Recombination analysis based on the HAstV-2 and HAstV-4 complete genomes

Complete genome sequences of previously unstudied human astrovirus subgenotypes – HAstV-2a and HAstV-2c – and two isolates of a rare genotype HAstV-4 have been determined. These isolates were recovered from fecal samples of young children hospitalized with acute intestinal infections in Novosibirsk (Russia). Three of the four sequenced isolates (HAstV-2a, HAstV-2c, and HAstV-4) are recombinants. It has been shown that all known HAstV-2 genomes have emerged via recombination; the HAstV-1 and HAstV-4 genotypes contain both recombinant and non-recombinant isolates; and all HAstV-3, HAstV-5, and HAstV-6 whole-genome sequences display no reliable signs of recombination. The average mutation accumulation rate has been determined based on an extended ORF2 fragment and amounts to 1.0 × 10⁻³ substitutions per site per year. The evolutionary chronology of current HAstV genotypes has been reconstructed.     

History and future of comparative analyses in sleep research

The comparative methods of evolutionary biology are a useful tool for investigating the functions of sleep. These techniques can help determine whether experimental results, derived from a single or few species, apply broadly across a specified group of animals. In this way, comparative analysis is a powerful complement to experimentation. The variation in the time mammalian species spend asleep has been most amenable for use with this approach, given the large number of mammals for which sleep data exist. Here, it is assumed that interspecific variation in the time spent asleep reflects underlying differences in the need for sleep. If true, then significant predictors of sleep times should provide insight into the function of sleep. Many such analyses have sought the evolutionary determinants of mammalian sleep by relating the time spent in the two basic states of sleep, rapid eye movement (REM) and non-REM sleep, to constitutive variables thought to be functionally related to sleep. However, the early analyses had several methodological problems, and recent re-analyses have overturned some widely accepted relationships, such as the idea that species with higher metabolic rates engage in more sleep. These more recent studies also provide evolutionarily broad support for a neurophysiological role for REM sleep. Furthermore, results from comparative analyses suggest that animals are particularly vulnerable to predation during REM sleep, a finding that lends further support to the notion that REM sleep must serve an important function. Here, we review the methodology and results of quantitative comparative studies of sleep. We highlight important developments in our understanding of the evolutionary determinants of sleep and emphasize relationships that address prevailing hypotheses for the functions of sleep. Lastly, we outline a possible future for comparative analyses, focusing on work in non-mammalian groups, the use of more physiologically meaningful variables, and electrophysiological sleep studies conducted in the wild.     

RT-PCR assay for detection of Lassa virus and related Old World arenaviruses targeting the L gene

This study describes an RT-PCR assay targeting the L RNA segment of arenaviruses. Conserved regions were identified in the polymerase domain of the L gene on the basis of published sequences for Lassa virus, lymphocytic choriomeningitis virus (LCMV), Pichinde virus and Tacaribe virus, as well as 15 novel sequences for Lassa virus, LCMV, Ippy virus, Mobala virus and Mopeia virus determined in this study. Using these regions as target sites, a PCR assay for detection of all known Old World arenaviruses was developed and optimized. The concentration that yields 95% positive results in a set of replicate tests (95% detection limit) was determined to be 4290 copies of Lassa virus L RNA per ml of serum, corresponding to 30 copies per reaction. The ability of the assay to detect various Old World arenaviruses was demonstrated with in vitro transcribed RNA, material from infected cell cultures and samples from patients with Lassa fever and monkeys with LCMV-associated callitrichid hepatitis. The L gene PCR assay may be applicable: (i) as a complementary diagnostic test for Lassa virus and LCMV; (ii) to identify unknown Old World arenaviruses suspected as aetiological agents of disease; and (iii) for screening of potential reservoir hosts for unknown Old World arenaviruses.     

Isolation and phylogenetic analysis of Mucambo virus (Venezuelan equine encephalitis complex subtype IIIA) in Trinidad

In the 1950s and 1960s, alphaviruses in the Venezuelan equine encephalitis (VEE) antigenic complex were the most frequently isolated arboviruses in Trinidad. Since then, there has been very little research performed with these viruses. Herein, we report on the isolation, sequencing, and phylogenetic analyses of Mucambo virus (MUCV; VEE complex subtype IIIA), including 6 recently isolated from Culex (Melanoconion) portesi mosquitoes and 11 previously isolated in Trinidad and Brazil. Results show that nucleotide and amino acid identities across the complete structural polyprotein for the MUCV isolates were 96.6-100% and 98.7-100%, respectively, and the phylogenetic tree inferred for MUCV was highly geographically- and temporally-structured. Bayesian analyses suggest that the sampled MUCV lineages have a recent common ancestry of approximately 198 years (with a 95% highest posterior density (HPD) interval of 63-448 years) prior to 2007, and an overall rate of evolution of 1.28 × 10^− 4 substitutions/site/yr.     

Genetic diversity and phylogenetic analysis of the attachment glycoprotein of phocine distemper viruses of the 2002 and 1988 epizootics

To investigate the possible origin and spread of the dramatic re-emergent 2002 distemper epizootic observed among seals in Danish Waters, we have sequenced wild-type genes of the attachment (H) glycoproteins of viruses from both the 2002 and 1988 epizootics. Phylogenetic analysis of the H genes of phocine distemper virus (PDV) together with other morbilliviruses, suggests that the re-emergent 2002 PDV is more closely related to a putative recent ancestral PDV than the 1988 PDV isolates. Moreover, upsurges of distemper disease in land-living carnivores linked in time and locality to the 2002 seal epizootic in Danish Waters was investigated and determined to be caused by canine distemper virus, the closest relative of PDV, revealing no direct epidemiological link to the seal epizootics.     

Complete Nucleotide Sequence of IT-227/82, An Avian Paramyxovirus Type-1 Strain of Pigeons (Columba Livia)

This paper describes the complete genome sequence of IT-227/82, a strain of avian paramyxovirus type-1 of pigeon (PPMV-1). IT-227/82 is an antigenic variant of Newcastle disease virus (NDV) of chickens. The genome is 15,192 nucleotides (nt) long, similarly to the previously published NDV strain ZJ1. It is, however, six nt longer than the genomes of NDV strains LaSota/46 and Beaudette C. The six-nt insertion was located in the 5′ non-coding region of the nucleoprotein (NP) gene. The presence of this six-nt insertion showed no correlation with the virulence or the reservoir of the NDV strains sequenced so far. The genome length of 15,186 or 15,192 nt can be connected however, to “old” (I, II, III and IV) and “new” (V, VI, VII and VIII) NDV genotypes, respectively. Comparison of open reading frames indicated that the PPMV-1 strain IT-227/82 encodes the longest W protein, (227 amino acids). The length of the W protein showed remarkable differences even within genotypes and cannot be regarded, therefore, as a phylogenetic feature. The haemagglutinin-neuraminidase protein of strain IT-227/82 consists of 571 amino acids, similarly to genotypes IV, V and VII NDV strains, while genotype I and II strains have longer HN proteins, 616 and 577 amino acids, respectively. The length of the haemagglutinin-neuraminidase protein possesses phylogenetic importance.     

An early work [1910-1913] in Biological Psychology by pioneer psychiatrist, criminologist and philosopher José Ingenieros, M.D. (1877-1925) of Buenos Aires

One of the earliest recorded works in Biological Psychology was published in 1910 by Argentine psychiatrist José Ingenieros (1877-1925), Professor of Experimental Psychology at the Faculty of Philosophy and Letters of the University of Buenos Aires. Ingenieros, a multifaceted personality and prolific author and educator famous for his lapidary aphorisms, has been considered a 'luminary' for generations. Trained as a physician, he was the first scientist to establish a comprehensive psychological system in Latin America. His long list of publications includes more than 300 titles generally divided in two periods: studies in mental pathology and criminology (1897-1908) and studies in philosophy, psychology and sociology (1908-1925). His works were never made particularly available to English-speaking audiences, despite the fact that certain of his books are still best-sellers in the Spanish-speaking world. We present an overview of Ingenieros' life and work, and a detailed account of his profoundly interesting work Principios de Psicología Biológica, in which he analyzes the development, evolution and social context of mental functions. We also provide an English translation of the Introduction contributed by Nobel laureate Wilhelm Ostwald (1853-1932) to the 1922 German edition of the work, pertinent to the energetic principles Ingenieros used and the study of Psychology as a natural science. It is a hope, 80 years after Ingenieros' parting, to bibliographically resurrect this champion of reason, who, until now, has not been given his due placement in the international psychological and biomedical literature.     

Genes of cathepsin L-like proteases in Trypanosoma rangeli isolates: Markers for diagnosis, genotyping and phylogenetic relationships

We have sequenced genes encoding cathepsin L-like (CatL-like) cysteine proteases from isolates of Trypanosoma rangeli from humans, wild mammals and Rhodnius species of Central and South America. Phylogenetic trees of sequences encoding mature CatL-like enzymes of T. rangeli and homologous genes from other trypanosomes, Leishmania spp. and bodonids positioned sequences of T. rangeli (rangelipain) closest to T. cruzi (cruzipain). Phylogenetic tree of kinetoplastids based on sequences of CatL-like was totally congruent with those derived from SSU rRNA and gGAPDH genes. Analysis of sequences from the CatL-like catalytic domains of 17 isolates representative of the overall phylogenetic diversity and geographical range of T. rangeli supported all the lineages (A–D) previously defined using ribosomal and spliced leader genes. Comparison of the proteolytic activities of T. rangeli isolates revealed heterogeneous banding profiles of cysteine proteases in gelatin gels, with differences even among isolates of the same lineage. CatL-like sequences proved to be excellent targets for diagnosis and genotyping of T. rangeli by PCR. Data from CatL-like encoding genes agreed with results from previous studies of kDNA markers, and ribosomal and spliced leader genes, thereby corroborating clonal evolution, independent transmission cycles and the divergence of T. rangeli lineages associated with sympatric species of Rhodnius.     

The brain in the early fossil jawless vertebrates: evolutionary information from an empty nutshell

Various 535-365 million year-old extinct jawless vertebrates taxa provide either direct or indirect information about brain and cranial nerve morphology. The paraphyletic group referred to as "ostracoderms", includes some forms in which the braincase closely encapsulated the brain, thereby providing relatively accurate data about its overall external morphology. Current morphology-based phylogenies suggests that "ostracoderms" are in fact jawless stem gnathostomes, and the closely similar aspect of their brain cavity suggests that it illustrates the ancestral condition of the gnathostome brain and fills the morphological gap between the brain condition of the extant cyclostomes and that of the extant jawed vertebrates.     

Cloning of stanniocalcin (STC) cDNAs of divergent teleost species: Monomeric STC supports monophyly of the ancient teleosts, the osteoglossomorphs

Molecular cloning of teleost stanniocalcin (STC) cDNAs was undertaken in two species of order Osteoglossiformes of subdivision Osteoglossomorpha and one species of each of orders Cypriniformes and Perciformes within the subdivision Euteleostei. The elephantnose (Gnathonemus petersii) and the butterflyfish (Pantadon buchholzi) are basal teleosts in different osteoglossiforme suborders yet their 218 amino acid (aa) mature hormones, from prehormones of 249 and 251aa, respectively, have only 10 cysteine residues. A substitution for cysteine at the intermonomeric disulfide linkage site, implies that their STCs exist as monomeric peptides, as is the case with STC from another osteoglossormorph, arawana [Amemiya, Y., Marra, L.E., Reyhani, N., Youson, J.H., 2002. Stanniocalcin from an ancient teleost: a monomeric form of the hormone and a possible extracorpuscular distribution. Mol. Cell. Endocrinol. 188, 141-150]. The STC cDNA of the generalized teleost and cyprinid, the white sucker (Catostomus commersoni), encodes a prehormone of 249aa with a signal peptide of 31aa and a mature protein of 218aa that possesses 11 cysteine residues. The latter feature is consistent with a previous analysis that white sucker mature STC is a glycosylated, homodimeric peptide [Amemiya, Y., Marra, L.E., Reyhani, N., Youson, J.H., 2002. Stanniocalcin from an ancient teleost: a monomeric form of the hormone and a possible extracorpuscular distribution. Mol. Cell. Endocrinol. 188, 141-150]. An open reading frame of the STC cDNA of the derived teleost and perciforme, the smallmouth bass (Micropterus dolomieui), encodes a prehormone of 255aa with a signal peptide of 33aa and a mature protein of 222aa. The position of the 11 cysteines in smallmouth bass STC suggests that it exists as a homodimeric peptide. A phylogenetic analysis, using the new STC-1 amino acid sequences and those in the gene data base provided strong support for monophyly of the Osteoglossomorpha and indicated, with positioning of white sucker and smallmouth bass, that this molecule has some utility as a taxonomic marker. This analysis also suggested that two STC-1 gene sequences exist in multiple fish genomes, and that they may be a product of the fish-specific genome duplication. The mutation in the osteoglossomorph STC likely occurred after the appearance of the first teleosts and before movement of the tectonic plates.