bluuebunny/crossref_metadata_2025 huggingface dataset:
Stimulation of mammalian translation initiation factor eIF4A activity by a small molecule inhibitor of eukaryotic translation
Authors: Bordeleau Marie-Eve , Matthews James , Wojnar Joanna M. , Lindqvist Lisa , Novac Olivia , Jankowsky Eckhard , Sonenberg Nahum , Northcote Peter , Teesdale-Spittle Paul , Pelletier Jerry
Published: July 2005

RNA helicases are the largest group of enzymes in eukaryotic RNA metabolism. The DEXD/H-box putative RNA helicases form the helicase superfamily II, whose members are defined by seven highly conserved amino acid motifs, making specific targeting of selected members a challenging pharmacological problem. The translation initiation factor eIF4A is the prototypical DEAD-box RNA helicase that works in conjunction with eIF4B and eIF4H and as a subunit of eIF4F to prepare the mRNA template for ribosome binding, possibly by unwinding the secondary structure proximal to the 5′ m
7
GpppN cap structure. We report the identification and characterization of a small molecule inhibitor of eukaryotic translation initiation that acts in an unusual manner by stimulating eIF4A-associated activities. Our results suggest that proper control of eIF4A helicase activity is necessary for efficient ribosome binding and demonstrate the feasibility of selectively targeting DEAD-box RNA helicases with small molecules.
Variable rate of singing and variable song duration are associated with high immediate early gene expression in two anterior forebrain song nuclei
Authors: Liu Wan-chun , Nottebohm Fernando
Published: July 2005

The duration of songs and the intervals between these songs are more variable when wild, adult, free-ranging chipping sparrows sing at dawn than when they sing during the day. The more variable delivery is used to interact with males, and the stereotyped delivery is used to attract females. In captive birds, however, the variability observed at dawn persists during the day. We quantified the expression of an immediate early gene, ZENK, in wild and captive birds and found that the level of song-associated ZENK expression in two song nuclei, Area X and lMAN, was positively related to variability in song duration and intersong interval and could be dissociated from the social context in which the song occurred. Thus, a combination of field and laboratory approaches helped us identify nuclei, context, and behavioral features associated with a change in gene expression thought to be a marker of behavioral variability.
Visceral adipose tissue-derived serine protease inhibitor: A unique insulin-sensitizing adipocytokine in obesity
Authors: Hida Kazuyuki , Wada Jun , Eguchi Jun , Zhang Hong , Baba Masako , Seida Aya , Hashimoto Izumi , Okada Tatsuo , Yasuhara Akihiro , Nakatsuka Atsuko , Shikata Kenichi , Hourai Shinji , Futami Junichiro , Watanabe Eijiro , Matsuki Yasushi , Hiramatsu Ryuji , Akagi Shigeru , Makino Hirofumi , Kanwar Yashpal S.
Published: July 2005

There is a rapid global rise in obesity, and the link between obesity and diabetes remains somewhat obscure. We identified an adipocytokine, designated as visceral adipose tissue-derived serpin (vaspin), which is a member of serine protease inhibitor family. Vaspin cDNA was isolated by from visceral white adipose tissues (WATs) of Otsuka Long-Evans Tokushima fatty (OLETF) rat, an animal model of abdominal obesity with type 2 diabetes. Rat, mouse, and human vaspins are made up of 392, 394, and 395 amino acids, respectively; exhibit ≈40% homology with α
1
-antitrypsin; and are related to serine protease inhibitor family. Vaspin was barely detectable in rats at 6 wk and was highly expressed in adipocytes of visceral WATs at 30 wk, the age when obesity, body weight, and insulin levels peak in OLETF rats. The tissue expression of vaspin and its serum levels decrease with worsening of diabetes and body weight loss at 50 wk. The expression and serum levels were normalized with the treatment of insulin or insulin-sensitizing agent, pioglitazone, in OLETF rats. Administration of vaspin to obese CRL:CD-1 (ICR) (ICR) mice fed with high-fat high-sucrose chow improved glucose tolerance and insulin sensitivity reflected by normalized serum glucose levels. It also led to the reversal of altered expression of genes relevant to insulin resistance, e.g., leptin, resistin, TNFα, glucose transporter-4, and adiponectin. In DNA chip analyses, vaspin treatment resulted in the reversal of expression in ≈50% of the high-fat high-sucrose-induced genes in WATs. These findings indicate that vaspin exerts an insulin-sensitizing effect targeted toward WATs in states of obesity.
On Beurling-type theorems in weighted 𝑙² and Bergman spaces
Authors: Shimorin Serguei
Published: July 2005

We prove that analytic operators satisfying certain series of operator inequalities possess the wandering subspace property. As a corollary, we obtain Beurling-type theorems for invariant subspaces in certain weighted

l
2

l^2

and Bergman spaces.
Means on solenoids
Authors: Krupski Paweł
Published: July 2005

It is determined which solenoids admit 2-argument continuous means.
Invariant complementation and projectivity in the Fourier algebra
Authors: Wood Peter
Published: July 2005

In this paper, we study the ideals in the Fourier algebra of a locally compact group

G
G

which are complemented by an invariant projection. In particular we show that when

G
G

is discrete, every ideal which is complemented by a completely bounded projection must be invariantly complemented. Perhaps surprisingly, this result does not depend of the amenability of the group or the algebra, but instead relies on the operator biprojectivity of the Fourier algebra for a discrete group.
Deformations of minimal Lagrangian submanifolds with boundary
Authors: Butscher Adrian
Published: July 2005

Let

L
L

be a special Lagrangian submanifold of a compact Calabi-Yau manifold

M
M

with boundary lying on the symplectic, codimension 2 submanifold

W
W

. It is shown how deformations of

L
L

which keep the boundary of

L
L

confined to

W
W

can be described by an elliptic boundary value problem, and two results about minimal Lagrangian submanifolds with boundary are derived using this fact. The first is that the space of minimal Lagrangian submanifolds near

L
L

with boundary on

W
W

is found to be finite dimensional and is parametrized over the space of harmonic 1-forms of

L
L

satisfying Neumann boundary conditions. The second is that if

W
′

W’

is a symplectic, codimension 2 submanifold sufficiently near

W
W

, then, under suitable conditions, there exists a minimal Lagrangian submanifold

L
′

L’

near

L
L

with boundary on

W
′

W’

.
A tall space with a small bottom
Authors: Juhász István , Shelah Saharon , Soukup Lajos , Szentmiklóssy Zoltán
Published: July 2005

We introduce a general method of constructing locally compact scattered spaces from certain families of sets and then, with the help of this method, we prove that ifκ>κ=κ\kappa ^{>\kappa } = \kappa, then there is such a space of heightκ+\kappa ^+with onlyκ\kappamany isolated points. This implies that there is a locally compact scattered space of heightω2{\omega }_2withω1\omega _1isolated points in ZFC, solving an old problem of the first author.
Unipotent flat bundles and Higgs bundles over compact Kähler manifolds
Authors: Lekaus Silke
Published: July 2005

We characterize those unipotent representations of the fundamental group

π
1

(
X
,
x
)

\pi _1(X,x)

of a compact Kähler manifold

X
X

, which correspond to a Higgs bundle whose underlying Higgs field is equal to zero. The characterization is parallel to the one that R. Hain gave of those unipotent representations of

π
1

(
X
,
x
)

\pi _1(X,x)

that can be realized as the monodromy of a flat connection on the holomorphically trivial vector bundle. We see that Hain’s result and ours follow from a careful study of Simpson’s correspondence between Higgs bundles and local systems.
On the power series coefficients of certain quotients of Eisenstein series
Authors: Berndt Bruce , Bialek Paul
Published: July 2005

In their last joint paper, Hardy and Ramanujan examined the coefficients of modular forms with a simple pole in a fundamental region. In particular, they focused on the reciprocal of the Eisenstein series

E
6

(
τ
)

E_6(\tau )

. In letters written to Hardy from nursing homes, Ramanujan stated without proof several more results of this sort. The purpose of this paper is to prove most of these claims.
Riemannian nilmanifolds and the trace formula
Authors: Gornet Ruth
Published: July 2005

This paper examines the clean intersection hypothesis required for the expression of the wave invariants, computed from the asymptotic expansion of the classical wave trace by Duistermaat and Guillemin. The main result of this paper is the calculation of a necessary and sufficient condition for an arbitrary Riemannian two-step nilmanifold to satisfy the clean intersection hypothesis. This condition is stated in terms of metric Lie algebra data. We use the calculation to show that generic two-step nilmanifolds satisfy the clean intersection hypothesis. In contrast, we also show that the family of two-step nilmanifolds that fail the clean intersection hypothesis are dense in the family of two-step nilmanifolds. Finally, we give examples of nilmanifolds that fail the clean intersection hypothesis.
ATP Production inChlamydomonas reinhardtiiFlagella by Glycolytic Enzymes
Authors: Mitchell Beth F. , Pedersen Lotte B. , Feely Michael , Rosenbaum Joel L. , Mitchell David R.
Published: July 2005

Eukaryotic cilia and flagella are long, thin organelles, and diffusion from the cytoplasm may not be able to support the high ATP concentrations needed for dynein motor activity. We discovered enzyme activities in the Chlamydomonas reinhardtii flagellum that catalyze three steps of the lower half of glycolysis (phosphoglycerate mutase, enolase, and pyruvate kinase). These enzymes can generate one ATP molecule for every substrate molecule consumed. Flagellar fractionation shows that enolase is at least partially associated with the axoneme, whereas phosphoglycerate mutase and pyruvate kinase primarily reside in the detergent-soluble (membrane + matrix) compartments. We further show that axonemal enolase is a subunit of the CPC1 central pair complex and that reduced flagellar enolase levels in the cpc1 mutant correlate with the reduced flagellar ATP concentrations and reduced in vivo beat frequencies reported previously in the cpc1 strain. We conclude that in situ ATP synthesis throughout the flagellar compartment is essential for normal flagellar motility.
PACdb: PolyA Cleavage Site and 3′-UTR Database
Authors: Brockman J. Michael , Singh Priyam , Liu Donglin , Quinlan Sean , Salisbury Jesse , Graber Joel H.
Published: July 2005

Summary: The PolyA Cleavage Site and 3′-UTR Database (PACdb) is a web-accessible database that catalogs putative 3′-processing sites and 3′-UTR sequences for multiple organisms. Sites have been identified primarily via expressed sequence tag-genome alignments, enabling delineation of both the specificities and heterogeneity of 3′-processing events.

Availability: By web browser or CGI: PACdb: http://harlequin.jax.org/pacdb/; AtPACdb: http://harlequin.jax.org/atpacdb/

Contact:  joel.graber@jax.org

Supplementary information: Available online at http://harlequin.jax.org/pacdb/supplemental.php
Inhibition of protein kinases C prevents murine cytomegalovirus replication
Authors: Kučić Natalia , Mahmutefendić Hana , Lučin Pero
Published: July 2005

For successful establishment of infection and initiation of the replication cycle, murine cytomegalovirus (MCMV) utilizes cellular structures and functions, including cell-membrane penetration, capsid dismantling and cytosolic transport of viral DNA into the nucleus. These early events of MCMV infections are dependent on cellular regulatory mechanisms, primarily protein phosphorylation. In the present study, protein kinase inhibitors were used to explore the role of protein phosphorylation mediated by protein kinases C (PKCs) in the very early events of MCMV infection. Inhibitory effects were determined by immunofluorescence and Western blot analysis of MCMV IE1 and E1 protein expression and by production of infectious virions in cell culture. It was found that H-7, a broadly specific inhibitor of cellular protein kinases, prevented virus replication in a dose-dependent and reversible manner, and that the block in replication occurred very early in infection. More specific PKC inhibitors (sangivamycin, calphostin C and bisindolylmaleimide II), Ca2+/calmodulin inhibitors (EDTA and W7) and phorbol esters (PMA) were used to dissect PKC-subclass contribution in the very early events of MCMV replication. The results indicate that the role of diacylglycerol/phorbol ester-dependent but calcium-independent PKCs is essential for establishment of MCMV infection in the host cell, starting at a very early stage of infection.
Gene-expression changes induced by Feline immunodeficiency virus infection differ in epithelial cells and lymphocytes
Authors: Dowling R. J. O. , Bienzle D.
Published: July 2005

Infection of cats with Feline immunodeficiency virus (FIV) is an important model for understanding comparative lentivirus biology. In vivo, FIV infects lymphocytes and monocyte/macrophages, but in vitro infection is commonly investigated in epithelial Crandell–Reese Feline Kidney (CRFK) cells. In this study, the transcriptional responses of CRFK cells and primary lymphocytes to infection with FIV 34TF, a cloned subtype A virus, and FIV USgaB01, a biological subtype B isolate, were determined. Reverse-transcribed mRNA from both cell types was hybridized to microarrays containing 1700 human expressed sequence tags in duplicate and data were analysed with Significance Analysis of Microarrays (sam) software. Results from six experiments assessing homeostatic cross-species hybridization excluded 3·48 % inconsistently detected transcripts. Analysis of data from five time points over 48 h after infection identified 132 and 24 differentially expressed genes in epithelial cells and lymphocytes, respectively. Genes involved in protein synthesis, the cell cycle, structure and metabolism were affected. The magnitude of gene-expression changes ranged from 0·62 to 1·62 and early gene induction was followed by downregulation after 4 h. Transcriptional changes in CRFK cells were distinct from those in lymphocytes, except for heat-shock cognate protein 71, which was induced at multiple time points in both cell types. These findings indicate that FIV infection induces transcriptional changes of a modest magnitude in a wide range of genes, which is probably reflective of the relatively non-cytopathic nature of virus infection.
Sequence variation divides Equine rhinitis B virus into three distinct phylogenetic groups that correlate with serotype and acid stability
Authors: Black Wesley D. , Hartley Carol A. , Ficorilli Nino P. , Studdert Michael J.
Published: July 2005

Equine rhinitis B virus (ERBV), genus Erbovirus, family Picornaviridae, occurs as two serotypes, ERBV1 and ERBV2, and the few isolates previously tested were acid labile. Of 24 ERBV1 isolates tested in the studies reported here, 19 were acid labile and five were acid stable. The two available ERBV2 isolates, as expected, were acid labile. Nucleotide sequences of the P1 region encoding the capsid proteins VP1, VP2, VP3 and VP4 were determined for five acid-labile and three acid-stable ERBV1 isolates and one acid-labile ERBV2 isolate. The sequences were aligned with the published sequences of the prototype acid-labile ERBV1.1436/71 and the prototype ERBV2.313/75. The three acid-stable ERBV1 were closely related in a phylogenetic group that was distinct from the group of six acid-labile ERBV1, which were also closely related to each other. The two acid-labile ERBV2 formed a third distinct group. One acid-labile ERBV1 had a chimeric acid-labile/acid-stable ERBV1 P1 sequence, presumably because of a recombination event within VP2 and this was supported by SimPlot analysis. ERBV1 rabbit antiserum neutralized acid-stable and acid-labile ERBV1 isolates similarly. Accordingly, three distinct phylogenetic groups of erboviruses exist that are consistent with serotype and acid stability phenotypes.
Characterization of internal ribosomal entry sites of Triatoma virus
Authors: Czibener Cecilia , Alvarez Diego , Scodeller Eduardo , Gamarnik Andrea V.
Published: July 2005

Triatoma virus (TrV) belongs to a new family of RNA viruses known asDicistroviridae. Nucleotide sequence comparisons between different dicistroviruses allowed two putative internal ribosomal entry sites (IRESs) in the TrV RNA to be defined: the 5′UTR IRES of 548 nt and the intergenic region (IGR) IRES of 172 nt. Using monocistronic and bicistronic RNAs, it was shown that the TrV genome contains two functional IRESs that mediate translation initiation in a cap-independent manner. In addition, it was found that the two TrV IRESs were able to direct efficient translation of reporter genes in microinjectedXenopusoocytes, suggesting minimum requirements for host factors. The IGR IRES begins with a non-canonical CUC; however, mutations of this triplet to AUG or CCU did not impair IRES function, indicating that the CUC is not essential for the initiation process. Furthermore, translation efficiency from two TrV IRESs was differentially modulated by IFN-αand viral infection.
Nucleotide sequence and genomic organization of a newly isolated densovirus infecting Dendrolimus punctatus
Authors: Wang Junping , Zhang Jiamin , Jiang Hong , Liu Chuanfeng , Yi Fuming , Hu Yuanyang
Published: July 2005

The nucleotide sequence of a novel icosahedral DNA virus infecting Dendrolimus punctatus has been determined. The genome is 5039 nt long and includes inverted terminal repeats of 200 nt containing 131 nt long J-shaped terminal hairpins. The ‘plus' strand of the genome contains three large open reading frames (ORFs), the left and the mid-ORFs (within the left ORF) in the left-half encoding the non-structural proteins and the right ORF in the right-half encoding viral capsid proteins. NS1 protein contains conserved replication initiation and DNA-dependent ATPase/helicase domains. VP1 protein contains a conserved PGY and phospholipase A2 motifs and shows high identities with VPs of Casphalia extranea densovirus and Bombyx mori densovirus-1 belonging to the genus Iteravirus. Phylogenetic analysis also revealed that this virus is most closely related to Casphalia extranea densovirus and Bombyx mori densovirus-1. Consequently, this virus was considered as a new third member of the genus Iteravirus of the subfamily Densovirinae, and designated Dendrolimus punctatus densovirus.
Murine cytomegalovirus resistant to antivirals has genetic correlates with human cytomegalovirus
Authors: Scott G. M. , Ng H.-L. , Morton C. J. , Parker M. W. , Rawlinson W. D.
Published: July 2005

Human cytomegalovirus (HCMV) resistance to antivirals is a significant clinical problem. Murine cytomegalovirus (MCMV) infection of mice is a well-described animal model for in vivo studies of CMV pathogenesis, although the mechanisms of MCMV antiviral susceptibility need elucidation. Mutants resistant to nucleoside analogues aciclovir, adefovir, cidofovir, ganciclovir, penciclovir and valaciclovir, and the pyrophosphate analogue foscarnet were generated by in vitro passage of MCMV (Smith) in increasing concentrations of antiviral. All MCMV antiviral resistant mutants contained DNA polymerase mutations identical or similar to HCMV DNA polymerase mutations known to confer antiviral resistance. Mapping of the mutations onto an MCMV DNA polymerase three-dimensional model generated using the Thermococcus gorgonarius Tgo polymerase crystal structure showed that the DNA polymerase mutations potentially confer resistance through changes in regions surrounding a catalytic aspartate triad. The ganciclovir-, penciclovir- and valaciclovir-resistant isolates also contained mutations within MCMV M97 identical or similar to recognized GCV-resistant mutations of HCMV UL97 protein kinase, and demonstrated cross-resistance to antivirals of the same class. This strongly suggests that MCMV M97 has a similar role to HCMV UL97 in the phosphorylation of nucleoside analogue antivirals. All MCMV mutants demonstrated replication-impaired phenotypes, with the lowest titre and plaque size observed for isolates containing mutations in both DNA polymerase and M97. These findings indicate DNA polymerase and protein kinase regions of potential importance for antiviral susceptibility and replication. The similarities between MCMV and HCMV mutations that arise under antiviral selective pressure increase the utility of MCMV as a model for in vivo studies of CMV antiviral resistance.
Structure of birnavirus-like particles determined by combined electron cryomicroscopy and X-ray crystallography
Authors: Pous Joan , Chevalier Christophe , Ouldali Malika , Navaza Jorge , Delmas Bernard , Lepault Jean
Published: July 2005

Birnaviruses possess a capsid with a single protein layer in contrast to most double-stranded RNA viruses infecting multicellular eukaryotes. Using freeze-drying and heavy metal shadowing, the capsids of two birnaviruses, infectious bursal disease virus (IBDV) and infectious pancreatic necrosis virus, as well as of an IBDV virus-like particle (VLP) are shown to follow the same T=13 laevo icosahedral geometry. The structure of the VLP was determined at a resolution of approximately 15 Å (1·5 nm) by a combination of electron cryomicroscopy and a recently developed three-dimensional reconstruction method, where the scattering density is expressed in terms of symmetry-adapted functions. This reconstruction methodology is well adapted to the icosahedral symmetry of viruses and only requires a small number of images to analyse. The atomic model of the external capsid protein, VP2, recently determined by X-ray crystallography, fits well into the VLP reconstruction and occupies all the electron densities present in the map. Thus, similarly to the IBDV virion, only VP2 forms the icosahedral layer of the VLP. The other components of both VLP and IBDV particles that play a crucial role in the capsid assembly, VP1, VP3 and the peptides arising from the processing of pVP2, do not follow the icosahedral symmetry, allowing them to be involved in other processes such as RNA packaging.
Sendai virus trailer RNA simultaneously blocks two apoptosis-inducing mechanisms in a cell type-dependent manner
Authors: Wiegand Marian , Bossow Sascha , Neubert Wolfgang J.
Published: July 2005

Induction of apoptosis during Sendai virus (SeV) infection has previously been documented to be triggered by initiator caspases (for strain F) or by a contribution of the cellular protein TIAR (T-cell-activated intracellular antigen-related) (for strain Z). Here, evidence was provided that both TIAR and caspases are simultaneously involved in apoptosis induction as a result of infection with SeV strain F. SeV F infection induced death in all tested cell lines, which could only be partially prevented through the pan-caspase inhibitor z-VAD-fmk. However, infection of seven different cell lines with the SeV mutant Fctr48z overexpressing a TIAR-sequestering RNA from the modified leader resulted in a cell type-dependent reduced cytopathic effect (CPE); in an earlier study a similar mutant derived from SeV Z was shown to prevent the induction of any CPE. Finally, blocking of caspases through z-VAD-fmk combined with Fctr48z infection led to complete abrogation of CPE, clearly demonstrating the existence of two separate mechanisms inducing cell death during SeV F infections. Interestingly, a cell type-specific interference between these two mechanisms could be detected during infection with the mutant virus Fctr48z: RNA transcribed from the mutated leader was able to trans-dominantly inhibit caspase-mediated apoptosis. Thus, virus-expressed factors enabling a well-balanced ratio of suppression and triggering of apoptosis seem to be essential for optimal virus replication.
Measles virus superinfection immunity and receptor redistribution in persistently infected NT2 cells
Authors: Ludlow Martin , McQuaid Stephen , Cosby S. Louise , Cattaneo Roberto , Rima Bert K. , Duprex W. Paul
Published: July 2005

A recombinant measles virus (MV) expressing red fluorescent protein (MVDsRed1) was used to produce a persistently infected cell line (piNT2-MVDsRed1) from human neural precursor (NT2) cells. A similar cell line (piNT2-MVeGFP) was generated using a virus that expresses enhanced green fluorescent protein. Intracytoplasmic inclusions containing the viral nucleocapsid protein were evident in all cells and viral glycoproteins were present at the cell surface. Nevertheless, the cells did not release infectious virus nor did they fuse to generate syncytia. Uninfected NT2 cells express the MV receptor CD46 uniformly over their surface, whereas CD46 was present in cell surface aggregates in the piNT2 cells. There was no decrease in the overall amount of CD46 in piNT2 compared to NT2 cells. Cell-to-cell fusion was observed when piNT2 cells were overlaid onto confluent monolayers of MV receptor-positive cells, indicating that the viral glycoproteins were correctly folded and processed. Infectious virus was released from the underlying cells, indicating that persistence was not due to gross mutations in the virus genome. Persistently infected cells were superinfected with MV or canine distemper virus and cytopathic effects were not observed. However, mumps virus could readily infect the cells, indicating that superinfection immunity is not caused by general soluble antiviral factors. As MVeGFP and MVDsRed1 are antigenically indistinguishable but phenotypically distinct it was possible to use them to measure the degree of superinfection immunity in the absence of any cytopathic effect. Only small numbers of non-fusing green fluorescent piNT2-MVDsRed1 cells (1 : 300 000) were identified in which superinfecting MVeGFP entered, replicated and expressed its genes.
Comparison of two alignment techniques within a single complex data set: POY versus Clustal
Authors: Terry Matthew D. , Whiting Michael F.
Published: July 2005

Sensitivity analyses can be performed with respect to different methodologies, differential analytical parameters or models within a single methodology, or alignment parameters. The latter investigations are particularly relevant when divergence and/or the size of molecular data sets make alignment of sequences difficult. Sensitivity analyses are often performed for analyses incorporating Direct Optimization (via POY), either to select optimal alignment parameters or to investigate the stability of topology across parameter sets. Such investigations are rarely, if ever, performed for Clustal alignments as some manual adjustments are nearly always incorporated in the final alignment. Exploration of the performance of both POY and Clustal for a large insect data set incorporating three genes (18S, 28S, H3) and morphology reveals that the performance of POY, as measured by and ILD metric, is predictable across the landscape topology with minimal incongruence when all parameters are treated equally. In contrast, Clustal alignment followed by parsimony analysis yields a landscape with less overall variance, but less predictable behaviour across the parameter topology.

© The Willi Hennig Society 2005.
Minority rule supertrees? MRP, Compatibility, and Minimum Flip may display the least frequent groups
Authors: Goloboff Pablo A.
Published: July 2005

New examples are presented, showing that supertree methods such as matrix representation with parsimony, minimum flip trees, and compatibility analysis of the matrix representing the input trees, produce supertrees that cannot be interpreted as displaying the groups present in the majority of the input trees. These methods may produce a supertree displaying some groups present in the minority of the trees, and contradicted by the majority. Of the three methods, compatibility analysis is the least used, but it seems to be the one that differs the least from majority rule consensus. The three methods are similar in that they choose the supertree(s) that best fit the set of input trees (quantified as some measure of the fit to the matrix representation of the input trees); in the case of complete trees, it is argued that, for a supertree method to be equivalent to majority rule or frequency difference consensus, two necessary (but not sufficient) conditions must be met. First, the measure of fit between a supertree and an input tree must be symmetrical. Second, the fit for a character representing a group must be measured as absolute: either it fits or it does not fit. In the restricted case of complete and equally resolved input trees, compatibility analysis (unlike MRP and minimum flipping) fulfils these two conditions: it is symmetrical (i.e., as long as the trees have the same taxon sets and are equally resolved, the number of characters in the matrix representation of tree A that require homoplasy in tree B is always the same as the number of characters in the matrix representation of tree B that require homoplasy in tree A) and it measures fit as all‐or‐none. In the case of just two complete and equally resolved input trees, the two conditions (symmetry and absolute fit) are necessary and sufficient, which explains why the compatibility analysis of such trees behaves as majority consensus. With more than two such trees, these conditions are still necessary but no longer sufficient for the equivalence; in such cases, the compatibility supertree may differ significantly from the majority rule consensus, even when these conditions apply (as shown by example). MRP and minimum flipping are asymmetric and measure various degrees of fit for each character, which explains why they often behave very differently from majority rule procedures, and why they are very likely to have groups contradicted by each of the input trees, or groups supported by a minority of the input trees.

© The Willi Hennig Society 2005.
Phylogenetic analysis of Themira (Sepsidae: Diptera): sensitivity analysis, alignment, and indel treatment in a multigene study
Authors: Laamanen Torsten R. , Meier Rudolf , Miller Michael A. , Hille Axel , Wiegmann Brian M.
Published: July 2005

In this study we use sensitivity analysis sensuWheeler (1995) for a matrix entirely composed of DNA sequences. We propose that not only congruence but also phylogenetic structure, as measured by character resampling, should be used to choose among competing weighting regimes. An extensive analysis of a five‐gene data set for Themira (Sepsidae: Diptera) reveals that even with different ways of partitioning the data, measures of topological congruence, character incongruence, and phylogenetic structure favor similar weighting regimes involving the down‐weighting of transitions. We furthermore use sensitivity analysis for obtaining empirical evidence that allows us to select weights for third positions, deciding between treating indels as fifth character states or missing values, and choosing between manual and computational alignments. For our data, sensitivity analysis favors manual alignment over a Clustal‐generated numerical alignment, the treatment of indels as fifth character states over considering them missing values, and equal weights for all positions in protein‐encoding genes over the down‐weighting of third positions. Among the topological congruence measures compared, symmetric tree distance performed best. Partitioned Bremer Support analysis reveals that COI contributes the largest amount of support for our phylogenetic tree for Themira.

© The Willi Hennig Society 2005.
Water‐repellent soil and its relationship to granularity, surface roughness and hydrophobicity: a materials science view
Authors: McHale G. , Newton M. I. , Shirtcliffe N. J.
Published: July 2005

Considerable soil water repellency has been observed at a wide range of locations worldwide. The soil exhibiting water repellency is found within the upper part of the soil profile. The reduced rate of water infiltration into these soils leads to severe runoff erosion, and reduction of plant growth. Soil water repellency is promoted by drying of soil, and can be induced by fire or intense heating of soil containing hydrophobic organic matter. Recent studies outside soil science have shown how enhancement of the natural water repellency of materials, both porous and granular, by surface texture (i.e. surface roughness, pattern and morphology) into super‐hydrophobicity is possible. The similarities between these super‐hydrophobic materials and observed properties of water‐repellent soil are discussed from a non‐soil scientist, materials‐based perspective. A simple model is developed for a hydrophobic granular surface and it is shown that this can provide a mechanism for enhancement of soil water repellency through the relative size and spacing of grains and pores. The model provides a possible explanation for why soil water repellency should be more prevalent under dry conditions than wet. Consequences for water runoff, raindrop splash and soil erosion are discussed.
Redox reactions and phosphorus release in re‐flooded soils of an altered wetland
Authors: Shenker M. , Seitelbach S. , Brand S. , Haim A. , Litaor M. I.
Published: July 2005

Phosphorus loss from land can be a major factor affecting surface water quality. We studied P‐release mechanisms in wetland soils that had been drained and cultivated for four decades and then re‐flooded. We measured redox, pH and solution composition in two sites in the field and in four peat and calcareous soils incubated in biogeochemical microcosms. The redox and pH measurements during the 120 days of incubation and the resulting soil solution composition indicated that the main process leading to P release is reductive dissolution of ferric hydroxides on which P was adsorbed and in which P was occluded. The molar Fe:P ratio increased with period of reduction from below 1 in the first week of re‐flooding to 15–60 after 120 days. This suggests an increased P‐retention capacity upon reoxidation of the soil solution, whether within the soil profile or in the drainage canals. Prolonged flooding of the calcite‐poor, gypsum‐rich peat soils increased the oversaturation of soil solutions with respect to hydroxyapatite and occasionally β‐Ca3(PO4)2(c), indicating that in spite of the large Ca concentration, the rate of Ca‐P precipitation was insufficient to maintain the saturation status of the Ca‐P system. In the calcareous soils the Ca‐P system effectively controlled the P activity in soil solution throughout the incubation period. In both cases the precipitation of Ca‐P minerals could be an important P‐retention mechanism.
Virus and microbial loop dynamics over an annual cycle in three contrasting Antarctic lakes
Authors: MADAN NANETTE J. , MARSHALL WILLIAM A. , LAYBOURN‐PARRY JOHANNA
Published: July 2005

1. Viral and microbial loop dynamics were investigated over an annual cycle in three contrasting saline Antarctic lakes – Highway Lake (salinity 4‰), Pendant Lake (salinity 19‰) and Ace Lake, a meromictic system (with a mixolimnion salinity of 18‰) in order to assess the importance of viruses in extreme, microbially dominated systems.

2. Virus like particles (VLP) showed no clear seasonal pattern, with high concentrations occurring in both winter and summer (range 0.89 × 107 ± 0.038 to 12.017 × 107 ± 1.28 mL−1). VLP abundances reflected lake productivity based on chlorophyll a concentrations. Bacterial abundances and biomass did not correlate with VLP numbers except in Pendant Lake, the most productive of the three lakes studied.

3. Pendant Lake supported the highest bacterial biomass (range Highway: 18.44 ± 1.35 to 59.43 ± 2.80 ng C mL−1; Ace: 14.42 ± 2.69 to 68.39 ± 2.95 ng C mL−1; Pendant: 31.36 ± 3.94 to 115.95 ± 4.49 ng C mL−1) so that virus to bacteria ratios (VBR) (range 30.48 ± 7.96 to 96.67 ± 8.21) were higher in Ace Lake (range 30.58 ± 3.98 to 80.037 ± 1.60) and Highway Lake (range 18.63 ± 3.12 to 126.74 ± 6.50).

4. Negative correlations occurred between VLP and cryptophytes (dominant phototrophic nanoflagellates), suggesting that they were not hosts to lytic viruses. Among the other protists only the heterotrophic nanoflagellates of Highway Lake (dominated by the marine choanoflagellate Diaphanoeca grandis) showed a positive correlation with VLP.

5. The VLP was negatively correlated with photosynthetically active radiation (PAR) and temperature, both of which increased with ice thinning and breakout, increasing viral decay. In winter VLP probably persisted in cold, dark water.

6. High VLP concentrations and high VBR (values at the upper end of those reported for marine and lacustrine systems) indicated that viruses, most of which were probably bacteriophage, are a major element within the microbial communities in extreme, saline lakes.
Is there competition among ciliates and nematodes?
Authors: BERGTOLD MATTHIAS , GÜNTER VIKTOR , TRAUNSPURGER WALTER
Published: July 2005

1. Biotic interaction between the ciliate Cyclidium glaucoma and the nematode Caenorhabditis elegans was investigated by manipulating the densities of the organisms in microcosms with and without sediment.

2. After 11 days the abundance of ciliates, nematodes and bacteria as well as extracellular enzyme activity were determined. Ciliates had a negative effect on nematode abundance in microcosms without sediment and in microcosms with sandy sediment, whereas in muddy sediment the effect was less distinctive. An effect of nematodes on ciliates was not observed.

3. The common resource bacteria were not affected negatively by the activity of the grazers. Overall grazer biomass increased with the addition of sediment to the microcosms, suggesting a rise of the carrying capacity in the experimental system. Especially in muddy sediment the abundance of bacteria and extracellular enzyme activity was higher compared to the microcosms without sediment.

4. The results of the experiment suggest a strong interspecific competition between nematodes and ciliates, where nematodes are, at least temporary, strongly affected.
Combining a regional climate model with a phytoplankton community model to predict future changes in phytoplankton in lakes
Authors: ALEX ELLIOTT J. , THACKERAY STEPHEN J. , HUNTINGFORD CHRIS , JONES RICHARD G.
Published: July 2005

1. Linking a regional climate model (RCM) configured for contemporary atmospheric greenhouse gas concentrations, with a phytoplankton community model (PROTECH) produced realistic simulations of 20 years of recent phytoplankton data from Bassenthwaite Lake, in the North‐West of England.

2. Meteorological drivers were derived from the RCM to represent a future climate scenario involving a 1% per annum compound increase in atmospheric CO2 concentrations until 2100. Using these drivers, PROTECH was run for another 20 year period representing the last two decades of the 21st century.

3. Comparison of these present and future simulations revealed likely impacts on the current seasonal phytoplankton development. Under future climate conditions, the simulated spring bloom showed an increase in cyanobacteria dominance caused by greater success of Planktothrix. Also, the summer cyanobacteria bloom declined earlier because of nutrient limitation caused by the increased spring growth. Overall productivity in the lake did not change.

4. Analysis showed that these predicted changes were driven by changes in water temperature, which were in turn triggered by the higher air temperatures predicted by the RCM.
A demographic model explains life‐history variation in Arabis fecunda
Authors: LESICA P. , YOUNG T. P.
Published: July 2005

The distinction between semelparity and iteroparity is one of the most fundamental in life‐history biology. Despite an abundance of theory proposed to explain the evolution of this dichotomy, few quantitative empirical tests exist.

We report here on life‐history variation in the perennial herb Arabis fecunda (Brassicaceae), in which differences in the frequency of iteroparity and terminal flowering (facultative semelparity) are expressed among populations. These differences are consistent over time, and a common garden experiment suggested that they may be at least partly genetically based.

An analysis of demographic data over a 5‐year period from three populations indicated that a simple demographic model of life‐history evolution is consistent with life‐history variation in this species. Individuals in populations with greater mean adult survival were more likely to express iteroparity than individuals in populations with lower adult survival.
How are animals with ornaments predicted to compensate for a bad start in life? A dynamic optimization model approach
Authors: LINDSTRÖM J. , METCALFE N. B. , ROYLE N. J.
Published: July 2005

Animals may compensate for a poor start in life by accelerated (‘catch up’) growth if conditions subsequently improve. Although this incurs costs, the occurrence of catch up growth across taxa suggests there are also considerable benefits to it.

A state‐dependent, dynamic optimization model was constructed to explore how and under what circumstances individuals are predicted to vary their compensatory resource allocation to somavssexual ornaments.

In the model, individuals of differing initial state either experienced a constant environment, or one in which initially poor resource availability subsequently improved. Individuals could allocate resources, at each time step, to body growth, somatic maintenance or a sexual ornament.

The results showed that resource allocation strategies are sensitive to the fitness return functions used. Consequently, there is a wide range of potential optimal adult phenotypes.

Four general patterns emerged. (i) Making specific predictions about compensatory resource allocation is difficult owing to the general lack of information about the shape of the fitness return functions. (ii) Complete compensation in expected fitness (such that a poor start does not reduce future fitness) is likely to occur rarely. (iii) If a sexual ornament is required for mating success, compensating individuals are likely to be smaller in body size than those experiencing a constant environment. (iv) Poor initial resource availability in life tends to delay sexual maturation.
Cichlid jaw mechanics: linking morphology to feeding specialization
Authors: HULSEY C. D. , GARCÍA DE LEÓN F. J.
Published: July 2005

The utility of the anterior jaw four‐bar linkage model and the trophic consequences of jaw protrusion were investigated in Heroine cichlids by examining the evolutionary relationships among maxillary kinematic transmission (KT), maximum jaw protrusion and dietary specialization on evasive prey.

In 31 species of Heroine cichlids, a four‐bar linkage model was used to generate kinematic predictions of maxillary KT, the angular amount of maxilla rotation per unit lower jaw rotation, expected during mouth opening. Maxillary KT averaged 0·79 and ranged from 0·58 in Herichthys tamasopoensis to 1·06 in Petenia splendida.

Because the maxilla pushes the toothed premaxilla out during jaw protrusion, we predicted higher maxillary KT should characterize species with greater maximum jaw protrusion. Maximum jaw protrusion ranged from 1·5 to 14·2% of cichlid standard length and was highly correlated with greater maxillary KT.

The proportion of fish and crustaceans in the diet of these cichlids was correlated with maximum protrusion, suggesting jaw protrusion may aid in the capture of evasive prey.

Phylogenetic independent contrasts indicate changes in anterior jaw mechanics may be necessary for diversification of cichlid jaw protrusion abilities, and the labile evolution of jaw protrusion in Heroine cichlids likely facilitated the repeated specialization on evasive prey during their diversification.
Estimating adhesive seed‐dispersal distances: field experiments and correlated random walks
Authors: MOUISSIE A. M. , LENGKEEK W. , VAN DIGGELEN R.
Published: July 2005

In this study we aimed to estimate distance distributions of adhesively dispersed seeds and the factors that determine them.

Seed attachment and detachment were studied using field experiments with a real sheep, a sheep dummy and a cattle dummy. Seed‐retention data were used in correlated random walk models to simulate adhesive seed dispersal.

Seed attachment to the sheep dummy was larger in quantity and in number of species, and stronger in relation to seed density in the vegetation, than was seed attachment to the cattle dummy. Species found on the real sheep were also found on the sheep dummy.

Detachment from sheep wool differed little between smooth, bristly, small or large seeds, but smooth seeds detached from cattle fur within a few metres. Seeds applied within reach of vegetation detached sooner than seeds applied higher on the dummy.

The simulations showed that sheep are long‐distance seed‐dispersal vectors for seeds of any morphology (99 percentile distance, 2·9 km). The virtual cattle and Fallow Deer dispersed bristly and hooked seeds over long distances (99 percentile distance, 435–840 m), but not smooth seeds. Wood Mouse simulations generated only short‐distance dispersal (99 percentile distance, 12 m).
Lactate and free glucose in supercooled hatchling Painted Turtles (Chrysemys picta) exposed to natural and semi‐natural thermal regimes
Authors: PACKARD M. J. , PACKARD G. C.
Published: July 2005

Hatchlings of the North American Painted Turtle, Chrysemys picta (Schneider 1783) typically spend their first winter of life inside a shallow, terrestrial hibernaculum (the natal nest) where they commonly are exposed for extended periods to ice and cold. Current evidence indicates that turtles withstand such exposure by resisting freezing and becoming supercooled.

Supercooled hatchlings held at constant temperatures in the laboratory experience circulatory impairment and stagnant hypoxia, and consequently rely on anaerobic metabolism to meet a portion of their energy needs. As a result, lactate accumulates in bodies of supercooled animals.

The first experiment in the current investigation demonstrated that unfrozen hatchlings exposed to subzero temperatures like those recorded in a natural hibernaculum contained elevated quantities of lactic acid (and free glucose). This finding validates the widespread reliance on laboratory studies to gain insights regarding the physiology of animals overwintering in the field.

In a second study, hatchling Painted Turtles held for 20 days at −6 °C contained nearly twice as much lactate as turtles sampled after 10 days at that temperature. Hatchlings held for 10 days at −6 °C and then for another 10 days at −3 °C also contained more lactate than turtles sampled after 10 days at −6 °C, but not as much as the hatchlings that spent 20 days at −6 °C. Thus, animals held for part of the time at the higher subzero temperature still relied on anaerobic metabolism, but not to the same extent as turtles held continuously at the lower temperature. In contrast, hatchlings held for 10 days at −6 °C and then for another 10 days at either 0 °C or +3 °C contained no more lactate than control animals that never were exposed to subzero temperatures. Hatchlings exposed for the second 10 days to either 0 °C or +3 °C apparently were able to catabolize or otherwise process all the lactate that was accumulated during the first 10 days of their treatment.

Free glucose in bodies of hatchlings was elevated in all animals exposed to subzero temperatures, even when the initial exposure was followed by 10 days at temperatures as high as +3 °C. This finding has important implications with regard to the substrate that is used to support intermediary metabolism in supercooled turtles as well as to the metabolic pathways that are used to remove accumulated lactate once body temperature of the turtles rises at least to 0 °C.