The CD4 T cell-deficient mouse mutation nackt (nkt) involves a deletion in the cathepsin L (Ctsl) gene

We recently reported a novel autosomal recessive mouse mutation designated nackt (nkt). Homozygous mutant mice have diffuse alopecia and a marked reduction in the proportion of CD4+ T cells in the thymus and peripheral lymphoid tissues. Here we show that the CD4 T-cell deficiency is due to a defect in the thymic microenvironment rather than the hematopoietic compartment. Furthermore, we identified the molecular basis of the mutant phenotype by demonstrating that the nkt mutation represents a 118-bp deletion of the cathepsin L (Ctsl) gene which is required for degradation of the invariant chain, a critical chaperone for major histocompatibility complex class II molecules. This finding explains the similarities in skin and immune defects observed in nkt/nkt and Ctsl -/- mice. The data reported here provide further in vivo evidence that the lysosomal cysteine protease cathepsin L plays a critical role in CD4+ T-cell selection in the thymus.     

Phylogenetic relationships and reticulation among Asian Elymus (Poaceae) allotetraploids: Analyses of three nuclear gene trees

This phylogenetic study focuses on a subset of the species in Elymus—specifically, the endemic Asian tetraploids presumed to combine the St genome from Pseudoroegneria with the Y genome from an unknown donor. The primary goals were to (1) determine whether the St and Y genomes are derived from phylogenetically distinct donors; (2) identify the closest relative, and potentially the likely donor, of the Y genome; and (3) interpret variation among StStYY species in terms of multiple origins and/or introgression. The goals were addressed using phylogenetic analyses of sequences from three low-copy nuclear genes: phosphoenolpyruvate carboxylase, β-amylase, and granule-bound starch synthase I. Data sets include 16 StStYY individuals representing nine species, along with a broad sample of representatives from most of the monogenomic (i.e., non-allopolyploid) genera in the tribe. To briefly summarize the results: (1) the data clearly support an allopolyploid origin for the Asian tetraploids, involving two distinct donors; (2) the Y genome was contributed by a single donor, or multiple closely-related donors; (3) the phylogenetic position of the Elymus Y genome varies among the three trees and its position is not strongly supported, so the identity of the donor remains a mystery; and (4) conflicts among the gene trees with regard to the St-genome sequences suggest introgression involving both Elymus and Pseudoroegneria.     

Cloning and expression pattern of the lysozyme C gene in zebrafish

Here, we report isolation and developmental expression pattern of the zebrafish lysozyme C gene. Amino acid sequence analysis showed that the zebrafish lysozyme C protein shared approximately 37-80% identities with the mouse, human, chicken, and carp counterparts. Whole-mount in situ hybridization showed that the lysozyme C gene was expressed in macrophages, as its expression was co-localized with the known myeloid lineage markers L-plastin and PU.1. At 20 hours postfertilization (hpf), most of the lysozyme C positive cells were localized in the yolksac and head mesenchyme but not in the intermediate cell mass, supporting the notion that the primitive macrophage originated from the yolksac (Development 126 (1999) 3735). At 36hpf, the lysozyme C positive cells scattered within the head and yolksac, and began to appear in the caudal part of axial vein. By 6 days postfertilization (dpf), the lysozyme C positive cells accumulated in the kidney where hematopoiesis had been indicated to take place after 4dpf (Dev. Dyn. 214 (1999) 323). Taken together, our results demonstrate that the lysozyme C gene is specifically expressed in myeloid lineage, suggesting that it could serve as an excellent marker for genetic screening of both primitive and definitive myeloid lineage development in zebrafish.     

Cadmium-induced ovarian pathophysiology is mediated by change in gene expression pattern of zinc transporters in zebrafish (Danio rerio)

This study explored the potential for expression pattern of genes encoding zinc (Zn) transporters to be involved in the cadmium (Cd)-induced reproductive toxicity in female of zebrafish. For this purpose, oocytes maturity and ovarian histology as well as Cd, Zn and metallothioneins (MTs) accumulation and expression of genes encoding Zrt-,Irt-related protein 10 (ZIP10), Zn transporter 1 (ZnT1) and zebrafish metallothionein (zMT) were examined in ovaries of adult zebrafish exposed to 0.4 mg/L Cd in water and supplemented with Zn (5 mg kg⁻¹) in their diet for 21 days. Cd-exposure decreased the expression of ZnT1 and caused up-regulation of ZIP10 and zMT gene expression. These changes were accompanied by increased Cd and MTs accumulation, decreased Zn contents as well as by histopathological damages in ovarian tissues. The co-exposure of fish to Cd and Zn abolished ZnT1 down-regulation and rendered a persistently increased ZIP10 mRNA level. This treatment also decreased Cd and MTs accumulation, reversed Cd-induced Zn depletion and partially restored Cd-induced histological changes in ovarian tissues. These results imply that the downregulation of ZnT1 as well as the overexpression of ZIP10, in responses to the ovarian Zn depletion induced by Cd, play a major role in Cd accumulation and consequently in its toxicity. The protective effect of dietary Zn supplementation against Cd-induced toxicity is mediated, at least in part, by the increase of Zn availability and subsequently the induction of ZnT1 gene expression.     

Cloning and expression pattern of vat-1 homolog gene in zebrafish

The VAT-1 protein is present in the electric organ of marine rays where it is suggested to play a central role in nerve signal transmission. VAT-1 homolog protein was also identified in mouse and human but its function remains to be determined. We have investigated VAT-1 homolog in zebrafish Danio rerio since it is an excellent model amenable to the combination of genetic, molecular and embryological studies. Amino acid sequence analysis shows that the zebrafish VAT-1 homolog shares approximately 51-61% identity with the electric ray, mouse, and human counterparts. By in situ hybridization, vat-1 homolog mRNA is first observed in the trigeminal nuclei at the 8-somite stage. At 20-somite stage, vat-1 homolog is detected in the brain, namely in primary clusters of neurons, in the epiphysis and in the hindbrain. vat-1 homolog is also present in the neural tube but this expression disappears after 72 h post-fertilization. At 24 h post-fertilization, vat-1 homolog starts to be expressed in the developing gut. At later stages, vat-1 homolog is present throughout the brain, appears in the maturing retina and the pharyngeal cavity.     

Phylogenetic relationships of allotetraploid Hordelymus europaeus (L.) Harz (Poaceae: Triticeae)

Phylogenetic analyses of sequence data from two plastid genes (rbcL and ndhF) and two single-copy nuclear genes (DMC1 and EF-G) are used to elucidate the origin of the tetraploid, monotypic Hordelymus europaeus. Previous data have mostly shown an allopolyploid origin of Hordelymus, but very recently it was suggested that Hordelymus is autoploid. The present analysis, including representatives from all basic genome types accepted in the Triticeae, lends support to an alloploid origin. There is substantial support for the progenitor of Psathyrostachys as female genome donor of Hordelymus. Individual nuclear gene trees disagree about the male genome donor, but combined analysis of all data weakly supports the common progenitor of Pseudoroegneria and Henrardia as the male genome donor.     

Phylogenetic relationships of the Temnocephaloidea (Platyhelminthes)

Temnocephala novaezealandiae (family Temnocephalidae) and Troglocaridicola mrazeki and Scutariella georgica (family Scutariellidae) were studied by electron microscopy in an attempt to reveal characters that would indicate their phylogenetic relationship to other members of the Platyhelminthes. Ultrastructural features of the epidermis in these temnocephaloideans are like those of the neoophoran turbellarians. The epidermis is syncytial, is honeycombed by a multitude of gland necks whose secretions produce an epidermal surface film, and is underlaid by a thick basement membrane. Some cells in the parenchyma are compartmentalized by intrusive cell processes from neighboring parenchymal cells in a fashion similar to parenchymal structure in the Monogenea and Digenea. The spermatozoa have a pair of free 9+1 flagella and contain aligned dense bodies. The Temnocephaloidea is evidently derived from an early rhabdocoel-turbellarian-like ancestor.     

Phylogenetic relationships in the skin-inhabiting Sarcoptoidea (Acari: Astigmata)

A phylogenetic analysis of relationships is carried out among the skin-inhabiting mites presently included in the families Rhyncoptidae, Audycoptidae and Sarcoptidae. The analysis included eight taxa (five genera of follicle associates and three subfamilies of skin-burrowing sarcoptids) and 41 characters, and generated a single most parsimonious tree of length 60 with a consistency index of 0.745. The genus Caenolestocoptes (Sarcoptidae, Caenolestocoptinae) is the sister group of the assemblage of Ursicoptes, Saimirioptes, Audycoptes (all Audycoptidae) and Rhyncoptes (Rhyncoptidae). Within the latter grouping Audycoptes is the sister group of Rhyncoptes. Based on these results the Caenolestocoptinae Fain & Lukoschus, 1976 and Audycoptidae Lavoipierre, 1964 are synonymised with the Rhyncoptidae Lawrence, 1956. The Rhyncoptidae (sensu nov.) appears to be the sister group of the Sarcoptidae (sensu stricto).The distribution pattern of follicle inhabitation and skin-burrowing in the Sarcoptoidea can be explained by one adaptation to follicle inhabitation (Rhyncoptidae), another to skin-burrowing (Sarcoptidae) and possibly a third in their common ancestor from living on the hairs or on the skin to living in the skin (follicles, burrows or both).New host and locality data for various taxa in the Rhyncoptidae (sensu nov.) are provided. The larva of Audycoptes lawrencei Lavoipierre, 1964, is described and the female redescribed.     

Phylogenetic relationships of fantails (Aves: Rhipiduridae)

We explore the phylogenetic relationships of fantails (Aves: Rhipiduridae) using molecular characters derived from two nuclear introns and two mitochondrial genes. Our results indicate that Rhipidura hypoxantha is not a true fantail, but rather a member of the Stenostiridae clade that is morphologically and behaviourally convergent with fantails. Within the true Rhipiduridae, we identified six distinct clades; however, phylogenetic relationships among these groups were unresolved. The only well-supported sister relationship was between members of the grey and the rufous fantail complexes. Clades recovered through our model-based phylogenetic analyses generally correspond to previously proposed fantail complexes based on morphological characters. The phylogenetic position of R. atra and R. diluta remain unclear, as sister relationships varied between analyses for the prior whereas the latter was placed as sister to the New Guinea thicket fantails, R. leucothorax and R. threnothorax ; yet significant node support was not recovered for either taxa. Biogeographically, fantails appear to have radiated rapidly and the six clades are not geographically restricted, but instead span South-east Asia, New Guinea, Australia and Pacific Islands.     

Phylogenetic relationships of the mockingbirds and thrashers (Aves: Mimidae)

The mockingbirds, thrashers and allied birds in the family Mimidae are broadly distributed across the Americas. Many aspects of their phylogenetic history are well established, but there has been no previous phylogenetic study that included all species in this radiation. Our reconstructions based on mitochondrial and nuclear DNA sequence markers show that an early bifurcation separated the Mimidae into two clades, the first of which includes North and Middle American taxa (Melanotis, Melanoptila, Dumetella) plus a small radiation that likely occurred largely within the West Indies (Ramphocinclus, Allenia, Margarops, Cinclocerthia). The second and larger radiation includes the Toxostoma thrasher clade, along with the monotypic Sage Thrasher (Oreoscoptes) and the phenotypically diverse and broadly distributed Mimus mockingbirds. This mockingbird group is biogeographically notable for including several lineages that colonized and diverged on isolated islands, including the Socorro Mockingbird (Mimus graysoni, formerly Mimodes) and the diverse and historically important Galapagos mockingbirds (formerly Nesomimus). Our reconstructions support a sister relationship between the Galapagos mockingbird lineage and the Bahama Mockingbird (M. gundlachi) of the West Indies, rather than the Long-tailed Mockingbird (M. longicaudatus) or other species presently found on the South American mainland. Relationships within the genus Toxostoma conflict with traditional arrangements but support a tree based on a preivous mtDNA study. For instance, the southern Mexican endemic Ocellated Thrasher (T. ocellatum) is not an isolated sister species of the Curve-billed thrasher (T. curvirostre).     

Phylogenetic relationships and classification of the Vespinae (Hymenoptera: Vespidae)

Abstract. The phylogenetic relationships of the genera, subgenera and species-groups of the Vespinae are analysed using cladistic techniques. The results are used as the basis for a natural classification of these wasps. The cladogram for the four genera recognized is: Vespa + (Provespa + (Dolichovespula + Vespula)). No subgenera are recognized; all those previously described are synonymized with the appropriate genus. The synonymies of Nyctovespa with Vespa and Rugovespula with Vespula are new.     

Phylogenetic relationships of the Australian lomatiines (Diptera: Bombyliidae)

Cladistic analysis is used to isolate the monophyletic group of genera that comprise the Australian Lomatiinae and to investigate the relationships between the Australian genera. Cladograms of genera in the Australian Tomophthalmae and Lomatiinae are presented. Myonema Roberts and Neosardus Roberts are placed in the Cylleniinae, Antonia Loew remains in the Antoniinae and Petrorossia Bezzi is placed in the Anthracinae. The relationship of the Australian lomatiines to the world fauna is discussed, as are the relationships between the Australian genera. Docidomyia White is included in the Lomatiinae and is the sister group of all other genera of the subfamily: Comptosia Macquart sens.lat.; Doddosia Edwards, Oncodosia Edwards and Paramonovomyia Evenhuis. The current diagnosis of the Lomatiinae is changed to reflect the inclusion of Docidomyia. The two subgenera of Comptosia sensu Edwards, Aleucosia Edwards and Comptosia , were not each others' closest relatives in the strict consensus tree. Thus Comptosia as currently recognized is paraphyletic and the two subgenera are treated as genera, Aleucosia stat.nov. and Comptosia stat.nov.     

Production and processing of a recombinant Fasciola hepatica cathepsin B-like enzyme (FhcatB1) reveals potential processing mechanisms in the parasite

The liver fluke, Fasciola hepatica, apparently uses a number of cysteine proteases during its life cycle, most likely for feeding, immune evasion and invasion of tissues. A cathepsin B-like enzyme (herein referred to as FhcatB1) appears to be a major enzyme secreted by the invasive, newly excysted juvenile flukes of this parasite. To examine the processing mechanisms for this enzyme, a recombinant form was expressed in Pichia pastoris and purified to yield a homogenous pool of the enzyme. The purified enzyme could be autoactivated at low pH via a bi-molecular mechanism, a process that was greatly accelerated by the presence of large, negatively charged molecules such as dextran sulfate. The enzyme could also apparently be processed to the correct size by an asparaginyl endopeptidase via cleavage in an unusual insertion N-terminal to the normal cleavage site used to yield the active form of the enzyme. Thus, there appear to be a number of ways in which this enzyme can be processed to its optimally active form prior to secretion by F. hepatica.