bluuebunny/crossref_metadata_2025 huggingface dataset:
Molecular Diagnosis of Old World Cutaneous Leishmaniasis and Species Identification by Use of a Reverse Line Blot Hybridization Assay
Authors: Nasereddin Abedelmajeed , Bensoussan-Hermano Esther , Schönian Gabriele , Baneth Gad , Jaffe Charles L.
Published: July 2008

Reverse line blot hybridization assays (RLB) have been used for the rapid diagnosis and genotyping of many pathogens. The leishmaniases are caused by a large number of species, and rapid, accurate parasite characterization is important in deciding on appropriate therapy. Fourteen oligonucleotide probes, 2 genus specific and 12 species specific (2 specific for
Leishmania major
, 3 for
L. tropica
, 1 for
L. infantum
, 3 for
L. donovani
, and 3 for
L. aethiopica
), were prepared by using DNA sequences in the internal transcribed spacer 1 (ITS1) region of the rRNA genes. Probe specificity was evaluated by amplifying DNA from 21 reference strains using biotinylated ITS1 PCR primers and the RLB. The genus-specific probes, PP and PP3′, recognized all
Leishmania
species examined, while the species-specific probes were able to distinguish between all the Old World
Leishmania
species. Titrations using purified parasite DNA showed that the RLB is 10- to 100-fold more sensitive than ITS1 PCR and can detect <0.1 pg DNA. The RLB was compared to kinetoplast DNA (kDNA) and ITS1 PCR by using 67 samples from suspected cutaneous leishmaniasis (CL) patients in Israel and the West Bank. The RLB accurately identified 58/59 confirmed positive samples as CL, a result similar to that found by kDNA PCR (59/59) and better than that by ITS1 PCR (50/59). The positive predictive value and negative predictive value of the RLB were 95.1% and 83.3%, respectively.
L. major
or
L. tropica
was identified by the RLB in 55 of the confirmed positive cases, a level of accuracy better than that of ITS1 PCR with restriction fragment length polymorphism (42/59). Thus, RLB can be used to diagnose and characterize Old World CL.
Comparative Study of Nasopharyngeal Aspirate and Nasal Swab Specimens for Diagnosis of Acute Viral Respiratory Infection
Authors: Sung Rita Y. T. , Chan Paul K. S. , Choi Kai C. , Yeung Apple C. M. , Li Albert M. , Tang Julian W. , Ip Margaret , Tsen Tracy , Nelson E. Anthony S.
Published: July 2008

Paired nasopharyngeal aspirate (NPA) and nasal swab (NS) samples from 475 children hospitalized for acute respiratory infection were studied for the detection of influenza virus, parainfluenza virus, respiratory syncytial virus, and adenovirus by immunofluorescence test, viral culture, and multiplex PCR assay. The overall sensitivity of viral detection with NPA specimens was higher than that obtained with NS specimens.
The NY-1 Hantavirus Gn Cytoplasmic Tail Coprecipitates TRAF3 and Inhibits Cellular Interferon Responses by Disrupting TBK1-TRAF3 Complex Formation
Authors: Alff Peter J. , Sen Nandini , Gorbunova Elena , Gavrilovskaya Irina N. , Mackow Erich R.
Published: July 2008

Pathogenic hantaviruses replicate within human endothelial cells and cause two diseases, hemorrhagic fever with renal syndrome and hantavirus pulmonary syndrome. In order to replicate in endothelial cells pathogenic hantaviruses inhibit the early induction of beta interferon (IFN-β). Expression of the cytoplasmic tail of the pathogenic NY-1 hantavirus Gn protein is sufficient to inhibit RIG-I- and TBK1-directed IFN responses. The formation of TBK1-TRAF3 complexes directs IRF-3 phosphorylation, and both IRF-3 and NF-κB activation are required for transcription from the IFN-β promoter. Here we report that the NY-1 virus (NY-1V) Gn tail inhibits both TBK1-directed NF-κB activation and TBK1-directed transcription from promoters containing IFN-stimulated response elements. The NY-1V Gn tail coprecipitated TRAF3 from cellular lysates, and analysis of TRAF3 deletion mutants demonstrated that the TRAF3 N terminus is sufficient for interacting with the NY-1V Gn tail. In contrast, the Gn tail of the nonpathogenic hantavirus Prospect Hill virus (PHV) failed to coprecipitate TRAF3 or inhibit NF-κB or IFN-β transcriptional responses. Further, expression of the NY-1V Gn tail blocked TBK1 coprecipitation of TRAF3 and infection by NY-1V, but not PHV, blocked the formation of TBK1-TRAF3 complexes. These findings indicate that the NY-1V Gn cytoplasmic tail forms a complex with TRAF3 which disrupts the formation of TBK1-TRAF3 complexes and downstream signaling responses required for IFN-β transcription.
Natural Killer Cells Regulate T-Cell Proliferation during Human Parainfluenza Virus Type 3 Infection
Authors: Noone Cariosa M. , Paget Elaine , Lewis Ellen A. , Loetscher Marius R. , Newman Robert W. , Johnson Patricia A.
Published: July 2008

Human parainfluenza virus type 3 (HPIV3) is a major respiratory pathogen in humans. Failure to induce immunological memory associated with HPIV3 infection has been attributed to inhibition of lymphocyte proliferation. We demonstrate that the inability of mixed lymphocytes to respond to virally infected antigen-presenting cells is due to an interleukin-2-dependent, nonapoptotic mechanism involving natural killer (NK) cells and their influence is exerted in a contact-dependent manner. These results suggest a novel regulatory mechanism for NK cells during HPIV3 infection, offering an explanation for viral persistence and poor memory responses.
Heparan Sulfate-Binding Foot-and-Mouth Disease Virus Enters Cells via Caveola-Mediated Endocytosis
Authors: O'Donnell Vivian , LaRocco Michael , Baxt Barry
Published: July 2008

Foot-and-mouth disease virus (FMDV) utilizes different cell surface macromolecules to facilitate infection of cultured cells. Virus, which is virulent for susceptible animals, infects cells via four members of the α
V
subclass of cellular integrins. In contrast, tissue culture adaptation of some FMDV serotypes results in the loss of viral virulence in the animal, accompanied by the loss of virus' ability to use integrins as receptors. These avirulent viral variants acquire positively charged amino acids on surface-exposed structural proteins, resulting in the utilization of cell surface heparan sulfate (HS) molecules as receptors. We have recently shown that FMDV serotypes utilizing integrin receptors enter cells via a clathrin-mediated mechanism into early endosomes. Acidification within the endosome results in a breakdown of the viral capsid, releasing the RNA, which enters the cytoplasm by a still undefined mechanism. Since there is evidence that HS internalizes bound ligands via a caveola-mediated mechanism, it was of interest to analyze the entry of FMDV by cell-surface HS. Using a genetically engineered variant of type O
1
Campos (O
1
C3056R) which can utilize both integrins and HS as receptors and a second variant (O
1
C3056R-KGE) which can utilize only HS as a receptor, we followed viral entry using confocal microscopy. After virus bound to cells at 4°C, followed by a temperature shift to 37°C, type O
1
C3056R-KGE colocalized with caveolin-1, while O
1
C3056R colocalized with both clathrin and caveolin-1. Compounds which either disrupt or inhibit the formation of lipid rafts inhibited the replication of O
1
C3056R-KGE. Furthermore, a caveolin-1 knockdown by RNA interference also considerably reduced the efficiency of O
1
C3056R-KGE infection. These results indicate that HS-binding FMDV enters the cells via the caveola-mediated endocytosis pathway and that caveolae can associate and traffic with endosomes. In addition, these results further suggest that the route of FMDV entry into cells is a function solely of the viral receptor.
Epstein-Barr Virus BART MicroRNAs Are Produced from a Large Intron prior to Splicing
Authors: Edwards Rachel Hood , Marquitz Aron R. , Raab-Traub Nancy
Published: July 2008

Latent Epstein-Barr virus (EBV) infection is associated with several lymphoproliferative disorders, including posttransplant lymphoma, Hodgkin's disease, and Burkitt's lymphoma, as well as nasopharyngeal carcinoma (NPC). Twenty-nine microRNAs (miRNAs) have been identified that are transcribed during latent infection from three clusters in the EBV genome. Two of the three clusters of miRNAs are made from the BamHI A rightward transcripts (BARTs), a set of alternatively spliced transcripts that are highly abundant in NPC but have not been shown to produce a detectable protein. This study indicates that while the BART miRNAs are located in the first four introns of the transcripts, processing of the pre-miRNAs from the primary transcript occurs prior to completion of the splicing reaction. Additionally, production of the BART miRNAs correlates with accumulation of a spliced mRNA in which exon 1 is joined directly to exon 3, suggesting that this form of the transcript may favor production of miRNAs. Sequence variations and processing of pre-miRNAs to the mature form also may account for various differences in miRNA abundance. Importantly, residual intronic pieces that result from processing of the pre-miRNAs were detected in the nucleus. The predicted structures of these pieces suggest there is a bias or temporal pattern to the production of the individual pre-miRNAs. These findings indicate that multiple factors contribute to the production of the BART miRNAs and to the apparent differences in abundance between the individual miRNAs of the cluster.
Human Parainfluenza Virus Type 1 C Proteins Are Nonessential Proteins That Inhibit the Host Interferon and Apoptotic Responses and Are Required for Efficient Replication in Nonhuman Primates
Authors: Bartlett Emmalene J. , Cruz Ann-Marie , Esker Janice , Castaño Adam , Schomacker Henrick , Surman Sonja R. , Hennessey Margaret , Boonyaratanakornkit Jim , Pickles Raymond J. , Collins Peter L. , Murphy Brian R. , Schmidt Alexander C.
Published: July 2008

Recombinant human parainfluenza virus type 1 (rHPIV1) was modified to create rHPIV1-P(C−), a virus in which expression of the C proteins (C′, C, Y1, and Y2) was silenced without affecting the amino acid sequence of the P protein. Infectious rHPIV1-P(C−) was readily recovered from cDNA, indicating that the four C proteins were not essential for virus replication. Early during infection in vitro, rHPIV1-P(C−) replicated as efficiently as wild-type (wt) HPIV1, but its titer subsequently decreased coincident with the onset of an extensive cytopathic effect not observed with wt rHPIV1. rHPIV1-P(C−) infection, but not wt rHPIV1 infection, induced caspase 3 activation and nuclear fragmentation in LLC-MK2 cells, identifying the HPIV1 C proteins as inhibitors of apoptosis. In contrast to wt rHPIV1, rHPIV1-P(C−) and rHPIV1-C
F170S
, a mutant encoding an F170S substitution in C, induced interferon (IFN) and did not inhibit IFN signaling in vitro. However, only rHPIV1-P(C−) induced apoptosis. Thus, the anti-IFN and antiapoptosis activities of HPIV1 were separable: both activities are disabled in rHPIV1-P(C−), whereas only the anti-IFN activity is disabled in rHPIV1-C
F170S
. In African green monkeys (AGMs), rHPIV1-P(C−) was considerably more attenuated than rHPIV1-C
F170S
, suggesting that disabling the anti-IFN and antiapoptotic activities of HPIV1 had additive effects on attenuation in vivo. Although rHPIV1-P(C−) protected against challenge with wt HPIV1, its highly restricted replication in AGMs and in primary human airway epithelial cell cultures suggests that it might be overattenuated for use as a vaccine. Thus, the C proteins of HPIV1 are nonessential but have anti-IFN and antiapoptosis activities required for virulence in primates.
Frequency and Spectrum of Genomic Integration of Recombinant Adeno-Associated Virus Serotype 8 Vector in Neonatal Mouse Liver
Authors: Inagaki Katsuya , Piao Chuncheng , Kotchey Nicole M. , Wu Xiaolin , Nakai Hiroyuki
Published: July 2008

Neonatal injection of recombinant adeno-associated virus serotype 8 (rAAV8) vectors results in widespread transduction in multiple organs and therefore holds promise in neonatal gene therapy. On the other hand, insertional mutagenesis causing liver cancer has been implicated in rAAV-mediated neonatal gene transfer. Here, to better understand rAAV integration in neonatal livers, we investigated the frequency and spectrum of genomic integration of rAAV8 vectors in the liver following intraperitoneal injection of 2.0 × 10
11
vector genomes at birth. This dose was sufficient to transduce a majority of hepatocytes in the neonatal period. In the first approach, we injected mice with a β-galactosidase-expressing vector at birth and quantified rAAV integration events by taking advantage of liver regeneration in a chronic hepatitis animal model and following partial hepatectomy. In the second approach, we performed a new, quantitative rAAV vector genome rescue assay by which we identified rAAV integration sites and quantified integrations. As a result, we find that at least ∼0.05% of hepatocytes contained rAAV integration, while the average copy number of integrated double-stranded vector genome per cell in the liver was ∼0.2, suggesting concatemer integration. Twenty-three of 34 integrations (68%) occurred in genes, but none of them were near the mir-341 locus, the common rAAV integration site found in mouse hepatocellular carcinoma. Thus, rAAV8 vector integration occurs preferentially in genes at a frequency of 1 in approximately 10
3
hepatocytes when a majority of hepatocytes are once transduced in the neonatal period. Further studies are warranted to elucidate the relationship between vector dose and integration frequency or spectrum.
Influenza A Virus Matrix Protein 1-Specific Human CD8+T-Cell Response Induced in Trivalent Inactivated Vaccine Recipients
Authors: Terajima Masanori , Cruz John , Leporati Anita M. , Orphin Laura , Babon Jenny Aurielle B. , Co Mary Dawn T. , Pazoles Pamela , Jameson Julie , Ennis Francis A.
Published: July 2008

Among 17 HLA-A2-positive healthy adults, CD8+T-cell responses against an HLA-A2-restricted matrix protein 1 (M1) epitope increased after immunization with trivalent inactivated influenza vaccine (TIV) in two individuals. The presence of M1 in TIV was confirmed by Western blotting. T-cell cytotoxicity assays showed that TIV is processed and the epitope is presented by antigen-presenting cells to an M1 epitope-specific CD8+T-cell line for specific lysis. These data show that TIV, which is formulated to contain surface glycoproteins to induce serotype-specific antibody responses, also contains M1, capable of inducing subtype cross-reactive CD8+T-cell responses in some vaccinees.
A Hepatitis C Virus
cis
-Acting Replication Element Forms a Long-Range RNA-RNA Interaction with Upstream RNA Sequences in NS5B
Authors: Diviney Sinéad , Tuplin Andrew , Struthers Madeleine , Armstrong Victoria , Elliott Richard M. , Simmonds Peter , Evans David J.
Published: July 2008

The genome of hepatitis C virus (HCV) contains
cis
-acting replication elements (CREs) comprised of RNA stem-loop structures located in both the 5′ and 3′ noncoding regions (5′ and 3′ NCRs) and in the NS5B coding sequence. Through the application of several algorithmically independent bioinformatic methods to detect phylogenetically conserved, thermodynamically favored RNA secondary structures, we demonstrate a long-range interaction between sequences in the previously described CRE (5BSL3.2, now SL9266) with a previously predicted unpaired sequence located 3′ to SL9033, approximately 200 nucleotides upstream. Extensive reverse genetic analysis both supports this prediction and demonstrates a functional requirement in genome replication. By mutagenesis of the Con-1 replicon, we show that disruption of this alternative pairing inhibited replication, a phenotype that could be restored to wild-type levels through the introduction of compensating mutations in the upstream region. Substitution of the CRE with the analogous region of different genotypes of HCV produced replicons with phenotypes consistent with the hypothesis that both local and long-range interactions are critical for a fundamental aspect of genome replication. This report further extends the known interactions of the SL9266 CRE, which has also been shown to form a “kissing loop” interaction with the 3′ NCR (P. Friebe, J. Boudet, J. P. Simorre, and R. Bartenschlager, J. Virol. 79:380-392, 2005), and suggests that cooperative long-range binding with both 5′ and 3′ sequences stabilizes the CRE at the core of a complex pseudoknot. Alternatively, if the long-range interactions were mutually exclusive, the SL9266 CRE may function as a molecular switch controlling a critical aspect of HCV genome replication.
A crustal-scale cross-section through the Tauern Window (eastern Alps) from geophysical and geological data
Authors: Lammerer B. , Gebrande H. , Lüschen E. , Veselá P.
Published: July 2008

A restorable geological cross-section through the entire crust of the Tauern Window is presented. It is drawn from surface geology and seismic data of the TRANSALP vibroseis section using balancing software. The architecture of the window is characterized by three horses in a large duplex structure and folded granitic sills. The duplex was later uplifted along two large faults at its northern rim. The first is a blind fault along the deep-reaching sub-Tauern ramp with a displacement of 17 km. The tip of the hanging wall block wedged underneath the Austroalpine and Penninic nappes and caused a triangle structure. This led to backthrusting and backfolding within the marginal rocks of the window. At the second one, the Tauern North Boundary Fault occurred in our retrodeformation, a throw of
c
. 3 km. A total shortening of the crust or parts of the crust of
c
. 60 km in north–south direction led to uplift of the Tauern Window.
Neotectonic faulting, uplift and seismicity in the central and western Swiss Alps
Authors: Ustaszewski Michaela , Pfiffner O. Adrian
Published: July 2008

Our study aims to characterize the post-glacial neotectonic activity by finding surface expressions of recently active tectonic faults. The central and western Swiss Alps were chosen as the study area because surface uplift rates are very high, indicating ongoing uplift of the external basement massifs. Moreover, the Valais area coincides with enhanced seismic activity. Active faults were searched by mapping lineaments on aerial photographs and subsequent field studies. Three main types of faults could be distinguished: gravitational faults (i.e. faults related to mass movements); tectonic faults; and composite faults (i.e. tectonic faults with a component of gravitational and post-glacial rebound-related reactivation). A large number of tectonic faults were found (over 1700), but only two unequivocally post-glacially active tectonic faults could be distinguished. Indications for their post-glacial (re-)activation are displaced Quaternary landforms or sediments. Large gravitational faults, as well as composite faults often correlate with deep-seated gravitational slope deformations (DSGSD). The latter occur mainly along valley slopes, particularly where a pervasive foliation strikes parallel to the valley. Fault orientations show correlations either with the regional main foliation (e.g. Aar and Gotthard massif), the orientation of valleys (e.g. Bedretto and Urseren valley), or pre-existing tectonic structures (e.g. faults parallel to joints that are perpendicular to the strike of major structures in the Helvetic nappes). Comparisons of fault orientations with orientations of nodal planes of earthquake focal mechanisms of the last 20 years show a poor indicative correlation. The central and western Swiss Alps host a large number of faults prone for reactivation in today's stress field. However, for most of these faults, no indications of their last phase of activity exist. The low number of unambiguously active tectonic faults suggests that the current strain is either predominantly aseismic or, alternatively, cumulated seismic moment is too low for producing surface rupture.
Tectonics and sedimentation during convergence of the ALCAPA and Tisza–Dacia continental blocks: the Pienide nappe emplacement and its foredeep (N. Romania)
Authors: Tischler M. , Matenco L. , Filipescu S. , Gröger H. R. , Wetzel A. , Fügenschuh B.
Published: July 2008

The juxtaposition of the ALCAPA and Tisza–Dacia continental blocks, although one of the key issues in the evolution of the Carpathians, is not well known in terms of associated effects on the sedimentary systems during frontal foreland development. Most of the contact between ALCAPA and Tisza–Dacia being covered by post-tectonic deposits, these effects can best be observed in northern Romania. Sedimentological data on facies, palaeocurrents and modal composition of sandstones combined with micropalaeontological data and 2D well-calibrated seismic lines constrain the tectonic history of the contact zone between ALCAPA and Tisza–Dacia. Pervasive deposition of sand-dominated siliciclastics beginning in late Early Oligocene (Late Rupelian) times is interpreted to reflect the onset of convergence between ALCAPA and Tisza–Dacia in the study area. The depocentre of coarse siliciclastic material migrates southward, finally forming a southeastward-thinning clastic wedge in the Transylvanian Basin. This Burdigalian-age clastic wedge is interpreted as fill of a flexural foreland basin that formed in response to the coeval thrusting of parts of ALCAPA (Pienides) over Tisza–Dacia. A shift from an E–W to SE–NW striking basin axis during Oligocene times towards a WSW–ENE oriented basin axis during Burdigalian times is interpreted as a result of clockwise rotation of Tisza–Dacia during basin formation.
Metamorphism of metasediments at the scale of an orogen: a key to the Tertiary geodynamic evolution of the Alps
Authors: Bousquet Romain , Oberhänsli Roland , Goffé Bruno , Wiederkehr Michael , Koller Friedrich , Schmid Stefan M. , Schuster Ralf , Engi Martin , Berger Alfons , Martinotti Giorgio
Published: July 2008

Major discoveries in metamorphic petrology, as well as other geological disciplines, have been made in the Alps. The regional distribution of Late Cretaceous–Tertiary metamorphic conditions, documented in post-Hercynian metasediments across the entire Alpine belt from Corsica–Tuscany in the west to Vienna in the east, is presented in this paper. In view of the uneven distribution of information, we concentrate on type and grade of metamorphism; and we elected to distinguish between metamorphic paths where either pressure and temperature peaked simultaneously, or where the maximum temperature was reached at lower pressures, after a significant temperature increase on the decompression path.

The results show which types of process caused the main metamorphic imprint: a subduction process in the western Alps, a collision process in the central Alps, and complex metamorphic structures in the eastern Alps, owing to a complex geodynamic and metamorphic history involving the succession of the two types of process. The western Alps clearly show a relatively simple picture, with an internal (high-pressure dominated) part thrust over an external greenschist to low-grade domain, although both metamorphic domains are structurally very complex. Such a metamorphic pattern is generally produced by subduction followed by exhumation along a cool decompression path. In contrast, the central Alps document conditions typical of subduction (and partial accretion), followed by an intensely evolved collision process, often resulting in a heating event during the decompression path of the early-subducted units. Subduction-related relics and (collisional/decompressional) heating phenomena in different tectonic edifices characterize the Tertiary evolution of the Eastern Alps. The Tuscan and Corsica terrains show two different kinds of evolution, with Corsica resembling the western Alps, whereas the metamorphic history in the Tuscan domain is complex owing to the late evolution of the Apennines. This study confirms that careful analysis of the metamorphic evolution of metasediments at the scale of an entire orogen may change the geodynamic interpretation of mountain belts.
Northern Apennine–Corsica orogenic system: an updated overview
Authors: Molli Giancarlo
Published: July 2008

The aim of this paper is to describe some aspects of the Northern Apennine/Corsica orogenic system, a classical and still-debated subject in the geology of the central Mediterranean. After a necessarily short historical outline, a general updated overview of the Northern Apennine and Corsica is presented. The results of recent research on metamorphic units representative of the former continental margins have been used to constrain some key events of the geological history of the Northern Apennine/Corsica orogenic system and its relationship with the western Alps. Many still-controversial topics are tackled in this paper, which calls for further data and studies. In particular, the early stages of the oceanic convergence recorded by the Ligurian units of the Apennine and by Corsican ophiolites need refinement of structural and chronological data sets. Similarly, the deep structure of the inner Northern Apennine is far from being well explored; nevertheless, three crustal-scale cross-sections across the Northern Apennine are presented to show differences in the crustal and near-surface architecture at the orogen scale and to discuss some points of the Apennine history, namely the relationships between shortening in the external and exhumation/extension in the internal domains, from the Oligocene onward.
Evolution of an Early Permian extensional detachment fault from synintrusive, mylonitic flow to brittle faulting (Grassi Detachment Fault, Orobic Anticline, southern Alps, Italy)
Authors: Froitzheim N. , Derks J. F. , Walter J. M. , Sciunnach D.
Published: July 2008

Lower Permian volcanic and sedimentary rocks of the Collio Formation in the Orobic Anticline do not rest with a depositional contact on the Variscan basement but are separated from it by the subhorizontal Grassi Detachment Fault, consisting of a cataclasite layer underlain by mylonite. Field relations indicate that both the cataclasite and the mylonite are Early Permian in age. The mylonite formed in a continuous process before, during, and after the intrusion of the Val Biandino Quartz Diorite in the footwall of the detachment fault. Microstructure and quartz texture of the mylonite indicate top-to-the-southeast displacement. Quartz textures of mylonite close to the intrusive bodies are characterized by c-axis single maxima near the Y-direction of the finite strain, indicating prism glide as the dominant gliding system and hence high temperatures (above
c.
500 °C) during mylonitization. This is explained by heat advection through the rising quartz diorite melt. During detachment faulting, the footwall of the Grassi Detachment Fault was bowed up to form a metamorphic core complex. The Ponteranica Conglomerate was deposited as a proximal, syntectonic fan-delta on the southeast side of the metamorphic core complex late in its evolution. The unconformity of the Verrucano Lombardo over the Collio Formation and the basement results from erosion of the topography created by detachment faulting, core complex updoming, and block tilting. These results indicate dramatic SE–NW stretching (in present-day coordinates) of the South-Alpine crust during the Early Permian. The return from the thickened, orogenic crust at the end of the Hercynian orogeny to the normal crustal thickness (
c.
30 km) of Late Permian and Early Triassic times was accommodated to a large extent by crustal extension, at least in this part of the southern Alps.
Tertiary cooling and exhumation history in the Maramures area (internal eastern Carpathians, northern Romania): thermochronology and structural data
Authors: Gröger H. R. , Fügenschuh B. , Tischler M. , Schmid S. M. , Foeken J. P. T.
Published: July 2008

The Tertiary kinematic history of the Maramures area is constrained by integrating thermochronological (fission track and (U–Th)/He analysis) data with field-based structural investigations. This study focuses on the tectonic evolution of the northern rim of the Tisza–Dacia block during collision with the European margin. Cretaceous nappe stacking, related metamorphism as well as Late Cretaceous exhumation are evidenced by zircon fission track data. Subsequent Palaeogene to Early Miocene sedimentation led to burial heating and annealing of fission tracks in apatite. Final tectonic uplift was initiated during the convergence of Tisza–Dacia with the European margin, associated with transpressional deformation (16 to 12 Ma). This led to Mid-Miocene exhumation, recorded by apatite fission track cooling ages in the western part of the study area. Transtension between 12 and 10 Ma caused brittle deformation along E–W trending strike-slip faults and SW–NE trending normal faults, delimiting blocks that were tilted towards the SW. This fragmentation of the crust led to enhanced exhumation at rates of 1 mm/a in the central part of the study area, as is documented by Middle to Late Miocene cooling ages (13 to 7 Ma). The outside estimate for the total amount of exhumation since Middle Miocene times is 7 km.
Violence, Gender, and Subjectivity
Authors: Das Veena
Published: July 2008

This review examines the interlocking of violence, gender, and subjectivity within the overarching framework of the sexualization of the social contract. Tracking the question of gendered belonging to the nation state, the article discusses the anthropological literature along with feminist and critical theory to shed light on the relation between reproduction and death as a way of giving life to the nation-state. Sexual and reproductive violence are closely linked to the social and cultural imaginaries of order and disorder; and violence, far from being an interruption of the ordinary, is folded into the ordinary.
Evolutionary Models of Women's Reproductive Functioning
Authors: Vitzthum Virginia J.
Published: July 2008

Life history theory posits that natural selection leads to the evolution of mechanisms that tend to allocate resources to the competing demands of growth, reproduction, and survival such that fitness is locally maximized. (That is, among alternative allocation patterns exhibited in a population, those having the highest inclusive fitness will become more common over generational time.) Strategic modulation of reproductive effort is potentially adaptive because investment in a new conception may risk one's own survival, future reproductive opportunities, and/or current offspring survival. Several physiological and behavioral mechanisms modulate reproductive effort in human females. This review focuses on the hormonal changes that vary the probability of ovulation, conception, and/or continuing pregnancy and discusses evolutionary models that predict how and why these hormonal changes occur. Anthropological field studies have yielded important insights into the environmental correlates of variation in ovarian steroids, but much remains to be learned about the evolutionary determinants, proximate mechanisms, and demographic significance of variation in women's reproductive functioning.
Adoption of the Unrelated Child: Some Challenges to the Anthropological Study of Kinship
Authors: Howell Signe
Published: July 2008

Adoption of children born by others is practiced in some form or another in all known societies. Although ethnographic monographs from all over the world have made numerous brief references to local adoption and/or fostering practices, very little sustained interpretative interest has, until recently, been directed at this social phenomenon. With the sudden and rapid increase in transnational adoption—people in Western Europe and North America adopt children from countries in the south and the former Soviet empire—a new-found anthropological interest in adoption has been observed. This review places adoption firmly within the tradition of theoretical kinship and explores the values attached to a perceived relationship between biological and social relatedness in a number of different social settings in which adoption is being practiced.
Alternative Kinship, Marriage, and Reproduction
Authors: Levine Nancy E.
Published: July 2008

This review examines the implications of new kinship practices for anthropological theory, with a special focus on recent research in gay and lesbian kinship and assisted reproduction. The article begins with an account of the theoretical contexts in which kinship studies have been conducted and a brief survey of some of the older literature on alternative systems of marriage and family formation in preindustrial and modern societies. The emphasis then turns to current discussions of how gay men and lesbian women are creating meaningful networks of kin and families and the ways in which these practices both follow and challenge traditional expectations for family life. The final section surveys the ways in which the new reproductive technologies have been utilized in Euro-American societies and how cultural ideas and values concerning kin relationships have shaped the transfer of these technologies to and their utilization in other societies.
Evolution in Archaeology
Authors: Shennan Stephen
Published: July 2008

This review begins with a brief outline of the key concepts of Darwinian archaeology. Its history is then summarized, beginning with its emergence as a significant theoretical focus within the discipline in the early 1980s; its main present-day currents are then presented, citing examples of recent work. The developments in archaeology are part of broader trends in anthropology and psychology and are characterized by the same theoretical disagreements. There are two distinct research traditions: one centered on cultural transmission and dual inheritance theory and the other on human behavioral ecology. The development of specifically archaeological methodologies within these two traditions for testing evolutionary hypotheses relating to diachronic questions using archaeological data is discussed. Finally, this review suggests that the greatest challenge for the future lies in finding ways of using archaeological data to address current major debates in evolutionary social science as a whole concerning, for example, the emergence of large-scale cooperation.
Evolutionary Perspectives on Religion
Authors: Boyer Pascal , Bergstrom Brian
Published: July 2008

Recent work in biology, cognitive psychology, and archaeology has renewed evolutionary perspectives on the role of natural selection in the emergence and recurrent forms of religious thought and behavior, i.e., mental representations of supernatural agents, as well as artifacts, ritual practices, moral systems, ethnic markers, and specific experiences associated with these representations. One perspective, inspired from behavioral ecology, attempts to measure the fitness effects of religious practices. Another set of models, representative of evolutionary psychology, explain religious thought and behavior as the output of cognitive systems (e.g., animacy detection, social cognition, precautionary reasoning) that are not exclusive to the religious domain. In both perpectives, the question remains open, whether religious thought and behavior constitute an adaptation or a by-product of adaptive cognitive function.
Reproduction and Inheritance: Goody Revisited
Authors: Hann Chris
Published: July 2008

According to Jack Goody, in a body of work that dates back to the 1950s, differences in the mode of inheritance between Eurasia and sub-Saharan Africa have multiple connections to domestic groups, kin terminology, politics and stratification, and above all, productive systems. Goody's theory is built on evolutionist assumptions and draws in part on statistical analysis of the Ethnographic Atlas. Theoretically and methodologically unfashionable among sociocultural anthropologists, his work has been largely ignored in recent decades. This article considers the standard criticisms and reviews pertinent recent work on kinship and property in rural Europe and in legal anthropology. Inheritance was supposed to lose its fundamental social significance in socialist societies, and it also came to play a smaller role in the social reproduction of advanced capitalist societies. However, this eclipse may prove to be temporary, and a reengagement with the topic on the part of anthropologists is overdue.
Assisted Reproductive Technologies and Culture Change
Authors: Inhorn Marcia C. , Birenbaum-Carmeli Daphna
Published: July 2008

In 1978, the world's first “test-tube” baby was born via in vitro fertilization (IVF). The past 30 years have seen the rapid evolution of many other assisted reproductive technologies (ARTs)—some are simple variants of IVF, whereas others bridge the fields of assisted reproduction and human genomics. As ARTs have evolved over time, so have social, cultural, legal, and ethical responses to them. Indeed, ARTs are a key symbol of our times, representing the growing prominence of biotechnologies in the configuration of individual, familial, and collective identities around the globe. This review highlights the scholarship of more than 50 anthropologists who are studying the effects of ARTs in many areas of social life, including the traditional anthropological domains of kinship, marriage, and the family, gender, religion, and biomedicine. Their research bespeaks both the destabilizing and the generative impacts of ARTs at the interface between science and society.
Sexuality Studies in Archaeology
Authors: Voss Barbara L.
Published: July 2008

Does sexuality have a past? A growing body of archaeological research on sexuality demonstrates that the sexual politics of the past were as richly varied and complex as those of the present. Furthermore, investigations of past sexualities have much to say about conventional archaeological topics such as state formation, subsistence and settlement systems, and the emergence and elaboration of symbolic systems, and they have made methodological and theoretical contributions to the archaeology of social identities and visual representations. To date, most research has clustered into five groupings: reproduction management, sexual representations, sexual identities, prostitution, and the sexual politics of institutions. The most intriguing new development is the growing application of queer theory as an archaeological methodology for investigating nonsexual as well as sexual matters. In particular, queer theory provides a methodological bridge between archaeological research on sexuality and research on other aspects of social identity.
The Epigenetics of rRNA Genes: From Molecular to Chromosome Biology
Authors: McStay Brian , Grummt Ingrid
Published: July 2008

In eukaryotes, the genes encoding ribosomal RNAs (rDNA) exist in two distinct epigenetic states that can be distinguished by a specific chromatin structure that is maintained throughout the cell cycle and is inherited from one cell to another. The fact that even in proliferating cells with a high demand of protein synthesis a fraction of rDNA is silenced provides a unique possibility to decipher the mechanism underlying epigenetic regulation of rDNA. This chapter summarizes our knowledge of the molecular mechanisms that establish and propagate the epigenetic state of rRNA genes, unraveling a complex interplay of DNA methyltransferases and histone-modifying enzymes that act in concert with chromatin remodeling complexes and RNA-guided mechanisms to define the transcriptional state of rDNA. We also review the critical role of the RNA polymerase I transcription factor UBF in the formation of active nucleolar organizer regions (NORs) and maintenance of the euchromatic state of rRNA genes.
Sister Chromatid Cohesion: A Simple Concept with a Complex Reality
Authors: Onn Itay , Heidinger-Pauli Jill M. , Guacci Vincent , Ünal Elçin , Koshland Douglas E.
Published: July 2008

In eukaryotes, the process of sister chromatid cohesion holds the two sister chromatids (the replicated chromosomes) together from DNA replication to the onset of chromosome segregation. Cohesion is mediated by cohesin, a four-subunit SMC (structural maintenance of chromosome) complex. Cohesin and cohesion are required for proper chromosome segregation, DNA repair, and gene expression. To carry out these functions, cohesion is regulated by elaborate mechanisms involving a growing list of cohesin auxiliary factors. These factors control the timing and position of cohesin binding to chromatin, activate chromatin-bound cohesin to become cohesive, and orchestrate the orderly dissolution of cohesion. The 45-nm ringlike architecture of soluble cohesin is compatible with dramatically different mechanisms for both chromatin binding and cohesion generation. Solving the mechanism of cohesion and its complex regulation presents significant challenges but offers the potential to provide important insights into higher-order chromosome organization and chromosome biology.
Systems Approaches to Identifying Gene Regulatory Networks in Plants
Authors: Long Terri A. , Brady Siobhan M. , Benfey Philip N.
Published: July 2008

Complex gene regulatory networks are composed of genes, noncoding RNAs, proteins, metabolites, and signaling components. The availability of genome-wide mutagenesis libraries; large-scale transcriptome, proteome, and metabalome data sets; and new high-throughput methods that uncover protein interactions underscores the need for mathematical modeling techniques that better enable scientists to synthesize these large amounts of information and to understand the properties of these biological systems. Systems biology approaches can allow researchers to move beyond a reductionist approach and to both integrate and comprehend the interactions of multiple components within these systems. Descriptive and mathematical models for gene regulatory networks can reveal emergent properties of these plant systems. This review highlights methods that researchers are using to obtain large-scale data sets, and examples of gene regulatory networks modeled with these data. Emergent properties revealed by the use of these network models and perspectives on the future of systems biology are discussed.
The Evolution, Regulation, and Function of Placenta-Specific Genes
Authors: Rawn Saara M. , Cross James C.
Published: July 2008

A number of placenta-specific genes (e.g., Tpbp, Plac1, Syncytin, and retrotransposon-associated genes such as Peg10, Rtl1, Endothelin B receptor, Insl4, Leptin, Midline1, and Pleiotrophin), enhancer elements (e.g., glycoprotein hormone α-subunit) and gene isoforms (e.g., 3βHSD, Cyp19), as well as placenta-specific members of gene families (e.g., Gcm1, Mash2, Rhox, Esx1, Cathepsin, PAG, TKDP, Psg, Siglec) have been identified. This review summarizes their evolution, regulation, and biochemical functions and discusses their significance for placental development and function. Strikingly, the number of unique, truly placenta-specific genes that have been discovered to date is very small. The vast majority of placenta-specific gene products have resulted from one of three mechanisms: evolution of placenta-specific promoters, evolution of large gene families with several placenta-specific members, or adoption of functions associated with endogenous retroviruses and retroelements. Interestingly, nearly all the examples of placenta-specific genes that have been discovered to date are not present in all placental mammals.
Study of High–Reynolds Number Isotropic Turbulence by Direct Numerical Simulation
Authors: Ishihara Takashi , Gotoh Toshiyuki , Kaneda Yukio
Published: July 2008

We review studies of the statistics of isotropic turbulence in an incompressible fluid at high Reynolds numbers using direct numerical simulation (DNS) from the viewpoint of fundamental physics. The Reynolds number achieved by the largest DNS, with 40963 grid points, is comparable with the largest Reynolds number in laboratory experiments. The high-quality DNS data in the inertial subrange and the dissipative range enable the examination of detailed statistics at small scales, such as the normalized energy-dissipation rate, energy and energy-flux spectra, the intermittency of the velocity gradients and increments, scaling exponents, and flow-field structure. We emphasize basic questions of turbulence, universality in the sense of Kolmogorov's theory, and the dependence of the statistics on the Reynolds number and scale.
Neuropsychological Assessment of Dementia
Authors: Salmon David P. , Bondi Mark W.
Published: July 2008

Neuropsychological studies show that cognitive deficits associated with Alzheimer's disease (AD) are distinct from age-associated cognitive decline. Quantitative and qualitative differences are apparent across many cognitive domains, but are especially obvious in episodic memory (particularly delayed recall), semantic knowledge, and some aspects of executive functions. The qualitatively distinct pattern of deficits is less salient in very old AD patients than in younger AD patients. Although decline in episodic memory is usually the earliest cognitive change that occurs prior to the development of the AD dementia syndrome, asymmetry in cognitive abilities may also occur in this “preclinical” phase of the disease and predict imminent dementia. Discrete patterns of cognitive deficits occur in AD and several neuropathologically distinct age-associated neurodegenerative disorders. Knowledge of these differences helps to clinically distinguish among various causes of dementia and provides useful models for understanding brain-behavior relationships that mediate cognitive abilities affected in various neurodegenerative diseases.
Regulation of cell surface expression of functional pacemaker channels by a motif in the B-helix of the cyclic nucleotide-binding domain
Authors: Nazzari Hamed , Angoli Damiano , Chow Sarah S. , Whitaker Gina , Leclair Leisha , McDonald Evan , Macri Vincenzo , Zahynacz Kristin , Walker Valerie , Accili Eric A.
Published: July 2008

Previous studies have suggested that a portion of the cyclic nucleotide-binding domain (CNBD) of the hyperpolarization-activated cyclic nucleotide-gated channel 2 (HCN2) “pacemaker” channel, composed of the A- and B-helices and the interceding β-barrel, confers two functions: inhibition of channel opening in response to hyperpolarization and promotion of cell surface expression. The sequence determinants required for each of these functions are unknown. In addition, the mechanism underlying plasma membrane targeting by this subdomain has been limitedly explored. Here we identify a four-amino acid motif (EEYP) in the B-helix that strongly promotes channel export from the endoplasmic reticulum (ER) and cell surface expression but does not contribute to the inhibition of channel opening. This motif augments a step in the trafficking pathway and/or the efficiency of correct folding and assembly.