bluuebunny/crossref_metadata_2025 huggingface dataset:
Systematic analysis of nucleation-dependent polymerization reveals new insights into the mechanism of amyloid self-assembly
Authors: Xue Wei-Feng , Homans Steve W. , Radford Sheena E.
Published: June 2008

Self-assembly of misfolded proteins into ordered fibrillar aggregates known as amyloid results in numerous human diseases. Despite an increasing number of proteins and peptide fragments being recognised as amyloidogenic, how these amyloid aggregates assemble remains unclear. In particular, the identity of the nucleating species, an ephemeral entity that defines the rate of fibril formation, remains a key outstanding question. Here, we propose a new strategy for analyzing the self-assembly of amyloid fibrils involving global analysis of a large number of reaction progress curves and the subsequent systematic testing and ranking of a large number of possible assembly mechanisms. Using this approach, we have characterized the mechanism of the nucleation-dependent formation of β
2
-microglobulin (β
2
m) amyloid fibrils. We show, by defining nucleation in the context of both structural and thermodynamic aspects, that a model involving a structural nucleus size approximately the size of a hexamer is consistent with the relatively small concentration dependence of the rate of fibril formation, contrary to expectations based on simpler theories of nucleated assembly. We also demonstrate that fibril fragmentation is the dominant secondary process that produces higher apparent cooperatively in fibril formation than predicted by nucleated assembly theories alone. The model developed is able to explain and predict the behavior of β
2
m fibril formation and provides a rationale for explaining generic properties observed in other amyloid systems, such as fibril growth acceleration and pathway shifts under agitation.
The FACT Spt16 “peptidase” domain is a histone H3–H4 binding module
Authors: Stuwe Tobias , Hothorn Michael , Lejeune Erwan , Rybin Vladimir , Bortfeld Miriam , Scheffzek Klaus , Ladurner Andreas G.
Published: June 2008

The FACT complex is a conserved cofactor for RNA polymerase II elongation through nucleosomes. FACT bears histone chaperone activity and contributes to chromatin integrity. However, the molecular mechanisms behind FACT function remain elusive. Here we report biochemical, structural, and mutational analyses that identify the peptidase homology domain of the
Schizosaccharomyces pombe
FACT large subunit Spt16 (Spt16-N) as a binding module for histones H3 and H4. The 2.1-Å crystal structure of Spt16-N reveals an aminopeptidase P fold whose enzymatic activity has been lost. Instead, the highly conserved fold directly binds histones H3–H4 through a tight interaction with their globular core domains, as well as with their N-terminal tails. Mutations within a conserved surface pocket in Spt16-N or posttranslational modification of the histone H4 tail reduce interaction
in vitro
, whereas the globular domains of H3–H4 and the H3 tail bind distinct Spt16-N surfaces. Our analysis suggests that the N-terminal domain of Spt16 may add to the known H2A–H2B chaperone activity of FACT by including a H3–H4 tail and H3–H4 core binding function mediated by the N terminus of Spt16. We suggest that these interactions may aid FACT-mediated nucleosome reorganization events.
The complement protein properdin binds apoptotic T cells and promotes complement activation and phagocytosis
Authors: Kemper Claudia , Mitchell Lynne M. , Zhang Lijuan , Hourcade Dennis E.
Published: June 2008

Apoptotic cells must be rapidly eliminated to avoid harmful inflammatory and autoimmune reactions. Innate immunity is designed/poised to identify dying cells by their unique surface-associated molecular patterns. Here we demonstrate for the first time, to our knowledge, that the human complement protein properdin binds to early apoptotic T cells and initiates complement activation, leading to C3b opsonization and ingestion by phagocytic cells. Properdin binding was facilitated by the glycosaminoglycan chains of surface proteoglycans. Properdin released by activated neutrophils was particularly effective at recognition of apoptotic T cells, whereas the binding activity of properdin in the serum appeared to be inhibited. “Properdin tagging” of apoptotic T cells also induced their uptake by phagocytes independent of complement activation or other complement proteins. Although our findings were made primarily with apoptotic T cells, they suggest that properdin could play a similar role during apoptosis of other cell types.
An epoxide hydrolase involved in the biosynthesis of an insect sex attractant and its use to localize the production site
Authors: Abdel-latief Mohatmed , Garbe Leif A. , Koch Markus , Ruther Joachim
Published: June 2008

Epoxide hydrolases (EHs) are enzymes occurring in virtually any living organism. They catalyze the hydrolysis of epoxide containing lipids and are involved in crucial mechanisms, such as the detoxification of xenobiotics or the regulation of inflammation and blood pressure. Here, we describe a function of a putative EH gene in the biosynthesis of a sex attractant in the jewel waspNasonia vitripennisand use this gene to localize the site of pheromone production. Males of this parasitic wasp release a mixture of (4R,5R)-(threo-) and (4R,5S)-(erythro-)5-hydroxy-4-decanolide (HDL) to attract virgin females. Using a stable isotope labeled precursor, we demonstrated that vernolic acid (erythro-12,13-epoxy-octadec-9Z-enoic acid) is converted byN. vitripennismales to threo-HDL. This suggested the involvement of an EH in hydrolyzing the fatty acid epoxide under inversion of the stereochemistry into the respective diol, which might be further processed by chain shortening and lactonization to HDL. We cloned a putativeN. vitripennisEH gene (Nasvi-EH1) encoding 470 amino acids and localized its transcripts in the male rectal papillae byinsituRT-PCR. Chemical analyses and histological studies confirmed that males synthesize the sex attractant in the rectal vesicle and release it via the anal orifice. Involvement ofNasvi-EH1in HDL biosynthesis was established by RNAi-mediated gene silencing. Injection ofNasvi-EH1dsRNA into male abdomens inhibited pheromone biosynthesis by 55% and suppressed the targeted gene transcripts in the rectal vesicle by 95%.
A generative, probabilistic model of local protein structure
Authors: Boomsma Wouter , Mardia Kanti V. , Taylor Charles C. , Ferkinghoff-Borg Jesper , Krogh Anders , Hamelryck Thomas
Published: June 2008

Despite significant progress in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology. One of the key remaining challenges is an efficient probabilistic exploration of the structural space that correctly reflects the relative conformational stabilities. Here, we present a fully probabilistic, continuous model of local protein structure in atomic detail. The generative model makes efficient conformational sampling possible and provides a framework for the rigorous analysis of local sequence–structure correlations in the native state. Our method represents a significant theoretical and practical improvement over the widely used fragment assembly technique by avoiding the drawbacks associated with a discrete and nonprobabilistic approach.
Chiral discrimination of the Japanese beetle sex pheromone and a behavioral antagonist by a pheromone-degrading enzyme
Authors: Ishida Yuko , Leal Walter S.
Published: June 2008

The sophistication of the insect olfactory system is elegantly demonstrated by the reception of sex pheromone by the Japanese beetle. In this insect, two olfactory receptor neurons housed in antennal sensilla placodea are highly sensitive. One neuron specifically detects the sex pheromone produced by conspecific females (
R
,
Z
)-5-(−)-(1-decenyl)oxacyclopentan-2-one [(
R
)-japonilure]. The other neuron is tuned to (
S
)-japonilure, a sex pheromone from a closely related species and a behavioral antagonist for the Japanese beetle. These chemical signals are enzymatically terminated by antennal esterases that open the lactone rings to form physiologically inactive hydroxyacids. We have isolated a pheromone-degrading enzyme, PjapPDE, from >100,000 antennae of the Japanese beetle. PjapPDE was demonstrated to be expressed only in the antennal tissues housing the pheromone-detecting sensilla placodea. Baculovirus expression generated recombinant PjapPDE with likely the same posttranslational modifications as the native enzyme. Kinetic studies with pure native and recombinant PjapPDE showed a clear substrate preference, with an estimated half-life
in vivo
for the sex pheromone and a behavioral antagonist of ≈30 and ≈90 ms, respectively.
Identification of the TFII-I family target genes in the vertebrate genome
Authors: Chimge Nyam-Osor , Makeyev Aleksandr V. , Ruddle Frank H. , Bayarsaihan Dashzeveg
Published: June 2008

GTF2I
and
GTF2IRD1
encode members of the TFII-I transcription factor family and are prime candidates in the Williams syndrome, a complex neurodevelopmental disorder. Our previous expression microarray studies implicated TFII-I proteins in the regulation of a number of genes critical in various aspects of cell physiology. Here, we combined bioinformatics and microarray results to identify TFII-I downstream targets in the vertebrate genome. These results were validated by chromatin immunoprecipitation and siRNA analysis. The collected evidence revealed the complexity of TFII-I-mediated processes that involve distinct regulatory networks. Altogether, these results lead to a better understanding of specific molecular events, some of which may be responsible for the Williams syndrome phenotype.
Neuroligin-1 is required for normal expression of LTP and associative fear memory in the amygdala of adult animals
Authors: Kim Juhyun , Jung Sang-Yong , Lee Yeon Kyung , Park Sangki , Choi June-Seek , Lee C. Justin , Kim Hye-Sun , Choi Yun-Beom , Scheiffele Peter , Bailey Craig H. , Kandel Eric R. , Kim Joung-Hun
Published: June 2008

Neuroligin-1 is a potent trigger for the
de novo
formation of synaptic connections, and it has recently been suggested that it is required for the maturation of functionally competent excitatory synapses. Despite evidence for the role of neuroligin-1 in specifying excitatory synapses, the underlying molecular mechanisms and physiological consequences that neuroligin-1 may have at mature synapses of normal adult animals remain unknown. By silencing endogenous neuroligin-1 acutely in the amygdala of live behaving animals, we have found that neuroligin-1 is required for the storage of associative fear memory. Subsequent cellular physiological studies showed that suppression of neuroligin-1 reduces NMDA receptor-mediated currents and prevents the expression of long-term potentiation without affecting basal synaptic connectivity at the thalamo-amygdala pathway. These results indicate that persistent expression of neuroligin-1 is required for the maintenance of NMDAR-mediated synaptic transmission, which enables normal development of synaptic plasticity and long-term memory in the amygdala of adult animals.
Epigenetic histone H3 lysine 9 methylation in metabolic memory and inflammatory phenotype of vascular smooth muscle cells in diabetes
Authors: Villeneuve Louisa M. , Reddy Marpadga A. , Lanting Linda L. , Wang Mei , Meng Li , Natarajan Rama
Published: June 2008

Diabetic patients continue to develop inflammation and vascular complications even after achieving glycemic control. This poorly understood “metabolic memory” phenomenon poses major challenges in treating diabetes. Recent studies demonstrate a link between epigenetic changes such as chromatin histone lysine methylation and gene expression. We hypothesized that H3 lysine-9 tri-methylation (H3K9me3), a key repressive and relatively stable epigenetic chromatin mark, may be involved in metabolic memory. This was tested in vascular smooth muscle cells (VSMC) derived from type 2 diabetic
db
/
db
mice. These cells exhibit a persistent atherogenic and inflammatory phenotype even after culture
in vitro
. ChIP assays showed that H3K9me3 levels were significantly decreased at the promoters of key inflammatory genes in cultured
db
/
db
VSMC relative to control
db
/+ cells. Immunoblotting demonstrated that protein levels of the H3K9me3 methyltransferase Suv39h1 were also reduced in
db
/
db
VSMC. Furthermore,
db
/
db
VSMC were hypersensitive to TNF-α inflammatory stimulus, which induced dramatic and sustained decreases in promoter H3K9me3 and Suv39h1 occupancy. Recruitment of corepressor HP1α was also reduced under these conditions in
db
/
db
cells. Overexpression of SUV39H1 in
db
/
db
VSMC reversed this diabetic phenotype. Conversely, gene silencing of SUV39H1 with shRNAs in normal human VSMC (HVSMC) increased inflammatory genes. HVSMC cultured in high glucose also showed increased inflammatory gene expression and decreased H3K9me3 at their promoters. These results demonstrate protective roles for H3K9me3 and Suv39h1 against the preactivated state of diabetic VSMC. Dysregulation of epigenetic histone modifications may be a major underlying mechanism for metabolic memory and sustained proinflammatory phenotype of diabetic cells.
Excess MCM proteins protect human cells from replicative stress by licensing backup origins of replication
Authors: Ibarra Arkaitz , Schwob Etienne , Méndez Juan
Published: June 2008

The six main minichromosome maintenance proteins (Mcm2–7), which presumably constitute the core of the replicative DNA helicase, are present in chromatin in large excess relative to the number of active replication forks. To evaluate the relevance of this apparent surplus of Mcm2–7 complexes in human cells, their levels were down-regulated by using RNA interference. Interestingly, cells continued to proliferate for several days after the acute (>90%) reduction of Mcm2–7 concentration. However, they became hypersensitive to DNA replication stress, accumulated DNA lesions, and eventually activated a checkpoint response that prevented mitotic division. When this checkpoint was abrogated by the addition of caffeine, cells quickly lost viability, and their karyotypes revealed striking chromosomal aberrations. Single-molecule analyses revealed that cells with a reduced concentration of Mcm2–7 complexes display normal fork progression but have lost the potential to activate “dormant” origins that serve a backup function during DNA replication. Our data show that the chromatin-bound “excess” Mcm2–7 complexes play an important role in maintaining genomic integrity under conditions of replicative stress.
RNA-binding Protein HuR Interacts with Thrombomodulin 5′Untranslated Region and Represses Internal Ribosome Entry Site–mediated Translation under IL-1β Treatment
Authors: Yeh Chiu-Hung , Hung Liang-Yi , Hsu Chin , Le Shu-Yun , Lee Pin-Tse , Liao Wan-Lin , Lin Yi-Tseng , Chang Wen-Chang , Tseng Joseph T.
Published: June 2008

Reduction in host-activated protein C levels and resultant microvascular thrombosis highlight the important functional role of protein C anticoagulant system in the pathogenesis of sepsis and septic shock. Thrombomodulin (TM) is a critical factor to activate protein C in mediating the anticoagulation and anti-inflammation effects. However, TM protein content is decreased in inflammation and sepsis, and the mechanism is still not well defined. In this report, we identified that the TM 5′ untranslated region (UTR) bearing the internal ribosome entry site (IRES) element controls TM protein expression. Using RNA probe pulldown assay, HuR was demonstrated to interact with the TM 5′UTR. Overexpression of HuR protein inhibited the activity of TM IRES, whereas on the other hand, reducing the HuR protein level reversed this effect. When cells were treated with IL-1β, the IRES activity was suppressed and accompanied by an increased interaction between HuR and TM 5′UTR. In the animal model of sepsis, we found the TM protein expression level to be decreased while concurrently observing the increased interaction between HuR and TM mRNA in liver tissue. In summary, HuR plays an important role in suppression of TM protein synthesis in IL-1β treatment and sepsis.
Anillin-mediated Targeting of Peanut to Pseudocleavage Furrows Is Regulated by the GTPase Ran
Authors: Silverman-Gavrila Rosalind V. , Hales Karen G. , Wilde Andrew
Published: June 2008

During early development in Drosophila, pseudocleavage furrows in the syncytial embryo prevent contact between neighboring spindles, thereby ensuring proper chromosome segregation. Here we demonstrate that the GTPase Ran regulates pseudocleavage furrow organization. Ran can exert control on pseudocleavage furrows independently of its role in regulating the microtubule cytoskeleton. Disruption of the Ran pathway prevented pseudocleavage furrow formation and restricted the depth and duration of furrow ingression of those pseudocleavage furrows that did form. We found that Ran was required for the localization of the septin Peanut to the pseudocleavage furrow, but not anillin or actin. Biochemical assays revealed that the direct binding of the nuclear transport receptors importin α and β to anillin prevented the binding of Peanut to anillin. Furthermore, RanGTP reversed the inhibitory action of importin α and β. On expression of a mutant form of anillin that lacked an importin α and β binding site, inhibition of Ran no longer restricted the depth and duration of furrow ingression in those pseudocleavage furrows that formed. These data suggest that anillin and Peanut are involved in pseudocleavage furrow ingression in syncytial embryos and that this process is regulated by Ran.
The Rho-Guanine Nucleotide Exchange Factor Domain of Obscurin Regulates Assembly of Titin at the Z-Disk through Interactions with Ran Binding Protein 9
Authors: Bowman Amber L. , Catino Dawn H. , Strong John C. , Randall William R. , Kontrogianni-Konstantopoulos Aikaterini , Bloch Robert J.
Published: June 2008

Obscurin is an ∼800-kDa protein composed of structural and signaling domains that organizes contractile structures in striated muscle. We have studied the Rho-GEF domain of obscurin to understand its roles in morphogenesis and signaling. We used adenoviral overexpression of this domain, together with ultrastructural and immunofluorescence methods, to examine its effect on maturing myofibrils. We report that overexpression of the Rho-GEF domain specifically inhibits the incorporation of titin into developing Z-disks and disrupts the structure of the Z-disk and Z/I junction, and alters features of the A/I junction. The organization of other sarcomeric markers, including α-actinin, was not affected. We identified Ran binding protein 9 (RanBP9) as a novel ligand of the Rho-GEF domain and showed that binding is specific, with an apparent binding affinity of 1.9 μM. Overexpression of the binding region of RanBP9 also disrupted the incorporation of titin into developing Z-disks. Immunofluorescence localization during myofibrillogenesis indicated that the Rho-GEF domain assembles into sarcomeres before RanBP9, which first occurs in myonuclei and later in development translocates to the myoplasm, where it colocalizes with obscurin. Both the Rho-GEF domain and its binding region on RanBP9 bind directly to the N-terminal Ig domains of titin, which flank the Z-disk. Our results suggest that the Rho-GEF domain interacts with RanBP9 and that both can interact with the N-terminal region of titin to influence the formation of the Z-disk and A/I junction.
Three Members of the LC8/DYNLL Family Are Required for Outer Arm Dynein Motor Function
Authors: Tanner Christopher A. , Rompolas Panteleimon , Patel-King Ramila S. , Gorbatyuk Oksana , Wakabayashi Ken-ichi , Pazour Gregory J. , King Stephen M.
Published: June 2008

The highly conserved LC8/DYNLL family proteins were originally identified in axonemal dyneins and subsequently found to function in multiple enzyme systems. Genomic analysis uncovered a third member (LC10) of this protein class in Chlamydomonas. The LC10 protein is extracted from flagellar axonemes with 0.6 M NaCl and cofractionates with the outer dynein arm in sucrose density gradients. Furthermore, LC10 is specifically missing only from axonemes of those strains that fail to assemble outer dynein arms. Previously, the oda12-1 insertional allele was shown to lack the Tctex2-related dynein light chain LC2. The LC10 gene is located ∼2 kb from that of LC2 and is also completely missing from this mutant but not from oda12-2, which lacks only the 3′ end of the LC2 gene. Although oda12-1 cells assemble outer arms that lack only LC2 and LC10, this strain exhibits a flagellar beat frequency that is consistently less than that observed for strains that fail to assemble the entire outer arm and docking complex (e.g., oda1). These results support a key regulatory role for the intermediate chain/light chain complex that is an integral and highly conserved feature of all oligomeric dynein motors.
Intrinsic disorder prediction from the analysis of multiple protein fold recognition models
Authors: McGuffin Liam J.
Published: June 2008

Motivation: Intrinsic protein disorder is functionally implicated in numerous biological roles and is, therefore, ubiquitous in proteins from all three kingdoms of life. Determining the disordered regions in proteins presents a challenge for experimental methods and so recently there has been much focus on the development of improved predictive methods. In this article, a novel technique for disorder prediction, called DISOclust, is described, which is based on the analysis of multiple protein fold recognition models. The DISOclust method is rigorously benchmarked against the top five methods from the CASP7 experiment. In addition, the optimal consensus of the tested methods is determined and the added value from each method is quantified.

Results: The DISOclust method is shown to add the most value to a simple consensus of methods, even in the absence of target sequence homology to known structures. A simple consensus of methods that includes DISOclust can significantly outperform all of the previous individual methods tested.

Availability:  http://www.reading.ac.uk/bioinf/DISOclust/

Contact:  l.j.mcguf.n@reading.ac.uk

Supplementary information: Supplementary data are available at http://www.reading.ac.uk/bioinf/DISOclust/suppl.pdf
Computational design of synthetic gene circuits with composable parts
Authors: Marchisio M.A. , Stelling J.
Published: June 2008

Motivation: In principle, novel genetic circuits can be engineered using standard parts with well-understood functionalities. However, no model based on the simple composition of these parts has become a standard, mainly because it is difficult to define signal exchanges between biological units as unambiguously as in electrical engineering. Corresponding concepts and computational tools for easy circuit design in biology are missing.

Results: Taking inspiration from (and slightly modifying) ideas in the ‘MIT Registry of Standard Biological Parts’, we developed a method for the design of genetic circuits with composable parts. Gene expression requires four kinds of signal carriers: RNA polymerases, ribosomes, transcription factors and environmental ‘messages’ (inducers or corepressors). The flux of each of these types of molecules is a quantifiable biological signal exchanged between parts. Here, each part is modeled independently by the ordinary differential equations (ODE) formalism and integrated into the software ProMoT (Process Modeling Tool). In this way, we realized a ‘drag and drop’ tool, where genetic circuits are built just by placing biological parts on a canvas and by connecting them through ‘wires’ that enable flow of signal carriers, as it happens in electrical engineering. Our simulations of well-known synthetic circuits agree well with published computational and experimental results.

Availability: The code is available on request from the authors.

Contact:  mario.marchisio@bsse.ethz.ch

Supplementary information:  Supplementary data are available at Bioinformatics online.
CellML and associated tools and techniques
Authors: Garny Alan , Nickerson David P , Cooper Jonathan , Santos Rodrigo Weber dos , Miller Andrew K , McKeever Steve , Nielsen Poul M.F , Hunter Peter J
Published: June 2008

We have, in the last few years, witnessed the development and availability of an ever increasing number of computer models that describe complex biological structures and processes. The multi-scale and multi-physics nature of these models makes their development particularly challenging, not only from a biological or biophysical viewpoint but also from a mathematical and computational perspective. In addition, the issue of sharing and reusing such models has proved to be particularly problematic, with the published models often lacking information that is required to accurately reproduce the published results.

The International Union of Physiological Sciences Physiome Project was launched in 1997 with the aim of tackling the aforementioned issues by providing a framework for the modelling of the human body. As part of this initiative, the specifications of the CellML mark-up language were released in 2001.

Now, more than 7 years later, the time has come to assess the situation, in particular with regard to the tools and techniques that are now available to the modelling community. Thus, after introducing CellML, we review and discuss existing editors, validators, online repository, code generators and simulation environments, as well as the CellML Application Program Interface. We also address possible future directions including the need for additional mark-up languages.
Plant speciation in continental island floras as exemplified byNigellain the Aegean Archipelago
Authors: Comes Hans Peter , Tribsch Andreas , Bittkau Christiane
Published: June 2008

Continental shelf island systems, created by rising sea levels, provide a premier setting for studying the effects of geographical isolation on non-adaptive radiation and allopatric speciation brought about by genetic drift. The Aegean Archipelago forms a highly fragmented complex of mostly continental shelf islands that have become disconnected from each other and the mainland in relatively recent geological times (ca<5.2 Ma). These ecologically fairly homogenous islands thus provide a suitable biogeographic context for assessing the relative influences of past range fragmentation, colonization, gene flow and drift on taxon diversification. Indeed, recent molecular biogeographic studies on the AegeanNigella arvensiscomplex, combining phylogenetic, phylogeographic and population level approaches, exemplify the importance of allopatry and genetic drift coupled with restricted gene flow in driving plant speciation in this continental archipelago at different temporal and spatial scales. While the recent (Late Pleistocene) radiation of AegeanNigella, as well as possible instances of incipient speciation (in the Cyclades), is shown to be strongly conditioned by (palaeo)geographic factors (including changes in sea level), shifts in breeding system (selfing) and associated isolating mechanisms have also contributed to this radiation. By contrast, founder event speciation has probably played only a minor role, perhaps reflecting a migratory situation typical for continental archipelagos characterized by niche pre-emption because of a long established resident flora. Overall, surveys of neutral molecular markers in AegeanNigellahave so far revealed population genetic processes that conform remarkably well to predictions raised by genetic drift theory. The challenge is now to gain more direct insights into the relative importance of the role of genetic drift, as opposed to natural selection, in the phenotypic and reproductive divergence among these Aegean plant species.
The strength and genetic basis of reproductive isolating barriers in flowering plants
Authors: Lowry David B , Modliszewski Jennifer L , Wright Kevin M , Wu Carrie A , Willis John H
Published: June 2008

Speciation is characterized by the evolution of reproductive isolation between two groups of organisms. Understanding the process of speciation requires the quantification of barriers to reproductive isolation, dissection of the genetic mechanisms that contribute to those barriers and determination of the forces driving the evolution of those barriers. Through a comprehensive analysis involving 19 pairs of plant taxa, we assessed the strength and patterns of asymmetry of multiple prezygotic and postzygotic reproductive isolating barriers. We then reviewed contemporary knowledge of the genetic architecture of reproductive isolation and the relative role of chromosomal and genic factors in intrinsic postzygotic isolation. On average, we found that prezygotic isolation is approximately twice as strong as postzygotic isolation, and that postmating barriers are approximately three times more asymmetrical in their action than premating barriers. Barriers involve a variable number of loci, and chromosomal rearrangements may have a limited direct role in reproductive isolation in plants. Future research should aim to understand the relationship between particular genetic loci and the magnitude of their effect on reproductive isolation in nature, the geographical scale at which plant speciation occurs, and the role of different evolutionary forces in the speciation process.
Plant species radiations: where, when, why?
Authors: Linder Hans Peter
Published: June 2008

The spatial and temporal patterns of plant species radiations are largely unknown. I used a nonlinear regression to estimate speciation and extinction rates from all relevant dated clades. Both are surprisingly high. A high species richness can be the result of either little extinction, thus preserving the diversity that dates from older radiations (a ‘mature radiation’), or a ‘recent and rapid radiation’. The analysis of radiations from different regions (Andes, New Zealand, Australia, southwest Africa, tropics and Eurasia) revealed that the diversity of Australia may be largely the result of mature radiations. This is in sharp contrast to New Zealand, where the flora appears to be largely the result of recent and rapid radiations. Mature radiations are characteristic of regions that have been climatically and geologically stable throughout the Neogene, whereas recent and rapid radiations are more typical of younger (Pliocene) environments. The hyperdiverse Cape and Neotropical floras are the result of the combinations of mature as well as recent and rapid radiations. Both the areas contain stable environments (the Amazon basin and the Cape Fold Mountains) as well as dynamic landscapes (the Andes and the South African west coast). The evolution of diversity can only be understood in the context of the local environment.
The relative importance of ecology and geographic isolation for speciation in anoles
Authors: Thorpe Roger S , Surget-Groba Yann , Johansson Helena
Published: June 2008

The biogeographic patterns in sexually reproducing animals in island archipelagos may be interpreted as reflecting the importance of allopatric speciation. However, as the forms are allopatric, their reproductive isolation is largely untestable. A historical perspective integrating geology and molecular phylogeny reveals specific cases where ancient precursor islands coalesce, which allows the application of population genetics to critically test genetic isolation. TheAnolispopulations on Martinique in the Lesser Antilles are one such case where species-level populations on ancient precursor islands (ca6–8 Myr BP) have met relatively recently. The distribution of the mtDNA lineages is tightly linked to the precursor island, but the population genetic analysis of microsatellite variation in large samples shows no evidence of restricted genetic exchange between these forms in secondary contact. This tests, and rejects, the hypothesis of simple allopatric speciation in these forms. By contrast, Martinique has pronounced environmental zonation, to which anoles are known to adapt. The population genetic analysis shows restricted genetic exchange across the ecotone between xeric coastal habitat and montane rainforest. This does not indicate full ecological speciation in these forms, but it does suggest the relative importance of the role of ecology in speciation in general.
Changes to gene expression associated with hybrid speciation in plants: further insights from transcriptomic studies inSenecio
Authors: Hegarty Matthew J , Barker Gary L , Brennan Adrian C , Edwards Keith J , Abbott Richard J , Hiscock Simon J
Published: June 2008

Interspecific hybridization is an important mechanism of speciation in higher plants. In flowering plants, hybrid speciation is usually associated with polyploidy (allopolyploidy), but hybrid speciation without genome duplication (homoploid hybrid speciation) is also possible, although it is more difficult to detect. The combination of divergent genomes within a hybrid can result in profound changes to both genome and transcriptome. Recent transcriptomic studies of wild and resynthesized homoploid and allopolyploid hybrids have revealed widespread changes to gene expression in hybrids relative to expression levels in their parents. Many of these changes to gene expression are ‘non-additive’, i.e. not simply the sum of the combined expression levels of parental genes. Some gene expression changes are far outside the range of gene expression in either parent, and can therefore be viewed as ‘transgressive’. Such profound changes to gene expression may enable new hybrids to survive in novel habitats not accessible to their parent species. Here, we give a brief overview of hybrid speciation in plants, with an emphasis on genomic change, before focusing discussion on findings from recent transcriptomic studies. We then discuss our current work on gene expression change associated with hybrid speciation in the genusSenecio(ragworts and groundsels) focusing on the findings from a reanalysis of gene expression data obtained from recent microarray studies of wild and resynthesized allopolyploidSenecio cambrensis. These data, showing extensive non-additive and transgressive gene expression changes inSeneciohybrids, are discussed in the light of findings from other model systems, and in the context of the potential importance of gene expression change to hybrid speciation in plants.
Quantum State Engineering and Precision Metrology Using State-Insensitive Light Traps
Authors: Ye Jun , Kimble H. J. , Katori Hidetoshi
Published: June 2008

Precision metrology and quantum measurement often demand that matter be prepared in well-defined quantum states for both internal and external degrees of freedom. Laser-cooled neutral atoms localized in a deeply confining optical potential satisfy this requirement. With an appropriate choice of wavelength and polarization for the optical trap, two electronic states of an atom can experience the same trapping potential, permitting coherent control of electronic transitions independent of the atomic center-of-mass motion. Here, we review a number of recent experiments that use this approach to investigate precision quantum metrology for optical atomic clocks and coherent control of optical interactions of single atoms and photons within the context of cavity quantum electrodynamics. We also provide a brief survey of promising prospects for future work.
Virus Attenuation by Genome-Scale Changes in Codon Pair Bias
Authors: Coleman J. Robert , Papamichail Dimitris , Skiena Steven , Futcher Bruce , Wimmer Eckard , Mueller Steffen
Published: June 2008

As a result of the redundancy of the genetic code, adjacent pairs of amino acids can be encoded by as many as 36 different pairs of synonymous codons. A species-specific “codon pair bias” provides that some synonymous codon pairs are used more or less frequently than statistically predicted. We synthesized de novo large DNA molecules using hundreds of over-or underrepresented synonymous codon pairs to encode the poliovirus capsid protein. Underrepresented codon pairs caused decreased rates of protein translation, and polioviruses containing such amino acid–independent changes were attenuated in mice. Polioviruses thus customized were used to immunize mice and provided protective immunity after challenge. This “death by a thousand cuts” strategy could be generally applicable to attenuating many kinds of viruses.
A Significant Upward Shift in Plant Species Optimum Elevation During the 20th Century
Authors: Lenoir J. , Gégout J. C. , Marquet P. A. , de Ruffray P. , Brisse H.
Published: June 2008

Spatial fingerprints of climate change on biotic communities are usually associated with changes in the distribution of species at their latitudinal or altitudinal extremes. By comparing the altitudinal distribution of 171 forest plant species between 1905 and 1985 and 1986 and 2005 along the entire elevation range (0 to 2600 meters above sea level) in west Europe, we show that climate warming has resulted in a significant upward shift in species optimum elevation averaging 29 meters per decade. The shift is larger for species restricted to mountain habitats and for grassy species, which are characterized by faster population turnover. Our study shows that climate change affects the spatial core of the distributional range of plant species, in addition to their distributional margins, as previously reported.
Tryptophan-Accelerated Electron Flow Through Proteins
Authors: Shih Crystal , Museth Anna Katrine , Abrahamsson Malin , Blanco-Rodriguez Ana Maria , Di Bilio Angel J. , Sudhamsu Jawahar , Crane Brian R. , Ronayne Kate L. , Towrie Mike , Vlček Antonín , Richards John H. , Winkler Jay R. , Gray Harry B.
Published: June 2008

Energy flow in biological structures often requires submillisecond charge transport over long molecular distances. Kinetics modeling suggests that charge-transfer rates can be greatly enhanced by multistep electron tunneling in which redox-active amino acid side chains act as intermediate donors or acceptors. We report transient optical and infrared spectroscopic experiments that quantify the extent to which an intervening tryptophan residue can facilitate electron transfer between distant metal redox centers in a mutant
Pseudomonas aeruginosa
azurin. Cu
I
oxidation by a photoexcited Re
I
-diimine at position 124 on a histidine(124)-glycine(123)-tryptophan(122)-methionine(121) β strand occurs in a few nanoseconds, fully two orders of magnitude faster than documented for single-step electron tunneling at a 19 angstrom donor-acceptor distance.
Deep Drilling into the Chesapeake Bay Impact Structure
Authors: Gohn G. S. , Koeberl C. , Miller K. G. , Reimold W. U. , Browning J. V. , Cockell C. S. , Horton J. W. , Kenkmann T. , Kulpecz A. A. , Powars D. S. , Sanford W. E. , Voytek M. A.
Published: June 2008

Samples from a 1.76-kilometer-deep corehole drilled near the center of the late Eocene Chesapeake Bay impact structure (Virginia, USA) reveal its geologic, hydrologic, and biologic history. We conducted stratigraphic and petrologic analyses of the cores to elucidate the timing and results of impact-melt creation and distribution, transient-cavity collapse, and ocean-water resurge. Comparison of post-impact sedimentary sequences inside and outside the structure indicates that compaction of the crater fill influenced long-term sedimentation patterns in the mid-Atlantic region. Salty connate water of the target remains in the crater fill today, where it poses a potential threat to the regional groundwater resource. Observed depth variations in microbial abundance indicate a complex history of impact-related thermal sterilization and habitat modification, and subsequent post-impact repopulation.
Compelling Cases for Change
Authors: Bowers C. Michael
Published: June 2008

Forensics Under Fire
. Are Bad Science and Dueling Experts Corrupting Criminal Justice?.
By Jim Fisher
. Rutgers University Press, Piscataway, NJ, 2008. 339 pp. $24.95. ISBN 9780813542713.

Discussing a number of high-profile cases, the author argues that current forensic practices fall far short of the field's public perceptions and potential.
Peaks of 20th-Century Presentation
Authors: Andersen Hanne
Published: June 2008

The Oxford Book of Modern Science Writing
.
Richard Dawkins, Ed.
. Oxford University Press, Oxford, 2008. 437 pp. $34.95, £20. ISBN 9780199216802.

These selections from writings by researchers over the past century cover such topics as what scientists study, who they are, what they think, and what they find delight in.
Influence of Host Interleukin-10 Polymorphisms on Development of Traveler's Diarrhea Due to Heat-Labile Enterotoxin-ProducingEscherichia coliin Travelers from the United States Who Are Visiting Mexico
Authors: Flores Jose , DuPont Herbert L. , Lee Stephanie A. , Belkind-Gerson Jaime , Paredes Mercedes , Mohamed Jamal A. , Armitige Lisa Y. , Guo Dong-Chuan , Okhuysen Pablo C.
Published: June 2008

Up to 60% of U.S. visitors to Mexico develop traveler's diarrhea (TD), mostly due to enterotoxigenicEscherichia coli(ETEC) strains that produce heat-labile (LT) and/or heat-stable (ST) enterotoxins. Distinct single-nucleotide polymorphisms (SNPs) within the interleukin-10 (IL-10) promoter have been associated with high, intermediate, or low production of IL-10. We conducted a prospective study to investigate the association of SNPs in the IL-10 promoter and the occurrence of TD in ETEC LT-exposed travelers. Sera from U.S. travelers to Mexico collected on arrival and departure were studied for ETEC LT seroconversion by using cholera toxin as the antigen. Pyrosequencing was performed to genotype IL-10 SNPs. Stools from subjects who developed diarrhea were also studied for other enteropathogens. One hundred twenty-one of 569 (21.3%) travelers seroconverted to ETEC LT, and among them 75 (62%) developed diarrhea. Symptomatic seroconversion was more commonly seen in subjects who carried a genotype producing high levels of IL-10; it was seen in 83% of subjects with the GG genotype versus 54% of subjects with the AA genotype at IL-10 gene position −1082 (P, 0.02), in 71% of those with the CC genotype versus 33% of those with the TT genotype at position −819 (P, 0.005), and in 71% of those with the CC genotype versus 38% of those with the AA genotype at position −592 (P, 0.02). Travelers with the GCC haplotype were more likely to have symptomatic seroconversion than those with the ATA haplotype (71% versus 38%;P, 0.002). Travelers genetically predisposed to produce high levels of IL-10 were more likely to experience symptomatic ETEC TD.
Effects of Multispecies Probiotic Combination on
Helicobacter pylori
Infection In Vitro
Authors: Myllyluoma E. , Ahonen A.-M. , Korpela R. , Vapaatalo H. , Kankuri E.
Published: June 2008

Probiotic bacteria alleviate many gastrointestinal symptoms, but the current trend of combining bacteria for additional benefit may make their effects more complex. We characterize four probiotics and their combination in terms of pathogen adhesion, barrier function, cell death, and inflammatory response in
Helicobacter pylori
-infected epithelial cells.
H. pylori
-infected Caco-2 cells were pretreated with
Lactobacillus rhamnosus
GG,
Lactobacillus rhamnosus
Lc705,
Propionibacterium freudenreichii
subsp.
shermanii
Js,
Bifidobacterium breve
Bb99, or all four organisms in combination. We evaluated the adhesion of
H. pylori
by in situ immunofluorescence; epithelial barrier function by measurement of transepithelial resistance; apoptosis by measurement of caspase 3 activation; cell membrane leakage by measurement of lactate dehydrogenase release; and inflammation by measurement of interleukin-8 (IL-8), IL-10, prostaglandin E
2
(PGE
2
), and leukotriene B
4
(LTB
4
) release. All probiotics inhibited
H. pylori
adhesion.
L. rhamnosus
GG,
L. rhamnosus
Lc705,
P. freudenreichii
subsp.
shermanii
Js, and the combination inhibited
H. pylori
-induced cell membrane leakage.
L. rhamnosus
GG,
L. rhamnosus
Lc705, and the combination initially improved epithelial barrier function but increased the
H. pylori
-induced barrier deterioration after incubation for 24 to 42 h.
L. rhamnosus
GG,
L. rhamnosus
Lc705, and
P. freudenreichii
subsp.
shermanii
Js inhibited
H. pylori
-induced IL-8 release, whereas
L. rhamnosus
GG,
L. rhamnosus
Lc705, and
B. breve
Bb99 suppressed PGE
2
release. None of these anti-inflammatory effects persisted when the probiotics were used in combination. The combination thus increased the levels of IL-8, PGE
2
, and LTB
4
released from
H. pylori
-infected epithelial cells. The proinflammatory actions of the individual components dominated the anti-inflammatory effects when the probiotic bacteria were used in combination. Our results stress that the therapeutic response can be optimized if probiotic strains are characterized before they are used in combination.
Differential Expression of Interleukin-4 (IL-4) and IL-4δ2 mRNA, but Not Transforming Growth Factor Beta (TGF-β), TGF-βRII, Foxp3, Gamma Interferon, T-bet, or GATA-3 mRNA, in Patients with Fast and Slow Responses to Antituberculosis Treatment
Authors: Djoba Siawaya Joel Fleury , Bapela Nchinya Bennedict , Ronacher Katharina , Beyers Nulda , van Helden Paul , Walzl Gerhard
Published: June 2008

This study investigated interleukin-4 (IL-4), IL-4δ2, transforming growth factor beta (TGF-β), TGF-βRII, Foxp3, GATA-3, T-bet, and gamma interferon (IFN-γ) transcription in peripheral blood samples of adult pulmonary tuberculosis patients prior to and after 1 week of therapy. Twenty patients with positive results for sputum culture forMycobacterium tuberculosiswere enrolled and treated with directly observed short-course antituberculosis chemotherapy. Early treatment response was assessed. At the end of the intensive phase of treatment (month 2), 12 patients remained sputum culture positive (slow responders) and 8 converted to a negative culture (fast responders). Only the expression levels of IL-4 (4-fold decrease) and IL-4δ2 (32-fold increase) changed significantly during the first week of therapy in the 20 patients. No baseline differences were present between the responder groups, but fast responders had significantly higher IL-4 transcripts than slow responders at week 1. Fast responders showed a 19-fold upregulation and slow responders a 47-fold upregulation of IL-4δ2 at week 1. Only slow responders also showed a significant decrease in IL-4 expression at week 1. There were no significant differences in expression of TGF-β, TGF-βRII, Foxp3, IFN-γ, and GATA-3 between the groups. These data show that differential IL-4-related gene expression in the early stage of antituberculosis treatment accompanies differential treatment responses and may hold promise as a marker for treatment effect.
Interleukin-23 Is Required for Development of Arthritis in Mice Vaccinated and Challenged withBorreliaSpecies
Authors: Kotloski Nicholas J. , Nardelli Dean T. , Peterson Sara Heil , Torrealba Jose R. , Warner Thomas F. , Callister Steven M. , Schell Ronald F.
Published: June 2008

We recently hypothesized that T helper 17 (Th17) cells and their associated cytokines are involved in the development of arthritis following infection withBorrelia burgdorferi. Here, we show that interleukin-23 (IL-23), a survival factor for Th17 cells, is required for the induction of arthritis in mice vaccinated withB. burgdorferistrain 297 and challenged with “Borrelia bissettii.” WhenBorrelia-vaccinated and -challenged mice were given antibodies to the p19 subunit of IL-23, they failed to develop the histopathological changes observed in untreated vaccinated and challenged mice. In addition, viableB. bissettiiorganisms stimulated the secretion of IL-17 fromBorrelia-immune lymph node cells during in vitro culture. When anti-IL-23 p19 antibody was included in cultures ofB. bissettiiorganisms andBorrelia-immune lymph node cells, the production of IL-17 was reduced to levels observed in cultures containing immune cells alone. Taken together, these results support the hypothesis that Th17 cell-associated cytokines are involved in the development ofBorrelia-mediated arthritis. These findings provide insight into previously overlooked immune mechanisms responsible for the development of Lyme arthritis.