primary and laboratory-adapted strains and was independent of the viral coreceptor-usage phenotype. Similar to HNPs, HD5 inhibits HIV-1 entry into the target cell by interfering with the reciprocal interaction between the external envelope glycoprotein, gp120, and CD4. At high concentrations, HD5 was also found to downmodulate expression of the CXCR4 coreceptor, but not of CCR5. Consistent with its broad spectrum of activity, antibody competition studies showed that HD5 binds to a region overlapping with the CD4- and coreceptor-binding sites of gp120, but not to the V3 loop region, which contains the major determinants of coreceptor-usage specificity.

Conclusion/Significance

These findings provide new insights into the first line of immune defense against HIV-1 at the mucosal level and open new perspectives for the development of preventive and therapeutic strategies.     

Prevalence of symbionts and trypanosome infections in tsetse flies of two villages of the “Faro and Déo” division of the Adamawa region of Cameroon

Background

Tsetse flies are vectors of human and animal African trypanosomiasis. In spite of many decades of chemotherapy and vector control, the disease has not been eradicated. Other methods like the transformation of tsetse fly symbionts to render the fly refractory to trypanosome infection are being evaluated. The aim of the present study was to evaluate the association between trypanosome infections and the presence of symbionts in these tsetse species. Tsetse flies were trapped in two villages of the “Faro and Déo” Division of the Adamawa region of Cameroon. In the field, tsetse fly species were identified and their infection by trypanosomes was checked by microscopy. In the laboratory, DNA was extracted from their midguts and the presence of symbionts (Sodalis glossinidius and Wolbachia sp.) and trypanosomes was checked by PCR. Symbionts/trypanosomes association tests were performed.

Results

Three tsetse fly species including Glossina tachinoides (90.1%), Glossina morsitans submorsitans (9.4%) and Glossina fuscipes fuscipes (0.5%) were caught. In all the population we obtained an occurrence rate of 37.2% for Sodalis glossinidius and 67.6% for Wolbachia irrespective to tsetse flies species. S. glossinidius and Wolbachia sp. occurrence rates were respectively 37 and 68% for G. tachinoides and 28.6 and 59.5% for G. m. submorsitans. Between Golde Bourle and Mayo Dagoum significant differences were observed in the prevalence of symbionts. Prevalence of trypanosomes were 34.8% for Glossina tachinoides and 40.5% for Glossina morsitans submorsitans. In G. tachinoides, the trypanosome infection rates were 11, 2.6 and 13.7%, respectively, for T. brucei s.l., T. congolense forest type and T. congolense savannah type. In G. m. submorsitans, these infection rates were 16.7, 9.5 and, 2.4% respectively, for T. brucei s.l., T. congolense forest type and T. congolense savannah type.

Conclusions

The rate of tsetse fly infection by trypanosomes was low compared to those obtained in HAT foci of south Cameroon, and this rate was not statistically linked to the rate of symbiont occurrence. This study allowed to show for the first time the presence of Wolbachia sp. in the tsetse fly sub-species Glossina morsitans submorsitans and Glossina tachinoides.

     

Asymmetric hybridization in Nicotiana by “gamma fusion” and progeny analysis of self-fertile hybrids

Summary Mesophyll protoplasts of the nitrate-reductase (NR)-deficient Nicotiana plumbaginifolia mutant, Nia26, were fused with -irradiated mesophyll protoplasts of Nicotiana sylvestris, V-42. Hybrid selection was based on complementation of NR deficiency by transfer of the donor NR gene to N. plumbaginifolia. Regenerated hybrids had different numbers of donor chromosomes in a tetraploid background of N. plumbaginifolia. The transfer and expression of different isozymes from the donor were also observed. Six self-fertile regenerants were obtained from 21 independently isolated cell colonies. Progeny analyses revealed: (1) the linkage of NR and shikimate dehydrogenase (ShDh); (2) a stabilization of the transmission rate of NR; and (3) the obtainment of mono- and disomic addition lines in the first and second progeny of the original regenerants. Southern hybridization analyses demonstrated unequivocally the presence of the NR gene from the donor partner in progeny plants.