bluuebunny/crossref_metadata_2025_split huggingface dataset:
High‐dose chemotherapy followed by autologous peripheral blood stem cell transplantation for recurrent primary mediastinal malignant germ cell tumor: A case report
Authors: Keino Dai , Kondoh Kensuke , Murata Shunsuke , Ohyama Ryo , Morimoto Mizuho , Muto Shinji , Fukuda Miho , Wakisaka Munechika , Kitagawa Hiroaki , Kinoshita Akitoshi 
Published: December 2013

AbstractA 15‐yr‐old boy presented with an anterior mediastinal mass, multiple lung metastases and obstruction of the left brachiocephalic vein, the superior vena cava and the subclavian vein. Tumor biopsy by CT guidance confirmed a diagnosis of GCT. Five courses of BEP therapy were performed, and CT of the chest revealed reduction in the anterior mediastinal mass and disappearance of the multiple lung metastases. We performed the anterior mediastinal mass extraction followed by adjuvant chemotherapy consisting of ICE and TIP. However, the AFP levels became elevated soon after. Abnormal accumulation was observed in the right upper lung by DW‐MRI. After the operation, two courses of TI chemotherapy and two courses of HDCT followed by auto‐PBSCT were performed. He was complicated with auditory disorder and renal dysfunction. Although HDCT followed by auto‐PBSCT was effective for the relapsed primary mediastinal GCT, a treatment strategy avoiding late complications is warranted.
Intestinal transplantation in children with multiple intestinal atresias and immunodeficiency
Authors: Fischer Ryan T. , Friend Brian , Talmon Geoffrey A. , Grant Wendy J. , Quiros‐Tejeira Ruben E. , Langnas Alan N. , Coccia Peter F. 
Published: December 2013

AbstractGVHD has been reported in 8–10% of children after small bowel transplant (SBTx). Immunodeficient children may be predisposed to aggressive, steroid‐resistant GVHD. There exists a unique association of immunodeficiency in children with MIA (MIAI). We report on our SBTx experience in patients with the diagnosis of MIAI, their high incidence of GVHD, and the possible role of stem cell transplantation in these patients. We performed a review of records from children that underwent SBTx or that we evaluated for SBTx at our institution. We focused on the diagnoses of atresia, multiple intestinal atresia, immunodeficiency, and GVHD in our patient population. Children with MIAI are likely to experience severe GVHD following SBTx. MIAI correlated with a 100% incidence of GVHD in these patients. Of the five patients with MIAI that underwent SBTx, three succumbed to severe GVHD within 1–6 months after SBTx. One patient received stem cell transplant prior to SBTx and did not develop severe GVHD, but died from influenza nine months after SBTx. Our unique patient survives long‐term, with engraftment of donor γ δ T cells. He has mild, persistent chronic GVHD. Atresia is a common referral diagnosis for SBTx. Patients with multiple atresias, especially MIAI, are at significant risk for the complication of GVHD following SBTx. We recommend careful immunologic assessment and antecedent stem cell transplant in children with MIAI prior to SBTx.
p‐Coumaroyl‐CoA:monolignol transferase (PMT) acts specifically in the lignin biosynthetic pathway in Brachypodium distachyon
Authors: Petrik Deborah L. , Karlen Steven D. , Cass Cynthia L. , Padmakshan Dharshana , Lu Fachuang , Liu Sarah , Le Bris Philippe , Antelme Sébastien , Santoro Nicholas , Wilkerson Curtis G. , Sibout Richard , Lapierre Catherine , Ralph John , Sedbrook John C. 
Published: December 2013

SummaryGrass lignins contain substantial amounts of p‐coumarate (pCA) that acylate the side‐chains of the phenylpropanoid polymer backbone. An acyltransferase, named p‐coumaroyl‐CoA:monolignol transferase (OsPMT), that could acylate monolignols with pCA in vitro was recently identified from rice. In planta, such monolignol‐pCA conjugates become incorporated into lignin via oxidative radical coupling, thereby generating the observed pCA appendages; however p‐coumarates also acylate arabinoxylans in grasses. To test the authenticity of PMT as a lignin biosynthetic pathway enzyme, we examined Brachypodium distachyon plants with altered BdPMT gene function. Using newly developed cell wall analytical methods, we determined that the transferase was involved specifically in monolignol acylation. A sodium azide‐generated Bdpmt‐1 missense mutant had no (<0.5%) residual pCA on lignin, and BdPMT RNAi plants had levels as low as 10% of wild‐type, whereas the amounts of pCA acylating arabinosyl units on arabinoxylans in these PMT mutant plants remained unchanged. pCA acylation of lignin from BdPMT‐overexpressing plants was found to be more than three‐fold higher than that of wild‐type, but again the level on arabinosyl units remained unchanged. Taken together, these data are consistent with a defined role for grass PMT genes in encoding BAHD (BEAT, AHCT, HCBT, and DAT) acyltransferases that specifically acylate monolignols with pCA and produce monolignol p‐coumarate conjugates that are used for lignification in planta.
Prevalence and Pathogenic Potential of Campylobacter Isolates from Free-Living, Human-Commensal American Crows
Authors: Weis Allison M. , Miller Woutrina A. , Byrne Barbara A. , Chouicha Nadira , Boyce Walter M. , Townsend Andrea K. 
Published: December 2013

ABSTRACTRecent studies have suggested a potential role for wild birds in zoonotic transmission ofCampylobacter jejuni, the leading cause of gastroenteritis in humans worldwide. In this study, we detectedCampylobacterspp. in 66.9% (85/127) of free-ranging American crows (Corvus brachyrhyncos) sampled in the Sacramento Valley of California in 2012 and 2013. Biochemical testing and sequence analysis of 16S rRNA revealed that 93% of isolates (n= 70) wereC. jejuni, with cytolethal distending toxin (CDT) and flagellin A genes detected by PCR in 20% and 46% of theC. jejuniisolates (n= 59), respectively. The high prevalence ofC. jejuni, coupled with the occurrence of known virulence markers CDT and flagellin A, demonstrates that crows shedCampylobacterspp. in their feces that are potentially pathogenic to humans. Crows are abundant in urban, suburban, and agricultural settings, and thus further study to determine their role in zoonotic transmission ofCampylobacterwill inform public health.
Multistrain Probiotic Modulation of Intestinal Epithelial Cells' Immune Response to a Double-Stranded RNA Ligand, Poly(I·C)
Authors: MacPherson Chad , Audy Julie , Mathieu Olivier , Tompkins Thomas A. 
Published: December 2013

ABSTRACT

A commercially available product containing three probiotic bacterial strains (
Lactobacillus helveticus
R0052,
Bifidobacterium longum
subsp.
infantis
R0033, and
Bifidobacterium bifidum
R0071) was previously shown in animal trials to modulate both T
H
1 and T
H
2 immune responses. Clinical studies on this combination of bacteria have also shown positive health effects against seasonal winter diseases and rotavirus infection. The goal of this study was to use a well-established
in vitro
intestinal epithelial (HT-29) cell model that has been shown to constitutively express double-stranded RNA (dsRNA) sensors (Toll-like receptor 3 [TLR3], retinoic acid-inducible gene I, melanoma differentiation-associated gene 5, and dsRNA-activated protein kinase). By using the HT-29 cell model, we wanted to evaluate whether or not this combination of three bacteria had the capacity to immune modulate the host cell response to a dsRNA ligand, poly(I·C). Using a custom-designed, two-color expression microarray targeting genes of the human immune system, we investigated the response of HT-29 cells challenged with poly(I·C) both in the presence and in the absence of the three probiotic bacteria. We observed that the combination of the three bacteria had a major impact on attenuating the expression of genes connected to proinflammatory T
H
1 and antiviral innate immune responses compared to that obtained by the poly(I·C)-only challenge. Major pathways through which the multistrain combination may be eliciting its immune-modulatory effect include the TLR3 domain-containing adapter-inducing beta interferon (TRIF), mitogen-activated protein kinase, and NF-κB signaling pathways. Such a model may be useful for selecting potential biomarkers for the design of future clinical trials.
High-Yield, Zero-Leakage Expression System with a Translational Switch Using Site-Specific Unnatural Amino Acid Incorporation
Authors: Minaba Masaomi , Kato Yusuke 
Published: December 2013

ABSTRACT

Synthetic biologists construct complex biological circuits by combinations of various genetic parts. Many genetic parts that are orthogonal to one another and are independent of existing cellular processes would be ideal for use in synthetic biology. However, our toolbox is still limited with respect to the bacterium
Escherichia coli
, which is important for both research and industrial use. The site-specific incorporation of unnatural amino acids is a technique that incorporates unnatural amino acids into proteins using a modified exogenous aminoacyl-tRNA synthetase/tRNA pair that is orthogonal to any native pairs in a host and is independent from other cellular functions. Focusing on the orthogonality and independency that are suitable for the genetic parts, we designed novel AND gate and translational switches using the unnatural amino acid 3-iodo-
l
-tyrosine incorporation system in
E. coli
. A translational switch was turned on after addition of 3-iodo-
l
-tyrosine in the culture medium within minutes and allowed tuning of switchability and translational efficiency. As an application, we also constructed a gene expression system that produced large amounts of proteins under induction conditions and exhibited zero-leakage expression under repression conditions. Similar translational switches are expected to be applicable also for eukaryotes such as yeasts, nematodes, insects, mammalian cells, and plants.
Molecular Characterization of a Novel
N
-Acetyltransferase from Chryseobacterium sp
Authors: Takenaka Shinji , Yoshida Kenji , Tanaka Kosei , Yoshida Ken-ichi 
Published: December 2013

ABSTRACT

N
-Acetyltransferase from
Chryseobacterium
sp. strain 5-3B is an acetyl coenzyme A (acetyl-CoA)-dependent enzyme that catalyzes the enantioselective transfer of an acetyl group from acetyl-CoA to the amino group of
l
-2-phenylglycine to produce (2
S
)-2-acetylamino-2-phenylacetic acid. We purified the enzyme from strain 5-3B and deduced the N-terminal amino acid sequence. The gene, designated
natA
, was cloned with two other hypothetical protein genes; the three genes probably form a 2.5-kb operon. The deduced amino acid sequence of NatA showed high levels of identity to sequences of putative
N
-acetyltransferases of
Chryseobacterium
spp. but not to other known arylamine and arylalkylamine
N
-acetyltransferases. Phylogenetic analysis indicated that NatA forms a distinct lineage from known
N
-acetyltransferases. We heterologously expressed recombinant NatA (rNatA) in
Escherichia coli
and purified it. rNatA showed high activity for
l
-2-phenylglycine and its chloro- and hydroxyl-derivatives. The

K
m

and
V
max
values for
l
-2-phenylglycine were 0.145 ± 0.026 mM and 43.6 ± 2.39 μmol · min
−1
· mg protein
−1
, respectively. The enzyme showed low activity for 5-aminosalicylic acid and 5-hydroxytryptamine, which are reported as good substrates of a known arylamine
N
-acetyltransferase and an arylalkylamine
N
-acetyltransferase. rNatA had a comparatively broad acyl donor specificity, transferring acyl groups to
l
-2-phenylglycine and producing the corresponding 2-acetylamino-2-phenylacetic acids (relative activity with acetyl donors acetyl-CoA, propanoyl-CoA, butanoyl-CoA, pentanoyl-CoA, and hexanoyl-CoA, 100:108:122:10:<1).
Active Ammonia Oxidizers in an Acidic Soil Are Phylogenetically Closely Related to Neutrophilic Archaeon
Authors: Wang Baozhan , Zheng Yan , Huang Rong , Zhou Xue , Wang Dongmei , He Yuanqiu , Jia Zhongjun 
Published: December 2013

ABSTRACT

All cultivated ammonia-oxidizing archaea (AOA) within the
Nitrososphaera
cluster (former soil group 1.1b) are neutrophilic. Molecular surveys also indicate the existence of
Nitrososphaera
-like phylotypes in acidic soil, but their ecological roles are poorly understood. In this study, we present molecular evidence for the chemolithoautotrophic growth of
Nitrososphaera
-like AOA in an acidic soil with pH 4.92 using DNA-based stable isotope probing (SIP). Soil microcosm incubations demonstrated that nitrification was stimulated by urea fertilization and accompanied by a significant increase in the abundance of AOA rather than ammonia-oxidizing bacteria (AOB). Real-time PCR analysis of
amoA
genes as a function of the buoyant density of the DNA gradient following the ultracentrifugation of the total DNA extracted from SIP microcosms indicated a substantial growth of soil AOA during nitrification. Pyrosequencing of the total 16S rRNA genes in the “heavy” DNA fractions suggested that archaeal communities were labeled to a much greater extent than soil AOB. Acetylene inhibition further showed that
13
CO
2
assimilation by nitrifying communities depended solely on ammonia oxidation activity, suggesting a chemolithoautotrophic lifestyle. Phylogenetic analysis of both
13
C-labeled
amoA
and 16S rRNA genes revealed that most of the active AOA were phylogenetically closely related to the neutrophilic strains
Nitrososphaera viennensis
EN76 and JG1 within the
Nitrososphaera
cluster. Our results provide strong evidence for the adaptive growth of
Nitrososphaera
-like AOA in acidic soil, suggesting a greater metabolic versatility of soil AOA than previously appreciated.
Identification and Upregulation of Biosynthetic Genes Required for Accumulation of Mycosporine-2-Glycine under Salt Stress Conditions in the Halotolerant Cyanobacterium Aphanothece halophytica
Authors: Waditee-Sirisattha Rungaroon , Kageyama Hakuto , Sopun Warangkana , Tanaka Yoshito , Takabe Teruhiro 
Published: December 2013

ABSTRACT

Mycosporine-like amino acids (MAAs) are valuable molecules that are the basis for important photoprotective constituents. Here we report molecular analysis of mycosporine-like amino acid biosynthetic genes from the halotolerant cyanobacterium
Aphanothece halophytica
, which can survive at high salinity and alkaline pH. This extremophile was found to have a unique MAA core (4-deoxygadusol)-synthesizing gene separated from three other genes.
In vivo
analysis showed accumulation of the mycosporine-2-glycine but not shinorine or mycosporine-glycine. Mycosporine-2-glycine accumulation was stimulated more under the stress condition of high salinity than UV-B radiation. The
Aphanothece
MAA biosynthetic genes also manifested a strong transcript level response to salt stress. Furthermore, the transformed
Escherichia coli
and
Synechococcus
strains expressing four putative
Aphanothece
MAA genes under the control of a native promoter were found to be capable of synthesizing mycosporine-2-glycine. The accumulation level of mycosporine-2-glycine was again higher under the high-salinity condition. In the transformed
E. coli
cells, its level was approximately 85.2 ± 0.7 μmol/g (dry weight). Successful production of a large amount of mycosporine in these cells provides a new opportunity in the search for an alternative natural sunscreen compound source.
Accumulation of Polyphosphate in Lactobacillus spp. and Its Involvement in Stress Resistance
Authors: Alcántara Cristina , Blasco Amalia , Zúñiga Manuel , Monedero Vicente 
Published: December 2013

ABSTRACT

Polyphosphate (poly-P) is a polymer of phosphate residues synthesized and in some cases accumulated by microorganisms, where it plays crucial physiological roles such as the participation in the response to nutritional stringencies and environmental stresses. Poly-P metabolism has received little attention in
Lactobacillus
, a genus of lactic acid bacteria of relevance for food production and health of humans and animals. We show that among 34 strains of
Lactobacillus
, 18 of them accumulated intracellular poly-P granules, as revealed by specific staining and electron microscopy. Poly-P accumulation was generally dependent on the presence of elevated phosphate concentrations in the culture medium, and it correlated with the presence of polyphosphate kinase (
ppk
) genes in the genomes. The
ppk
gene from
Lactobacillus
displayed a genetic arrangement in which it was flanked by two genes encoding exopolyphosphatases of the Ppx-GppA family. The
ppk
functionality was corroborated by its disruption (LCABL_27820 gene) in
Lactobacillus casei
BL23 strain. The constructed
ppk
mutant showed a lack of intracellular poly-P granules and a drastic reduction in poly-P synthesis. Resistance to several stresses was tested in the
ppk
-disrupted strain, showing that it presented a diminished growth under high-salt or low-pH conditions and an increased sensitivity to oxidative stress. These results show that poly-P accumulation is a characteristic of some strains of lactobacilli and may thus play important roles in the physiology of these microorganisms.
FigA, a Putative Homolog of Low-Affinity Calcium System Member Fig1 in Saccharomyces cerevisiae, Is Involved in Growth and Asexual and Sexual Development in Aspergillus nidulans
Authors: Zhang Shizhu , Zheng Hailin , Long Nanbiao , Carbó Natalia , Chen Peiying , Aguilar Pablo S. , Lu Ling 
Published: December 2013

ABSTRACT

Calcium-mediated signaling pathways are widely employed in eukaryotes and are implicated in the regulation of diverse biological processes. In
Saccharomyces cerevisiae
, at least two different calcium uptake systems have been identified: the high-affinity calcium influx system (HACS) and the low-affinity calcium influx system (LACS). Compared to the HACS, the LACS in fungi is not well known. In this study, FigA, a homolog of the LACS member Fig1 from
S. cerevisiae
, was functionally characterized in the filamentous fungus
Aspergillus nidulans
. Loss of
figA
resulted in retardant hyphal growth and a sharp reduction of conidial production. Most importantly, FigA is essential for the homothallic mating (self-fertilization) process; further, FigA is required for heterothallic mating (outcrossing) in the absence of HACS
midA
. Interestingly, in a
figA
deletion mutant, adding extracellular Ca
2+
rescued the hyphal growth defects but could not restore asexual and sexual reproduction. Furthermore, quantitative PCR results revealed that
figA
deletion sharply decreased the expression of
brlA
and
nsdD
, which are known as key regulators during asexual and sexual development, respectively. In addition, green fluorescent protein (GFP) tagging at the C terminus of FigA (FigA::GFP) showed that FigA localized to the center of the septum in mature hyphal cells, to the location between vesicles and metulae, and between the junctions of metulae and phialides in conidiophores. Thus, our findings suggest that FigA, apart from being a member of a calcium uptake system in
A. nidulans
, may play multiple unexplored roles during hyphal growth and asexual and sexual development.
Solanesyl Diphosphate Synthase, an Enzyme of the Ubiquinone Synthetic Pathway, Is Required throughout the Life Cycle of Trypanosoma brucei
Authors: Lai De-Hua , Poropat Estefanía , Pravia Carlos , Landoni Malena , Couto Alicia S. , Pérez Rojo Fernando G. , Fuchs Alicia G. , Dubin Marta , Elingold Igal , Rodríguez Juan B. , Ferella Marcela , Esteva Mónica I. , Bontempi Esteban J. , Lukeš Julius 
Published: December 2013

ABSTRACT

Ubiquinone 9 (UQ9), the expected product of the long-chain solanesyl diphosphate synthase of
Trypanosoma brucei
(TbSPPS), has a central role in reoxidation of reducing equivalents in the mitochondrion of
T. brucei
. The ablation of TbSPPS gene expression by RNA interference increased the generation of reactive oxygen species and reduced cell growth and oxygen consumption. The addition of glycerol to the culture medium exacerbated the phenotype by blocking its endogenous generation and excretion. The participation of TbSPPS in UQ synthesis was further confirmed by growth rescue using UQ with 10 isoprenyl subunits (UQ10). Furthermore, the survival of infected mice was prolonged upon the downregulation of TbSPPS and/or the addition of glycerol to drinking water. TbSPPS is inhibited by 1-[(
n
-oct-1-ylamino)ethyl] 1,1-bisphosphonic acid, and treatment with this compound was lethal for the cells. The findings that both UQ9 and ATP pools were severely depleted by the drug and that exogenous UQ10 was able to fully rescue growth of the inhibited parasites strongly suggest that TbSPPS and UQ synthesis are the main targets of the drug. These two strategies highlight the importance of TbSPPS for
T. brucei
, justifying further efforts to validate it as a new drug target.
A preliminary evaluation of the effects of opioids on innate and adaptive human in vitro immune function
Authors: Boland Jason W , Foulds Gemma A , Ahmedzai Sam H , Pockley A Graham 
Published: December 2013

BackgroundStudies have demonstrated that whereas some opioids have little effect on immunity (eg, buprenorphine), others can be immunosuppressive (eg, morphine) or immunostimulatory (eg, tramadol). However, a variety of approaches have been used, especially in vitro and animal models, and the findings are variable. We hypothesised that opioids have differential effects on immunity via direct actions on neutrophils, monocytes, natural killer (NK) and T cells, and this is the first study to systematically evaluate the influence of eight opioids on neutrophil and monocyte phagocytosis and oxidative burst responses, NK cell cytotoxicity and T cell responsiveness in vitro.MethodsPeripheral blood was obtained from healthy volunteers, and the effects of clinically relevant concentrations of morphine, tramadol, fentanyl, buprenorphine, methadone, oxycodone, diamorphine and codeine on phagocytosis and oxidative burst responses were determined using whole blood flow cytometry. The influence of opioids on the capacity of resting and IL-2 stimulated isolated peripheral blood mononuclear cells (PBMCs) to kill NK cell-sensitive K562 cells, and the responsiveness of PBMC subpopulations to IL-2 and polyclonal stimulation were also evaluated.ResultsMethadone, oxycodone and diamorphine inhibited the production of IL-6 by IL-2 stimulated PBMCs. None of the opioids consistently influenced the other measured immune parameters, although there was a trend for morphine, tramadol, fentanyl and buprenorphine to inhibit phagocytosis and oxidative burst responses toEscherichia coli.ConclusionsPreliminary studies using standardised in vitro methodologies have demonstrated that some therapeutic opioids suppress IL-6 production. Although this might potentially suppress bacterial defence mechanisms, it would have little direct effect on anticancer immunity. These findings should be confirmed in larger in vitro and clinical studies.