bluuebunny/crossref_metadata_2025 huggingface dataset:
Alternative editing of cytochrome c oxidase III mRNA in trypanosome mitochondria generates protein diversity
Authors: Ochsenreiter Torsten , Hajduk Stephen L
Published: September 2006

Trypanosomes use RNA editing to produce most functional mitochondrial messenger RNA. Precise insertion and deletion of hundreds of uridines is necessary to make full‐length cytochrome c oxidase III (COXIII) mRNA. We show that COXIII mRNA can be alternatively edited by a mechanism using an alternative guide RNA to make a stable mRNA. This alternatively edited mRNA is translated to produce a unique protein that fractionates with mitochondrial membranes and colocalizes with mitochondrial proteins in situ. Alternative RNA editing represents a previously unknown mechanism generating protein diversity and, as such, represents an important function for RNA editing.
Asn‐ and Asp‐mediated interactions between transmembrane helices during translocon‐mediated membrane protein assembly
Authors: Meindl‐Beinker Nadja M , Lundin Carolina , Nilsson IngMarie , White Stephen H , von Heijne Gunnar
Published: September 2006

Inter‐helix hydrogen bonding involving asparagine (Asn, N), glutamine (Gln, Q), aspartic acid (Asp, D) or glutamic acid (Glu, E) can drive efficient di‐ or trimerization of transmembrane helices in detergent micelles and lipid bilayers. Likewise, Asn–Asn and Asp–Asp pairs can promote the formation of helical hairpins during translocon‐mediated membrane protein assembly in the endoplasmic reticulum. By in vitro translation of model integral membrane protein constructs in the presence of rough microsomes, we show that Asn‐ or Asp‐mediated interactions with a neighbouring transmembrane helix can enhance the membrane insertion efficiency of a marginally hydrophobic transmembrane segment. Our observations suggest that inter‐helix hydrogen bonds can form during Sec61 translocon‐assisted insertion and thus could be important for membrane protein assembly.
wasted away
, a
Drosophila
mutation in triosephosphate isomerase, causes paralysis, neurodegeneration, and early death
Authors: Gnerer Joshua P. , Kreber Robert A. , Ganetzky Barry
Published: September 2006

To identify genes required for maintaining neuronal viability, we screened our collection of
Drosophila
temperature-sensitive paralytic mutants for those exhibiting shortened lifespan and neurodegeneration. Here, we describe the characterization of
wasted away
(
wstd
), a recessive, hypomorphic mutation that causes progressive motor impairment, vacuolar neuropathology, and severely reduced lifespan. We demonstrate that the affected gene encodes the glycolytic enzyme, triosephosphate isomerase (Tpi). Mutations causing Tpi deficiency in humans are also characterized by progressive neurological dysfunction, neurodegeneration, and early death. In Tpi-deficient flies and humans, a decrease in ATP levels did not appear to cause the observed phenotypes because ATP levels remained normal. We also found no genetic evidence that the mutant
Drosophila
Tpi was misfolded or involved in aberrant protein–protein associations. Instead, we favor the hypothesis that mutations in Tpi lead to an accumulation of methylglyoxal and the consequent enhanced production of advanced glycation end products, which are ultimately responsible for the death and dysfunction of Tpi-deficient neurons. Our results highlight an essential protective role of Tpi and support the idea that advanced glycation end products may also contribute to pathogenesis of other neurological disorders.
Holomorphic continuation of generalized Jacquet integrals for degenerate principal series
Authors: Wallach Nolan
Published: September 2006

This paper introduces a class of parabolic subgroups of real reductive groups (called “very nice”). For these parabolic subgroups we study the generalized Whittaker vectors for their degenerate principal series. It is shown that there is a holomorphic continuation of the Jacquet integrals associated with generic characters of their unipotent radicals. Also, in this context an analogue of the “multiplicity one” theorem is proved. Included is a complete classification of these parabolic subgroups (due to K. Baur and the author). These parabolic subgroups include all known examples of such continuations and multiplicity theorems.
Assessment of Bone Mineral Density in Duchenne Muscular Dystrophy Using the Lateral Distal Femur
Authors: Harcke H Theodore , Kecskemethy Heidi H , Conklin Dolores , Scavina Mena , Mackenzie William G , McKay Charles P
Published: September 2006

Objectives:

To document lateral distal femur (LDF) bone mineral density (BMD) values in children with Duchenne muscular dystrophy (DMD) and to examine the potential for these measures to aid in their care.

Methods:

Forty-seven boys with DMD had a total of 82 studies of BMD at multiple sites (whole body, lumbar spine, distal femur). Measures were converted to age-adjusted z-scores and analyzed for ambulatory status, steroid use, and fracture history.

Results:

Bone mineral density z-scores were significantly lower in the whole body and LDF in children who were partially ambulatory and nonambulatory when compared with children who were always ambulatory. With a positive history of fracture, mean LDF z-scores were significantly lower when compared with mean z-scores of children with no fractures. Lateral distal femur BMD correlated with ambulation and fracture better than whole body and lumbar spine BMD.

Conclusions:

The LDF is recommended as a more sensitive alternative to lumbar spine for measure of BMD in children with DMD.
A Woman With Spontaneous Focal Muscle Movements
Authors: Perez Angel S , Bertorini Tulio E , Narayanaswami Pushpa
Published: September 2006

The present case is about a patient who had rolling muscle contractions, which were electrically silent. She was diagnosed as having Rippling Muscle Disease, in her case; this disorder was likely autoimmune associated. RMD can be hereditary, acquired due to de novo mutations, or have autoimmune etiology. Most of the time RMD is associated with myasthenia gravis. Depending of the form of RMD, patients respond to dantrolene and/or immunossupresants.
Where do all the maternal effects go? Variation in offspring body size through ontogeny in the live-bearing fishPoecilia parae
Authors: Lindholm Anna K , Hunt John , Brooks Robert
Published: September 2006

Maternal effects are an important source of adaptive variation, but little is known about how they vary throughout ontogeny. We estimate the contribution of maternal effects, sire genetic and environmental variation to offspring body size from birth until 1 year of age in the live-bearing fishPoecilia parae. In both the sexes, maternal effects on body size were initially high in juveniles, and then declined to zero at sexual maturity. In sons, this was accompanied by a sharp rise in sire genetic variance, consistent with the expression of Y-linked loci affecting male size. In daughters, all variance components decreased with time, consistent with compensatory growth. There were significant negative among-dam correlations between early body size and the timing of sexual maturity in both sons and daughters. However, there was no relationship between early life maternal effects and adult longevity, suggesting that maternal effects, although important early in life, may not always influence late life-history traits.
Testing hypotheses of Pleistocene population history using coalescent simulations: phylogeography of the pygmy nuthatch (Sitta pygmaea)
Authors: Spellman Garth M , Klicka John
Published: September 2006

In this paper, we use mitochondrial NADH dehydrogenase subunit 2 sequences to test Pleistocene refugial hypotheses for the pygmy nuthatch (Sitta pygmaea). Pygmy nuthatches are a common resident of long-needle pine forests in western North America and demonstrate a particular affinity with ponderosa pine (Pinus ponderosa). Palaeoecological and genetic data indicate that ponderosa pine was isolated in two Pleistocene refugia corresponding to areas in the southern Sierra Nevada in the west and southern Arizona and New Mexico in the east. We use coalescent simulations to test the hypothesis that pygmy nuthatches tracked the Pleistocene history of their preferred habitat and persisted in two refugia during the periods of glacial maxima. Coalescent simulation of population history does not support the hypothesis of two Pleistocene refugia for the pygmy nuthatch. Instead, our data are consistent with a single refuge model. Nucleotide diversity is greatest in the western populations of southern and coastal California. We suggest that the pygmy nuthatch expanded from a far western glacial refuge into its current distribution since the most recent glacial maximum.
Sexual selection predicts advancement of avian spring migration in response to climate change
Authors: Spottiswoode Claire N , Tøttrup Anders P , Coppack Timothy
Published: September 2006

Global warming has led to earlier spring arrival of migratory birds, but the extent of this advancement varies greatly among species, and it remains uncertain to what degree these changes are phenotypically plastic responses or microevolutionary adaptations to changing environmental conditions. We suggest that sexual selection could help to understand this variation, since early spring arrival of males is favoured by female choice. Climate change could weaken the strength of natural selection opposing sexual selection for early migration, which would predict greatest advancement in species with stronger female choice. We test this hypothesis comparatively by investigating the degree of long-term change in spring passage at two ringing stations in northern Europe in relation to a synthetic estimate of the strength of female choice, composed of degree of extra-pair paternity, relative testes size and degree of sexually dichromatic plumage colouration. We found that species with a stronger index of sexual selection have indeed advanced their date of spring passage to a greater extent. This relationship was stronger for the changes in the median passage date of the whole population than for changes in the timing of first-arriving individuals, suggesting that selection has not only acted on protandrous males. These results suggest that sexual selection may have an impact on the responses of organisms to climate change, and knowledge of a species' mating system might help to inform attempts at predicting these.
Experimentally induced change in infectious period affects transmission dynamics in a social group
Authors: Naug Dhruba , Smith Brian
Published: September 2006

A key component of any epidemiological model is the infectious period, which greatly affects the dynamics and persistence of an infection. Social organization, leading to behavioural and spatial heterogeneities among potential susceptibles, interacts with infectious period to create different risk categories within a group. Using the honeybee (
Apis mellifera
) colony as a social model, a protocol that creates different infectious periods in individual bees and another that follows the diffusion of a transmittable tracer within a colony, we show experimentally how a short infectious period results in an epidemic process with low prevalence confined only to individuals at the outer edge of a group, while a long infectious period results in high prevalence distributed more universally among all the group members. We call this finding an evidence of ‘organizational immunity’ in a social network and propose that the honeybee colony provides a unique opportunity to test its role in social transmission processes.
From record performance to hypoxia tolerance: respiratory transition in damselfish larvae settling on a coral reef
Authors: Nilsson Göran E , Östlund-Nilsson Sara , Penfold Rose , Grutter Alexandra S
Published: September 2006

The fastest swimming fishes in relation to size are found among coral reef fish larvae on their way to settle on reefs. By testing two damselfishes,Chromis atripectoralisandPomacentrus amboinensis, we show that the high swimming speeds of the pre-settlement larvae are accompanied by the highest rates of oxygen uptake ever recorded in ectothermic vertebrates. As expected, these high rates of oxygen uptake occur at the cost of poor hypoxia tolerance. However, hypoxia tolerance is needed when coral reef fishes seek nocturnal shelter from predators within coral colonies, which can become severely hypoxic microhabitats at night. When the larvae settle on the reef, we found that they go through a striking respiratory transformation, i.e. the capacity for rapid oxygen uptake falls, while the ability for high-affinity oxygen uptake at low oxygen levels is increased. This transition to hypoxia tolerance is needed when they settle on the reef; this was strengthened by our finding that small resident larvae ofAcanthochromis polyacanthus, a damselfish lacking a planktonic larval stage, do not display such a transition, being well adapted to hypoxia and showing relatively low maximum rates of oxygen uptake that change little with age.
Submillimetre-wave lines of H
2
D
+
and D
2
H
+
as probes into chemistry in cold dark clouds
Authors: Amano Takayoshi
Published: September 2006

We discuss past and recent progress of our continuing project of submillimetre-wave spectroscopic investigations of H
2
D
+
and D
2
H
+
. Three new lines of H
2
D
+
in the 2.5–3.5 THz range are measured with a tunable far-infrared laser system. Since these molecules are very light asymmetric molecules, analysis based on a conventional effective Hamiltonian is not very useful in predicting the transition frequencies to the accuracy of the order of several MHz or better. In this respect, any addition of new accurate measurements of transition frequencies is important. In this paper, some discussions will be made on

and its deuterated species as probable interstellar species in cold dark clouds. In particular,

, which is predicted to be abundant in cold dark clouds, can be (indirectly) detected by observing

.
Starkeya koreensis sp. nov., isolated from rice straw
Authors: Im Wan-Taek , Aslam Zubair , Lee Myungjin , Ten Leonid N. , Yang Deok-Chun , Lee Sung-Taik
Published: September 2006

A facultatively chemolithoautotrophic, Gram-negative, aerobic, highly curved rod-shaped, non-motile, non-spore-forming bacterium, strain Jip08T, was isolated from rice straw in Daejeon, South Korea. Strain Jip08T produced colourless colonies (1.0–1.5 mm) on R2A medium after 3 days. On the basis of 16S rRNA gene sequence similarity, strain Jip08T was shown to belong to the α-2 subclass of the Proteobacteria, and was most closely related to Starkeya novella IAM 12100T (98.6 %), Angulomicrobium tetraedale DSM 5895T (98.1 %), Angulomicrobium amanitiforme NCIMB 1785T (98.0 %), Ancylobacter aquaticus ATCC 25396T (96.6 %) and Methylorhabdus multivorans DM13T (95.8 %), all of which belong to the family Hyphomicrobiaceae. The genomic DNA G+C content of strain Jip08T was 69 mol%. Chemotaxonomic data [major ubiquinone, Q-10; major fatty acids, C18 : 1 isomer (summed feature of C18 : 1
ω7c/ω9t/ω12t), C19 : 0 cyclo ω8c and C16 : 0], 16S rRNA gene sequence analyses and some morphological and physiological features supported the affiliation of strain Jip08T to the genus Starkeya. However, DNA–DNA hybridization data and some phenotypic properties showed that strain Jip08T could be distinguished from the single known Starkeya species and represented a novel species, for which the name Starkeya koreensis sp. nov. is proposed. The type strain is Jip08T (=KCTC 12212T=NBRC 100963T=IAM 15215T).
Proposal of Roseburia faecis sp. nov., Roseburia hominis sp. nov. and Roseburia inulinivorans sp. nov., based on isolates from human faeces
Authors: Duncan Sylvia H. , Aminov Rustam I. , Scott Karen P. , Louis Petra , Stanton Thaddeus B. , Flint Harry J.
Published: September 2006

Seven recently cultured bacterial isolates, although similar in their 16S rRNA gene sequences toRoseburia intestinalisL1-82T(DSM 14610T), were not sufficiently related for inclusion within existing species, forming three separate clusters in a 16S rRNA gene phylogenetic tree. The isolates, which were obtained from human stools, were Gram-variable or Gram-negative, strictly anaerobic, slightly curved rods; cells from all strains measured approximately 0.5×1.5–5.0 μm and were motile. Two strains belonging to one cluster (A2-181 and A2-183T) were the only strains that were able to grow on glycerol and that failed to grow on any of the complex substrates tested (inulin, xylan and amylopectin). Strains belonging to a second cluster (represented by M6/1 and M72/1T) differed from the other isolates in their ability to grow on sorbitol. Isolates belonging to a third cluster (L1-83 and A2-194T) were the only strains that failed to grow on xylose and that gave good growth on inulin (strains M6/1 and M72/1Tgave weak growth). All strains were net acetate utilizers. The DNA G+C contents of representativeRoseburiastrains A2-183T, A2-194T, M72/1TandR. intestinalisL1-82Twere 47.4, 41.4, 42.0 and 42.6 mol%, respectively. Based on 16S rRNA gene sequence similarity, three novelRoseburiaspecies are proposed, with the namesRoseburia hominissp. nov. (type strain A2-183T=DSM 16839T=NCIMB 14029T),Roseburia inulinivoranssp. nov. (type strain A2-194T=DSM 16841T=NCIMB 14030T) andRoseburia faecissp. nov. (type strain M72/1T=DSM 16840T=NCIMB 14031T).
Paracoccus homiensis sp. nov., isolated from a sea-sand sample
Authors: Kim Byung-Yong , Weon Hang-Yeon , Yoo Seung-Hee , Kwon Soon-Wo , Cho Yang-Hee , Stackebrandt Erko , Go Seung-Joo
Published: September 2006

Strain DD-R11T, isolated from a sea-sand sample from Homi Cape, Pohang city, South Korea, was a Gram-negative, aerobic, motile, non-spore-forming, rod- to ovoid-shaped bacterium. Colonies grown on marine agar were circular, convex and colourless to creamy white. Growth occurred between 10 and 40 °C (optimum 25–30 °C) and at pH 5.0–9.0 (optimum pH 6.0–8.0). The strain could grow in up to 15 % NaCl (optimum 3–5 % NaCl). According to 16S rRNA gene sequence analysis, the strain was a member of the genus Paracoccus in the Alphaproteobacteria. Sequence similarities to type strains of the genus Paracoccus were between 94.6 and 98.3 %, showing the highest sequence similarity to Paracoccus zeaxanthinifaciens ATCC 21588T. The DNA–DNA relatedness value of strain DD-R11T and P. zeaxanthinifaciens ATCC 21588T was 27 %. Strain DD-R11T was characterized by having ubiquinone 10 as the major respiratory quinone and C18 : 1
ω7c as the predominant fatty acid. The DNA G+C content was 63.0 mol%. On the basis of its phenotypic and genotypic characteristics, it is suggested that DD-R11T represents a novel species of the genus Paracoccus, for which the name Paracoccus homiensis sp. nov. is proposed, with DD-R11T (=KACC 11518T=DSM 17862T) as the type strain.
Paenibacillus sepulcri sp. nov., isolated from biodeteriorated mural paintings in the Servilia tomb
Authors: Šmerda Jakub , Sedláček Ivo , Páčová Zdena , Krejčí Eva , Havel Ladislav
Published: September 2006

In 2001, a Gram-variable, facultatively anaerobic, endospore-forming bacterium isolated from biodeteriorated mural paintings in the Servilia tomb of the Roman necropolis of Carmona was deposited asPaenibacillusstrain LMG 19508. Subsequently, the strain was characterized in detail using phenotypic and molecular methods. The 16S rRNA gene sequence confirmed that the strain belongs to the genusPaenibacillusand indicated its relationship toPaenibacillus mendeliiCCM 4839T(96.7 % sequence similarity). The predominant menaquinone was MK-7. The cell wall containedmeso-diaminopimelic acid of the A1γtype. The DNA G+C content (50 mol%) and the major fatty acid (anteiso-C15 : 0) of strain LMG 19508Twere also consistent with its affiliation to the genusPaenibacillus. DNA–DNA hybridization distinguished strain LMG 19508Tfrom other phylogenetically relatedPaenibacillusspecies. Therefore, the isolate represents a novel species, for which the namePaenibacillus sepulcrisp. nov. is proposed. The type strain is CCM 7311T(=LMG 19508T).
Updated phylogeny of the genus Aeromonas
Authors: Saavedra M. J. , Figueras M. J. , Martínez-Murcia A. J.
Published: September 2006

Recent phylogenetic studies of the genusAeromonasbased ongyrBandrpoDgene sequences have improved the phylogeny based on 16S rRNA gene sequences first published in 1992, particularly in the ability to split closely related species. These studies did not include the recently described speciesAeromonas simiaeandAeromonas molluscorumand only a single strain ofAeromonas culicicolawas available for analysis at that time. In the present work, theseAeromonasspecies and newly isolated strains ofA. culicicolawere examined. Sequence analysis indicates thatA. simiaeandA. molluscorumbelong to non-described phylogenetic lines of descent within this genus, which supports the original description of both species. The most closely related species areAeromonas schubertiiandAeromonas encheleia, respectively, which is consistent with 16S rRNA gene sequencing results. However, while the five strains ofA. molluscorumshowed nucleotide differences in theirgyrBandrpoDgene sequences, the only two knownA. simiaestrains exhibited identical gene sequences, suggesting that they are isolates of the same strain. On the basis of therpoDgene sequence phylogeny,A. culicicolastrains from the original description and new isolates from drinking water and ornamental fish clustered within the speciesAeromonas veronii, suggesting inconsistencies with previous results. Other strains with previously controversial taxonomy and new isolates from other studies were included in this study in order to clarify their phylogenetic affiliation at the species level.
Morganella psychrotolerans sp. nov., a histamine-producing bacterium isolated from various seafoods
Authors: Emborg Jette , Dalgaard Paw , Ahrens Peter
Published: September 2006

Mesophilic Morganella morganii (n=6) and psychrotolerant M. morganii-like isolates from various seafoods (n=13), as well as clinical M. morganii isolates (n=3), were characterized by using a polyphasic approach including multi-locus sequencing. Based on the phylogenetic analysis, the 22 strains were divided into two distinct groups comprising mesophilic and psychrotolerant isolates, respectively. This classification was supported by DNA–DNA hybridization studies, whereby a psychrotolerant isolate (strain U2/3T) showed 41.0 and 17.8 % relatedness to the type strains of the mesophilic species Morganella morganii subsp. morganii (strain LMG 7874T) and Morganella morganii subsp. sibonii (strain DSM 14850T), respectively. Analysis of the 16S rRNA gene sequences showed a similarity of 98.6 % between mesophilic and psychrotolerant isolates. However, fragments of seven protein-encoding housekeeping genes (atpD, dnaN, gyrB, hdc, infB, rpoB and tuf) all showed less than 90.9 % sequence similarity between the two groups. The psychrotolerant isolates grew at 0–2 °C and also differed from the mesophilic M. morganii isolates with respect to growth at 37 °C and in 8.5 % (w/v) NaCl and fermentation of d-galactose. The psychrotolerant strains appear to represent a novel species, for which the name Morganella psychrotolerans sp. nov. is proposed. The type strain is U2/3T (=LMG 23374T=DSM 17886T).
Roseomonas aquatica sp. nov., isolated from drinking water
Authors: Gallego Virginia , Sánchez-Porro Cristina , García Maria Teresa , Ventosa Antonio
Published: September 2006

Strain TR53T, a Gram-negative, non-motile, non-spore-forming and strictly aerobic coccobacillus, isolated from the drinking water distribution system of Seville, Spain, was subjected to polyphasic taxonomic analysis using a combination of phenotypic, genotypic and phylogenetic features. Phylogenetic analysis of 16S rRNA gene sequences showed that strain TR53T had highest similarity to members of the genus Roseomonas, with sequence similarity values between 95.7 % (to Roseomonas genomospecies 5 strain ATCC 49960) and 94.0 % (to Roseomonas gilardii subsp. rosea ATCC 49956T). On the basis of its phenotypic characteristics, 16S rRNA gene sequence data and DNA G+C content (68.6 mol%), strain TR53T represents a novel species of the genus Roseomonas, for which the name Roseomonas aquatica sp. nov. is proposed. The type strain of Roseomonas aquatica is TR53T (=CECT 7131T=JCM 13556T).
Lishizhenia caseinilytica gen. nov., sp. nov., a marine bacterium of the phylum Bacteroidetes
Authors: Lau Ken W. K. , Ren Jianping , Wai Natalie L. M. , Qian Pei-Yuan , Wong Po-Keung , Wu Madeline
Published: September 2006

A light-orange, aerobic bacterium, strain UST040201-001T, that degrades casein, gelatin and Tween 20, was isolated in February 2004 from a sand-filtered seawater sample from Port Shelter, Hong Kong SAR, China. The strain possessed menaquinone-6 and its 16S rRNA gene sequence shared only 90.1 % similarity with that of Brumimicrobium glaciale IC156T. Phylogenetic analysis showed that UST040201-001T formed a distinct lineage within the family Cryomorphaceae. Its ecophysiological and biochemical characteristics suggest that this strain represents a novel genus and species within the phylum Bacteroidetes. The name Lishizhenia caseinilytica gen. nov., sp. nov. is proposed. The type strain of Lishizhenia caseinilytica is UST040201-001T (=NRRL B-41434T=JCM 13821T).
Thiomicrospira halophila sp. nov., a moderately halophilic, obligately chemolithoautotrophic, sulfur-oxidizing bacterium from hypersaline lakes
Authors: Sorokin Dimitry Yu. , Tourova Tatjana P. , Kolganova Tatjana V. , Spiridonova Elizaveta M. , Berg Ivan A. , Muyzer Gerard
Published: September 2006

Enrichments at 2 M NaCl and pH 7.5–8, with thiosulfate or sulfide as electron donor, inoculated with sediments from hypersaline chloride–sulfate lakes of the Kulunda Steppe (Altai, Russia) resulted in the domination of two different groups of moderately halophilic, chemolithoautotrophic, sulfur-oxidizing bacteria. Under fully aerobic conditions with thiosulfate, bacteria belonging to the genus Halothiobacillus dominated while, under microaerophilic conditions, a highly motile, short vibrio-shaped phenotype outcompeted the halothiobacilli. Three genetically and phenotypically highly similar vibrio-shaped isolates were obtained in pure culture and one of them, strain HL 5T, was identified as a member of the Thiomicrospira crunogena cluster by 16S rRNA gene sequencing. The new isolates were able to grow with thiosulfate as electron donor within a broad salinity range from 0.5 to 3.5 M NaCl with an optimum at 1.5 M and within a pH range from 6.5 to 8.5 with an optimum at pH 7.5–7.8. Comparative analysis of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) gene sequences demonstrated that strain HL 5T possessed two genes, cbbL-1 and cbbL-2, of the form I RuBisCO and a cbbM gene of the form II RuBisCO, similar to the other members of the Thiomicrospira crunogena cluster. On the basis of phenotypic and genetic comparison, the new halophilic isolates are proposed to be placed into a novel species, Thiomicrospira halophila sp. nov. (type strain HL 5T=DSM 15072T=UNIQEM U 221T).
Micromonospora coriariae sp. nov., isolated from root nodules of Coriaria myrtifolia
Authors: Trujillo Martha E. , Kroppenstedt Reiner M. , Schumann Peter , Carro Lorena , Martínez-Molina Eustoquio
Published: September 2006

An actinomycete strain, NAR01T, was isolated from root nodules of a Coriaria plant. The 16S rRNA gene sequence of strain NAR01T showed most similarity to the type strains of Micromonospora endolithica (98.94 %) and Micromonospora chersina (98.4 %). The chemotaxonomic results obtained confirmed the taxonomic position of the isolate within the genus Micromonospora, and revealed differences at the species level. Physiological and biochemical tests showed that strain NAR01T could be clearly distinguished from its closest phylogenetic neighbours, while DNA–DNA hybridization results indicated that the isolate represents a novel species. On the basis of these results, strain NAR01T (=DSM 44875T=LMG 23557T) is proposed as the type strain of the novel species Micromonospora coriariae sp. nov.
Burkholderia ferrariae sp. nov., isolated from an iron ore in Brazil
Authors: Valverde Angel , Delvasto Pedro , Peix Alvaro , Velázquez Encarna , Santa-Regina Ignacio , Ballester Antonio , Rodríguez-Barrueco Claudino , García-Balboa Camino , Igual José M.
Published: September 2006

A Gram-negative, non-spore-forming bacterial strain with the ability to solubilize highly insoluble phosphatic minerals was isolated from a high-phosphorous iron ore from Minas Gerais State, Brazil. This strain, designated FeGl01T, was subjected to a polyphasic taxonomic investigation. Comparative 16S rRNA gene sequence analysis indicated that it formed a distinct phylogenetic lineage within the genus Burkholderia together with several other species of the genus, e.g. Burkholderia sacchari, Burkholderia tropica and Burkholderia unamae. Partial nucleotide sequencing and analysis of the recA gene roughly corroborated the phylogenetic position of strain FeGl01T within the genus Burkholderia. The chemotaxonomic properties of strain FeGl01T, such as ubiquinone Q-8 as the predominant quinone system and C16 : 0, C17 : 0 cyclo, C18 : 1
ω7c and C19 : 0
ω8c cyclo as the major fatty acids, were also consistent with its classification within the genus Burkholderia. DNA–DNA hybridization experiments between strain FeGl01T and the type strains of B. unamae, B. sacchari and B. tropica yielded reassociation values of 40 % or lower, which, together with qualitative and quantitative differences in fatty acid composition and with differences in several phenotypic traits, support the separation of the new isolate from the phylogenetically most closely related species. Therefore, it is suggested that strain FeGl01T represents a novel species of the genus Burkholderia, for which the name Burkholderia ferrariae sp. nov. is proposed. The type strain is FeGl01T (=LMG 23612T=CECT 7171T=DSM 18251T).
Reclassification of Thermoterrabacterium ferrireducens as Carboxydothermus ferrireducens comb. nov., and emended description of the genus Carboxydothermus
Authors: Slobodkin A. I. , Sokolova T. G. , Lysenko A. M. , Wiegel J.
Published: September 2006

Similarities in phylogeny and metabolic properties between the type species of two monospecific genera of thermophilic anaerobic bacteria, Carboxydothermus hydrogenoformans and Thermoterrabacterium ferrireducens, and analysis of their recently available 16S rRNA gene sequences warranted clarification of their taxonomic positions. We have determined that the value of DNA–DNA hybridization between the type strains is 53 %. Additional physiological studies revealed that C. hydrogenoformans Z-2901T is capable of Fe(III) reduction with H2 as an electron donor and ferrihydrite as an electron acceptor. T. ferrireducens JW/AS-Y7T is able to grow and utilize CO with ferrihydrite as an electron acceptor without hydrogen or acetate production. We therefore reclassify Thermoterrabacterium ferrireducens as Carboxydothermus ferrireducens comb. nov. (type strain JW/AS-Y7T=DSM 11255T=VKM B-2392T). The description of the genus Carboxydothermus is emended to include such important physiological properties as growth on organic compounds and capacity for Fe(III) reduction.
The effect of St John’s wort extracts on CYP3A: a systematic review of prospective clinical trials
Authors: Whitten D. L. , Myers S. P. , Hawrelak J. A. , Wohlmuth H.
Published: September 2006

Aim

The aim of this systematic review was to assess the quality and outcomes of clinical trials investigating the effect of St John’s wort extracts on the metabolism of drugs by CYP3A.

Methods

Prospective clinical trials assessing the effect of St John’s wort (SJW) extracts on metabolism by CYP3A were identified through computer‐based searches (from their inception to May 2005) of Medline, Cinahl, PsycINFO, AMED, Current Contents and Embase, hand‐searches of bibliographies of relevant papers and consultation with manufacturers and researchers in the field. Two reviewers selected trials for inclusion, independently extracted data and recorded details on study design.

Results

Thirty‐one studies met the eligibility criteria. More than two‐thirds of the studies employed a before‐and‐after design, less than one‐third of the studies used a crossover design, and only three studies were double‐blind and placebo controlled. In 12 studies the SJW extract had been assayed, and 14 studies stated the specific SJW extract used. Results from 26 studies, including all of the 19 studies that used high‐dose hyperforin extracts (>10 mg day−1), had outcomes consistent with CYP3A induction. The three studies using low‐dose hyperforin extracts (<4 mg day−1) demonstrated no significant effect on CYP3A.

Conclusion

There is reasonable evidence to suggest that high‐dose hyperforin SJW extracts induce CYP3A. More studies are required to determine whether decreased CYP3A induction occurs after low‐dose hyperforin extracts. Future studies should adopt study designs with a control phase or control group, identify the specific SJW extract employed and provide quantitative analyses of key constituents.
T cell receptor excision circles (TRECs), CD4+, CD8+ and their CD45RO+ and CD45RA+ subpopulations in hepatitis C virus (HCV)-HIV-co-infected patients during treatment with interferon alpha plus ribavirin: analysis in a population on effective antiretroviral therapy
Authors: Arizcorreta A , Márquez M , Fernández-Gutiérrez C , Guzmán E Pérez , Brun F , Rodríguez-Iglesias M , Girón-González J A
Published: September 2006

Interferon (IFN)-α induced CD4+ T lymphopenia is a toxic effect of the treatment of chronic hepatitis C virus (HCV) in human immunodeficiency virus (HIV)-co-infected patients. To increase the knowledge about this secondary effect, we performed an analysis of the evolution of the T cell receptor excision circles (TRECs), CD4+ and CD8+ T cells and of their CD45RO+ and CD45RA+ subpopulations during the treatment of chronic hepatitis HCV with peginterferon alpha (pegIFN-α) + ribavirin. Twenty HCV/HIV-co-infected patients, with undetectable HIV load after highly active antiretroviral therapy (HAART), were treated with pegIFN-α + ribavirin. TRECs were determined using real-time polymerase chain reaction. CD4+ and CD8+ T cells and their CD45RO+ and CD45RA+ subpopulations were analysed by two-colour flow cytometry. Median baseline CD4+ and CD8+ T cells were 592 mm3 and 874 mm3, respectively. Median baseline CD45RO+ subpopulation was 48% for CD4+ T and 57% for CD8+ T lymphocytes. A progressive decrease in both T cell populations, as well as of their CD45RO+ and CD45RA+ subpopulations, was detected, with a difference between the baseline and nadir levels approaching 50%. The evolution of T cell populations and TRECs was independent of the response to the treatment. T lymphocytes and their subpopulations returned to baseline levels at 24 weeks after the end of treatment, with the exception of the T CD4+ CD45RA+ subpopulation. The ratio of CD4+ CD45RO+/CD4+ CD45RA+ increased from 0·89 (baseline) to 1·44 (24 weeks after the end of the therapy). TRECs/ml did not return to the basal values. In conclusion, a significant reduction of CD4+ and CD8+ T cells, and of their CD45RA+ and CD45RO+ subpopulations, in HIV/HCV co-infected patients treated with pegIFN-α was observed. Both subpopulations increased after the suppression of treatment, but the CD4+ CD45RA subpopulation did not reach the basal levels as a consequence, at least in part, of a decrease in thymic production.
El Niño effects in the Palmyra Atoll region: oceanographic changes and bigeye tuna (Thunnus obesus) catch rate variability
Authors: HOWELL EVAN A. , KOBAYASHI DONALD R.
Published: September 2006

A generalized additive model (GAM) was constructed to separate and quantify the effects of fishery‐based (operational) and oceanographic parameters on the bigeye tuna (Thunnus obesus) catch rates at Palmyra Atoll in the central Tropical Pacific. Bigeye catch, the number of hooks per set, and set location from 4884 longline sets spanning January 1994 to December 2003 were used with a temporally corresponding El Niño‐Southern Oscillation (ENSO) indicator built from sea surface height (SSH) data. Observations of environmental data combined with the results from the GAM indicated that there is an increase in bigeye catch rates corresponding to an increase in eastward advection during the winter months of El Niño events. A seasonal pattern with higher bigeye catch rates from December to April and a spatial pattern with higher rates to the northeast and northwest of the atoll were observed during this study period. It is hypothesized that the combination of the eastward advection of the warm pool coupled with vertical changes in temperature during the winter months of El Niño events increases the availability of bigeye tuna in this region. This increase in availability may be due to a change in exploitable population size, location, or both.
Distribution of jack mackerel (Trachurus japonicus) larvae and juveniles in the East China Sea, with special reference to the larval transport by the Kuroshio Current
Authors: SASSA CHIYUKI , KONISHI YOSHINOBU , MORI KEN
Published: September 2006

Horizontal distribution patterns of jack mackerel (Trachurus japonicus) larvae and juveniles were investigated in the East China Sea between 4 February and 30 April 2001. A total of 1549 larvae and juveniles were collected by bongo and neuston nets at 357 stations. The larvae were concentrated in the frontal area between the Kuroshio Current and shelf waters in the upstream region of the Kuroshio. The abundance of small larvae (<3 mm notochord length) was highest in the southern East China Sea (SECS) south of 28°N, suggesting that the principal spawning ground is formed in the SECS from late winter to spring. Jack mackerel also spawned in the northern and central East China Sea (NECS and CECS, respectively), as some small larvae were also collected in these areas. In the SECS, the abundance of small larvae was highest in February and gradually decreased from March to April. The habitat temperature of small larvae in the SECS and CECS (20–26°C) was higher than that in the NECS (15–21°C), suggesting higher growth rates in the SECS and CECS than in the NECS. The juveniles (10‐ to 30‐mm standard length) became abundant in the NECS off the west coast of Kyushu Island and CECS in April and were collected in association with scyphozoans typical of the Kuroshio waters. However, juveniles were rarely collected in the SECS, where the small larvae were concentrated. Considering the current systems in the study area, a large number of the eggs and larvae spawned and hatched in the SECS would be transported northeastward by the Kuroshio and its branches into the jack mackerels’ nursery grounds, such as the shallow waters off the west coast of Kyushu and the Pacific coast of southern Japan.
Proximate composition and mineral contents of the blue crab (Callinectes sapidus) breast meat, claw meat and hepatopancreas
Authors: Küçükgülmez Aygül , Çelik Mehmet , Yanar Yasemen , Ersoy Beyza , Çikrikçi Mustafa
Published: September 2006

The objective of this study was to determine the nutritional composition of the breast, claw meat and hepatopancreas of the blue crab (Callinectes sapidus). Samples were subjected to proximate (protein, fat, ash and moisture) and calcium, magnesium, phosphorus, potassium and sodium (Ca, Mg, P, K and Na) analyses. Protein, fat, ash and moisture of the breast, claw meat and hepatopancreas of the blue crab averaged 19.05, 0.59, 2.10 and 76.85 g/100 g, respectively. The results have revealed that this species is a rich source of protein, Ca, Mg, P and Na. Claw meat had higher protein concentrations (19.55 g/100 g) than both breast meat and hepatopancreas (18.81 g/100 g). Na was predominant element among minerals analysed. There were significant differences between Ca, Mg, P, K and Na contents of claw, breast meat and hepatopancreas of the blue crab. Information on the nutrient composition is needed to facilitate the processing, utilisation and marketing of blue crab products. Blue crab could balance human nutrition and could be used as an alternative dietary supplement of proteins and mineral matter.
Melatonin Receptors on Ovine Pars Tuberalis: Characterization and Autoradiographicai Localization
Authors: Morgan Peter J. , Williams Lynda M. , Davidson Gary , Lawson Wilfred , Howell Edward
Published: September 2006

The functional significance of the pars tuberalis (PT) of the mammalian adenohypophysis has remained an enigma (1, 2). One view of its function is that it acts as an auxiliary gland to support the endocrine role of the pars distalis (PD) (2), as it has been shown to contain immunocytochemically identifiable thyrotrophs and gonadotrophs (1). Many of the cells of the PT are, however, ultrastructurally unique suggesting an independent function for this tissue. Our recent demonstration that the PT of the rat is a major binding site for the ligand iodomelatonin lends further support to this idea (3). We have utilized the highly specific ligand [125l]melatonin, and have demonstrated that it binds exclusively, with very high affinity, to the PT but not the PD of the adult sheep adenohypophysis. These findings support the conclusion that the PT has a distinct role in relation to melatonin action and seasonal reproduction.
Regulation of Basal and Stimulated Prolactin Release in Prolactin‐Secreting Rat Pituitary Tumors*
Authors: Lafond J. , Bouvier C. , Forget H. , Lagace G. , Kaufman S. , Collu R.
Published: September 2006

To better understand the mechanisms of the inhibitory effects of dopamine on pituitary prolactin release, we have utilized an estrone‐induced, benign and dopamine‐sensitive rat pituitary adenoma and two malignant, transplantable and dopamine‐resistant rat pituitary tumors, 7315a and MITW15. Enzymatically dispersed and Percoll purified cells obtained from the three tissues were incubated for 30 min in media with or without Na+ and in the presence or the absence of dopamine and/or various prolactin releasers for evaluating the secretion of prolactin under baseline and experimental conditions. In some experiments, the cells were pretreated for 16 h with pertussis toxin to evaluate the eventual presence and role of pertussis toxin‐sensitive G proteins. Dopamine inhibited baseline prolactin release by adenomatous lactotrophs in a Na+‐dependent manner, but was totally inactive with 7315a and MtTW15 cells. The Ca2+ channel agonist BAY K 8644 stimulated prolactin release with all three preparations and its effects were enhanced by a Na+‐free medium. Dopamine antagonized the stimulatory effects of BAY K 8644 with adenomatous and 7315a cells only, even in the absence of Na+. Pertussis toxin pretreatment significantly increased baseline prolactin release by adenomatous and MtTW15 cells and abolished dopamine inhibition of adenomatous lactotrophs baseline hormone release. BAY K 8644, TRH and vasoactive intestinal peptide, stimulated prolactin release by adenomatous cells and this effect was antagonized by dopamine in a pertussis toxin‐sensitive manner. All prolactin releasers, except TRH, were effective also with 7315a cells, and its actions were not blocked by pertussin toxin. The stimulatory effects of BAY K 8644 and vasoactive intestinal peptide on 7315a cells were enhanced by pertussis toxin pretreatment. The results obtained with an almost pure preparation of adenomatous lactotrophs confirm the existence of a dual mechanism of dopamine inhibitory action on prolactin release: 1) a Na+‐dependent action exerted on baseline, and 2) a Na+‐independent action exerted on stimulated prolactin release. They also indicate that both actions are exerted through pertussis toxin‐sensitive G proteins. Furthermore, our results show the presence in transplantable pituitary tumors 7315a and MtTW15 of multiple and diverse anomalies in the regulation of prolactin release probably due, at least partly, to anomalies of one or more G proteins and/or neurotransmitter receptors.
Levels of Transcripts Encoding a Member of the Protein Kinase C Family in the Paraventricular and Supraoptic Nuclei are Increased by Hyperosmolality
Authors: Young W. Scott
Published: September 2006

The distribution of mRNA transcripts for the six known protein kinase C (PKC) genes has been investigated by quantitative in situ hybridization histochemistry. PKC‐δ transcripts were detected only in the thalamus and PKC‐ζ was found in several areas including the supraoptic (SON) and paraventricular (PVN) nuclei. Activation of magnocellular cells in the SON and PVN following 7 days of saline‐loading resulted in increased levels of PKC‐ζ transcripts in both of these nuclei.
Dynamic Changes in Neuropeptide Y Concentrations in the Median Eminence in Association with Preovulatory Luteinizing Hormone Release in the Rat
Authors: Sahu Abhiram , Jacobson William , Crowley William R. , Kalra Satya P.
Published: September 2006

Neuropeptide Y (NPY) stimulates luteinizing hormone (LH) release in the rat by a dual action, one in the hypothalamus to excite LH‐releasing hormone (LHRH) release and the other at the level of pituitary gonadotrophs to activate and/or potentiate LH release induced by LHRH. Because NPY produces effects similar to norepinephrine with which it may comprise an excitatory hypothalamic circuit, it was hypothesized that NPY concentrations in the hypothalamus would change in a time‐ and site‐specific manner in association with the preovulatory LH surge on proestrus. Concentrations of NPY in individual nuclei of the preoptic‐tuberal pathway and serum LH levels were estimated by radioimmunoassays in rats during diestrus 2 and proestrus. On proestrus, serum LH levels were basal between 1000 and 1400 h, rose significantly at 1500 h and plateaued between 1600 and 1800 h. Of the five neural sites examined, only NPY in the median eminence displayed marked fluctuations in close association with the LH surge. NPY concentrations were low between 1000 and 1300 h, and rose abruptly at 1400 h (P<0.05) preceding the onset of LH rise at 1500 h. These elevated levels were maintained until 1600 h, during which time serum LH rose to a plateau and then fell at 1800 h to the low range seen between 1000 and 1300 h. In contrast, the pattern of changes in NPY levels in the arcuate nucleus, suprachiasmatic nucleus and medial preoptic area, three additional sites in the preoptic‐tuberal pathway known to participate in the preovulatory LH surge, were markedly different from that seen in the median eminence. In each of these three sites, NPY levels rose significantly at 1800 h from the values at 1000 to 1200 h with a slightly different time‐course of increment. None of these areas exhibited changes in NPY concentrations on diestrus 2; NPY concentrations also were unaltered on diestrus 2 or proestrus in the ventromedial nucleus. The present observations of site‐specific, dynamic changes in NPY levels on proestrus, in a manner previously documented for LHRH, support the hypothesis that a subset of NPY neurons terminating in the median eminence may be a component of excitatory neural circuitry that either independently or in co‐action with the adrenergic system is responsible for the induction of preovulatory LH release.