bluuebunny/crossref_metadata_2025_split huggingface dataset:
Above‐ and below‐ground competition between intercropped winter wheat Triticum aestivum and white clover Trifolium repens
Authors: THORSTED MARIAN D. , WEINER JACOB , OLESEN JØRGEN E. 
Published: March 2006

Summary

Intercropping of white clover and cereals has recently been promoted for low‐input farming systems because it offers several benefits for sustainability, but the practical use of this system has been limited by the relatively low wheat yields. Very little is known about competition between the two species in this intercropping system and its implications for production.
To investigate the interaction between white clover and wheat, we separated above‐ and below‐ground competition in the field in a fully factorial additive design. The treatments were with and without clover, with and without below‐ground partitions between rows of the two species, and with and without above‐ground partitions. Above‐ground biomass of both species was harvested three times over the growing season, and the wheat biomass was analysed for nitrogen content.
When wheat was grown without clover, its biomass was much reduced by below‐ground partitions and slightly reduced by above‐ground partitions. Presence of both above‐ and below‐ground partitions did not result in lower wheat biomass than below‐ground partitions alone.
Total biomass was higher when both species were present, and this biomass was reduced by below‐ground partitions and, to a lesser degree, by above‐ground partitions. In mixture, below‐ground partitions reduced wheat biomass and increased clover biomass at the last harvest, whereas above‐ground partitions reduced clover biomass and increased wheat biomass.
The interaction between the two species was dominated by competition for soil nutrients, but competition for light influenced the partitioning of biomass production between the two species. Mingling of the roots of both species is important for maximizing soil resource utilization, whereas shoots performed almost as well without mingling.
Synthesis and applications. The results suggest that competition between wheat and clover for nitrogen is reduced by nitrogen fixation because clover obtains some of its nitrogen from fixation. Increased availability of nitrogen to the intercropped wheat late in the growing season could increase grain protein content. Our results suggest possibilities for improved management of competition between the two species to optimize resource utilization, biomass production and wheat yields. Goals for yield should be based on a specific component, such as total biomass, grain yield and grain quality, because these yield components can behave differently when another species is present.
Habitat connectivity and matrix restoration: the wider implications of agri‐environment schemes
Authors: DONALD PAUL F. , EVANS ANDY D. 
Published: March 2006

Summary

The spread and intensification of agriculture are recognized as two of the most important global threats to wildlife. There are clear links between agricultural change and declines in biodiversity across a wide range of agricultural systems, and convincing evidence that reversing these changes leads to a recovery in wildlife populations.
Nearly 4 billion euros are now paid annually through agri‐environment schemes (AES) to farmers in Europe and North America to make environmental improvements to their land. Where appropriately designed and targeted, these schemes have proved successful in reversing declines in farmland wildlife populations.
We argue that insights gained from island biogeography and metapopulation theory, and from theoretical and empirical assessments of landscape connectivity suggest that AES may carry substantial wider benefits, which so far have not been considered in the design and deployment of such schemes. ‘Softening’ agricultural land could offset some of the negative impacts on biodiversity of the loss and fragmentation of non‐agricultural habitats; could allow species to adapt to climate change; could slow the spread of alien and invasive species; and could contribute positively to the coherence of key biodiversity and protected area networks. Indeed, AES might represent the only viable way to counter these threats.
We outline a number of ways in which these wider benefits could be taken account of in the design of AES and suggest a number of characteristics of the species most likely to benefit from them.
Synthesis and applications. Agri‐environment schemes might bring significant environmental benefits to habitats other than farmland by restoring the agricultural matrix that separates them. Theoretical and empirical research suggests that matrix restoration improves a number of ecosystem functions. Where they are available, AES might therefore represent a viable mechanism for addressing a range of pandemic environmental problems such as global climate change. Little consideration has so far been given to these wider conservation applications in the design, deployment and monitoring of AES.
Studying phenotypic evolution using multivariate quantitative genetics
Authors: McGUIGAN KATRINA 
Published: March 2006

AbstractQuantitative genetics provides a powerful framework for studying phenotypic evolution and the evolution of adaptive genetic variation. Central to the approach is G, the matrix of additive genetic variances and covariances. G summarizes the genetic basis of the traits and can be used to predict the phenotypic response to multivariate selection or to drift. Recent analytical and computational advances have improved both the power and the accessibility of the necessary multivariate statistics. It is now possible to study the relationships between G and other evolutionary parameters, such as those describing the mutational input, the shape and orientation of the adaptive landscape, and the phenotypic divergence among populations. At the same time, we are moving towards a greater understanding of how the genetic variation summarized by G evolves. Computer simulations of the evolution of G, innovations in matrix comparison methods, and rapid development of powerful molecular genetic tools have all opened the way for dissecting the interaction between allelic variation and evolutionary process. Here I discuss some current uses of G, problems with the application of these approaches, and identify avenues for future research.
Molecular ecology of zebra mussel invasions
Authors: MAY GEMMA E. , GELEMBIUK GREGORY W. , PANOV VADIM E. , ORLOVA MARINA I. , LEE CAROL EUNMI 
Published: March 2006

AbstractThe invasion of the zebra mussel, Dreissena polymorpha, into North American waters has resulted in profound ecological disturbances and large monetary losses. This study examined the invasion history and patterns of genetic diversity among endemic and invading populations of zebra mussels using DNA sequences from the mitochondrial cytochrome oxidase I (COI) gene. Patterns of haplotype frequency indicate that all invasive populations of zebra mussels from North America and Europe originated from the Ponto‐Caspian Sea region. The distribution of haplotypes was consistent with invasive populations arising from the Black Sea drainage, but could not exclude the possibility of an origin from the Caspian Sea drainage. Similar haplotype frequencies among North American populations of D. polymorpha suggest colonization by a single founding population. There was no evidence of invasive populations arising from tectonic lakes in Turkey, while lakes in Greece and Macedonia contained only Dreissena stankovici. Populations in Turkey might be members of a sibling species complex of D. polymorpha. Ponto‐Caspian derived populations of D. polymorpha (θ = 0.0011) and Dreissena bugensis (one haplotype) exhibited low levels of genetic diversity at the COI gene, perhaps as a result of repeated population bottlenecks. In contrast, geographically isolated tectonic lake populations exhibited relatively high levels of genetic diversity (θ = 0.0032 to 0.0134). It is possible that the fluctuating environment of the Ponto‐Caspian basin facilitated the colonizing habit of invasive populations of D. polymorpha and D. bugensis. Our findings were concordant with the general trend of destructive freshwater invaders in the Great Lakes arising from the Ponto‐Caspian Sea basin.
Inferring population history from fine‐scale spatial genetic analysis in Oryza rufipogon (Poaceae)
Authors: XU XIAN , LU BAO‐RONG , CHEN YOLANDA H. , XU MING , RONG JUN , YE PINGYANG , CHEN JIAKUAN , SONG ZHIPING 
Published: March 2006

AbstractDetermining the genetic structure of an in situ conserved population can provide insight into the dynamics of population genetic processes associated with successful plant conservation. We used 21 microsatellite loci to analyse the genetic relationships among individuals (n= 813) collected from a small Oryza rufipogon population conserved since 1993 in Hunan Province of China. The analysis revealed four distinct genetic subpopulations (FST= 0.145) without geographic isolation. One subpopulation was composed of possible introgressed individuals, two subpopulations were composed of seed recruits and their descendants, and the fourth subpopulation consisted of reintroduced individuals, seed recruits and their descendants. Positive spatial genetic structures were detected by spatial autocorrelation statistics at the population (c. 63 m) and subpopulation levels (11–30 m), but the degree of autocorrelation was stronger at the population level. These results showed that prejudging the cryptic structure is important before autocorrelation analysis for the entire population. Our study suggests that population history can be a significant determinant on population structure for plant restoration projects.
Genetic relationships among marine and freshwater populations of the European three‐spined stickleback (Gasterosteus aculeatus) revealed by microsatellites
Authors: MÄKINEN H. S. , CANO J. M. , MERILÄ J. 
Published: March 2006

AbstractTo assess the population genetic structure of the three‐spined stickleback,Gasterosteus aculeatus, variability at 18 microsatellite loci was examined in 1724 individuals from 74 locations covering most of the species distribution range in Europe. The results revealed high overall degree of differentiation (FST = 0.21) but contrasting level of divergence and genetic variability between habitat types. Marine populations were genetically relatively uniform even across great geographical distances as compared to substantial differentiation among freshwater populations. Analysis of molecular variance indicated low but significant (2.7%) variation in allele frequencies between geographical regions, but a negligible effect of habitat type (0.2%). The phylogenetic pattern was not explained by habitat type, but a weak signal of populations clustering according to geographical or water system origin was found. The results support the view that three‐spined stickleback marine ancestors colonized northern European fresh waters during the postglacial marine submergencec. 10 000 years ago, whereas in the Mediterranean region colonization probably dates back to the Pleistocene. The independent origins of river and lake populations indicate that they originate from multiple colonizations rather than sharing common ancestry. In the continuous marine environment, the low degree of differentiation among populations can be explained by gene flow among subpopulations and large effective population size buffering divergence in neutral markers. In contrast, among postglacially established freshwater populations differentiation appears to be driven by genetic drift and isolation. The stepwise mutations appear to have contributed to the population differentiation in the southern part of the three‐spined stickleback distribution range.
Genetic variation and population differentiation in the lichen‐forming ascomyceteXanthoria parietinaon the island Storfosna, central Norway
Authors: LINDBLOM LOUISE , EKMAN STEFAN 
Published: March 2006

AbstractGenetic diversity and fine‐scale population structure in the lichen‐forming ascomyceteXanthoria parietinawas investigated using sequence variation in part of the intergenic spacer (IGS) and the complete internal transcribed spacer (ITS) regions of the nuclear ribosomal DNA. Sampling included 213 and 225 individuals, respectively, from seven populations in two different habitats, bark and rock, on the island Storfosna off the central west coast of Norway. Both markers revealed significant variation and a total of 10 IGS and 16 ITS haplotypes were found. There were no signs of significant positive spatial autocorrelation at any spatial size class down to 10% of transect length, nor did we find significant deviations from neutrality or signs of historical population expansion. Analysis of molecular variance (amova) indicated that most of the genetic variance observed was within populations, but when populations were grouped according to habitat, more than a quarter of the variance was explained among groups. Pairwise comparisons of populations (FST, exact tests of population differentiation) revealed significant differentiation between populations in different habitats (on bark or rock), but not between populations in the same habitat. Haplotype networks show that internal and presumably old haplotypes are shared between habitats, whereas terminal haplotypes tend to be unique to a habitat, mostly bark. We interpret the observed pattern to mean that there is no evidence of restricted gene flow between populations in the same habitat at the present spatial scale (interpopulation distances one or a few kilometres). On the other hand, differentiation between habitats is considerable, which we attribute to restricted gene flow between habitats (habitat isolation). Evidence suggests that the observed differentiation did not evolve locally. Estimates of divergence time between populations in the respective habitats indicate that an ancestral population started to diverge at least 34 000 years ago but probably much further back in time.
Multiple introductions promote range expansion of the molluscCyclope neritea(Nassariidae) in France: evidence from mitochondrial sequence data
Authors: SIMON‐BOUHET B. , GARCIA‐MEUNIER P. , VIARD F. 
Published: March 2006

AbstractSince the 1970s, the nassariid gastropodCyclope neriteahas been extending its range north along the French Atlantic coasts from the Iberian Peninsula. This may be due to natural spread because of the recent warming of the northeastern Atlantic. However, human‐mediated introductions related to shellfish culture may also be a probable explanation for this sudden range expansion. To examine these two hypotheses, we carried out a comprehensive study based on mitochondrial gene sequences (cytochrome oxidase I) of the five recently colonized French bays as well as 14 populations located in the recognized native range of the species. From a total of 594 individuals, we observed 29 haplotypes to split into three divergent clades. In the native range, we observed a low molecular diversity, strong genetic structure and agreement between geography and gene genealogies. Along the French coasts, we observed the opposite: high genetic diversity and low genetic structure. Our results show that recurrent human‐mediated introductions from several geographical areas in the native range may be a source for the French Atlantic populations. However, despite the low dispersal ability ofC. neritea, the isolation‐by‐distance pattern in France suggested that this gastropod may have been present (although unnoticed) on the French Atlantic coasts before the 1970s. AsC. neriteashows characteristics of a cryptogenic species, the classification of Atlantic populations as either native or introduced is not straightforward. Cryptogenic species should be studied further to determine the status of new populations close to their recognized native range.
INVITED REVIEW: Microbial ecology in the age of genomics and metagenomics: concepts, tools, and recent advances
Authors: XU JIANPING 
Published: March 2006

AbstractMicrobial ecology examines the diversity and activity of micro‐organisms in Earth's biosphere. In the last 20 years, the application of genomics tools have revolutionized microbial ecological studies and drastically expanded our view on the previously underappreciated microbial world. This review first introduces the basic concepts in microbial ecology and the main genomics methods that have been used to examine natural microbial populations and communities. In the ensuing three specific sections, the applications of the genomics in microbial ecological research are highlighted. The first describes the widespread application of multilocus sequence typing and representational difference analysis in studying genetic variation within microbial species. Such investigations have identified that migration, horizontal gene transfer and recombination are common in natural microbial populations and that microbial strains can be highly variable in genome size and gene content. The second section highlights and summarizes the use of four specific genomics methods (phylogenetic analysis of ribosomal RNA, DNA–DNA re‐association kinetics, metagenomics, and micro‐arrays) in analysing the diversity and potential activity of microbial populations and communities from a variety of terrestrial and aquatic environments. Such analyses have identified many unexpected phylogenetic lineages in viruses, bacteria, archaea, and microbial eukaryotes. Functional analyses of environmental DNA also revealed highly prevalent, but previously unknown, metabolic processes in natural microbial communities. In the third section, the ecological implications of sequenced microbial genomes are briefly discussed. Comparative analyses of prokaryotic genomic sequences suggest the importance of ecology in determining microbial genome size and gene content. The significant variability in genome size and gene content among strains and species of prokaryotes indicate the highly fluid nature of prokaryotic genomes, a result consistent with those from multilocus sequence typing and representational difference analyses. The integration of various levels of ecological analyses coupled to the application and further development of high throughput technologies are accelerating the pace of discovery in microbial ecology.
Three‐dimensional structure of Mycoplasma pneumoniae’s attachment organelle and a model for its role in gliding motility
Authors: Henderson Gregory P. , Jensen Grant J. 
Published: March 2006

SummaryWhile most motile bacteria propel themselves with flagella, other mechanisms have been described including retraction of surface‐attached pili, secretion of polysaccharides, or movement of motors along surface protein tracks. These have been referred to collectively as forms of ‘gliding’ motility. Despite being simultaneously one of the smallest and simplest of all known cells, Mycoplasma pneumoniae builds a surprisingly large and complex cell extension known as the attachment organelle that enables it to glide. Here, three‐dimensional images of the attachment organelle were produced with unprecedented clarity and authenticity using state‐of‐the‐art electron cryotomography. The attachment organelle was seen to contain a multisubunit, jointed, dynamic motor much larger than a flagellar basal body and comparable in complexity. A new model for its function is proposed wherein inchworm‐like conformational changes of its electron‐dense core are leveraged against a cytoplasmic anchor and transmitted to the surface through layered adhesion proteins.
Relapsing fever spirochaetes produce a serine protease that provides resistance to oxidative stress and killing by neutrophils
Authors: Guyard Cyril , Battisti James M. , Raffel Sandra J. , Schrumpf Merry E. , Whitney Adeline R. , Krum Jonathan G. , Porcella Stephen F. , Rosa Patricia A. , DeLeo Frank R. , Schwan Tom G. 
Published: March 2006

SummaryThe spirochaetes that cause tick‐borne relapsing fever and Lyme disease are closely related human pathogens, yet they differ significantly in their ecology and pathogenicity. Genome sequencing of two species of relapsing fever spirochaetes, Borrelia hermsii and Borrelia turicatae, identified a chromosomal open reading frame, designated bhpA, not present in the Lyme disease spirochaete Borrelia burgdorferi. The predicted amino acid sequence of bhpA was homologous with the HtrA serine proteases, which are involved with stress responses and virulence in other bacteria. B. hermsii produced an active serine protease that was recognized by BhpA antibodies and the recombinant BhpA protein‐degraded β‐casein. bhpA was transcribed in vitro at all growth temperatures and transcription levels were slightly elevated at higher temperatures. These results correlated with the synthesis of BhpA during B. hermsii infection in mice. With the exception of Borrelia recurrentis, the bhpA gene, protein and enzymatic activity were found in all relapsing fever spirochaetes, but not in Lyme disease or related spirochaetes. Heterologous expression of bhpA in B. burgdorferi increased the spirochaete's resistance to both oxidative stress and killing by human neutrophils. Therefore, we propose that bhpA encodes a unique and functional serine protease in relapsing fever spirochaetes. This periplasmic enzyme may prevent the accumulation of proteins damaged by the innate immune response and contribute to the ability of the relapsing fever spirochaetes to achieve high cell densities in blood.
Self‐control in DNA site‐specific recombination mediated by the tyrosine recombinase TnpI
Authors: Vanhooff Virginie , Galloy Christine , Agaisse Hervé , Lereclus Didier , Révet Bernard , Hallet Bernard 
Published: March 2006

SummaryTn4430is a distinctive transposon of the Tn3family that encodes a tyrosine recombinase (TnpI) to resolve replicative transposition intermediates. The internal resolution site of Tn4430(IRS, 116 bp) contains two inverted repeats (IR1 and IR2) at the crossover core site, and two additional TnpI binding motifs (DR1 and DR2) adjacent to the core. Deletion analysis demonstrated that DR1 and DR2 are not required for recombinationin vivoandin vitro. Their function is to provide resolution selectivity to the reaction by stimulating recombination between directly oriented sites on a same DNA molecule. In the absence of DR1 and/or DR2, TnpI‐mediated recombination of supercoiled DNA substrates gives a mixture of topologically variable products, while deletion between two wild‐type IRSs exclusively produces two‐noded catenanes. This demonstrates that TnpI binding to the accessory motifs DR1 and DR2 contributes to the formation of a specific synaptic complex in which catalytically inert recombinase subunits act as architectural elements to control recombination sites pairing and strand exchange. A model for the organization of TnpI/IRS recombination complex is presented.
Self‐compartmentalized bacterial proteases and pathogenesis
Authors: Butler Susan M. , Festa Richard A. , Pearce Michael J. , Darwin K. Heran 
Published: March 2006

SummaryProtein degradation is required for homeostasis of all living organisms. Self‐compartmentalized ATP‐dependent proteases are required for virulence of several pathogenic bacteria. Among the proteases implicated are ClpP and Lon, as well as the more recently identified bacterial proteasome. It is generally assumed that when a pathogen invades a host, microbial proteins become irreversibly damaged and need to be degraded. However, recent data suggest that proteolysis is also essential for virulence gene regulation. In this review, we will discuss what is known about the relationship between ATP‐dependent proteolysis and pathogenesis. In addition, we will propose other potential roles these chambered proteases may have in bacterial virulence. Importantly, these proteases show promise as targets for antimicrobial therapy.