bluuebunny/crossref_metadata_2025 huggingface dataset:
Elevated levels of gene expression for collagen and decorin in human gingival overgrowth
Authors: Dannewitz Bettina , Edrich Christina , Tomakidi Pascal , Kohl Annette , Gabbert Olaf , Staehle Hans‐Jörg , Steinberg Thorsten
Published: June 2006

Objectives: It has been demonstrated that extracellular matrix molecules are involved in cyclosporine‐induced gingival overgrowth (GO). However, for many of these molecules, it remains unclear whether their abundance is modulated on the protein and gene expression level.

Material and Methods: To contribute to this clarification, we have analysed the protein and mRNA expression of type‐I collagen (COL1) and decorin (DC) in native specimens obtained from five patients with GO, and matched normal tissue using indirect immunofluorescence (IIM), in situ hybridization (ISH) and quantitative polymerase chain reaction (PCR).

Results: IIF revealed a largely co‐localized although remarkably increased abundance for COL1 and DC in GO. This increase coincided with an up‐regulated gene expression observed for both molecules, as detected by ISH and quantitative PCR.

Conclusions: Analysis of our data clearly demonstrates elevated levels for COL1 and DC and shows for the first time in native human tissue that involvement of these genes in GO is not confined to the protein level but also includes the transcriptional level.
Population consequences of behaviour in the European bitterling (Rhodeus sericeus Cyprinidae)
Authors: Smith C. , Reichard M. , Douglas A. , Jurajda P.
Published: June 2006

Abstract –  The European bitterling is a freshwater fish with an unusual spawning symbiosis with freshwater mussels. Female bitterling possess long ovipositors that they use to place their eggs onto the gills of a mussel. Males fertilise the eggs by releasing sperm into the inhalant siphon of the mussel. The embryos develop inside the mussel for approximately a month, eventually leaving the mussel as actively swimming larvae. Because they use a discrete spawning site that can be readily manipulated they represent an ideal model for linking reproductive decisions with population dynamics. Bitterling have been used in field and large‐scale pool experiments, in combination with modelling and population and genetic studies to investigate the population consequences of behaviour. Here we show how male mating tactics, female mate and oviposition decisions, and aggressive interference competition among juveniles, may have significant impacts on bitterling population size and population genetics.
Reproductive ecology of two cyprinid fishes in an oligotrophic lake near the southern limits of their distribution range
Authors: Tarkan A. S.
Published: June 2006

Abstract –  The reproductive activities of two dominant fish species, roach Rutilus rutilus and rudd Scardinius erythrophthalmus were investigated from August 2000 to July 2002 in an oligotrophic lake, Lake Sapanca, in the northwest of Turkey. A total of 907 roach and 593 rudd individuals were examined. Macroscopic appearance of ovary, gonadosomatic index and oocyte diameter frequency distribution suggested that the spawning season of roach and rudd were from early April (13 °C) to late May (18 °C) and from early May (17.5 °C) to late June (23.5 °C), respectively. The spawning cycles of both species showed the same tendency in two successive years. The estimated mean total lengths at first maturity (LT50) were 12.26 and 14.98 cm for male and female roach, respectively, and 7.12 and 8.10 cm for male and female rudd, respectively. The sizes at 50% maturity corresponded to 3 years for roach and 1 year for rudd, for both sexes. The ratio of males to females was 1.3:1 and 1.2:1 for roach and rudd, respectively. The average condition factor K was 1.21 for rudd and 1.14 for roach, and it was not affected by sex or reproductive effort. Absolute fecundity varied from 7829 to 95,387 eggs between ages 3 and 9 for roach and from 1807 to 35,629 eggs between ages 1 and 7 for rudd. Comparisons of these results with earlier studies from more northern regions revealed that spawning of both species in this area started earlier, but spawning temperature and the duration of spawning was approximately the same.
Protracted spawning of St Lawrence River northern pike (Esox lucius): simulated effects on survival, growth, and production
Authors: Farrell J. M. , Mead J. V. , Murry B. A.
Published: June 2006

Abstract –  An individual‐based early life history model demonstrated that the timing and distribution of St Lawrence River northern pike (Esox lucius) spawning could affect subsequent young‐of‐year (YOY) production during nursery and influence year‐class formation. Three different spawning patterns have emerged from empirical studies, where egg deposition occurred along the entire littoral gradient beginning in seasonally flooded emergent habitats in tributaries, progressing to submerged aquatic vegetation in shallow bays, and ending in deep water littoral habitats (up to 6 m). The spawning period is protracted, and typically lasts 6–8 weeks due to the presence of a strong thermal gradient. The model used temperature as the driving variable to predict egg abundance, stage‐specific development, growth, survival, and ultimately relative production of YOY northern pike within 1‐ha plots representative of the three habitats. Earlier spawning (mean 21 days) and higher mean daily survival and growth yielded higher YOY net production for tributaries (mean = 3095.4 g ha−1, SD = 2028.6) relative to the shallow bay habitat (202.5 g ha−1, SD = 125.7). In contrast, deep littoral habitat represented an ecological sink with little production (<0.9 g ha−1). The results demonstrate the importance of the linkage between spawning and nursery processes in determining reproductive success.
Annual movement of adult pike (Esox lucius L.) in a lowland river
Authors: Koed A. , Balleby K. , Mejlhede P. , Aarestrup K.
Published: June 2006

Abstract –  The movement of ten radio‐tagged adult pikes (57–113 cm) in the River Gudenå, Denmark, was investigated from September 1998 to September 1999. The movements of pike were characterised by long resident periods in the submergent vegetation, interrupted by short excursions to nearby areas. Two periods with more intense movement were observed; one period during early winter; and one period during spring from mid‐March to mid‐May. The increased movement during early winter may have been initiated by a slight temperature increase at this time, whereas the increased movement during spring coincided with the spawning of pike. Despite suitable spawning areas nearby the areas where pike resided most of the year, several pike, mainly females, migrated to distant localities during spring.
Laboratory‐based reproduction success of ruffe, Gymnocephalus cernuus (L.), in brackish water is determined by maternal properties
Authors: Albert A. , Vetemaa M. , Saat T.
Published: June 2006

Abstract – Body length, age, egg size, embryo salinity tolerance and length at hatching of the freshwater (salinity <0.1 ppt, Lake Peipsi) and brackish‐water (salinity 2–6 ppt, Pärnu and Matsalu Bay) ruffe, Gymnocephalus cernuus (L.), were examined to reveal their reproductive success in moderate salinity. Eggs of females originating from brackish water were significantly larger than eggs of freshwater females. No correlation between egg size and female size and age was found in brackish‐water populations. In the freshwater population there was a small negative correlation between egg size and female size, but no correlation with female age. Fertilisation by sperm of males of different origin (brackish water or freshwater) produced no significant differences at any critical developmental stage (fertilisation, gastrulation, hatching) in the development of eggs from brackish‐water or freshwater females at 3.3, 5.5, 7.7 and 9.9 ppt salinity. Survival rates in different salinity depended only on female origin; embryonic salinity tolerance was higher in ruffe inhabiting brackish water. Obviously, embryo salinity tolerance in ruffe is determined by egg qualities.
Patterns of movement of adult northern pike (Esox luciusL.) in a regulated river
Authors: Vehanen T. , Hyvärinen P. , Johansson K. , Laaksonen T.
Published: June 2006

Abstract – We performed a tagging study on one of the spawning populations of northern pike (Esox luciusL.) of the River Kajaaninjoki in Finland. Northern pike is the main predator in many lakes and rivers in the northern hemisphere. Previous tagging studies have shown a general tendency to sedentary behaviour by pike. Whether individuals in a fish population adapt a sedentary or moving strategy may affect population persistence. To study if the spawning population consists of sedentary or moving individuals and the pattern of movements, we tagged 40 pike with radio transmitters and followed them from May 2002 to June 2003. Pike were caught and tagged during the spawning season in the mouth of the River Kajaaninjoki which flows into one of the largest lakes in Finland, Lake Oulujärvi. Our results suggest that the pike spawning population consisted of sedentary pike (N = 16) dwelling the whole year in the river, and moving pike (N = 24) which moved to Lake Oulujärvi after the spawning period. Pike exhibited homing behaviour, as most of the migrating pike returned to the same spawning area in the following year. Large pike had a higher movement rate than small pike during the summer and seasonally the movement rate was lowest during the spring and highest during the summer.
Upstream migration of chum salmon through a restored segment of the Shibetsu River
Authors: Akita M. , Makiguchi Y. , Nii H. , Nakao K. , Sandahl J. F. , Ueda H.
Published: June 2006

Abstract –  A segment of the Shibetsu River was restored to reconstruct the ecological condition of the previously canalized river stretch to a more natural, meandering state. In this study, we investigated the upstream migration of chum salmon (Oncorhynchus keta) using radio transmitters to track the horizontal position of fish and data loggers to detect the vertical swimming depth of fish, simultaneously. The monitored salmon travelled near the bottom of the water column and along the riverbanks, and tended to hold in deep, slow current areas in the canalized river. In the restored segment, the fish swam at more shallow depths and against stronger currents. Although the three tracked fish all reached the confluent point and chose to enter the restored segment, they did not remain in the segment for long. This indicates that the restored area facilitates the upward migration of the chum salmon.
Investigating the role of brain‐derived neurotrophic factor in relapsing–remitting multiple sclerosis
Authors: Liguori M. , Fera F. , Gioia M. C. , Valentino P. , Manna I. , Condino F. , Cerasa A. , La Russa A. , Clodomiro A. , Paolillo A. , Nisticò R. , Vercillo L. , Cittadella R. , Quattrone A.
Published: June 2006

Multiple sclerosis (MS) is a common, heterogeneous disorder of the central nervous system with a complex trait composed of both genetic and environmental factors. Recently, scientific interest has increased in defining factors that possibly contribute to brain functional plasticity; the results might be useful to assess the relationship between MS lesion burden and clinical events, as well as explaining the well‐known phenotypic heterogeneity of the disease. In this study, we explored the effect of the Val66Met brain‐derived neurotrophic factor (BDNF) functional polymorphism on cognitive performances and volumetric measurements obtained by magnetic resonance imaging of the brain in a selected population of relapsing–remitting MS (RRMS) patients, with relatively short disease duration and minimal clinical disability, compared to gender, age and educational‐level matched healthy subjects. We found that in the RRMS group, the BDNF Met‐allele was significantly associated with the lower volume of cerebral grey matter (GM) (P = 0.005). Furthermore, a significant (P = 0.013) interaction effect between ‘MS‐status’ and the BDNF genotype was found for GM volumes, with the result that patients carrying the BDNF Met‐allele showed a higher risk of developing global GM atrophy than the homozygous Val/Val. No BDNF‐related impact on global neuropsychological functions resulted in either RRMS patients or controls. Our data seem to be consistent with the reported influence of BDNF in neuronal plasticity, thus suggesting that the Met‐allele might have a negative prognostic effect on cortical morphometry in RRMS patients.
Acceptability, feasibility and affordability of infant feeding options for HIV‐infected women: a qualitative study in south‐west Nigeria
Authors: Abiona Titilayo C. , Onayade Adedeji A. , Ijadunola Kayode T. , Obiajunwa Perpetua O. , Aina Olabisi I. , Thairu Lucy N.
Published: June 2006

The objective of this study was to explore the acceptability, feasibility, affordability, safety and sustainability of replacement feeding options for HIV‐infected mothers in Ile‐Ife, in south‐west Nigeria. Six focus group discussions were conducted with a purposive sample of mothers, fathers and grandmothers. The HIV status of all participants was unknown to investigators. All text data were analysed using the Text‐based Beta Software program. With regard to the acceptability of replacement feeds, respondents perceived the stigma associated with not breastfeeding to be an important consideration. In this community, breastfeeding is the norm – even though it is not necessarily exclusive. For infected mothers who choose to breastfeed exclusively and then to wean their infants before 6 months of age, respondents did not anticipate early cessation of breastfeeding to be problematic. Respondents noted that acceptable replacement foods included infant formula, soy milk and cow’s milk. Barriers to replacement feeding that were mentioned included: the high costs of replacement foods and fuel for cooking; an unreliable supply of electrical power; poor access to safe water; and poor access to storage facilities. The research confirms the difficulty of replacement feeding for HIV‐infected mothers in sub‐Saharan Africa. The results also provide the basis for new issues and hypothesis for future research in other communities with similar socio‐cultural and economic characteristics.
Relative validity of a dietary interview for assessing infant diet and compliance in a dietary intervention trial
Authors: Vähätalo Liisa , Bärlund Sonja , Hannila Marja‐Leena , Uusitalo Ulla , Pigg Hanna‐Mari , Salonen Marja , Nucci Anita , Krischer Jeffrey P. , Knip Mikael , Åkerblom Hans K. , Virtanen Suvi M. ,   the TRIGR Study Group
Published: June 2006

The objective of this study was to assess the relative validity of a dietary interview method for use in an infant population. A dietary interview covering a 1‐month period was completed during a study visit at 3 or 6 months of age. It included structured questions and a short food frequency questionnaire (FFQ). The information was compared with data from two 48‐h recall interviews conducted during the month previous to the study visit. The agreement between the FFQ and 48‐h recalls was analysed as proportion of subjects classified into the same categories of consumption frequency and by the kappa analysis. A total of 100 subjects, at the age of 2–3 months (n = 50) and 5–6 months (n = 50), were included. The kappa values for breastmilk and study formula ranged from 0.82 to 0.95, indicating very good agreement. The agreement for other foods and vitamin D supplementation ranged from fair to very good. We also found a strong correlation for the reported amount of study formula consumed per feeding at 3 months (rs = 0.87, n = 24) and 6 months of age (rs = 0.73, n = 35) between the questionnaire and 48‐h recall data. However, the average amount of study formula per feeding was significantly higher when estimated for a 1‐month period, compared with a mean calculated from the two 48‐h recalls. As a conclusion, the interview was found to be a useful tool for assessing diet and compliance in a dietary intervention for infants.
Physiological and biochemical response of potato (Solanum tuberosum L. cv. Kara) to O3 and antioxidant chemicals: possible roles of antioxidant enzymes
Authors: Hassan I.A.
Published: June 2006

An Egyptian cultivar of potato (Solanum tuberosum L. cv. Kara) was grown in the field at two locations in northern Egypt: a ‘rural’ and a ‘suburban’ site, from October 2000 and November 2002. The antiozonant ethylenediurea (EDU) and the fungicide chlorothalonil (1,3‐benzenedicarbonitrile‐2,4,5,6 tetrachloroisophthalnitrile) were applied as a foliar spray to plants at both sites. It was found that foliar injury symptoms were reduced greatly in plants treated with EDU and/or chlorothalonil, and the yield of treated plants was higher than that of the untreated ones, with the EDU having a greater protection than chlorothalonil. Antiozonant (EDU) and fungicide (chlorothalonil) combination sprays were even more effective in reducing O3 injury. Moreover, the percentage of protection was higher in the rural area than in the suburban one, and this was associated with higher levels of O3 recorded in the rural area. The response to O3, EDU, and chlorothalonil of the leaf antioxidant scavenger system was examined. Antiozonant‐treated plants had the highest reduced glutathione/oxidised glutathione ratio. The results suggest that EDU and chlorothalonil do not act directly as antiozonant to inhibit O3 injury but act through maintaining some antioxidant enzymes during O3 exposure. To the best of knowledge, this is the first report demonstrating the marked enhancement of yield and plant oxidative enzymes by fungicides as a mechanism of protecting plants against noxious oxidative stress from the environment in the developing world.
Pathotypes of Plasmodiophora brassicae, the cause of clubroot, in Australia
Authors: Donald E.C. , Cross S.J. , Lawrence J.M. , Porter I.J.
Published: June 2006

Variation in pathogenicity of Plasmodiophora brassicae in Australia was studied using the European Clubroot Differential series of brassica hosts. From 41 collections of P. brassicae originating from important vegetable brassica production regions in Victoria, Western Australia, Tasmania, Queensland and New South Wales, 23 triplet codes were generated. These were more similar to populations of P. brassicae reported from the USA than those from Europe. The most common Australian pathotypes had triplet codes of 16/3/12 and 16/3/31 and were each assigned seven times to pathogen collections originating from three states of Australia. Other codes that occurred more than once were 16/2/31, which was assigned to six collections from four states of Australia, and 16/19/31, which was assigned twice to collections originating from Western Australia.
A histochemical study of the reproductive structures in the flatworm Dugesia leporii (Platyhelminthes, Tricladida)
Authors: Corso Gavina , Manconi Renata , Stocchino Giacinta A.
Published: June 2006

Abstract. The functional morphology and the topographic distribution of tissues in the reproductive system of specimens of Dugesia leporii, an endemic Sardinian free‐living planarian, are investigated. Data are provided on the nature of epithelial and glandular secretions, spermatophores, and cocoons by histochemistry, light microscopy, and scanning electron microscopy. All secreting epithelial cells produce strongly acidic sulfated glycoproteins. Glandular cells secrete strongly acidic sulfated glycoproteins or keratohyalin‐like material in the penis bulb, and prekeratin‐like material in atrial glands. Secretions of the bursa copulatrix may be involved in the activation of sperm while material produced by the bursa canal and oviducts probably serves to propel spermatophores or sperm and eggs. Mucous secretion of the seminal vesicle may serve to dilute and activate sperm before copulation. The viscous secrete of the ejaculatory duct and vasa deferentia may play a protective role to maintain sperm viability. Materials produced by the penis papilla and atrium probably lubricate the epithelial surface. The bilayered wall of spermatophore made of keratohyalin‐like material and strongly acidic sulfated glycoproteins is produced by two gland types of the penis bulb. The bilayered shell of cocoon made of prekeratin‐like and keratohyalin‐like materials is secreted by both atrial glands and vitelline cells. The cocoon stalk is made of keratohyalin‐like material produced by cement glands. Shell glands, producing GAG, are not involved in cocoon formation, but they may be implicated in the dilution and activation of seminal material to favor sperm movement toward the oviducts.
Ultrastructure of the male gonad and male gametogenesis in the clam shrimp Eulimnadia texana (Crustacea, Branchiopoda, Spinicaudata)
Authors: Scanabissi Franca , Cesari Michele , Reed Sadie K. , Weeks Stephen C.
Published: June 2006

Abstract. The ultrastructure of the male gonad of Eulimnadia texana (Branchiopoda, Spinicaudata) has been observed for the first time to investigate the sexuality of a well‐studied case of androdioecy in the animal kingdom. The male gonad is a double structure located in the hemocoel throughout the entire body length on each side of the midgut. Male gametes originate from the wall and mature centripetally toward the lumen; the proliferative activity is very high and continuous and therefore the mature gonad is full of numerous germ cells. Inside the lumen several degenerative stages are found mixed with sperm cells and spermatids, the latter two being not easily distinguishable because of the slight differences between them. The evolutionary meaning of the degenerative process in E. texana male gametes is difficult to explain, and we propose some hypotheses about its possible role or cause in the studied population: (a) to help build spermatophores, (b) to act as a trophic component for viable sperm, (c) as a manifestation of inbreeding depression, and/or (d) to regulate the number of sperm cells.
Characterization and comparison of digestive proteinases of the Cortez swimming crab, Callinectes bellicosus, and the arched swimming crab, Callinectes arcuatus
Authors: Díaz‐Tenorio Lourdes M. , García‐Carreño Fernando L. , Navarrete del Toro M. Ángeles
Published: June 2006

Abstract. Protease activity in the midgut gland, gastric chamber, and gastric juice from the crabs Callinectes bellicosus and Callinectes arcuatus was characterized by several methods, confirming that the composition of digestive proteases is the same in the gastric juice and the midgut gland. Gastric juice was suitable for the identification and characterization of the proteinases trypsin and chymotrypsin. Such enzymes were presented as isotrypsins and isochymotrypsins. Proteinase composition evaluated by SDS‐PAGE and substrate‐SDS‐PAGE showed differences between species, but not between gender. Proteinases were thermostable at 40°–50°C for 1 h and showed maximum activity at pH 6–8, making the use of digestive proteinases for evaluations of protein digestibility by the pHstat method possible. We propose using gastric juice as a source of digestive enzymes for in vitro studies of enzymes in digestibility assays and characterization procedures.
A new species of Xyloplax (Echinodermata: Asteroidea: Concentricycloidea) from the northeast Pacific: comparative morphology and a reassessment of phylogeny
Authors: Mah Christopher L.
Published: June 2006

Abstract. Xyloplax janetae n. sp. is described from the northeast Pacific Ocean. This is the third species recognized for the monogeneric Concentricycloidea. Skeletal structures are elaborated by scanning electron microscopy and compared with those of Xyloplax medusiformis from New Zealand and Xyloplax turnerae from the Bahamas. Critical‐point‐dried specimens show fibrous connective tissue emerging from openings on the abactinal surface, on the abactinal spine bases, and at broken cross sections of the adambulacral spines. Knob‐like structures emerging through the stereom openings of the abactinal spine base are also observed. Tube feet have round, swollen knobs and show few striations relative to other asteroids. Cosmopolitan bathyal–abyssal echinoderm species tend to exhibit few morphological differences over broad geographic ranges; this generalization is true of Xyloplax. The Concentricycloidea is proposed as an infraclass within the Asteroidea, as the sister branch to the Neoasteroidea (the crown‐group asteroids) within the subclass Ambuloasteroidea. The hypothesis presented is compatible with recent phylogenetic data supporting affinities between Xyloplax and the Asteroidea. Characters plesiomorphic in basal neoasteroids are consistent with a sister‐group relationship to concentricycloids. Actinal plate presence, an important synapomorphy for the Neoasteroidea, is absent from concentricycloids. The substantial morphological departure of Xyloplax is considered to be associated with the post‐Paleozoic diversification of crown‐group asteroids rather than from modification of an established and conservative morphology.
PHASE: A Novel Approach to Pharmacophore Modeling and 3D Database Searching
Authors: Dixon Steven L. , Smondyrev Alexander M. , Rao Shashidhar N.
Published: June 2006

Pharmacophore modeling and 3D database searching are now recognized as integral components of lead discovery and lead optimization, and the continuing need for improved pharmacophore‐based tools has driven the development of PHASE. By employing a novel, tree‐based partitioning algorithm, PHASE exhaustively identifies spatial arrangements of functional groups that are common and essential to the biologic activity of a set of high affinity ligands. These pharmacophore hypotheses are validated in a number of ways, including their ability to: (i) rationalize the binding affinities of a training set of molecules of varying activity, (ii) successfully predict the affinities of a test set of molecules, and (iii) selectively retrieve known actives from a database of drug‐like molecules. In addition, PHASE uniquely offers the ability to distinguish multiple binding modes through a bi‐directional clustering approach applied to bit string representations of the ligand/hypothesis space.
Insight into the Binding Mode for Cyclopentapeptide Antagonists of the CXCR4 Receptor
Authors: Våbenø Jon , Nikiforovich Gregory V. , Marshall Garland R.
Published: June 2006

The finding that the chemokine receptor CXCR4 is involved in T‐cell HIV entry has encouraged the development of antiretroviral drugs targeting this receptor. Additional evidence that CXCR4 plays a crucial role in both angiogenesis and metastasis provides further motivation for the development of a CXCR4 inhibitor for therapeutic applications in oncology. To facilitate the design of such ligands, we have investigated the possible binding modes for cyclopentapeptide CXCR4 antagonists by docking 11 high/medium affinity cyclopentapeptides to a developed three‐dimensional model of the CXCR4 G‐protein‐coupled receptor's transmembrane region. These ligands, expected to bind in the same mode to the receptor, were docked in the previously deduced receptor‐bound conformation [Våbenøet al., in press; doi 10.1002/bip.20508]. Ligand–receptor complexes were generated using an automated docking procedure that allowed ligand flexibility. By comparing the resulting ligand poses, only two binding modes common for all 11 compounds were identified. Inspection of these two ligand–receptor complexes identified several CXCR4 contact residues shown by mutation to be interaction sites for ligands and important for HIV gp120 binding. Thus, the results provide further insight into the mechanism by which these cyclopentapeptides block HIV entry as well as a basis for rational design of CXCR4 mutants to map potential contacts with small peptide ligands.
Patterns of stable isotope signatures in willow warbler Phylloscopus trochilus feathers collected in Africa
Authors: Bensch Staffan , Bengtsson Göran , Åkesson Susanne
Published: June 2006

We conducted stable isotope analyses of nitrogen and carbon on feathers obtained from willow warblers in Africa to find an explanation for a previously observed pattern of different δ15N and δ13C values across a migratory divide in central Scandinavia. A new data set confirms that north Scandinavian birds of the subspecies P. t. acredula have higher δ15N values than south Scandinavian birds of the subspecies P. t. trochilus. In Africa, we found significant differences for both δ15N and δ13C values among feathers collected from major geographical regions as well as between countries within regions. Isotope signatures of δ15N and δ13C in Scandinavian acredula matched well with those of willow warblers sampled in southern parts of Africa, but differed from samples obtained in East and West Africa. Isotope signatures in Scandinavian trochilus did not agree with the pattern in any of the three African regions (West, East or South). However, a more detailed analysis of the isotopic data in feathers from countries within West Africa, which is the wintering region of Swedish trochilus based on ringing recoveries, revealed a correspondence with samples from Liberia, the Ivory Coast and Nigeria.
Replication Control of Staphylococcal Multiresistance Plasmid pSK41: an Antisense RNA Mediates Dual-Level Regulation of Rep Expression
Authors: Kwong Stephen M. , Skurray Ronald A. , Firth Neville
Published: June 2006

Replication of staphylococcal multiresistance plasmid pSK41 is negatively regulated by the antisense transcript RNAI. pSK41 minireplicons bearing
rnaI
promoter (P

rnaI

) mutations exhibited dramatic increases in copy number, approximately 40-fold higher than the copy number for the wild-type replicon. The effects of RNAI mutations on expression of the replication initiator protein (Rep) were evaluated using transcriptional and translational fusions between the
rep
control region and the
cat
reporter gene. The results suggested that when P

rnaI

is disrupted, the amount of
rep
mRNA increases and it becomes derepressed for translation. These effects were reversed when RNAI was provided in
trans
, demonstrating that it is responsible for significant negative regulation at two levels, with the greatest repression exerted on
rep
translation initiation. Mutagenesis provided no evidence for RNAI-mediated transcriptional attenuation as a basis for the observed reduction in
rep
message associated with expression of RNAI. However, RNA secondary-structure predictions and supporting mutagenesis data suggest a novel mechanism for RNAI-mediated repression of
rep
translation initiation, where RNAI binding promotes a steric transition in the
rep
mRNA leader to an alternative thermodynamically stable stem-loop structure that sequesters the
rep
translation initiation region, thereby preventing translation.
Dynamic Metabolic Adjustments and Genome Plasticity Are Implicated in the Heat Shock Response of the Extremely Thermoacidophilic ArchaeonSulfolobus solfataricus
Authors: Tachdjian Sabrina , Kelly Robert M.
Published: June 2006

Approximately one-third of the open reading frames encoded in theSulfolobus solfataricusgenome were differentially expressed within 5 min following an 80 to 90°C temperature shift at pH 4.0. This included many toxin-antitoxin loci and insertion elements, implicating a connection between genome plasticity and metabolic regulation in the early stages of stress response.
Crystal Structure of Pyridoxal Kinase from the
Escherichia coli pdxK
Gene: Implications for the Classification of Pyridoxal Kinases
Authors: Safo Martin K. , Musayev Faik N. , di Salvo Martino L. , Hunt Sharyn , Claude Jean-Baptiste , Schirch Verne
Published: June 2006

The
pdxK
and
pdxY
genes have been found to code for pyridoxal kinases, enzymes involved in the pyridoxal phosphate salvage pathway. Two pyridoxal kinase structures have recently been published, including
Escherichia coli
pyridoxal kinase 2 (ePL kinase 2) and sheep pyridoxal kinase, products of the
pdxY
and
pdxK
genes, respectively. We now report the crystal structure of
E. coli
pyridoxal kinase 1 (ePL kinase 1), encoded by a
pdxK
gene, and an isoform of ePL kinase 2. The structures were determined in the unliganded and binary complexes with either MgATP or pyridoxal to 2.1-, 2.6-, and 3.2-Å resolutions, respectively. The active site of ePL kinase 1 does not show significant conformational change upon binding of either pyridoxal or MgATP. Like sheep PL kinase, ePL kinase 1 exhibits a sequential random mechanism. Unlike sheep pyridoxal kinase, ePL kinase 1 may not tolerate wide variation in the size and chemical nature of the 4′ substituent on the substrate. This is the result of differences in a key residue at position 59 on a loop (loop II) that partially forms the active site. Residue 59, which is His in ePL kinase 1, interacts with the formyl group at C-4′ of pyridoxal and may also determine if residues from another loop (loop I) can fill the active site in the absence of the substrate. Both loop I and loop II are suggested to play significant roles in the functions of PL kinases.
The Orphan Response Regulator DigR Is Required for Synthesis of Extracellular Matrix Fibrils inMyxococcus xanthus
Authors: Overgaard Martin , Wegener-Feldbrügge Sigrun , Søgaard-Andersen Lotte
Published: June 2006

InMyxococcus xanthus, two-component systems have crucial roles in regulating motility behavior and development. Here we describe an orphan response regulator, consisting of an N-terminal receiver domain and a C-terminal DNA binding domain, which is required for A and type IV pilus-dependent gliding motility. Genetic evidence suggests that phosphorylation of the conserved, phosphorylatable aspartate residue in the receiver domain is required for DigR activity. Consistent with the defect in type IV pilus-dependent motility, adigRmutant is slightly reduced in type IV pilus biosynthesis, and the composition of the extracellular matrix fibrils is abnormal, with an increased content of polysaccharides and decreased accumulation of the FibA metalloprotease. By using genome-wide transcriptional profiling, 118 genes were identified that are directly or indirectly regulated by DigR. These 118 genes include only 2,agmQandcheY4, previously implicated in A and type IV pilus-dependent motility, respectively. In silico analyses showed that 36% of the differentially expressed genes are likely to encode exported proteins. Moreover, four genes encoding homologs of extracytoplasmic function (ECF) sigma factors, which typically control aspects of cell envelope homeostasis, are differentially expressed in adigRmutant. We suggest that the DigR response regulator has an important function in cell envelope homeostasis and that the motility defects in adigRmutant are instigated by the abnormal cell envelope and abnormal expression ofagmQandcheY4.
Lesions in Teichoic Acid Biosynthesis in
Staphylococcus aureus
Lead to a Lethal Gain of Function in the Otherwise Dispensable Pathway
Authors: D'Elia Michael A. , Pereira Mark P. , Chung Yu Seon , Zhao Wenjun , Chau Andrew , Kenney Teresa J. , Sulavik Mark C. , Black Todd A. , Brown Eric D.
Published: June 2006

An extensive study of teichoic acid biosynthesis in the model organism
Bacillus subtilis
has established teichoic acid polymers as essential components of the gram-positive cell wall. However, similar studies pertaining to therapeutically relevant organisms, such as
Staphylococcus aureus
, are scarce. In this study we have carried out a meticulous examination of the dispensability of teichoic acid biosynthetic enzymes in
S. aureus
. By use of an allelic replacement methodology, we examined all facets of teichoic acid assembly, including intracellular polymer production and export. Using this approach we confirmed that the first-acting enzyme (TarO) was dispensable for growth, in contrast to dispensability studies in
B. subtilis
. Upon further characterization, we demonstrated that later-acting gene products (TarB, TarD, TarF, TarIJ, and TarH) responsible for polymer formation and export were essential for viability. We resolved this paradox by demonstrating that all of the apparently indispensable genes became dispensable in a
tarO
null genetic background. This work suggests a lethal gain-of-function mechanism where lesions beyond the initial step in wall teichoic acid biosynthesis render
S. aureus
nonviable. This discovery poses questions regarding the conventional understanding of essential gene sets, garnered through single-gene knockout experiments in bacteria and higher organisms, and points to a novel drug development strategy targeting late steps in teichoic acid synthesis for the infectious pathogen
S. aureus
.
Cohesion-Defective Mutants ofMyxococcus xanthus
Authors: Bonner Pamela J. , Shimkets Lawrence J.
Published: June 2006

Cohesion ofMyxococcus xanthuscells involves interaction of a cell surface cohesin with a component of the extracellular matrix. In this work, two previously isolated cohesion-defective (fbd) mutants were characterized. ThefbdAandfbdBgenes do not encode the cohesins but are necessary for their production. Both mutants produce type IV pili, suggesting that PilA is not a major cohesin.
Expression of SarX, a Negative Regulator of
agr
and Exoprotein Synthesis, Is Activated by MgrA in
Staphylococcus aureus
Authors: Manna Adhar C. , Cheung Ambrose L.
Published: June 2006

The expression of genes involved in the pathogenesis of
Staphylococcus aureus
is known to be controlled by global regulatory loci, including
agr
,
sarA
,
saeRS
,
arlRS
, and
sarA
-like genes. As part of our continuing efforts to understand the regulatory mechanisms that involve
sarA
-like genes, we describe here the characterization of a novel transcriptional regulator called SarX, a member of the SarA protein family. The transcription of
sarX
was growth phase dependent and was expressed maximally during the stationary phase of growth, which was significantly decreased in the
mgrA
mutant. MgrA acted as an activator of
sarX
expression as confirmed by transcriptional fusion and Northern blot analyses. Purified MgrA protein bound to the upstream region of the
sarX
promoter as demonstrated by gel shift assay. The expression levels of various potential target genes involved in virulence and regulation, specifically those affected by
sarA
and
mgrA
, were analyzed with isogenic
sarX
mutant strains. Our data indicated that SarX acted as a repressor of the
agr
locus and consequently target genes regulated by the
agr
system. We propose that SarX is an important regulator in the SarA protein family and may be part of the common pathway by which
agr
and members of the
sarA
gene family control virulence in
S. aureus
.
The BBA01 Protein, a Member of Paralog Family 48 fromBorrelia burgdorferi, Is Potentially Interchangeable with the Channel-Forming Protein P13
Authors: Pinne Marija , Denker Katrin , Nilsson Elin , Benz Roland , Bergström Sven
Published: June 2006

TheBorrelia burgdorferigenome exhibits redundancy, with many plasmid-carried genes belonging to paralogous gene families. It has been suggested that certain paralogs may be necessary in various environments and that they are differentially expressed in response to different conditions. The chromosomally locatedp13gene which codes for a channel-forming protein belongs to paralog family 48, which consists of eight additional genes. Of the paralogous genes from family 48, the BBA01 gene has the highest homology top13. Herein, we have inactivated the BBA01 gene inB. burgdorferistrain B31-A. This mutant shows no apparent phenotypic difference compared to the wild type. However, analysis of BBA01 in a C-terminal protease A (CtpA)-deficient background revealed that like P13, BBA01 is posttranslationally processed at its C terminus. Elevated BBA01 expression was obtained in strains with the BBA01 gene introduced on the shuttle vector compared to the wild-type strain. We could further demonstrate that BBA01 is a channel-forming protein with properties surprisingly similar to those of P13. The single-channel conductance, of about 3.5 nS, formed by BBA01 is comparable to that of P13, which together with the high degree of sequence similarity suggests that the two proteins may have similar and interchangeable functions. This is further strengthened by the up-regulation of the BBA01 protein and its possible localization in the outer membrane in ap13knockout strain, thus suggesting that P13 can be replaced by BBA01.
Chromosome Condensation in the Absence of the Non-SMC Subunits of MukBEF
Authors: Wang Qinhong , Mordukhova Elena A. , Edwards Andrea L. , Rybenkov Valentin V.
Published: June 2006

MukBEF is a bacterial SMC (structural maintenance of chromosome) complex required for chromosome partitioning inEscherichia coli. We report that overproduction of MukBEF results in marked chromosome condensation. This condensation is rapid and precedes the effects of overproduction on macromolecular synthesis. Condensed nucleoids are often mispositioned; however, cell viability is only mildly affected. The overproduction of MukB leads to a similar chromosome condensation, even in the absence of MukE and MukF. Thus, the non-SMC subunits of MukBEF play only an auxiliary role in chromosome condensation. MukBEF, however, was often a better condensin than MukB. Furthermore, the chromosome condensation by MukB did not rescue the temperature sensitivity of MukEF-deficient cells, nor did it suppress the high frequency of anucleate cell formation. We infer that the role of MukBEF in stabilizing chromatin architecture is more versatile than its role in controlling chromosome size. We further propose that MukBEF could be directly involved in chromosome segregation.
Expression of Genes Coding for GerA and GerK Spore Germination Receptors Is Dependent on the Protein Phosphatase PrpE
Authors: Hinc Krzysztof , Nagórska Krzysztofa , Iwanicki Adam , Węgrzyn Grzegorz , Séror Simone J. , Obuchowski Michał
Published: June 2006

The ability of
Bacillus subtilis
to form spores is a strategy for survival under unfavorable environmental conditions. It is equally crucial to break spore dormancy and return to vegetative growth at the appropriate time. Here we present data showing that the PrpE phosphatase is involved in the control of expression of genes coding for GerA receptors, which are necessary for
l
-alanine-induced spore germination. Moreover, PrpE is also involved in aspartic acid, glucose, fructose, and potassium (AGFK)-induced spore germination by controlling expression of genes coding for GerK receptors. In the absence of PrpE, the production of spores was essentially normal. However,
l
-alanine-induced spore germination and, to a lesser extent, the AGFK-induced pathway were abolished. In contrast, the germination pathway dependent on Ca
2+
-dipicolinate or dodecylamine remained intact. A protein phosphatase PrpE-green fluorescent protein fusion was localized to the prespore and to the dormant spore, consistent with a role in controlling expression of genes coding for GerA receptors. We propose that PrpE is an important element in a signal transduction pathway in
Bacillus subtilis
that controls the expression of genes coding for germination receptors.
SOME PROBLEMATICAL ASPECTS OF AuAu AND PbPb COLLISIONS AND THE COMBINATIONAL APPROACH
Authors: DE BHASKAR , BISWAS S. K. , BHATTACHARYYA S.
Published: June 2006

The present work is an attempt to analyze some of the so-called problematical aspects of both the AuAu and PbPb collisions at high energies. In the framework of a phenomenological theory, called here the combinational approach (CA), we have attempted to obtain in this work the nature of the ratios of (i) invariant cross-sections in AuAu and PbPb reactions to the binary-scaled PP interaction cross-section values and (ii) the latest spurt of values on secondary proton-to-pion (p/π) ratios which have stirred much excitements recently. To our surprise, at least up to nearly pT = 4 GeV/c , we find no exotic or novel nuclear-medium effects with regard to the explanation for both observations. And in this domain it is seen that our model reproduces the reported experimental features modestly well. However, the region beyond pT = 4 GeV/c apparently necessitates introduction of various second-order effects arising out of multiple collisions involving the interacting partons; and needs to be explored separately by more detailed and in-depth future studies.
B PHYSICS ON THE LATTICE: PRESENT AND FUTURE
Authors: WINGATE MATTHEW
Published: June 2006

Recent experimental measurements and lattice QCD calculations are now reaching the precision (and accuracy) needed to over-constrain the CKM parameters [Formula: see text] and [Formula: see text]. In this brief review, we discuss the current status of lattice QCD calculations needed to connect the experimental measurements of B meson properties to quark flavor-changing parameters. Special attention is given to B→πℓν, which is becoming a competitive way to determine |Vub|, and to [Formula: see text] mixings, which now include reliable extrapolation to the physical light quark mass. The combination of the recent measurement of the Bs mass difference and current lattice calculations dramatically reduces the uncertainty in |Vtd|. We present an outlook for reducing dominant lattice QCD uncertainties entering CKM fits and remark on lattice calculations for other decay channels.
Transcriptional and posttranscriptional regulation of endothelial nitric oxide synthase expression
Authors: Searles Charles D.
Published: June 2006

The ability of the endothelium to produce nitric oxide is essential to maintenance of vascular homeostasis; disturbance of this ability is a major contributor to the pathogenesis of vascular disease. In vivo studies have demonstrated that expression of endothelial nitric oxide synthase (eNOS) is vital to endothelial function and have led to the understanding that eNOS expression is subject to modest but significant degrees of regulation. Subsequently, numerous physiological and pathophysiological stimuli have been identified that modulate eNOS expression via mechanisms that alter steady-state eNOS mRNA levels. These mechanisms involve changes in the rate of eNOS gene transcription (transcriptional regulation) and alteration of eNOS mRNA processing and stability (posttranscriptional regulation). In cultured endothelial cells, shear stress, transforming growth factor-β1, lysophosphatidylcholine, cell growth, oxidized linoleic acid, 3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors, and hydrogen peroxide have been shown to increase eNOS expression. In contrast, tumor necrosis factor-α, hypoxia, lipopolysaccaride, thrombin, and oxidized LDL can decrease eNOS mRNA levels. For many of these stimuli, both transcriptional and posttranscriptional mechanisms contribute to regulation of eNOS expression. Recent studies have begun to further define signaling pathways responsible for changes in eNOS expression and have characterized cis- and trans-acting regulatory elements. In addition, a role has been identified for epigenetic control of eNOS mRNA levels. This review will discuss transcriptional and posttranscriptional regulation of eNOS with emphasis on the molecular mechanisms that have been identified for these processes.