Specificity of the hepatitis C virus NS3 serine protease: effects of substitutions at the 3/4A, 4A/4B, 4B/5A, and 5A/5B cleavage sites on polyprotein processing.

Cleavage at four sites (3/4A, 4A/4B, 4B/5A, and 5A/5B) in the hepatitis C virus polyprotein requires a viral serine protease activity residing in the N-terminal one-third of the NS3 protein. Sequence comparison of the residues flanking these cleavage sites reveals conserved features including an acidic residue (Asp or Glu) at the P6 position, a Cys or Thr residue at the P1 position, and a Ser or Ala residue at the P1' position. In this study, we used site-directed mutagenesis to assess the importance of these and other residues for NS3 protease-dependent cleavages. Substitutions at the P7 to P2' positions of the 4A/4B site had varied effects on cleavage efficiency. Only Arg at the P1 position or Pro at P1' substantially blocked processing at this site. Leu was tolerated at the P1 position, whereas five other substitutions allowed various degrees of cleavage. Substitutions with positively charged or other hydrophilic residues at the P7, P3, P2, and P2' positions did not reduce cleavage efficiency. Five substitutions examined at the P6 position allowed complete cleavage, demonstrating that an acidic residue at this position is not essential. Parallel results were obtained with substrates containing an active NS3 protease domain in cis or when the protease domain was supplied in trans. Selected substitutions blocking or inhibiting cleavage at the 4A/4B site were also examined at the 3/4A, 4B/5A, and 5A/5B sites. For a given substitution, a site-dependent gradient in the degree of inhibition was observed, with a 3/4A site being least sensitive to mutagenesis, followed by the 4A/4B, 4B/5A, and 5A/5B sites. In most cases, mutations abolishing cleavage at one site did not affect processing at the other serine protease-dependent sites. However, mutations at the 3/4A site which inhibited cleavage also interfered with processing at the 4B/5A site. Finally, during the course of these studies an additional NS3 protease-dependent cleavage site has been identified in the NS4B region.     

Sindbis virus attachment: isolation and characterization of mutants with impaired binding to vertebrate cells.

Sindbis virus can infect a broad range of insect and vertebrate cell types. The ability to restrict tissue tropism and target virus infection to specific cell types would expand the usefulness of engineered alphaviruses as gene expression vectors. In this study, virus pools derived from libraries of full-length Sindbis virus cDNA clones containing random insertion mutations in the PE2 or E1 virion glycoprotein gene were screened for mutants defective for binding to vertebrate cells. Binding-competent mutants were depleted by serial adsorption to chicken embryo fibroblast (CEF) monolayers at 4 degrees C, and the remaining population was amplified by immune-enhanced infection of P388D1 cells. From the PE2 libraries, 12 candidate mutants showing reduced cytopathic effects on CEF monolayers were isolated and three representative mutants, NB1, NB2, and NB12, were characterized in detail. Insertion mutations for NB1 and NB12 were found near the PE2 cleavage site, whereas the insertion in NB2 occurred between residues 69 and 74 of E2. Although virion assembly and release occurred normally for all three mutants, PE2 cleavage was completely (NB1) or partially (NB12) blocked for the mutants with insertions near the PE2 cleavage site. Both NB1 and NB2 were defective for binding to CEF and BHK-21 cells. Mild trypsin digestion of isolated NB1 virions resulted in PE2 cleavage and partially restored binding to CEF. Besides defective binding, NB1 also exhibited slower CEF penetration kinetics. Consistent with previous work, these results implicate PE2 cleavage and domains in the N-terminal portion of E2 as important determinants of alphavirus binding and penetration. Binding-defective mutants such as NB2, which exhibit normal particle assembly, release, and penetration, may be useful for future efforts to target Sindbis virus infection.     

Segregation analysis of fat mass and other body composition measures derived from underwater weighing.

Segregation patterns of three body composition measures which were derived from underwater weighing were evaluated in a random sample of 176 French-Canadian families. Two of the variables can be considered as primary partitions of weight (fat mass [FM] and fat-free mass [FFM]), while the remaining variable (percent body fat [%BF]) is a derived index combining the measures of both fat and fat-free weight. This study represents the first report investigating major gene effects for these measures. Segregation analyses revealed that a major locus hypothesis could not be rejected for two of the three phenotypes. The single exception was FFM, for which nearly 60% of the variance was accounted for by a non-Mendelian major effect, which may reflect environmentally based commingling or may be in part a function of gene-environment interactions or correlations. In contrast to the results for FFM, the results for each of FM and %BF were similar and suggested a major locus which accounted for 45% of the variance, with an additional 22%-26% due to a multifactorial component. Given the similarity of the major gene characteristics for these two phenotypes, the possibility that the same gene underlies both measures warrants investigation. A reasonable hypothesis is to consider genes that may influence nutrient partitioning, as the family of candidate genes to receive the major attention.     

Geographic differences in Blainville's beaked whale (Mesoplodon densirostris) echolocation clicks

Aim

Understanding cetacean species' distributions and population structure over space and time is necessary for effective conservation and management. Geographic differences in acoustic signals may provide a line of evidence for population-level discrimination in some cetacean species. We use acoustic recordings collected over broad spatial and temporal scales to investigate whether global variability in echolocation click peak frequency could elucidate population structure in Blainville's beaked whale (Mesoplodon densirostris), a cryptic species well-studied acoustically.

Location

North Pacific, Western North Atlantic and Gulf of Mexico.

Time period

2004–2021.

Major taxa studied

Blainville's beaked whale.

Methods

Passive acoustic data were collected at 76 sites and 150 cumulative years of data were analysed to extract beaked whale echolocation clicks. Using an automated detector and subsequent weighted network clustering on spectral content and interclick interval of clicks, we determined the properties of a primary cluster of clicks with similar characteristics per site. These were compared within regions and across ocean basins and evaluated for suitability as population-level indicators.

Results

Spectral averages obtained from primary clusters of echolocation clicks identified at each site were similar in overall shape but varied in peak frequency by up to 8 kHz. We identified a latitudinal cline, with higher peak frequencies occurring in lower latitudes.

Main conclusions

It may be possible to acoustically delineate populations of Blainville's beaked whales. The documented negative correlation between signal peak frequency and latitude could relate to body size. Body size has been shown to influence signal frequency, with lower frequencies produced by larger animals, which are subsequently more common in higher latitudes for some species, although data are lacking to adequately investigate this for beaked whales. Prey size and depth may shape frequency content of echolocation signals, and larger prey items may occur in higher latitudes, resulting in lower signal frequencies of their predators.     

Epidermal glands in Squamata: morphology and histochemistry of the pre-cloacal glands in Amphisbaena alba (Amphisbaenia)

Summary Pre-cloacal glands occur in some species of amphisbaenians. Although these glands are important in systematics, their biology and chemistry are little known. The pre-cloacal glands of Amphisbaena alba are of the holocrine type. They are made up of a glandular body and a duct. The glandular body is conical to elongate and is formed of clongatc lobules separated one from another by collagen septa. Each lobule is composed, at its periphery, of germinative cells, and within of polyhedral secretory cells, of different degrees of differentiation. The germinative cells, set on a basal lamina, are basophilic and their cytoplasm is fairly electron dense. The polyhedral cells display bulky cytoplasm, filled with spherical granules, wrapped in membranes and differing in their electron densities. Towards the lumen of the gland, these granules are increasingly eosinophilic and have an affinity for orange G. The secretion is discharged into the duct leading to the pore, which is situated in the central region of the scale. This secretion shows positive histochemical results for mucopolysaccharides and proteins. The similarity between the epidermal glands of lizards and those of A. alba raises the suggestion that the glands have equivalent functions, possibly in the course of intra- or interspecific communication.     

Biofeedback treatments of generalized anxiety disorder: Preliminary results

Forty-five individuals with generalized anxiety (38 with GAD as defined by DSM-III) were randomized to 4 treatment conditions or a waiting list control. Patients received 8 sessions of either frontal EMG biofeedback, biofeedback to increase EEG alpha, biofeedback to decrease EEG alpha, or a pseudomeditation control condition. All treated subjects showed significant reductions in STAI-Trait Anxiety and psychophysiologic symptoms on the Psychosomatic Symptom Checklist. Only alpha-increase biofeedback subjects showed significant reductions in heart rate reactivity to stressors at a separate psychophysiological testing session. Decreased self-report of anxiety was maintained at 6 weeks posttreatment.     

Spontaneous allelic variant in deafness–blindness gene Ush1g resulting in an expanded phenotype

Relationships between novel phenotypic behaviors and specific genetic alterations are often discovered using target-specific, directed mutagenesis or phenotypic selection following chemical mutagenesis. An alternative approach is to exploit deficiencies in DNA repair pathways that maintain genetic integrity in response to spontaneously induced damage. Mice deficient in the DNA glycosylase NEIL1 show elevated spontaneous mutations, which arise from translesion DNA synthesis past oxidatively induced base damage. Several litters of Neil1 knockout mice included animals that were distinguished by their backwards-walking behavior in open-field environments, while maintaining frantic forward movements in their home cage environment. Other phenotypic manifestations included swim test failures, head tilting and circling. Mapping of the mutation that conferred these behaviors showed the introduction of a stop codon at amino acid 4 of the Ush1g gene. Ush1g^bw/bw null mice displayed auditory and vestibular defects that are commonly seen with mutations affecting inner-ear hair-cell function, including a complete lack of auditory brainstem responses and vestibular-evoked potentials. As in other Usher syndrome type I mutant mouse lines, hair cell phenotypes included disorganized and split hair bundles, as well as altered distribution of proteins for stereocilia that localize to the tips of row 1 or row 2. Disruption to the bundle and kinocilium displacement suggested that USH1G is essential for forming the hair cell's kinocilial links. Consistent with other Usher type 1 models, Ush1g^bw/bw mice had no substantial retinal degeneration compared with Ush1g^bw/+ controls. In contrast to previously described Ush1g alleles, this new allele provides the first knockout model for this gene.