NMR dynamic studies suggest that allosteric activation regulates ligand binding in chicken liver bile acid-binding protein

Apo chicken liver bile acid-binding protein has been structurally characterized by NMR. The dynamic behavior of the protein in its apo- and holo-forms, complexed with chenodeoxycholate, has been determined via (15)N relaxation and steady state heteronuclear (15)N((1)H) nuclear Overhauser effect measurements. The dynamic parameters were obtained at two pH values (5.6 and 7.0) for the apoprotein and at pH 7.0 for the holoprotein, using the model free approach. Relaxation studies, performed at three different magnetic fields, revealed a substantial conformational flexibility on the microsecond to millisecond time scales, mainly localized in the C-terminal face of the beta-barrel. The observed dynamics are primarily caused by the protonation/deprotonation of a buried histidine residue, His(98), located on this flexible face. A network of polar buried side chains, defining a spine going from the E to J strand, is likely to provide the long range connectivity needed to communicate motion from His(98) to the EF loop region. NMR data are accompanied by molecular dynamics simulations, suggesting that His(98) protonation equilibrium is the triggering event for the modulation of a functionally important motion, i.e. the opening/closing at the protein open end, whereas ligand binding stabilizes one of the preexisting conformations (the open form). The results presented here, complemented with an analysis of proteins belonging to the intracellular lipid-binding protein family, are consistent with a model of allosteric activation governing the binding mechanism. The functional role of this mechanism is thoroughly discussed within the framework of the mechanism for the enterohepatic circulation of bile acids.     

Molt and growth of an estuarine crab, Chasmagnathus granulatus (Brachyura: Varunidae), in Mar Chiquita coastal lagoon, Argentina

Juvenile and adult growth of Chasmagnathus granulatus was studied in the laboratory in terms of molt increment in size (MI) and the intermolt period (IP), comparing data obtained from short‐term (STE) and long‐term (LTE) laboratory experiments. Crabs in a pre‐molt condition were collected for STE, including the entire size range of the species. Larger crabs remained in the laboratory no more than 14 days; the average time to molt was 5.8 ± 3.1 days. We registered the molt of 94 females, 64 males and 34 undifferentiated juveniles and calculated their MI. Moreover, 24 males and four females were reared in the laboratory over 3 years (LTE). Hiatt diagrams did not show sex‐specific differences between juveniles of both sexes, but revealed differences between juveniles and adults in each sex as well as between adults of both sexes. The MI decreased gradually with size; this pattern was described with a quadratic model. The IP increased exponentially with size. The presence of regenerating limbs diminished the MI. The abdomen of females reached its final shape and maximum relative width at functional maturity. Growth curves for both sexes were calculated using the von Bertalanffy model, but this model yielded an underestimation of the actual maximum size of this crab.     

Histamine-immunoreactive neurons in the hypothalamus of cats

The localization of histaminergic neurons in the cat brain was determined immunohistochemically with an antibody against histamine. We found that histamine-immunoreactive neurons are observed exclusively in the posterior hypothalamus of colchicine treated cats. The larger group of neurons was found in the ventrolateral part of the posterior hypothalamus, including the tuberomammillary nucleus. Histamine-positive neurons were also observed in the supramammillary area and adjacent posterior hypothalamic area, as well as in the peri- and premammillary regions. In addition, numerous histamine immunoreactive fibers were detected, not only in the posterior hypothalamus, but also in other brain areas, such as the preoptic area of the anterior hypothalamus.     

The influence of habitat, season and tidal regime in the activity of the intertidal crab Neohelice (=Chasmagnathus) granulata

The activity pattern of intertidal crabs is influenced by factors that usually change rhythmically following tidal and/or diel cycles, and is often associated with the use of refuges. The movement activity of the burrowing crab Neohelice granulata was compared among three populations from SW Atlantic coastal areas where they face different tidal regimes, water salinities, substrata and biological factors. At each site, we examined the seasonal activity of the crabs (individuals collected in pitfall traps) in two types of habitat: mudflat and salt marsh. The working hypothesis is that the activity would vary according to the diverse environmental conditions encountered at geographical and local scales. Crab activity varied between sites and seasons showing to be more intense when habitats were covered by water. The most active groups were large males, followed by large non-ovigerous females. Ovigerous females were almost inactive. Most crabs were near or inside burrows at low tides in Mar Chiquita and Bahía Blanca, but they were active at both low and high tides in San Antonio during spring and summer. N. granulata were active in a wide range of temperatures: from 10 to 37 °C at low tides and at temperatures as low as 2 °C when covered by water. Differences of activity between mudflat and salt marsh varied among sites depending on flooding frequencies. Movement activity of N. granulata varied both in space and in time; crabs move under very different abiotic conditions (e.g., low or high tide, daylight or night, low and high temperature) and their movement may also be prevented or elicited by biotic conditions like burrow complexity, food quality and predation pressure. The wide set of conditions under which N. granulata can be active may explain why this is the only semiterrestrial crab inhabiting latitudes higher than 40°S in South America.     

Feather ornaments are dynamic traits in the Great Tit Parus major

In behavioural studies it has been common to quantify plumage colours or ornaments over a range of dates and link them to fitness characteristics without accounting for seasonal changes in these traits. Such changes are likely to be widespread among birds, yet we lack assessments of this variability within individuals. We studied both within‐ and between‐individual temporal changes in Great Tit Parus major ornaments, specifically the melanin‐based black breast stripe and the pigment‐free white cheek patch. During the non‐breeding season both ornaments varied. In juveniles and adult females, the area of the breast stripe first rose and then, from near the end of December, decreased. In adult males there was a linear decrease. In the cheek patch, the irregularity of the cheek borders showed either a linear (adults) or a non‐linear (juveniles) increase as the season progressed. In individuals repeatedly sampled during the same winter, the decrease in the size of the breast stripe was larger for males than females and there was an overall decrease in the regularity of the cheek borders. There was no relationship between the size of the breast stripe and the white cheek patch irregularities or the cheek patch area. These results imply that more attention should be paid to quantification, within individuals, of the components of expression of phenotypic traits. In addition, we suggest that further research should focus on explaining the causes and functions of ornament change.     

Outbreak of human herpesvirus type 1 infection in nonhuman primates (Callithrix penincillata)

Human herpesvirus type 1 (HHV-1) is widely dispersed among the human population. Although infection is often asymptomatic in humans, nonhuman primates develop a severe and often fatal infection. In August 2006, 13 black-tufted marmosets (Callithrix penincillata) from a group of 14 presented with clinical apathy, anorexia, and ataxia. Physical examination revealed conjunctivitis, erosive or ulcerative lesions on the skin, and swollen lymph nodes. Of the 14 animals captured, 10 died. Grossly, ulcers and erosions were observed on the skin of face, nasal planum, lips, and oral mucosa. Histologically, superficial vesicular and erosive stomatitis with associated basophilic intranuclear inclusion bodies in the squamous epithelium were observed. Swabs from oral lesions and tissue samples from necropsied animals were positive for HHV-1 by nested polymerase chain reaction for eight animals.     

Use of vector control to protect people from sleeping sickness in the focus of Bonon (Côte d’Ivoire)

BackgroundGambian human African trypanosomiasis (gHAT) is a neglected tropical disease caused by Trypanosoma brucei gambiense transmitted by tsetse flies (Glossina). In Côte d’Ivoire, Bonon is the most important focus of gHAT, with 325 cases diagnosed from 2000 to 2015 and efforts against gHAT have relied largely on mass screening and treatment of human cases. We assessed whether the addition of tsetse control by deploying Tiny Targets offers benefit to sole reliance on the screen-and-treat strategy.Methodology and principal findingsIn 2015, we performed a census of the human population of the Bonon focus, followed by an exhaustive entomological survey at 278 sites. After a public sensitization campaign, ~2000 Tiny Targets were deployed across an area of 130 km² in February of 2016, deployment was repeated annually in the same month of 2017 and 2018. The intervention’s impact on tsetse was evaluated using a network of 30 traps which were operated for 48 hours at three-month intervals from March 2016 to December 2018. A second comprehensive entomological survey was performed in December 2018 with traps deployed at 274 of the sites used in 2015. Sub-samples of tsetse were dissected and examined microscopically for presence of trypanosomes. The census recorded 26,697 inhabitants residing in 331 settlements. Prior to the deployment of targets, the mean catch of tsetse from the 30 monitoring traps was 12.75 tsetse/trap (5.047–32.203, 95%CI), i.e. 6.4 tsetse/trap/day. Following the deployment of Tiny Targets, mean catches ranged between 0.06 (0.016–0.260, 95%CI) and 0.55 (0.166–1.794, 95%CI) tsetse/trap, i.e. 0.03–0.28 tsetse/trap/day. During the final extensive survey performed in December 2018, 52 tsetse were caught compared to 1,909 in 2015, with 11.6% (5/43) and 23.1% (101/437) infected with Trypanosoma respectively.ConclusionsThe annual deployment of Tiny Targets in the gHAT focus of Bonon reduced the density of Glossina palpalis palpalis by >95%. Tiny Targets offer a powerful addition to current strategies towards eliminating gHAT from Côte d’Ivoire.     

Topology independent protein structural alignment

Background  

Identifying structurally similar proteins with different chain topologies can aid studies in homology modeling, protein folding, protein design, and protein evolution. These include circular permuted protein structures, and the more general cases of non-cyclic permutations between similar structures, which are related by non-topological rearrangement beyond circular permutation. We present a method based on an approximation algorithm that finds sequence-order independent structural alignments that are close to optimal. We formulate the structural alignment problem as a special case of the maximum-weight independent set problem, and solve this computationally intensive problem approximately by iteratively solving relaxations of a corresponding integer programming problem. The resulting structural alignment is sequence order independent. Our method is also insensitive to insertions, deletions, and gaps.     

Ecological connectivity assessment in a strongly structured fire salamander (Salamandra salamandra) population

Small populations are more prone to extinction if the dispersal among them is not adequately maintained by ecological connections. The degree of isolation between populations could be evaluated measuring their genetic distance, which depends on the respective geographic (isolation by distance, IBD) and/or ecological (isolation by resistance, IBR) distances. The aim of this study was to assess the ecological connectivity of fire salamander Salamandra salamandra populations by means of a landscape genetic approach. The species lives in broad‐leaved forest ecosystems and is particularly affected by fragmentation due to its habitat selectivity and low dispersal capability. We analyzed 477 biological samples collected in 47 sampling locations (SLs) in the mainly continuous populations of the Prealpine and Eastern foothill lowland (PEF) and 10 SLs in the fragmented populations of the Western foothill (WF) lowland of Lombardy (northern Italy). Pairwise genetic distances (Chord distance, D_C) were estimated from allele frequencies of 16 microsatellites loci. Ecological distances were calculated using one of the most promising methodology in landscape genetics studies, the circuit theory, applied to habitat suitability maps. We realized two habitat suitability models: one without barriers (EcoD) and a second one accounting for the possible barrier effect of main roads (EcoD_b). Mantel tests between distance matrices highlighted how the Log‐D_C in PEF populations was related to log‐transformed geographic distance (confirming a prevalence of IBD), while it was explained by the Log‐EcoD, and particularly by the Log‐EcoD_b, in WF populations, even when accounting for the confounding effect of geographic distance (highlighting a prevalence of IBR). Moreover, we also demonstrated how considering the overall population, the effect of Euclidean or ecological distances on genetic distances acting at the level of a single group (PEF or WF populations) could not be detected, when population are strongly structured.     

Urinary neopterin in malignant lymphoma.

Urinary neopterin levels were studied in 96 patients with malignant lymphomas. Twenty-eight had Hodgkin's disease and 68 non-Hodgkin's lymphoma. Neopterin excretion was significantly related to the clinical stage of the disease. Mean neopterin excretion in patients with active disease (634 +/- 527 mumol neopterin/mol creatinine) was significantly higher (p = 0.000) than in patients in complete remission (198 +/- 105 mumol neopterin/mol creatinine). Mean neopterin levels of patients in stage III-IV were higher than for patients in stage I-II. These findings were the same in patients with Hodgkin's disease and those with non-Hodgkin's lymphoma (659 +/- 593-425 +/- 316 mumol neopterin/mol creatinine), regardless of the histological subtype. A significant correlation was found between neopterin excretion, ESR (r = 0.31; p = 0.003) and hemoglobin (r = -0.40; p = 0.000). Longitudinal analysis showed a trend towards a correlation between response to therapy and neopterin excretion. These findings suggest that neopterin may be a useful prognostic marker in non-Hodgkin's lymphoma.