bluuebunny/crossref_metadata_2025 huggingface dataset:
Migraine management in children - Review of strategies and Recommendations
Authors: Kundu Narayan Chandra , Ahmad Quadruddin
Published: September 2007

Headache is a frequent health problem in children and adolescents. It is estimated that headache occurs in around 70% of adolescents and 25% of younger children. This ranks headache and migraine in the top five health problems of childhood. Headache in children is often considered as an excuse to abstain from studies and school; and thus not taken seriously by adults. This article highlights the importance of headache in children and provides evidence based treatment guidelines in this group of patient.

(J Bangladesh Coll Phys Surg 2007; 25 : 77-85)
Percutaneous Coronary Intervention (PCI) in the Era of Drug-Eluting Stents
Authors: Momenuzzaman NAM , Begum Fatema , Malik Fazilatunnesa , Ghafur Shakil
Published: September 2007

Angioplasty opened the stenotic coronary artery but faced complication like abrupt vessel closure. Deployment of bare metal stent within the lesion solved the problem but another complication like restenosis emerged. Neointimal hyperplasia and vessel wall remodeling were identified as the underlying mechanism and lead to the development of drug eluting stent. In the selected patient group, drug eluting stent (sirolimus and paclitaxel) are proved to be extremely promising in respect to reduction of target vessel failure, clinical restenosis (target vessel revascularization), binary restenosis, stent thrombosis and other parameters. Importantly initial positive outcome persisted in the subsequent later follow ups. Outcome in the unfavourable groups are also encouraging but needs few more studies and follow ups. There are scopes for future improvement also. With the immense success, drug eluting stents are increasingly used worldwide and becoming an integral part of percutaneous coronary intervention.

(J Bangladesh Coll Phys Surg 2007; 25 : 86-91)
Cervical Ectopic Pregnancy: Case Report
Authors: Banu Laila Parveen , Chowdhury Sameena , Begum Kohinoor , Islam Ferdousi , Tasnim Saria
Published: September 2007

A thirty year old lady para 3+0 presented with complaints of amenorrhoea for eight weeks and slight per vaginal bleeding for 28 days with frequent bouts of profuse bleeding. Total abdominal hysterectomy was done. Naked eye examination of the specimen was suggestive of cervical ectopic pregnancy (CEP). Histopathology report confirmed cervical implantation of placenta. CEP is an extremely rare life threatening form of ectopic pregnancy.

(J Bangladesh Coll Phys Surg 2007; 25 : 92-94)
Control of twospotted spider mite Tetranychus urticae Koch (Acari: Tetranychidae) by some selected chemicals
Authors: Hossain S , Haque MM , Nader N
Published: September 2007

The experiment was conducted to study the effectiveness of four commonly used chemicals viz., deltamethrin, cypermethrin, malathion and sulphur against two-spotted spider mite (TSSM), Tetranychus urticae Koch on potted bean plants and on excised leaf discs. Mite population remained significantly lower in all treated plots except malathion treatment. The population of T. urticae differed significantly due to different chemicals and it remained lower up to 4th week on single-sprayed plants, which again increased. But in double-sprayed plants mite population was checked and remained significantly lower. The estimated LC50 values for cypermethrin, malathion, deltamethrin and sulphur were 2.9956, 15.8663, 0.5386 and 20.7045 nl.cm-2 respectively when the chemicals were sprayed before mite release. But the LC50 values for these chemicals sprayed after mite release were estimated 1.8110, 8.2746, 0.2192 and 6.8308 nl.cm-2. The use of chemicals is essential for better yield of crops. Among the four tested chemicals the pyrithroids (cypermethrin and deltamethrin) were found more effective against the TSSM than the other two.

Key words: Two-spotted spider mite, Tetranychus urticae, bean, deltamethrin, cypermethrin, malathion, sulphur

Univ. j. zool. Rajshahi Univ. Vol.25 2006 p.15-18
Toxic and repellent action of sugarcane bagasse-based lignin against some stored grain insect pests
Authors: Khanam LA Muslima , Talukder D , Hye MA
Published: September 2007

Laboratory experiments were carried out to investigate the efficacy of sugarcane bagasse-based lignin against four stored grain insect pests viz., Tribolium castaneum, Tribolium confusum, Sitophilus oryzae and Callosobruchus maculatus. Mortality was assessed after 24, 48 and 72 h of treatment and LD50 values were calculated at the respective time intervals. It was observed that T. castaneum is more susceptible to the lignin than the other test insects. Repellent activity of the product was conducted for T. castaneum and T. confusum. All the concentrations of the product were found to be repellent to both the insect species. Strong repellent activity was observed at concentrations of 471.57 and 628.76 µg.cm-2 to T. confusum showing the repellency of class V activity.

Key words: Bagasse-based lignin, toxicity, repellency, Tribolium castaneum, T. confusum, Sitophilus oryzae, Callosobruchus maculatus

Univ. j. zool. Rajshahi Univ. Vol.25 2006 p.27-30
Present status of pond fishery resources and livelihood of the fish farmers at Mohanpur Upazila in Rajshahi District
Authors: Zaman Tanjeena , Jewel MAS , Bhuiyan AS
Published: September 2007

A survey was conducted in Mohanpur Upazila, Rajshahi to determine the pond fishery resources and the livelihood status of fish farmers for a period of nine months (August 2005-April 2006). The survey was conducted on 90 fish farmers of 52 villages under 6 unions. Data were collected through personal visit and interviews following a detailed questionnaire. Pond sizes of the area varied from 15 to above 180 decimal of which maximum ponds (57.8%) were operated by single owner. Field observation revealed that 65.5% ponds were used for fish culture, whereas 28.5% and 6% ponds were culturable and derelict, respectively. Among the fish farmers 23.3% was illiterate whereas 14.4, 8.9 and 6.7% were educated upto primary, secondary and higher secondary or above level, respectively. Agriculture (51.1%) is the principal occupation of the pond owners followed by aquaculture (18.9%). The highest percentage (33%) fish farmers earned Tk. 25,000-50,000 per year, 32% earned Tk. 50,000-1,00,000 an the rest 25% earned above Tk. 1,25,000 annually. Fish farmers were found to face various problems such as social, economical and technical problems, which were identified during the study. Necessary overcome efforts are also suggested according to the problems.

Key words: Pond fishery resources, fish farmers, livelihood status

Univ. j. zool. Rajshahi Univ. Vol.25 2006 p.31-35
Effects of cypermethrin alone and in combination with leaf and seed extracts of neem against adult Tribolium castaneum (Herbst)
Authors: Khalequzzaman M , Khanom Makhsuda
Published: September 2007

Cypermethrin was applied either alone or in combination with leaf and seed extracts of neem (Azadirachta indica A. Juss) to four strains of the adult red flour beetle Tribolium castaneum (Herbst) and the mortality was assessed after 24 and 48 hrs of treatments. The LD50 values were calculated as 0.0072, 0.0105, 0.0056 and 0.0124 μgcm-2 after 24 hours and 0.0041, 0.0076, 0.0046 and 0.0097 μgcm-2 after 48 hours of treatment for the Local, CR-1, FSS-II and CTC-12 strains respectively. The results showed synergism when applied in combined doses of cypermethrin and leaf and seed extracts with petroleum spirit, ethyl acetate and methanol. Leaf extract in acetone had an insignificant effect showing its inertness with cypermethrin excepting 24 hrs after treatment of Local strain and 48 hrs after treatment of CTC-12 strain. Seed extract in methanol in Local strain showed insignificant effect after 24 hrs of treatment but a synergistic effect occurred after 48 hrs of treatment.

Key words: Cypermethrin, Azadirachta indica, Tribolium castaneum, synergism

Univ. j. zool. Rajshahi Univ. Vol.25 2006 p.45-40
Jojoba oil analysis by high pressure liquid chromatography and gas chromatography/mass spectrometry
Authors: Spencer Gayland F. , Plattner Ronald D. , Miwa Thomas
Published: September 2007

Two analytical procedures for determining com‐positions of jojoba liquid wax esters are described and compared. One, the more tedious, involves separation of wax ester homologs by high pressure liquid chro‐matography followed by determination of the acid and alcohol moieties from each homolog. The second allows rapid determination of wax ester composition by gas Chromatographic separation of hydrogenated jojoba wax esters according to chain length, followed immediately by ancillary mass spectrometric identifi‐cation of the acid and alcohol moieties. Double bonds in the alkyl chains in jojoba liquid waxes were almost exclusively (98%) ω‐9, when examined by gas chro‐matography/mass spectrometry (GC/MS) and ozonolysis/GC/MS.
Rapid determination of residual hexane in oils by gas chromatography using pyrolyzer
Authors: Hirayama S. , Imai C.
Published: September 2007

A simple, direct gas Chromatographic (GC) tech‐nique is described for the quantitative determination of residual hexane in extracted vegetable oils. The method is rapid and sensitive to one ppm hexane. A platinum boat, on which sample oil was placed, is inserted into a pyrolysis chamber in a pyrolyzer at‐tached to a GC, and heated at 150 C for 60 sec to carry the evaporated hexane into the GC with a carrier gas. In the method, the column of GC may be used without the possibility of contamination because the sample is not injected directly into the GC. The method should be useful for the quality con‐trol of solvent extracted oil products.
Changes in phospholipid levels during high moisture storage of soybeans
Authors: Chapman G. W. , Robertson J. A.
Published: September 2007

Fungicide‐treated and untreated commercial soy‐beans were stored at high temperature and humidity (35 C and 85% RH) in separate environmental chambers. Crude oil was extracted from the beans periodically during a 23‐day storage period and its phospholipids separated by three‐solvent system, two‐dimensional thin layer chromatography. The amount of phospholipids was determined by spectro‐photometric assay of inorganic phosphate liberated after perchloric acid digestion. The level of phospho‐lipids increased substantially during storage in treated and untreated soybean samples. Phosphatidic acid, phosphatidyl inositol, phosphatidyl ethanolamine, and phosphatidyl choline were the major phospho‐lipids. Phosphatidyl choline was the principal phos‐pholipid in extracted crude oil from treated and untreated beans during storage. The major phospho‐lipid levels increased more rapidly during the first 6 days of storage than during the remainder of the period in both samples. The data indicated that increased phospholipid levels occurred independently of mold growth and could have been the result of water imbibition and germination of the beans during storage.
trans Fatty acid content of commercial margarine samples determined by gas liquid chromatography on OV‐ 275
Authors: Ottenstein D. M. , Wittings LA. , Walker G. , Mahadevan V. , Pelick N.
Published: September 2007

Gas liquid chromatography (GLC) of margarine methyl esters on a 20 ft × 1/8 in. column containing 15% OV‐275 on 100/120 mesh Chromosorb P AW‐DMCS at 220 C provided practical separations oftrans octadecamonoenoates from the correspondingcis‐isomers and oftrans, trans‐ andcis,trans‐ octa‐decadienoates from the correspondingcis.cis‐isomers.Trans content by GLC was in reasonable agreement (±1–2%) with totaltrans content by infrared analysis in six of seven commercial margarine samples.
Characterization of a monoterpenoid ether from the essential oil of sagebrush (Artemisia tridentata)
Authors: Buttkus H. , Bose R. J.
Published: September 2007

From the essential oil of sagebrush(Artemisia tridentata) a component of the general composition C10H16O was isolated. From its nuclear magnetic resonance, mass and infrared spectra an isoprenoid monoterpene, containing a substituted furanyl‐cyclopropane fused ring system, l,6,6‐trimethyl‐4‐ethenyl‐exo‐2‐oxabicyclo [3.1.0] hexane, is proposed as its structure.
Nea Presidential Address, 1991: Sixteenth-Century European Expansion and the Economic Decline of Africa (In Honor of Walter Rodney)
Authors: Boston Thomas D.
Published: September 2007

Prior to the sixteenth century, the Indian Ocean trading network was one of the wealthiest commercial regions in the world. It included states of East Africa, the Arabian peninsula, the Indian subcontinent, Southeast Asia, China and Japan. By circumnavigating Africa, Portugal was the first European nation to gain access to the region. Through the exercise of naval superiority, blockading of strategic shipping lanes, imposition of duties and expulsion of Swahili and Muslim merchants, Portugal exercised a mercantile monopoly which ultimately led to the region's rapid economic decline. Using rare historical documents from Portugal and Africa, this study traces the effects of Portuguese expansion on the economies of East Africa and trade in the Indian Ocean.
Recent U.S. Economic Policies and the Central Caribbean Economies
Authors: Coppin Addington
Published: September 2007

This study examines the trade and investment performances of three economies in the Central Caribbean region since the Caribbean Basin Initiative (CBI) and associated programs. We find that the rapid growth in nontraditional exports from these economies to the United States did not necessarily translate into net foreign exchange earnings. On a per capita basis, export-related investment in Haiti was much lower than in the other two economies — Jamaica and the Dominican Republic. As a percentage of the labor force, gross employment gains for Jamaica have been significantly larger than those in either the Dominican Republic or Haiti. It appears that the policies favoring expansion in the offshore sector may foster employment opportunities of females, especially where traditional sectors are in decline.
The evolutionary emergence of cell type-specific genes inferred from the gene expression analysis of
Hydra
Authors: Hwang Jung Shan , Ohyanagi Hajime , Hayakawa Shiho , Osato Naoki , Nishimiya-Fujisawa Chiemi , Ikeo Kazuho , David Charles N. , Fujisawa Toshitaka , Gojobori Takashi
Published: September 2007

Cell lineages of cnidarians including
Hydra
represent the fundamental cell types of metazoans and provides us a unique opportunity to study the evolutionary diversification of cell type in the animal kingdom.
Hydra
contains epithelial cells as well as a multipotent interstitial cell (I-cell) that gives rise to nematocytes, nerve cells, gland cells, and germ-line cells. We used cDNA microarrays to identify cell type-specific genes by comparing gene expression in normal
Hydra
with animals lacking the I-cell lineage, so-called epithelial
Hydra
. We then performed
in situ
hybridization to localize expression to specific cell types. Eighty-six genes were shown to be expressed in specific cell types of the I-cell lineage. An additional 29 genes were expressed in epithelial cells and were down-regulated in epithelial animals lacking I-cells. Based on the above information, we constructed a database (
http://hydra.lab.nig.ac.jp/hydra/
), which describes the expression patterns of cell type-specific genes in
Hydra
. Most genes expressed specifically in either I-cells or epithelial cells have homologues in higher metazoans. By comparison, most nematocyte-specific genes and approximately half of the gland cell- and nerve cell-specific genes are unique to the cnidarian lineage. Because nematocytes, gland cells, and nerve cells appeared along with the emergence of cnidarians, this suggests that lineage-specific genes arose in cnidarians in conjunction with the evolution of new cell types required by the cnidarians.
Suppression of oncogenic properties of c-Myc by LKB1-controlled epithelial organization
Authors: Partanen Johanna I. , Nieminen Anni I. , Mäkelä Tomi P. , Klefstrom Juha
Published: September 2007

Cellular organization into epithelial architecture maintains structural integrity and homeostasis by suppressing cell proliferation and apoptosis. However, it is unclear whether the epithelial organization is sufficient to block induction of cell-autonomous cell cycle progression and apoptotic sensitivity by activated oncogenes. We show that chronic activation of oncogenic c-Myc, starting in the developing 3D organotypic mammary acinar structures, results in hyperproliferation and transformed acinar morphology. Surprisingly, acute c-Myc activation in mature quiescent acini with established epithelial architecture fails to reinitiate the cell cycle or transform these structures. c-Myc does reinitiate the cell cycle in quiescent, but structurally unorganized, acini, which demonstrates that proper epithelial architecture is needed for the proliferation blockade. The capability of c-Myc to reinitiate the cell cycle in acinar structures is also restored by the loss of LKB1, a human homologue of the cell polarity protein PAR4. The epithelial architecture also restrains the apoptotic activity of c-Myc, but coactivation of c-Myc and a complementary TNF-related apoptosis-inducing ligand death receptor pathway can induce a strong Bim and Bid-mediated apoptotic response in the established acini. The results together expose surprising proliferation and apoptosis resistance of organized epithelial structures and identify a role for the polarity regulator LKB1 in the development of c–Myc-resistant cell organization.
T helper 1 cells stimulated with ovalbumin and IL-18 induce airway hyperresponsiveness and lung fibrosis by IFN-γ and IL-13 production
Authors: Hayashi Nobuki , Yoshimoto Tomohiro , Izuhara Kenji , Matsui Kiyoshi , Tanaka Toshio , Nakanishi Kenji
Published: September 2007

We previously reported that ovalbumin (OVA) and IL-18 nasally administered act on memory type T helper (Th)1 cells to induce airway hyperresponsiveness (AHR) and inflammation, which is characterized by peribronchial infiltration with neutrophils and eosinophils. Here, we report this administration also induces lung fibrosis in an IL-13-dependent manner. Th1 cells secrete several cytokines, including IFN-γ and bronchogenic cytokine IL-13, when stimulated with antigen (Ag) and IL-18. However, IL-13 blockade failed to attenuate AHR, although this treatment inhibited eosinophilic infiltration. To understand the mechanism by which Th1 cells induce AHR after Ag plus IL-18 challenge, we established “passive” and “active” Th1 mice by transferring OVA-specific Th1 cells into naïve BALB/c mice or by immunizing naïve BALB/c mice with OVA/complete Freund's adjuvant, respectively. Administration of Ag and IL-18 induced both types of Th1 mice to develop AHR, airway inflammation, and lung fibrosis. Furthermore, this treatment induced deposition of periostin, a novel component of lung fibrosis. Neutralization of IL-13 or IFN-γ during Ag plus IL-18 challenges inhibited the combination of eosinophilic infiltration, lung fibrosis, and periostin deposition or the combination of neutrophilic infiltration and AHR, respectively. We also found that coadministration of OVA and LPS into Th1 mice induced AHR and airway inflammation via endogenous IL-18. Thus, IL-18 becomes a key target molecule for the development of a therapeutic regimen for the treatment of Th1-cell-induced bronchial asthma.
Altered sensitivities to morphine and cocaine in scaffold protein tamalin knockout mice
Authors: Ogawa Masaaki , Miyakawa Tsuyoshi , Nakamura Kenji , Kitano Jun , Furushima Kenryo , Kiyonari Hiroshi , Nakayama Rika , Nakao Kazuki , Moriyoshi Koki , Nakanishi Shigetada
Published: September 2007

Tamalin is a scaffold protein that interacts with metabotropic glutamate receptors and the kinase-deficient neurotrophin TrkCT1 receptor and forms a protein complex with multiple protein-trafficking and intracellular signaling molecules. In culture, tamalin promotes intracellular trafficking of group 1 metabotropic glutamate receptors through its interaction with guanine nucleotide exchange factor cytohesins and causes actin reorganization and membrane ruffling via the TrkCT1/cytohesin-2 signaling mechanism. However, how tamalin serves its physiological function
in vivo
has remained elusive. In this study, we generated tamalin knockout (Tam
−/−
KO) mice and investigated behavioral alterations resulting from their deficiency in functional tamalin. Targeted deletion of functional tamalin altered neither the overall brain architecture nor the general behavior of the mice under ordinary conditions. However, Tam
−/−
KO mice showed a decrease in sensitivity to acute morphine-induced hyperlocomotion and morphine analgesic effects in the hot-plate test. Furthermore, tamalin deficiency impaired the ability of the animals to show conditioned place preference after repeated morphine administration and to display locomotor sensitization by chronic cocaine treatment. Upon
in vivo
microdialysis analysis of the nucleus accumbens, Tam
−/−
KO and wild-type mice showed no genotypic differences in their response patterns of extracellular dopamine and glutamate before or after morphine administration. These results demonstrate that the tamalin scaffold protein plays a unique role in both acute and adaptive behavioral responses to morphine and cocaine and could regulate common neural substrates implicated in drugs of abuse.
MitoNEET is a uniquely folded 2Fe–2S outer mitochondrial membrane protein stabilized by pioglitazone
Authors: Paddock Mark L. , Wiley Sandra E. , Axelrod Herbert L. , Cohen Aina E. , Roy Melinda , Abresch Edward C. , Capraro Dominique , Murphy Anne N. , Nechushtai Rachel , Dixon Jack E. , Jennings Patricia A.
Published: September 2007

Iron–sulfur (Fe–S) proteins are key players in vital processes involving energy homeostasis and metabolism from the simplest to most complex organisms. We report a 1.5 Å x-ray crystal structure of the first identified outer mitochondrial membrane Fe–S protein, mitoNEET. Two protomers intertwine to form a unique dimeric structure that constitutes a new fold to not only the ≈650 reported Fe–S protein structures but also to all known proteins. We name this motif the NEET fold. The protomers form a two-domain structure: a β-cap domain and a cluster-binding domain that coordinates two acid-labile 2Fe–2S clusters. Binding of pioglitazone, an insulin-sensitizing thiazolidinedione used in the treatment of type 2 diabetes, stabilizes the protein against 2Fe–2S cluster release. The biophysical properties of mitoNEET suggest that it may participate in a redox-sensitive signaling and/or in Fe–S cluster transfer.
Optimization of primer design for the detection of variable genomic lesions in cancer
Authors: Bashir Ali , Liu Yu-Tsueng , Raphael Benjamin J. , Carson Dennis , Bafna Vineet
Published: September 2007

Primer approximation multiplex PCR (PAMP) is a new experimental protocol for efficiently assaying structural variation in genomes. PAMP is particularly suited to cancer genomes where the precise breakpoints of alterations such as deletions or translocations vary between patients. The design of PCR primer sets for PAMP is challenging because a large number of primer pairs are required to detect alterations in the hundreds of kilobases range that can occur in cancer. These sets of primers must achieve high coverage of the region of interest, while avoiding primer dimers and satisfying the physico-chemical constraints of good PCR primers. We describe a natural formulation of these constraints as a combinatorial optimization problem. We show that the PAMP primer design problem is NP-hard, and design algorithms based on simulated annealing and integer programming, that provide good solutions to this problem in practice.

The algorithms are applied to a test region around the known CDKN2A deletion, which show excellent results even in a 1:49 mixture of mutated:wild-type cells. We use these test results to help set design parameters for larger problems. We can achieve near-optimal designs for regions close to 1 Mb.

Contact:  abashir@ucsd.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Mining biological networks for unknown pathways
Authors: Cakmak Ali , Ozsoyoglu Gultekin
Published: September 2007

Motivation: Biological pathways provide significant insights on the interaction mechanisms of molecules. Presently, many essential pathways still remain unknown or incomplete for newly sequenced organisms. Moreover, experimental validation of enormous numbers of possible pathway candidates in a wet-lab environment is time- and effort-extensive. Thus, there is a need for comparative genomics tools that help scientists predict pathways in an organism's biological network.

Results: In this article, we propose a technique to discover unknown pathways in organisms. Our approach makes in-depth use of Gene Ontology (GO)-based functionalities of enzymes involved in metabolic pathways as follows: Model each pathway as a biological functionality graph of enzyme GO functions, which we call pathway functionality template.Locate frequent pathway functionality patterns so as to infer previously unknown pathways through pattern matching in metabolic networks of organisms.

We have experimentally evaluated the accuracy of the presented technique for 30 bacterial organisms to predict around 1500 organism-specific versions of 50 reference pathways. Using cross-validation strategy on known pathways, we have been able to infer pathways with 86% precision and 72% recall for enzymes (i.e. nodes). The accuracy of the predicted enzyme relationships has been measured at 85% precision with 64% recall.

Availability: Code upon request.

Contact:  ali.cakmak@case.edu

Supplementary information: Supplementary data are available at Bioinformatics online.
Life under pressure: insights from electronic data-storage tags into cod swimbladder function
Authors: van der Kooij Jeroen , Righton David , Strand Espen , Michalsen Kathrine , Thorsteinsson Vilhjalmur , Svedäng Henrik , Neat Francis C. , Neuenfeldt Stefan
Published: September 2007

van der Kooij, J., Righton, D., Strand, E., Michalsen, K., Thorsteinsson, V., Svedäng, H., Neat, F. C., and Neuenfeldt, S. 2007. Life under pressure: insights from electronic data-storage tags into cod swimbladder function. – ICES Journal of Marine Science. 64: 1293–1301. The behavioural response of cod (Gadus morhua) to sudden pressure reductions was investigated in a large electronic-tagging experiment using data collected from 141 cod tagged in five different areas of the Northeast Atlantic. More than 40% of cod exhibited a characteristic equilibration behaviour after a rapid pressure reduction caused either by capture before tagging, or by pressure reduction during a rapid ascent from the seabed, or when migrating to deeper water. The equilibration allowed the cod to regain demersal residence. The rate of descent averaged 10 m d−1 (ranging from 2 to 23 m d−1) over periods of less than a day to 1 month. Descent rates for cod on the Icelandic shelf were inversely related to fish length, i.e. smaller fish descended more rapidly, findings consistent with results achieved in the past under laboratory conditions. Modelling of swimbladder volume during equilibration suggested that cod were negatively buoyant for most of the time. The results imply that swimbladder functionality is retained after the probable barotrauma that would follow a large and rapid ascent, and that rates of gas exchange into the swimbladder may be naturally variable. These findings have implications for assumptions on discard mortality, the interpretation of cod behaviour, and its impact on biomass estimates obtained from acoustic surveys.
When will the eel recover? A full life-cycle model
Authors: Åström Mårten , Dekker Willem
Published: September 2007

Åström M., and Dekker W. 2007. When will the eel recover? A full life-cycle model. – ICES Journal of Marine Science, 64: 000–000: –. The European eel population has declined over the past decades in most of its distribution area, and the stock is outside safe biological limits. The EU has taken up the challenge to design a management system that ensures the escapement of 40% of spawning-stock biomass, relative to unexploited, unpolluted circumstances in unobstructed rivers. This ultimately aims to restore the spawning stock to a level at which glass eel production is not impaired, i.e. to restore to full historical glass eel recruitment. To explore the trajectory from the current depleted state to full recruitment recovery, we developed a simple model of stock dynamics, based on a simplified stock–recruitment relationship and the conventional dynamic pool assumptions. Recruitment trajectories under different future fishery regimes are explored, for the medium (one generation time) and long time-span (until full recruitment recovery). Reducing fisheries to zero, recovery is expected within ∼80 years, whereas under an ultimately sustainable fishing regime of just 10% of the current rate of fishing mortality, recovery may take more than 200 years. Moreover, management regimes, apparently leading to slight recovery of the stock in the coming 5–15 years, might still be unsustainable in the long run.
Classification of ‘Sarraceniospora aurea’ Furihata et al. 1989 as Actinocorallia aurea sp. nov.
Authors: Tamura Tomohiko , Hatano Kazunori , Suzuki Ken-ichiro
Published: September 2007

Phylogenetic analysis of ‘Sarraceniospora aurea’ NBRC 14752 and strain NBRC 15120, based on 16S rRNA gene sequences, revealed that these organisms are related to members of the genus Actinocorallia. These organisms contained glutamic acid, alanine and meso-diaminopimelic acid as cell-wall amino acids and the menaquinones MK-9(H4), MK-9(H6) and MK-9(H8). The chemotaxonomic characteristics of the strains were consistent with those of the genus Actinocorallia. However, DNA–DNA hybridization and phenotypic characteristics revealed that the strains differed from the recognized species of the genus Actinocorallia. Therefore, we propose that ‘Sarraceniospora aurea’ NBRC 14752 and strain NBRC 15120 be reclassified in the genus Actinocorallia as a novel species, Actinocorallia aurea sp. nov. (type strain NBRC 14752T=DSM 44434T).
Francisella philomiragia subsp. noatunensis subsp. nov., isolated from farmed Atlantic cod (Gadus morhua L.)
Authors: Mikalsen J. , Olsen A. B. , Tengs T. , Colquhoun D. J.
Published: September 2007

Seven bacterial isolates from farmed Atlantic cod displaying chronic granulomatous disease were characterized by phenotypic and molecular taxonomic methods. The isolates were Gram-negative, facultatively intracellular, non-motile, strictly aerobic coccobacilli which produced H2S from cysteine-supplemented media and are therefore phenotypically consistent with members of the genus Francisella. Comparison of 16S rRNA gene sequences and six partial housekeeping gene sequences (groEL, shdA, rpoB, rpoA, pgm and atpA) confirmed the organism as a member of the genus Francisella, with Francisella philomiragia as its closest relative (99.3 % 16S rRNA gene sequence similarity, 92.2–99.0 % housekeeping gene sequence similarity). Despite the close relationship with F. philomiragia, isolates from Atlantic cod could be readily distinguished phenotypically and genetically from F. philomiragia ATCC 25015T. DNA–DNA hybridization studies revealed a mean reassociation value of 68 %. Thus, on the basis of phenotypic and molecular genetic evidence, we propose that the strains isolated from Atlantic cod should be recognized as Francisella philomiragia subsp. noatunensis subsp. nov. with the type strain 2005/50/F292-6CT (=NCIMB 14265T=LMG 23800T). Francisella philomiragia ATCC 25015T (=DSM 735T) is reclassified as Francisella philomiragia subsp. philomiragia subsp. nov.
Desulfovibrio marinus sp. nov., a moderately halophilic sulfate-reducing bacterium isolated from marine sediments in Tunisia
Authors: Ben Dhia Thabet O. , Fardeau M.-L. , Suarez-Nuñez C. , Hamdi M. , Thomas P. , Ollivier B. , Alazard D.
Published: September 2007

Two novel sulfate-reducing bacterial strains, designated E-2T and IMP-2, were isolated from geographically distinct locations. Strain E-2T was recovered from marine sediments near Sfax (Tunisia), whereas strain IMP-2 originated from oilfield production fluids in the Gulf of Mexico. Cells were Gram-negative, non-sporulated, motile, vibrio-shaped or sigmoid. They were strictly anaerobic, mesophilic and moderately halophilic. Sulfate, sulfite, thiosulfate and elemental sulfur served as electron acceptors, but not nitrate or nitrite. H2 (with acetate as carbon source), formate, fumarate, lactate, malate, pyruvate, succinate and fructose were used as electron donors in the presence of sulfate as terminal electron acceptor. Lactate was oxidized incompletely to acetate. Fumarate and pyruvate were fermented. Desulfoviridin and c-type cytochromes were present. 16S rRNA gene sequence analysis of the two strains showed that they were phylogenetically similar (99.0 % similarity) and belonged to the genus Desulfovibrio, with Desulfovibrio indonesiensis and Desulfovibrio gabonensis as their closest phylogenetic relatives. The G+C content of the DNA was respectively 60.4 and 62.7 mol% for strains E-2T and IMP-2. DNA–DNA hybridization experiments revealed that the novel strains had a high genomic relatedness, suggesting that they belong to the same species. We therefore propose that the two isolates be affiliated to a novel species of the genus Desulfovibrio, Desulfovibrio marinus sp. nov. The type strain is strain E-2T (=DSM 18311T =JCM 14040T).
Salinicoccus siamensis sp. nov., isolated from fermented shrimp paste in Thailand
Authors: Pakdeeto Amnat , Tanasupawat Somboon , Thawai Chitti , Moonmangmee Somporn , Kudo Takuji , Itoh Takashi
Published: September 2007

Fifteen strains of moderately halophilic, Gram-positive cocci were isolated from a traditional fermented shrimp paste (‘ka-pi’) produced in Thailand. These bacteria were strictly aerobic, non-motile, non-sporulating and catalase- and oxidase-positive. They produced orange pigment and grew in the presence of 1.5–25 % (w/v) NaCl. They grew optimally in 10 % (w/v) NaCl, at pH 8.5 and at 37 °C. The cell-wall peptidoglycan was ofl-Lys type. Menaquinone with six isoprene units (MK-6) was a major component. The dominant cellular fatty acids were anteiso-C15 : 0and iso-C15 : 0. DNA G+C contents were in the range 44.5–47.5 mol%. Comparative 16S rRNA gene sequence analyses indicated that representative strain PN1-2Twas related most closely toSalinicoccus roseusJCM 14630T, with 97.3 % similarity. The other novel strains were included in the same species based on their levels of DNA–DNA relatedness to strain PN1-2T(≥76.6 %) but showed low DNA–DNA relatedness toS. roseusJCM 14630T(21.7 %). On the basis of the phenotypic and molecular data presented, the 15 novel strains are suggested to represent a single novel species of the genusSalinicoccus, for which the nameSalinicoccus siamensissp. nov. is proposed. The type strain is PN1-2T(=JCM 12822T=PCU 242T=TISTR 1562T).
Streptomyces durmitorensis sp. nov., a producer of an FK506-like immunosuppressant
Authors: Savic Miloje , Bratic Ivana , Vasiljevic Branka
Published: September 2007

Screening of soil samples from the Durmitor National Park, Serbia and Montenegro, for strains producing immunosuppressants with a similar mechanism of action to FK506 resulted in the isolation of the actinomycete strain MS405T. Isolate MS405T was found to have morphological and phenotypic properties that were consistent with its classification as a Streptomyces strain. The DNA G+C content of strain MS405T was 72 mol%. 16S rRNA gene sequence data confirmed the taxonomic position of the strain, following the generation of phylogenetic trees by using various treeing algorithms. On the basis of 16S rRNA gene sequence similarity, strain MS405T was shown to belong to the Streptomyces albidoflavus ‘supercluster’, being related to Streptomyces aureus DSM 41785T (99.59 % similarity) and Streptomyces kanamyceticus DSM 40500T (99.32 %). The 16S–23S rRNA internally transcribed spacer (ITS) region exhibited variations in length and sequence composition, showing limited usefulness in phylogenetic analyses. However, DNA relatedness values support the classification of this isolate within a novel species. A number of physiological and biochemical tests distinguished strain MS405T from its closest phylogenetic neighbours. Therefore, strain MS405T represents a novel species, for which the name Streptomyces durmitorensis sp. nov. is proposed, with the type strain MS405T (=DSM 41863T =CIP 108995T).
Aestuariimicrobium kwangyangense gen. nov., sp. nov., an ll-diaminopimelic acid-containing bacterium isolated from tidal flat sediment
Authors: Jung Seo-Youn , Kim Hee-Sik , Song Jae Jun , Lee Seung-Goo , Oh Tae-Kwang , Yoon Jung-Hoon
Published: September 2007

Four Gram-positive, catalase-positive, short rod- or coccoid-shaped bacterial strains, R27T, R44, R45 and R47, were isolated from an enrichment culture with diesel oil-degradation activity and their taxonomic positions were investigated using a polyphasic approach. Phenotypic, phylogenetic and genetic similarities indicated that strains R27T, R44, R45 and R47 belong to the same species. Phylogenetic analysis based on 16S rRNA gene sequences showed that the four strains form a distinct evolutionary lineage within the familyPropionibacteriaceae. The novel four strains had cell-wall peptidoglycan based onll-diaminopimelic acid, MK-9(H4) as the predominant menaquinone and anteiso-C15 : 0as the major cellular fatty acid. The DNA G+C contents were 68.8–69.2 mol%. These chemotaxonomic properties, together with phylogenetic distinctiveness, distinguish the four novel strains from recognized members of the familyPropionibacteriaceae. On the basis of phenotypic, chemotaxonomic, phylogenetic and genetic data, strains R27T, R44, R45 and R47 are classified as representatives of a new genus and novel species,Aestuariimicrobium kwangyangensegen. nov., sp. nov., within the familyPropionibacteriaceae. The type strain ofAestuariimicrobium kwangyangensesp. nov. is R27T(=KCTC 19182T=JCM 14204T).
Pseudovibrio japonicus sp. nov., isolated from coastal seawater in Japan
Authors: Hosoya Shoichi , Yokota Akira
Published: September 2007

A Gram-negative, motile, rod-shaped bacterium (WSF2T) was isolated from coastal seawater of the Boso Peninsula in Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain WSF2T represented a separate lineage within the genus Pseudovibrio. The DNA G+C content of strain WSF2T was 51.7 mol%. DNA–DNA hybridization values between strain WSF2T and the type strains of Pseudovibrio species were significantly lower than those accepted as the phylogenetic definition of a species. Furthermore, some biochemical characteristics indicated that strain WSF2T differed from other Pseudovibrio species. Based on these characteristics, it is proposed that the isolate represents a novel species, Pseudovibrio japonicus sp. nov. The type strain is WSF2T (=IAM 15442T=NCIMB 14279T=KCTC 12861T).
Aureispira maritima sp. nov., isolated from marine barnacle debris
Authors: Hosoya Shoichi , Arunpairojana Vullapa , Suwannachart Chatrudee , Kanjana-Opas Akkharawit , Yokota Akira
Published: September 2007

A novel gliding marine bacterium (strain 59SAT) was isolated from marine barnacle debris. A phylogenetic analysis based on 16S rRNA gene sequences showed that the isolate formed a distinct lineage within the genus Aureispira in the family ‘Saprospiraceae’. The DNA G+C content of strain 59SAT was 38.7 mol%, the major respiratory quinone was MK-7 and the predominant cellular fatty acids were 20 : 4ω6c and 16 : 0. On the basis of the data from DNA–DNA hybridization, physiological and chemotaxonomic analyses and 16S rRNA gene sequence comparisons, strain 59SAT represents a novel species of the genus Aureispira, for which the name Aureispira maritima sp. nov. is proposed. The type strain is 59SAT (=IAM 15439T=TISTR 1726T).
On species descriptions based on a single strain: proposal to introduce the status species proponenda (sp. pr.)
Authors: Felis Giovanna E. , Dellaglio Franco
Published: September 2007

A survey of the descriptions of novel bacterial species published in the period 1996–2006 revealed that a large number of taxonomic descriptions are still based on one or a few strains. This situation determines that not only species descriptions, but also proposals to create higher ranks, are actually based on very few strains, which could produce a highly biased scenario. The encouragement to include a reasonable number of strains in species descriptions has been largely disregarded after its proposal, since acceptance of such descriptions relies mainly on editors' and reviewers' opinions. This observation and other considerations lead us to propose the creation of the status species proponenda (sp. pr.), as a compromise between the need for scientific description of biodiversity and exchange of data and the good taxonomic practice of including a sufficient number of strains in descriptions of species and higher taxonomic ranks.
Modestobacter versicolor sp. nov., an actinobacterium from biological soil crusts that produces melanins under oligotrophy, with emended descriptions of the genus Modestobacter and Modestobacter multiseptatus Mevs et al. 2000
Authors: Reddy Gundlapally S. N. , Potrafka Ruth M. , Garcia-Pichel Ferran
Published: September 2007

A novel isolate, CP153-2T, was obtained from topsoil biological crusts in the Colorado Plateau (USA). Colonies were black in colour due to melanin-like pigments when grown on oligotrophic medium, but not when grown on copiotrophic medium. Induction of melanogenesis was independent of growth phase or illumination conditions, including exposure to UVB and UVA radiation, but exposure to UVB could enhance total pigment production and growth under low nitrogen prevented its synthesis. This mode of regulation was previously unknown among melanin-producing bacteria. Polyphasic characterization of the strain revealed that cells were short, straight to curved or irregular rods that developed into pairs and formed multiseptate short filaments, with rare bud-like cells. Short rods were typically motile by means of flagella; multicellular structures tended to be sessile. Cells stained Gram-positive, grew at 4–30 °C and had a narrow range of pH tolerance (pH 5–9). The major fatty acids were iso-C15:0 iso-C16 : 0, anteiso-C15 : 0 and C18 : 1; MK-9(H4) was the major respiratory quinone. Its peptidoglycan contained meso-diaminopimelic acid. Based on 16S rRNA gene sequence similarity data, its closest relative (98.1 % similarity) was Modestobacter multiseptatus DSM 44406T, which is similar morphologically. Based on the above characteristics, strain CP153-2T was also assigned to the genus Modestobacter. However, CP153-2T had a relatedness of only 49.9 % in whole-genome reassociation comparisons with the type strain of M. multiseptatus and thus formally represents a novel species, for which the name Modestobacter versicolor sp. nov. is proposed. Additional evidence in support of a novel species comes from phenotypic and chemotaxonomic characteristics. Strain CP153-2T (=ATCC BAA-1040T =DSM 16678T) is the type strain of M. versicolor.
Reclassification of Graphium tectonae as Parascedosporium tectonae gen. nov., comb. nov., Pseudallescheria africana as Petriellopsis africana gen. nov., comb. nov. and Pseudallescheria fimeti as Lophotrichus fimeti comb. nov.
Authors: Gilgado Fèlix , Gené Josepa , Cano Josep , Guarro Josep
Published: September 2007

During a biodiversity survey of Argentinian soil fungi, we recovered a rareScedosporium-like fungus which was proven to be genetically and morphologically different from known species ofScedosporium(anamorph ofPseudallescheria) and relatives and is proposed here as representing a new genus. This genus is mainly characterized by producing sympodial conidia from denticulate conidiogenous cells. This isolate was morphologically identical toGraphium tectonaeand thus the new combinationParascedosporium tectonaegen. nov., comb. nov. is proposed. Sequence analysis of four regions of three genes, i.e.β-tubulin (two loci), calmodulin and the internal transcribed spacer region of the 5.8S rRNA, confirmed our proposal. Both the phylogenetic analysis and morphological studies excludedPseudallescheria africanaandPseudallescheria fimetifrom the genusPseudallescheria. The former is proposed as a member of the new genusPetriellopsis, and the latter has been accommodated inLophotrichus. The type strains ofParascedosporium tectonaegen. nov., comb. nov.,Petriellopsis africanagen. nov., comb. nov. andLophotrichus fimeticomb. nov. are respectively CBS 127.84T, CBS 311.72Tand CBS 129.78T.
Loktanella atrilutea sp. nov., isolated from seawater in Japan
Authors: Hosoya Shoichi , Yokota Akira
Published: September 2007

A Gram-negative, rod-shaped bacterium, IG8T, was isolated from seawater off the Sanriku coast, Japan. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IG8T represented a separate lineage within the genus Loktanella; the highest 16S rRNA gene sequence similarity values were found with the type strains of Loktanella
salsilacus (98.6 %) and Loktanella fryxellensis (98.4 %). DNA–DNA hybridization values between strain IG8T and the type strains of L. salsilacus (27.9–36.1 %) and L. fryxellensis (11.3–31.0 %) were clearly below 70 %, the generally accepted limit for species delineation. The DNA G+C content of strain IG8T was 66.3 mol%. On the basis of DNA–DNA hybridization, some biochemical characteristics and 16S rRNA gene sequence comparison, it is proposed that the isolate represents a novel species, Loktanella atrilutea sp. nov. The type strain is IG8T (=IAM 15450T=NCIMB 14280T).
Pelobacter seleniigenes sp. nov., a selenate-respiring bacterium
Authors: Narasingarao Priya , Häggblom Max M.
Published: September 2007

Strain KMT is a novel bacterium with the unique metabolic abilities of being able to respire selenate as the electron acceptor using acetate as the carbon substrate and possessing the ability to grow fermentatively on short-chain organic acids such as lactate, citrate and pyruvate. Strain KMT was isolated from a sediment enrichment culture of a highly impacted wetland system in New Jersey, USA. Strain KMT is able to reduce selenate as well as selenite to elemental selenium. The unique metabolic capabilities of strain KMT include the respiration of nitrate, poorly crystalline Fe(III) and anthraquinone disulfonate. Phylogenetic analysis of the 16S rRNA gene of the novel isolate indicates that strain KMT groups within the family Geobacteraceae in the class Deltaproteobacteria with approximately 96–97 % 16S rRNA gene sequence similarity to the closest known organisms Malonomonas rubra Gra Mal 1T, Pelobacter acidigallici Ma Gal 2T and species of the genus Desulfuromusa. Recognized species of the genera Malonomonas and Pelobacter cannot use any inorganic electron acceptors, while strains of the genus Desulfuromusa do not ferment organic substrates. This contrasts with the ability of strain KMT to ferment organic compounds as well as to couple selenate reduction to acetate utilization. Based on 16S rRNA gene phylogeny and metabolic properties, strain KMT represents a novel species for which the name Pelobacter seleniigenes sp. nov. (type strain KMT=DSM 18267T=ATCC BAA-1388T) is proposed. Based on the phylogenetic grouping of species of the genus Pelobacter within the Desulfuromusa cluster, it is suggested that Malonomonas rubra Gra Mal 1T should also be included in this group.