bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time‐averaging and fidelity of modern death assemblages: building a taphonomic foundation for conservation palaeobiology
Authors: Kidwell Susan M. 
Published: May 2013

AbstractEcosystems today are under growing pressure, with human domination at many scales. It is difficult, however, to gauge what has changed or been lost – and why – in the absence of data from periods before human activities. Actualistic taphonomic studies, originally motivated to understand preservational controls on deep‐time fossil records, are now providing insights into modern death assemblages as historical archives of present‐day ecosystems, turning taphonomy on its head. This article reviews the past 20 years of work on the temporal resolution and ability of time‐averaged skeletal assemblages to capture ecological information faithfully, focusing primarily on molluscs from soft‐sediment seafloors. Two promising arenas for ‘applied taphonomy’ are then highlighted: (1) using live‐dead mismatch – that is, observed discordance in the diversity, species composition, and distribution of living animals and co‐occurring skeletal remains – to recognize recent anthropogenic change, and (2) using time‐averaged death assemblages as windows into regional diversity and long‐term baselines, as a supplement or substitute for conventional live‐collected data. Meta‐analysis and modelling find that, in unaltered habitats, live‐dead differences in community‐level attributes can be generated largely or entirely by time‐averaging of natural spatial and temporal variability in living assemblages, on time frames consistent with the range of shell ages observed in death assemblages. Time‐averaging coarsens the temporal and spatial resolution of biological information in predictable ways; by comparison, taphonomic bias of information arising from differential preservation, production and transport of shells is surprisingly modest. Several challenges remain for basic taphonomic research, such as empirical and analytical methods of refining the temporal resolution of death assemblages; assessing the fate of resolution and fidelity with progressive burial; and expanding our understanding of the dynamics of skeletal accumulation in other groups and settings. Rather than shunning human‐impacted areas as inappropriate analogues of the deep past, we should capitalize on them to explore the fundamental controls on skeletal accumulation and to develop robust protocols for bringing time‐averaged death assemblages into the toolkits of conservation biology and environmental management.
A Triassic seed with an angiosperm‐like wind dispersal mechanism
Authors: Axsmith Brian J. , Fraser Nicholas C. , Corso Taryn 
Published: May 2013

AbstractThe earliest record of a seed with a pappus‐like, parachute seed dispersal mechanism, Edenia villisperma gen. et sp. nov., is described from the Upper Triassic of the eastern United States. The seed is small and roughly triangular. Clusters of long hairs emerge from a whorl of at least five circular scars just below the proximal end. This morphology indicates that the hair clusters represent modified lateral structures similar to the pappus of several eudicot angiosperm groups, but probably representing a case of convergent evolution of a similar structure in a gymnosperm. The seeds are usually found isolated, but one specimen indicates that they were born tightly packed together on an axis. A few earlier records exist of dispersal hairs, but this is the first clearly indicating a pappus‐like structure. Although the exact affinities of Edenia are uncertain, this seed demonstrates that plants with highly advanced wind dispersal mechanisms occurred at least 55 million years earlier than previously thought.
Marker‐free genetic engineering of the chloroplast in the green microalga Chlamydomonas reinhardtii
Authors: Chen Hsu‐Ching , Melis Anastasios 
Published: May 2013

SummaryThe work applied a transgene expression method based on the replacement of an inactive rbcL gene as the selection marker in Chlamydomonas reinhardtii chloroplasts. The native rbcL gene in strain CC2653 has a point mutation that causes early translation termination, thus resulting in a photosynthesis mutant. Recovery of rbcL function for selection is offered along with the heterologous expression of the alcohol dehydrogenase ADH1 gene from Saccharomyces cerevisiae in the Chlamydomonas chloroplast. The CrCpADH1 gene was inserted via double homologous recombination in the psaB‐rbcL chloroplast intergenic region of recipient strain CC2653, using the psaB and rbcL gene sequences for the double homologous recombination. This transformation conferred a functional rbcL gene and expression of the CrCpADH1 transgene in the recipient strain. This method alleviated the need to use antibiotics for selection, resulting in a negligible number of false positives during screening, and attaining a transformation efficiency greater than 90%. The approach also ensured segregation of chloroplast DNA copies, so as to achieve homoplasmy of the transformant chloroplast DNA, with a concomitant elimination of recipient strain Cp DNA. High levels of steady‐state CrCpADH1 transcripts were detected in the homoplasmic transformants. However, CrCpADH1 protein levels were attenuated under continuous illumination growth conditions due to oxygen accumulation in the cells. Under conditions of low oxygen partial pressure, or anoxia, accumulation of CrCpADH1 protein in the cells and ethanol in the growth medium was observed. A metabolic pathway for ethanol production is proposed in Chlamydomonas, mediated by the chloroplast‐localized CrCpADH1 transgenic enzyme.
Adult stem cells for chronic lung diseases
Authors: Mora Ana L. , Rojas Mauricio 
Published: May 2013

AbstractIdiopathic pulmonary fibrosis (IPF) and chronic obstructive pulmonary disease (COPD) are chronic, progressive and lethal lung diseases. The incidence of IPF and COPD increases with age, independent of exposure to common environmental risk factors. At present, there is limited understanding of the relationship between ageing and the development of chronic lung diseases. One hypothesis is that chronic injury drives to exhaustion the local and systemic repair responses in the lung. These changes are accentuated during ageing where there is a progressive accumulation of senescent cells. Recently, stem cells have emerged as a critical reparative mechanism for lung injury. In this review, we discuss the repair response of bone marrow‐derived mesenchymal stem cells (B‐MSC) after lung injury and how their function is affected by ageing. Our own work has demonstrated a protective role of B‐MSC in several animal models of acute and chronic lung injury. We recently demonstrated the association, using animal models, between age and an increase in the susceptibility to develop severe injury and fibrosis. At the same time, we have identified functional differences between B‐MSC isolated from young and old animals. Further studies are required to understand the functional impairment of ageing B‐MSC, ultimately leading to a rapid stem cell depletion or fatigue, interfering with their ability to play a protective role in lung injury. The elucidation of these events will help in the development of rational and new therapeutic strategies for COPD and IPF.
Cytoskeleton‐dependent endomembrane organization in plant cells: an emerging role for microtubules
Authors: Brandizzi Federica , Wasteneys Geoffrey O. 
Published: May 2013

SummaryMovement of secretory organelles is a fascinating yet largely mysterious feature of eukaryotic cells. Microtubule‐based endomembrane and organelle motility utilizing the motor proteins dynein and kinesin is commonplace in animal cells. In contrast, it has been long accepted that intracellular motility in plant cells is predominantly driven by myosin motors dragging organelles and endomembrane‐bounded cargo along actin filament bundles. Consistent with this, defects in the acto‐myosin cytoskeleton compromise plant growth and development. Recent findings, however, challenge the actin‐centric view of the motility of critical secretory organelles and distribution of associated protein machinery. In this review, we provide an overview of the current knowledge on actin‐mediated organelle movement within the secretory pathway of plant cells, and report on recent and exciting findings that support a critical role of microtubules in plant cell development, in fine‐tuning the positioning of Golgi stacks, as well as their involvement in cellulose synthesis and auxin polar transport. These emerging aspects of the biology of microtubules highlight adaptations of an ancestral machinery that plants have specifically evolved to support the functioning of the acto‐myosin cytoskeleton, and mark new trends in our global appreciation of the complexity of organelle movement within the plant secretory pathway.
Efficacy of Liposomal Amphotericin B and Posaconazole in Intratracheal Models of Murine Mucormycosis
Authors: Luo Guanpingsheng , Gebremariam Teclegiorgis , Lee Hongkyu , French Samuel W. , Wiederhold Nathan P. , Patterson Thomas F. , Filler Scott G. , Ibrahim Ashraf S. 
Published: May 2013

ABSTRACT

Mucormycosis is a life-threatening fungal infection almost uniformly affecting diabetics in ketoacidosis or other forms of acidosis and/or immunocompromised patients. Inhalation of
Mucorales
spores provides the most common natural route of entry into the host. In this study, we developed an intratracheal instillation model of pulmonary mucormycosis that hematogenously disseminates into other organs using diabetic ketoacidotic (DKA) or cyclophosphamide-cortisone acetate-treated mice. Various degrees of lethality were achieved for the DKA or cyclophosphamide-cortisone acetate-treated mice when infected with different clinical isolates of
Mucorales
. In both DKA and cyclophosphamide-cortisone acetate models, liposomal amphotericin B (LAmB) or posaconazole (POS) treatments were effective in improving survival, reducing lungs and brain fungal burdens, and histologically resolving the infection compared with placebo. These models can be used to study mechanisms of infection, develop immunotherapeutic strategies, and evaluate drug efficacies against life-threatening
Mucorales
infections.
Pharmacodynamics Modeling To Optimize Dosage Regimens of Sulbactam
Authors: Jaruratanasirikul Sutep , Wongpoowarak Wibul , Aeinlang Nanchanit , Jullangkoon Monchana 
Published: May 2013

ABSTRACT
The aim of this study was to reveal population pharmacokinetics and assess the efficacies of various dosage regimens of sulbactam in terms of the probability of target attainment with this agent over a range of MICs. Monte Carlo simulations were performed to determine the probability of attaining specific pharmacodynamic targets. The results indicated that a regimen consisting of a 4-h infusion of 3 g of sulbactam every 8 h would be an alternative treatment option for less-susceptible pathogens.
Fetal Safety of Macrolides
Authors: Bahat Dinur Anat , Koren Gideon , Matok Ilan , Wiznitzer Arnon , Uziel Elia , Gorodischer Rafael , Levy Amalia 
Published: May 2013

ABSTRACT
Macrolide antibiotics are largely used in pregnancy for different bacterial infections. Their fetal safety has been studied by several groups, yielding opposing results. In particular, there have been studies claiming an association between macrolides and cardiovascular malformations. Exposure in early infancy has been associated with pyloric stenosis and intussusception. This has led to an avoidance in prescribing macrolides to pregnant women in several Scandinavian countries. The Objectives of the present study was to investigate the fetal safety of this class of drug by linking a large administrative database of drug dispensing and pregnancy outcome in Southern Israel. A computerized database of medications dispensed from 1999 to 2009 to all women registered in the Clalit health maintenance organization in southern Israel was linked with two computerized databases containing maternal and infant hospitalization records. Also, medical pregnancy termination data were analyzed. The following confounders were controlled for: maternal age, ethnicity, maternal pregestational diabetes, parity, and the year the mother gave birth or went through medical pregnancy termination. First- and third-trimester exposures to macrolide antibiotics as a group and to individual drugs were analyzed. During the study period there were 105,492 pregnancies among Clalit women that met the inclusion criteria. Of these, 104,380 ended in live births or dead fetuses and 1,112 in abortion due to medical reasons. In the first trimester of pregnancy, 1,033 women were exposed to macrolides. There was no association between macrolides and either major malformations [odds ratio (OR), 1.08; 95% confidence interval (CI), 0.84 to 1.38)] or specific malformations, after accounting for maternal age, parity, ethnicity, prepregnancy diabetes, and year of exposure. During the third trimester of pregnancy, 959 women were exposed to macrolides. There was no association between such exposure and perinatal mortality, low birth weight, low Apgar score, or preterm delivery. Similarly, no associations were demonstrated with pyloric stenosis or intussusception. Use of macrolides in the first trimester of pregnancy is not associated with an increased risk of major malformations. Exposure in the third trimester is not likely to increase neonatal risks for pyloric stenosis or intussusception in a clinically meaningful manner.
H-NS Plays a Role in Expression of Acinetobacter baumannii Virulence Features
Authors: Eijkelkamp Bart A. , Stroeher Uwe H. , Hassan Karl A. , Elbourne Liam D. H. , Paulsen Ian T. , Brown Melissa H. 
Published: May 2013

ABSTRACT

Acinetobacter baumannii
has become a major problem in the clinical setting with the prevalence of infections caused by multidrug-resistant strains on the increase. Nevertheless, only a limited number of molecular mechanisms involved in the success of
A. baumannii
as a human pathogen have been described. In this study, we examined the virulence features of a hypermotile derivative of
A. baumannii
strain ATCC 17978, which was found to display enhanced adherence to human pneumocytes and elevated levels of lethality toward
Caenorhabditis elegans
nematodes. Analysis of cellular lipids revealed modifications to the fatty acid composition, providing a possible explanation for the observed changes in hydrophobicity and subsequent alteration in adherence and motility. Comparison of the genome sequences of the hypermotile variant and parental strain revealed that an insertion sequence had disrupted an
hns
-like gene in the variant. This gene encodes a homologue of the histone-like nucleoid structuring (H-NS) protein, a known global transcriptional repressor. Transcriptome analysis identified the global effects of this mutation on gene expression, with major changes seen in the autotransporter Ata, a type VI secretion system, and a type I pilus cluster. Interestingly, isolation and analysis of a second independent hypermotile ATCC 17978 variant revealed a mutation to a residue within the DNA binding region of H-NS. Taken together, these mutants indicate that the phenotypic and transcriptomic differences seen are due to loss of regulatory control effected by H-NS.
Bovine Respiratory Syncytial Virus and Histophilus somni Interaction at the Alveolar Barrier
Authors: Agnes J. T. , Zekarias B. , Shao M. , Anderson M. L. , Gershwin L. J. , Corbeil L. B. 
Published: May 2013

ABSTRACT

Our previous studies showed that
Histophilus somni
and bovine respiratory syncytial virus (BRSV) act synergistically
in vivo
to cause more severe bovine respiratory disease than either agent alone causes. Since
H. somni
surface and secreted immunoglobulin binding protein A (IbpA) causes retraction of bovine alveolar type 2 (BAT2) cells and invasion between BAT2 cells
in vitro
, we investigated mechanisms of BRSV-plus-
H. somni
infection at the alveolar barrier. BRSV treatment of BAT2 cells prior to treatment with IbpA-rich
H. somni
concentrated culture supernatant (CCS) resulted in increased BAT2 cell rounding and retraction compared to those with either treatment alone. This mimicked the increased alveolar cell thickening in calves experimentally infected with BRSV followed by
H. somni
compared to that in calves infected with BRSV or
H. somni
alone. BRSV-plus-
H. somni
CCS treatment of BAT2 cells also enhanced paracellular migration. The effect of matrix metalloproteinases (MMPs) was investigated as well because microarray analysis revealed that treatment with BRSV plus
H. somni
synergistically upregulated BAT2 cell expression of
mmp1
and
mmp3
compared to that in cells treated with either agent alone. Enzyme-linked immunosorbent assay (ELISA) confirmed that MMP1 and MMP3 protein levels were similarly upregulated. In collagen I and collagen IV (targets for MMP1 and MMP3, respectively) substrate zymography, digestion was increased with supernatants from dually treated BAT2 cells compared with those from singly treated cells. Enhanced breakdown of collagen IV in the basal lamina and of fibrillar collagen I in the adjacent interstitium in the dual infection may facilitate dissemination of
H. somni
infection.
Human Leukocyte Antigens and Cellular Immune Responses to Anthrax Vaccine Adsorbed
Authors: Ovsyannikova Inna G. , Pankratz V. Shane , Vierkant Robert A. , Pajewski Nicholas M. , Quinn Conrad P. , Kaslow Richard A. , Jacobson Robert M. , Poland Gregory A. 
Published: May 2013

ABSTRACT

Interindividual variations in vaccine-induced immune responses are in part due to host genetic polymorphisms in the human leukocyte antigen (HLA) and other gene families. This study examined associations between HLA genotypes, haplotypes, and homozygosity and protective antigen (PA)-specific cellular immune responses in healthy subjects following immunization with Anthrax Vaccine Adsorbed (AVA). While limited associations were observed between individual HLA alleles or haplotypes and variable lymphocyte proliferative (LP) responses to AVA, analyses of homozygosity supported the hypothesis of a “heterozygote advantage.” Individuals who were homozygous for any HLA locus demonstrated significantly lower PA-specific LP than subjects who were heterozygous at all eight loci (median stimulation indices [SI], 1.84 versus 2.95,
P
= 0.009). Similarly, we found that class I (HLA-A) and class II (HLA-DQA1 and HLA-DQB1) homozygosity was significantly associated with an overall decrease in LP compared with heterozygosity at those three loci. Specifically, individuals who were homozygous at these loci had significantly lower PA-specific LP than subjects heterozygous for HLA-A (median SI, 1.48 versus 2.13,
P
= 0.005), HLA-DQA1 (median SI, 1.75 versus 2.11,
P
= 0.007), and HLA-DQB1 (median SI, 1.48 versus 2.13,
P
= 0.002) loci, respectively. Finally, homozygosity at an increasing number (≥4) of HLA loci was significantly correlated with a reduction in LP response (
P
< 0.001) in a dose-dependent manner. Additional studies are needed to reproduce these findings and determine whether HLA-heterozygous individuals generate stronger cellular immune response to other virulence factors (
Bacillus anthracis
LF and EF) than HLA-homozygous subjects.
The Dot/Icm Effector SdhA Is Necessary for Virulence of Legionella pneumophila in Galleria mellonella and A/J Mice
Authors: Harding Clare R. , Stoneham Charlotte A. , Schuelein Ralf , Newton Hayley , Oates Clare V. , Hartland Elizabeth L. , Schroeder Gunnar N. , Frankel Gad 
Published: May 2013

ABSTRACT

Legionella pneumophila
is an intracellular bacterium that resides within amoebae and macrophages in a specialized compartment termed the
Legionella
-containing vacuole (LCV). As well as providing an intracellular niche for replication, the LCV helps to prevent the release of bacterial components into the cytoplasm. Recognition of these components as danger signals by the host activates immune responses leading to clearance of the bacterium. Here, we examined the role of two important virulence factors of
L. pneumophila
, the potent danger signal flagellin and the translocated Dot/Icm type IVB secretion system effector SdhA, which is crucial to maintain LCV integrity, in the
Galleria mellonella
infection model. We demonstrate that flagellin expression does not contribute to virulence, replication, or induction of clearance mechanisms. Conversely, SdhA expression is important for virulence. We found that in the absence of SdhA, the LCV in hemocytes showed signs of instability and leakage. Furthermore, in contrast to wild-type
L. pneumophila
, a Δ
sdhA
mutant caused a transient depletion of hemocytes and reduced mortality. Analysis of the Δ
sdhA
mutant in the A/J mouse model also showed a significant replication defect. Together, our data underline the crucial importance of SdhA in infection across different model organisms.
Hypoxia-Inducible Factor 1-Regulated Lysyl Oxidase Is Involved in Staphylococcus aureus Abscess Formation
Authors: Beerlage Christiane , Greb Jessica , Kretschmer Dorothee , Assaggaf Mohammad , Trackman Philip C. , Hansmann Martin-Leo , Bonin Michael , Eble Johannes A. , Peschel Andreas , Brüne Bernhard , Kempf Volkhard A. J. 
Published: May 2013

ABSTRACT

Hypoxia-inducible factor 1 (HIF-1) is the key transcription factor involved in the adaptation of mammals to hypoxia and plays a crucial role in cancer angiogenesis. Recent evidence suggests a leading role for HIF-1 in various inflammatory and infectious diseases. Here we describe the role of HIF-1 in
Staphylococcus aureus
infections by investigating the HIF-1-dependent host cell response. For this purpose, transcriptional profiling of HIF-1α-deficient HepG2 and control cells, both infected with
Staphylococcus aureus
, was performed. Four hours after infection, the expression of 190 genes, 24 of which were regulated via HIF-1, was influenced.
LOX
(encoding lysyl oxidase) was one of the upregulated genes with a potential impact on the course of
S. aureus
infection. LOX is an amine oxidase required for biosynthetic cross-linking of extracellular matrix components. LOX was upregulated
in vitro
in different cell cultures infected with
S. aureus
and also
in vivo
, in kidney abscesses of mice intravenously infected with
S. aureus
and in clinical skin samples from patients with
S. aureus
infections. Inhibition of LOX by β-aminopropionitrile (BAPN) did not affect the bacterial load in kidneys or blood but significantly influenced abscess morphology and collagenization. Our data provide evidence for a crucial role of HIF-1-regulated LOX in abscess formation.