bluuebunny/crossref_metadata_2025_split huggingface dataset:
The FliK protein and flagellar hook‐length control
Authors: Waters Richard C. , O'Toole Paul W. , Ryan Kieran A. 
Published: April 2007

AbstractThe bacterial flagellum is a highly complex prokaryotic organelle. It is the motor that drives bacterial motility, and despite the large amount of energy required to make and operate flagella, motile organisms have a strong adaptive advantage. Flagellar biogenesis is both complex and highly coordinated and it typically involves at least three two‐component systems. Part of the flagellum is a type III secretion system, and it is via this structure that flagellar components are exported. The assembly of a flagellum occurs in a number of stages, and the “checkpoint control” protein FliK functions in this process by detecting when the flagellar hook substructure has reached its optimal length. FliK then terminates hook export and assembly and transmits a signal to begin filament export, the final stage in flagellar biosynthesis. As yet the exact mechanism of how FliK achieves this is not known. Here we review what is known of the FliK protein and discuss the evidence for and against the various hypotheses that have been proposed in recent years to explain how FliK controls hook length, FliK as a molecular ruler, the measuring cup theory, the role of the FliK N terminus, the infrequent molecular ruler theory, and the molecular clock theory.
Endozoochory varies with ecological scale and context
Authors: Anne Bråthen Kari , T. González Victoria , Iversen Marianne , Killengreen Siw , T. Ravolainen Virve , A. Ims Rolf , G. Yoccoz Nigel 
Published: April 2007

Several studies on endozoochory have established large herbivores as important for seed dispersal, yet no studies have evaluated how endozoochory is dependent on ecological scale and context. Here we address effects of reindeer density on endozoochory in a hierarchical, multi‐scale study, encompassing several ecological contexts.We found reindeer density effects on endozoochory to vary with spatial scale. Higher reindeer densities at the level of landscape areas, as indexed through faeces abundance, were related to both less species and lower abundance of emerging plants from faeces. In contrast, there was no effect of higher reindeer densities at the level of herding districts (i.e. large scale assemblages of landscapes). Lack of consistency between scales reflects ecological hierarchy, indicating that reindeer density effects on endozoochory best matches at the scale of landscapes.Pasture seed plant composition was only partly an important ecological factor. That is, ericoid species, the dominating plants in the pastures, were also the most abundant seed plants found to emerge from the faeces. However, most herbaceous seed plant species in the pastures were not emerging from the faeces and the few that emerged were positively related to the site fertility and altitude of the pasture.Studies addressing endozoochory of ruminants are typically concerned with seed plants, whereas in this study we also found indications of that diaspores of ferns are viable after passing the digestive tract of large herbivores. Vascular spore plants were even more abundant in the faeces than were vascular seed plants.Results from this study demonstrate that reindeer may counteract a potentially negative impact on seed limitation from their grazing by returning viable seeds in their faeces. However, in Finnmark, northern Norway, this effect is only marginal, relates only to a very few species and individuals and shows ecological scale and context dependence.
Faulting, seismic‐stratigraphic architecture and Late Quaternary evolution of the Gulf of Alkyonides Basin–East Gulf of Corinth, Central Greece
Authors: Sakellariou D. , Lykousis V. , Alexandri S. , Kaberi H. , Rousakis G. , Nomikou P. , Georgiou P. , Ballas D. 
Published: April 2007

ABSTRACTSwath bathymetry, single‐channel seismic profiling, gravity and box coring, 210Pb down‐core radiochemical analyses and sequence stratigraphic analysis in the Gulf of Alkyonides yielded new data on the evolution of the easternmost part of the Gulf of Corinth. Three fault segments, the South Strava, West Alkyonides and East Alkyonides faults, dipping 45, 30 and 45°, respectively, northwards, form the southern tectonic boundary of the Alkyonides Basin. Two 45° southwards dipping segments, the Domvrena and Germeno Faults, form the northern tectonic margin. The Alkyonides Basin architecture is the result of a complex interaction between fault dynamics and the effects of changes in climate and sea/lake level. Chrono‐stratigraphic interpretation of the seismic stratigraphy through correlation of the successive seismic packages with lowstands and highstands of the Late Quaternary indicates that the evolution of the basin started 0.40–0.45 Ma BP and can be divided in two stages. Subsidence of the basin floor during the early stage was uniform across the basin and the mean sedimentation rate was 1.0 m kyear−1. Vertical slip acceleration on the southern tectonic margin since 0.13 Ma BP resulted in the present asymmetric character of the basin. Subsidence concentrated close to the southern margin and sedimentation rate increased to 1.4 m kyear−1 in the newly formed depocentre of the basin. Actual (last 100 year) sedimentation rates were calculated to >2 mm year−1, but are significantly influenced by the presence of episodic gravity flow deposits. Total vertical displacement of 1.1 km is estimated between the subsiding Alkyonides Basin floor and the uplifting Megara Basin since the onset of basin subsidence at a mean rate of 2.4–2.75 m kyear−1, recorded on the East Alkyonides Fault. Gravity coring in the Strava Graben and in the lower northern margin of Alkyonides Basin proved the presence of whitish to olive grey laminated mud below thin marine sediments. Aragonite crystals and absence of the marine coccolithophora Emiliania huxleyi indicate sedimentation in lacustrine environment during the last lowstand glacial interval.
The size–grain hypothesis: do macroarthropods see a fractal world?
Authors: KASPARI MICHAEL , WEISER MICHAEL 
Published: April 2007

Abstract1. In the size–grain hypothesis (a) long legs allow walking organisms to step over gaps and pores in substrate but prohibit them from entering those gaps; (b) the world is more rugose for small organisms; and (c) the relative cost of long legs increases as organisms grow smaller. The hypothesis predicts a positive allometry of leg length ( = massbwhereb> 0.33 of isometry), a pattern that robustly holds for ants.2. Toward testing for leg length allometries in other taxa, arthropods were extracted from the Panama leaf litter and measured. Three common taxa (spiders, diplopods, Coleoptera) yieldedbs that exceeded 0.33 while three others (Acarina, Pseudoscorpiones, and Collembola) did not. The exponentbtended to increase (P =0.06,n= 7) with an arthropod taxon’s average body mass.3. Since leg length in cursorial organisms tends toward isometry in very small and very large taxa (i.e. mammals) this suggests that the size–grain hypothesis may best apply at a transition zone of intermediate body mass: the macroarthropods.4. Body length was a robust predictor of mass in all groups despite variation in shape.
Genetic variation in Holocene bowhead whales from Svalbard
Authors: BORGE T. , BACHMANN L. , BJØRNSTAD G. , WIIG Ø. 
Published: April 2007

AbstractBowhead whales (Balaena mysticetus) are distributed in the Arctic in five putative stocks. All stocks have been heavily depleted due to centuries of exploitation. In the present study, nucleotide sequence variation of the mitochondrial control region was determined from bone remains of 99 bowhead whales. The bones, 14C dated from recent to more than 50 000 bp, were collected on Svalbard (Spitsbergen) and are expected to relate to ancestors of the today nearly extinct Spitsbergen stock. Fifty‐eight haplotypes were found, a few being frequent but many only found in one individual. The most abundant haplotypes of the Spitsbergen stock are the same as those most abundant in the extant Bering‐Chukchi‐Beaufort (BCB) Seas stock of bowhead whales. Although FST indicates a slight but statistically significant genetic differentiation between the Spitsbergen and the BCB stocks this was not considered informative due to the very high levels of genetic diversity of mitochondrial DNA haplotypes in both bowhead whale stocks. Other measures such as KST also indicated very low genetic differentiation between the two populations. Nucleotide diversity and haplotype diversity showed only minor differences between the Spitsbergen and BCB stocks. The data suggest that the historic Spitsbergen stock — before the severe bottleneck caused by whaling — did not have substantially more genetic variation than the extant BCB stock. The similar haplotypes of the Holocene Svalbard samples and the current BCB stock indicate significant migration between these two stocks and question the current designation of five distinct stocks of bowhead whales in the Arctic.
Social kin associations and genetic structuring of striped dolphin populations (Stenella coeruleoalba) in the Mediterranean Sea
Authors: GASPARI STEFANIA , AZZELLINO ARIANNA , AIROLDI SABINA , HOELZEL A. RUS 
Published: April 2007

AbstractWe investigated hierarchical patterns of genetic subdivision, and assessed kinship within and between social groups of striped dolphins (Stenella coeruleoalba) in the Tyrrhenian Sea. A total of 165 samples were analysed at eight microsatellite DNA loci, including outgroup samples from the Adriatic, Scotland and Spain for population‐level comparisons. We found population genetic structure within the Mediterranean basin, including small but significant differentiation between the Adriatic and Tyrrhenian Seas (FST = 0.0047, P = 0.008), and between putative ‘inshore’ and ‘offshore’ (FST = 0.0217, P = 0.005) populations in the Tyrrhenian Sea. Assessment of kinship within and among 12 association groups showed higher average kinship for females within than between groups, and smaller groups showed higher average kinship. Comparisons of relatedness for both sexes showed a significant difference between males and females, with females more likely to associate with adult kin. Together these data emphasize the importance of the social cohesion of kin in small groups to the structuring of striped dolphin populations in this environment.
Molecular evidence of host‐associated genetic divergence in the holly leafminer Phytomyza glabricola (Diptera: Agromyzidae): apparent discordance among marker systems
Authors: SCHEFFER SONJA J. , HAWTHORNE DAVID J. 
Published: April 2007

AbstractHost races play a central part in understanding the role of host plant mediated divergence and speciation of phytophagous insects. Of greatest interest are host‐associated populations that have recently diverged; however, finding genetic evidence for very recent divergences is difficult because initially only a few loci are expected to evolve diagnostic differences. The holly leafminer Phytomyza glabricola feeds on two hollies, Ilex glabra and I. coriacea, that are broadly sympatric throughout most of their ranges. The leafminer is often present on both host plants and exhibits a dramatic life history difference on the two hosts, suggesting that host races may be present. We collected 1393 bp of mitochondrial cytochrome oxidase I (COI) sequence and amplified fragment length polymorphism (AFLP) data (45 polymorphic bands) from sympatric populations of flies reared from the two hosts. Phylogenetic and frequency analysis of mitochondrial COI sequence data uncovered considerable variation but no structuring by the host plant, and only limited differentiation among geographical locations. In contrast, analysis of AFLP frequency data found a significant effect with host plant, and a much smaller effect with geographical location. Likewise, neighbour‐joining analysis of AFLP data resulted in clustering by host plant. The AFLP data indicate that P. glabricola is most likely comprised of two host races. Because there were no fixed differences in mitochondrial or AFLP data, this host‐associated divergence is likely to have occurred very recently. P. glabricola therefore provides a new sympatric system for exploring the role of geography and ecological specialization in the speciation of phytophagous insects.
Case studies and mathematical models of ecological speciation. 1. Cichlids in a crater lake
Authors: GAVRILETS SERGEY , VOSE AARON , BARLUENGA MARTA , SALZBURGER WALTER , MEYER AXEL 
Published: April 2007

AbstractA recent study of a pair of sympatric species of cichlids in Lake Apoyo in Nicaragua is viewed as providing probably one of the most convincing examples of sympatric speciation to date. Here, we describe and study a stochastic, individual‐based, explicit genetic model tailored for this cichlid system. Our results show that relatively rapid (< 20 000 generations) colonization of a new ecological niche and (sympatric or parapatric) speciation via local adaptation and divergence in habitat and mating preferences are theoretically plausible if: (i) the number of loci underlying the traits controlling local adaptation, and habitat and mating preferences is small; (ii) the strength of selection for local adaptation is intermediate; (iii) the carrying capacity of the population is intermediate; and (iv) the effects of the loci influencing nonrandom mating are strong. We discuss patterns and timescales of ecological speciation identified by our model, and we highlight important parameters and features that need to be studied empirically to provide information that can be used to improve the biological realism and power of mathematical models of ecological speciation.
Estimating the number of whales entering trade using DNA profiling and capture‐recapture analysis of market products
Authors: BAKER C. SCOTT , COOKE JUSTIN G. , LAVERY SHANE , DALEBOUT MEREL L. , MA YONG‐UN , FUNAHASHI NAOKO , CARRAHER COLM , BROWNELL ROBERT L. 
Published: April 2007

AbstractSurveys of commercial markets combined with molecular taxonomy (i.e. molecular monitoring) provide a means to detect products from illegal, unregulated and/or unreported (IUU) exploitation, including the sale of fisheries bycatch and wild meat (bushmeat). Capture‐recapture analyses of market products using DNA profiling have the potential to estimate the total number of individuals entering the market. However, these analyses are not directly analogous to those of living individuals because a ‘market individual’ does not die suddenly but, instead, remains available for a time in decreasing quantities, rather like the exponential decay of a radioactive isotope. Here we use mitochondrial DNA (mtDNA) sequences and microsatellite genotypes to individually identify products from North Pacific minke whales (Balaenoptera acutorostrata ssp.) purchased in 12 surveys of markets in the Republic of (South) Korea from 1999 to 2003. By applying a novel capture‐recapture model with a decay rate parameter to the 205 unique DNA profiles found among 289 products, we estimated that the total number of whales entering trade across the five‐year survey period was 827 (SE, 164; CV, 0.20) and that the average ‘half‐life’ of products from an individual whale on the market was 1.82 months (SE, 0.24; CV, 0.13). Our estimate of whales in trade (reflecting the true numbers killed) was significantly greater than the officially reported bycatch of 458 whales for this period. This unregulated exploitation has serious implications for the survival of this genetically distinct coastal population. Although our capture‐recapture model was developed for specific application to the Korean whale‐meat markets, the exponential decay function could be modified to improve the estimates of trade in other wildmeat or fisheries markets or abundance of living populations by noninvasive genotyping.
Phylogeography of spruce beetles (Dendroctonus rufipennis Kirby) (Curculionidae: Scolytinae) in North America
Authors: MAROJA LUANA S. , BOGDANOWICZ STEVEN M. , WALLIN KIMBERLY F. , RAFFA KENNETH F. , HARRISON RICHARD G. 
Published: April 2007

AbstractTree‐feeding insects that are widespread in north temperate regions are excellent models for studying how past glaciations have impacted differentiation and speciation. We used mitochondrial DNA (mtDNA) sequences and allele frequencies at nine microsatellite loci to examine genetic population structure across the current range of the spruce beetle (Dendroctonus rufipennis), an economically important insect in North America. Two major haplotype groups occur across northern North America, from Newfoundland to Alaska, on white spruce (Picea glauca), and a third distinctive haplotype group occurs throughout the Rocky Mountains on Engelmann spruce (Picea engelmannii). The two mtDNA lineages found in northern populations are 3–4% divergent from each other and from the lineages found in the Rocky Mountains. Analyses of microsatellite data also suggest the existence of major population groupings associated with different geographical regions. In the Pacific Northwest, concordant contact zones for genetically distinct populations of spruce beetles and their principal hosts appear to reflect recent secondary contact. Although we could detect no evidence of historical mtDNA gene flow between allopatric population groups, patterns of variation in the Pacific Northwest suggest recent hybridization and introgression. Together with the pollen record for spruce, they also suggest that beetles have spread from at least three glacial refugia. A minimum estimate of divergence time between the Rocky Mountain and northern populations was 1.7 Myr (million years), presumably reflecting the combined effects of isolation during multiple glacial cycles.
Plant cells must pass a K+ threshold to re‐enter the cell cycle
Authors: Sano Toshio , Becker Dirk , Ivashikina Natalya , Wegner Lars H. , Zimmermann Ulrich , Roelfsema M. Rob G. , Nagata Toshiyuki , Hedrich Rainer 
Published: April 2007

SummaryPotassium is an inevitable component of plant life, and potassium channels play a pivotal role in plant growth and development. The role of potassium and of K+ channels in plant cell division and cell‐cycle progression, however, has not been determined so far. K+ channel blocker studies with synchronized tobacco BY‐2 cells revealed that K+ uptake is required for proper cell‐cycle progression during the transition from G1 to S phase. Electrophysiological studies (patch‐clamp and voltage‐clamp techniques) showed a cell‐cycle dependency of K+ channel activities and reduced driving force for K+ uptake in dividing cells. Among the four Shaker‐like K+ channel genes expressed in BY‐2 cells, NKT1 represents an inwardly rectifying K+ channel that mediates K+ uptake. NKT1 is transcriptionally induced during G1 phase, while transcripts of the outward‐rectifier NTORK1 dominate S phase. Elongating BY‐2 cells appeared hyperpolarized (−101 ± 11 mV), and had elevated osmotic pressure and approximately twice the turgor pressure when compared with depolarized (−64 ± 8 mV) dividing cells. This indicates that cells have to gain a threshold K+ level to re‐enter the cell cycle. Based on these findings, turgor regulation through modulation of K+ channel density in plant cell division and cell‐cycle progression is discussed.
A simplified method for the analysis of transcription factor–promoter interactions that allows high‐throughput data generation
Authors: Berger Bettina , Stracke Ralf , Yatusevich Ruslan , Weisshaar Bernd , Flügge Ulf‐Ingo , Gigolashvili Tamara 
Published: April 2007

SummaryTransient expression systems are intensively used to study the transactivation potential of transcription factors and to confirm target promoters. Here we present a novel system based on the high‐efficiency transformation of cultured Arabidopsis thaliana cells by agrobacteria. To demonstrate the potential of this system, we compared it with a commonly used protoplast transfection assay, and studied the regulation of phenylpropanoid biosynthetic pathway genes by various transcription factors. Both systems led to comparable results on the regulation of the promoters tested. However, the agrobacterium‐mediated co‐transformation assay needs significantly less time, requires only mixing of cultured plant cells with agrobacteria, is less labour‐intensive and allows handling of multiple assays in parallel, making it suitable for medium‐ to high‐throughput analyses. In addition, the binary vectors used are the same for both cell‐based assays and stable plant transformations.
Sex ratio, sex‐specific chick mortality and sexual size dimorphism in birds
Authors: BENITO M. M. , GONZÁLEZ‐SOLÍS J. 
Published: April 2007

AbstractIt has been suggested that sexual size dimorphism (SSD) may influence sex ratios at different life stages. Higher energy requirements during growth associated with larger body size could lead to a greater mortality of the larger sex and ultimately to an overproduction of the smaller sex. To explore the associations between SSD and hatching and fledging sex ratio we performed a species‐level analysis and a phylogenetically controlled analysis, based on 83 bird species. Overall, there was a significant inverse relationship between the degree of SSD and the proportion of males at hatching and fledging. Sex‐specific mortality related to SSD showed a weak but persistent negative tendency, suggesting a mortality bias towards the larger sex. These results suggest that changes in relation to SSD may take place mainly at the conception stage, but could be adjusted during growth. However, conclusions should be treated cautiously as these relationships weaken when additional variables are considered.
Storage of buffy‐coat‐derived platelets in additive solutions at 4 °C and 22 °C: flow cytometry analysis of platelet glycoprotein expression
Authors: Sandgren P. , Hansson M. , Gulliksson H. , Shanwell A. 
Published: April 2007

Background  The aim of our in vitro study is to compare the effects on platelet membrane glycoproteins that play an important role in the main functions of platelets, when platelets are stored for a period of 21 days at 4 °C or 22 °C.Study Design and Methods  Platelet concentrates (PC) were prepared from pooled buffy‐coats (BC) for paired studies (total eight pools from 80 BCs) by using the OrbiSac system. We divided each pool into two PCs and stored them at 4 °C or 22 °C.Results  The activation marker CD62 remained almost unchanged during storage in all units. The expression of CD63 was higher in PCs stored at 22 °C than in those stored at 4 °C. No significant difference in CD41 expression was detected over time. The expression of CD42b declined during storage and even more in PCs stored at 4 °C until day 21 [day 14: mean flourscence intensity: 32·5 ± 13·1 vs. 46·5 ± 19·1], but the percentage of platelets expressing CD42b remained high in platelets stored at 4 °C, but gradually decreased at 22 °C (day 14: 95·0 ± 1·5 vs. 59·0 ± 9·9). Storage at 4 °C reduced the rate of glycolysis and maintained the pH better after day 10 than in PCs stored at 22 °C (day 14: 7·009 ± 0·067 vs. 7·233 ± 0·125). The concentration of regulated upon activation of normal T‐cells expressed and secreted was higher in PCs stored at 22 °C than at 4 °C (day 7: 414·7 ± 32·3 vs. 49·6 ± 19·0). No response to extent of shape change and no swirling were detected at 4 °C.Conclusion  Platelets stored at 4 °C retain their in vitro characteristics better than those stored at 22 °C, except for parameters that reflect changes in shape. Storage at 4 °C is not associated with an increased expression of glycoprotein (GpIb, GpIIb/IIIa) and platelet activation markers (CD62p and CD63) as compared with storage at 22 °C.