bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phenotypic Differences in Leucocyte Populations among Healthy Preterm and Full‐Term Newborns
Authors: Quinello C. , Silveira‐Lessa A. L. , Ceccon M. E. J. R. , Cianciarullo M. A. , Carneiro‐Sampaio M. , Palmeira P. 
Published: April 2014

AbstractThe immune system of neonates has been considered functionally immature, and due to their high susceptibility to infections, the aim of this study was to analyse the phenotypic differences in leucocyte populations in healthy preterm and full‐term newborns. We evaluated the absolute numbers and frequencies of dendritic cells (DCs) and DC subsets, monocytes and T and B lymphocytes and subsets in the cord blood of healthy moderate and very preterm (Group 1), late preterm (Group 2) and full‐term (Group 3) newborns and in healthy adults, as controls, by flow cytometry. The analyses revealed statistically higher absolute cell numbers in neonates compared with adults due to the characteristic leucocytosis of neonates. We observed a lower frequency of CD80+ myeloid and plasmacytoid DCs in Group 1 and reduced expression of TLR‐4 on myeloid DCs in all neonates compared with adults. TLR‐2+ monocytes were reduced in Group 1 compared with Groups 2 and 3, and TLR‐4+ monocytes were reduced in Groups 1 and 2 compared with Group 3. The frequencies and numbers of naïve CD4+ T and CD19+ B cells were higher in the three groups of neonates compared with adults, while CD4+ effector and effector memory T cells and CD19+ memory B cells were elevated in adults compared with neonates, as expected. Our study provides reference values for leucocytes in cord blood from term and preterm newborns, which may facilitate the identification of immunological deficiencies in protection against extracellular pathogens.
The heterogeneous HLA genetic composition of the Brazilian population and its relevance to the optimization of hematopoietic stem cell donor recruitment
Authors: Fabreti‐Oliveira R. A. , Nascimento E. , Fonseca C. G. , Santos M. A. 
Published: April 2014

AbstractThe aim of this study was to investigate the human leukocyte antigen (HLA) molecular variation across the Brazilian population in order to determine possible regional differences, which would be highly relevant to optimizing donor recruitment strategies in hematopoietic stem cell transplantation (HSCT) and understanding the population genetic background of this heterogeneous country. HLA data of 551 HSCT donors from five Brazilian regions were characterized by high‐resolution DNA alleles at the HLA‐A, ‐B, ‐C, ‐DRB1 and ‐DQB1 loci and compared with other populations in Brazil and worldwide populations. Allele and haplotype frequencies were estimated. The analysis was performed to assess Hardy–Weinberg equilibrium (HWE) and linkage disequilibrium (LD) among different loci in each recruitment center. Genetic variation was explored through genetic distance analyzed by using a new algorithm based on linear algebra, taking into account geographic regions of Brazil. The results indicated a heterogeneous genetic composition of the Brazilian population, such that HLA allele and haplotype frequencies exhibit different distributions among Brazilian regions, which has important implications for donor matching. In addition, a pronounced differentiation was observed by the absence of clustering of the regional populations in the reduced‐dimension space. These data may be useful for increasing donor recruitment with more genetic representativeness in the Brazilian Volunteer Bone Marrow Donors Registry (REDOME).
Independent contribution of bronchoalveolar lavage and serum galactomannan in the diagnosis of invasive pulmonary aspergillosis
Authors: Fisher C.E. , Stevens A.M. , Leisenring W. , Pergam S.A. , Boeckh M. , Hohl T.M. 
Published: April 2014

AbstractThe optimal combination of galactomannan index (GMI) testing for the diagnosis of invasive pulmonary aspergillosis (IPA) remains unclear. For diagnostic approaches that are triggered by clinical signs and symptoms in high‐risk patients, institutional variation remains, with some centers routinely relying on only serum GMI or bronchoalveolar lavage (BAL) GMI testing. In addition, use of mold‐active agents before diagnosis of IPA is becoming increasingly common, and understanding the effect of these drugs on test yield is important when making time‐critical treatment decisions. In a single‐center cohort of 210 allogeneic hematopoietic cell transplant recipients, we found that serum and BAL GMI testing contributed independently to IPA diagnosis, supporting the practice of sending both tests simultaneously to ensure a timely diagnosis of IPA. BAL GMI sensitivity was not affected by receipt of mold‐active therapy in our cohort.
Intrinsic properties of rostral ventrolateral medulla presympathetic and bulbospinal respiratory neurons of juvenile rats are not affected by chronic intermittent hypoxia
Authors: Almado Carlos Eduardo L. , Leão Ricardo M. , Machado Benedito H. 
Published: April 2014

New Findings
What is the central question of this study?
What is the effect of chronic intermittent hypoxia (a neurogenic model of hypertension that also induces active expiration) on intrinsic electrophysiological properties of rostral ventrolateral medulla presympathetic and putative expiratory neurons recorded in brainstem slices of juvenile rats (postnatal day 35)?
What is the main finding and its importance?
Presympathetic neurons and phrenic nucleus‐projecting neurons of rostral ventrolateral medulla present characteristics of intrinsic pacemakers, and chronic intermittent hypoxia produces no changes in their intrinsic electrophysiological properties.
The presympathetic neurons in the rostral ventrolateral medulla (RVLM) are considered to be the source of the sympathetic activity, and there is experimental evidence that these cells present intrinsic autodepolarization. There is also evidence that an important respiratory neuronal population located in the RVLM/Bötzinger complex (BötC) corresponds to augmenting expiratory neurons (aug‐E), which send projections to the phrenic nucleus in the spinal cord. However, the pacemaker activity of presympathetic neurons and the intrinsic properties of aug‐E neurons had not been evaluated in brainstem slices of juvenile rats (postnatal day 35). Chronic intermittent hypoxia (CIH) is a sympathetic‐mediated hypertension model, which seems to produce an associated increase in the activity of aug‐E neurons. In this study, we evaluated the effects of CIH on the intrinsic properties of RVLM/BötC presympathetic and phrenic nucleus‐projecting neurons (aug‐E) in brainstem slices of juvenile rats (postnatal day 35). We observed that all presympathetic neurons presented spontaneous action potential firing (n = 18), which was not abolished by ionotropic receptor antagonism. In addition, exposure to 10 days of CIH produced no changes in their intrinsic passive properties, firing pattern or excitability. Most aug‐E neurons presented spontaneous firing in control conditions (13 of 15 neurons), and this characteristic was preserved after blocking fast synaptic transmission (12 of 15 neurons), clearly demonstrating their intrinsic pacemaker activity. Chronic intermittent hypoxia also produced no changes in intrinsic passive properties, frequency and pattern of discharge or excitability of the aug‐E neurons. The present study shows that: (i) it is possible to record the electrophysiological properties of RVLM/BötC presympathetic and aug‐E neurons in brainstem slices from juvenile rats; (ii) these neurons present characteristics of intrinsic pacemakers; and (iii) their intrinsic properties were not altered by chronic intermittent hypoxia.
Fluorescence-Based Quasicontinuous and
In Situ
Monitoring of Biofilm Formation Dynamics in Natural Marine Environments
Authors: Fischer M. , Friedrichs G. , Lachnit T. 
Published: April 2014

ABSTRACT

Analyzing the dynamics of biofilm formation helps to deepen our understanding of surface colonization in natural environments. While methods for screening biofilm formation in the laboratory are well established, studies in marine environments have so far been based upon destructive analysis of individual samples and provide only discontinuous snapshots of biofilm establishment. In order to explore the development of biofilm over time and under various biotic and abiotic conditions, we applied a recently developed optical biofilm sensor to quasicontinuously analyze marine biofilm dynamics
in situ
. Using this technique in combination with microscope-assisted imaging, we investigated biofilm formation from its beginning to mature multispecies biofilms. In contrast to laboratory studies on biofilm formation, a smooth transition from initial attachment to colony formation and exponential growth could not be observed in the marine environment. Instead, initial attachment was followed by an adaptation phase of low growth and homogeneously distributed solitary bacterial cells. Moreover, we observed a diurnal variation of biofilm signal intensity, suggesting a transient state of biofilm formation of bacteria. Overall, the biofilm formation dynamics could be modeled by three consecutive development stages attributed to initial bacterial attachment, bacterial growth, and attachment and growth of unicellular eukaryotic microorganisms. Additional experiments showed that the presence of seaweed considerably shortened the adaptation phase in comparison with that on control surfaces but yielded similar growth rates. The outlined examples highlight the advantages of a quasicontinuous
in situ
detection that enabled, for the first time, the exploration of the initial attachment phase and the diurnal variation during biofilm formation in natural ecosystems.
Bacterial Symbionts of a Devastating Coffee Plant Pest, the Stinkbug Antestiopsis thunbergii (Hemiptera: Pentatomidae)
Authors: Matsuura Yu , Hosokawa Takahiro , Serracin Mario , Tulgetske Genet M. , Miller Thomas A. , Fukatsu Takema 
Published: April 2014

ABSTRACT

Stinkbugs of the genus
Antestiopsis
, so-called antestia bugs or variegated coffee bugs, are notorious pests of coffee plants in Africa. We investigated the symbiotic bacteria associated with
Antestiopsis thunbergii
, a major coffee plant pest in Rwanda. PCR, cloning, sequencing, and phylogenetic analysis of bacterial genes identified four distinct bacterial lineages associated with
A. thunbergii
: a gammaproteobacterial gut symbiont and symbionts representing the genera
Sodalis
,
Spiroplasma
, and
Rickettsia
.
In situ
hybridization showed that the gut symbiont densely occupied the lumen of midgut crypts, whereas the
Sodalis
symbiont, the
Spiroplasma
symbiont, and the
Rickettsia
symbiont sparsely and sporadically infected various cells and tissues. Diagnostic PCR survey of 154
A. thunbergii
individuals collected at 8 localities in Rwanda revealed high infection frequencies (100% for the gut symbiont, 51.3% for the
Sodalis
symbiont, 52.6% for the
Spiroplasma
symbiont, and 24.0% for the
Rickettsia
symbiont). These results suggest that the gut symbiont is the primary symbiotic associate of obligate nature for
A. thunbergii
, whereas the
Sodalis
symbiont, the
Spiroplasma
symbiont, and the
Rickettsia
symbiont are the secondary symbiotic associates of facultative nature. We observed high coinfection frequencies, i.e., 7.8% of individuals with quadruple infection with all the symbionts, 32.5% with triple infections with the gut symbiont and two of the secondary symbionts, and 39.6% with double infections with the gut symbiont and any of the three secondary symbionts, which were statistically not different from the expected coinfection frequencies and probably reflected random associations. The knowledge of symbiotic microbiota in
A. thunbergii
will provide useful background information for controlling this devastating coffee plant pest.
Phosphate Starvation in Fungi Induces the Replacement of Phosphatidylcholine with the Phosphorus-Free Betaine Lipid Diacylglyceryl-
N
,
N
,
N
-Trimethylhomoserine
Authors: Riekhof Wayne R. , Naik Surabhi , Bertrand Helmut , Benning Christoph , Voelker Dennis R. 
Published: April 2014

ABSTRACT

Diacylglyceryl-
N
,
N
,
N
-trimethylhomoserine (DGTS) is a phosphorus-free betaine-lipid analog of phosphatidylcholine (PtdCho) synthesized by many soil bacteria, algae, and nonvascular plants. Synthesis of DGTS and other phosphorus-free lipids in bacteria occurs in response to phosphorus (P) deprivation and results in the replacement of phospholipids by nonphosphorous lipids. The genes encoding DGTS biosynthetic enzymes have previously been identified and characterized in bacteria and the alga
Chlamydomonas reinhardtii
. We now report that many fungal genomes, including those of plant and animal pathogens, encode the enzymatic machinery for DGTS biosynthesis, and that fungi synthesize DGTS during P limitation. This finding demonstrates that replacement of phospholipids by nonphosphorous lipids is a strategy used in divergent eukaryotic lineages for the conservation of P under P-limiting conditions. Mutants of
Neurospora crassa
were used to show that DGTS synthase encoded by the
BTA1
gene is solely responsible for DGTS biosynthesis and is under the control of the fungal phosphorus deprivation regulon, mediated by the NUC-1/Pho4p transcription factor. Furthermore, we describe the rational reengineering of lipid metabolism in the yeast
Saccharomyces cerevisiae
, such that PtdCho is completely replaced by DGTS, and demonstrate that essential processes of membrane biogenesis and organelle assembly are functional and support growth in the engineered strain.
A New Strategy of RNA Interference That Targets Heterologous Sequences Reveals CITFA1 as an Essential Component of Class I Transcription Factor A in Trypanosoma brucei
Authors: Park Sung Hee , Nguyen Bao N. , Kirkham Justin K. , Nguyen Tu N. , Günzl Arthur 
Published: April 2014

ABSTRACT

Conditional gene silencing by RNA interference in
Trypanosoma brucei
can be inconclusive if knockdowns are inefficient or have off-target effects. To enable efficient, specific silencing of single-copy genes in mammalian-infective, bloodstream form trypanosomes, we developed a system that targets the heterologous and functional
Trypanosoma cruzi
U2AF35
3′ untranslated region (UTR) (Tc3) or, alternatively, the sequence of the PTP tag, which can be fused to any mRNA of interest. Two cell lines were created, single-marker Tc3 (smTc3) and smPTP, which conditionally express Tc3 and PTP double-stranded RNA (dsRNA), respectively. The system depends on manipulating both alleles of the gene of interest so that cells exclusively express the target mRNA as a fusion to one of these heterologous sequences. We generated allele integration vectors in which the C-terminal part of a gene's coding sequence can be fused to either heterologous sequence in a single cloning step. We first tested this system with
CITFA7
, which encodes a well-characterized subunit of the class I transcription factor A (CITFA), an essential factor for transcription initiation by RNA polymerase I. Targeting either Tc3 or PTP fused to the
CITFA7
mRNA resulted in gene knockdowns that were as efficient and specific as targeting the endogenous
CITFA7
mRNA. Moreover, application of this system to
CITFA1
, which could not be silenced by established methods, demonstrated that the gene encodes an essential CITFA subunit that mediates binding of the transcription factor complex to RNA polymerase I promoters.
Distinct and Redundant Roles of Protein Tyrosine Phosphatases Ptp1 and Ptp2 in Governing the Differentiation and Pathogenicity of Cryptococcus neoformans
Authors: Lee Kyung-Tae , Byun Hyo-Jeong , Jung Kwang-Woo , Hong Joohyeon , Cheong Eunji , Bahn Yong-Sun 
Published: April 2014

ABSTRACT

Protein tyrosine phosphatases (PTPs) serve as key negative-feedback regulators of mitogen-activated protein kinase (MAPK) signaling cascades. However, their roles and regulatory mechanisms in human fungal pathogens remain elusive. In this study, we characterized the functions of two PTPs, Ptp1 and Ptp2, in
Cryptococcus neoformans
, which causes fatal meningoencephalitis.
PTP1
and
PTP2
were found to be stress-inducible genes, which were controlled by the MAPK Hog1 and the transcription factor Atf1. Ptp2 suppressed the hyperphosphorylation of Hog1 and was involved in mediating vegetative growth, sexual differentiation, stress responses, antifungal drug resistance, and virulence factor regulation through the negative-feedback loop of the HOG pathway. In contrast, Ptp1 was not essential for Hog1 regulation, despite its Hog1-dependent induction. However, in the absence of Ptp2, Ptp1 served as a complementary PTP to control some stress responses. In differentiation, Ptp1 acted as a negative regulator, but in a Hog1- and Cpk1-independent manner. Additionally, Ptp1 and Ptp2 localized to the cytosol but were enriched in the nucleus during the stress response, affecting the transient nuclear localization of Hog1. Finally, Ptp1 and Ptp2 played minor and major roles, respectively, in the virulence of
C. neoformans
. Taken together, our data suggested that PTPs could be exploited as novel antifungal targets.
Histidine Degradation via an Aminotransferase Increases the Nutritional Flexibility of Candida glabrata
Authors: Brunke Sascha , Seider Katja , Richter Martin Ernst , Bremer-Streck Sibylle , Ramachandra Shruthi , Kiehntopf Michael , Brock Matthias , Hube Bernhard 
Published: April 2014

ABSTRACTThe ability to acquire nutrients during infections is an important attribute in microbial pathogenesis. Amino acids are a valuable source of nitrogen if they can be degraded by the infecting organism. In this work, we analyzed histidine utilization in the fungal pathogen of humansCandida glabrata. Hemiascomycete fungi, likeC. glabrataorSaccharomyces cerevisiae, possess no gene coding for a histidine ammonia-lyase, which catalyzes the first step of a major histidine degradation pathway in most other organisms. We show thatC. glabratainstead initializes histidine degradation via the aromatic amino acid aminotransferase Aro8. AlthoughARO8is also present inS. cerevisiaeand is induced by extracellular histidine, the yeast cannot use histidine as its sole nitrogen source, possibly due to growth inhibition by a downstream degradation product. Furthermore,C. glabratarelies only on Aro8 for phenylalanine and tryptophan utilization, sinceARO8, but not its homologueARO9, was transcriptionally activated in the presence of these amino acids. Accordingly, anARO9deletion had no effect on growth with aromatic amino acids. In contrast, inS. cerevisiae,ARO9is strongly induced by tryptophan and is known to support growth on aromatic amino acids. Differences in the genomic structure of theARO9gene betweenC. glabrataandS. cerevisiaeindicate a possible disruption in the regulatory upstream region. Thus, we show that, in contrast toS. cerevisiae,C. glabratahas adapted to use histidine as a sole source of nitrogen and that the aromatic amino acid aminotransferase Aro8, but not Aro9, is the enzyme required for this process.
Arginine Deiminase in Staphylococcus epidermidis Functions To Augment Biofilm Maturation through pH Homeostasis
Authors: Lindgren J. K. , Thomas V. C. , Olson M. E. , Chaudhari S. S. , Nuxoll A. S. , Schaeffer C. R. , Lindgren K. E. , Jones J. , Zimmerman M. C. , Dunman P. M. , Bayles K. W. , Fey P. D. 
Published: April 2014

ABSTRACT

Allelic replacement mutants were constructed within arginine deiminase (
arcA1
and
arcA2
) to assess the function of the arginine deiminase (ADI) pathway in organic acid resistance and biofilm formation of
Staphylococcus epidermidis
1457. A growth-dependent acidification assay (pH ∼5.0 to ∼5.2) determined that strain 1457 devoid of arginine deiminase activity (1457 ΔADI) was significantly less viable than the wild type following depletion of glucose and in the presence of arginine. However, no difference in viability was noted for individual 1457 Δ
arcA1
(native) or Δ
arcA2
(arginine catabolic mobile element [ACME]-derived) mutants, suggesting that the native and ACME-derived ADIs are compensatory in
S. epidermidis
. Furthermore, flow cytometry and electron paramagnetic resonance spectroscopy results suggested that organic acid stress resulted in oxidative stress that could be partially rescued by the iron chelator dipyridyl. Collectively, these results suggest that formation of hydroxyl radicals is partially responsible for cell death via organic acid stress and that ADI-derived ammonia functions to counteract this acid stress. Finally, static biofilm assays determined that viability, ammonia synthesis, and pH were reduced in strain 1457 ΔADI following 120 h of growth in comparison to strain 1457 and the
arcA1
and
arcA2
single mutants. It is hypothesized that ammonia synthesis via the ADI pathway is important to reduce pH stress in specific microniches that contain high concentrations of organic acids.
Involvement of
rppH
in Thermoregulation in Pseudomonas syringae
Authors: Hockett Kevin L. , Ionescu Michael , Lindow Steven E. 
Published: April 2014

ABSTRACT

Temperature, among other environmental factors, influences the incidence and severity of many plant diseases. Likewise, numerous traits, including the expression of virulence factors, are regulated by temperature. Little is known about the underlying genetic determinants of thermoregulation in plant-pathogenic bacteria. Previously, we showed that the expression of both
fliC
(encoding flagellin) and
syfA
(encoding a nonribosomal polypeptide synthetase) was suppressed at high temperatures in
Pseudomonas syringae
. In this work, we used a high-throughput screen to identify mutations that conferred overexpression of
syfA
at elevated temperatures (28°C compared to 20°C). Two genes, Psyr_2474, encoding an acyl-coenzyme A (CoA) dehydrogenase, and Psyr_4843, encoding an ortholog of RppH, which in
Escherichia coli
mediates RNA turnover, contribute to thermoregulation of
syfA
. To assess the global role of
rppH
in thermoregulation in
P. syringae
, RNA sequencing was used to compare the transcriptomes of an
rppH
deletion mutant and the wild-type strain incubated at 20°C and 30°C. The disruption of
rppH
had a large effect on the temperature-dependent transcriptome of
P. syringae
, affecting the expression of 569 genes at either 20°C or 30°C but not at both temperatures. Intriguingly, RppH is involved in the thermoregulation of ribosome-associated proteins, as well as of RNase E, suggesting a prominent role of
rppH
on the proteome in addition to its effect on the transcriptome.