Immunogenetic evidence for the phylogenetic sister group relationship of dogs and bears (Mammalia, Carnivora: Canidae and Crsidae). a comparative determinant analysis of carnivoran albumin, c3 complement and immunoglobulin micro-chain

Thirty-seven antigenic determinants were identified in the albumins, the immunoglobulin micro- and IgG(Fc) chains, and the C3 proteins of 51 carnivoran (sub)species from 31 genera, and in 12 noncarnivoran mammals. In addition to 19 determinants plesiomorphic for Carnivora as an order, 18 synapomorphic epitopes of carnivoran families revealed nine phylogenetic reaction groups: (1) canids, (2) ursids, (3) the racoon, (4) the Weddell seal, (5) the lesser panda, (6) the harbour seal, (7) mustelids, (8) viverrids and hyaenas, and (9) felids. These data identify Canoidea (Canidae, Ursidae, Phocidae, Procyonidae, Ailuridae, Mustelidae) and Feloidea (Viverridae, Hyaenidae, Felidae) as two fundamentally differentiated lineages of Carnivora, and confirm the inclusion of seals among the former. The Ursidae are the sister group of the Canidae. The antigenic determinants in the studied proteins do not subdivide the Canidae, Ursidae and Felidae into immunologically differentiated lineages.     

Two Japanese wildcats, the Tsushima cat and the Iriomote cat, show the same mitochondrial DNA lineage as the leopard cat Felis bengalensis

We previously revealed, based on mitochondrial DNA sequence analysis, that the Iriomote cat is very closely related to the leopard cat Felis bengalensis, which is widespread in Asia [24]. In this study, in order to understand the phylogenetic status of the Tsushima cat which is the other wildcat in Japan, partial sequences (402 bases) of the mitochondrial cytochrome b region were determined and compared with those of the Iriomote cat and other feline species. The phylogenetic tree of the cytochrome b sequences indicated that the Tsushima cat and the Iriomote cat have the same mitochondrial DNA lineage as the leopard cat. One or two transitional substitutions were observed among the two Japanese wildcats and the leopard cat. The divergence time (approximately 100,000 years ago) of the Tsushima cat and the leopard cat, estimated by sequence data, was in concordance with the formation date of the Tsushima Island. These results suggest that genetic drift after geographic isolation has brought fixation of some genetic and morphological characters to the Tsushima cat and the Iriomote cat, while these two Japanese wildcats are still genetically close to the continental leopard cat. Considering morphological differences and molecular phylogeny, it is reasonable for the two Japanese wildcats to be classified as two subspecies of F. bengalensis.     

Microsporidia are related to Fungi: evidence from the largest subunit of RNA polymerase II and other proteins

We have determined complete gene sequences encoding the largest subunit of the RNA polymerase II (RBP1) from two Microsporidia, Vairimorpha necatrix and Nosema locustae. Phylogenetic analyses of these and other RPB1 sequences strongly support the notion that Microsporidia are not early-diverging eukaryotes but instead are specifically related to Fungi. Our reexamination of elongation factors EF-1alpha and EF-2 sequence data that had previously been taken as support for an early (Archezoan) divergence of these amitochondriate protists show such support to be weak and likely caused by artifacts in phylogenetic analyses. These EF data sets are, in fact, not inconsistent with a Microsporidia + Fungi relationship. In addition, we show that none of these proteins strongly support a deep divergence of Parabasalia and Metamonada, the other amitochondriate protist groups currently thought to compose early branches. Thus, the phylogenetic placement among eukaryotes for these protist taxa is in need of further critical examination.     

Genetic and phylogenetic divergence of feline immunodeficiency virus in the puma (Puma concolor)

Feline immunodeficiency virus (FIV) is a lentivirus which causes an AIDS-like disease in domestic cats (Felis catus). A number of other felid species, including the puma (Puma concolor), carry a virus closely related to domestic cat FIV. Serological testing revealed the presence of antibodies to FIV in 22% of 434 samples from throughout the geographic range of the puma. FIV-Pco pol gene sequences isolated from pumas revealed extensive sequence diversity, greater than has been documented in the domestic cat. The puma sequences formed two highly divergent groups, analogous to the clades which have been defined for domestic cat and lion (Panthera leo) FIV. The puma clade A was made up of samples from Florida and California, whereas clade B consisted of samples from other parts of North America, Central America, and Brazil. The difference between these two groups was as great as that reported among three lion FIV clades. Within puma clades, sequence variation is large, comparable to between-clade differences seen for domestic cat clades, allowing recognition of 15 phylogenetic lineages (subclades) among puma FIV-Pco. Large sequence divergence among isolates, nearly complete species monophyly, and widespread geographic distribution suggest that FIV-Pco has evolved within the puma species for a long period. The sequence data provided evidence for vertical transmission of FIV-Pco from mothers to their kittens, for coinfection of individuals by two different viral strains, and for cross-species transmission of FIV from a domestic cat to a puma. These factors may all be important for understanding the epidemiology and natural history of FIV in the puma.     

Cytoplasmic creatine kinases from giant pandas

The muscle and brain creatine kinases of giant panda have been isolated and purified. The purified muscle and brain enzymes (MM and BB) are homogeneous on both the polyacrylamide gel electrophoresis in the presence and absence of SDS. Both enzymes are dimers, consisting of two identical subunits each with a molecular weight of 42,000 daltons. The characteristics of muscle and brain enzymes have been studied, respectively. The hybridized enzyme, MB, was prepared by hybridization of MM and BB. The kinetic parameters of MM, BB and MB were determined, respectively. The results from modification of SH groups show that the SH groups of panda creatine kinases are essential for their activity and among the all SH groups in the enzyme only one per subunit is essential for enzymatic activity.     

Molecular evolution of the photolyase-blue-light photoreceptor family

The photolyase-blue-light photoreceptor family is composed of cyclobutane pyrimidine dimer (CPD) photolyases, (6-4) photolyases, and blue-light photoreceptors. CPD photolyase and (6-4) photolyase are involved in photoreactivation for CPD and (6-4) photoproducts, respectively. CPD photolyase is classified into two subclasses, class I and II, based on amino acid sequence similarity. Blue-light photoreceptors are essential light detectors for the early development of plants. The amino acid sequence of the receptor is similar to those of the photolyases, although the receptor does not show the activity of photoreactivation. To investigate the functional divergence of the family, the amino acid sequences of the proteins were aligned. The alignment suggested that the recognition mechanisms of the cofactors and the substrate of class I CPD photolyases (class I photolyases) are different from those of class II CPD photolyases (class II photolyases). We reconstructed the phylogenetic trees based on the alignment by the NJ method and the ML method. The phylogenetic analysis suggested that the ancestral gene of the family had encoded CPD photolyase and that the gene duplication of the ancestral proteins had occurred at least eight times before the divergence between eubacteria and eukaryotes.     

Coevolution of the Monogenoidea (Platyhelminthes) based on a revised hypothesis of parasite phylogeny

A revised hypothesis for the phylogeny of the Subclass Polyonchoinea (Monogenoidea) was constructed employing phylogenetic systematics. The Acanthocotylidae (formerly of the Order Capsalidea) is transferred to the Order Gyrodactylidea based on this analysis. The new phylogeny is used to determine coevolutionary relationships of the familial taxa of Monogenoidea with their hosts. The coevolutionary analysis suggests that the Monogenoidea apparently underwent sympatric speciation or dispersal while parasitic on ancestral Gnathostomata, resulting in two primary clades: the Polyonchoinea and the Oligonchoinea + Polystomatoinea. The two parasite clades apparently cospeciated independently with divergence of the Chondrichthyes and Osteichthyes. In the Polyonchoinea, the clade associated with Chondrichthyes experienced primary extinction within the Holocephala, but coevolved into the Loimoidae and Monocotylidae in the Galeomorphii and Squalea (Elasmobranchii), respectively. Within the Osteichthyes, polyonchoineans experienced primary extinction with the divergence of Sarcopterygii, Polypteriformes and Acipenseriformes. They demonstrate primary dispersal from the Neopterygii into the Squalea (as Amphibdellatinea), Actinistia (as Neodactylodiscinea) and Urodela (as Lagarocotylidea). Secondary dispersals of polyonchoineans occurred in the Gyrodactylidae to the Polypteriformes, Urodela and Anura; in the Acanthocotylidae to the Myxinoidea and Squalea; in the Capsalidae to the Acipenseriformes and Elasmobranchii; and in the Monocotylidae to the Holocephala. The Oligonchoinea and Polystomatoinea developed upon divergence of the Chondrichthyes and Osteichthyes. Oligonchoineans cospeciated within the Chondrichthyes, with the Chimaericolidea developing within the Holocephala and the ancestor of the Diclybothriidea + Mazocraeidea within the Elasmobranchii. Two cases of primary dispersal occurred within this clade: the Diclybothriidae to the Acipenseriformes and the ancestor of mazocraeidean families to the Neopterygii (both Osteichthyes). Secondary dispersal within the Oligonchoinea includes host switching of the common ancestor of Callorhynchocotyle (Hexabothriidae) to the Holocephala. Polystomatoineans coevolved within the Osteichthyes, but experienced primary extinctions in the Actinopterygii, Actinistia, Dipnoi and Amniota. Coevolution of the Sphyranuridae and Polystomatidae occurred with divergence of the Urodela and Anura, respectively. Secondary dispersal of Polystomatids to the Urodela, Dipnoi and Amniota is suggested. A preliminary phylogenetic analysis of the Polystomatoinea suggests that primary extinction with secondary dispersal of polystomatids to the Dipnoi may not be necessary to explain extant parasite distributions, since Concinnocotyla (Concinnocotylinae) appears to represent the sister taxon of the remaining Polystomatidae + Sphyranuridae.     

Predictive value of contact investigation for identifying recent transmission of Mycobacterium tuberculosis

BACKGROUND: Abciximab (ReoPro; Eli Lilly and Co, Indianapolis, IN) is a monoclonal antibody that binds to the platelet glycoprotein IIb/IIIa receptor and produces powerful inhibition of platelet function. Clinical trials of abciximab in patients undergoing coronary angioplasty have demonstrated a reduction in thrombotic complications and have encouraged the widespread use of this agent. We have observed a substantial incidence of excessive bleeding among patients who receive abciximab and subsequently require emergency cardiac operations. METHODS: The records of 11 consecutive patients who required emergency cardiac operations after administration of abciximab and failed angioplasty or stent placement were reviewed. RESULTS: The interval from the cessation of abciximab administration to operation was critical in determining the degree of coagulopathy after cardiopulmonary bypass. The median values for postoperative chest drainage (1,300 versus 400 mL; p < 0.01), packed red blood cells transfused (6 versus 0 U; p = 0.02), platelets transfused (20 versus 0 packs; p = 0.02), and maximum activated clotting time (800 versus 528 seconds; p = 0.01) all were significantly greater in the early group (cardiac operation < 12 hours after abciximab administration; n = 6) compared with the late (cardiac operation >12 hours after abciximab administration; n = 5) group. CONCLUSIONS: This report suggests that the antiplatelet agent abciximab is associated with substantial bleeding when it is administered within 12 hours of operation.     

Nucleotide sequence and restriction fragment-length polymorphism analysis of human T-cell lymphotropic virus type II (HTLV-II) in southern Europe: evidence for the HTLV-IIa and HTLV-IIb subtypes

Human T-cell lymphotropic virus type II (HTLV-II) has been subtyped into two major groups, IIa and IIb, according to molecular studies involving env gene sequencing. Subsequently, this retrovirus was further subclassified by examining the long terminal repeat (LTR), the most divergent genomic region. Sequence analysis and restriction fragment-length polymorphism (RFLP) applied to the LTR region identified either four or five groups within the IIa subtype (depending on the restriction enzyme sets used) and six within the IIb subtype. In this study, we analyzed the LTR sequences of 29 samples obtained from HTLV-II-infected individuals living in Spain and Italy, which included 24 injecting drug users (IDUs), three blood donors, and two subjects at risk for HIV/HTLV infection. Sequence analysis and phylogenetic analysis of 720 base pairs of the LTR performed in 10 Spanish samples showed that all of these samples belonged to IIb subtype, with a divergence of 7.5% and 1.66% compared with MoT (IIa) and NRA/G12 (IIb) isolates, respectively. RFLP analysis demonstrated the presence of the IIb 4-subtype restriction pattern in 26 samples, a IIb5-subtype pattern in one Italian IDU, and a IIa0-subtype pattern in two Italian samples (blood donors), according to W.M. Switzer's nomenclature. This is the first report of the presence of IIb5 in Southern Europe and IIa0 among Italian blood donors. RFLP correlated with nucleotide sequence and phylogenetic data obtained in this study, demonstrating the ability of the RFLP method to predict the phylogroup of HTLV-II-infected samples.     

Highlights of the sixth report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure

The vertebrates are traditionally classified into two distinct groups, Agnatha (jawless vertebrates) and Gnathostomata (jawed vertebrates). Extant agnathans are represented by hagfishes (Myxiniformes) and lampreys (Petromyzontiformes), frequently grouped together within the Cyclostomata. Whereas the recognition of the Gnathostomata as a clade is commonly acknowledged, a consensus has not been reached regarding whether or not Cyclostomata represents a clade. In the present study we have used newly established sequences of the protein-coding genes of the mitochondrial DNA molecule of the hagfish to explore agnathan and gnathostome relationships. The phylogenetic analysis of Pisces, using echinoderms as outgroup, placed the hagfish as a sister group of Vertebrata sensu stricto, i.e., the lamprey and the gnathostomes. The phylogenetic analysis of the Gnathostomata identified a basal divergence between gnathostome fishes and a branch leading to birds and mammals, i.e., between "Anamnia" and Amniota. The lungfish has a basal position among gnathostome fishes with the teleosts as the most recently evolving lineage. The findings portray a hitherto unrecognized polarity in the evolution of bony fishes. The presently established relationships are incompatible with previous molecular studies.     

Placement shift, sibling relationship quality, and child outcomes in foster care: A controlled study.

Sibling unity during family transitions is considered a protective factor for child behavior problems, but there is little empirical support for the widespread child protection policy of placing siblings together in foster care. In a prospective study of 156 maltreated children, siblings were classified in 1 of 3 placement groups: continuously together (n = 110), continuously apart (n = 22), and disrupted placement (siblings placed together were separated; n = 24). Changes in child adjustment as a function of sibling relationship and placement group were examined. Sibling positivity predicted lower child problems at follow-up (about 14 months later), while sibling negativity predicted higher child problems. Placement group did not affect child behavior problems at follow-up; however, compared to siblings in continuous placement (either together or apart), siblings in disrupted placement with high initial behavior problems were rated as having fewer problems at follow-up, while siblings in disrupted placement with low initial behavior problems were rated as having more problems at follow-up. These findings highlight the importance of considering relationships between siblings and the risk that one poses to another before early placement decisions are made. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

B-cell and T-regulatory cell dysfunction in six Chinese children with hypogammaglobulinaemia

We model the non-local mechanisms of genomic evolution and propose methods for studying the evolutionary divergence of species based on these models. Mechanisms include the movement of segments of genomes within a single chromosome (transpositions), the reciprocal translocation of segments between two chromosomes, and the inversion of segments. Each of these is studied in the context of a different type of genomic data. We introduce the theory of phylogenetic invariants for evolutionary inference based on very long macromolecular sequences.     

Granule-bound starch synthase: structure, function, and phylogenetic utility

Interest in the use of low-copy nuclear genes for phylogenetic analyses of plants has grown rapidly, because highly repetitive genes such as those commonly used are limited in number. Furthermore, because low-copy genes are subject to different evolutionary processes than are plastid genes or highly repetitive nuclear markers, they provide a valuable source of independent phylogenetic evidence. The gene for granule-bound starch synthase (GBSSI or waxy) exists in a single copy in nearly all plants examined so far. Our study of GBSSI had three parts: (1) Amino acid sequences were compared across a broad taxonomic range, including grasses, four dicotyledons, and the microbial homologs of GBSSI. Inferred structural information was used to aid in the alignment of these very divergent sequences. The informed alignments highlight amino acids that are conserved across all sequences, and demonstrate that structural motifs can be highly conserved in spite of marked divergence in amino acid sequence. (2) Maximum-likelihood (ML) analyses were used to examine exon sequence evolution throughout grasses. Differences in probabilities among substitution types and marked among-site rate variation contributed to the observed pattern of variation. Of the parameters examined in our set of likelihood models, the inclusion of among-site rate variation following a gamma distribution caused the greatest improvement in likelihood score. (3) We performed cladistic parsimony analyses of GBSSI sequences throughout grasses, within tribes, and within genera to examine the phylogenetic utility of the gene. Introns provide useful information among very closely related species, but quickly become difficult to align among more divergent taxa. Exons are variable enough to provide extensive resolution within the family, but with low bootstrap support. The combined results of amino acid sequence comparisons, maximum-likelihood analyses, and phylogenetic studies underscore factors that might affect phylogenetic reconstruction. In this case, accommodation of the variable rate of evolution among sites might be the first step in maximizing the phylogenetic utility of GBSSI.     

Vaccine-induced canine distemper in a lesser panda

A fatal disease occurred in a lesser panda (Ailurus fulgens) 2 weeks after vaccination with modified live distemper vaccine. The disease clinically resembled canine distemper. Pathologically there was giant cell pneumonia, with canine distemper viral inclusion bodies in pulmonary and digestive tract epithelium. Viral isolates were indicative of an attenuated strain rather than virulent types.     

Distinct annexin subfamilies in plants and protists diverged prior to animal annexins and from a common ancestor

Annexin homologues in the kingdoms of Planta and Protista were characterized by molecular sequence analysis to determine their phylogenetic and structural relationship with annexins of Animalia. Sequence fragments from 19 plant annexins were identified in sequence databases and composite sequences were also assembled from expressed sequence tags for Arabidopsis thaliana. Length differences in protein aminotermini and evidence for unique exon splice sites indicated that plant annexins were distinct from those of animals. A third annexin gene of Giardia lamblia (Anx21-Gla) was identified as a distant relative to other protist annexins and to those of higher eukaryotes, thus providing a suitable outgroup for evolutionary reconstruction of the family tree. Rooted evolutionary trees portrayed protist, plant, and Dictyostelium annexins as early, monophyletic ramifications prior to the appearance of closely related animal annexin XIII. Molecular phylogenetic analyses of DNA and protein sequence alignments revealed at least seven separate plant subfamilies, represented by Anx18 (alfalfa, previously classified), Anx22 (thale cress), Anx23 (thale cress, cotton, rape and cabbage), Anx24 (bell pepper and tomato p34), Anx25 (strawberry, horseradish, pea, soybean, and castor bean), Anx26-Zma, and Anx27-Zma (maize). Other unique subfamilies may exist for rice, tomato p35, apple, and celery annexins. Consensus sequences compiled for each eukaryotic kingdom showed some breakdown of the "annexin-fold" motif in repeats 2 and 3 of protist and plant annexins and a conserved codon deletion in repeat 3 of plants. The characterization of distinct annexin genes in plants and protists reflects their comparable diversity among animal species and offers alternative models for the comparative study of structure-function relationships within this important gene family.     

Functional knockout of the transient outward current, long-QT syndrome, and cardiac remodeling in mice expressing a dominant-negative Kv4 alpha subunit

Amino acid changes S180A (S-->A at site 180), H197Y, Y277F, T285A, and A308S are known to shift the maximum wavelength of absorption (lambda max) of red and green visual pigments toward blue, essentially in an additive fashion. To test the generality of this "five-sites" rule, we have determined the partial amino acid sequences of red and green pigments from five mammalian orders (Artiodactyla, Carnivora, Lagomorpha, Perissodactyla, and Rodentia). The result suggests that cat (Felis catus), dog (Canis familiaris), and goat (Capra hircus) pigments all with AHYTA at the five critical sites have lambda max values of approximately 530 nm, whereas rat (Rattus norvegicus) pigment with AYYTS has a lambda max value of approximately 510 nm, which is accurately predicted by the five-sites rule. However, the observed lambda max values of the orthologous pigments of European rabbit (Oryctolagus cuniculus), white-tailed deer (Odocoileus virginianus), gray squirrel (Sciurus carolinensis), and guinea pig (Cavia procellus) are consistently more than 10 nm higher than the predicted values, suggesting the existence of additional molecular mechanisms for red and green color vision. The inferred amino acid sequences of ancestral organisms suggest that the extant mammalian red and green pigments appear to have evolved from a single ancestral green-red hybrid pigment by directed amino acid substitutions.