bluuebunny/crossref_metadata_2025_split huggingface dataset:
Variable Transcriptional Activity of Endogenous Retroviruses in Human Breast Cancer
Authors: Frank Oliver , Verbeke Caroline , Schwarz Norbert , Mayer Jens , Fabarius Alice , Hehlmann Rüdiger , Leib-Mösch Christine , Seifarth Wolfgang 
Published: December 2007

ABSTRACTHuman endogenous retroviruses (HERVs) account for up to 9% of the human genome and include more than 800 elements related to betaretroviruses. While mouse mammary tumor virus (MMTV) is the accepted etiological agent of mammary tumors in mice, the role of retroviral elements in human breast cancer remains elusive. Here, we performed a comprehensive microarray-based analysis of overall retroviral transcriptional activities in 46 mammary gland tissue specimens representing pairs of nonmalignant and tumor samples from 23 patients. An analysis of nonmalignant tissue samples revealed a distinct, mammary gland-specific HERV expression profile that consists of 18 constitutively active HERV taxa. For corresponding tumor samples, a general trend toward lower levels of HERV transcription was observed, suggesting common regulatory mechanisms. In various subsets of patients, however, increased transcript levels of single class I HERV families (HERV-T, HERV-E, and HERV-F) and several class II families, including HML-6, were detected. An analysis of transcribed HML-6 sequences revealed either the activation of some or the increased activity of several proviral loci. No evidence for MMTV or human MMTV-like virus transcripts was found, indicating that transcriptionally active, MMTV analogous, exogenous viruses were not present in the breast cancer samples analyzed.
Chronic CD4+T-Cell Activation and Depletion in Human Immunodeficiency Virus Type 1 Infection: Type I Interferon-Mediated Disruption of T-Cell Dynamics
Authors: Sedaghat Ahmad R. , German Jennifer , Teslovich Tanya M. , Cofrancesco Joseph , Jie Chunfa C. , Talbot C. Conover , Siliciano Robert F. 
Published: December 2007

ABSTRACTThe mechanism of CD4+T-cell depletion during chronic human immunodeficiency virus type 1 (HIV-1) infection remains unknown. Many studies suggest a significant role for chronic CD4+T-cell activation. We assumed that the pathogenic process of excessive CD4+T-cell activation would be reflected in the transcriptional profiles of activated CD4+T cells. Here we demonstrate that the transcriptional programs of in vivo-activated CD4+T cells from untreated HIV-positive (HIV+) individuals are clearly different from those of activated CD4+T cells from HIV-negative (HIV−) individuals. We observed a dramatic up-regulation of cell cycle-associated and interferon-stimulated transcripts in activated CD4+T cells of untreated HIV+individuals. Furthermore, we find an enrichment of proliferative and type I interferon-responsive transcription factor binding sites in the promoters of genes that are differentially expressed in activated CD4+T cells of untreated HIV+individuals compared to those of HIV−individuals. We confirm these findings by examination of in vivo-activated CD4+T cells. Taken together, these results suggest that activated CD4+T cells from untreated HIV+individuals are in a hyperproliferative state that is modulated by type I interferons. From these results, we propose a new model for CD4+T-cell depletion during chronic HIV-1 infection.
Coronavirus Escape from Heptad Repeat 2 (HR2)-Derived Peptide Entry Inhibition as a Result of Mutations in the HR1 Domain of the Spike Fusion Protein
Authors: Bosch Berend Jan , Rossen John W. A. , Bartelink Willem , Zuurveen Stephanie J. , de Haan Cornelis A. M. , Duquerroy Stephane , Boucher Charles A. B. , Rottier Peter J. M. 
Published: December 2007

ABSTRACT
Peptides based on heptad repeat (HR) domains of class I viral fusion proteins are considered promising antiviral drugs targeting virus cell entry. We have analyzed the evolution of the mouse hepatitis coronavirus during multiple passaging in the presence of an HR2-based fusion inhibitor. Drug-resistant variants emerged as a result of multiple substitutions in the spike fusion protein, notably within a 19-residue segment of the HR1 region. Strikingly, one mutation, an A1006V substitution, which consistently appeared first in four independently passaged viruses, was the main determinant of the resistance phenotype, suggesting that only limited options exist for escape from the inhibitory effect of the HR2 peptide.
Genome Organization and Reverse Genetic Analysis of a Type I Feline Coronavirus
Authors: Tekes Gergely , Hofmann-Lehmann Regina , Stallkamp Iris , Thiel Volker , Thiel Heinz-Jürgen 
Published: December 2007

ABSTRACTIn this study we report the complete sequence and genome organization of the serotype I feline coronavirus (FCoV) strain Black. Furthermore, a reverse genetic system was established for this FCoV strain by cloning a full-length cDNA copy into vaccinia virus. This clone served as basis for the generation of recombinant FCoV (recFCoV) that was shown to bear the same features in vitro as the parental FCoV. Using this system, accessory 3abc genes in the FCoV genome were replaced by green fluorescent protein (recFCoV-GFP) andRenillaluciferase genes (recFCoV-RL). In addition, we showed that feline CD14+blood monocytes and dendritic cells can be easily detected after infection with recFCoV-GFP. Thus, our established reverse genetic system provides a suitable tool to study the molecular biology of serotype I FCoV.
Insights in the Neoproterozoic–Early Cambrian transition of NW Argentina: facies, environments and fossils in the proto-margin of western Gondwana
Authors: Aceñolaza G. , Aceñolaza F. 
Published: December 2007

Abstract

In NW Argentina, over 3000 metres of highly tectonized and metamorphosed siliciclastics of the Puncoviscana Formation underlie the more fossiliferous Cambro–Ordovician strata of the Mesón and Santa Victoria groups. Historically regarded as the non-fossiliferous ‘basal Precambrian shield’ of the region, its age was later found to be in part Phanerozoic, with the discovery of Early Cambrian trace fossils, and more recently refined with geochronological data. Widespread siliciclastic deposits characterize this sequence. A review of trace fossils in the Puncoviscana Formation has added new taxa. Trace fossil assemblages denote? geographical belts, indicating shallower marine conditions to the east (
Nereites
association) and deeper to the west (
Oldhamia
association). Such assemblages related to the palaeomorphology of the basin also represent different temporal levels, and in so doing reflect the overall evolution of the Puncoviscana Sea through time. The use of taxa that characterize Siberian stages in order to date parts of the Puncoviscana Formation should be abandoned as Siberian stages are defined by a specific set of fossils that are absent in the strata of NW Argentina. Thus, careful systematic studies and re-evaluation of the strata and fauna in the Puncoviscana Basin are the only way to improve understanding of the Neoproterozoic–Cambrian transition in the Andean margin of South America.
First Early Cambrian Radiolaria
Authors: Braun A. , Chen J. , Waloszek D. , Maas A. 
Published: December 2007

Abstract
Radiolarian skeletons are known from a limestone concretion collected from a black shale succession and from black cherts of the Yangtze Platform, China. Both occurrences are of earliest Cambrian age. The findings, reported in this paper, represent the oldest known fossil Radiolaria. Their spherical skeletons display a morphology typical of spherical radiolarians from Ordovician and younger faunas. This occurrence of radiolarians with radial symmetry and, most probably, a planktonic lifestyle can now be traced back into the earliest Cambrian. Thus, radiolarians have been part of the early oceanic plankton and likely played a significant role in the silica cycle of the oceans along with siliceous sponges.
Ventogyrus
, a possible siphonophore-like trilobozoan coelenterate from the Vendian Sequence (late Neoproterozoic), northern Russia
Authors: Fedonkin M. A. , Ivantsov A. Y. 
Published: December 2007

Abstract

Complex internal anatomy is documented for the first time in a Neoproterozoic soft-bodied invertebrate. New data suggests that
Ventogyru
s, originally described as a sessile, boat-shaped form belonging to the enigmatic Neoproterozoic group Petalonamae, is actually composed of three, identical modules, arranged around an axial rod. Each module has one longitudinal and numerous transverse septa, which delimit chambers of decreasing size from one end to the other. Three distinct longitudinal channels with alternating lateral branches make up an internal network, perhaps a circulatory system.
Ventogyrus
is a most unusual form, particularly in the quality of its three dimensional preservation of a complex internal structure and a three-fold symmetry, a symmetry shared by many Ediacarans.
Morphology and taphonomy of an Ediacaran frond:
Charnia
from the Avalon Peninsula of Newfoundland
Authors: Laflamme M. , Narbonne G. M. , Greentree C. , Anderson M. M. 
Published: December 2007

Abstract

The Ediacaran frond
Charnia
, known mainly from fragmentary leaf-like fronds from around the world, is represented by completely preserved specimens with holdfasts in the Mistaken Point biota of Newfoundland. Previous reconstructions of
Charnia
from two-dimensional impressions were significantly oversimplified, resulting in three-dimensional reconstructions which highlighted a sheet-like morphology. Overlapping relationships and internal structures are rarely (if ever) preserved, and only through detailed photography together with both landmark and traditional morphometric analyses of numerous complete
Charnia
specimens can the preservational biases be removed.
Charnia
is reinterpreted here as having a series of individual overlapping primary branches attached to an internal central stalk, and with individual branches constrained by an internal, organic skeleton and/or attachments between adjacent branches. Three species,
C. masoni
Ford 1958
,
C. wardi
Narbonne & Gehling 2003
, and
C. antecedens
sp. nov. can be distinguished on the basis of length/width ratios and the degree of attachment of adjacent branches. Morphological, taphonomical, and ecological studies at Mistaken Point imply that
Charnia
was a sessile, epibenthic frond that fed from suspension in this deep-water volcaniclastic setting. Evolution of more rigorous connections between the primary branches allowed
Charnia
to migrate into more turbulent, shallower-water habitats by the late Ediacaran.
Comparative taphonomy of Vendian genera
Beltanelloides
and
Nemiana
: taxonomy and lifestyle
Authors: Leonov M. V. 
Published: December 2007

Abstract

Taphonomic analysis of new material from Vendian sequences of the White Sea and southwestern Ukraine provides data for a better definition of both the widely distributed fossil taxa of
Beltanelloides
and
Nemiana.
A new type of
Beltanelloides
preservation is described, so it is now possible to attribute some sandstone imprints to this taxon.
Nemiana simplex
seems to have a lifestyle and level of body organization comparable with that of sponges. The narrow range of facies in which
Nemiana
occurs, when compared to the much broader range of
Beltanelloides
, is compelling evidence for a benthic lifestyle of
Nemiana
.
Vendian
Hiemalora
from Arctic Siberia reinterpreted as holdfasts of benthic organisms
Authors: Serezhnikova E. A. 
Published: December 2007

Abstract

Hiemalora
Fedonkin, 1982 is based on cosmopolitan fossils of the late Vendian (Ediacaran) Neoproterozoic sequences. There is no consensus on the nature and systematic position of these organisms. Taphonomic and morphological observations of extensive collections of
Hiemalora pleiomorphus
from Khatyspyt Formation (Arctic Siberia) indicate that this fossil is just a part of an unknown organism. Most probably
Hiemalora
represents a form with a thick-walled body, possessing a cone-like attachment bearing radial processes that resemble sponge root offshoots or algal rhizoids. Originally these structures penetrated the soft sediment and served as anchors as well as a source of symbiotic nutrition. Various imprints of
Hiemalora
could represent different sections of conic-shaped bodies. Probably, there were several organisms referred to as
Hiemalora
that had a similar substrate attachment organ.
A new reconstruction of
Protolyellia
(Early Cambrian psammocoral)
Authors: Savazzi E. 
Published: December 2007

Abstract

A new reconstruction of
Protolyellia
(psammocoral) from the Mickwitzia sandstone, Early Cambrian of south-central Sweden, is proposed. Observations, conceptual analysis and physical modelling indicate that the distinctive honeycomb or (less frequently) ridge sculpture of the upper side of the sand-button was a wrinkle pattern in a flexible epithelium. Wrinkling was caused by contraction of a subepithelial muscle layer joined to the epithelium by connective tissue. Fine-grained sand particles adhering on, or embedded within, the epithelium preserved its surface relief after the soft parts decomposed. The sand-bearing epithelium covered a subcylindrical structure attached around the periphery of the sand-button and extending upwards. This structure is occasionally preserved felled horizontally near a sand-button, but is more commonly found as isolated shreds. Sudden burial caused the lower portion of this structure to contract and wrinkle against the tissues containing the sand-button. After the soft parts decomposed, sediment compaction pasted the wrinkled layer onto the sand-button, thus producing the typical preservation mode. The wrinkle pattern of
Protolyellia
differs from those of Recent cnidarians, and suggests that
Protolyellia
did not possess mesenteries.
Protolyellia
may be more distantly related to modern cnidarians than previously assumed. In addition, alternative affinities with Ediacaran frond-bearing forms cannot be excluded.
Poriferan paraphyly and its implications for Precambrian palaeobiology
Authors: Sperling E. A. , Pisani D. , Peterson K. J. 
Published: December 2007

Abstract

Well-supported molecular phylogenies, combined with knowledge of modern biology, can lead to new inferences about the sequence of character acquisition in early animal evolution, the taxonomic affinity of enigmatic Precambrian and Cambrian fossils, and the Proterozoic Earth system in general. In this paper we demonstrate, in accordance with previous molecular studies, that sponges are paraphyletic, and that calcisponges are more closely related to eumetazoans than they are to demosponges. In addition, our Bayesian analysis finds the Homoscleromorpha, previously grouped with the demosponges, to be even more closely related to eumetazoans than are the calcisponges. Hence there may be at least three separate extant ‘poriferan’ lineages, each with their own unique skeleton. Because spiculation is convergent within ‘Porifera’, differences between skeletonization processes in enigmatic Cambrian taxa such as
Chancelloria
and modern sponges does not mean that these Problematica are not organized around a poriferan body plan, namely a benthic, sessile microsuspension feeding organism. The shift from the anoxic and sulphidic deep ocean that characterized the mid-Proterozoic to the well-ventilated Phanerozoic ocean occurs before the evolution of macrozooplanton and nekton, and thus cannot have been caused by the advent of faecal pellets. However, the evolution and ecological dominance of sponges during this time interval provides both a mechanism for the long-term generation of isotopically-light CO
2
that would be recorded in carbon isotopic excusions such as the ‘Shuram’ event, and an alternative mechanism for the drawdown and sequestration of dissolved organic carbon within the sediment.
Towards a morphospace for the Ediacara biota
Authors: Antcliffe J. B. , Brasier M. D. 
Published: December 2007

Abstract

The Ediacara biota of the late Neoproterozoic is justly famous as a biological puzzle. Studies of Ediacaran biology have commonly used analogy with living organisms as a cipher for the decoding of biological affinity, and consequently the life mode and habit. Here, we discuss the problems of using such analogous reasoning and put forward our alternative approach, that of using Morphospace Analysis for the study of growth, form and phylogeny. This tool, we suggest, has the potential to be used for testing the unity of an evolutionary clade, such as ‘rangeomorphs’ and ‘dickinsoniomorphs’. Preliminary data from the members of the Ediacara biota do indeed show such a unity within our preliminary morphospace model (all
k
values are low). This method reveals no clear relationships, between these forms and more recent biological groups such as the sea pens or the Foraminifera.
The nature of vendobionts
Authors: Seilacher A. 
Published: December 2007

Abstract
The notion that the majority of Ediacaran fossils do not represent stem groups to modern metazoan phyla is now increasingly accepted. Nevertheless, the further claim of the vendobiont hypothesis needs to be elaborated: that these large and seemingly complex organisms were not truly multicellular. Arguments for interpreting vendobionts as an extinct class of rhizopodan Protozoa are: (1) negative allometry of the quilts; (2) presence of a loosely englutinated, but sandy fill skeleton similar to the xenophyophorian stercomare; (3) a disparity of designs and lifestyles that would be incompatible with metazoan bauplans and feeding strategies; (4) unusual patterns of regeneration; (5) resting traces of some mobile, epibenthic species.
Theoretical morphology of quilt structures in Ediacaran fossils
Authors: Tojo B. , Saito R. , Kawakami S. , Ohno T. 
Published: December 2007

Abstract

Vendobiont type fossils are characterized by possessing ‘gliding symmetry’, in which quilts of the different vanes consisting the body of the Vendobionta meet along the seam with small offset. Because two, three or more vanes are joined along this seam and the quilts of different vanes can be variously offset along the seam, a variety of gliding symmetry exists among Vendobionta. Our theoretical consideration here predicts that the number of possible gliding symmetry is one, two and three for organisms having two, three and four vanes, respectively. We also predict that a special combination of morphological types appear alternatively during the growth of the Vendobionta with two vanes. Further, we were able to identify the existence of two types in gliding symmetry predicted by us for
Pteridinium
specimens with three vanes. Detailed examination of the gliding symmetry of other Vendobionta, therefore, may give important clues in solving riddles veiling the vendobiont relationships.
The Verdun Syndrome: simultaneous origin of protective armour and infaunal shelters at the Precambrian–Cambrian transition
Authors: Dzik J. 
Published: December 2007

Abstract
All of the structurally identifiable latest Ediacaran and earliest Cambrian infaunal trace fossils represent shelters of animals feeding above the sediment surface. It is the case with the most complete and oldest radiometrically dated Precambrian–Cambrian transition strata along the Khorbusuonka River in northern Siberia, in the basal Cambrian succession at Meishucun in southern China, richest in small shelly fossils, as well as in the type succession of the Vendian in Podolia, Ukraine. The oldest traces of feeding within the mud are known from no earlier than the late Tommotian of Siberia, Mongolia, Sweden, and Poland. This suggests that the invention of hydraulic mechanisms of sediment penetration was enforced by predation, not by trophic needs. Various ways to protect the body by secretion of a mineral skeleton or building tubes by collected mineral grains were developed by other animals at the same time. Predation may thus appear to be the triggering mechanism for the ‘Cambrian explosion’. Subsequent increase in the depth of bioturbation resulted in a profound change of taphonomic conditions, artificially enhancing the effects of evolution.
The Cambrian ‘basement’ of gastropod evolution
Authors: Parkhaev P. Y. 
Published: December 2007

Abstract
The oldest gastropods are known from the uppermost Nemakit-Daldynian to lowermost Tommotian deposits. However, to trace ancestry before this time, when most metazoans did not possess shells, is difficult. Study of the oldest gastropods, diagnosed and discussed here, sheds some light on the earliest stages of evolution of major gastropod branches. It appears that the subclass Archaeobranchia served as the base for this early radiation.
Fleshing out the Ediacaran period
Authors: Gehling J. G. 
Published: December 2007

Abstract
The Flinders Ranges Ediacaran succession preserves an apparently primary palaeomagnetic record, distinctive stratigraphic events such as the Acraman ejecta layer, and fossils of the Ediacara biota at three well-separated levels. The fossil assemblage of the Ediacara Member includes both trace fossils and body fossils, and shares at least 65% of its taxa with the White Sea assemblages in northern Russia, suggesting they were coeval. Globally, Ediacaran successions are diverse in their lithostratigraphy but share many characteristics of biota, isotope signatures and events which can be calibrated with radiometric dating. Available radiometric dating of Ediacaran successions supports the concept of distinct Avalon (575 Ma–565 Ma), White Sea (558 Ma–555 Ma) and Nama (549 Ma–543 Ma) associations as a temporal succession rather than being controlled by environment or palaeobiogeography. The challenge to document the tempo and pattern of evolution of early animals and the associated changes in global climate make the subdivision and calibration of the Ediacaran a vital task for the next decade.
Microstratigraphy of the Late Ediacaran to the Ordovician in NW Iran (Takab area)
Authors: Jafari S. M. , Shemirani A. , Hamdi B. 
Published: December 2007

Abstract

Platform sediments of Iran span the Late Ediacaran and extend into the Palaeozoic. They are primarily clastic and carbonaceous in nature, deposited in coastal and lagoonal settings. They crop out in the Takab area, as the Soltanieh Formation (Late Proterozoic to Atdabanian), the Barut Formation (Early Bottomian), the Zaigun Formation (Middle Bottomian), the Lalun Formation (Late Bottomian) and the Mila Formation (Middle Cambrian to Early Ordovician). A Precambrian–Cambrian assemblage has been identified at the base of Member 3 and the top of Member 2 in the Soltanieh Formation. The Soltanieh Formation consists of shallow marine sediments. Vertical microfacies variation reflects two regressive sequences, the earliest Cambrian System being a regressive cycle. The presence of
Chuaria
and
Vendotaenia
in the Soltanieh Formation allows correlation of Iranian sequences to those elsewhere in the world, indicating a late Neoproterozoic age. Detailed facies analyses of the Soltanieh, Barut, Zaigun, Lalun, and Mila formations allow refined palaeoenvironmental reconstructions to be made for the Ediacaran–Cambrian/Ordovician in Iran.
Sprigg, Glaessner and Wade and the discovery and international recognition of the Ediacaran fauna
Authors: Turner S. , Vickers-Rich P. 
Published: December 2007

Abstract
Reg Sprigg was a young geologist when he found Ediacaran fossils in the hills of the western Flinders Ranges of South Australia. At first not taken seriously by his mentors, the reality of his fossils and the true age of his finds were recognized by the late 1940s.
Research on these oldest known metazoans of the time was then carried out by Martin Glaessner and his student, Mary Wade, who first studied Foraminifera. Sprigg was not included in this research but took a different path pursuing a career as an economic geologist and founding Santos. Wade and Glaessner interpreted their Ediacaran fossils as worms and jellyfish, but more recent interpretations have led to very different conclusions.