Interaction between genetic and inductive factors controlling the expression of dispersal and dormancy morphs in dimorphic astigmatic mites

Some astigmatic mites display dimorphic deutonymphs (hypopus) which are facultatively intercalated in their development cycle between protonymph and tritonymph. Such species, among them Glycyphagus privatus and Glycyphagus ornatus show three potential developmental pathways: (1) to bypass the hypopus stage and develop directly from the protonymph to the tritonymph and the subsequent reproductive stage when conditions are favorable; (2) to leave the original site and disperse by means of a phoretic hypopus morph; or (3) to survive inimical life conditions in the natal environment by means of a sedentary hypopus morph. By producing both dispersing (and afterwards at the arrival site reproducing) and sedentary (drought-hardy and dormancy-prone) progeny each single parent attains a selective advantage through a risk-reducing insurance against irregularly fluctuating and often fatal life conditions of their temporary patch habitats. Both genetic heterogeneity and ecological plasticity for hypopus production adapt the Glycyphagus species to cope with variation in the environment. Both traits (for dispersal and survival) are extremely polymorphic with genotypes ranging from low to high propensities for production of each hypopus type. There is a substantial environmental effect on genetic expression such that expression of both morphs depends on the quality of food. This ecological response allows a fast reaction of the mite to the current trophic environment. Phoretic morphs are predominantly expressed at favorable trophic conditions and sedentary morphs at poor trophic conditions. Ecological influences may override genetic propensities and vice versa. Although selection imposed by changing environmental patterns adjusts the frequencies of genotypes over generations and provides for long-term adaptation, the short-term process of environmental induction adapts the population within a generation to transient-habitat disturbances. The interaction of genetic and ecological determinants explains the varying proportions of directly developing mites, phoretic hypopodes, and sedentary hypopodes, in a population at any moment.     

Human Tetherin Exerts Strong Selection Pressure on the HIV-1 Group N Vpu Protein

HIV-1 groups M and N emerged within the last century following two independent cross-species transmissions of SIVcpz from chimpanzees to humans. In contrast to pandemic group M strains, HIV-1 group N viruses are exceedingly rare, with only about a dozen infections identified, all but one in individuals from Cameroon. Poor adaptation to the human host may be responsible for this limited spread of HIV-1 group N in the human population. Here, we analyzed the function of Vpu proteins from seven group N strains from Cameroon, the place where this zoonosis originally emerged. We found that these N-Vpus acquired four amino acid substitutions (E15A, V19A and IV25/26LL) in their transmembrane domain (TMD) that allow efficient interaction with human tetherin. However, despite these adaptive changes, most N-Vpus still antagonize human tetherin only poorly and fail to down-modulate CD4, the natural killer (NK) cell ligand NTB-A as well as the lipid-antigen presenting protein CD1d. These functional deficiencies were mapped to amino acid changes in the cytoplasmic domain that disrupt putative adaptor protein binding sites and an otherwise highly conserved ßTrCP-binding DSGxxS motif. As a consequence, N-Vpus exhibited aberrant intracellular localization and/or failed to recruit the ubiquitin-ligase complex to induce tetherin degradation. The only exception was the Vpu of a group N strain recently discovered in France, but originally acquired in Togo, which contained intact cytoplasmic motifs and counteracted tetherin as effectively as the Vpus of pandemic HIV-1 M strains. These results indicate that HIV-1 group N Vpu is under strong host-specific selection pressure and that the acquisition of effective tetherin antagonism may lead to the emergence of viral variants with increased transmission fitness.     

Physical properties of a genomic condensed chromatin fragment

We have studied the physical properties of a segment of condensed chromatin that lies upstream of the chicken beta-globin locus. This segment can be excised from an avian erythroleukemia cell line by restriction enzyme digestion and released from the nucleus as an essentially homogeneous fragment about 15.5 kbp long. Because of this homogeneity we could measure its sedimentation coefficient quite accurately by a combination of sucrose gradient and analytical ultracentrifugation. By measuring additionally the buoyant density of the cross-linked particle in CsCl we could deduce the total mass of the particle, hence its frictional coefficient, f, directly related to its shape. The measured value of f is consistent with a rod-like particle of the approximate length and diameter proposed earlier for the 30 nm chromatin fiber. The method is generally applicable to homogeneous particles of unique sequence at genomic abundance.     

Distribution of phytoplankton pigments in nine European estuaries and implications for an estuarine typology

Phytoplankton pigments were studied by LiquidChromatography (HPLC) in nine West Europeanestuaries. Three estuaries, i.e. the Rhine,Scheldt and the Gironde were sampled four timesto cover the different seasons, whereas theother six estuaries were sampled once. Pigmentdistributions in estuaries reflect bothriverine inputs as well as autochthonousblooms. Fucoxanthin was the most commonaccessory photosynthetic pigment showing thatDiatoms were the most common group in thestudied estuaries and were particularlydominant during autumn and winter. In the veryturbid Gironde estuary, degradation processeswere predominant between salinities 1 and 20,while Diatoms, Dinoflagellates and Cryptophytesbloomed above 20 salinity during spring andsummer. This contrasted with the highlyeutrophic but less turbid Scheldt, wherephytoplanktonic blooms occurred at lowsalinities close to the city of Antwerp. In theScheldt, we observed both a tenfold fluctuationof phytoplankton biomass and a fluctuatingpigment diversity index. In contrast,chlorophyll a was always low in theGironde, but we observed large variations ofpigment diversity among samplings duringdifferent seasons. Distribution of pheopigmentsshowed that the maximum turbidity zone (MTZ)was a highly reactive region for heterotrophicphytoplankton degradation. The Scheldt and theThames were the most anthropogenic influencedestuaries contrasting with the Gironde estuarythat has a less urbanised watershed. Anestuarine typology is proposed based on threeclusters emerging from a correspondenceanalysis of pigment variables and variablescharacterising the anthropogenic impact andphysical forcing.     

Drosophila chibby is required for basal body formation and ciliogenesis but not for Wg signaling

Centriole-to-basal body conversion, a complex process essential for ciliogenesis, involves the progressive addition of specific proteins to centrioles. CHIBBY (CBY) is a coiled-coil domain protein first described as interacting with β-catenin and involved in Wg-Int (WNT) signaling. We found that, in Drosophila melanogaster, CBY was exclusively expressed in cells that require functional basal bodies, i.e., sensory neurons and male germ cells. CBY was associated with the basal body transition zone (TZ) in these two cell types. Inactivation of cby led to defects in sensory transduction and in spermatogenesis. Loss of CBY resulted in altered ciliary trafficking into neuronal cilia, irregular deposition of proteins on spermatocyte basal bodies, and, consequently, distorted axonemal assembly. Importantly, cby(1/1) flies did not show Wingless signaling defects. Hence, CBY is essential for normal basal body structure and function in Drosophila, potentially through effects on the TZ. The function of CBY in WNT signaling in vertebrates has either been acquired during vertebrate evolution or lost in Drosophila.     

Presence of and phosphate release from polyphosphates or phytate phosphate in lake sediments

NaOH is often used as an extractant for thefractionation of sediment-bound phosphates. Besidesorthophosphate, a certain quantity of phosphate whichis called ‘non-reactive NaOH-extractable phosphate’is also extracted. In recent literature it has beensuggested that this fraction consists of bacterialpolyphosphates and might be responsible for the phosphate release from aquatic sediments under anoxicconditions. In a previous publication we have already shown thatNaOH is not an accurate extractant as both theconcentration of NaOH and the duration of theextraction have an influence on the quantity ofphosphate extracted, due to the hydrolysis of organicphosphates. In this article we show that cold NaOH does not onlyextract iron-bound phosphate but phytate phosphate aswell. Non-reactive phosphate in this extract was notrelated to the presence of polyphosphate, but mainlyto phytate and humic phosphates. As it has been shownthat phytate may disappear from sediments when theybecome anoxic, we suggest that phytate mineralizationmay be an important mechanism for anoxic phosphaterelease from sediments. This revised version was published online in July 2006 with corrections to the Cover Date.     

Engineering antibiotic production and overcoming bacterial resistance

Progress in DNA technology, analytical methods and computational tools is leading to new developments in synthetic biology and metabolic engineering, enabling new ways to produce molecules of industrial and therapeutic interest. Here, we review recent progress in both antibiotic production and strategies to counteract bacterial resistance to antibiotics. Advances in sequencing and cloning are increasingly enabling the characterization of antibiotic biosynthesis pathways, and new systematic methods for de novo biosynthetic pathway prediction are allowing the exploration of the metabolic chemical space beyond metabolic engineering. Moreover, we survey the computer-assisted design of modular assembly lines in polyketide synthases and non-ribosomal peptide synthases for the development of tailor-made antibiotics. Nowadays, production of novel antibiotic can be tranferred into any chosen chassis by optimizing a host factory through specific strain modifications. These advances in metabolic engineering and synthetic biology are leading to novel strategies for engineering antimicrobial agents with desired specificities.     

Serum Vaspin Levels Are Associated with the Development of Clinically Manifest Arthritis in Autoantibody-Positive Individuals

Objectives

We have previously shown that overweight may increase the risk of developing rheumatoid arthritis (RA) in autoantibody positive individuals. Adipose tissue could contribute to the development of RA by production of various bioactive peptides. Therefore, we examined levels of adipokines in serum and synovial tissue of subjects at risk of RA.

Methods

Fifty-one individuals positive for immunoglobulin M rheumatoid factor (IgM-RF) and/or anti-citrullinated protein antibodies (ACPA), without arthritis, were included in this prospective study. Levels of adiponectin, vaspin, resistin, leptin, chemerin and omentin were determined in baseline fasting serum samples (n = 27). Synovial tissue was obtained by arthroscopy at baseline and we examined the expression of adiponectin, resistin and visfatin by immunohistochemistry.

Results

The development of clinically manifest arthritis after follow-up was associated with baseline serum vaspin levels (HR1.5 (95% CI 1.1 to 2.2); p = 0.020), also after adjustment for overweight (HR1.7 (95% CI 1.1 to 2.5); p = 0.016). This association was not seen for other adipokines. Various serum adipokine levels correlated with BMI (adiponectin r = -0.538, leptin r = 0.664; chemerin r = 0.529) and systemic markers of inflammation such as CRP levels at baseline (adiponectin r = -0.449, omentin r = -0.557, leptin r = 0.635, chemerin r = 0.619, resistin r = 0.520) and ESR (leptin r = 0.512, chemerin r = 0.708), p-value<0.05. Synovial expression of adiponectin, resistin and visfatin was not associated with development of clinically manifest arthritis.

Conclusions

In this exploratory study, serum adipokines were associated with an increased inflammatory state in autoantibody-positive individuals at risk of developing RA. Furthermore, serum vaspin levels may assist in predicting the development of arthritis in these individuals.     

5-Propynylamino alpha-deoxyuridine promotes DNA duplex stabilization of anionic and neutral but not cationic alpha-oligonucleotides

Incorporation of 5-propynylamino and 5-propynyl alpha-2'-deoxyuridine into alpha-oligonucleotides (alpha-ON) allows high-affinity targeting of complementary DNA for alpha-ON with anionic and neutral backbone but not for cationic alpha-ON, revealing clues on the role of the amino group of the propynylamino on the formation of DNA duplexes.     

Cellular Responses during Morphological Transformation in Azospirillum brasilense and Its flcA Knockout Mutant

FlcA is a response regulator controlling flocculation and the morphological transformation of Azospirillum cells from vegetative to cyst-like forms. To understand the cellular responses of Azospirillum to conditions that cause morphological transformation, proteins differentially expressed under flocculation conditions in A. brasilense Sp7 and its flcA knockout mutant were investigated. Comparison of 2-DE protein profiles of wild-type (Sp7) and a flcA deletion mutant (Sp7-flcAΔ) revealed a total of 33 differentially expressed 2-DE gel spots, with 22 of these spots confidently separated to allow protein identification. Analysis of these spots by liquid chromatography-tandem mass spectrometry (LC-MS/MS) and MASCOT database searching identified 48 proteins (≥10% emPAI in each spot). The functional characteristics of these proteins included carbon metabolism (beta-ketothiolase and citrate synthase), nitrogen metabolism (Glutamine synthetase and nitric oxide synthase), stress tolerance (superoxide dismutase, Alkyl hydroperoxidase and ATP-dependent Clp protease proteolytic subunit) and morphological transformation (transducer coupling protein). The observed differences between Sp7 wild-type and flcA ⁻ strains enhance our understanding of the morphological transformation process and help to explain previous phenotypical observations. This work is a step forward in connecting the Azospirillum phenome and genome.