bluuebunny/crossref_metadata_2025 huggingface dataset:
Xylem of early angiosperms: Nuphar (Nymphaeaceae) has novel tracheid microstructure1
Authors: Carlquist Sherwin , Schneider Edward L. , Hellquist C. Barre
Published: December 2008

SEM studies of xylem of stems of Nuphar reveal a novel feature, not previously reported for any angiosperm. Pit membranes of tracheid end walls are composed of coarse fibrils, densest on the distal (outside surface, facing the pit of an adjacent cell) surface of the pit membrane of a tracheid, thinner, and disposed at various levels on the lumen side of a pit membrane. The fibrils tend to be randomly oriented on the distal face of the pit membrane; the innermost fibrils facing the lumen take the form of longitudinally oriented strands. Where most abundantly present, the fibrils tend to be disposed in a spongiform, three‐dimensional pattern. Pores that interconnect tracheids are present within the fibrillar meshwork. Pit membranes on lateral walls of stem tracheids bear variously diminished versions of this pattern. Pits of root tracheids are unlike those of stems in that the lumen side of pit membranes bears a reticulum revealed on the outer surface of the tracheid after most of the thickness of a pit membrane is shaved away by the sectioning process. No fibrillar texturing is visible on the root tracheid pits when they are viewed from the inside of a tracheid. Tracheid end walls of roots do contain pores of various sizes in pit membranes. These root and stem patterns were seen in six species representing the two sections of Nuphar, plus one intersectional hybrid, as well as in one collection of Nymphaea, included for purposes of comparison. Differences between root and stem tracheids with respect to microstructure are consistent in all species studied. Microstructural patterns reported here for stem tracheid pits of Nymphaeaceae are not like those of Chloranthaceae, Illiciaceae, or other basal angiosperms. They are not referable to any of the patterns reported for early vascular plants. The adaptational nature of the pit membrane structure in these tracheids is not apparent; microstructure of pit membranes in basal angiosperms is more diverse than thought prior to study with SEM.
Expression and hypoxic up‐regulation of neuroglobin in human glioblastoma cells
Authors: Emara Marwan , Salloum Nicole , Allalunis-Turner Joan
Published: December 2008

Neuroglobin is a recently identified globin molecule that is expressed predominantly in the vertebrate brain. Neuroglobin expression increases in oxygen‐deprived neurons, suggesting it protects neurons from ischemic cell death. We report that neuroglobin transcript and protein are expressed in human glioblastoma cells, and that this expression increases in hypoxia in vitro. We also show that neuroglobin is up‐regulated in hypoxic microregions of glioblastoma tumor xenografts. Our finding of hypoxic up‐regulation of neuroglobin in human glioblast oma cells may provide insight into how tumor cells adapt to and survive in hypoxic microenvironments.
Partielle epiphyseale Brückenbildung mit zunehmendem Genu varum bei kortikalem Enchondrom – ein Fallbericht
Authors: Niethard M. , Rogalski M. , Deja M. , Zacher J.
Published: December 2008

Einleitung: Trauma oder Infektionen können die Epiphysenfuge des Kniegelenks zerstören und zu einer partiellen epiphysären Brückenbildung führen. Dies führt zu einer Längendifferenz und Achsabweichung. Es gibt nur wenig Informationen über tumorähnliche Läsionen als auslösender Faktor für diese Veränderungen. Wir suchten einen Lösungsansatz, der das Wachstumspotenzial als Einflussfaktor mit einbezieht und ausnutzt, um der Patientin spätere aufwendige Korrekturen zu ersparen. Methodik: Wir berichten über ein 6-jähriges Mädchen mit progredienter Varusdeformität des linken Kniegelenks und Abnahme der Gehstrecke. Nativ-Röntgen und MRT-Diagnostik zeigten eine gutartige Läsion im Sinne eines Enchondroms des mediodistalen Femurs, wobei die mediale Epiphysenfuge betroffen war. Die frühzeitig auftretende und rasch
fortschreitende Achsdeformität war Anlass für folgende Operationen: 1. Resektion der gutartigen Läsion und arthroskopisch gestützte Resektion der epiphysealen Knochenbrücke mit Fettgewebs-Interponat. 2. Laterale Hemiepiphyseodese mittels Eight-plate. Histologisch zeigte sich ein kortikales Enchondrom als Ursache für die o.a. Wachstumsstörung. Während der Nachbeobachtung (vierteljährliche klinische und radiologische Untersuchung) stellten wir ein nahezu normales Wachstumsverhalten der mediodistalen Femurepiphyse mit konsekutiver Achskorrektur fest. Ergebnisse: 1 Jahr postoperativ erreichten wir durch operative Intervention (Resektion und temporäre laterale Hemiepiphyseodese) eine vollständige Achskorrektur in Bezug auf die Gegenseite. Die Eight-plate wurde bereits entfernt. Die Nachbeobachtung wird bis zum vollständigen Wachstumsabschluss fortgeführt. Schlussfolgerung: Eine
partielle epiphyseale Brückenbildung wird nur in seltenen Fällen durch gutartige Knochentumoren verursacht. Durch Resektion mit anschließendem Fettgewebs-Interponat und temporärer Hemiepiphyseodese kann eine Achskorrektur während des Wachstums erzielt werden. Das Fortschreiten einer Deformität mit später resultierenden ausgedehnten chirurgischen Verfahren konnte vermieden werden.
Cytokinins are central regulators of cambial activity
Authors: Matsumoto-Kitano Miho , Kusumoto Takami , Tarkowski Petr , Kinoshita-Tsujimura Kaori , Václavíková Kateřina , Miyawaki Kaori , Kakimoto Tatsuo
Published: December 2008

The roots and stems of dicotyledonous plants thicken by the cell proliferation in the cambium. Cambial proliferation changes in response to environmental factors; however, the molecular mechanisms that regulate cambial activity are largely unknown. The quadruple
Arabidopsis thaliana
mutant
atipt1;3;5;7
, in which 4 genes encoding cytokinin biosynthetic isopentenyltransferases are disrupted by T-DNA insertion, was unable to form cambium and showed reduced thickening of the root and stem. The
atipt3
single mutant, which has moderately decreased levels of cytokinins, exhibited decreased root thickening without any other recognizable morphological changes. Addition of exogenously supplied cytokinins to
atipt1;3;5;7
reactivated the cambium in a dose-dependent manner. When an
atipt1;3;5;7
shoot scion was grafted onto WT root stock, both the root and shoot grew normally and
trans
-zeatin-type (
t
Z-type) cytokinins in the shoot were restored to WT levels, but isopentenyladenine-type cytokinins in the shoot remained unchanged. Conversely, when a WT shoot was grafted onto an
atipt1;3;5;7
root, both the root and shoot grew normally and isopentenyladenine-type cytokinins in the root were restored to WT levels, but
t
Z-type cytokinins were only partially restored. Collectively, it can be concluded that cytokinins are important regulators of cambium development and that production of cytokinins in either the root or shoot is sufficient for normal development of both the root and shoot.
Memory T-lymphocyte survival does not require T-cell receptor expression
Authors: Leignadier Julie , Hardy Marie-Pierre , Cloutier Marilyne , Rooney Julie , Labrecque Nathalie
Published: December 2008

The factors controlling memory T (Tm)-cell longevity are still poorly defined, and their identification is pivotal to the design of a vaccine conferring long-term protection against infection. Tm cells have the ability to survive in the absence of the T-cell receptor (TCR)–MHC interaction. This does not exclude a possible role for TCR-intrinsic ligand-independent constitutive signaling in Tm-cell homeostasis. Using a unique TCR tetracycline-inducible expression system, we show that the ablation of TCR expression, which abrogates any possible signaling via the TCR, did not influence the survival and self-renewal of antigen-specific CD8+Tm cells even when they have to compete with endogenous T cells for survival factors. Moreover, CD8+Tm-cell functionality was not altered even on prolonged maintenance in the absence of TCR-MHC interactions. Furthermore, our results show that a subset of CD4+Tm cells can survive in the absence of TCR expression in nonlymphopenic hosts.
Drosophila
D1 dopamine receptor mediates caffeine-induced arousal
Authors: Andretic Rozi , Kim Young-Cho , Jones Frederick S. , Han Kyung-An , Greenspan Ralph J.
Published: December 2008

The arousing and motor-activating effects of psychostimulants are mediated by multiple systems. In
Drosophila
, dopaminergic transmission is involved in mediating the arousing effects of methamphetamine, although the neuronal mechanisms of caffeine (CAFF)-induced wakefulness remain unexplored. Here, we show that in
Drosophila
, as in mammals, the wake-promoting effect of CAFF involves both the adenosinergic and dopaminergic systems. By measuring behavioral responses in mutant and transgenic flies exposed to different drug-feeding regimens, we show that CAFF-induced wakefulness requires the
Drosophila
D1 dopamine receptor (
dDA1
) in the mushroom bodies. In WT flies, CAFF exposure leads to downregulation of
dDA1
expression, whereas the transgenic overexpression of
dDA1
leads to CAFF resistance. The wake-promoting effects of methamphetamine require a functional dopamine transporter as well as the dDA1, and they engage brain areas in addition to the mushroom bodies.
Development of tough, low-density titanium-based bulk metallic glass matrix composites with tensile ductility
Authors: Hofmann Douglas C. , Suh Jin-Yoo , Wiest Aaron , Lind Mary-Laura , Demetriou Marios D. , Johnson William L.
Published: December 2008

The mechanical properties of bulk metallic glasses (BMGs) and their composites have been under intense investigation for many years, owing to their unique combination of high strength and elastic limit. However, because of their highly localized deformation mechanism, BMGs are typically considered to be brittle materials and are not suitable for structural applications. Recently, highly-toughened BMG composites have been created in a Zr–Ti-based system with mechanical properties comparable with high-performance crystalline alloys. In this work, we present a series of low-density, Ti-based BMG composites with combinations of high strength, tensile ductility, and excellent fracture toughness.
Screening plasmonic materials using pyramidal gratings
Authors: Gao Hanwei , Henzie Joel , Lee Min Hyung , Odom Teri W.
Published: December 2008

Surface plasmon polaritons (SPPs) are responsible for exotic optical phenomena, including negative refraction, surface enhanced Raman scattering, and nanoscale focusing of light. Although many materials support SPPs, the choice of metal for most applications has been based on traditional plasmonic materials (Ag, Au) because there have been no side-by-side comparisons of the different materials on well-defined, nanostructured surfaces. Here, we report a platform that not only enabled rapid screening of a wide range of metals under different excitation conditions and dielectric environments, but also identified new and unexpected materials for biosensing applications. Nanopyramidal gratings were used to generate plasmon dispersion diagrams for Al, Ag, Au, Cu, and Pd. Surprisingly, the SPP coupling efficiencies of Cu and Al exceeded widely used plasmonic materials under certain excitation conditions. Furthermore, grazing angle excitation led to the highest refractive index sensitivities (figure of merit >85) reported at optical frequencies because of extremely narrow SPP resonances (full-width-at-half-minimum <6 nm or 7 meV). Finally, our screening process revealed that Ag, with the highest sensitivity, was not necessarily the preferred material for detecting molecules. We discovered that Au and even Pd, a weak plasmonic material, showed comparable index shifts on formation of a protein monolayer.
Aglycosylated immunoglobulin G1variants productively engage activating Fc receptors
Authors: Sazinsky Stephen L. , Ott René G. , Silver Nathaniel W. , Tidor Bruce , Ravetch Jeffrey V. , Wittrup K. Dane
Published: December 2008

Immunoglobulin G plays a vital role in adaptive immunity and antibody-based therapy through engagement of its Fc region by the Fcγ receptors (FcγRs) on immune cells. In addition to specific protein-protein contacts, N-linked glycosylation of the IgG Fc has been thought to be essential for the recognition of Fc by FcγR. This requirement for the N-linked glycan has limited biomanufacture of therapeutic antibodies by restricting it to mammalian expression systems. We report here aglycosylated Fc domain variants that maintain engagement to FcγRs, both in vitro and in vivo, demonstrating that Fc glycosylation is not strictly required for the activation of immune cells by IgG. These variants provide insight into how the N-linked glycan is used biologically in the recognition of Fc by FcγRs, as well as represent a step toward the production in alternative expression systems of antibody-based therapeutics capable of eliciting immune effector functions.
CTLA-4 blockade enhances polyfunctional NY-ESO-1 specific T cell responses in metastatic melanoma patients with clinical benefit
Authors: Yuan Jianda , Gnjatic Sacha , Li Hao , Powel Sarah , Gallardo Humilidad F. , Ritter Erika , Ku Geoffrey Y. , Jungbluth Achim A. , Segal Neil H. , Rasalan Teresa S. , Manukian Gregor , Xu Yinyan , Roman Ruth-Ann , Terzulli Stephanie L. , Heywood Melanie , Pogoriler Evelina , Ritter Gerd , Old Lloyd J. , Allison James P. , Wolchok Jedd D.
Published: December 2008

Blockade of inhibitory signals mediated by cytotoxic T lymphocyte-associated antigen 4 (CTLA-4) has been shown to enhance T cell responses and induce durable clinical responses in patients with metastatic melanoma. The functional impact of anti-CTLA-4 therapy on human immune responses is still unclear. To explore this, we analyzed immune-related adverse events and immune responses in metastatic melanoma patients treated with ipilimumab, a fully human anti-CTLA-4 monoclonal antibody. Fifteen patients were selected on the basis of availability of suitable specimens for immunologic monitoring, and eight of these showed evidence of clinical benefit. Five of the eight patients with evidence of clinical benefit had NY-ESO-1 antibody, whereas none of seven clinical non-responders was seropositive for NY-ESO-1. All five NY-ESO-1 seropositive patients had clearly detectable CD4+and CD8+T cells against NY-ESO-1 following treatment with ipilimumab. One NY-ESO-1 seronegative clinical responder also had a NY-ESO-1 CD4+and CD8+T cell response, possibly related to prior vaccination with NY-ESO-1. Among five clinical non-responders analyzed, only one had a NY-ESO-1 CD4+T cell response and this patient did not have detectable anti-NY-ESO-1 antibody. Overall, NY-ESO-1-specific T cell responses increased in frequency and functionality during anti-CTLA-4 treatment, revealing a polyfunctional response pattern of IFN-γ, MIP-1β and TNF-α. We therefore suggest that CTLA-4 blockade enhanced NY-ESO-1 antigen-specific B cell and T cell immune responses in patients with durable objective clinical responses and stable disease. These data provide an immunologic rationale for the efficacy of anti-CTLA-4 therapy and call for immunotherapeutic designs that combine NY-ESO-1 vaccination with CTLA-4 blockade.
Genetic analysis of crawling and swimming locomotory patterns in
C. elegans
Authors: Pierce-Shimomura Jonathan T. , Chen Beth L. , Mun James J. , Ho Raymond , Sarkis Raman , McIntire Steven L.
Published: December 2008

Alternative patterns of neural activity drive different rhythmic locomotory patterns in both invertebrates and mammals. The neuro-molecular mechanisms responsible for the expression of rhythmic behavioral patterns are poorly understood. Here we show that
Caenorhabditis elegans
switches between distinct forms of locomotion, or crawling versus swimming, when transitioning between solid and liquid environments. These forms of locomotion are distinguished by distinct kinematics and different underlying patterns of neuromuscular activity, as determined by
in vivo
calcium imaging. The expression of swimming versus crawling rhythms is regulated by sensory input. In a screen for mutants that are defective in transitioning between crawl and swim behavior, we identified
unc-79
and
unc-80
, two mutants known to be defective in NCA ion channel stabilization. Genetic and behavioral analyses suggest that the NCA channels enable the transition to rapid rhythmic behaviors in
C. elegans. unc-79
,
unc-80
, and the NCA channels represent a conserved set of genes critical for behavioral pattern generation.
Dynamic cross-frequency couplings of local field potential oscillations in rat striatum and hippocampus during performance of a T-maze task
Authors: Tort Adriano B. L. , Kramer Mark A. , Thorn Catherine , Gibson Daniel J. , Kubota Yasuo , Graybiel Ann M. , Kopell Nancy J.
Published: December 2008

Oscillatory rhythms in different frequency ranges mark different behavioral states and are thought to provide distinct temporal windows that coherently bind cooperating neuronal assemblies. However, the rhythms in different bands can also interact with each other, suggesting the possibility of higher-order representations of brain states by such rhythmic activity. To explore this possibility, we analyzed local field potential oscillations recorded simultaneously from the striatum and the hippocampus. As rats performed a task requiring active navigation and decision making, the amplitudes of multiple high-frequency oscillations were dynamically modulated in task-dependent patterns by the phase of cooccurring theta-band oscillations both within and across these structures, particularly during decision-making behavioral epochs. Moreover, the modulation patterns uncovered distinctions among both high- and low-frequency subbands. Cross-frequency coupling of multiple neuronal rhythms could be a general mechanism used by the brain to perform network-level dynamical computations underlying voluntary behavior.
Early visual brain areas reflect the percept of an ambiguous scene
Authors: Parkkonen Lauri , Andersson Jesper , Hämäläinen Matti , Hari Riitta
Published: December 2008

When a visual scene allows multiple interpretations, the percepts may spontaneously alternate despite the stable retinal image and the invariant sensory input transmitted to the brain. To study the brain basis of such multi-stable percepts, we superimposed rapidly changing dynamic noise as regional tags to the Rubin vase-face figure and followed the corresponding tag-related cortical signals with magnetoencephalography. The activity already in the earliest visual cortical areas, the primary visual cortex included, varied with the perceptual states reported by the observers. These percept-related modulations most likely reflect top-down influences that accentuate the neural representation of the perceived object in the early visual cortex and maintain the segregation of objects from the background.
Dispersions and adjusted frequencies in corpora
Authors: Gries Stefan Th.
Published: December 2008

The most frequent statistics in corpus linguistics are frequencies of occurrence and frequencies of co-occurrence of two or more linguistic variables. However, such frequencies in isolation may sometimes be misleading since they do not take into consideration the degree of dispersion of the relevant linguistic variable. Many dispersion measures and adjusted frequency measures have been suggested but are neither widely known nor applied. Another unfortunate aspect of such measures is that many also come with a variety of problems. I pursue three objectives with this article. First, I want to raise awareness of this issue and make the available measures more widely known, so I present an overview of many measures of dispersion and adjusted frequencies. Second, I propose a conceptually simple alternative measure, DP, explain and exemplify it, and compare it to previously discussed measures. Third and most importantly, I urge corpus linguists to explore the notion of dispersion in more detail and outline a few proposals which steps to take next.
Evolution of signalling systems with multiple senders and receivers
Authors: Skyrms Brian
Published: December 2008

Sender–receiver games are simple, tractable models of information transmission. They provide a basic setting for the study the evolution of meaning. It is possible to investigate not only the equilibrium structure of these games but also the dynamics of evolution and learning—with sometimes surprising results. Generalizations of the usual binary game to interactions with multiple senders, multiple receivers or both provide the elements of signalling networks. These can be seen as the loci of information processing, group decisions, and teamwork.
Behavioural social choice: a status report
Authors: Regenwetter Michel , Grofman Bernard , Popova Anna , Messner William , Davis-Stober Clintin P , Cavagnaro Daniel R
Published: December 2008

Behavioural social choice
has been proposed as a social choice parallel to seminal developments in other decision sciences, such as
behavioural decision theory
,
behavioural economics
,
behavioural finance
and
behavioural game theory
. Behavioural paradigms compare how rational actors
should
make certain types of decisions with how real decision makers behave
empirically
. We highlight that important theoretical predictions in social choice theory change dramatically under even minute violations of standard assumptions. Empirical data violate those critical assumptions. We argue that the nature of preference distributions in electorates is ultimately an empirical question, which social choice theory has often neglected. We also emphasize important insights for research on decision making by individuals. When researchers aggregate individual choice behaviour in laboratory experiments to report summary statistics, they are implicitly applying social choice rules. Thus, they should be aware of the potential for aggregation paradoxes. We hypothesize that such problems may substantially mar the conclusions of a number of (sometimes seminal) papers in behavioural decision research.
The Arabidopsis Abscisic Acid Catabolic GeneCYP707A2Plays a Key Role in Nitrate Control of Seed Dormancy
Authors: Matakiadis Theodoros , Alboresi Alessandro , Jikumaru Yusuke , Tatematsu Kiyoshi , Pichon Olivier , Renou Jean-Pierre , Kamiya Yuji , Nambara Eiji , Truong Hoai-Nam
Published: December 2008

Nitrate releases seed dormancy in Arabidopsis (Arabidopsis thaliana) Columbia accession seeds in part by reducing abscisic acid (ABA) levels. Nitrate led to lower levels of ABA in imbibed seeds when included in the germination medium (exogenous nitrate). Nitrate also reduced ABA levels in dry seeds when provided to the mother plant during seed development (endogenous nitrate). Transcript profiling of imbibed seeds treated with or without nitrate revealed that exogenous nitrate led to a higher expression of nitrate-responsive genes, whereas endogenous nitrate led to a profile similar to that of stratified or after-ripened seeds. Profiling experiments indicated that the expression of the ABA catabolic gene CYP707A2 was regulated by exogenous nitrate. The cyp707a2-1 mutant failed to reduce seed ABA levels in response to both endogenous and exogenous nitrate. In contrast, both endogenous and exogenous nitrate reduced ABA levels of the wild-type and cyp707a1-1 mutant seeds. The CYP707A2 mRNA levels in developing siliques were positively correlated with different nitrate doses applied to the mother plants. This was consistent with a role of the CYP707A2 gene in controlling seed ABA levels in response to endogenous nitrate. The cyp707a2-1 mutant was less sensitive to exogenous nitrate for breaking seed dormancy. Altogether, our data underline the central role of the CYP707A2 gene in the nitrate-mediated control of ABA levels during seed development and germination.
Mapping Metabolic and Transcript Temporal Switches during Germination in Rice Highlights Specific Transcription Factors and the Role of RNA Instability in the Germination Process
Authors: Howell Katharine A. , Narsai Reena , Carroll Adam , Ivanova Aneta , Lohse Marc , Usadel Björn , Millar A. Harvey , Whelan James
Published: December 2008

Transcriptome and metabolite profiling of rice (Oryza sativa) embryo tissue during a detailed time course formed a foundation for examining transcriptional and posttranscriptional processes during germination. One hour after imbibition (HAI), independent of changes in transcript levels, rapid changes in metabolism occurred, including increases in hexose phosphates, tricarboxylic acid cycle intermediates, and γ-aminobutyric acid. Later changes in the metabolome, including those involved in carbohydrate, amino acid, and cell wall metabolism, appeared to be driven by increases in transcript levels, given that the large group (over 6,000 transcripts) observed to increase from 12 HAI were enriched in metabolic functional categories. Analysis of transcripts encoding proteins located in the organelles of primary metabolism revealed that for the mitochondrial gene set, a greater proportion of transcripts peaked early, at 1 or 3 HAI, compared with the plastid set, and notably, many of these transcripts encoded proteins involved in transport functions. One group of over 2,000 transcripts displayed a unique expression pattern beginning with low levels in dry seeds, followed by a peak in expression levels at 1 or 3 HAI, before markedly declining at later time points. This group was enriched in transcription factors and signal transduction components. A subset of these transiently expressed transcription factors were further interrogated across publicly available rice array data, indicating that some were only expressed during the germination process. Analysis of the 1-kb upstream regions of transcripts displaying similar changes in abundance identified a variety of common sequence motifs, potential binding sites for transcription factors. Additionally, newly synthesized transcripts peaking at 3 HAI displayed a significant enrichment of sequence elements in the 3′ untranslated region that have been previously associated with RNA instability. Overall, these analyses reveal that during rice germination, an immediate change in some metabolite levels is followed by a two-step, large-scale rearrangement of the transcriptome that is mediated by RNA synthesis and degradation and is accompanied by later changes in metabolite levels.
The Acid Growth Theory of auxin-induced cell elongation is alive and well.
Authors: Rayle D L , Cleland R E
Published: December 2008

Plant cells elongate irreversibly only when load-bearing bonds in the walls are cleaved. Auxin causes the elongation of stem and coleoptile cells by promoting wall loosening via cleavage of these bonds. This process may be coupled with the intercalation of new cell wall polymers. Because the primary site of auxin action appears to be the plasma membrane or some intracellular site, and wall loosening is extracellular, there must be communication between the protoplast and the wall. Some "wall-loosening factor" must be exported from auxin-impacted cells, which sets into motion the wall loosening events. About 20 years ago, it was suggested that the wall-loosening factor is hydrogen ions. This idea and subsequent supporting data gave rise to the Acid Growth Theory, which states that when exposed to auxin, susceptible cells excrete protons into the wall (apoplast) at an enhanced rate, resulting in a decrease in apoplastic pH. The lowered wall pH then activates wall-loosening processes, the precise nature of which is unknown. Because exogenous acid causes a transient (1-4 h) increase in growth rate, auxin must also mediate events in addition to wall acidification for growth to continue for an extended period of time. These events may include osmoregulation, cell wall synthesis, and maintenance of the capacity of walls to undergo acid-induced wall loosening. At present, we do not know if these phenomena are tightly coupled to wall acidification or if they are the products of multiple independent signal transduction pathways.
Starch Granule Biosynthesis in Arabidopsis Is Abolished by Removal of All Debranching Enzymes but Restored by the Subsequent Removal of an Endoamylase
Authors: Streb Sebastian , Delatte Thierry , Umhang Martin , Eicke Simona , Schorderet Martine , Reinhardt Didier , Zeeman Samuel C.
Published: December 2008

Several studies have suggested that debranching enzymes (DBEs) are involved in the biosynthesis of amylopectin, the major constituent of starch granules. Our systematic analysis of all DBE mutants of Arabidopsis thaliana demonstrates that when any DBE activity remains, starch granules are still synthesized, albeit with altered amylopectin structure. Quadruple mutants lacking all four DBE proteins (Isoamylase1 [ISA1], ISA2, and ISA3, and Limit-Dextrinase) are devoid of starch granules and instead accumulate highly branched glucans, distinct from amylopectin and from previously described phytoglycogen. A fraction of these glucans are present as discrete, insoluble, nanometer-scale particles, but the structure and properties of this material are radically altered compared with wild-type amylopectin. Superficially, these data support the hypothesis that debranching is required for amylopectin synthesis. However, our analyses show that soluble glucans in the quadruple DBE mutant are degraded by α- and β-amylases during periods of net accumulation, giving rise to maltose and branched malto-oligosaccharides. The additional loss of the chloroplastic α-amylase AMY3 partially reverts the phenotype of the quadruple DBE mutant, restoring starch granule biosynthesis. We propose that DBEs function in normal amylopectin synthesis by promoting amylopectin crystallization but conclude that they are not mandatory for starch granule synthesis.
Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites
Authors: Sasaki Shin , Mello Cecilia C. , Shimada Atsuko , Nakatani Yoichiro , Hashimoto Shin-ichi , Ogawa Masako , Matsushima Kouji , Gu Sam Guoping , Kasahara Masahiro , Ahsan Budrul , Sasaki Atsushi , Saito Taro , Suzuki Yutaka , Sugano Sumio , Kohara Yuji , Takeda Hiroyuki , Fire Andrew , Morishita Shinichi
Published: December 2008

Might DNA sequence variation reflect germline genetic activity and underlying chromatin structure? We investigated this question using medaka (Japanese killifish,
Oryzias latipes
), by comparing the genomic sequences of two strains (Hd-rR and HNI) and by mapping ∼37.3 million nucleosome cores from Hd-rR blastulae and 11,654 representative transcription start sites from six embryonic stages. We observed a distinctive ∼200–base pair (bp) periodic pattern of genetic variation downstream of transcription start sites; the rate of insertions and deletions longer than 1 bp peaked at positions of approximately +200, +400, and +600 bp, whereas the point mutation rate showed corresponding valleys. This ∼200-bp periodicity was correlated with the chromatin structure, with nucleosome occupancy minimized at positions 0, +200, +400, and +600 bp. These data exemplify the potential for genetic activity (transcription) and chromatin structure to contribute to molding the DNA sequence on an evolutionary time scale.
The Sphingolipid Transporter Spns2 Functions in Migration of Zebrafish Myocardial Precursors
Authors: Kawahara Atsuo , Nishi Tsuyoshi , Hisano Yu , Fukui Hajime , Yamaguchi Akihito , Mochizuki Naoki
Published: December 2008

Sphingosine-1-phosphate (S1P) is a secreted lipid mediator that functions in vascular development; however, it remains unclear how S1P secretion is regulated during embryogenesis. We identified a zebrafish mutant,
ko157
, that displays cardia bifida (two hearts) resembling that in the
S1P receptor-2
mutant. A migration defect of myocardial precursors in the
ko157
mutant is due to a mutation in a multipass transmembrane protein, Spns2, and can be rescued by S1P injection. We show that the export of S1P from cells requires Spns2.
spns2
is expressed in the extraembryonic tissue yolk syncytial layer (YSL), and the introduction of
spns2
mRNA in the YSL restored the cardiac defect in the
ko157
mutant. Thus, Spns2 in the YSL functions as a S1P transporter in S1P secretion, thereby regulating myocardial precursor migration.
Modular Spectral Imaging System for Discrimination of Pigments in Cells and Microbial Communities
Authors: Polerecky Lubos , Bissett Andrew , Al-Najjar Mohammad , Faerber Paul , Osmers Harald , Suci Peter A. , Stoodley Paul , de Beer Dirk
Published: December 2008

Here we describe a spectral imaging system for minimally invasive identification, localization, and relative quantification of pigments in cells and microbial communities. The modularity of the system allows pigment detection on spatial scales ranging from the single-cell level to regions whose areas are several tens of square centimeters. For pigment identification in vivo absorption and/or autofluorescence spectra are used as the analytical signals. Along with the hardware, which is easy to transport and simple to assemble and allows rapid measurement, we describe newly developed software that allows highly sensitive and pigment-specific analyses of the hyperspectral data. We also propose and describe a number of applications of the system for microbial ecology, including identification of pigments in living cells and high-spatial-resolution imaging of pigments and the associated phototrophic groups in complex microbial communities, such as photosynthetic endolithic biofilms, microbial mats, and intertidal sediments. This system provides new possibilities for studying the role of spatial organization of microorganisms in the ecological functioning of complex benthic microbial communities or for noninvasively monitoring changes in the spatial organization and/or composition of a microbial community in response to changing environmental factors.
TatABC Overexpression Improves
Corynebacterium glutamicum
Tat-Dependent Protein Secretion
Authors: Kikuchi Yoshimi , Itaya Hiroshi , Date Masayo , Matsui Kazuhiko , Wu Long-Fei
Published: December 2008

The twin-arginine translocation (Tat) pathway in
Corynebacterium glutamicum
has been described previously. The minimal functional Tat system in
C. glutamicum
required TatA and TatC but did not require TatB, although this component was required for maximal efficiency of Tat-dependent secretion. We previously demonstrated that
Chryseobacterium proteolyticum
pro-protein glutaminase (pro-PG) and
Streptomyces mobaraensis
pro-transglutaminase (pro-TG) could be secreted via the Tat pathway in
C. glutamicum
. Here we report that the amounts of pro-PG secreted were more than threefold larger when TatC or TatAC was overexpressed, and there was a further threefold increase when TatABC was overexpressed. These results show that the amount of TatC protein is the first bottleneck and the amount of TatB protein is the second bottleneck in Tat-dependent protein secretion in
C. glutamicum
. In addition, the amount of pro-TG that accumulated via the Tat pathway when TatABC was overexpressed with the TorA signal peptide in
C. glutamicum
was larger than the amount that accumulated via the Sec pathway. We concluded that TatABC overexpression improves Tat-dependent pro-PG and pro-TG secretion in
C. glutamicum
.
Novel Evolutionary Engineering Approach for Accelerated Utilization of Glucose, Xylose, and Arabinose Mixtures by Engineered
Saccharomyces cerevisiae
Strains
Authors: Wisselink H. Wouter , Toirkens Maurice J. , Wu Qixiang , Pronk Jack T. , van Maris Antonius J. A.
Published: December 2008

Lignocellulosic feedstocks are thought to have great economic and environmental significance for future biotechnological production processes. For cost-effective and efficient industrial processes, complete and fast conversion of all sugars derived from these feedstocks is required. Hence, simultaneous or fast sequential fermentation of sugars would greatly contribute to the efficiency of production processes. One of the main challenges emerging from the use of lignocellulosics for the production of ethanol by the yeast
Saccharomyces cerevisiae
is efficient fermentation of
d
-xylose and
l
-arabinose, as these sugars cannot be used by natural
S. cerevisiae
strains. In this study, we describe the first engineered
S. cerevisiae
strain (strain IMS0003) capable of fermenting mixtures of glucose, xylose, and arabinose with a high ethanol yield (0.43 g g
−1
of total sugar) without formation of the side products xylitol and arabinitol. The kinetics of anaerobic fermentation of glucose-xylose-arabinose mixtures were greatly improved by using a novel evolutionary engineering strategy. This strategy included a regimen consisting of repeated batch cultivation with repeated cycles of consecutive growth in three media with different compositions (glucose, xylose, and arabinose; xylose and arabinose; and only arabinose) and allowed rapid selection of an evolved strain (IMS0010) exhibiting improved specific rates of consumption of xylose and arabinose. This evolution strategy resulted in a 40% reduction in the time required to completely ferment a mixture containing 30 g liter
−1
glucose, 15 g liter
−1
xylose, and 15 g liter
−1
arabinose.
Genetic Diversity and Host Range of Rhizobia Nodulating
Lotus tenuis
in Typical Soils of the Salado River Basin (Argentina)
Authors: Estrella María Julia , Muñoz Socorro , Soto María José , Ruiz Oscar , Sanjuán Juan
Published: December 2008

A total of 103 root nodule isolates were used to estimate the diversity of bacteria nodulating
Lotus tenuis
in typical soils of the Salado River Basin. A high level of genetic diversity was revealed by repetitive extragenic palindromic PCR, and 77 isolates with unique genomic fingerprints were further differentiated into two clusters, clusters A and B, after 16S rRNA restriction fragment length polymorphism analysis. Cluster A strains appeared to be related to the genus
Mesorhizobium
, whereas cluster B was related to the genus
Rhizobium
. 16S rRNA sequence and phylogenetic analysis further supported the distribution of most of the symbiotic isolates in either
Rhizobium
or
Mesorhizobium
: the only exception was isolate BA135, whose 16S rRNA gene was closely related to the 16S rRNA gene of the genus
Aminobacter.
Most
Mesorhizobium
-like isolates were closely related to
Mesorhizobium amorphae
,
Mesorhizobium mediterraneum
,
Mesorhizobium tianshanense
, or the broad-host-range strain NZP2037, but surprisingly few isolates grouped with
Mesorhizobium loti
type strain NZP2213.
Rhizobium
-like strains were related to
Rhizobium gallicum
,
Rhizobium etli
, or
Rhizobium tropici
, for which
Phaseolus vulgaris
is a common host. However, no
nodC
or
nifH
genes could be amplified from the
L. tenuis
isolates, suggesting that they have rather divergent symbiosis genes. In contrast,
nodC
genes from the
Mesorhizobium
and
Aminobacter
strains were closely related to
nodC
genes from narrow-host-range
M. loti
strains. Likewise,
nifH
gene sequences were very highly conserved among the Argentinian isolates and reference
Lotus
rhizobia. The high levels of conservation of the
nodC
and
nifH
genes suggest that there was a common origin of the symbiosis genes in narrow-host-range
Lotus
symbionts, supporting the hypothesis that both intrageneric horizontal gene transfer and intergeneric horizontal gene transfer are important mechanisms for the spread of symbiotic capacity in the Salado River Basin.
Complete Genome Sequence ofMacrococcus caseolyticusStrain JSCS5402, Reflecting the Ancestral Genome of the Human-Pathogenic Staphylococci
Authors: Baba Tadashi , Kuwahara-Arai Kyoko , Uchiyama Ikuo , Takeuchi Fumihiko , Ito Teruyo , Hiramatsu Keiichi
Published: December 2008

We isolated the methicillin-resistantMacrococcus caseolyticusstrain JCSC5402 from animal meat in a supermarket and determined its whole-genome nucleotide sequence. This is the first report on the genome analysis of a macrococcal species that is evolutionarily closely related to the human pathogensStaphylococcus aureusandBacillus anthracis. The essential biological pathways ofM. caseolyticusare similar to those of staphylococci. However, the species has a small chromosome (2.1 MB) and lacks many sugar and amino acid metabolism pathways and a plethora of virulence genes that are present inS. aureus. On the other hand,M. caseolyticuspossesses a series of oxidative phosphorylation machineries that are closely related to those in the familyBacillaceae. We also discovered a probable primordial form of aMacrococcusmethicillin resistance gene complex,mecIRAm, on one of the eight plasmids harbored by theM. caseolyticusstrain. This is the first finding of a plasmid-encoding methicillin resistance gene.Macrococcusis considered to reflect the genome of ancestral bacteria before the speciation of staphylococcal species and may be closely associated with the origin of the methicillin resistance gene complex of the notorious human pathogen methicillin-resistantS. aureus.
The YjbH Protein ofBacillus subtilisEnhances ClpXP-Catalyzed Proteolysis of Spx
Authors: Garg Saurabh K. , Kommineni Sushma , Henslee Luke , Zhang Ying , Zuber Peter
Published: December 2008

The global transcriptional regulator Spx ofBacillus subtilisis controlled at several levels of the gene expression process. It is maintained at low concentrations during unperturbed growth by the ATP-dependent protease ClpXP. Under disulfide stress, Spx concentration increases due in part to a reduction in ClpXP-catalyzed proteolysis. Recent studies of Larsson and coworkers (Mol. Microbiol. 66:669-684, 2007) implicated the product of theyjbHgene as being necessary for the proteolytic control of Spx. In the present study, yeast two-hybrid analysis and protein-protein cross-linking showed that Spx interacts with YjbH. YjbH protein was shown to enhance the proteolysis of Spx in reaction mixtures containing ClpXP protease but not ClpCP protease. An N-terminal truncated form of YjbH with a deletion of residues 1 to 24 (YjbHΔ1-24) showed no proteolysis enhancement activity. YjbH is specific for Spx as it did not accelerate proteolysis of the ClpXP substrate green fluorescent protein (GFP)-SsrA, a GFP derivative with a C-terminal SsrA tag that is recognized by ClpXP. Using inductively coupled plasma atomic emission spectroscopy and 4-(2-pyridylazo) resorcinol release experiments, YjbH was found to contain zinc atoms. Zinc analysis of YjbHΔ1-24revealed that the N-terminal histidine-rich region is indispensable for the coordination of at least one Zn atom. A Zn atom coordinated by the N-terminal region was rapidly released from the protein upon treatment with a strong oxidant. In conclusion, YjbH is proposed to be an adaptor for ClpXP-catalyzed Spx degradation, and a model of YjbH redox control involving Zn dissociation is presented.
The
Bacillus anthracis
Protein MprF Is Required for Synthesis of Lysylphosphatidylglycerols and for Resistance to Cationic Antimicrobial Peptides
Authors: Samant Shalaka , Hsu Fong-Fu , Neyfakh Alexander A. , Lee Hyunwoo
Published: December 2008

During inhalational anthrax,
Bacillus anthracis
survives and replicates in alveolar macrophages, followed by rapid invasion into the host's bloodstream, where it multiplies to cause heavy bacteremia.
B. anthracis
must therefore defend itself from host immune functions encountered during both the intracellular and the extracellular stages of anthrax infection. In both of these niches, cationic antimicrobial peptides are an essential component of the host's innate immune response that targets
B. anthracis
. However, the genetic determinants of
B. anthracis
contributing to resistance to these peptides are largely unknown. Here we generated Tn
917
transposon mutants in the ΔANR strain (pXO1
−
pXO2
−
) of
B. anthracis
and screened them for altered protamine susceptibility. A protamine-sensitive mutant identified carried the transposon inserted in the BA1486 gene encoding a putative membrane protein homologous to MprF known in several gram-positive pathogens. A mutant strain with the BAS1375 gene (the orthologue of BA1486) deleted in the Sterne 34F2 strain (pXO1
+
pXO2
−
) of
B. anthracis
exhibited hypersusceptibility not only to protamine but also to α-helical cathelicidin LL-37 and β-sheet defensin human neutrophil peptide 1 compared to the wild-type Sterne strain. Analysis of membrane lipids using isotopic labeling demonstrated that the BAS1375 deletion mutant is unable to synthesize lysinylated phosphatidylglycerols, and this defect is rescued by genetic complementation. Further, we determined the structures of these lysylphosphatidylglycerols by using various mass spectrometric analyses. These results demonstrate that in
B. anthracis
a functional MprF is required for the biosynthesis of lysylphosphatidylglycerols, which is critical for resistance to cationic antimicrobial peptides.
The Response Regulator RpaB Binds to the Upstream Element of Photosystem I Genes To Work for Positive Regulation under Low-Light Conditions in
Synechocystis
sp. Strain PCC 6803
Authors: Seino Yurie , Takahashi Tomoko , Hihara Yukako
Published: December 2008

The coordinated high-light response of genes encoding subunits of photosystem I (PSI) is achieved by the AT-rich region located just upstream of the core promoter in
Synechocystis
sp. strain PCC 6803. The upstream element enhances the basal promoter activity under low-light conditions, whereas this positive regulation is lost immediately after the shift to high-light conditions. In this study, we focused on a high-light regulatory 1 (HLR1) sequence included in the upstream element of every PSI gene examined. A gel mobility shift assay revealed that a response regulator RpaB binds to the HLR1 sequence in PSI promoters. Base substitution in the HLR1 sequence or decrease in copy number of the
rpaB
gene resulted in decrease in the promoter activity of PSI genes under low-light conditions. These observations suggest that RpaB acts as a transcriptional activator for PSI genes. It is likely that RpaB binds to the HLR1 sequence under low-light conditions and works for positive regulation of PSI genes and for negative regulation of high-light-inducible genes depending on the location of the HLR1 sequence within target promoters.
Complete Genome Sequence of
Haemophilus parasuis
SH0165
Authors: Yue Min , Yang Fan , Yang Jian , Bei Weicheng , Cai Xuwang , Chen Lihong , Dong Jie , Zhou Rui , Jin Meilin , Jin Qi , Chen Huanchun
Published: December 2008

Haemophilus parasuis
is the causative agent of Glässer's disease, which produces big losses in swine populations worldwide.
H. parasuis
SH0165, belonging to the dominant serovar 5 in China, is a clinically isolated strain with high-level virulence. Here, we report the first completed genome sequence of this species.