bluuebunny/crossref_metadata_2025 huggingface dataset:
Profundibacterium mesophilum gen. nov., sp. nov., a novel member in the family

Rhodobacteraceae

isolated from deep-sea sediment in the Red Sea, Saudi Arabia
Authors: Lai Pok Yui , Miao Li , Lee On On , Liu Ling-Li , Zhou Xiao-Jian , Xu Ying , Al-Suwailem Abdulaziz , Qian Pei-Yuan
Published: June 2012

A slow-growing, strictly aerobic, Gram-negative, coccus bacterial strain, designated KAUST100406-0324T, was isolated from sea-floor sediment collected from the Red Sea, Saudi Arabia. The catalase- and oxidase-positive strain was non-sporulating and only slightly halophilic. Optimum growth occurred at 20–25 °C and at pH values ranging from 7.0 to 8.0. The major cellular fatty acids of the strain were unsaturated C18 : 1ω6c and/or C18 : 1ω7c, C18 : 1ω7c 11-methyl and C16 : 1ω7c and/or C16 : 1ω6c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine and two unidentified phospholipids. Ubiquinone 10 was the predominant lipoquinone. The DNA G+C content of strain KAUST100406-0324T was 64.0 mol%. Phylogenetic analysis of 16S rRNA gene sequences revealed that the novel strain belonged to the family

Rhodobacteraceae

of the class

Alphaproteobacteria

but formed a distinct evolutionary lineage from other bacterial species with validly published names. The 16S rRNA gene sequence of the novel strain was distantly related, but formed a monophyletic cluster with, those of bacteria from two moderately halophilic genera,

Hwanghaeicola

and

Maribius

. The similarity of the sequence between the novel strain KAUST100406-0324T and the type strains

Hwanghaeicola aestuarii

Y26T (accession number FJ230842),

Maribius pelagius

B5-6T (DQ514326) and

Maribius salinus

CL-SP27T (AY906863) were 94.5 %, 95.2 % and 95.3 %, respectively. Based on the physiological, phylogenetic and chemotaxonomic characteristics presented in this study, we propose that this strain represents a novel species of a new genus in the family

Rhodobacteraceae

, for which the name of Profundibacterium mesophilum gen. nov., sp. nov. was proposed, with KAUST100406-0324T ( = JCM 17872T  = NRRL B-59665T) as the type strain.
Phycicoccus badiiscoriae sp. nov., a novel actinomycete isolated from scoria
Authors: Lee Soon Dong
Published: June 2012

An actinomycete strain, designated Sco-B23T, was isolated from a brown-coloured layer of scoria collected near Darangshi Oreum (a small mountain) in Jeju, Republic of Korea. Cells of the organism were Gram-positive, non-endospore-forming, non-motile cocci and grew at 20–35 °C, at pH 5.1–11.1 and with 0–1 % (w/v) NaCl. Colonies were circular, translucent and moderate yellow in colour with entire margins. On the basis of 16S rRNA gene sequence analysis, the isolate belonged to the genus

Phycicoccus

and formed a monophyletic line between a

Phycicoccus bigeumensis

–

Phycicoccus dokdonensis

cluster and a

Phycicoccus aerophilus

–

Phycicoccus ginsenosidimutans

cluster. Levels of 16S rRNA gene sequence similarity between strain Sco-B23T and the type strains of Phycicoccus species were:

P. bigeumensis

(98.8 %),

P. dokdonensis

(98.7 %),

P. aerophilus

(97.7 %),

P. ginsenosidimutans

(97.7 %),

P. cremeus

(96.9 %) and

P. jejuensis

(96.5 %). Chemotaxonomic analyses showed that the isolate possessed meso-diaminopimelic acid as the diamino acid of the peptidoglycan, MK-8(H4) as the predominant menaquinone, a polar lipid profile including diphosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unknown phospholipid and two unknown lipids, predominant fatty acids represented by iso-C15 : 0, C17 : 1
cis9, iso-C16 : 0 and iso-C14 : 0, and DNA G+C content of 69.7 mol%. DNA–DNA relatedness between strain Sco-B23T and the close relatives within the genus

Phycicoccus

was below 18.1 %. On the basis of phenotypic features and DNA–DNA hybridization data, strain Sco-B23T represents a novel species of the genus

Phycicoccus

, for which the name Phycicoccus badiiscoriae sp. nov. is proposed. The type strain is Sco-B23T ( = KCTC 19807T  = KACC 15111T  = NBRC 107918T).
Reclassification of Agromonas oligotrophica into the genus Bradyrhizobium as Bradyrhizobium oligotrophicum comb. nov.
Authors: Ramírez-Bahena Martha-Helena , Chahboune Rajaa , Peix Alvaro , Velázquez Encarna
Published: June 2012

Agromonas oligotrophicaJCM 1494Twas isolated in Japan in 1983, and the name was validly published in 1985. Analysis of the 16S rRNA gene sequence showed thatAgromonas oligotrophicaLMG 10732T( = JCM 1494T) is located within the genusBradyrhizobium, withBradyrhizobium denitrificansLMG 8443Tas its closest relative, showing 99.6 % 16S rRNA gene sequence identity. However,Agromonas oligotrophicaLMG 10732TandBradyrhizobium denitrificansLMG 8443Tcan be distinguished by housekeeping gene sequence analysis, phenotypic characterization and DNA–DNA hybridization.Agromonas oligotrophicais also genotypically and phenotypically different from the remaining species of the genusBradyrhizobium, and we therefore propose the reclassification ofAgromonas oligotrophicainto the genusBradyrhizobiumasBradyrhizobium oligotrophicumcomb. nov. (type strain LMG 10732T = JCM 1494T = ATCC 43045T).
Ferrimonas sediminum sp. nov., isolated from coastal sediment of an amphioxus breeding zone
Authors: Ji Shiqi , Zhao Rui , Li Zhao , Li Bingyu , Shi Xiaochong , Zhang Xiao-Hua
Published: June 2012

A Gram-stain-negative, facultatively anaerobic rod with a polar flagellum, designated strain JYr13T, was isolated from coastal sediment of an amphioxus breeding zone located in Qingdao, China. The isolate utilized Fe(III) oxyhydroxide, Fe(III) citrate, SeO3
2– and SeO4
2– as electron acceptors. Strain JYr13T grew optimally at 25–28 °C, pH 7.0–8.0 and in presence of 3 % (w/v) NaCl. Strain JYr13T contained menaquinone-7 and ubiquinones Q-7 and Q-8 as the predominant isoprenoid quinones, and C18 : 1ω9c, iso-C15 : 0, C17 : 1ω8c and C16 : 0 as the major fatty acids. The DNA G+C content of strain JYr13T was 59 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that the closest phylogenetic neighbour of strain JYr13T was

Ferrimonas kyonanensis

DSM 18153T (96.0 % 16S rRNA gene sequence similarity). Based on the phenotypic, chemotaxonomic and phylogenetic distinctiveness, strain JYr13T is considered to represent a novel species of the genus

Ferrimonas

, for which the name Ferrimonas sediminum sp. nov. is proposed. The type strain is JYr13T ( = DSM 23317T = LMG 25564T).
Corallomonas stylophorae gen. nov., sp. nov., a halophilic bacterium isolated from the reef-building coral Stylophora pistillata
Authors: Chen Ming-Hui , Sheu Shih-Yi , Chen Chaolun Allen , Wang Jih-Terng , Chen Wen-Ming
Published: June 2012

A heterotrophic marine bacterium, designated strain KTSW-6T, was isolated from the reef-building coral Stylophora pistillata in Kenting, Taiwan. Cells of strain KTSW-6T were Gram-stain-negative, facultatively anaerobic, halophilic, non-motile rods surrounded by a thick glycocalyx-like coat and forming creamy white colonies. Growth occurred at 15–37 °C (optimum, 25–30 °C), at pH 7.0–9.0 (optimum, pH 7.5–8.0) and with 0.5–7 % NaCl (optimum, 3–4 %). Polar lipids comprised phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, an uncharacterized aminophospholipid and three uncharacterized phospholipids (PL1–PL3). The respiratory quinones of strain KTSW-6T were Q-8 (62 %) and Q-7 (38 %). Major cellular fatty acids were summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c, 29.6 %), C18 : 1ω7c (27.6 %) and C16 : 0 (19.5 %). The major cellular hydroxy fatty acid was C10 : 0 3-OH. The DNA G+C content of strain KTSW-6T was 48.6 mol%. 16S rRNA gene sequence analysis indicated that strain KTSW-6T belongs to the family

Oceanospirillaceae

of the order

Oceanospirillales

, class

Gammaproteobacteria

. Strain KTSW-6T shared 92.7 % 16S rRNA gene sequence similarity with

Neptuniibacter caesariensis

MED92T and 92.0 % with

Neptunomonas naphthovorans

NAG-2N-126T. On the basis of the genotypic and phenotypic data, strain KTSW-6T represents a novel species of a new genus of the

Oceanospirillaceae

, for which the name Corallomonas stylophorae gen. nov., sp. nov. is proposed. The type strain of Corallomonas stylophorae is KTSW-6T ( = BCRC 80176T = LMG 25553T).
Rhodococcus cerastii sp. nov. and Rhodococcus trifolii sp. nov., two novel species isolated from leaf surfaces
Authors: Kämpfer P. , Wellner S. , Lohse K. , Lodders N. , Martin K.
Published: June 2012

Two Gram-positive, non-endospore-forming rods, strains C5T and T8T
, were isolated from the phyllospheres of Cerastium holosteoides and Trifolium repens, respectively, and were studied in detail for their taxonomic position. 16S rRNA gene sequence analysis allocated both isolates clearly to the genus

Rhodococcus

. Isolate C5T was most closely related to

Rhodococcus fascians

and

Rhodococcus yunnanensis

, showing 99.2 % gene sequence similarity to both species. Strain T8T revealed the highest 16S rRNA gene sequence similarity to

Rhodococcus corynebacterioides

(98.8 %) and

Rhodococcus kroppenstedtii

(98.6 %). The quinone system of both strains was composed of dihydrogenated menaquinones with eight (major amount) as well as nine, seven and six isoprenoid units (MK-8H2, MK-9H2 MK-7H2 MK-6H2).The polar lipid profiles of strains C5T and T8T consisted of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside and one unknown phospholipid. Additionally, strain C5T contained one unknown glycolipid, and strain T8T three unknown aminolipids. The fatty acid profiles contained major amounts of C16 : 0, C18 : 1ω9c and 10-methyl C18 : 0, which supported the grouping of the two isolates in the genus

Rhodococcus

. Physiological/biochemical characterization and DNA–DNA hybridizations with the type strains of the most closely related species allowed a clear phenotypic and genotypic differentiation of both strains. For this reason, we propose strain C5T ( = LMG 26203T  = CCM 7906T) as the type strain of a novel species with the name Rhodococcus cerastii sp. nov., and strain T8T ( = LMG 26204T  = CCM 7905T) as the type strain of a second novel species with the name Rhodococcus trifolii sp. nov.
CBX3 regulates efficient RNA processing genome-wide
Authors: Smallwood Andrea , Hon Gary C. , Jin Fulai , Henry Ryan E. , Espinosa Joaquín M. , Ren Bing
Published: June 2012

CBX5, CBX1, and CBX3 (HP1α, β, and γ, respectively) play an evolutionarily conserved role in the formation and maintenance of heterochromatin. In addition, CBX5, CBX1, and CBX3 may also participate in transcriptional regulation of genes. Recently, CBX3 binding to the bodies of a subset of genes has been observed in human and murine cells. However, the generality of this phenomenon and the role CBX3 may play in this context are unknown. Genome-wide localization analysis reveals CBX3 binding at genic regions, which strongly correlates with gene activity across multiple cell types. Depletion of CBX3 resulted in down-regulation of a subset of target genes. Loss of CBX3 binding leads to a more dramatic accumulation of unspliced nascent transcripts. In addition, we observed defective recruitment of splicing factors, including SNRNP70, to CBX3 target genes. Collectively, our data suggest a role for CBX3 in aiding in efficient cotranscriptional RNA processing.
Influence of asymmetrical mating patterns and male reproductive success on the maintenance of sexual polymorphism inAcer pictumsubsp.mono(Aceraceae)
Authors: SHANG HUI , LUO YI‐BO , BAI WEI‐NING
Published: June 2012

Populations ofAcerspecies often contain more than three sex phenotypes with complex sexual polymorphism including duodichogamy, protandry and protogyny. We identified the mechanisms that maintain sexual polymorphism inAcer pictumsubsp.mono, a temperate tree from northern China, by investigating maternal mating patterns and male reproductive success. We used paternity analyses to estimate rates of outcrossing and disassortative mating, as well as male outcrossed siring success, in a population ofA. pictumsubsp.monowith uneven sex phenotype ratios (duodichogamous 69.1%, protandrous 19.6%, protogynous 11.3%). We used a pollen‐transfer model to investigate whether the unequal ratios of sex phenotypes could be explained by the observed patterns of mating. Most progeny resulted from outcrossing, particularly disassortative among the sex phenotypes. Although the duodichogamous phenotype showed a significant amount of intraphenotypic mating, the frequency did not exceed that of disassortative mating. We detected no significant differences in male outcrossed siring success among the sex phenotypes. The pollen‐transfer model demonstrated that sex phenotype ratios could be maintained by the observed mating pattern in the population. Our results indicate that disassortative mating among the sex phenotypes can maintain sexual polymorphism inA. pictumsubsp.monoand that ratios biased towards duodichogamy can result from frequent intraphenotypic mating in this phenotype.
Limited gene flow among brown bear populations in far Northern Europe? Genetic analysis of the east–west border population in the Pasvik Valley
Authors: SCHREGEL JULIA , KOPATZ ALEXANDER , HAGEN SNORRE B. , BRØSETH HENRIK , SMITH MARTIN E. , WIKAN STEINAR , WARTIAINEN INGVILD , ASPHOLM PAUL E. , ASPI JOUNI , SWENSON JON E. , MAKAROVA OLGA , POLIKARPOVA NATALIA , SCHNEIDER MICHAEL , KNAPPSKOG PER M. , RUOKONEN MINNA , KOJOLA ILPO , TIRRONEN KONSTANTIN F. , DANILOV PJOTR I. , EIKEN HANS GEIR
Published: June 2012

Noninvasively collected genetic data can be used to analyse large‐scale connectivity patterns among populations of large predators without disturbing them, which may contribute to unravel the species’ roles in natural ecosystems and their requirements for long‐term survival. The demographic history of brown bears (Ursus arctos) in Northern Europe indicates several extinction and recolonization events, but little is known about present gene flow between populations of the east and west. We used 12 validated microsatellite markers to analyse 1580 hair and faecal samples collected during six consecutive years (2005–2010) in the Pasvik Valley at 70°N on the border of Norway, Finland and Russia. Our results showed an overall high correlation between the annual estimates of population size (Nc), density (D), effective size (Ne) andNe/Ncratio. Furthermore, we observed a genetic heterogeneity of ∼0.8 and highNe/Ncratios of ∼0.6, which suggests gene flow from the east. Thus, we expanded the population genetic study to include Karelia (Russia, Finland), Västerbotten (Sweden) and Troms (Norway) (477 individuals in total) and detected four distinct genetic clusters with low migration rates among the regions. More specifically, we found that differentiation was relatively low from the Pasvik Valley towards the south and east, whereas, in contrast, moderately high pairwiseFSTvalues (0.91–0.12) were detected between the east and the west. Our results indicate ongoing limits to gene flow towards the west, and the existence of barriers to migration between eastern and western brown bear populations in Northern Europe.
Regulation of cambial activity in relation to environmental conditions: understanding the role of temperature in wood formation of trees
Authors: Begum Shahanara , Nakaba Satoshi , Yamagishi Yusuke , Oribe Yuichiro , Funada Ryo
Published: June 2012

The timing of cambial reactivation plays an important role in determination of the amount and quality of wood and the environmental adaptivity of trees. Environmental factors, such as temperature, influence the growth and development of trees. Temperatures from late winter to early spring affect the physiological processes that are involved in the initiation of cambial cell division and xylem differentiation in trees. Cumulative elevated temperatures from late winter to early spring result in earlier initiation of cambial reactivation and xylem differentiation in tree stems and an extended growth period. However, earlier cambial reactivation increases the risk for frost damage because the cold tolerance of cambium decreases after cambial reactivation. The present review focuses on temperature regulation on the timing of cambial reactivation and xylem differentiation in trees, and also highlights recent advances in our understanding of seasonal changes in the cold stability of microtubules in trees. The review also summarizes the present understanding of the relationships between the timing of cambial reactivation, the start of xylem differentiation and changes in levels of storage materials in trees, as well as an attempt to identify the source of energy for cell division and differentiation. A better understanding of the mechanisms that regulate wood formation in trees and the influence of environmental conditions on such mechanisms should help in efforts to improve and enhance the exploitation of wood for commercial applications and to prepare for climatic change.
Seed size: a priority trait in cereal crops
Authors: Kesavan Markkandan , Song Jong Tae , Seo Hak Soo
Published: June 2012

Crop production and productivity must be increased to provide a balanced diet for the global population. The entire genome sequences of crop species allow the elucidation of genes that regulate important traits related to the final crop seed yield, which frequently depends mainly on seed size. Seed size is a major factor that controls seed quantity and it is strongly affected by various biotic, abiotic and genetic factors. Epigenetic marks in the genome and phytohormones are also important factors affecting seed growth and development. Several genes are known to be involved in the control of seed size, but their interaction and functional characterization have yet to be resolved. In this review, we discuss the different factors that govern seed size in cereal crops and Arabidopsis.
Is Sperm Freezability Related to the Post‐Thaw Lipid Peroxidation and the Formation of Reactive Oxygen Species in Boars?
Authors: Gómez‐Fernández J , Gómez‐Izquierdo E , Tomás C , Mocé E , de Mercado E
Published: June 2012

Contents

The aim of the present study was to determine whether the levels of reactive oxygen species (ROS) substances production and the levels of lipid peroxidation of the sperm membrane were related to the quality that the ejaculates exhibited after cryopreservation in boars. Ejaculates from 42 healthy boars were used in this study and they were cryopreserved with the lactose‐egg yolk extender (LEY). Several sperm quality parameters were assessed by flow cytometry in samples incubated for 30 and 150 min at 37°C after thawing: the percentage of sperm with intact plasma membrane (SIPM), intracellular reactive oxygen substances production through mean of DCF fluorescence intensity of total sperm (mean‐DCF) and the percentage of viable and non‐viable sperm containing oxidized BODIPY (VSOB and NVSOB). In addition, the percentages of total motile (TMS) and progressively motile sperm (PMS) were assessed at the same incubation times with a computer‐assisted sperm analysis system. The classification of the ejaculates into good or bad freezers was performed through hierarchical cluster analysis from SIPM and TMS at 150 min post‐thawing. The ejaculates of those males classified as good freezers exhibited higher (p < 0.05) SPIM, TMS and PMS than the bad freezers, although both groups presented similar (p > 0.05) VSOB, NVSOB and mean‐DCF. Therefore, these results show that lipid peroxidation and the amount of reactive oxygen substances in the sperm after cryopreservation are similar between boars classified as good or bad freezers.
Environmental Justice Storytelling: Angels and Isotopes at Yucca Mountain, Nevada
Authors: Houston Donna
Published: June 2012

Abstract:  This paper discusses the productive role of storytelling in community struggles for environmental justice. The individual and collective task of environmental justice storytelling highlights where the politics of pollution intersect with geographical imaginations. Storytelling takes on a productive role in transforming localized and individual emotions and experiences of environmental injustice into public knowledge that is performed in the world. This paper draws on a case study of nuclear waste disposal at Yucca Mountain in Nevada. I focus on how storytelling enacts scenarios of environmental witnessing and transformation that hold together a plurality of presences, absences, action and imagination, past histories and hope for the future.
Neurosarcoidosis‐related intracranial haemorrhage: three new cases and a systematic review of the literature
Authors: O'Dwyer J. P. , Al‐Moyeed B. A. , Farrell M. A. , Pidgeon C. N. , Collins D. R. , Fahy A. , Gibney J. , Swan N. , Dempsey O. J. , Kidd D. P. , Reid J. M. , Smyth S. , McCabe D. J. H.
Published: June 2012

Background and purpose

Intracranial haemorrhage in neurosarcoidosis (NS‐ICH) is rare, poorly understood and the diagnosis of NS may not be immediately apparent.

Methods

The clinical features of three new NS‐ICH cases are described including new neuropathological findings and collated with cases from a systematic literature review.

Results

Cases: (i) A 41‐year‐old man with headaches, hypoandrogenism and encephalopathy developed a cerebellar haemorrhage. He had neuropathological confirmation of NS with biopsy‐proven angiocentric granulomata and venous disruption. He responded to immunosuppressive therapy. (ii) A 41‐year‐old man with no history of hypertension was found unconscious. A subsequently fatal pontine haemorrhage was diagnosed. Liver biopsy revealed sarcoid granulomas. (iii) A 36‐year‐old man with raised intracranial pressure headaches presented with a seizure and a frontal haemorrhage. Hilar lymph node biopsy confirmed sarcoidosis, and he was treated successfully. Systematic review: Twelve other published cases were identified and collated with our cases. Average age was 36 years and M:F = 2.3:1; 46% presented with neurological symptoms and 31% had CNS‐isolated disease. Immediate symptoms of ICH were acute/worsening headache or seizures (60%). ICH was supratentorial (62%), infratentorial (31%) or subarachnoid (7%). Forty percent had definite NS, 53% probable NS and 7% possible NS (Zajicek criteria). Antigranulomatous/immunosuppressive therapy regimens varied and 31% died.

Conclusions

This series expands our knowledge of the pathology of NS‐ICH, which may be of arterial or venous origin. One‐third have isolated NS. Clinicians should consider NS in young‐onset ICH because early aggressive antigranulomatous therapy may improve outcome.
Whole genome amplification in large neurons of the terrestrial slug Limax
Authors: Yamagishi Miki , Ito Etsuro , Matsuo Ryota
Published: June 2012

J. Neurochem. (2012) 122, 727–737.

The brain of gastropod mollusks contains giant neurons whose nuclei are enlarged with a large amount of genomic DNA. Such DNA is produced by repeated endoreplication. We have previously demonstrated that the frequency of the neuronal DNA endoreplication is correlative to the body growth of the adult land slug and to the increase in the amount of transcripts within the neuron. However, it has long been controversial whether the neuronal DNA endoreplication entails whole genome amplification (polyploidy), or whether only the necessary genomic loci are amplified (polyteny, polysomy, or cis‐amplification by unequal recombination). In the present study, we adopted two modern techniques – quantitative genomic PCR and 5′‐bromodeoxyuridine labeling – to distinguish between these two possibilities. Our results demonstrated that multiple genomic loci were amplified to the same extent irrespective of the transcriptional activities at these loci. Moreover, the visceral giant cell, the biggest neuron in the slug’s brain, was estimated to contain approximately 10 000‐times as much genomic DNA as the haploid amount. The 5′‐bromodeoxyuridine‐labeling experiments also revealed a uniform DNA synthesis within the nucleus. These results strongly support the idea that the giant neurons contain a polyploid genome rather than a locus‐specific amplified genome.
Vimentin participates in microglia activation and neurotoxicity in cerebral ischemia
Authors: Jiang Susan X. , Slinn Jacqueline , Aylsworth Amy , Hou Sheng T.
Published: June 2012

J. Neurochem. (2012) 122, 764–774.

Microglia are the ‘immune cells’ of the brain and their activation plays a vital role in the pathogenesis of many neurodegenerative diseases. Activated microglia produce high levels of pro‐inflammatory factors, such as TNFα, causing neurotoxicity. Here we show that vimentin played a key role in controlling microglia activation and neurotoxicity during cerebral ischemia. Deletion of vimentin expression significantly impaired microglia activation in response to LPS in vitro and transient focal cerebral ischemia in vivo. Reintroduction of the functional vimentin gene back into vimentin knockout microglia restored their response to LPS. More importantly, impairment of microglia activation significantly protected brain from cerebral ischemia‐induced neurotoxicity. Collectively, we demonstrate a previously unknown function of vimentin in controlling microglia activation.
Photoperiodic expression of two RALDH enzymes and the regulation of cell proliferation by retinoic acid in the rat hypothalamus
Authors: Shearer Kirsty D. , Stoney Patrick N. , Nanescu Sonia E. , Helfer Gisela , Barrett Perry , Ross Alexander W. , Morgan Peter J. , McCaffery Peter
Published: June 2012

J. Neurochem. (2012) 122, 789–799.

Retinoic acid (RA) has been found to regulate hypothalamic function, but precisely where it acts is unknown. This study shows expression of retinaldehyde dehydrogenase (RALDH) enzymes in tanycytes that line the third ventricle in an area overlapping with the site of hypothalamic neural stem cells. The influence of RA was examined on the proliferation of progenitors lining the third ventricle using organotypic slice cultures. As has been shown in other regions of neurogenesis, RA was found to inhibit proliferation. Investigations of the dynamics of RALDH1 expression in the rat hypothalamus have shown that this enzyme is in tanycytes under photoperiodic control with highest levels during long versus short days. In parallel to this shift in RA synthesis, cell proliferation in the third ventricle was found to be lowest during long days when RA was highest, implying that RALDH1 synthesized RA may regulate neural stem cell proliferation. A second RA synthesizing enzyme, RALDH2 was also present in tanycytes lining the third ventricle. In contrast to RALDH1, RALDH2 showed little change with photoperiodicity, but surprisingly the protein was present in the apparent absence of mRNA transcript and it is hypothesized that the endocytic tanycytes may take this enzyme up from the cerebrospinal fluid (CSF).
Investigating the utility of human embryonic stem cell‐derived neurons to model ageing and neurodegenerative disease using whole‐genome gene expression and splicing analysis
Authors: Patani Rickie , Lewis Patrick A. , Trabzuni Daniah , Puddifoot Clare A. , Wyllie David J. A. , Walker Robert , Smith Colin , Hardingham Giles E. , Weale Michael , Hardy John , Chandran Siddharthan , Ryten Mina
Published: June 2012

J. Neurochem. (2012) 122, 738–751.

A major goal in regenerative medicine is the predictable manipulation of human embryonic stem cells (hESCs) to defined cell fates that faithfully represent their somatic counterparts. Directed differentiation of hESCs into neuronal populations has galvanized much interest into their potential application in modelling neurodegenerative disease. However, neurodegenerative diseases are age‐related, and therefore establishing the maturational comparability of hESC‐derived neural derivatives is critical to generating accurate in vitro model systems. We address this issue by comparing genome‐wide, exon‐specific expression analyses of pluripotent hESCs, multipotent neural precursor cells and a terminally differentiated enriched neuronal population to expression data from post‐mortem foetal and adult human brain samples. We show that hESC‐derived neuronal cultures (using a midbrain differentiation protocol as a prototypic example of lineage restriction), while successful in generating physiologically functional neurons, are closer to foetal than adult human brain in terms of molecular maturation. These findings suggest that developmental stage has a more dominant influence on the cellular transcriptome than regional identity. In addition, we demonstrate that developmentally regulated gene splicing is common, and potentially a more sensitive measure of maturational state than gene expression profiling alone. In summary, this study highlights the value of genomic indices in refining and validating optimal cell populations appropriate for modelling ageing and neurodegeneration.
Involvement of dopaminergic neuronal cystatin C in neuronal injury‐induced microglial activation and neurotoxicity
Authors: Dutta Garima , Barber David S. , Zhang Ping , Doperalski Nicholas J. , Liu Bin
Published: June 2012

J. Neurochem. (2012) 122, 752–763.

Factors released from injured dopaminergic (DA) neurons may trigger microglial activation and set in motion a vicious cycle of neuronal injury and inflammation that fuels progressive DA neurodegeneration in Parkinson’s disease. In this study, using proteomic and immunoblotting analysis, we detected elevated levels of cystatin C in conditioned media (CM) from 1‐methyl‐4‐phenylpyridinium and dieldrin‐injured rat DA neuronal cells. Immunodepletion of cystatin C significantly reduced the ability of DA neuronal CM to induce activation of rat microglial cells as determined by up‐regulation of inducible nitric oxide synthase, production of free radicals and release of proinflammatory cytokines as well as activated microglia‐mediated DA neurotoxicity. Treatment of the cystatin C‐containing CM with enzymes that remove O‐ and sialic acid‐, but not N‐linked carbohydrate moieties markedly reduced the ability of the DA neuronal CM to activate microglia. Taken together, these results suggest that DA neuronal cystatin C plays a role in the neuronal injury‐induced microglial activation and neurotoxicity. These findings from the rat DA neuron‐microglia in vitro model may help guide continued investigation to define the precise role of cystatin C in the complex interplay among neurons and glia in the pathogenesis of Parkinson’s disease.
Ancient DNA identifies post‐glacial recolonisation, not recent bottlenecks, as the primary driver of contemporary mtDNA phylogeography and diversity in Scandinavian brown bears
Authors: Bray Sarah C.E. , Austin Jeremy J. , Metcalf Jessica L. , Østbye Kjartan , Østbye Eivind , Lauritzen Stein‐Erik , Aaris‐Sørensen Kim , Valdiosera Cristina , Adler Christina J , Cooper Alan
Published: June 2012

Aim

Brown bear populations in Scandinavia show a strong mitochondrial DNA (mtDNA) phylogeographic structure and low diversity relative to other parts of Europe. Identifying the timing and origins of this mtDNA structure is important for conservation programs aimed at restoring populations to a natural state. Therefore, it is essential to identify whether contemporary genetic structure is linked to post‐glacial recolonisation from divergent source populations or an artefact of demographic impacts during recent population bottlenecks. We employed ancient DNA techniques to investigate the timing and potential causes of these patterns.

Location

Scandinavia and Europe.

Methods

Ancient mtDNA sequences from 20 post‐glacial Scandinavian bears were used to investigate phylogeographic structure and genetic diversity over the last 6000 years. MtDNA from 19 Holocene Norwegian bears was compared with 499 sequences from proximate extant populations in Sweden, Finland, Estonia and western Russia. A single mtDNA sequence from a Holocene Denmark sample was compared with 149 ancient and modern bears from Western Europe.

Results

All nineteen Holocene Norwegian samples are identical to or closely related to the most common mtDNA haplotype found in northern Europe today. MtDNA diversity was low and not significantly different from extant populations in northern Europe. In Denmark, we identified a single mtDNA haplotype that is previously unrecorded from Scandinavia.

Main conclusions

The current discrete phylogeographic structure and lack of mtDNA diversity in Scandinavia is attributed to serial founder effects during post‐glacial recolonisation from divergent source populations rather than an artefact of recent anthropogenic impacts. In contrast to previous interpretations, the recolonisation of southern Scandinavia may not have been limited to bears from a single glacial refugium. Results highlight the importance of conserving the long‐term evolutionary separation between northern and southern populations and identify southern Scandinavia as an important reservoir of mtDNA diversity that is under threat in other parts of Europe.
Stable‐hydrogen isotope measures of natal dispersal reflect observed population declines in a threatened migratory songbird
Authors: Studds Colin E. , McFarland Kent P. , Aubry Yves , Rimmer Christopher C. , Hobson Keith A. , Marra Peter P. , Wassenaar Leonard I.
Published: June 2012

Aim

Measuring dispersal is crucial for estimating demographic rates that inform conservation plans for rare and threatened species. We evaluated natal dispersal patterns in Bicknell's thrush (Catharus bicknelli) across most of the breeding range using a 10‐year data set of stable‐hydrogen isotope ratios in feathers (δ2HF) grown on the natal area and sampled 1 year later at the first breeding site.

Location

North‐eastern United States and south‐eastern Canada.

Methods

We used δ2HF values of adult thrushes sampled at 25 breeding sites as prior information for assigning first‐time breeders to their natal site. We calculated the minimum distance birds moved from their natal to first breeding site and fit these data to three statistical distributions for characterizing the importance of long‐distance dispersal: the exponential, Weibull and half‐Cauchy. Finally, we assessed differences in the probability of dispersal across the breeding range and through time to understand spatio‐temporal variation in demographic connectivity.

Results

The δ2HF values of first‐time breeders were lower compared with those of adults, a difference that was greater at the southern compared with northern breeding range extreme. Assignment tests accounting for age differences in δ2HF suggested that most birds dispersed < 200 km from their natal area and within the centre of the breeding range, whereas comparatively few individuals dispersed up to 700 km. A Weibull distribution provided the best fit to these data. Two of three corrections for age differences in δ2HF indicated that natal dispersal probability declined by 30–38% from 1996 to 2005.

Main conclusions

Our findings suggest that estimating natal dispersal with δ2HF measurements may contribute to understanding the resilience of geographically isolated Bicknell's thrush populations. Declining natal dispersal may be symptomatic of observed population declines and could compound this trend by limiting demographic exchange between habitat patches predicted to be increasingly isolated by natural and anthropogenic habitat changes.
The impact of aging on mitochondrial function and biogenesis pathways in skeletal muscle of sedentary high‐ and low‐functioning elderly individuals
Authors: Joseph Anna‐Maria , Adhihetty Peter J. , Buford Thomas W. , Wohlgemuth Stephanie E. , Lees Hazel A. , Nguyen Linda M.‐D. , Aranda Juan M. , Sandesara Bhanu D. , Pahor Marco , Manini Todd M. , Marzetti Emanuele , Leeuwenburgh Christiaan
Published: June 2012

Age‐related loss of muscle mass and strength (sarcopenia) leads to a decline in physical function and frailty in the elderly. Among the many proposed underlying causes of sarcopenia, mitochondrial dysfunction is inherent in a variety of aged tissues. The intent of this study was to examine the effect of aging on key groups of regulatory proteins involved in mitochondrial biogenesis and how this relates to physical performance in two groups of sedentary elderly participants, classified as high‐ and low‐functioning based on the Short Physical Performance Battery test. Muscle mass was decreased by 38% and 30% in low‐functioning elderly (LFE) participants when compared to young and high‐functioning elderly participants, respectively, and positively correlated to physical performance. Mitochondrial respiration in permeabilized muscle fibers was reduced (41%) in the LFE group when compared to the young, and this was associated with a 30% decline in cytochrome c oxidase activity. Levels of key metabolic regulators, SIRT3 and PGC‐1α, were significantly reduced (50%) in both groups of elderly participants when compared to young. Similarly, the fusion protein OPA1 was lower in muscle from elderly subjects; however, no changes were detected in Mfn2, Drp1 or Fis1 among the groups. In contrast, protein import machinery components Tom22 and cHsp70 were increased in the LFE group when compared to the young. This study suggests that aging in skeletal muscle is associated with impaired mitochondrial function and altered biogenesis pathways and that this may contribute to muscle atrophy and the decline in muscle performance observed in the elderly population.
The use of multiple 8 compression suturing as a novel procedure to preserve fertility in patients with placenta accreta: case series
Authors: Shazly Sherif A.‐E.M. , Badee Ahmed Y.A. , Ali Mohammed K.
Published: June 2012

Placenta accreta/percreta is a serious cause of intractable post‐partum haemorrhage during caesarean section and a common cause of peripartum hysterectomy. In this case series, we evaluated the use of multiple 8 sutures as a novel procedure to preserve the uterus in these cases. Seven women with placenta accreta/percreta were initially managed with bilateral uterine artery ligation. The procedure was resorted to in cases that did not respond to ligation (five women). Women were followed up for up to 24 months to report complications.
Implementation and audit of ‘Fast‐Track Surgery’ in gynaecological oncology surgery
Authors: Sidhu Verinder S. , Lancaster Letitia , Elliott David , Brand Alison H.
Published: June 2012

Background

Fast‐track surgery is a multidisciplinary approach to surgery that results in faster recovery from surgery and decreased length of stay (LOS).

Aims

The aims of this study were as follows: (i) to report on the processes required for the introduction of fast‐track surgery to a gynaecological oncology unit and (ii) to report the results of a clinical audit conducted after the protocol's implementation.

Methods

A fast‐track protocol, specific to our unit, was developed after a series of multidisciplinary meetings. The protocol, agreed upon by those involved in the care of women in our unit, was then introduced into clinical practice. An audit was conducted of all women undergoing laparotomy, with known or suspected malignancy. Information on LOS, complication and readmission rates was collected. Descriptive statistics and Poisson regression were used for statistical analysis.

Results

The developed protocol involved a multidisciplinary approach to pre‐, intra‐ and postoperative care. The audit included 104 consecutive women over a 6‐month period, who were followed for 6 weeks postoperatively. The median LOS was 4 days. The readmission rate was 7% and the complication rate was 19% (1% intraoperative, 4% major and 14% minor). Multivariate analysis revealed that increased duration of surgery and increasing age were predictors of longer LOS.

Conclusion

The development of a fast‐track protocol is achievable in a gynaecological oncology unit, with input from a multidisciplinary team. Effective implementation of the protocol can result in a short LOS, with acceptable complication and readmission rates when applied non‐selectively to gynaecological oncology patients.
The Rise and Fall of a Regulator: Adventure Sports in the United Kingdom
Authors: Ball‐King Laurence , Watt John , Ball David J.
Published: June 2012

Following a tragic accident in 1993 involving the deaths of teenagers while kayaking a new regulatory regime was imposed upon some adventure sports providers in the United Kingdom. In particular, a new regulatory body, the Adventure Activities Licensing Authority (AALA), was established to oversee the sector. Yet in 2010, a government‐sponsored review recommended that AALA be abolished and this recommendation has been quickly accepted by government. This article explores the background to these developments through documentation, interviews with those affected by the AALA regime, and court cases. Evidence reported here, perhaps surprising, is that AALA itself is seen in a very positive light by many, even those it regulates. What may have happened is that AALA became caught up in a wider debate about the place and management of risk in life beyond the workplace, which has been simmering in the United Kingdom for a decade or more, and of which it fell foul. It may also be that adventure sports, because they entail voluntary engagement with high consequence hazards, starkly expose serious questions about the application of conventional, factory‐originated risk assessment approaches to life in general.
Model Uncertainty and Model Averaging in the Estimation of Infectious Doses for Microbial Pathogens
Authors: Moon Hojin , Kim Steven B. , Chen James J. , George Nysia I. , Kodell Ralph L.
Published: June 2012

Food‐borne infection is caused by intake of foods or beverages contaminated with microbial pathogens. Dose‐response modeling is used to estimate exposure levels of pathogens associated with specific risks of infection or illness. When a single dose‐response model is used and confidence limits on infectious doses are calculated, only data uncertainty is captured. We propose a method to estimate the lower confidence limit on an infectious dose by including model uncertainty and separating it from data uncertainty. The infectious dose is estimated by a weighted average of effective dose estimates from a set of dose‐response models via a Kullback information criterion. The confidence interval for the infectious dose is constructed by the delta method, where data uncertainty is addressed by a bootstrap method. To evaluate the actual coverage probabilities of the lower confidence limit, a Monte Carlo simulation study is conducted under sublinear, linear, and superlinear dose‐response shapes that can be commonly found in real data sets. Our model‐averaging method achieves coverage close to nominal in almost all cases, thus providing a useful and efficient tool for accurate calculation of lower confidence limits on infectious doses.
Long‐Term Outcomes of Cardiovascular Implantable Electronic Devices in Patients with Staphylococcus aureus Bacteremia
Authors: OBEID KARAM M. , SZPUNAR SUSAN , KHATIB RIAD
Published: June 2012

Background:

The use of cardiovascular implantable electronic devices (CIEDs) is increasing. Staphylococcus aureus bacteremia (SAB) poses a risk for hematogenous seeding of the device. Our aim is to identify risk factors associated with secondary CIED infection, due to hematogenous seeding, during SAB from an unrelated primary focus.

Methods:

All patients with SAB and CIED were screened. Patients with SAB due to a primary source unrelated to the CIED were included. Patients were classified into cases if CIED infection was documented and controls without CIED infection during a minimum of 12 weeks follow‐up. A retrospective review of patients’ charts was done.

Results:

Thirty patients with CIED and SAB from an unrelated focus were identified. CIED infection developed in 11 patients (36.7%). No significant differences were noted between cases and controls in the source, time‐to‐therapy, and time‐to‐intervene but infected devices were more likely to be implantable cardioverter‐defibrillators (ICD) versus permanent pacemakers (PPMs) (9/11 [81.8%] vs 2/11 [18.2%] respectively, crude odds ratio 12.6, 95% confidence interval 10.8–14.4; P = 0.003).

Conclusion:

Hematogenous seeding of a CIED during SAB from an unrelated focus is not uncommon. The risk factors for CIED seeding are unknown but ICD devices seem to be at greater risk when compared to PPM. The reasons are not yet clear. Larger studies are needed to better define risk factors and design preventive measures. (PACE 2012; 35:961–965)
Closed Loop Stimulation is Effective in Improving Heart Rate and Blood Pressure Response to Mental Stress: Report of a Single‐Chamber Pacemaker Study in Patients with Chronotropic Incompetent Atrial Fibrillation
Authors: PROIETTI RICCARDO , MANZONI GIANMAURO , DI BIASE LUIGI , CASTELNUOVO GIANLUCA , LOMBARDI LEONIDA , FUNDARÒ CAMILLA , VEGLIANTE NADIA , PIETRABISSA GIADA , SANTANGELI PASQUALE , CANBY ROBERT A. , SAGONE ANTONIO , VIECCA MAURIZIO , NATALE ANDREA
Published: June 2012

Introduction:

Closed‐loop stimulation (CLS) is a form of rate‐adaptive pacing capable of providing an effective pacing rate profile not only during physical exercise but also during mental stress. To test its effectiveness, CLS and accelerometer sensor (AS) rate response were compared intraindividually during a mental stress test (MST).

Methods:

Thirty‐six patients (mean age 78.9 ± 6.4 years) implanted with a pacemaker with the CLS algorithm (Cylos, Biotronik, Berlin, Germany) underwent MSTs in different pacing configurations: nonrate‐adaptive mode (VVI), AS mode (VVIR), and CLS mode, respectively. A modified Stroop test was used in order to induce mental stress. Heart rate (HR), systolic blood pressure (SBP), diastolic blood pressure, and pacing percentage burden were collected for 5 minutes before, during, and 5 minutes after the test.

Results:

Mean peak‐HR during MST was significantly higher in CLS configuration than in VVIR and VVI modes (92.8 ± 12.6 vs 78.9 ± 6.5 vs 77.8 ± 7.5; P ≤ 0.001). The average HR increase during MST was also higher in CLS configuration than in VVIR and VVI modes (22.7 ± 16.7 vs 8.2 ± 8.6 vs 6.6 ± 6.3; P ≤ 0.001). The percentage of pacing beats during MST was higher in CLS configuration than with the other two algorithms (48.4 ± 17.9 vs 27.4 ± 17.5 vs 25.8 ± 17.6; P ≤ 0.001). The average peak‐SBP was significantly higher during MST in CLS mode than in VVIR and VVI configurations (172.6 ± 15.5 vs 156.7 ± 12.2 vs 145.5 ± 13.7; P ≤ 0.001). The mean SBP increase showed a similar behavior (51.8 ± 24.7 vs 18.4 ± 13.7 vs 16.4 ± 10.3; P ≤ 0.001).

Conclusion:

CLS algorithm in a single‐chamber device is more effective than AS in detecting an hemodynamic demand due to an emotional stress and supplying a proper HR increase. These results are even more surprising compared to previous data in dual‐chamber pacemakers, because they imply that CLS algorithm can provide an appropriate rate‐modulation in patients with AF and chronotropic incompetence.
(PACE 2012; 35:990–998)
Growth of Calcium Hydroxide Islands in Tricalcium Silicate‐Based Cements at Early Age
Authors: Xie Tiantian , Biernacki Joseph J.
Published: June 2012

Microstructural characteristics of hydrated triclinic tricalcium silicate [C3S(t)], monoclinic tricalcium silicate (alite), and type I portland cement at ages between time zero and 28 days were observed using electron microscopy. Image analysis was used to follow the development of calcium hydroxide (Ca(OH)2) and calcium silicate hydrate at micro‐ and meso‐length scales. In all cases, easily recognizable islands of Ca(OH)2 were noted to form, though the morphology and rate of formation differed for the three cement types. The formation of these islands was found to influence hydration by hindering the reaction of unhydrated cement particles that are embedded within their largely Ca(OH)2‐bearing matrix. Such may be important features to include and validate in developing microstructural and other forms of computational models. The extent to which such microstructural features influence the local rates of reaction seems to depend, at least in part, upon the crystallography of the C3S.