bluuebunny/crossref_metadata_2025 huggingface dataset:
A secretory pathway-localized cation diffusion facilitator confers plant manganese tolerance
Authors: Peiter Edgar , Montanini Barbara , Gobert Anthony , Pedas Pai , Husted Søren , Maathuis Frans J. M. , Blaudez Damien , Chalot Michel , Sanders Dale
Published: May 2007

Manganese toxicity is a major problem for plant growth in acidic soils, but cellular mechanisms that facilitate growth in such conditions have not been clearly delineated. Established mechanisms that counter metal toxicity in plants involve chelation and cytoplasmic export of the metal across the plasma or vacuolar membranes out of the cell or sequestered into a large organelle, respectively. We report here that expression of the
Arabidopsis
and poplar MTP11 cation diffusion facilitators in a manganese-hypersensitive yeast mutant restores manganese tolerance to wild-type levels. Microsomes from yeast expressing
AtMTP11
exhibit enhanced manganese uptake. In accord with a presumed function of MTP11 in manganese tolerance,
Arabidopsis mtp11
mutants are hypersensitive to elevated levels of manganese, whereas plants overexpressing
MTP11
are hypertolerant. In contrast, sensitivity to manganese deficiency is slightly decreased in mutants and increased in overexpressing lines. Promoter-GUS studies showed that
AtMTP11
is most highly expressed in root tips, shoot margins, and hydathodes, but not in epidermal cells and trichomes, which are generally associated with manganese accumulation. Surprisingly, imaging of MTP11–EYFP fusions demonstrated that MTP11 localizes neither to the plasma membrane nor to the vacuole, but to a punctate endomembrane compartment that largely coincides with the distribution of the trans-Golgi marker sialyl transferase. Golgi-based manganese accumulation might therefore result in manganese tolerance through vesicular trafficking and exocytosis. In accord with this proposal,
Arabidopsis mtp11
mutants exhibit enhanced manganese concentrations in shoots and roots. We propose that Golgi-mediated exocytosis comprises a conserved mechanism for heavy metal tolerance in plants.
Inhibition of GLI-mediated transcription and tumor cell growth by small-molecule antagonists
Authors: Lauth Matthias , Bergström Åsa , Shimokawa Takashi , Toftgård Rune
Published: May 2007

The developmentally important Hedgehog (Hh) signaling pathway has recently been implicated in several forms of solid cancer. Current drug development programs focus on targeting the protooncogene Smoothened, a key transmembrane pathway member. These drug candidates, albeit promising, do not address the scenario in which pathway activation occurs downstream of Smoothened, as observed in cases of medulloblastoma, glioma, pericytoma, breast cancer, and prostate cancer. A cellular screen for small-molecule antagonists of GLI-mediated transcription, which constitutes the final step in the Hh pathway, revealed two molecules that are able to selectively inhibit GLI-mediated gene transactivation. We provide genetic evidence of downstream pathway blockade by these compounds and demonstrate the ineffectiveness of upstream antagonists such as cyclopamine in such situations. Mechanistically, both inhibitors act in the nucleus to block GLI function, and one of them interferes with GLI1 DNA binding in living cells. Importantly, the discovered compounds efficiently inhibitedin vitrotumor cell proliferation in a GLI-dependent manner and successfully blocked cell growth in anin vivoxenograft model using human prostate cancer cells harboring downstream activation of the Hh pathway.
Integrated network analysis identifies nitric oxide response networks and dihydroxyacid dehydratase as a crucial target in
Escherichia coli
Authors: Hyduke Daniel R. , Jarboe Laura R. , Tran Linh M. , Chou Katherine J. Y. , Liao James C.
Published: May 2007

Nitric oxide (NO) is used by mammalian immune systems to counter microbial invasions and is produced by bacteria during denitrification. As a defense, microorganisms possess a complex network to cope with NO. Here we report a combined transcriptomic, chemical, and phenotypic approach to identify direct NO targets and construct the biochemical response network. In particular, network component analysis was used to identify transcription factors that are perturbed by NO. Such information was screened with potential NO reaction mechanisms and phenotypic data from genetic knockouts to identify active chemistry and direct NO targets in
Escherichia coli
. This approach identified the comprehensive
E. coli
NO response network and evinced that NO halts bacterial growth via inhibition of the branched-chain amino acid biosynthesis enzyme dihydroxyacid dehydratase. Because mammals do not synthesize branched-chain amino acids, inhibition of dihydroxyacid dehydratase may have served to foster the role of NO in the immune arsenal.
Low-intensity transplant regimens facilitate recruitment of donor-specific regulatory T cells that promote hematopoietic engraftment
Authors: Weng Ling , Dyson Julian , Dazzi Francesco
Published: May 2007

Low- or reduced-intensity conditioning regimens for allogeneic hemopoietic stem cell transplantation are effective at establishing donor hematopoietic engraftment and host-vs.-graft (HvG) tolerance. We investigated the mechanisms of HvG tolerance induction and maintenance in an animal model in which transplantation of sublethally irradiated female recipients with bone marrow (BM) from syngeneic male donors produces mixed chimerism. Splenocytes from chimeric mice inhibited HY-specific CD8+T cell responses bothin vitroandin vivo, and their adoptive transfer facilitated donor hematopoietic engraftment. These properties were contained within the CD4+CD25+population. The conditioning protocol alone led to a proportional expansion of regulatory T cells (Tregs), but the inhibitory activity was induced only if male BM was infused. The administration of anti-CD25-depleting antibodies to conditioned recipients at time of BM transplantation prevented donor-recipient chimerism but did not affect engraftment if performed after the establishment of chimerism, thus indicating that recipient Tregsare required for the generation but not the maintenance of HvG tolerance. We conclude that donor-specific Tregsof recipient origin are recruited when the donor antigens are present during reduced-intensity conditioning-induced Tregexpansion.
The theory of facilitated variation
Authors: Gerhart John , Kirschner Marc
Published: May 2007

This theory concerns the means by which animals generate phenotypic variation from genetic change. Most anatomical and physiological traits that have evolved since the Cambrian are, we propose, the result of regulatory changes in the usage of various members of a large set of conserved core components that function in development and physiology. Genetic change of the DNA sequences for regulatory elements of DNA, RNAs, and proteins leads to heritable regulatory change, which specifies new combinations of core components, operating in new amounts and states at new times and places in the animal. These new configurations of components comprise new traits. The number and kinds of regulatory changes needed for viable phenotypic variation are determined by the properties of the developmental and physiological processes in which core components serve, in particular by the processes' modularity, robustness, adaptability, capacity to engage in weak regulatory linkage, and exploratory behavior. These properties reduce the number of regulatory changes needed to generate viable selectable phenotypic variation, increase the variety of regulatory targets, reduce the lethality of genetic change, and increase the amount of genetic variation retained by a population. By such reductions and increases, the conserved core processes facilitate the generation of phenotypic variation, which selection thereafter converts to evolutionary and genetic change in the population. Thus, we call it a theory of facilitated phenotypic variation.
Profiling signaling polarity in chemotactic cells
Authors: Wang Yingchun , Ding Shi-Jian , Wang Wei , Jacobs Jon M. , Qian Wei-Jun , Moore Ronald J. , Yang Feng , Camp David G. , Smith Richard D. , Klemke Richard L.
Published: May 2007

Cell movement requires morphological polarization characterized by formation of a leading pseudopodium (PD) at the front and a trailing rear at the back. However, little is known about how protein networks are spatially integrated to regulate this process at the system level. Here, we apply global proteome profiling in combination with newly developed quantitative phosphoproteomics approaches for comparative analysis of the cell body (CB) and PD proteome of chemotactic cells. The spatial relationship of 3,509 proteins and 228 distinct sites of phosphorylation were mapped revealing networks of signaling proteins that partition to the PD and/or the CB compartments. The major network represented in the PD includes integrin signaling, actin regulatory, and axon guidance proteins, whereas the CB consists of DNA/RNA metabolism, cell cycle regulation, and structural maintenance. Our findings provide insight into the spatial organization of signaling networks that control cell movement and provide a comprehensive system-wide profile of proteins and phosphorylation sites that control cell polarization.
Evolution of individuality during the transition from unicellular to multicellular life
Authors: Michod Richard E.
Published: May 2007

Individuality is a complex trait, yet a series of stages each advantageous in itself can be shown to exist allowing evolution to get from unicellular individuals to multicellular individuals. We consider several of the key stages involved in this transition: the initial advantage of group formation, the origin of reproductive altruism within the group, and the further specialization of cell types as groups increase in size. How do groups become individuals? This is the central question we address. Our hypothesis is that fitness tradeoffs drive the transition of a cell group into a multicellular individual through the evolution of cells specialized at reproductive and vegetative functions of the group. We have modeled this hypothesis and have tested our models in two ways. We have studied the origin of the genetic basis for reproductive altruism (somatic cells specialized at vegetative functions) in the multicellular
Volvox carteri
by showing how an altruistic gene may have originated through cooption of a life-history tradeoff gene present in a unicellular ancestor. Second, we ask why reproductive altruism and individuality arise only in the larger members of the volvocine group (recognizing that high levels of kinship are present in all volvocine algae groups). Our answer is that the selective pressures leading to reproductive altruism stem from the increasing cost of reproduction with increasing group size. Concepts from population genetics and evolutionary biology appear to be sufficient to explain complexity, at least as it relates to the problem of the major transitions between the different kinds of evolutionary individuals.
Biological design in science classrooms
Authors: Scott Eugenie C. , Matzke Nicholas J.
Published: May 2007

Although evolutionary biology is replete with explanations for complex biological structures, scientists concerned about evolution education have been forced to confront “intelligent design” (ID), which rejects a natural origin for biological complexity. The content of ID is a subset of the claims made by the older “creation science” movement. Both creationist views contend that highly complex biological adaptations and even organisms categorically cannot result from natural causes but require a supernatural creative agent. Historically, ID arose from efforts to produce a form of creationism that would be less vulnerable to legal challenges and that would not overtly rely upon biblical literalism. Scientists do not use ID to explain nature, but because it has support from outside the scientific community, ID is nonetheless contributing substantially to a long-standing assault on the integrity of science education.
Functional information and the emergence of biocomplexity
Authors: Hazen Robert M. , Griffin Patrick L. , Carothers James M. , Szostak Jack W.
Published: May 2007

Complex emergent systems of many interacting components, including complex biological systems, have the potential to perform quantifiable functions. Accordingly, we define “functional information,”I(Ex), as a measure of system complexity. For a given system and function,x(e.g., a folded RNA sequence that binds to GTP), and degree of function,Ex(e.g., the RNA–GTP binding energy),I(Ex) = −log2[F(Ex)], whereF(Ex) is the fraction of all possible configurations of the system that possess a degree of function ≥Ex. Functional information, which we illustrate with letter sequences, artificial life, and biopolymers, thus represents the probability that an arbitrary configuration of a system will achieve a specific function to a specified degree. In each case we observe evidence for several distinct solutions with different maximum degrees of function, features that lead to steps in plots of information versus degree of function.
Full restoration of peripheral Foxp3
+
regulatory T cell pool by radioresistant host cells in
scurfy
bone marrow chimeras
Authors: Komatsu Noriko , Hori Shohei
Published: May 2007

Mutations in the gene encoding the transcription factor Foxp3 lead to fatal autoimmune pathology in mice and humans, which is associated with a deficiency in Foxp3
+
regulatory T cells (T
reg
). It has also been proposed that Foxp3 inactivation in nonhematopoietic tissues, particularly in thymic epithelium, is required for the pathogenesis, because Foxp3 mutant
scurfy
bone marrow cells fail to transmit the disease to lethally irradiated WT hosts. We demonstrate here that the lack of pathology in these radiation chimeras is due to the presence of radioresistant endogenous Foxp3
+
T
reg
of the host. In addition, chimeras carrying the
scurfy
mutation only in nonhematopoietic cells exhibit no evidence of autoimmune pathology. Thus, Foxp3 deficiency in nonhematopoietic cells does not contribute to the
scurfy
disease. Furthermore, our analyses of radiation chimeras revealed that the peripheral T
reg
pool is fully and specifically restored and maintained by radioresistant endogenous T
reg
or adoptively transferred exogenous T
reg
through “homeostatic” proliferation in the absence of T
reg
production from
scurfy
donor bone marrow cells. These results thus provide evidence that the autoimmune pathology in
scurfy
mice results indeed from a T
reg
deficiency and illustrate a robust homeostatic mechanism that strictly controls the size of peripheral T
reg
pool by fine-tuning of homeostatic proliferation.
The frailty of adaptive hypotheses for the origins of organismal complexity
Authors: Lynch Michael
Published: May 2007

The vast majority of biologists engaged in evolutionary studies interpret virtually every aspect of biodiversity in adaptive terms. This narrow view of evolution has become untenable in light of recent observations from genomic sequencing and population-genetic theory. Numerous aspects of genomic architecture, gene structure, and developmental pathways are difficult to explain without invoking the nonadaptive forces of genetic drift and mutation. In addition, emergent biological features such as complexity, modularity, and evolvability, all of which are current targets of considerable speculation, may be nothing more than indirect by-products of processes operating at lower levels of organization. These issues are examined in the context of the view that the origins of many aspects of biological diversity, from gene-structural embellishments to novelties at the phenotypic level, have roots in nonadaptive processes, with the population-genetic environment imposing strong directionality on the paths that are open to evolutionary exploitation.
Opening of connexin 43 hemichannels is increased by lowering intracellular redox potential
Authors: Retamal Mauricio A. , Schalper Kurt A. , Shoji Kenji F. , Bennett Michael V. L. , Sáez Juan C.
Published: May 2007

Nonjunctional membrane in many cells contains connexin gap junction hemichannels (or connexons) that can open to allow permeation of small molecules. Opening of Cx43 hemichannels is infrequent in normal extracellular Ca
2+
and enhanced by low Ca
2+
, positive membrane potentials, and dephosphorylation of critical residues. Here we report that lowering intracellular redox potential increases Cx43 hemichannel open probability under otherwise normal conditions. We studied dye uptake and single-channel activity in HeLa cells transfected with wild-type Cx43, Cx43 with enhanced GFP attached to its C terminus (Cx43-EGFP), and Cx43 with enhanced GFP attached to its N terminus (EGFP-Cx43). Dithiothreitol [(DTT) 10 mM], a membrane permeant-reducing agent, increased the rate of dye uptake by cells expressing Cx43 and Cx43-EGFP, but not by parental cells or cells expressing EGFP-Cx43. Induced dye uptake was blocked by La
3+
, by a peptide gap junction and hemichannel blocker (gap 26), and by flufenamic acid. DTT increased Cx43-EGFP hemichannel opening at positive voltages. Bath application of reduced glutathione, a membrane impermeant-reducing agent, did not increase dye uptake, but glutathione in the recording pipette increased hemichannel opening at positive voltages, suggesting that it acted intracellularly. DTT caused little change in levels of surface Cx43 or Cx43-EGFP, or in intracellular pH. These findings suggest that lowering intracellular redox potential increases the opening of Cx43 and Cx43-EGFP hemichannels, possibly by action on cytoplasmic cysteine residues in the connexin C terminus.
Prandiology of
Drosophila
and the CAFE assay
Authors: Ja William W. , Carvalho Gil B. , Mak Elizabeth M. , de la Rosa Noelle N. , Fang Annie Y. , Liong Jonathan C. , Brummel Ted , Benzer Seymour
Published: May 2007

Studies of feeding behavior in genetically tractable invertebrate model systems have been limited by the lack of proper methodology. We introduce the Capillary Feeder (CAFE), a method allowing precise, real-time measurement of ingestion by individual or grouped fruit flies on the scale of minutes to days. Using this technique, we conducted the first quantitative analysis of prandial behavior in
Drosophila melanogaster
. Our results allow the dissection of feeding into discrete bouts of ingestion, defining two separate parameters, meal volume and frequency, that can be uncoupled and thus are likely to be independently regulated. In addition, our long-term measurements show that flies can ingest as much as 1.7× their body mass over 24 h. Besides the study of appetite, the CAFE can be used to monitor oral drug delivery. As an illustration, we used the CAFE to test the effects of dietary supplementation with two compounds, paraquat and ethanol, on food ingestion and preference. Paraquat, a prooxidant widely used in stress tests, had a strong anorexigenic effect. In contrast, in a feeding preference assay, ethanol-laced food, but not ethanol by itself, acted as an attractant.
Evolution of nematode-trapping cells of predatory fungi of the Orbiliaceae based on evidence from rRNA-encoding DNA and multiprotein sequences
Authors: Yang Ying , Yang Ence , An Zhiqiang , Liu Xingzhong
Published: May 2007

Among fungi, the basic life strategies are saprophytism, parasitism, and predation. Fungi in Orbiliaceae (Ascomycota) prey on animals by means of specialized trapping structures. Five types of trapping devices are recognized, but their evolutionary origins and divergence are not well understood. Based on comprehensive phylogenetic analysis of nucleotide sequences of three protein-coding genes (RNA polymerase II subunit gene,
rpb2
; elongation factor 1-α gene,
ef1-α
; and ß tubulin gene,
bt
) and ribosomal DNA in the internal transcribed spacer region, we have demonstrated that the initial trapping structure evolved along two lineages yielding two distinct trapping mechanisms: one developed into constricting rings and the other developed into adhesive traps. Among adhesive trapping devices, the adhesive network separated from the others early and evolved at a steady and gentle speed. The adhesive knob evolved through stalk elongation, with a final development of nonconstricting rings. Our data suggest that the derived adhesive traps are at a highly differentiated stage. The development of trapping devices is felicitous proof of adaptive evolution.
Evidence for regulatory function of nucleus-encoded factors on mRNA stabilization and translation in the chloroplast
Authors: Raynaud Cécile , Loiselay Christelle , Wostrikoff Katia , Kuras Richard , Girard-Bascou Jacqueline , Wollman Francis-André , Choquet Yves
Published: May 2007

A salient feature of organelle gene expression is the requirement for nucleus-encoded factors that act posttranscriptionally in a gene-specific manner. A central issue is to understand whether these factors are merely constitutive or have a regulatory function. In the unicellular alga
Chlamydomonas reinhardtii
, expression of the chloroplast
petA
gene-encoding cytochrome
f
, a major subunit of the cytochrome

b
6
f

complex, depends on two specific nucleus-encoded factors: MCA1, required for stable accumulation of the
petA
transcript, and TCA1, required for its translation. We cloned the
TCA1
gene, encoding a pioneer protein, and transformed appropriate mutant strains with tagged versions of
MCA1
and
TCA1
. In transformed strains expressing decreasing amounts of MCA1 or TCA1, the concentration of these factors proved limiting for
petA
mRNA accumulation and cytochrome
f
translation, respectively. This observation suggests that in exponentially growing cells, the abundance of MCA1 sets the pool of
petA
transcripts, some of which are TCA1-selected for an assembly-dependent translation of cytochrome
f
. We show that MCA1 is a short-lived protein. Its abundance varies rapidly with physiological conditions that deeply affect expression of the
petA
gene
in vivo
, for instance in aging cultures or upon changes in nitrogen availability. We observed similar but more limited changes in the abundance of TCA1. We conclude that in conditions where
de novo
biogenesis of cytochrome

b
6
f

complexes is not required, a rapid drop in MCA1 exhausts the pool of
petA
transcripts, and the progressive loss of TCA1 further prevents translation of cytochrome
f
.
Review of micromachined thermopiles for infrared detection
Authors: Graf A , Arndt M , Sauer M , Gerlach G
Published: May 2007

During the last few years, thermopiles have come increasingly under the spotlight of commercial infrared sensing. This growing interest has motivated us to write an overview of micromachined thermopiles. The first part deals with theSeebeckeffect and discusses the most important physical parameters with their interactions. We also describe the main noise sources and give a derivation of the figures of merit and their relevance for thermopile detectors. In the second part, a number of material systems, techniques and micromachined structures are discussed on the basis of different examples. We explain the motivation behind miniaturized thermopile detectors and give a functional explanation of physical interrelations. Finally, different applications are presented and discussed in terms of their future potential.
Recycling Endosomes of Polarized Epithelial Cells Actively Sort Apical and Basolateral Cargos into Separate Subdomains
Authors: Thompson Anthony , Nessler Randy , Wisco Dolora , Anderson Eric , Winckler Bettina , Sheff David
Published: May 2007

The plasma membranes of epithelial cells plasma membranes contain distinct apical and basolateral domains that are critical for their polarized functions. However, both domains are continuously internalized, with proteins and lipids from each intermixing in supranuclear recycling endosomes (REs). To maintain polarity, REs must faithfully recycle membrane proteins back to the correct plasma membrane domains. We examined sorting within REs and found that apical and basolateral proteins were laterally segregated into subdomains of individual REs. Subdomains were absent in unpolarized cells and developed along with polarization. Subdomains were formed by an active sorting process within REs, which precedes the formation of AP-1B–dependent basolateral transport vesicles. Both the formation of subdomains and the fidelity of basolateral trafficking were dependent on PI3 kinase activity. This suggests that subdomain and transport vesicle formation occur as separate sorting steps and that both processes may contribute to sorting fidelity.
Nudel Modulates Kinetochore Association and Function of Cytoplasmic Dynein in M Phase
Authors: Liang Yun , Yu Wei , Li Yan , Yu Lihou , Zhang Qiangge , Wang Fubin , Yang Zhenye , Du Juan , Huang Qiongping , Yao Xuebiao , Zhu Xueliang
Published: May 2007

The microtubule-based motor cytoplasmic dynein/dynactin is a force generator at the kinetochore. It also transports proteins away from kinetochores to spindle poles. Regulation of such diverse functions, however, is poorly understood. We have previously shown that Nudel is critical for dynein-mediated protein transport, whereas mitosin, a kinetochore protein that binds Nudel, is involved in retention of kinetochore dynein/dynactin against microtubule-dependent stripping. Here we demonstrate that Nudel is required for robust localization of dynein/dynactin at the kinetochore. It localizes to kinetochores after nuclear envelope breakdown, depending mostly (∼78%) on mitosin and slightly on dynein/dynactin. Depletion of Nudel by RNA interference (RNAi) or overexpression of its mutant incapable of binding either Lis1 or dynein heavy chain abolishes the kinetochore protein transport and mitotic progression. Similar to mitosin RNAi, Nudel RNAi also leads to increased stripping of kinetochore dynein/dynactin in the presence of microtubules. Taking together, our results suggest a dual role of kinetochore Nudel: it activates dynein-mediated protein transport and, when interacting with both mitosin and dynein, stabilizes kinetochore dynein/dynactin against microtubule-dependent stripping to facilitate the force generation function of the motor.
Exogenous MAL Reroutes Selected Hepatic Apical Proteins into the Direct Pathway in WIF-B Cells
Authors: Ramnarayanan Sai Prasad , Cheng Christina A. , Bastaki Maria , Tuma Pamela L.
Published: May 2007

Unlike simple epithelial cells that directly target newly synthesized glycophosphatidylinositol (GPI)-anchored and single transmembrane domain (TMD) proteins from the trans-Golgi network to the apical membrane, hepatocytes use an indirect pathway: proteins are delivered to the basolateral domain and then selectively internalized and transcytosed to the apical plasma membrane. Myelin and lymphocyte protein (MAL) and MAL2 have been identified as regulators of direct and indirect apical delivery, respectively. Hepatocytes lack endogenous MAL consistent with the absence of direct apical targeting. Does MAL expression reroute hepatic apical residents into the direct pathway? We found that MAL expression in WIF-B cells induced the formation of cholesterol and glycosphingolipid-enriched Golgi domains that contained GPI-anchored and single TMD apical proteins; polymeric IgA receptor (pIgA-R), polytopic apical, and basolateral resident distributions were excluded. Basolateral delivery of newly synthesized apical residents was decreased in MAL-expressing cells concomitant with increased apical delivery; pIgA-R and basolateral resident delivery was unchanged. These data suggest that MAL rerouted selected hepatic apical proteins into the direct pathway.
Nest-mate recognition template of guard honeybees (Apis mellifera) is modified by wax comb transfer
Authors: Couvillon Margaret J , Caple Jamie P , Endsor Samuel L , Kärcher Martin , Russell Trudy E , Storey Darren E , Ratnieks Francis L.W
Published: May 2007

In recognition, discriminators use sensory information to make decisions. For example, honeybee (Apis mellifera) entrance guards discriminate between nest-mates and intruders by comparing their odours with a template of the colony odour. Comb wax plays a major role in honeybee recognition. We measured the rejection rates of nest-mate and non-nest-mate worker bees by entrance guards before and after a unidirectional transfer of wax comb from a ‘comb donor’ hive to a ‘comb receiver’ hive. Our results showed a significant effect that occurred in one direction. Guards in the comb receiver hive became more accepting of non-nest-mates from the comb donor hive (rejection decreased from 70 to 47%); however, guards in the comb donor hive did not become more accepting of bees from the comb receiver hive. These data strongly support the hypothesis that the transfer of wax comb increases the acceptance of non-nest-mates not by changing the odour of the bees, but by changing the template used by guards.
The rate of metabolism in marine animals: environmental constraints, ecological demands and energetic opportunities
Authors: Seibel Brad A , Drazen Jeffrey C
Published: May 2007

The rates of metabolism in animals vary tremendously throughout the biosphere. The origins of this variation are a matter of active debate with some scientists highlighting the importance of anatomical or environmental constraints, while others emphasize the diversity of ecological roles that organisms play and the associated energy demands. Here, we analyse metabolic rates in diverse marine taxa, with special emphasis on patterns of metabolic rate across a depth gradient, in an effort to understand the extent and underlying causes of variation. The conclusion from this analysis is that low rates of metabolism, in the deep sea and elsewhere, do not result from resource (e.g. food or oxygen) limitation or from temperature or pressure constraint. While metabolic rates do decline strongly with depth in several important animal groups, for others metabolism in abyssal species proceeds as fast as in ecologically similar shallow-water species at equivalent temperatures. Rather, high metabolic demand follows strong selection for locomotory capacity among visual predators inhabiting well-lit oceanic waters. Relaxation of this selection where visual predation is limited provides an opportunity for reduced energy expenditure. Large-scale metabolic variation in the ocean results from interspecific differences in ecological energy demand.
Analysis of morphometry and mitochondrial DNA sequences from two Trichiurus species in waters of the western North Pacific: taxonomic assessment and population structure
Authors: Tzeng C. H. , Chen C. S. , Chiu T. S.
Published: May 2007

The species status of cutlassfishes (Trichiurus spp.) in waters of the western North Pacific (five hydrographic areas) was examined using the full‐length (consisting of 1141 base pairs) DNA sequence of the mitochondrial cytochrome b gene (mtCyt b) and truss network‐based morphometrics. Two historically confusing Trichiurus morphs are suggested to be two separate species because a decisive difference in the genetic and morphometric data between Trichiurus japonicus and Trichiurus lepturus, using a restricted congener, Trichiurus brevis as the out‐group was found. Of all 241 polymorphic sites in mtCyt b at the P0·95 level, 192 sites fixed within species and variable between species was found. Two‐level AMOVA (species and hydrographic areas) results showed significant species differences, while no hydrographic structuring was found within species. Both maximum parsimony and neighbour‐joining distance trees supported clear branches for T. japonicus and T. lepturus at 100% bootstrap support. Discriminant function analysis with adjusted body size performed on the morphometric data of T. japonicus and T. lepturus revealed a decisive specific gap of non‐overlapping scattering. Combining mtCyt b findings with documented geological events in the western North Pacific, the authors postulate that T. japonicus was evolved peripherally from T. lepturus in middle Miocene, and these two partially sympatric species were achieved secondarily after the Pliocene when intermediate temperatures were located in the subtropical transitions.
Relationships among four genera of mojarras (Teleostei: Perciformes: Gerreidae) from the western Atlantic and their tentative placement among percomorph fishes
Authors: Chen W.‐J. , Ruiz‐Carus R. , Ortí G.
Published: May 2007

A phylogenetic study of the percoid family Gerreidae at both lower and higher taxonomic levels is presented based on DNA sequence data of four genes: mitochondrial 12S and 16S, and nuclear genes rhodopsin and recombination activating gene 1 (RAG1). The taxonomic sampling includes four genera of Gerreidae from the western Atlantic, 39 additional percomorph representatives and two outgroups. Phylogenetic results confirm the monophyly of the Gerreidae and suggest that the family is divided into two sub‐groups (Diapterus auratus plus Eugerres plumieri and Eucinostomus gula plus Gerres cinereus), which correspond to two previously defined taxonomic assemblages characterized by the shape of the preoperculum. Gerreids are placed at an intermediate position in the percomorph tree between two basal clades (L and Q) and a terminal clade N (grouping tetraodontiforms, acanthuroids, lophiiforms, caproids and several percoids). In addition, topology tests indicate that two traditional assemblages, Labroidei (seven representatives sampled) and Percoidei (22 representatives sampled) are not natural groups. Labrids and scarids appear to be more closely related to gerreids and to the members of clade N than to any other basal percomorphs, including their labroid ‘allies’ sampled in this study, Embiotocidae, Pomacentridae and Cichlidae, which are all nested within clade Q that also includes atherinomorphs, mugiliforms and Chandidae. The percoid taxa included in this study are widely distributed among various percomorph lineages. The percomorph phylogeny obtained is highly congruent with results from recent molecular studies.
Molecular data confirm the validity of the Portuguese blenny (Parablennius ruber, Valenciennes, 1836) and its presence in Western Europe
Authors: Almada V. C. , Domingues V. S. , Monteiro N. M. , Almada F. , Santos R. S.
Published: May 2007

DNA sequence analysis confirms the distinction betweenParablennius ruberandParablennius gattorugine, simultaneously validating the presence of the former species in Western Europe where it has been reported for >150 years. A possible scenario involving speciation ofP. ruberat the Azores and subsequent transport of larvae to Europe, a process that may be still occurring nowadays, could explain this pattern of occurrence.
Genetic differentiation among populations of the shortfinned eel Anguilla australis from East Australia and New Zealand
Authors: Shen K. N. , Tzeng W. N.
Published: May 2007

Variability at seven microsatellite loci was used to survey the genetic population structure of the shortfinned eel Anguilla australis. Samples were collected from six estuaries along the east coast of Australia and from three estuaries around New Zealand. Hierarchical analysis of molecular variance of the five loci with good fit to Hardy–Weinberg genotypic proportions detected highly significant differences among samples (FST= 0·016, P < 0·001). The fixation index between countries (FCT= 0·012, P < 0·001) was more than double the index among samples within countries (FSC= 0·005, P < 0·05). An unweighted pair‐group method with arithmetic mean (UPGMA) tree also supported the separation of Australian and New Zealand populations, as did assignment tests, which correctly assigned 80 and 84% of the individuals to Australia and New Zealand, respectively. Isolation‐by‐distance appeared among samples overall (r= 0·807, P < 0·001), but not among samples within countries (r= 0·027, P > 0·05 in Australia; r= 0·762, P > 0·05 in New Zealand). These findings indicate that populations of A. australis in East Australia and in New Zealand may be reproductively isolated from one another. Genetic differentiation among populations of A. australis was two‐ to 10‐fold higher than that among populations of other temperate eels in the North Atlantic Ocean, suggesting that two group of A. australis may reflect sub‐species. Anguilla australis in the two countries have different genetic structures and thus require separate management. Genetic isolation between Australian and New Zealand populations indicates that juveniles recruit independently into these two regions from geographically or temporally isolated spawning areas.
Transgene activity following somatic transgenesis in Nile tilapia Oreochromis niloticus
Authors: Brooks C. , Hwang G. , Maclean N.
Published: May 2007

A detailed study was made of the persistence and expression of a plasmid‐enclosed reporter gene construct after intramuscular injection into the somatic muscle tissue of juvenile Nile tilapia Oreochromis niloticus and also the effect of injecting a potentially growth‐promoting gene construct. The plasmid‐enclosed DNA proved stable at the site of injection, lasting in some cases for up to 6 months, and was, at a very low frequency, detected in gonad tissue, indicating occasional substantial movement from the injected muscle site. It was observed that the reporter gene and regulatory sequences were also functional within the somatic cells. In a comparison of expression levels by direct somatic injection, the 1·6 kb tilapia β‐actin regulatory sequence (tiβAP) resulted in c. three‐fold higher β‐galactosidase activity than the 4·7 kb carp β‐actin regulatory sequence (cβAP) when spliced to the lacZ gene. The enhancer element near the end of first intron in the tiβAP, when co‐injected with tiβAP/lacZ plasmid at a 3:1 ratio, drove significantly higher reporter activity in somatic cells than the tiβAP/lacZ sequence alone. The introduction of a growth‐promoting construct, the Nile tilapia growth hormone gene driven by a tiβAP, yielded no detectable growth enhancement.
Species‐specific genetic markers for identification of early life‐history stages of Cape hakes, Merluccius capensis and Merluccius paradoxus in the southern Benguela Current
Authors: Von Der Heyden S. , Lipinski M. R. , Matthee C. A.
Published: May 2007

The correct identification of fish egg and larval stages is crucial for inferring spawning areas and subsequent dispersal routes for marine fishes. The authors use species‐specific mtDNA polymerase chain reaction to estimate proportions of Merluccius capensis and Merluccius paradoxus eggs and larvae and to elucidate early life stage distribution patterns in the southern Benguela system.
Phylogeny of Branchiopoda (Crustacea) based on a combined analysis of morphological data and six molecular loci
Authors: Richter Stefan , Olesen Jørgen , Wheeler Ward C.
Published: May 2007

The phylogenetic relationships of branchiopod crustaceans have been in the focus of a number of recent morphological and molecular systematic studies. Although agreeing in some respects, major differences remain. We analyzed molecular sequences and morphological characters for 43 branchiopods and two outgroups. The branchiopod terminals comprise all eight “orders”. The molecular data include six loci: two nuclear ribosomal genes (18S rRNA, 28S rRNA), two mitochondrial ribosomal genes (12S rRNA, 16S rRNA), one nuclear protein coding gene (elongation factor 1α), and one mitochondrial protein coding gene (cytochrome c oxidase subunit I). A total of 65 morphological characters were analyzed dealing with different aspects of branchiopod morphology, including internal anatomy and larval characters. The morphological analysis resulted in a monophyletic Phyllopoda, with Notostraca as the sister group to the remaining taxa supporting the Diplostraca concept (“Conchostraca” + Cladocera). “Conchostraca” is not supported but Cyclestheria hislopi is the sister group to Cladocera (constituting together Cladoceromorpha) and Spinicaudata is closer to Cladoceromorpha than to Laevicaudata. Cladocera is supported as monophyletic. The combined analysis under equal weighting gave results in some respects similar to the morphological analysis. Within Phyllopoda, Cladocera, Cladoceromorpha and Spinicaudata + Cladoceromorpha are monophyletic. The combined analysis is different from the morphological analysis with respect to the position of Notostraca and Laevicaudata. Here, Laevicaudata is the sister group to the remaining Phyllopoda and Notostraca is sister group to Spinicaudata and Cladoceromorpha. A sensitivity analysis using 20 different parameter sets (different insertion–deletion [indel]/substitution and transversion/transition ratios) show the monophyly of Anostraca, Notostraca, Laevicaudata, Spinicaudata, Cladoceromorpha, Cladocera, and within Cladocera, of Onychopoda and Gymnomera under all or almost all (i.e., 19 of 20) parameter sets. Analyses with an indel‐to‐transversion ratio up to 2 result in monophyletic Phyllopoda, with Laevicaudata as sister group to the remaining Phyllopoda and with Spinicaudata and Cladoceromorpha as sister groups. Almost all analyses (including those with higher indel weights) result in the same topology when only ingroup taxa are considered.

© The Willi Hennig Society 2007.
Naming taxa from cladograms: some confusions, misleading statements, and necessary clarifications
Authors: Dubois Alain
Published: May 2007

Hillis (2006) recently published a rebuttal of my analysis (Dubois, 2006c) of a paper by Hillis and Wilcox (2005) on the taxonomy and nomenclature of American ranid frogs. His paper consists not only in a reply to my paper, as it contains in fact three distinct kinds of statements: (1) an attempt to “save” the new generic nomina proposed by Hillis and Wilcox (2005) from being considered nomina nuda under the Code; (2) another plea for the superiority of the Phylocode over the Code, especially as regards the absence of a Rule of Coordination and the substitution of “phylogenetic definition” of nomina to the use of onomatophores for the allocation of nomina to taxa; (3) a plea for “taxonomic stability” in order not to upset the traditional use of nomina and to please users of electronic data bases. These three points are here commented, as follows: (1) even with the best goodwill, under the rules of the Code it is possible to “save” only three or four of the seven new nomina of Hillis and Wilcox (2005), the others being indeed nomina nuda; furthermore, three of these seven nomina are definitively useless and redundant, being junior objective synonyms of other generic nomina; (2) the well‐known arguments against the Phylocode do not need to be repeated in detail once again, the most important one being that replacement of a secular nomenclatural system by another one, whose theoretical and practical superiority is highly questionable, would cause considerable chaos and detract taxonomists from their urgent task of accelerating the collection, study and description of the living species of our planet; (3) the claim for taxonomic and nomenclatural stability ignores the importance of the taxonomic impediment and sends a misleading message to the scientific community and to society as a whole: in the present situation of our knowledge, taxonomic stability is ignorance, and the science of taxonomy would have much to lose to adapt its concepts and practices to the needs of databases at the expense of scientific quality. It is once again stressed that, for the quality and accuracy of communication between evolutionary biologists, and above all with other biologists and non‐biologists, it is urgent that scientific periodicals impose the use of different systems of notation of nomina following distinct nomenclatural systems, such as the Code and the Phylocode.

© The Willi Hennig Society 2007.
Species: kinds of individuals or individuals of a kind
Authors: Rieppel Olivier
Published: May 2007

The “species‐as‐individuals” thesis takes species, or taxa, to be individuals. On grounds of spatiotemporal boundedness, any biological entity at any level of complexity subject to evolutionary processes is an individual. From evolutionary theory flows an ontology that does not countenance universal properties shared by evolving entities. If austere nominalism were applied to evolving entities, however, nature would be reduced to a mere flow of passing events, each one a blob in space–time and hence of passing interest only. Yet if there is genuine biodiversity in nature, if nature is genuinely carved into species, and taxa, then these evolutionary entities will be genuinely differentiated into specific kinds, each species being one of its kind. Given the fact that evolving entities have un‐sharp boundaries, an appropriately weak, “non‐essentialist” concept of natural kind has to be invoked that does not allow for strong identity conditions. The thesis of this paper is that species are not either individuals, or natural kinds. Instead, species are complex wholes (particulars, individuals) that instantiate a specific natural kind.

© The Willi Hennig Society 2007.
K‐ras oncogene silencing strategy reduces tumor growth and enhances gemcitabine chemotherapy efficacy for pancreatic cancer treatment
Authors: Réjiba Soukaina , Wack Séverine , Aprahamian Marc , Hajri Amor
Published: May 2007

Pancreatic adenocarcinoma remains a fatal disease characterized by rapid tumor progression, high metastatic potential and profound chemoresistance. Gemcitabine is the current standard chemotherapy for advanced pancreatic cancer, but it is still far from optimal and novel therapeutic strategies are needed urgently. Mutations in the k‐ras gene have been found in more than 90% of pancreatic cancers and are believed to play a key role in this malignancy. Thus, the goal of this study was to investigate the impact of k‐ras oncogene silencing on pancreatic tumor growth. Additionally, we examined whether combining k‐ras small interfering RNA (siRNA) with gemcitabine has therapeutic potential for pancreatic cancer. The treatment of tumor cell cultures with the corresponding k‐ras siRNA resulted in a significant inhibition of k‐ras endogenous expression and cell proliferation. In vivo, tumor xenografts were significantly reduced with k‐ras siRNAGAT delivered by electroporation. Moreover, combined treatment with pSsik‐rasGAT plus gemcitabine resulted in strong growth inhibition of orthotopic pancreatic tumors. Survival rate was significantly prolonged and the mean tumor volume was dramatically reduced in mice receiving the combined treatment compared with single agents. Collectively, these findings show that targeting mutant k‐ras through specific siRNA might be effective for k‐ras oncogene silencing and tumor growth inhibition. The improvement of gemcitabine‐based chemotherapy suggests that this strategy might be used therapeutically against human pancreatic cancer to potentiate the effects of conventional therapy. (Cancer Sci 2007; 98: 1128–1136)