bluuebunny/crossref_metadata_2025 huggingface dataset:
Nocardioides

salsibiostraticola sp. nov., isolated from biofilm formed in coastal seawater
Authors: Cho Yirang , Jang Gwang Il , Hwang Chung Yeon , Kim Eun-Hye , Cho Byung Cheol
Published: May 2013

A Gram-staining-positive, non-motile, aerobic, non-spore-forming and short rod-shaped bacterial strain, PAMC 26527T, was isolated from biofilm formed in coastal seawater of the Norwegian Sea. Analysis of the 16S rRNA gene sequence of strain PAMC 26527T revealed a clear affiliation with the genus

Nocardioides

. Based on phylogenetic analysis, strain PAMC 26527T showed the closest phylogenetic relationship with

Nocardioides caricicola

YC6903T with 16S rRNA gene sequence similarity of 96.3 %. Strain PAMC 26527T grew in the presence of 0–5.0 % sea salts. The optimum temperature and pH for growth were 20 °C and pH 7.5. The major cellular fatty acids of strain PAMC 26527T were iso-C16 : 0, C17 : 1ω8c and C18 : 1ω9c and the major isoprenoid quinone was MK-8(H4). Cell-wall analysis showed that strain PAMC 26527T contained ll-diaminopimelic acid. The genomic DNA G+C content was 69.3 mol%. The combined phenotypic, chemotaxonomic and phylogenetic data showed that strain PAMC 26527T could be clearly distinguished from recognized members of the genus

Nocardioides

. Thus, strain PAMC 26527T should be classified as representing a novel species in the genus

Nocardioides

, for which the name

Nocardioides

salsibiostraticola sp. nov. is proposed. The type strain is PAMC 26527T ( = KCTC 29158T = JCM 18743T).
Dyella

kyungheensis sp. nov., isolated from soil of a cornus fruit field
Authors: Son Heung-Min , Yang Jung-Eun , Yi Eun-Ji , Park YongJin , Won Kyung-Hwa , Kim Ju-Han , Han Chang-Kyun , Kook MooChang , Yi Tae-Hoo
Published: May 2013

A Gram-reaction-negative, aerobic, motile by one polar flagellum, yellow-pigmented, rod-shaped bacterium, designated strain THG-B117T, was isolated from soil of a cornus fruit field of Hoengseong province in South Korea and its taxonomic position was investigated by a polyphasic study. Strain THG-B117T grew well at 25–30 °C and at pH 6.0–8.0 in the absence of NaCl on nutrient agar. On the basis of 16S rRNA gene sequence similarity, strain THG-B117T was shown to belong to the family

Xanthomonadaceae

and be related to

Dyella japonica

XD53T (98.7 % similarity),

Dyella terrae

JS14-6T (98.0 %),

Dyella koreensis

BB4T (96.9 %),

Dyella soli

JS12-10T (96.9 %) and

Dyella thiooxydans

ATSB10T (96.7 %). DNA–DNA hybridization experiments showed that DNA relatedness between strain THG-B117T and its phylogenetically closest neighbours was below 45.1 %. The G+C content of the genomic DNA of strain THG-B117T was 64.8 mol%. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, diphosphatidylglycerol, unidentified aminolipids, unidentified aminophospholipids and unidentified phospholipids. Phenotypic and chemotaxonomic data (major ubiquinone was Q-8, and major fatty acids were iso-C15 : 0, iso-C16 : 0, iso-C17 : 0 and iso-C17 : 1ω9c) supported the affiliation of strain THG-B117T with the genus

Dyella

. The results of physiological and biochemical tests suggested that strain THG-B117T was different genotypically and phenotypically from recognized species of the genus

Dyella

, and represents a novel species of this genus. The name

Dyella

kyungheensis sp. nov. is proposed, with the type strain THG-B117T ( = KACC 16981T = JCM 18747T).
Micromonospora

schwarzwaldensis sp. nov., a producer of telomycin, isolated from soil
Authors: Gurovic Maria Soledad Vela , Müller Sebastian , Domin Nicole , Seccareccia Ivana , Nietzsche Sandor , Martin Karin , Nett Markus
Published: May 2013

A Gram-stain-positive, spore-forming actinomycete strain (HKI0641T) was isolated from a soil sample collected in the Black Forest, Germany. During screening for antimicrobial natural products this bacterium was identified as a producer of the antibiotic telomycin. Morphological characteristics and chemotaxonomic data indicated that the strain belonged to the genus

Micromonospora

. The peptidoglycan of strain HKI0641T contained meso-diaminopimelic acid, and the fatty acid profile consisted predominantly of anteiso-C15 : 0, iso-C15 : 0, iso-C16 : 0 and C16 : 0. MK-10(H4), MK-10(H2) and MK-10 were identified as the major menaquinones. To determine the taxonomic positioning of strain HKI0641T, we computed a binary tanglegram of two rooted phylogenetic trees that were based upon 16S rRNA and gyrB gene sequences. The comparative analysis of the two common classification methods strongly supported the phylogenetic affiliation with the genus

Micromonospora

, but it also revealed discrepancies in the assignment at the level of the genomic species. 16S rRNA gene sequence analysis identified

Micromonospora coxensis

DSM 45161T (99.1 % sequence similarity) and

Micromonospora marina

DSM 45555T (99.0 %) as the nearest taxonomic neighbours, whereas the gyrB sequence of strain HKI0641T indicated a closer relationship to

Micromonospora aurantiaca

DSM 43813T (95.1 %). By means of DNA–DNA hybridization experiments, it was possible to resolve this issue and to clearly differentiate strain HKI0641T from other species of the genus

Micromonospora

. The type strains of the aforementioned species of the genus

Micromonospora

could be further distinguished from strain HKI0641T by several phenotypic properties, such as colony colour, NaCl tolerance and the utilization of carbon sources. The isolate was therefore assigned to a novel species of the genus

Micromonospora

, for which the name

Micromonospora

schwarzwaldensis sp. nov. is proposed. The type strain is HKI0641T ( = DSM 45708T = CIP 110415T).
Dual function of the McaS small RNA in controlling biofilm formation
Authors: Jørgensen Mikkel Girke , Thomason Maureen K. , Havelund Johannes , Valentin-Hansen Poul , Storz Gisela
Published: May 2013

Many bacterial small RNAs (sRNAs) regulate gene expression through base-pairing with mRNAs, and it has been assumed that these sRNAs act solely by this one mechanism. Here we report that the multicellular adhesive (McaS) sRNA of Escherichia coli uniquely acts by two different mechanisms: base-pairing and protein titration. Previous work established that McaS base pairs with the mRNAs encoding master transcription regulators of curli and flagella synthesis, respectively, resulting in down-regulation and up-regulation of these important cell surface structures. In this study, we demonstrate that McaS activates synthesis of the exopolysaccharide β-1,6 N-acetyl-D-glucosamine (PGA) by binding the global RNA-binding protein CsrA, a negative regulator of pgaA translation. The McaS RNA bears at least two CsrA-binding sequences, and inactivation of these sites compromises CsrA binding, PGA regulation, and biofilm formation. Moreover, ectopic McaS expression leads to induction of two additional CsrA-repressed genes encoding diguanylate cyclases. Collectively, our study shows that McaS is a dual-function sRNA with roles in the two major post-transcriptional regulons controlled by the RNA-binding proteins Hfq and CsrA.
Human ALKBH7 is required for alkylation and oxidation-induced programmed necrosis
Authors: Fu Dragony , Jordan Jennifer J. , Samson Leona D.
Published: May 2013

Programmed necrosis has emerged as a crucial modulator of cell death in response to several forms of cellular stress. In one form of programmed necrotic cell death, induced by cytotoxic alkylating agents, hyperactivation of poly-ADP-ribose polymerase (PARP) leads to cellular NAD and ATP depletion, mitochondrial dysfunction, reactive oxygen species formation, and ensuing cell death. Here, we show that the protein encoded by the human AlkB homolog 7 (ALKBH7) gene plays a pivotal role in DNA-damaging agent-induced programmed necrosis by triggering the collapse of mitochondrial membrane potential and large-scale loss of mitochondrial function that lead to energy depletion and cellular demise. Depletion of ALKBH7 suppresses necrotic cell death induced by numerous alkylating and oxidizing agents while having no effect on apoptotic cell death. Like wild-type cells, ALKBH7-depleted cells undergo PARP hyperactivation and NAD depletion after severe DNA damage but, unlike wild-type cells, exhibit rapid recovery of intracellular NAD and ATP levels. Consistent with the recovery of cellular bioenergetics, ALKBH7-depleted cells maintain their mitochondrial membrane potential, plasma membrane integrity, and viability. Our results uncover a novel role for a mammalian AlkB homolog in programmed necrosis, presenting a new target for therapeutic intervention in cancer cells that are resistant to apoptotic cell death.
Molecular antagonism between X-chromosome and autosome signals determines nematode sex
Authors: Farboud Behnom , Nix Paola , Jow Margaret M. , Gladden John M. , Meyer Barbara J.
Published: May 2013

Sex is determined in Caenorhabditis elegans by the ratio of X chromosomes to the sets of autosomes, the X:A signal. A set of genes called X signal elements (XSEs) communicates X-chromosome dose by repressing the masculinizing sex determination switch gene xol-1 (XO lethal) in a dose-dependent manner. xol-1 is active in 1X:2A embryos (males) but repressed in 2X:2A embryos (hermaphrodites). Here we showed that the autosome dose is communicated by a set of autosomal signal elements (ASEs) that act in a cumulative, dose-dependent manner to counter XSEs by stimulating xol-1 transcription. We identified new ASEs and explored the biochemical basis by which ASEs antagonize XSEs to determine sex. Multiple antagonistic molecular interactions carried out on a single promoter explain how different X:A values elicit different sexual fates. XSEs (nuclear receptors and homeodomain proteins) and ASEs (T-box and zinc finger proteins) bind directly to several sites on xol-1 to counteract each other's activities and thereby regulate xol-1 transcription. Disrupting ASE- and XSE-binding sites in vivo recapitulated the misregulation of xol-1 transcription caused by disrupting cognate signal element genes. XSE- and ASE-binding sites are distinct and nonoverlapping, suggesting that direct competition for xol-1 binding is not how XSEs counter ASEs. Instead, XSEs likely antagonize ASEs by recruiting cofactors with reciprocal activities that induce opposite transcriptional states. Most ASE- and XSE-binding sites overlap xol-1's −1 nucleosome, which carries activating chromatin marks only when xol-1 is turned on. Coactivators and corepressors tethered by proteins similar to ASEs and XSEs are known to deposit and remove such marks. The concept of a sex signal comprising competing XSEs and ASEs arose as a theory for fruit flies a century ago. Ironically, while the recent work of others showed that the fly sex signal does not fit this simple paradigm, our work shows that the worm signal does.
Advanced Proteomic Analyses Yield a Deep Catalog of Ubiquitylation Targets in Arabidopsis
Authors: Kim Do-Young , Scalf Mark , Smith Lloyd M. , Vierstra Richard D.
Published: May 2013

The posttranslational addition of ubiquitin (Ub) profoundly controls the half-life, interactions, and/or trafficking of numerous intracellular proteins. Using stringent two-step affinity methods to purify Ub-protein conjugates followed by high-sensitivity mass spectrometry, we identified almost 950 ubiquitylation substrates in whole Arabidopsis thaliana seedlings. The list includes key factors regulating a wide range of biological processes, including metabolism, cellular transport, signal transduction, transcription, RNA biology, translation, and proteolysis. The ubiquitylation state of more than half of the targets increased after treating seedlings with the proteasome inhibitor MG132 (carbobenzoxy-Leu-Leu-Leu-al), strongly suggesting that Ub addition commits many to degradation by the 26S proteasome. Ub-attachment sites were resolved for a number of targets, including six of the seven Lys residues on Ub itself with a Lys-48>Lys-63>Lys-11>>>Lys-33/Lys-29/Lys-6 preference. However, little sequence consensus was detected among conjugation sites, indicating that the local environment has little influence on global ubiquitylation. Intriguingly, the level of Lys-11–linked Ub polymers increased substantially upon MG132 treatment, revealing that they might be important signals for proteasomal breakdown. Taken together, this proteomic analysis illustrates the breadth of plant processes affected by ubiquitylation and provides a deep data set of individual targets from which to explore the roles of Ub in various physiological and developmental pathways.
The α/β Hydrolase CGI-58 and Peroxisomal Transport Protein PXA1 Coregulate Lipid Homeostasis and Signaling in Arabidopsis
Authors: Park Sunjung , Gidda Satinder K. , James Christopher N. , Horn Patrick J. , Khuu Nicholas , Seay Damien C. , Keereetaweep Jantana , Chapman Kent D. , Mullen Robert T. , Dyer John M.
Published: May 2013

COMPARATIVE GENE IDENTIFICATION-58 (CGI-58) is a key regulator of lipid metabolism and signaling in mammals, but its underlying mechanisms are unclear. Disruption of CGI-58 in either mammals or plants results in a significant increase in triacylglycerol (TAG), suggesting that CGI-58 activity is evolutionarily conserved. However, plants lack proteins that are important for CGI-58 activity in mammals. Here, we demonstrate that CGI-58 functions by interacting with the PEROXISOMAL ABC-TRANSPORTER1 (PXA1), a protein that transports a variety of substrates into peroxisomes for their subsequent metabolism by β-oxidation, including fatty acids and lipophilic hormone precursors of the jasmonate and auxin biosynthetic pathways. We also show that mutant cgi-58 plants display changes in jasmonate biosynthesis, auxin signaling, and lipid metabolism consistent with reduced PXA1 activity in planta and that, based on the double mutant cgi-58 pxa1, PXA1 is epistatic to CGI-58 in all of these processes. However, CGI-58 was not required for the PXA1-dependent breakdown of TAG in germinated seeds. Collectively, the results reveal that CGI-58 positively regulates many aspects of PXA1 activity in plants and that these two proteins function to coregulate lipid metabolism and signaling, particularly in nonseed vegetative tissues. Similarities and differences of CGI-58 activity in plants versus animals are discussed.
Automatic processing of macromolecular crystallography X-ray diffraction data at the ESRF
Authors: Monaco Stéphanie , Gordon Elspeth , Bowler Matthew W. , Delagenière Solange , Guijarro Matias , Spruce Darren , Svensson Olof , McSweeney Sean M. , McCarthy Andrew A. , Leonard Gordon , Nanao Max H.
Published: May 2013

The development of automated high-intensity macromolecular crystallography (MX) beamlines at synchrotron facilities has resulted in a remarkable increase in sample throughput. Developments in X-ray detector technology now mean that complete X-ray diffraction datasets can be collected in less than one minute. Such high-speed collection, and the volumes of data that it produces, often make it difficult for even the most experienced users to cope with the deluge. However, the careful reduction of data during experimental sessions is often necessary for the success of a particular project or as an aid in decision making for subsequent experiments. Automated data reduction pipelines provide a fast and reliable alternative to user-initiated processing at the beamline. In order to provide such a pipeline for the MX user community of the European Synchrotron Radiation Facility (ESRF), a system for the rapid automatic processing of MX diffraction data from single and multiple positions on a single or multiple crystals has been developed. Standard integration and data analysis programs have been incorporated into the ESRF data collection, storage and computing environment, with the final results stored and displayed in an intuitive manner in the ISPyB (information system for protein crystallography beamlines) database, from which they are also available for download. In some cases, experimental phase information can be automatically determined from the processed data. Here, the system is described in detail.
meso-Tetrakis[4-(heptyloxy)phenyl]porphyrin
Authors: Zhao Hong-Bin , Chen Liang , Wang Bang-Ying , Liao Jun-Xu , Xu Yong-Jun
Published: May 2013

The core of the novel title centrosymmetric porphyrin derivative, C72H86N4O4, with long flexible hexyloxy substituents, is almost planar, which is anticipated to facilitate π-electron delocalization and lead to a significant deviation between the planes of the benzene rings and the molecular plane. The two N-bound H atoms on the pyrrole rings are disordered and the occupancy factors refined to a ratio of 0.28 (2):0.72 (2).
(2S,3S)-2,6-Dimethylheptane-1,3-diol, the oxygenated side chain of 22(S)-hydroxycholestrol, and its synthetic precursor (R)-4-benzyl-3-[(2R,3S)-3-hydroxy-2,6-dimethylheptanoyl]-1,3-oxazolidin-2-one
Authors: Høgmoen Åstrand Ove Alexander , Iqbal Zeshan , Sandberg Marcel , Kase Eili T. , Görbitz Carl Henrik , Rongved Pål
Published: May 2013

(2S,3S)-2,6-Dimethylheptane-1,3-diol, C9H20O2, (I), was synthesized from the ketone (R)-4-benzyl-3-[(2R,3S)-3-hydroxy-2,6-dimethylheptanoyl]-1,3-oxazolidin-2-one, C19H27NO4, (II), containing C atoms of known chirality. In both structures, strong hydrogen bonds between the hydroxy groups form tape motifs. The contribution from weaker C—H...O hydrogen bonds is much more evident in the structure of (II), which furthermore contains an example of a direct short Osp3...Csp2contact that represents a usually unrecognized type of intermolecular interaction.
Temporal dynamics of direct reciprocal and indirect effects in a host–parasite network
Authors: Pilosof Shai , Fortuna Miguel A. , Vinarski Maxim V. , Korallo‐Vinarskaya Natalia P. , Krasnov Boris R.
Published: May 2013

Temporal variation in the direct and indirect influence that hosts and parasites exert on each other is still poorly understood. However, variation in species' influence due to species and interactions turnover can have important consequences for host community dynamics and/or for parasite transmission dynamics, and eventually for the risk of zoonotic diseases.

We used data on a network of small mammals and their ectoparasites surveyed over 6 years to test hypotheses exploring (i) the temporal variability in direct and indirect influences species exert on each other in a community, and (ii) the differences in temporal variability of direct/indirect influences between temporally persistent (TP) and temporally intermittent species.

We modelled the temporal variation in (i) direct reciprocal influence between hosts and parasites (hosts providing resources to parasites and parasites exploiting the resources of hosts), using an asymmetry index, and (ii) indirect influence among species within a community (e.g. facilitation of parasite infestation by other parasites), using betweenness centrality. We also correlated asymmetry and centrality to examine the relationship between them.

Network dynamics was determined by TP species but even those species had strong among‐species heterogeneity in the temporal variation of the direct/indirect effects they exerted. In addition, there was a significant positive linear correlation between asymmetry and centrality.

We conclude that the temporal dynamics of host–parasite interactions is driven by TP hosts. However, even within this group of persistent species, some exhibit large temporal variation, such that the functional roles they play (e.g. in promoting parasite transmission) change over time. In addition, parasites having a large negative impact on hosts are also those facilitating the spread of other parasites through the entire host community. Our results provide new insights into community dynamics and can be applied in the management of antagonistic networks aimed at preventing disease outbreaks.
Extrarenal roles of the with‐no‐lysine[K] kinases (WNKs)
Authors: Siew Keith , O'Shaughnessy Kevin M
Published: May 2013

Identified over a decade ago, the with‐no‐lysine[K] kinases (WNKs) have been the subsequent focus of intense research into the renal handling of Na+, Cl− and K+ and several rare monogenetic diseases. However, the potential extrarenal roles for WNKs have been less well explored.

Thiazides and Gordon syndrome are known to have effects on bone mineral density, Ca2+ and PO43− homeostasis, which were originally assumed to be an indirect effect through the kidney. However, current data suggest a complex and direct role for WNKs in the physiology of bone.

The WNKs also modulate systemic blood pressure at several levels, including the vascular resistance vessels, where they cause vasoconstriction by altering the abundance of the transient receptor potential canonical channel 3 and/or phosphorylation of the Na+−K+−2Cl− cotransporter 1 in vascular smooth muscle cells.

The WNKs and many of the cation‐coupled Cl− cotransporters they regulate are highly expressed in the central nervous system and recent work suggests that WNK dysfunction may have a role in the development of autism, schizophrenia and hereditary sensory and autonomic neuropathy Type 2.

Finally, the WNK–sterile 20 kinase signalling axis represents an evolutionarily ancient mechanism for maintaining osmotic homeostasis, but a rapidly expanding body of evidence also shows a role in immunity and cellular regulation.
Impact of non‐cardiovascular surgery on reactive hyperaemia and arterial endothelial function
Authors: Hu Yan Jun , Wei An Ning , Chook Ping , Yin Yuehui , Cheng William , Wu Meng Jun , Celermajer David S , Woo Kam Sang
Published: May 2013

Vascular reactivity is a surrogate marker for atherosclerosis and is predictive of cardiovascular outcome. Non‐cardiovascular surgery is associated with perioperative cardiovascular complications in high‐risk patients.

To evaluate the impact of non‐cardiovascular surgery on reactive hyperaemia and arterial endothelial function and to investigate the relationships between endothelial dysfunction and invasive (laparotomy) or minimally invasive (laparoscopic) surgery, we prospectively evaluated 106 patients undergoing abdominal surgery under general anaesthesia (71 laparotomy, 35 laparoscopy). Measurements of blood pressure, heart rate and pain (on a visual analogue scale (VAS)) were undertaken. Brachial endothelium‐dependent flow‐mediated dilation (FMD), endothelium‐independent dilation, nitroglycerin (NTG)‐induced dilation and reactive hyperaemia were measured with high‐resolution B‐mode ultrasound on preoperative Day 1 (baseline), as well as 2 h and 1 and 7 days postoperatively.

Blood pressure and heart rate were significantly higher 2 h postoperatively. Pain, as measured on the VAS, was higher (P < 0.01) and reactive hyperaemia and FMD were significantly lower (P < 0.001) at 2 h and 1 day postoperatively compared with values at baseline and on postoperative Day 7. By postoperative Day 7, FMD had recovered to baseline levels. Patients undergoing laparoscopic surgery had less FMD reduction on Days 1 and 7 (7.5 ± 1.5% and 7.9 ± 1.5%, respectively) compared with those undergoing laparotomy (6.4 ± 1.6% (P = 0.001) and 7.0 ± 1.6% (P = 0.006), respectively), consistent with potential cardiovascular benefit. Responses to NTG were stable throughout. Backward multivariate linear regression analysis indicated that FMD was independently related to age and VAS (model R = 0.486; F = 6.4; P < 0.001).

Reactive hyperaemia and arterial endothelial function are significantly reduced in the early postoperative period, particularly after laparotomy compared with laparoscopy, which may be related to postoperative cardiovascular events.
DNAbarcoding commercially important fish species ofTurkey
Authors: Keskİn Emre , Atar Hasan H.
Published: May 2013

DNAbarcoding was used in the identification of 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. A total of 1765DNAbarcodes using a 654‐bp‐long fragment of the mitochondrial cytochrome c oxidase subunit I gene were generated for 89 commercially important freshwater and marine fish species found in Turkish ichthyofauna. These species belong to 70 genera, 40 families and 19 orders from class Actinopterygii, and all were associated with a distinctDNAbarcode. Nine and 12 of theCOIbarcode clusters represent the first species records submitted to theBOLDand GenBank databases, respectively. AllCOIbarcodes (except sequences of first species records) were matched with reference sequences of expected species, according to morphological identification. Average nucleotide frequencies of the data set were calculated asT = 29.7%,C = 28.2%,A = 23.6% andG = 18.6%. Average pairwise genetic distance among individuals were estimated as 0.32%, 9.62%, 17,90% and 22.40% for conspecific, congeneric, confamilial and within order, respectively. Kimura 2‐parameter genetic distance values were found to increase with taxonomic level. For most of the species analysed in our data set, there is a barcoding gap, and an overlap in the barcoding gap exists for only two genera. Neighbour‐joining trees were drawn based onDNAbarcodes and all the specimens clustered in agreement with their taxonomic classification at species level. Results of this study supportedDNAbarcoding as an efficient molecular tool for a better monitoring, conservation and management of fisheries.
Curve Fit: a pixel‐level raster regression tool for mapping spatial patterns
Authors: De Jager Nathan R. , Fox Timothy J.
Published: May 2013

Despite the fact that pixels (i.e. picture elements) are the basic sampling units of maps, we are aware of no software package or tool that allows users to model changes that may occur at such fine spatial resolutions over broad geographic extents.

Curve Fit is an extension to the application ArcMap that allows users to conduct linear or nonlinear regression analysis on the range of values found within input raster data sets (geo‐referenced images), independently for each pixel.

Outputs consist of raster surfaces of regression model parameter estimates, standard errors, goodness‐of‐fit estimates and multimodel inference measures.

Curve fit outputs characterize continuous spatial or temporal change across a series of raster data sets.
The neurobiological correlates of childhood adversity and implications for treatment
Authors: Tyrka A. R. , Burgers D. E. , Philip N. S. , Price L. H. , Carpenter L. L.
Published: May 2013

Objective

This article provides an overview of research on the neurobiological correlates of childhood adversity and a selective review of treatment implications.

Method

Findings from a broad array of human and animal studies of early adversity were reviewed.

Results

Topics reviewed include neuroendocrine, neurotrophic, neuroimaging, and cognitive effects of adversity, as well as genetic and epigenetic influences. Effects of early‐life stress on treatment outcome are considered, and development of treatments designed to address the neurobiological abnormalities is discussed.

Conclusion

Early adversity is associated with abnormalities of several neurobiological systems that are implicated in the development of psychopathology and other medical conditions. Early‐life stress negatively impacts treatment outcome, and individuals may require treatments that are specific to this condition.
Genetics of serum and muscle lipids in pigs
Authors: Casellas J. , Vidal O. , Pena R. N. , Gallardo D. , Manunza A. , Quintanilla R. , Amills M.
Published: May 2013

Pork meat is one of the most important sources of animal protein in the human diet. Its nutritional properties are partly determined by intramuscular fat content and composition, with existing general consensus about the detrimental effects of cholesterol and saturated fat on cardiovascular health in humans. Because of their physiological resemblance, pigs can be also used as a valuable animal model to study the genetics of human diseases such as atherosclerosis, obesity and dyslipidaemias. Heritability estimates and QTL maps of porcine muscle and serum lipid traits evidence that a considerable amount of genetic variance determining these phenotypes exists, but its molecular basis remains mostly unknown. The recent advent of high‐throughput genotyping and sequencing technologies has revolutionised the field of animal genomics. With these powerful tools, finding needles in the genomic haystack has become increasingly feasible. However, these methodological advances should not be deemed as magic bullets. The goal of identifying the many polymorphisms that shape the variability of lipid phenotypes is so challenging that success can be achieved only under the scope of large international consortia.
Investigating gene expression differences in two chicken groups with variable propensity to feather pecking
Authors: Wysocki Michal , Preuss Siegfried , Stratz Patrick , Bennewitz Jörn
Published: May 2013

Feather pecking is a major welfare problem in egg production. It may be caused by genetic, physiological and environmental factors. The main aim of this study was to uncover gene expression variability in brain tissue between individuals from high feather pecking and low feather pecking groups using the Chicken Gene Expression Microarray. In total, 313 signals were initially identified as significant (P ≤ 0.05) for the fold change higher than two. A subset of functional candidate genes including downregulated (GLUL, TSPO, MAOA) and upregulated (HTR1B, SIP1, PSEN1) transcripts was subjected to quantitative PCR validation. The significance level and direction of the fold change in gene expression observed by the microarray analysis were confirmed for four genes (HTR1B, SIP1, PSEN1 and GLUL). Newly identified candidate genes play an important role in neurotransmission and psychopathological disorders and can be considered as potential genetic components involved in complex feather pecking behavior. It can be concluded that this study has revealed some interesting differences in gene expression between high and low feather pecking groups and helped to approach elucidation of the genetic foundations of feather pecking.
Design, Synthesis, and Evaluation of Indolebutylamines as a Novel Class of Selective Dopamine D3 Receptor Ligands
Authors: Du Peng , Xu Lili , Huang Jiye , Yu Kunqian , Zhao Rui , Gao Bo , Jiang Hualiang , Zhao Weili , Zhen Xuechu , Fu Wei
Published: May 2013

A series of indolebutylamine derivatives were designed, synthesized, and evaluated as a novel class of selective ligands for the dopamine 3 receptor. The most potent compound 11q binds to dopamine 3 receptor with a Ki value of 124 nm and displays excellent selectivity over the dopamine 1 receptor and dopamine 2 receptor. Investigation based on structural information indicates that site S182 located in extracellular loop 2 may account for high selectivity of compounds. Interaction models of the dopamine 3 receptor‐11q complex and structure‐activity relationships were discussed by integrating all available experimental and computational data with the eventual aim to discover potent and selective ligands to dopamine 3 receptor.
PON1‐108 TT and PON1‐192 RR genotypes are more frequently encountered in Greek PCOS than non‐PCOS women, and are associated with hyperandrogenaemia
Authors: Paltoglou George , Tavernarakis George , Christopoulos Panagiotis , Vlassi Margarita , Gazouli Maria , Deligeoroglou Efthimios , Creatsas George , Mastorakos George
Published: May 2013

Objective

To investigate the frequencies of three paraoxonase (PON)1 polymorphisms in Greek polycystic ovary syndrome (PCOS) and non‐PCOS women, and their genotypes association with hyperandrogenaemia and insulin resistance.

Design

Case–control genetic association study.

Setting

University Hospital Endocrine Unit.

Patients

A total of 142 PCOS cases (NIH criteria) and 112 controls.

Main Outcome Measure

Genotyping of the c.–108C>T (PON1‐108), the c.163T>A (PON1‐55) and the c.575A>G (PON1‐192) polymorphisms and measurement of baseline androgen and insulin resistance profile.

Results

The PON1‐108 TT and PON1‐192 RR genotypes were more frequently encountered in the PCOS than in the control group. The PON1‐192 R allele frequency was greater in the PCOS than in the control group. Comparing the PCOS and the control groups, statistical significances favoured a recessive and a dominant genetic model, respectively, for the single PON1‐108 T and PON1‐192 R alleles. Free Androgen Index (FAI) levels were higher in patients with PON1‐108 TT, whereas Testosterone, FAI and Dehydroepiandrosterone sulphate (DHEAS) levels were higher in patients with PON1‐192 RR than patients with the wild or the heterozygous genotype.

Conclusions

The decreased PON1 activity‐associated PON1‐108 TT and the PON1‐192 RR genotypes are more frequently found in Greek PCOS women and are associated with hyperandrogenaemia. Hyperandrogenaemia must depend also on other genetic factors because the same genotypes were not associated with hyperandrogenaemia in the control group. Through identification of the involved polymorphisms, women with PCOS could potentially have a better therapeutic screening.
Whole‐Genome mRNA Expression Profiling Identifies Functional and Prognostic Signatures in Patients with Mesenchymal Glioblastoma Multiforme
Authors: Bao Zhao‐Shi , Zhang Chuan‐Bao , Wang Hong‐Jun , Yan Wei , Liu Yan‐Wei , Li Ming‐Yang , Zhang Wei
Published: May 2013

Background

The Cancer Genome Atlas (TCGA) has divided patients with glioblastoma multiforme (GBM) into four subtypes based on mRNA expression microarray. The mesenchymal subtype, with a larger proportion, is considered a more lethal one. Clinical outcome prediction is required to better guide more personalized treatment for these patients.

Aims

The objective of this study was to identify a mRNA expression signature to improve outcome prediction for patients with mesenchymal GBM.

Results

For signature identification and validation, we downloaded mRNA expression microarray data from TCGA as training set and data from Rembrandt and GSE16011 as validation set. Cox regression and risk‐score analysis were used to develop the 4 signatures, which were function and prognosis associated as revealed by Gene Ontology (GO) analysis and Gene Set Variation Analysis (GSVA). Patients who had high‐risk scores according to the signatures had poor overall survival compared with patients who had low‐risk scores.

Conclusions

The signatures were identified as risk predictors that patients who had a high‐risk score tended to have unfavorable outcome, demonstrating their potential for personalizing cancer management.
Association between EXOC3L2 rs597668 Polymorphism and Alzheimer's Disease
Authors: Shang Hong , Fu Jin , Zhang Xue‐Mei , Song Rong‐Rong , Wang Wei‐Zhi
Published: May 2013

Background

EXOC3L2 gene rs597668 polymorphism was identified to be significantly associated with Alzheimer's disease (AD) in Caucasian population. However, recent studies reported consistent and inconsistent results in Caucasian and Asian populations.

Aims

In order to assess this association, we performed a meta‐analysis of rs597668 polymorphism using RevMan (v.5.1) software.

Methods

We searched PubMed and Google scholar databases and selected 4 independent publications, which included 16 independent studies. We conducted sensitivity analysis and evaluated the publication bias. In the end, we calculated the odds ratio (OR) using fixed effect model (Mantel‐Haenszel).

Results

We observed significant association between rs597668 polymorphism and AD using allele model (P = 0.006, OR = 1.09, 95% CI 1.03–1.16) and the dominant model (P = 0.008, OR = 1.11, 95% CI 1.03–1.21).

Discussion and Conclusions

To our knowledge, this is the first study that assesses the association between rs597668 polymorphism and AD by meta‐analysis. We believe that our findings will be very useful for future genetic studies in AD.
The results of surgery for colorectal hepatic metastases following expansion of the indications in 2005
Authors: Zhong Y. , Zhu D. , Liang L. , Ye Q. , Wei Y. , Ren L. , Pan X. , Fan J. , Xu J. , Qin X.
Published: May 2013

Aim

Safety and survival were investigated in patients treated according to expanded surgical indications for colorectal hepatic metastases.

Method

A retrospective analysis of all consecutive patients who underwent resection of colorectal hepatic metastases at Zhongshan Hospital from 2000 to 2010 was conducted. The patients were divided into two groups based on a change in the surgical indications introduced in 2005. Patients in Group I underwent hepatic surgery between 2000 and 2004 and those in Group II between 2005 and 2010. The clinicopathological data and survival rates of both groups were analysed.

Results

There were 530 patients who underwent hepatic surgery between 2000 and 2010. After the expansion of surgical indications, the rate of surgical resection rose from 25.1 to 35.1% (P < 0.05). There was no significant difference in perioperative mortality (2.2% vs 0.9%) or morbidity (20.9% vs 29.8%). Recurrence occurred in 27.5% and 36.7% in Groups I and II, respectively, and 5‐year overall survival was 43% and 49%, respectively (not significant).

Conclusion

Expanding the indications for surgical resection of hepatic metastases increased the resection rate but had no significant effect on survival.
Colorectal neoplasia in long‐standing ulcerative colitis – a prospective study from a low‐prevalence area
Authors: Shivakumar B. M. , Lakshmankumar B. , Rao L. , Bhat G. , Suvarna D. , Pai C. G.
Published: May 2013

Aim

Despite increasing recognition of ulcerative colitis (UC) in Asia in recent decades, reports on the occurrence of colorectal neoplasia (CRN) in UC are scarce and surveillance for this complication is not routinely practised in this region. We aimed to assess the outcome of a newly initiated pilot screening programme for screening CRN among UC patients in India.

Method

In this prospective study from an academic hospital setting, patients with UC at high risk of CRN were offered screening by magnifying chromocolonoscopy and the frequency of neoplastic lesions was assessed.

Results

Twenty‐nine (70.7%) of 41 eligible patients [a median age of 46 (interquartile range 36–54.5) years; 17 (58.6%) men] enrolled for surveillance; 41 colonoscopies were undertaken over 42 months. The median disease duration was 10 (interquartile range 7.5–14.5) years. Sixteen (55.1%) had extensive colitis. On initial screening, low‐grade dysplasia (LGD) was seen in five (17.2%) and high‐grade dysplasia (HGD) in three (10.3%). Of these three, one accepted proctocolectomy immediately, one underwent surgery for adenocarcinoma and one refused surgery. Twelve follow‐up colonoscopies in nine patients revealed three new LGD.

Conclusions

High‐grade dysplasia and subsequent adenocarcinoma can be detected with careful follow‐up in Indian patients with long‐standing UC but acceptance of surveillance and subsequent therapy are suboptimal. We found evidence that screening and surveillance programmes are useful for detecting neoplasias in UC, and need to be customized for this region.
Spent green tea leaves for decolourisation of raw textile industry wastewater
Authors: Weng Chih‐Huang , Lin Yao‐Tung , Chen Yen‐Jung , Sharma Yogesh Chandra
Published: May 2013

True colour measurements of wastewater samples, in terms of American Dye Manufacturers' Institute values, were used to evaluate the effectiveness of decolourisation of textile wastewater using spent green tea leaf powder waste. Raw wastewater samples with a true colour of 868 ADMI were used in the batch adsorption experiments. Results revealed that the true colour removal efficiency of the raw textile wastewater was high in acidic solution and at high temperature, indicating an endothermic nature of the system. The major functional groups of the green tea leaf powder waste involved in adsorption were identified by Fourier Transform‐infrared spectroscopy analysis. Adsorption kinetic data were modelled using the modified Freundlich and intraparticle diffusion kinetics equations. Fitting results of the Langmuir adsorption isotherm showed that the adsorption capacity of the green tea leaf powder waste was 775 ADMI g−1, which is higher than that of powder activated carbon (526 ADMI g−1). The low activation energy values (13.9 kJ mol−1) suggested that adsorption was governed by a diffusion process and the reaction involved a physisorption mechanism. From the perspectives of waste utilisation, remarkable colour adsorption capacity and inexpensive and abundant availability, green tea leaf waste is an attractive alternative for decolourisaton of textile wastewater. Because high temperature favours colour removal, green tea leaf powder can be directly applied in raw textile wastewater treatment.
Synthesis, characterisation and electrochemical investigation of phthalocyanines with pendant 4‐{2‐[2‐(4‐tert‐butylphenoxy)ethoxy]ethoxy} substituents
Authors: Acar İrfan , Topçu Saim , Bıyıklıoğlu Zekeriya , Kantekin Halit
Published: May 2013

In this study, a novel metal‐free phthalocyanine and three metallophthalocyanines carrying four 2‐[2‐(4‐tert‐butylphenoxy)ethoxy groups on the periphery were prepared by cyclotetramerisation of a dinitrile derivative in the presence of the corresponding divalent metal salts [zinc(ii), cobalt(ii), copper(ii)]. These new phthalocyanine compounds have been characterised by infrared, 1H and 13C nuclear magnetic resonance and electrospray mass spectroscopies and elemental analysis. The electrochemical properties of the metal‐free, zinc(ii) and cobalt(ii) phthalocyanines were investigated by cyclic voltammetry and differential pulse voltammetry methods. The cobalt complex showed a metal‐based reduction process, while the metal‐free and zinc(ii) phthalocyanines showed ligand‐based electron transfer processes. It has been found that the absorption spectra substantially depend on concentration. It has been shown that these changes are attributable to the association of the phthalocyanine molecule. The number of molecules in the associates and the equilibrium constants for this association are determined.
Thirty days of resveratrol supplementation does not affect postprandial incretin hormone responses, but suppresses postprandial glucagon in obese subjects
Authors: Knop F. K. , Konings E. , Timmers S. , Schrauwen P. , Holst J. J. , Blaak E. E.
Published: May 2013

Aims

Resveratrol, a natural polyphenolic compound produced by various plants (e.g. red grapes) and found in red wine, has glucose‐lowering effects in humans and rodent models of obesity and/or diabetes. The mechanisms behind these effects have been suggested to include resveratrol‐induced secretion of the gut incretin hormone glucagon‐like peptide‐1. We investigated postprandial incretin hormone and glucagon responses in obese human subjects before and after 30 days of resveratrol supplementation.

Methods

Postprandial plasma responses of the incretin hormones glucagon‐like peptide‐1 and glucose‐dependent insulinotropic polypeptide and glucagon were evaluated in 10 obese men [subjects characteristics (mean ± standard error of the mean): age 52 ± 2 years; BMI 32 ± 1 kg/m2, fasting plasma glucose 5.5 ± 0.1 mmol/l] who had been given a dietary supplement of resveratrol (Resvida® 150 mg/day) or placebo for 30 days in a randomized, double‐blind, crossover design with a 4‐week washout period. At the end of each intervention period a standardized meal test (without co‐administration of resveratrol) was performed.

Results

Resveratrol supplementation had no impact on fasting plasma concentrations or postprandial plasma responses (area under curve values) of glucose‐dependent insulinotropic polypeptide (11.2 ± 2.1 vs. 11.8 ± 2.2 pmol/l, P = 0.87; 17.0 ± 2.2 vs. 14.8 ± 1.6 min × nmol/l, P = 0.20) or glucagon‐like peptide‐1 (15.4 ± 1.0 vs. 15.2 ± 0.9 pmol/l, P = 0.84; 5.6 ± 0.4 vs. 5.7 ± 0.3 min × nmol/l, P = 0.73). Resveratrol supplementation significantly suppressed postprandial glucagon responses (4.4 ± 0.4 vs. 3.9 ± 0.4 min × nmol/l, P = 0.01) without affecting fasting glucagon levels (15.2 ± 2.2 vs. 14.5 ± 1.5 pmol/l, P = 0.56).

Conclusions

Our data suggest that 30 days of resveratrol supplementation does not affect fasting or postprandial incretin hormone plasma levels in obese humans, but suppresses postprandial glucagon responses.
Doppler Markers of Elevated Left Atrial and Ventricular Filling Pressure in a Critically Ill Patient
Authors: Caselli Stefano , Serdoz Andrea , Ramamurthi Alamelu , Pandian Natesa G. , De Paola Domenico , Serdoz Roberto
Published: May 2013

Accurate assessment of intracardiac flows by Doppler echocardiography may add important hemodynamic information in the critically ill patient. Detailed analysis of flow gradients through different sites and their correlation with timing of cardiac events may help us in better understanding the pathophysiology of the underlying disease. We report the clinical case of a 78‐year‐old patient with septic shock, in whom an A‐dip of aortic regurgitation, shortening of diastolic filling, and diastolic mitral regurgitation were detected by Doppler analysis. Pathophysiologic explanation of these phenomena and their evolution after inotropic drug infusion are reported.
The Incremental Value of RT Three‐Dimensional TEE in the Evaluation of Prosthetic Mitral Valve Ring Thrombosis Complicated with Thromboembolism
Authors: Gürsoy Ozan Mustafa , Karakoyun Süleyman , Kalçık Macit , Özkan Mehmet
Published: May 2013

Purpose: Although nonobstructive prosthetic valve thrombosis (PVT) does not develop hemodynamic compromise, it carries potential risk for thromboembolism. Real time three‐dimensional transesophageal echocardiography (RT‐3DTEE), has emerged as a complementary tool in depicting “en face” views of prosthesis compared with two‐dimensional transesophageal echocardiography (2DTEE). We aimed to evaluate the utility of RT‐3DTEE in assessment of mitral ring‐located thrombosis. Method: We present 3 cases of mechanical mitral valve thrombosis complicated by thromboembolism, who were all examined and followed‐up by 2D transthoracic echocardiography (TTE), 2DTEE, and RT‐3DTEE. Result: The consequencies of thromboembolism in the patients were coronary embolism, transient ischemic attack, and ischemic stroke, respectively. They were all inadequately anticoagulated at the time of admission. 2DTTE and TEE examination was unsatisfactory; RT‐3DTEE depicted nonobstructive mitral ring thrombosis in each of the patients. The patients were followed up under effective anticoagulation and antiplatelet therapy. RT‐3DTEE was able to demonstrate the evolution of thrombus size in each of the patients. Conclusion: Nonobstructive ring‐located PVT which poses risk for thromboembolism, may be diagnosed with certainty and imaged with clarity utilizing RT‐3DTEE.
The Role of Three‐Dimensional Echocardiography in Diagnosis and Management of Ruptured Sinus of Valsalva Aneurysm
Authors: Vatankulu Mehmet Akif , Tasal Abdurrahman , Erdogan Ercan , Sonmez Osman , Goktekin Omer
Published: May 2013

Mini‐Abstract

A 29‐year‐old man was admitted to our outpatient clinic with exertional dyspnea. Transesophageal echocardiography (TEE) revealed a ruptured sinus of Valsalva aneurysm into the right ventricle. Real time three‐dimensional (3D) TEE, used to visualize the relationship between the rupture, the aortic valve, and the right ventricle, revealed the precise shape, size, and location of the defect. The defect was closed using a 16/10 mm Amplatzer duct occluder under real time 3DTEE guidance. 3DTEE provided more accurate delineation of the defect location and orientation than other imaging techniques and may aid in the selection of an appropriate device for closure.