Portion Of Flank Research Articles

An integrated approach of advanced methods for mapping geologic structures and sedimentary thickness in Ukelle and adjoining region (Southeast Nigeria)

High-resolution aeromagnetic data were enhanced using recent and advanced filters to map the geologic structures of the Ukelle and adjoin region (Southeast Nigeria). Aeromagnetic data were reduced to the equator (RTE) and upward continued to 100 m. Subsequently, enhancement operations like the tilt angle of the horizontal gradient (TAHG), logistic function of the horizontal gradient (LTHG), and fast sigmoid function (FSED) operations were carried out. The results from these filters indicated that the ENE-WSW, NE-SW, NNE-SSW, and NNW-SSE orientations dominate the structural pattern of the Ukelle region. In addition, the edge filters delineated NE-SW trending synclinal structures that match the location of thick (500-1400 m) sedimentation obtained by the tilt-depth (TD) method. Furthermore, the structural map obtained from remote sensing data validated the lineament orientations and position of the NE-SW trending synclinal structure. The results also showed that the study location’s southeastern and northwestern flanking portions, controlled by extensive Santonian igneous intrusions and metamorphisms, are characterized by high lineaments and thin (0-500 m) sedimentation. The observed thin sedimentation is believed to be caused by widespread Santonian tectonic events in the area. At the same time, related geologic structures served as migration pathways and accumulation zones for rift mineralization.

A new species of Corydoras (Siluriformes: Callichthyidae) from the rio Madre de Dios basin, Peruvian Amazon, with comments on Corydoras aeneus identity

Abstract A new species of Corydoras is described from tributaries to the rio Araza, an affluent of the rio Inambari, itself a tributary to the rio Madre de Dios, rio Madeira basin in the Peruvian Amazon. The new species can be distinguished from its congeners by the following features: (I) absence of contact between the posterior process of the parieto-supraoccipital and the nuchal plate, (II) a single, large conspicuous dark brown or black blotch on anterodorsal portion of flank; blotch somewhat rounded to roughly diamond shaped, and (III) absence of dark blotches on fins. General comments on the identity of Corydoras aeneus are also provided.

Taxonomic review of the typical long-snouted species of Corydoras (Siluriformes: Callichthyidae) from the río de La Plata basin

Abstract The typical long-snouted species of Corydoras from the río de La Plata basin were reviewed herein, and the previously proposed synonymy of Corydoras ellisae was corroborated. Corydoras areio and C. aurofrenatus are diagnosed from their congeners, excluding those in lineage 1, by the following features: temporal sensory canal in sphenotic with two pores; upper tooth plate of branchial arch with three or four series of teeth; fleshy flap at mouth corner. Corydoras areio differs from all lineage 1 congeners by having infraorbital 2 with relatively wider posterior laminar expansion; absence of large patches of black pigmentation on the body and absence of conspicuous concentration of dark brown or black chromatophores on anterior portion of the dorsal fin; and presence of blotches on flanks not aligned in longitudinal series. Corydoras aurofrenatus differs from all lineage 1 congeners by having ventral surface of head and trunk densely covered by small, not coalescent platelets; middle portion of flank with two or three dark brown or black patches (below the dorsal-fin, below the adipose-fin base, and on the caudal peduncle base, diffuse and variably present), patches decreasing in size posteriorly; poorly developed fleshy flap at the corner of mouth; anteroventral portion of cleithrum exposed.

The ribosomal intergenic spacer (IGS) in the potato and tobacco cyst nematodes, Globodera pallida, G. rostochiensis and G. tabacum

The potato cyst nematodes Globodera pallida and G. rostochiensis (PCN), and tobacco cyst nematode (TCN), G. tabacum, are the most important parasitic nematodes of potato and tobacco worldwide. Ribosomal DNA provides useful molecular data for diagnostics, the study of polymorphisms and for evolutionary research in eukaryotic organisms including nematodes. Here we present data on the structure and organization of a rarely studied part of the intergenic spacer (IGS) region of the PCN and TCN genome of cyst nematodes. This region has shown potential for diagnostic purposes and population studies in other organisms including nematodes. In nematodes, the ribosomal RNA gene cluster comprises three genes: 5.8S, 18S and 28S rRNA, which are separated by spacer regions: the intergenic spacer (IGS), non-transcribed spacer (NTS), externally transcribed spacer (EST) and the internally transcribed spacer (ITS). The intergenic spacer (IGS) region consists of an external transcribed spacer (ETS) and a non-transcribed spacer (NTS) which is located between the 28S of one repeat and the 18S gene of the next repeat within the rRNA genes cluster. In this study, the first flanking portion of the IGS was amplified, cloned and sequenced from PCN and TCN. Primers were then designed to amplify the whole IGS sequence. PCR amplification of IGS from G. tabacum, G. pallida, and G. rostochiensis yielded respectively: a single amplicon of 3 kb, three amplicons sized 2.5, 2.6 and 2.9 kb, and two amplicons sized 2.8 and 2.9 kb. Results showed that Globodera spp. has more than one variant copy of the IGS, with both long and short repetitive DNA elements. An approximately 400 bp long region without any internal repetitive elements, were identified in a position between the two repetitive regions suggesting that there is a 5S gene in the IGS of these species.

Electrical resistivity tomography (ERT) based subsurface characterisation of Pakhi Landslide, Garhwal Himalayas, India

Pakhi landslide is one of the major debris slides of retrogressive nature along national highway (NH-58) corridor from Rishikesh to Badrinath in Garhwal Himalayas, India. The present work is the first such attempt in one of the landslides in Indian Himalayas and in the present case study, the subsurface characterization of the landslide was carried out with an aim to correlate the subsurface lithology, slip surface and geometry of the landslide using borehole investigation and electrical resistivity tomography (ERT) techniques. The results from ERT survey along and across the landslide could help to delineate different strata layers; thereby deciphering the probable slip surface of the landslide activity. Further, based on the landslide model drawn from the ERT interpretations, it can be stated that the crown portion of the right flank is more vulnerable to sliding phenomenon and that of the left flank is more prone to erosion. The results obtained from both the borehole investigation and ERT techniques are observed to be in great agreement and could complement each other for subsurface detailed investigation of landslide. The integration of both these techniques provides useful information about the landslide activities and defines the geometry of the landslide. Hence, it will be quite helpful in planning mitigation strategies as well as usefulness of each of these techniques.

Study of ice-related flow features around Tanaica Montes, Mars: Implications for late amazonian debris-covered glaciation

Lobate debris aprons (LDA) and lineated valley fill (LVF) have been broadly recognized in the mid-latitudes of Mars and their subsequent analyses using data from the SHAllow RADar (SHARAD) instrument has suggested evidence for contemporary ice preserved beneath these features. In this study, we conduct detailed characterization of newly identified LDA flow units within the Tanaica Montes region (39.55˚ N, 269.17˚ E) of Mars to assess and understand the similarities in their emplacement with respect to LDA flow units mapped in other regions of Mars. We utilize the Mars Reconnaissance Orbiter (MRO) Context Camera (CTX) images and SHAllow RADar (SHARAD) datasets for geomorphic and subsurface analysis and Mars Global Surveyor (MGS) Mars Orbiter Laser Altimeter (MOLA) point tracks for topographic analysis. Geomorphic observation of LDA flow units surrounding the montes flanks and massif walls reveal integrated pattern of convergence and divergence and evidence of bending and deflection within the flow lines that resulted in concentric, loop-like flow patterns in the downslope. Brain-terrain texture and craters with varying morphological characteristics (ring-mold type) is suggestive that LDAs may be similar to ice-rich, debris-covered glaciers. MOLA point track based convex-up topographic profiles of LDAs suggest that their thickness vary in the range of ∼100–200 m in both the northwestern and southeastern portions of study region. Further, the slope values of mapped LDA surfaces within the study region are within ∼0.1˚–4˚. The extent of mapped LDAs within the study region is such that some of the low elevation (∼0.8–1.3 km) portions of montes flanks are surrounded by relatively less extent (up to ∼0.5–0.8 km) of LDA flow units. Geomorphic and topographic evidence for flow units that appear to be superposed on the main LDA body collectively suggest the possibility of episodic glacial activity in the region. Furthermore, based on the alignment of subsurface reflectors with the surrounding plains when a permittivity of ice (3.2) is assumed and the radargram is depth-corrected, we infer that some of the portions of LDA flow units have preserved ice in their subsurface up to ∼300–500 m depth. Crater size frequency distribution of craters counted on LDA surface indicates that the best-fit age is ∼110 Ma. In addition, the LDA surfaces exhibit different best-fit ages for different types of crater morphologies (bowl-shaped, ring-mold and infilled craters) included in the crater count statistics. Together, these observations and the interpretations suggest that most, if not all, of the LDAs in the study region are like classical LDAs mapped in other regions of Mars (e.g. along the mid-latitude dichotomy boundary and eastern Hellas region). These results indicate that a widespread accumulation and preservation of ice has occurred during the Late Amazonian as suggested in previous studies.

On the Mechanisms of Rain Formation in an Idealized Supercell Storm

Abstract Deep convective storms produce raindrops through three mechanisms: condensation and coalescence growth of cloud liquid droplets (i.e., warm processes), melting of ice hydrometeors, and shedding from wet hailstones. To investigate the relative importance of these mechanisms and their contributions to exotic drop size distributions (DSDs) observed near the surface in supercell storms, an idealized simulation of a supercell is performed using a modified version of the Morrison two-moment microphysics scheme. The modified scheme includes separate categories for warm, shed, and melted rain. Rain originating from melting ice dominates the rain mass at low levels, especially along the right forward-flank precipitation shield, whereas shed-rain drops dominate a region within the left forward flank. Warm rain is only dominant in the upshear portion of the rear flank of the storm at low levels, though it dominates the total rain mass within the main updraft aloft. The warm-rain mass at low levels is associated with strong low-level downdrafts, consistent with previously published hypotheses based on polarimetric radar observations. Raindrops produced via warm processes are smaller on average than those produced by shedding and melting; drops in the latter class tend to be the largest. Overall, the simulations fail to reproduce the diverse nature of observed supercell DSDs, although the modified microphysics scheme does increase the variability of surface DSDs compared to the Control run. This implies that more sophisticated treatment of rain microphysics is needed to capture the natural variability of supercell DSDs, including the ability to evolve the DSD spectral shape through sedimentation and collisional processes.

Development and evolution of detachment faulting along 50 km of the Mid‐Atlantic Ridge near 16.5°N

AbstractA multifaceted study of the slow spreading Mid‐Atlantic Ridge (MAR) at 16.5°N provides new insights into detachment faulting and its evolution through time. The survey included regional multibeam bathymetry mapping, high‐resolution mapping using AUV Sentry, seafloor imaging using the TowCam system, and an extensive rock‐dredging program. At different times, detachment faulting was active along ∼50 km of the western flank of the study area, and may have dominated spreading on that flank for the last 5 Ma. Detachment morphologies vary and include a classic corrugated massif, noncorrugated massifs, and back‐tilted ridges marking detachment breakaways. High‐resolution Sentry data reveal a new detachment morphology; a low‐angle, irregular surface in the regional bathymetry is shown to be a finely corrugated detachment surface (corrugation wavelength of only tens of meters and relief of just a few meters). Multiscale corrugations are observed 2–3 km from the detachment breakaway suggesting that they formed in the brittle layer, perhaps by anastomosing faults. The thin wedge of hanging wall lavas that covers a low‐angle (6°) detachment footwall near its termination are intensely faulted and fissured; this deformation may be enhanced by the low angle of the emerging footwall. Active detachment faulting currently is limited to the western side of the rift valley. Nonetheless, detachment fault morphologies also are present over a large portion of the eastern flank on crust >2 Ma, indicating that within the last 5 Ma parts of the ridge axis have experienced periods of two‐sided detachment faulting.

A basin modeling and organic geochemistry study in the Vallecitos syncline, San Joaquin Basin, California

The Vallecitos syncline is a westerly structural extension of the San Joaquin Basin. The Vallecitos oil field, comprised of eight separate areas that produce from Cretaceous and Paleogene reservoirs, accounted for 5.4 MMB of oil and 5.6 BCF associated of gas through 2010. However, exploration for oil and gas in the Vallecitos area is challenging due to structural complexity and limited data. The purpose of this study is to evaluate whether source rocks are actively generating petroleum in the Vallecitos syncline and to improve our understanding of burial history and timing of hydrocarbon generation. We conducted biomarker analysis on twenty-two oil samples from the Vallecitos syncline. Source-related biomarkers show two genetic groups of oil, which originated from two different source rocks. These results differ from earlier published interpretations in which the Kreyenhagen Formation is the only source rock in the Vallecitos syncline, and suggest that the Cretaceous Moreno Formation in the syncline also is an active source rock.Stratigraphic evidence and modeling suggest that late Cenozoic episodes of erosion due to folding and uplift removed significant overburden on the flanks of the syncline. To better understand the petroleum systems and clarify the total active source rocks in the area, 2D burial histories were generated through the Vallecitos syncline. A published cross-section through the deepest part of the syncline was selected to conduct thermal history, basin evolution, and migration analyses. The 2D model results indicate that the lower Kreyenhagen Formation has various maturities within the formation at different locations in the present-day syncline. The basal part of the Kreyenhagen Formation is in the dry gas window and maturity decreases away from the central part to the flanks. It remains immature along shallow portions of the present-day flanks. In contrast, the basal part of the Moreno Formation achieved extremely high maturity (past the gas generation zone) but is in the oil generation zone on the flanks of the syncline at shallow depth. All of our geochemical and 2D model results suggest that there are two active source rocks in the Vallecitos syncline. Accordingly, we propose that there are two active petroleum systems in the Vallecitos syncline.

The ribosomal intergenic spacer (IGS) region in Schistosoma japonicum: Structure and comparisons with related species

The intergenic spacer (IGS) between the 28S and 18S ribosomal RNA genes was PCR-amplified, sequenced and characterized for Schistosoma japonicum from mainland China, and compared with those of other Schistosoma species. Excluding flanking portions of the 28S and 18S genes, the IGS in the longest sequenced amplicon from S. japonicum IGS was 1457bp in length. However, intra-specific and intra-individual variation was noted. The IGS region of S. japonicum is strikingly different in structure from those of African Schistosoma species for which data are available. S. japonicum has a shorter IGS and largely lacks a long region of complex repeats seen in the African species. However, careful comparisons with African species highlighted the presence of a few shared repeat motifs that were not apparent from study of African species only. Such motifs presumably have functional significance. Discovery of such motifs may in general be aided by comparisons of relatively distant taxa rather than of sibling taxa.

Relationship between the flank sliding of the South East Crater (Mt. Etna, Italy) and the paroxysmal event of November 16, 2006

Over the last 2 years, the south east crater (SEC) at Mt. Etna (Italy) has been characterised by the intermittent emission of lava flows, often accompanied by paroxysmal episodes with violent strombolian activity and/or lava fountains. One of the most intense and intriguing episodes occurred on November 16, 2006 during strombolian and effusive activity from the very top of the SEC. At the eastern base of the crater, a violent and short-lasting outburst generated a 300-m-high eruptive curtain of finely fragmented magma and steam, which collapsed in a few seconds giving rise to a small but significant pyroclastic flow. The paroxysm was preceded by progressive sliding of the eastern flank of the SEC edifice, which led to the formation of a large niche. Previously published models explain the outburst as due to rapid vaporisation of water contained in sediments on contact with hot lava flowing along the flank of the SEC or, alternatively, to gravitational collapse of a destabilised portion of the eastern flank of the crater. However, several lines of evidence suggest that these models do not adequately explain the paroxysm, which we propose was associated with the explosive emission of magma during the rapid opening of an ESE-WNW-oriented fracture at the eastern base of the SEC. Moreover, geochemical data of the products associated with this episode show that they are the most primitive and gas-rich among those erupted during the entire 2006 period. We suggest that the paroxysm of November 16, 2006, which occurred at base of the SEC, was a magma outburst due to rapid ground fracturing related to a drop in confining pressure upon the underlying dyke consequent to the sliding of the eastern flank of the SEC cone. Specifically, the unloaded shallow portion of the feeding dyke did not restrain the arrival of a new batch of gas-rich magma, which worked its way out by fracturing the base of the niche at its weakest point. This paroxysm appears significant because it reveals the potential development of syn-eruptive dynamics acting directly on the uppermost portion of the plumbing system which is able to generate pyroclastic flows even on basaltic volcanoes such as Mount Etna.

A New Species of the Scinax catharinae Species Group (Anura: Hylidae) from Minas Gerais, Southeastern Brazil

A new species of tree frog from the Scinax catharinae species group is described, discovered in the Municipality of Ouro Preto, southeastern Brazil. The new species is related to Scinax flavoguttatus, but differs from this species mainly by the light green color on its inguinal regions and hidden portions of flanks and thighs, by its subovoid snout, by its developed nuptial pad, and by its smaller males and females. Additionally, we describe the tadpole which is characterized by: dorsal position of nostril; dorsolateral eyes; gold spots between nostrils and eyes, short spiracle; spiracle opening on the midline of dorsal and ventral surface of body; absence of tail flagellum; oral disc with a short dorsal gap, surrounded by a uniseriate marginal papillae; M- shaped upper jaw sheath; tooth row formula 2(2)/3.

Hazards from pyroclastic density currents at Mt. Etna (Italy)

Despite the recent recognition of Mount Etna as a periodically violently explosive volcano, the hazards from various types of pyroclastic density currents (PDCs) have until now received virtually no attention at this volcano. Large-scale pyroclastic flows last occurred during the caldera-forming Ellittico eruptions, 15–16 ka ago, and the risk of them occurring in the near future is negligible. However, minor PDCs can affect much of the summit area and portions of the upper flanks of the volcano. During the past ~ 20 years, small pyroclastic flows or base-surge-like vapor and ash clouds have occurred in at least 8 cases during summit eruptions of Etna. Four different mechanisms of PDC generation have been identified during these events: (1) collapse of pyroclastic fountains (as in 2000 and possibly in 1986); (2) phreatomagmatic explosions resulting from mixing of lava with wet rock (2006); (3) phreatomagmatic explosions resulting from mixing of lava with thick snow (2007); (4) disintegration of the unstable flanks of a lava dome-like structure growing over the rim of one of the summit craters (1999). All of these recent PDCs were of a rather minor extent (maximum runout lengths were about 1.5 km in November 2006 and March 2007) and thus they represented no threat for populated areas and human property around the volcano. Yet, events of this type pose a significant threat to the lives of people visiting the summit area of Etna, and areas in a radius of 2 km from the summit craters should be off-limits anytime an event capable of producing similar PDCs occurs. The most likely source of further PDCs in the near future is the Southeast Crater, the youngest, most active and most unstable of the four summit craters of Etna, where 6 of the 8 documented recent PDCs originated. It is likely that similar hazards exist in a number of volcanic settings elsewhere, especially at snow- or glacier-covered volcanoes and on volcano slopes strongly affected by hydrothermal alteration.

Molecular organization of 5S rDNA in bitterlings (Cyprinidae)

Molecular organization and nucleotide sequences of the 5S rRNA gene and NTS were investigated in freshwater fish, bitterlings (Acheilognathinae), including 10 species/subspecies of four genera, Acheilognathus, Pseudoperilampus, Rhodeus, and Tanakia, to understand the evolutionary trait of 5S rDNA arrays. Southern hybridization analysis revealed a general trend with tandem repeats of 5S rDNA in all the examined bitterlings. Sequence analysis demonstrated a conserved 120 bp sequence of the 5S rRNA gene and a short NTS of 56-67 bp with two distinct portions, a conserved (5'-flanking portion; at positions -1 to -38) and a variable part (3'-flanking portion), in 6 of 10 species/subspecies examined. The conserved NTS region was most likely an external promoter so far observed in various vertebrates, whereas the variable NTS region could be divided into two types due to its nucleotide polymorphisms. Molecular phylogeny using the 5S rRNA gene and NTS sequences suggested the occurrence of 5S rDNA duplication before speciation and a concerted evolution for the gene and conserved NTS regions, but a birth-and-death process to maintain the variable NTS region. Thus, the 5S rDNA in the examined bitterlings might have evolved under a mixed process of evolution.

The impact of Scotian Shelf Water “cross-over” on the plankton dynamics on Georges Bank: A 3-D experiment for the 1999 spring bloom

The 1999 March SeaWiFS images detected an intense phytoplankton bloom on the southern flank of Georges Bank (GB). The bloom covered a large portion of the southern flank between the 60 and 200 m isobaths, and later extended to and connected with an even larger patch near the Northeast Peak (NEP) and Browns Bank. A three-dimensional (3-D) model experiment was conducted to examine the cause of the bloom and the impact of Scotian Shelf Water on the spring phytoplankton bloom dynamics. The finite volume coastal ocean model (FVCOM) provided the hydrodynamic fields for Lagrangian particle trajectory, tracer and biological model experiments. Process-oriented modeling experiments showed that the formation and maintenance of the phytoplankton bloom on the southeastern flank of GB is related to the weak stratification caused by the transport of the colder but fresher Scotian Shelf Water across the Northeast Channel (NEC). With sufficient nutrients from the slope, the bloom could result from in situ growth of phytoplankton near the slope where the stabilizing salinity front is located. The model results suggest that the timing and location of the phytoplankton bloom on the southern flank of GB is sensitive to the spatial distribution of temperature and salinity on the bank, the flow fields across the NEC, and the location of the salinity front near the shelf break. r 2006 Elsevier Ltd. All rights reserved.

Multiple, non-allelic, intein-coding sequences in eukaryotic RNA polymerase genes.

BackgroundInteins are self-splicing protein elements. They are translated as inserts within host proteins that excise themselves and ligate the flanking portions of the host protein (exteins) with a peptide bond. They are encoded as in-frame insertions within the genes for the host proteins. Inteins are found in all three domains of life and in viruses, but have a very sporadic distribution. Only a small number of intein coding sequences have been identified in eukaryotic nuclear genes, and all of these are from ascomycete or basidiomycete fungi.ResultsWe identified seven intein coding sequences within nuclear genes coding for the second largest subunits of RNA polymerase. These sequences were found in diverse eukaryotes: one is in the second largest subunit of RNA polymerase I (RPA2) from the ascomycete fungus Phaeosphaeria nodorum, one is in the RNA polymerase III (RPC2) of the slime mould Dictyostelium discoideum and four intein coding sequences are in RNA polymerase II genes (RPB2), one each from the green alga Chlamydomonas reinhardtii, the zygomycete fungus Spiromyces aspiralis and the chytrid fungi Batrachochytrium dendrobatidis and Coelomomyces stegomyiae. The remaining intein coding sequence is in a viral relic embedded within the genome of the oomycete Phytophthora ramorum. The Chlamydomonas and Dictyostelium inteins are the first nuclear-encoded inteins found outside of the fungi.These new inteins represent a unique dataset: they are found in homologous proteins that form a paralogous group. Although these paralogues diverged early in eukaryotic evolution, their sequences can be aligned over most of their length. The inteins are inserted at multiple distinct sites, each of which corresponds to a highly conserved region of RNA polymerase. This dataset supports earlier work suggesting that inteins preferentially occur in highly conserved regions of their host proteins.ConclusionThe identification of these new inteins increases the known host range of intein sequences in eukaryotes, and provides fresh insights into their origins and evolution. We conclude that inteins are ancient eukaryote elements once found widely among microbial eukaryotes. They persist as rarities in the genomes of a sporadic array of microorganisms, occupying highly conserved sites in diverse proteins.

P3-289: Protein sequence

Histones are basic nuclear proteins that are responsible for the nucleosome structure within the chromosomal fiber in eukaryotes. See 142711. Albig et al. (1996) identified a gene, which they called H3.4, encoding a member of the H3 class of histones. Albig and Doenecke (1997) designated this gene H3t. By sequence analysis, Albig et al. (1996) found that H3t differs by 4 amino acid residues from the consensus mammalian H3 structure, and shows the consensus promoter and 3–prime flanking portions typical of replication–dependent histones. Preliminary data indicated that H3t is expressed in testicular cells. By analysis of a somatic cell hybrid panel and by fluorescence in situ hybridization, Albig et al. (1996) mapped the H3t gene to 1q42, outside the gene clusters that contain the other replication–dependent H3 genes. Histones are the basic nuclear proteins responsible for the nucleosome structure of the chromosomal fiber in eukaryotes. Two each of the core histones (H2A, H2B, H3, and H4) form an octamer, as the protein moiety of the core structure of the nucleosome. The linker histone H1 is involved in sealing 2 rounds of nucleosome DNA at the surface of the nucleosome core and is also involved in the formation of higher order structures of chromatin. Because of their function in organizing chromosomal structure, histones contribute to virtually all chromosomal processes, such as gene regulation, chromosome condensation, recombination, and replication.

Austrolebias varzeae, a new annual fish from the upper rio Uruguay basin, southern Brazil (Cyprinodontiformes: Rivulidae)

Austrolebias varzeae n. sp. is described from rio da Várzea floodplains, upper rio Uruguay basin, southern Brazil. It seems to be closely related to A. carvalhoi (Myers), with which it shares a similar color pattern of male and an apomorphic morphology of the autopalatine. The new species differs from A. carvalhoi by having more anal-fin rays in males and more caudal-fin rays. Austrolebias varzeae is distinguished from all other species of the genus by a unique color pattern, in which there are three distinctively darker and narrower bars on the anterior portion of male flank. Putative close relationships between A. varzeae and A. carvalhoi suggest a closely related biogeographic history between upper Uruguay and upper Iguaçu River basins, corroborated by a biogeographic pattern of the anablepid genus Jenynsia.

T cell receptor CDR3 loop length repertoire is determined primarily by features of the V(D)J recombination reaction.

The third complementarity-determining region (CDR) of the TCR alpha and beta chains forms loops that engage amino acid residues of peptides complexed with MHC. This interaction is central to the specific discrimination of antigenic-peptide-MHC complexes by the TCR. The TCRbeta chain CDR3 loop is encoded by the Dbeta gene segment and flanking portions of the Vbeta and Jbeta gene segments. The joining of these gene segments is imprecise, leading to significant variability in the TCRbeta chain CDR3 loop length and amino acid composition. In marked contrast to other pairing antigen-receptor chains, the TCR beta and alpha chain CDR3 loop size distributions are relatively narrow and closely matched. Thus, pairing of TCR alpha and beta chains with relatively similar CDR3 loop sizes may be important for generating a functional repertoire of alpha beta TCR. Here we show that the TCRbeta chain CDR3 loop size distribution is minimally impacted by TCRbeta chain or alpha beta TCR selection during thymocyte development. Rather, this distribution is determined primarily at the level of variable-region gene assembly, and is critically dependent on unique features of the V(D)J recombination reaction that ensure Dbeta gene segment utilization.

Molecular evidence for phylogenetic relationships among buntings and American sparrows (Emberizidae)

To help clarify controversial phylogenetic relationships within the family Emberizidae, we sequenced 1238 bp of mitochondrial DNA from the cytochrome b gene and a flanking portion of ND5. Although the longspurs (Calcarius) and the snow buntings (Plectrophenax) have been grouped with the Old World buntings (Emberiza) in traditional classifications, our molecular phylogenies constructed with maximum likelihood and maximum parsimony place these genera basal to a clade in which the Old World buntings and North American sparrows are sister groups. Contrary to the hypothesis that the radiation within Emberiza is recent following a westward expansion of emberizid stock into Eurasia from North America, we found that the level of genetic divergence among Old World buntings approximates those among different genera in North American sparrows. Thus the radiation of the Emberizidae seems to have occurred at roughly the same time in the Palaearctic and Nearctic. Our results are consistent with earlier analyses of allozymes, but sequences from multiple genes and new morphological analyses are required to fully resolve phylogenetic relationships within the Emberizidae.