bluuebunny/crossref_metadata_2025_split huggingface dataset:
Capercaillie in the Alps: genetic evidence of metapopulation structure and population decline
Authors: Segelbacher Gernot , Storch Ilse 
Published: March 2003

AbstractIn the Alps, the capercaillie is distributed in a metapopulation pattern with local populations on mountain ranges separated by farmland valleys. Habitat deterioration, primarily related to human land use, resulted in population declines and range contractions became obvious. At the edge of a species’ range, lower connectivity and less gene flow may render populations more susceptible to decline and extinction than in the core of the range. If this were true for the capercaillie in the Alps, edge populations should be subject to limited gene flow and should show genetic signs of a more severe population decline than core populations. To test this hypothesis, we used microsatellite DNA typing techniques. We assessed genetic variation within and among 18 local capercaillie populations across the Alps in relation to geographical distribution within the metapopulation system. All populations showed high levels of genetic variation in terms of average number of alleles, allelic richness and heterozygosity. Excess heterozygosity suggested a recent population decline, that was more pronounced in edge than core populations. We found high gene flow, but also significant differentiation among populations. Differentiation among edge populations was related to geographical distance, and appeared to be a recent process, most probably caused by reduced gene flow after population decline. In the core group, the high mountains of the central Alps seem to limit dispersal, and genetic drift was the most likely explanation for the observed differentiation among populations. We conclude that maintaining connectivity within the metapopulation system is vital for capercaillie conservation in the Alps.
Phylogeographical variation of chloroplast DNA in holm oak (Quercus ilex L.)
Authors: Lumaret R. , Mir C. , Michaud H. , Raynal V. 
Published: March 2003

AbstractVariation in the lengths of restriction fragments (RFLPs) of the whole chloroplast DNA molecule was studied in 174 populations of Quercus ilex L. sampled over the entire distribution of this evergreen and mainly Mediterranean oak species. By using five endonucleases, 323 distinct fragments were obtained. From the 29 and 17 cpDNA changes identified as site and length mutations, respectively, 25 distinct chlorotypes were distinguished, mapped and treated cladistically with a parsimony analysis, using as an outgroup Q. alnifolia Poech, a closely related evergreen oak species endemic to Cyprus where Q. ilex does not grow. The predominant role of Q. ilex as maternal parent in hybridization with other species was reflected by the occurrence of a single very specific lineage of related chlorotypes, the most ancestral and recent ones being located in the southeastern and in the northwestern parts of the species’ geographical distribution, respectively. The lineage was constituted of two clusters of chlorotypes observed in the ‘ilex’ morphotyped populations of the Balkan and Italian Peninsulas (including the contiguous French Riviera), respectively. A third cluster was divided into two subclusters identified in the ‘rotundifolia’ morphotyped populations of North Africa, and of Iberia and the adjacent French regions, respectively. Postglacial colonization probably started from three distinct southerly refugia located in each of the three European peninsulas, and a contact area between the Italian and the Iberian migration routes was identified in the Rhône valley (France). Chlorotypes identical or related to those of the Iberian cluster were identified in the populations from Catalonia and the French Languedoc region, which showed intermediate morphotypes, and in the French Atlantic populations which possessed the ‘ilex’ morphotype, suggesting the occurrence of adaptive morphological changes in the northern part of the species’ distribution.
A DNA‐based method for identification of krill species and its application to analysing the diet of marine vertebrate predators
Authors: Jarman S. N. , Gales N. J. , Tierney M. , Gill P. C. , Elliott N. G. 
Published: March 2003

AbstractAccurate identification of species that are consumed by vertebrate predators is necessary for understanding marine food webs. Morphological methods for identifying prey components after consumption often fail to make accurate identifications of invertebrates because prey morphology becomes damaged during capture, ingestion and digestion. Another disadvantage of morphological methods for prey identification is that they often involve sampling procedures that are disruptive for the predator, such as stomach flushing or lethal collection. We have developed a DNA‐based method for identifying species of krill (Crustacea: Malacostraca), an enormously abundant group of invertebrates that are directly consumed by many groups of marine vertebrates. The DNA‐based approach allows identification of krill species present in samples of vertebrate stomach contents, vomit, and, more importantly, faeces. Utilizing samples of faeces from vertebrate predators minimizes the impact of dietary studies on the subject animals. We demonstrate our method first on samples of Adelie penguin (Pygoscelis adeliae) stomach contents, where DNA‐based species identification can be confirmed by prey morphology. We then apply the method to faeces of Adelie penguins and to faeces of the endangered pygmy blue whale (Balaenoptera musculus brevicauda). In each of these cases, krill species consumed by the predators could be identified from their DNA present in faeces or stomach contents.
Introgression patterns in the mosaic hybrid zone betweenMytilus edulisandM. galloprovincialis
Authors: Bierne N. , Borsa P. , Daguin C. , Jollivet D. , Viard F. , Bonhomme F. , David P. 
Published: March 2003

AbstractHybrid zones are fascinating systems to investigate the structure of genetic barriers. Marine hybrid zones deserve more investigation because of the generally high dispersion potential of planktonic larvae which allows migration on scales unrivalled by terrestrial species. Here we analyse the genetic structure of the mosaic hybrid zone between the marine musselsMytilus edulisandM. galloprovincialis, using three length‐polymorphic PCR loci as neutral and diagnostic markers on 32 samples along the Atlantic coast of Europe. Instead of a single genetic gradient fromM. galloprovincialison the Iberian Peninsula toM. edulispopulations in the North Sea, three successive transitions were observed in France. From South to North, the frequency of alleles typical ofM. galloprovincialisfirst decreases in the southern Bay of Biscay, remains low in Charente, then increases in South Brittany, remains high in most of Brittany, and finally decreases again in South Normandy. The two enclosed patches observed in the midst of the mosaic hybrid zone in Charente and Brittany, although predominantlyM. edulis‐like andM. galloprovincialis‐like, respectively, are genetically original in two respects. First, considering only the various alleles typical of one species, the patches show differentiated frequencies compared to the reference external populations. Second, each patch is partly introgressed by alleles of the other species. When introgression is taken into account, linkage disequilibria appear close to their maximum possible values, indicating a strong genetic barrier within all transition zones. Some pre‐ or postzygotic isolation mechanisms (habitat specialization, spawning asynchrony, assortative fertilization and hybrid depression) have been documented in previous studies, although their relative importance remains to be evaluated. We also provided evidence for a recent migratory ‘short‐cut’ connectingM. edulis‐like populations of the Charente patch to an externalM. edulispopulation in Normandy and thought to reflect artificial transfer of spat for aquaculture.
Phylogeography and molecular rates of subterranean aquatic Stenasellid Isopods with a peri‐Tyrrhenian distribution
Authors: Ketmaier V. , Argano R. , Caccone A. 
Published: March 2003

AbstractThe subterranean Isopods belonging to the genus Stenasellus have an interesting disjunct distribution in the peri‐Tyrrhenian area with morphologically closely related taxa occurring in Sardinia, Corsica, Tuscany and in the Pyrenees phreatic and interstitial waters. Because the dispersal capacities of these organisms are limited, their distribution has been associated traditionally with the tectonic events leading to the separation of the Sardinia–Corsica microplate from the Pyrenees and its subsequent movement towards the Italian peninsula. We sequenced a fragment of the mtDNA cytochrome oxidase I gene (COI) for multiple populations of the S. racovitzai species‐group (Corsica, Sardinia, Tuscany) and S. virei (Pyrenees). We found that multiple phylogenetic analyses always gave the same topology, which is consistent with the genetic relations found using allozyme data, and with the palaeogeography of the area. The molecular data suggest that a combination of vicariance and dispersal events explain most effectively the present distribution pattern of these organisms. We also calculated COI rates and calibrated them against absolute time, taking advantage of the availability of two geologically based time estimates. Rates on all substitutions are similar to those published for other crustaceans for the same COI fragment, including taxonomically and ecologically distant groups. Rates on third codon positions or on transversions are generally lower than those found in other crustaceans.
A potential role for periplasmic superoxide dismutase in blocking the penetration of external superoxide into the cytosol of Gram‐negative bacteria
Authors: Korshunov Sergei S. , Imlay James A. 
Published: March 2003

SummarySuperoxide is a key component of the antibacterial weaponry of phagocytes. Presumably, for this rea‐son, strains of Salmonella typhimurium express a periplasmic superoxide dismutase (SOD) that is essential for full virulence. Because most anions cannot easily penetrate lipid membranes, it is thought that the phagosomal superoxide either damages an unknown target on the bacterial surface or reacts with nitric oxide to form peroxynitrite (HOONO), a toxic oxidant that can freely enter bacteria. However, in this study, we tested whether superoxide itself could penetrate membranes. Superoxide that was generated at high pH (>7.5) very slowly reduced cytochrome c that was encapsulated inside lipid vesicles. It did so much more quickly at lower pH (<7). Under the latter conditions, more superoxide was protonated and uncharged (HO2·), and the penetrance of superoxide was proportional to the concentration of this species. The permeability coefficient of HO2· was determined to be 9 × 10–4 cm sec–1, just slightly lower than that of water and far higher than the value of the anionic form (O2–, <10–7 cm sec–1). When Escherichia coli mutants that lack periplasmic SOD were exposed to super‐oxide at pH 6.5, cytosolic fumarase B was damaged. Damage was minimal at higher pH or in strains that contained periplasmic SOD. Thus, in the acidic phagolysosome, superoxide may be able to penetrate and attack cytosolic targets of captive bacteria. This process may contribute to the potency of the oxidative burst. One role of periplasmic SOD may be to avert this damage. In contrast, periplasmic SOD was ineffective at lowering the extracellular super‐oxide concentration and, therefore, may have little impact upon HOONO formation.
Role of the ribosomal stalk components in the resistance of Aspergillus fumigatus to the sordarin antifungals
Authors: Santos Cruz , Ballesta Juan P. G. 
Published: March 2003

Summary Aspergillus fumigatus, an important human nosocomial pathogen, is resistant
to sordarin derivatives, a new family of antifungals that inhibit protein synthesis
by interaction with the EF‐2–ribosomal stalk complex. To explore the role
of the A. fumigatus ribosome in the resistance mechanism, the fungal stalk
proteins were biochemically and genetically characterized and expressed in the sensitive
Saccharomyces cerevisiae. Two acidic phosphoproteins homologous to the 12
kDa P1 and P2 proteins described in other organisms were found together with the
34 kDa P0 protein, the third stalk component. The genes encoding each fungal stalk
protein were expressed in mutant S. cerevisiae strains lacking the equivalent
proteins. Both AfP1 and AfP2 proteins interact with their yeast counterparts of the
opposite type and bind to the ribosomal particles in the presence of either the S.
cerevisiae or the A. fumigatus P0 protein. The A. fumigatus acidic
phosphoproteins did not alter the yeast ribosome sordarin sensitivity. On the contrary,
the presence of the fungal P0 induces in vivo and in vitro resistance
to sordarin derivatives when present in the yeast ribosome. The mutations A117→E,
P122→R and G124→V in A. fumigatus
P0 reduce the resistance capacity of the protein. An S. cerevisiae strain
with the complete ribosomal stalk of A. fumigatus was obtained, which could be useful for the screening of new antifungals against this pathogenic fungus.
A putative three‐dimensional targeting motif of polygalacturonase (PehA), a protein secreted through the type II (GSP) pathway in Erwinia carotovora
Authors: Palomäki Tiina , Pickersgill Richard , Riekki Ruusu , Romantschuk Martin , Saarilahti Hannu T. 
Published: March 2003

SummaryIntramolecular information specifying protein secretion through the type II (GSP) pathway of Gram‐negative bacteria was investigated. Two regions of the polygalacturonase (PehA) of Erwinia carotovora containing residues proposed to be included in a targeting motif were located, one close to the C‐terminus between residues 342 and 369 and another between residues 84 and 135 in the large central loops. The regions were required together to promote secretion. Further residues in the middle of the protein were required for proper positioning of the regions, suggesting that they were both involved in interaction with the GSP. To our knowledge, this is the first time that a possible three‐dimensional targeting motif has been defined. At least one of the motifs comprises a cluster on the surface of the protein. The two motifs are structurally dissimilar, suggesting that there are two distinct recognition regions in the GSP apparatus. Finally, we propose that the targeting motifs are of a complex conformational nature with some variability accommodated, as illustrated by the observation that many mutations exhibited no clear phenotype individually but, in combination, severely compromised secretion.
Regulation of transcription by the activity of the Shigella flexneri type III secretion apparatus
Authors: Mavris Maria , Page Anne‐Laure , Tournebize Régis , Demers Brigitte , Sansonetti Philippe , Parsot Claude 
Published: March 2003

SummaryThe virulence plasmid‐encoded type III secretion system of Shigella flexneri

consists of the Mxi–Spa secretion apparatus, secreted proteins IpaA–D

and IpgD involved in entry of bacteria into epithelial cells, cytoplasmic chaperones

IpgC and IpgE and 15 other secreted proteins of unknown function, including VirA

and members of the IpaH family. The activity of the Mxi–Spa apparatus is regulated

by external signals, and transcription of virA and ipaH genes is specifically

induced in conditions of active secretion. We present genetic evidence that regulation

of these genes involves both MxiE, the transcriptional activator of the AraC family

encoded by the mxi operon, and IpgC, the chaperone for IpaB and IpaC. We also

show that together MxiE and IpgC are sufficient to activate virA and ipaH9.8

promoters in Escherichia coli. In S. flexneri, increasing the expression of IpgC led to a concomitant increase in IpaH production in conditions of non‐secretion. This suggests that the activity of secretion is sensed by the presence of free IpgC, which acts as a coactivator to allow MxiE to activate transcription at its target promoters.
The pivotal role of guanine phosphoribosyltransferase in purine salvage by Giardia lamblia
Authors: Munagala Narsimha , Wang Ching C. 
Published: March 2003

Summary Giardia lamblia is an anaerobic binucleate flagellated protozoan known to
lack de novo synthesis of purine nucleotides. Our previous metabolic studies
indicated two major parallel pathways mediated by adenine phosphoribosyltransferase
(APRT) and guanine phosphoribosyltransferase (GPRT) that constitute the primary route
of purine salvage in this organism. To verify further that these enzymes play a pivotal
role in replenishing the purine ribonucleotide pool and are required for replicative
growth of Giardia, a knock‐out of GPRT gene expression in this organism
was attempted. A hammerhead ribozyme flanked by two arms of GPRT antisense RNA (GPRZ)
was designed, synthesized and found capable of cleaving a GPRT mRNA fragment in
vitro at the designated site. GPRZ cDNA was then cloned into a viral vector pC631pac,
derived from the genome of giardiavirus (GLV), and its transcript was introduced
into GLV‐infected Giardia trophozoites by electroporation. Stable transformants
selected under increasing concentrations of puromycin displayed parallel increases
in ribozyme levels and associated decreases in GPRT mRNA levels, GPRT enzyme activity
and replicative cell growth to less than 10–20% of wild‐type levels.
Metabolite analyses showed specific depletion of the guanine ribonucleotide pools
in parallel with slower cell growth. We conclude that GPRT plays an essential role
in supplying guanine nucleotides required for growth and multiplication of Giardia, emphasizing its potential as a bona fide target for antigiardiasis chemotherapy.
Nitric oxide scavenging and detoxification by the Mycobacterium tuberculosis haemoglobin, HbN in Escherichia coli
Authors: Pathania Ranjana , Navani Naveen K. , Gardner Anne M. , Gardner Paul R. , Dikshit Kanak L. 
Published: March 2003

SummaryNitric oxide (NO), generated in large amounts within the macrophages, controls and restricts the growth of internalized human pathogen, Mycobacterium tuberculosis H37Rv. The molecular mechanism by which tubercle bacilli survive within macrophages is currently of intense interest. In this work, we have demonstrated that dimeric haemoglobin, HbN, from M. tuberculosis exhibits distinct nitric oxide dioxygenase (NOD) activity and protects growth and cellular respiration of heterologous hosts, Escherichia coli and Mycobacterium smegmatis, from the toxic effect of exogenous NO and the NO‐releasing compounds. A flavohaemoglobin (HMP)‐deficient mutant of E. coli, unable to metabolize NO, acquired an oxygen‐dependent NO consumption activity in the presence of HbN. On the basis of cellular haem content, the specific NOD activity of HbN was nearly 35‐fold higher than the single‐domain Vitreoscilla haemoglobin (VHb) but was sevenfold lower than the two‐domain flavohaemoglobin. HbN‐dependent NO consumption was sustained with repeated addition of NO, demonstrating that HbN is catalytically reduced within E. coli. Aerobic growth and respiration of a flavohaemoglobin (HMP) mutant of E. coli was inhibited in the presence of exogenous NO but remained insensitive to NO inhibition when these cells produced HbN, VHb or flavohaemoglobin. M. smegmatis, carrying a native HbN very similar to M. tuberculosis HbN, exhibited a 7.5‐fold increase in NO uptake when exposed to gaseous NO, suggesting NO‐induced NOD activity in these cells. In addition, expression of plasmid‐encoded HbN of M. tuberculosis in M. smegmatis resulted in 100‐fold higher NO consumption activity than the isogenic control cells. These results provide strong experimental evidence in support of NO scavenging and detoxification function for the M. tuberculosis HbN. The catalytic NO scavenging by HbN may be highly advantageous for the survival of tubercle bacilli during infection and pathogenesis.
The tetracycline resistance protein Tet(○) perturbs the conformation of the ribosomal decoding centre
Authors: Connell Sean R. , Trieber Catharine A. , Stelzl Ulrich , Einfeldt Edda , Taylor Diane E. , Nierhaus Knud H. 
Published: March 2003

SummaryTet(○) is an elongation factor‐like protein found in clinical isolates of Campylobacter jejuni that confers resistance to the protein‐synthesis inhibitor tetracycline. Tet(○) interacts with the 70S ribosome and promotes the release of bound tetracycline, however, as shown here, it does not form the same functional interaction with the 30S subunit. Chemical probing demonstrates that Tet(○) changes the reactivity of the 16S rRNA to dimethyl sulphate (DMS). These changes cluster within the decoding site, where C1214 is protected and A1408 is enhanced to DMS reactivity. C1214 is close to, but does not overlap, the primary tetracycline‐binding site, whereas A1408 is in a region distinct from the Tet(○) binding site visualized by cryo‐EM, indicating that Tet(○) induces long‐range rearrangements that may mediate tetracycline resistance. Tetracycline enhances C1054 to DMS modification but this enhancement is inhibited in the presence of Tet(○) unlike the tetracycline‐dependent protection of A892 which is unaffected by Tet(○). C1054 is part of the primary binding site of tetracycline and A892 is part of the secondary binding site. Therefore, the results for the first time demonstrate that the primary tetracycline binding site is correlated with tetracycline's inhibitory effect on protein synthesis.
MglA, a small GTPase, interacts with a tyrosine kinase to control type IV pili‐mediated motility and development of Myxococcus xanthus
Authors: Thomasson Bobbie , Link Jason , Stassinopoulos Angela G. , Burke Neal , Plamann Lynda , Hartzell Patricia L. 
Published: March 2003

SummaryThe mglA gene encodes a 22 kDa GTPase that is critical for single‐cell (A) gliding, type IV pili‐mediated (S) gliding and development of Myxococcus xanthus. To identify components that interact with MglA to control these processes, second‐site mutations that restore movement to non‐motile mglA mutants were sought. An allele‐specific extragenic suppressor of mglA8, named mas815 (mglA8 suppressor 15), was obtained. mas815 does not bypass the requirement for MglA, yet it restores type IV pili‐mediated motility and starvation‐induced development. Single‐cell (A) motility is not restored. The suppressing mutation maps to the 3′ end of a gene, masK, in an operon immediately upstream of the mglBA operon. masK encodes a protein of the STY kinase family. When the masK gene was used as bait against a library carrying M. xanthus DNA in the yeast two‐hybrid system, eight positive, independent clones containing fusions of mglA to GAL4 were obtained, thus confirming the interaction between MglA and MasK. MasK, expressed in Escherichia coli, was shown to phosphorylate at a tyrosine residue(s). The gain‐of‐function in the masK815 mutant was correlated with increased production of extracellular fibrils, which are required for adhesion, cell–cell contact and sensing phosphatidylethanolamine chemoattractants. These data suggest that the interaction between MasK and MglA is an essential part of a signal transduction pathway controlling motility and development.