Temperature dependence of fast carbonyl backbone dynamics in chicken villin headpiece subdomain

Temperature-dependence of protein dynamics can provide information on details of the free energy landscape by probing the characteristics of the potential responsible for the fluctuations. We have investigated the temperature-dependence of picosecond to nanosecond backbone dynamics at carbonyl carbon sites in chicken villin headpiece subdomain protein using a combination of three NMR relaxation rates: ¹³C′ longitudinal rate, and two cross-correlated rates involving dipolar and chemical shift anisotropy (CSA) relaxation mechanisms, ¹³C′/¹³C′-¹³C^α CSA/dipolar and ¹³C′/¹³C′–¹⁵N CSA/dipolar. Order parameters have been extracted using the Lipari-Szabo model-free approach assuming a separation of the time scales of internal and molecular motions in the 2–16°C temperature range. There is a gradual deviation from this assumption from lower to higher temperatures, such that above 16°C the separation of the time scales is inconsistent with the experimental data and, thus, the Lipari-Szabo formalism can not be applied. While there are variations among the residues, on the average the order parameters indicate a markedly steeper temperature dependence at backbone carbonyl carbons compared to that probed at amide nitrogens in an earlier study. This strongly advocates for probing sites other than amide nitrogen for accurate characterization of the potential and other thermodynamics characteristics of protein backbone.     

Sedimentation of photosynthetic pigments during the bloom of the green sulfur bacterium <Emphasis Type="Italic">Chlorobium phaeobacteroides</Emphasis> in Lake Kinneret: spatial patterns

Sediment fluxes were studied in the subtropical Lake Kinneret (Israel) in 2006, 2007, and 2008 from mid-June to October, when lake was chemically stratified and the green sulfur bacterium Chlorobium phaeobacteroides formed a dense population in the anoxic metalimnion. The rate of seston accumulation in traps was measured with sedimentation traps positioned along an offshore transect connecting the littoral zone and lake center. The sediment fluxes increased from the lake center towards the littoral, while the percentage of organic material (OM) decreased correspondingly. High fluxes of bacteriochlorophyll e (BChl e—a signature pigment of Chl. phaeobacteroides) and chlorophyll a (Chl a—a marker for eukaryotic algae and cyanobacteria) were detected in all locations. The relative contributions of Chl a and BChl e to the bulk of the accumulated OM were higher in traps positioned below the thermocline in the pelagic zone than in traps located near the shore line. The presence of BChl e in traps exposed to oxic conditions in the littoral, where Chl. phaeobacteroides does not develop, implies horizontal translocation of cells from the lake center towards its periphery. We assume that seiche-mediated movement of particles embedded in the metalimnetic waters is the most probable explanation for the existence of Chl. phaeobacteroides tracer in an oxic environment, but do not exclude the possibility of resuspension of settled particles as source for BChl e in littoral traps. The green sulfur bacteria are potentially important component of the sediment flux of photosynthesizing organisms in a thermally stratified lake and should be taken into account when carbon budget are constructed.     

Pattern of occurrence of supraneural coelomopores and intertentacular organs in Gymnolaemata (Bryozoa) and its evolutionary implications

The evolution of bryozoan female gonopores (the supraneural coelomopore (SNP) and the intertentacular organ (ITO)) is considered in the light of two alternative hypotheses. In the first hypothesis it is proposed that the ITO originated from the shortening and fusion of two tentacles possessing terminal pore(s), with further transformation into a simple pore. In the alternative hypothesis it is suggested that the ITO evolved from a coelomopore with a contribution from the basal parts of two disto-medial tentacles in an ancestor. Favouring the second hypothesis, in this paper we present a hypothetical scenario, according to which the earliest gymnolaemate bryozoans with uniserial growth and a broadcasting reproductive pattern possessed the supraneural coelomopore (SNP). This could serve both as a female gonopore and as a conduit for sperm entry. Evolution of large colonies of closely packed zooids led to development of the tube-like intertentacular organ (ITO) that is formed by epithelial proliferation of the basal parts of two dorso-medial tentacles. This prevented egg swallowing in the situation when water exchange was hampered within the large colony. The ITO independently evolved in both ctenostome and cheilostome gymnolaemates when multiserial colonies appeared. Evolution of brooding in species with colonies of closely packed zooids led to reduction of the ITO, except for the cheilostomes Tendra and Thalamoporella that acquired brooding independently. A rudimentary ITO also “survived” in two ctenostomes with the “mixed” type of brooding. An alternative, analogous organ—the ovipositor—has evolved in the cheilostome taxon Schizoporella.     

The Urinary Cytokine/Chemokine Signature of Renal Hyperfiltration in Adolescents with Type 1 Diabetes

Objective

Urinary cytokine/chemokine levels are elevated in adults with type 1 diabetes (T1D) exhibiting renal hyperfiltration. Whether this observation extends to adolescents with T1D remains unknown. Our first objective was to determine the relationship between hyperfiltration and urinary cytokines/chemokines in normotensive, normoalbuminuric adolescents with T1D using GFR_cystatin. Our second aim was to determine the relationship between urine and plasma levels of inflammatory biomarkers, to clarify the origin of these factors.

Methods

Urine and serum cytokines/chemokines (Luminex platform) and GFR_cystatin were measured in normofiltering (n = 111, T1D-N, GFR<135 ml/min/1.73 m²) and hyperfiltering (n = 31, T1D-H, GFR≥135 ml/min/1.73 m²) adolescents with T1D (ages 10–16), and in age and sex matched healthy control subjects (HC, n = 59).

Results

We noted significant step-wise increases in urinary cytokine/chemokine excretion according to filtration status with highest levels in T1D-H, with parallel trends in serum analyte concentrations. After adjusting for serum glucose at the time of sampling, differences in urinary cytokine excretion were not statistically significant. Only serum IL-2 significantly differed between HC and T1D (p = 0.0076).

Conclusions

Hyperfiltration is associated with increased urinary cytokine/chemokine excretion in T1D adolescents, and parallel trends in serum cytokine concentration. The GFR-associated trends in cytokine excretion may be driven by the effects of ambient hyperglycemia. The relationship between hyperfiltration, glycemia, and variations in serum and urine cytokine expression and their impact on future renal and systemic vascular complications requires further study.     

Distribution,growth, production,and ecological significance of the clam Unio terminalis in Lake Kinneret,Israel

The distribution, body composition, growth rate, and population structure of Unio terminalis were measured at different sites of Lake Kinneret (Israel). Maximum clam density was found on the muddy sand between 0.3–6 m depth. Clams were most abundant in the River Jordan inlet zone, where they showed the highest growth rate. This was probably related to both highest food availability and the highest density of fish hosting Unio glochidia in this area. U. terminalis in Lake Kinneret has a more massive shell and ash content as compared with the European Unio species. The annual P/B ratios of U. terminalis populations at different sites were similar and ranged within 0.17–0.18. The computated filtration capacity and energetic budget permit the assumption that the U. terminalis population plays a substantial role in removal of organic particles from the water in the Kinneret shallow inshore zone (up to 15 m depth), and in nutrient recycling.     

Free Radicals in Mercury-Resistant Bacteria Indicate a Novel Metabolic Pathway

A mercury resistant-soil bacterium P.10.15, identified as a close relative of Pseudomonas veronii, was shown to accumulate a specific compound in the stationary phase of growth. This compound is converted to a long-lived free radical under oxidizing conditions, as registered by its EPR signal at room temperature. The compound was purified by ion-exchange and gel-filtration chromatography and identified by mass spectroscopy, 2D NMR, and EPR as a trisaccharide -D-GlcpNOH,CH₃-(16)--D-Glcp-(11)--D-Glcp, or, in other words, as 6-O-(2-deoxy-2-{N-methyl}hydroxylamino--D-glucopyranosyl)---trehalose, previously discovered in Micrococcus luteus (lysodeikticus) and named lysodektose. It is suggested that the compound is a novel intermediate of a previously unknown basic metabolic pathway of trehalose transformation in bacteria, a potential target for antibacterial drug development.     

Motion of polymer ends in homopolymer and heteropolymer collapse.

To investigate the polymer coil-to-globule transition we performed simulations for the kinetics of homopolymer and heteropolymer collapse. Our stimulations made use of abstract models of long flexible polymers to obtain extensive statistical sampling. For a variety of these models, the simulations suggest that collapse of long polymers is dominated by diffusion of the polymer ends, which accrete monomers and small aggregates. The growth of the end aggregate was found to be nearly linear in time for homopolymers and largely unaffected by variations in microstructure. In contrast, for heteropolymers the presence of non-aggregating (hydrophilic) monomers dramatically slows and alters the growth of the end mass. In models simulated, the end mass grows roughly as the cube root of time, but still dominates aggregation along the contour. In a model where only pairwise bonding is allowed, the collapse is uniform since more flexible end motion does not result in continued end accretion. The possible significance of our results for biopolymer kinetics is discussed.     

The ability of bacteria to synthesize a new cyclopyrophosphate correlates with their tolerance to redox-cycling drugs: on a crossroad of chemotherapy, environmental toxicology and immunobiochemical problems.

Many redox-cyclers were recently shown to induce, in some bacterial species, large-scale biosynthesis of a new 2-methylbutan-1,2,3,4-tetraol-2,4-cyclopyrophosphate believed to be involved in anti-stress reactions. In the present study Mycobacterium smegmatis, Micrococcus luteus and Brevibacterium ammoniagenes were shown to begin synthesis of the new cyclopyrophosphate when cultivated in a medium containing furacilin or furadonin (widely used nitrofuran antibacterial drugs) and to maintain close to normal growth rates, whereas Staphylococcus aureus, Bacillus subtilis and Escherichia coli were inhibited by the drugs and were unable to synthesize the cyclopyrophosphate compound. Preferential binding of Mg2+ and Cd2+ with one or other phosphoryl groups of the cyclopyrophosphate, which was indicated by selective changes of 31P-NMR chemical shifts and intramolecular hydrogen bonding, is suggested as a reason for this selectivity.     

Sexual reproduction of the placental brooder Celleporella hyalina (Bryozoa,Cheilostomata) in the White Sea

The evolution of parental care is a central field in many ecological and evolutionary studies, but integral approaches encompassing various life-history traits are not common. Else, the structure, development and functioning of the placental analogues in invertebrates are poorly understood. Here, we describe the life-history, sexual colony dynamics, oogenesis, fertilization and brooding in the boreal-Arctic cheilostome bryozoan Celleporella hyalina. This placental brooder incubates its progeny in calcified protective chambers (ovicells) formed by polymorphic sexual zooids. We conducted a detailed ultrastructural study of the ovary and oogenesis, and provide evidence of both auto- and heterosynthetic mechanisms of vitellogenesis. We detected sperm inside the early oocyte and within funicular strands, and discuss possible variants of fertilization. We also detail the development and functioning of the placental analogue (embryophore) in the various stages of embryonic incubation as well as embryonic histotrophic nourishment. In contrast to all known cheilostome placentas, the main part of embryophore of C. hyalina is not a single cell layer. Rather, it is a massive “nutritive tissue” whose basal part is associated with funicular strands presumably providing transport function. C. hyalina shows a mixture of reproductive traits with macrolecithal oogenesis and well-developed placenta. These features give it an intermediate position in the continuum of variation of matrotrophic provisioning between lecithotrophic and placentotrophic cheilostome brooders. The structural and developmental differences revealed in the placental analogue of C. hyalina, together with its position on the bryozoan molecular tree, point to the independent origin of placentation in the family Hippothoidae.     

Mitochondrial DNA Variant in COX1 Subunit Significantly Alters Energy Metabolism of Geographically Divergent Wild Isolates in Caenorhabditis elegans

Mitochondrial DNA (mtDNA) sequence variation can influence the penetrance of complex diseases and climatic adaptation. While studies in geographically defined human populations suggest that mtDNA mutations become fixed when they have conferred metabolic capabilities optimally suited for a specific environment, it has been challenging to definitively assign adaptive functions to specific mtDNA sequence variants in mammals. We investigated whether mtDNA genome variation functionally influences Caenorhabditis elegans wild isolates of distinct mtDNA lineages and geographic origins. We found that, relative to N2 (England) wild-type nematodes, CB4856 wild isolates from a warmer native climate (Hawaii) had a unique p.A12S amino acid substitution in the mtDNA-encoded COX1 core catalytic subunit of mitochondrial complex IV (CIV). Relative to N2, CB4856 worms grown at 20 °C had significantly increased CIV enzyme activity, mitochondrial matrix oxidant burden, and sensitivity to oxidative stress but had significantly reduced lifespan and mitochondrial membrane potential. Interestingly, mitochondrial membrane potential was significantly increased in CB4856 grown at its native temperature of 25 °C. A transmitochondrial cybrid worm strain, chpIR (M, CB4856 > N2), was bred as homoplasmic for the CB4856 mtDNA genome in the N2 nuclear background. The cybrid strain also displayed significantly increased CIV activity, demonstrating that this difference results from the mtDNA-encoded p.A12S variant. However, chpIR (M, CB4856 > N2) worms had significantly reduced median and maximal lifespan relative to CB4856, which may relate to their nuclear–mtDNA genome mismatch. Overall, these data suggest that C. elegans wild isolates of varying geographic origins may adapt to environmental challenges through mtDNA variation to modulate critical aspects of mitochondrial energy metabolism.