bluuebunny/crossref_metadata_2025 huggingface dataset:
Survival behaviour of swamp wallabies during prescribed burning and wildfire
Authors: Garvey Nathan , Ben-Ami Dror , Ramp Daniel , Croft David B.
Published: March 2010

Context. Prescribed (or controlled) burning is frequently advocated as a means of reducing fuel loads in peri-urban forests to minimise the risk of high-intensity wildfires. An important consideration in prescribed burns is the impact on native wildlife.

Aims. An opportunity arose to follow the movements of radio-collared peri-urban swamp wallabies during a prescribed burn and after an unexpected wildfire in the same location a short time later. Movement data was used to assess the relative impacts of the prescribed burn and wildfire on mortality, emigration and habitat use; the behavioural responses and methods of avoidance used by swamp wallabies in response to an oncoming fire front; and the management implications for wildlife that inhabit fire-prone habitats in proximity to human settlement where wildfire mitigation is necessary.

Methods. Here we report on the movements of radio-collared swamp wallabies, Wallabia bicolor, before, during and after a prescribed fire and after a wildfire on the same site 6 months later.

Key results. No radio-collared swamp wallabies were killed during the prescribed burn and only one wallaby was observed to emigrate from the area post-fire. This contrasted to the wildfire where one wallaby died during or just after the fire and another perished in the post-fire environment a few months later. The wildfire also increased emigration post-fire.

Conclusions. We demonstrate that wallabies can avoid fire fronts and that this avoidance behaviour may be more successful during cooler fires. The prescribed burn provided a suitable habitat for wallabies but did not result in a shift in habitat preference.

Implications. Mitigation of the impact of prescribed burns on swamp wallabies may be achieved by allowing sufficient time for habitat complexity to re-establish between burns.
Predator-baiting experiments for the conservation of rock-wallabies in Western Australia: a 25-year review with recent advances
Authors: Kinnear J. E. , Krebs C. J. , Pentland C. , Orell P. , Holme C. , Karvinen R.
Published: March 2010

Predation is widely believed to be the main threatening process for many native vertebrates in Australia. For 25 years, predator-baiting experiments have been used in the Western Australian Central Wheatbelt to control red fox predation on rock-wallabies and other endangered marsupial prey elsewhere. We review here the history of a series of baiting experiments designed to protect rock-wallaby colonies by controlling red foxes with 1080 poison baits. We continue to support the conclusion that red foxes can reduce or exterminate rock-wallaby populations in Western Australia. Research trials from 1990 to 2008 have uniformly shown a dramatic recovery of rock-wallaby populations once red foxes are baited. Baiting experiments are often black boxes and their success should not blind us to their weaknesses. Ideally, what we would like to measure are the functional responses of predators to prey abundance directly. As a contribution towards this goal, we describe new technology that enables one to determine which predator killed which prey, at exactly what time, with improved research and management outcomes.
From combinatorial peptide selection to drug prototype (I): Targeting the vascular endothelial growth factor receptor pathway
Authors: Giordano Ricardo J. , Cardó-Vila Marina , Salameh Ahmad , Anobom Cristiane D. , Zeitlin Benjamin D. , Hawke David H. , Valente Ana P. , Almeida Fábio C. L. , Nör Jacques E. , Sidman Richard L. , Pasqualini Renata , Arap Wadih
Published: February 2010

Inhibition of blood vessel formation is a viable therapeutic approach in angiogenesis-dependent diseases. We previously used a combinatorial screening on vascular endothelial growth factor (VEGF)-activated endothelial cells to select the sequence CPQPRPLC and showed that the motif Arg-Pro-Leu targets VEGF receptor-1 and neuropilin-1. Here, we evaluated and validated
D
(LPR), a derivative molecule with strong antiangiogenesis attributes. This prototype drug markedly inhibits neovascularization in three mouse models: Matrigel-based assay, functional human/murine blood vessel formation, and retinopathy of prematurity. In addition to its systemic activity,
D
(LPR) also inhibits retinal angiogenesis when administered in an eye-drop formulation. Finally, in preliminary studies, we have showed targeted drug activity in an experimental tumor-bearing mouse model. These results show that drugs targeting extracellular domains of VEGF receptors are active, affect signal transduction, and have potential for clinical application. On a larger context, this study illustrates the power of ligand-directed selection plus retro-inversion for rapid drug discovery and development.
From combinatorial peptide selection to drug prototype (II): Targeting the epidermal growth factor receptor pathway
Authors: Cardó-Vila Marina , Giordano Ricardo J. , Sidman Richard L. , Bronk Lawrence F. , Fan Zhen , Mendelsohn John , Arap Wadih , Pasqualini Renata
Published: February 2010

The epidermal growth factor receptor (EGFR), a tyrosine kinase, is central to human tumorigenesis. Typically, three classes of drugs inhibit tyrosine kinase pathways: blocking antibodies, small kinase inhibitors, and soluble ligand receptor traps/decoys. Only the first two types of EGFR-binding inhibitory drugs are clinically available; notably, no EGFR decoy has yet been developed. Here we identify small molecules mimicking EGFR and that functionally behave as soluble decoys for EGF and TGFα, ligands that would otherwise activate downstream signaling. After combinatorial library selection on EGFR ligands, a panel of binding peptides was narrowed by structure–function analysis. The most active motif was CVRAC (EGFR 283–287), which is necessary and sufficient for specific EGFR ligand binding. Finally, a synthetic retro-inverted derivative,
D
(CARVC), became our preclinical prototype of choice. This study reveals an EGFR-decoy drug candidate with translational potential.
Comparing the use of the empty number line in England and the Netherlands
Authors: Murphy Carol
Published: February 2010

Efforts to meet the needs of children's learning in arithmetic has led to an increased emphasis on the teaching of mental calculation strategies in England. This has included the adoption of didactical tools such as the empty number line (ENL) that was developed as part of the realistic mathematics movement in the Netherlands. It has been claimed that the English use of the ENL differs from that of the Dutch. In this study curriculum guidance materials are examined to investigate these differences. Two examples of teaching sequences are provided to illustrate them further. It is proposed that the different uses stem from different pedagogical principles. The implications of the English use are discussed in relation to the presentation of mental calculation strategies in an algorithmic way.
ON THE RELIABILITY OF ZEUS-3D
Authors: Clarke David A.
Published: February 2010

Recent and not-so-recent critiques of the widely used magnetohydrodynamics (MHD)
code, ZEUS-3D, challenge its reliability and efficiency
suggesting that its MHD algorithm is capable of “significant errors” in some
simple one-dimensional shock-tube problems. I show that these concerns are
either inapplicable in multi-dimensional astrophysical applications, or result
from a misuse of the code rather than “flaws” in its design. I also describe a
few multi-dimensional test problems including one for super-Alfvénic turbulence,
and highlight some recent innovations and improvements to the code now available
online.
Some homological properties of the category 𝒪, II
Authors: Mazorchuk Volodymyr
Published: March 2010

We show, in full generality, that Lusztig’s

a

\mathbf {a}

-function describes the projective dimension of both indecomposable tilting modules and indecomposable injective modules in the regular block of the BGG category

O

\mathcal {O}

, proving a conjecture from the first paper. On the way we show that the images of simple modules under projective functors can be represented in the derived category by linear complexes of tilting modules. These complexes, in turn, can be interpreted as the images of simple modules under projective functors in the Koszul dual of the category

O

\mathcal {O}

. Finally, we describe the dominant projective modules and also the projective-injective modules in some subcategories of

O

\mathcal {O}

and show how one can use categorification to decompose the regular representation of the Weyl group into a direct sum of cell modules, extending the results known for the symmetric group (type

A
A

).
Exploiting sequence similarity to validate the sensitivity of SNP arrays in detecting fine-scaled copy number variations
Authors: Wong Gerard , Leckie Christopher , Gorringe Kylie L. , Haviv Izhak , Campbell Ian G. , Kowalczyk Adam
Published: February 2010

Motivation: High-density single nucleotide polymorphism (SNP) genotyping arrays are efficient and cost effective platforms for the detection of copy number variation (CNV). To ensure accuracy in probe synthesis and to minimize production costs, short oligonucleotide probe sequences are used. The use of short probe sequences limits the specificity of binding targets in the human genome. The specificity of these short probeset sequences has yet to be fully analysed against a normal reference human genome. Sequence similarity can artificially elevate or suppress copy number measurements, and hence reduce the reliability of affected probe readings. For the purpose of detecting narrow CNVs reliably down to the width of a single probeset, sequence similarity is an important issue that needs to be addressed.

Results: We surveyed the Affymetrix Human Mapping SNP arrays for probeset sequence similarity against the reference human genome. Utilizing sequence similarity results, we identified a collection of fine-scaled putative CNVs between gender from autosomal probesets whose sequence matches various loci on the sex chromosomes. To detect these variations, we utilized our statistical approach, Dectecting REcurrent Copy number change using rank-order Statistics (DRECS), and showed that its performance was superior and more stable than the t-test in detecting CNVs. Through the application of DRECS on the HapMap population datasets with multi-matching probesets filtered, we identified biologically relevant SNPs in aberrant regions across populations with known association to physical traits, such as height, covered by the span of a single probe. This provided empirical confirmation of the existence of naturally occurring narrow CNVs as well as the sensitivity of the Affymetrix SNP array technology in detecting them.

Availability: The MATLAB implementation of DRECS is available at http://ww2.cs.mu.oz.au/∼gwong/DRECS/index.html

Contact:  gwong@csse.unimelb.edu.au

Supplementary information:  Supplementary information is available at Bioinformatics online.
BioNet: an R-Package for the functional analysis of biological networks
Authors: Beisser Daniela , Klau Gunnar W. , Dandekar Thomas , Müller Tobias , Dittrich Marcus T.
Published: February 2010

Motivation: Increasing quantity and quality of data in transcriptomics and interactomics create the need for integrative approaches to network analysis. Here, we present a comprehensive R-package for the analysis of biological networks including an exact and a heuristic approach to identify functional modules.

Results: The BioNet package provides an extensive framework for integrated network analysis in R. This includes the statistics for the integration of transcriptomic and functional data with biological networks, the scoring of nodes as well as methods for network search and visualization.

Availability: The BioNet package and a tutorial are available from http://bionet.bioapps.biozentrum.uni-wuerzburg.de

Contact:  marcus.dittrich@biozentrum.uni-wuerzburg.de; tobias.mueller@biozentrum.uni-wuerzburg.de
Salicylic Acid Is Involved in the Nb-Mediated Defense Responses to Potato virus X in Solanum tuberosum
Authors: Sánchez Gerardo , Gerhardt Nadia , Siciliano Florencia , Vojnov Adrián , Malcuit Isabelle , Marano María Rosa
Published: March 2010

To evaluate the role of salicylic acid (SA) in Nb-mediated hypersensitive resistance to Potato virus X (PVX) avirulent strain ROTH1 in Solanum tuberosum, we have constructed SA-deficient transgenic potato plant lines by overexpressing the bacterial enzyme salicylate hydroxylase (NahG), which degrades SA. Evaluation of these transgenic lines revealed hydrogen peroxide accumulation and spontaneous lesion formation in an age- and light-dependent manner. In concordance, NahG potato plants were more sensitive to treatment with methyl viologen, a reactive oxygen species–generating compound. In addition, when challenged with PVX ROTH1, NahG transgenic lines showed a decreased disease-resistance response to infection and were unable to induce systemic acquired resistance. However, the avirulent viral effector, the PVX 25-kDa protein, does induce expression of the pathogenesis-related gene PR-1a in NahG potato plants. Taken together, our data indicate that SA is involved in local and systemic defense responses mediated by the Nb gene in Solanum tuberosum. This is the first report to show that basal levels of SA correlate with hypersensitive resistance to PVX.
The PedsQL™ in Pediatric Patients with Duchenne Muscular Dystrophy: Feasibility, Reliability, and Validity of the Pediatric Quality of Life Inventory Neuromuscular Module and Generic Core Scales
Authors: Davis Sarah E , Hynan Linda S , Limbers Christine A , Andersen C Mariam , Greene Medrith C , Varni James W , Iannaccone Susan T
Published: February 2010

Objective:

To evaluate the reliability and validity of the PedsQL™ 3.0 Neuromuscular Module (NMM) in assessing health-related quality of life in the Duchenne muscular dystrophy (DMD) population for use as a secondary outcome measure in phase III clinical trials.

Background:

DMD is the most common genetic form of muscular dystrophy in childhood. Clinical trials are underway to evaluate modalities of treatment. The NMM was developed based on interviews of patients with DMD and spinal muscular atrophy. To determine the PedsQL™ reliability and validity, we administered the NMM to patients with DMD and their caregivers.

Design/Methods:

Boys 8 to 18 years old with DMD were recruited from a neuromuscular disease clinic. At baseline, the child and caregiver completed the NMM and the PedsQL™ 4.0 Generic Core Scales (GC). The NMM was repeated 2 to 6 weeks later. Reliability was assessed using Cronbach's coefficient alpha (internal consistency) and intraclass correlation (ICC) (test-retest consistency). Construct validity was assessed by comparing baseline child and caregiver NMM total scores with the GC Total Score, forced vital capacity, cardiac ejection fraction, and ambulatory status.

Results:

Forty-four children and their caregivers completed the study. Internal consistency reliability of the total scale score of the NMM was demonstrated (Child α = 0.85; Caregiver α = 0.87). Test-retest reliability of the NMM was also demonstrated (Child ICC = 0.75, P = 0.001; Caregiver ICC = 0.85, P < 0.001). Validity of the total scale score of the NMM when compared with the GC Total Scale Score was supported (Child r (41) = 0.63, P < 0.001; Caregiver r (42) = 0.64, P < 0.001). Validity of the NMM compared with forced vital capacity was also supported (Child r (38) = 0.35, P = 0.032; Caregiver r (39) = 0.41, P = 0.01). The NMM parent-proxy-report and child self-report “About My Child's Neuromuscular Disease” scale was significantly related to wheelchair use (P < 0.008 and 0.016, respectively); the GC "Child Self-Report “Physical Health” scale was also significantly related to wheelchair use (P < 0.001). We were unable to conduct any analysis with ejection fraction because of the small number of children across all categories.

Conclusions:

The PedsQL™ NMM is a reliable measure of disease-specific health-related quality of life in the DMD population and may be used as an outcome measure in clinical trials.
Asymmetric Phenotype Associated With Rare Myelin Protein Zero Mutation
Authors: Souayah Nizar , Tick Chong Peter Siao
Published: February 2010

Myelin protein zero (MPZ) mutations cause demyelinating neuropathies that range from severe neonatal to milder adult forms. We report a 36-year-old man who developed weakness of his left little finger adduction 3 years earlier. The weakness progressed to his other limbs. Examination revealed mildly high-arched feet with asymmetric weakness of ulnar-innervated muscles (left > right) and asymmetric weakness of peroneal-innervated muscles (right > left). Motor nerve conduction velocities ranged from 18.4 to 24.4 m/s in the upper extremities and from 14.8 to 22.7 in the lower extremities. Left median partial motor conduction block was noted at the forearm segment. Genetic testing demonstrated MPZ mutation with ARG98HIS amino acid change. The patient's father is a 68-year-old man who was asymptomatic and who was noticed to have high-arched feet and asymmetric leg muscle atrophy and weakness (right > left). The patient's 2-year-old son is “clumsy” with history of neonatal laryngomalacia. He has flat feet, areflexia, and difficulty standing on individual right versus left leg. The patient's paternal grandfather had high-arched feet and hearing loss. We conclude that ARG98HIS MPZ mutation may cause hereditary and relatively mild and asymmetric demyelinating sensorimotor polyneuropathy.
Superficial Siderosis Mimicking Amyotrophic Lateral Sclerosis
Authors: Driver-Dunckley Erika D , Hoxworth Joseph M , Patel Naresh P , Bosch E Peter , Goodman Brent P
Published: February 2010

We report a case of superficial siderosis erroneously diagnosed as amyotrophic lateral sclerosis. The patient's symptoms began 18 years prior with unilateral upper extremity weakness, fasciculations, and hyperreflexia. The patient then developed ataxia and hearing loss 15 years after his original symptoms. The magnetic resonance images revealed superficial siderosis involving the spinal cord and brain. We want to attract attention to superficial siderosis as a rare amyotrophic lateral sclerosis mimic disorder.
GD1a-Associated Pure Motor Guillain-Barré Syndrome With Hyperreflexia and Bilateral Papillitis
Authors: Neuwirth Christoph , Mojon Daniel , Weber Markus
Published: February 2010

A patient with acute purely motor polyneuropathy with positive GD1a ganglioside antibodies who presented with paresis in combination with hyperreflexia is reported. Neurophysiological tests revealed features compatible with acute motor axonal neuropathy. Therapy with intravenous immunoglobulin led to rapid clinical improvement. However, at the time when signs of active denervation appeared on electromyographic testing, the patient developed bilateral papillitis. The pathogenesis of pure motor Guillain-Barré syndrome with hyperreflexia and papillitis is discussed.
The Neuromuscular Manifestations of Amyloidosis
Authors: Simmons Zachary , Specht Charles S
Published: February 2010

Amyloidosis is a systemic disease that may be acquired or hereditary and which results in the deposition of amyloid fibrils in a variety of tissues causing their progressive dysfunction. Although the clinical presentation often is dominated by cardiac or renal failure, peripheral neuropathy may be a significant or the initial manifestation, resulting in presentation to the neurologist. Diagnosis often is challenging and may require multiple diagnostic procedures, including more than one biopsy. Acquired and hereditary amyloidosis can be definitively distinguished from one another only by immunohistochemical staining or molecular genetic testing. Treatment remains a challenge, although chemotherapy and autologous stem cell transplantation offer hope for those with primary systemic amyloidosis, whereas liver transplantation is effective for some forms of hereditary amyloid neuropathy. Much less commonly, myopathy may be a clinically significant manifestation of amyloidosis.
Evolution of sexual dimorphism in bill size and shape of hermit hummingbirds (Phaethornithinae): a role for ecological causation
Authors: Temeles Ethan J. , Miller Jill S. , Rifkin Joanna L.
Published: March 2010

Unambiguous examples of ecological causation of sexual dimorphism are rare, and the best evidence involves sexual differences in trophic morphology. We show that moderate female-biased sexual dimorphism in bill curvature is the ancestral condition in hermit hummingbirds (Phaethornithinae), and that it is greatly amplified in species such asGlaucis hirsutusandPhaethornis guy, where bills of females are 60 per cent more curved than bills of males. In contrast, bill curvature dimorphism is lost or reduced in a lineage of short-billed hermit species and in specialistEutoxeressicklebill hermits. In the hermits, males tend to be larger than females in the majority of species, although size dimorphism is typically small. Consistent with earlier studies of hummingbird feeding performance, both raw regressions of traits and phylogenetic independent contrasts supported the prediction that dimorphism in bill curvature of hermits is associated with longer bills. Some evidence indicates that differences between sexes of hermit hummingbirds are associated with differences in the use of food plants. We suggest that some hermit hummingbirds provide model organisms for studies of ecological causation of sexual dimorphism because their sexual dimorphism in bill curvature provides a diagnostic clue for the food plants that need to be monitored for studies of sexual differences in resource use.
The beak of the other finch: coevolution of genetic covariance structure and developmental modularity during adaptive evolution
Authors: Badyaev Alexander V.
Published: March 2010

The link between adaptation and evolutionary change remains the most central and least understood evolutionary problem. Rapid evolution and diversification of avian beaks is a textbook example of such a link, yet the mechanisms that enable beak's precise adaptation and extensive adaptability are poorly understood. Often observed rapid evolutionary change in beaks is particularly puzzling in light of the neo-Darwinian model that necessitates coordinated changes in developmentally distinct precursors and correspondence between functional and genetic modularity, which should preclude evolutionary diversification. I show that during first 19 generations after colonization of a novel environment, house finches (Carpodacus mexicanus) express an array of distinct, but adaptively equivalent beak morphologies—a result of compensatory developmental interactions between beak length and width in accommodating microevolutionary change in beak depth. Directional selection was largely confined to the elimination of extremes formed by these developmental interactions, while long-term stabilizing selection along a single axis—beak depth—was mirrored in the structure of beak's additive genetic covariance. These results emphasize three principal points. First, additive genetic covariance structure may represent a historical record of the most recurrent developmental and functional interactions. Second, adaptive equivalence of beak configurations shields genetic and developmental variation in individual components from depletion by natural selection. Third, compensatory developmental interactions among beak components can generate rapid reorganization of beak morphology under novel conditions and thus greatly facilitate both the evolution of precise adaptation and extensive diversification, thereby linking adaptation and adaptability in this classic example of Darwinian evolution.
Inquilinus ginsengisoli sp. nov., isolated from soil of a ginseng field
Authors: Jung Hae-Min , Lee Jung-Sook , Bae Heon-Meen , Yi Tae-Hoo , Kim Se-Young , Lee Sung-Taik , Im Wan-Taek
Published: February 2010

A Gram-reaction-negative, chemo-organotrophic, non-motile, non-spore-forming, rod-shaped bacterium (strain Gsoil 080T) was isolated from soil collected in a ginseng field in Pocheon Province, South Korea, and was investigated by using a polyphasic taxonomic approach. Comparative 16S rRNA gene sequence analysis showed that strain Gsoil 080Twas related most closely toInquilinus limosusstrains AU0476Tand AU1979 (98.9 % similarity to both). Strain Gsoil 080Tshared ≤91.3 % 16S rRNA gene sequence similarity with the type strains of other recognized species examined. The genusInquilinusbelongs to the familyRhodospirillaceaein the orderRhodospirillales, classAlphaproteobacteria. The predominant ubiquinone was Q-10 and the major fatty acids were summed feature 7 (C18 : 1ω9c/ω12t/ω7c) and C19 : 0cycloω8c. The G+C content of the genomic DNA of strain Gsoil 080Twas 69.9 mol%. The level of DNA–DNA relatedness between strain Gsoil 080TandI. limosusLMG 20952Twas 12 %. The results of genotypic analyses in combination with chemotaxonomic and physiological data demonstrated that strain Gsoil 080Trepresents a novel species of the genusInquilinus, for which the nameInquilinus ginsengisolisp. nov. is proposed. The type strain is Gsoil 080T(=KCTC 12574T=LMG 23638T).
Flavobacterium beibuense sp. nov., isolated from marine sediment
Authors: Fu Yuanyuan , Tang Xixiang , Lai Qiliang , Zhang Chunhua , Zhong Huanzi , Li Weiwei , Liu Yuhui , Chen Liang , Sun Fengqin , Shao Zongze
Published: February 2010

A taxonomic study was carried out on strain F44-8T, which was isolated from a crude-oil-degrading consortium, enriched from marine sediment of the Beibu Gulf, PR China. The 16S rRNA gene sequence of strain F44-8T showed highest similarities to those of Flavobacterium frigoris LMG 21922T (93.3 %), Flavobacterium terrae R2A1-13T (93.3 %) and Flavobacterium gelidilacus LMG 21477T (93.1 %). Sequence similarities to other members of the genus Flavobacterium were <93.0 %. The dominant fatty acids of strain F44-8T were iso-C15 : 0, summed feature 3 (iso-C15 : 0 2-OH and/or C16 : 1
ω7c), iso-C15 : 1 G and iso-C17 : 0 3-OH. The DNA G+C content of strain F44-8T was 38.6 mol%. These results are consistent with characteristics of members of the genus Flavobacterium. Strain F44-8T could, however, be readily distinguished from all known Flavobacterium species by a number of phenotypic features. Therefore, according to the phenotypic and 16S rRNA gene sequence data, strain F44-8T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium beibuense sp. nov. is proposed (type strain F44-8T =CCTCC AB 209067T =LMG 25233T =MCCC 1A02877T).
Auritidibacter ignavus gen. nov., sp. nov., of the family Micrococcaceae isolated from an ear swab of a man with otitis externa, transfer of the members of the family Yaniellaceae Li et al. 2008 to the family Micrococcaceae and emended description of the suborder Micrococcineae
Authors: Yassin A. F. , Hupfer H. , Siering C. , Klenk H.-P. , Schumann P.
Published: February 2010

A Gram-reaction-positive, aerobic, catalase-positive, non-spore-forming, rod-shaped bacterium designated IMMIB L-1656Twas isolated from an ear swab of a man and characterized using a polyphasic approach. 16S rRNA gene sequence analysis indicated that strain IMMIB L-1656Tis related to members of the familyMicrococcaceae(<95.1 % sequence similarity). Anaylsis using different phylogenetic algorithms consistently grouped strain IMMIB L-1656Twith members of the genusYaniella. The organism posessed a cell-wall murein based onl-lysine (variation A4α, typel-Lys–Gly–l-Glu), MK-10 as the predominant menaquinone and long-chain cellular fatty acids of straight-chain and branched-chain saturated types (with iso-C15 : 0and anteiso-C17 : 0predominating). The polar lipids included diphosphatidylglycerol, phosphatidylglycerol and phosphatidylinositol in addition to unknown glycolipids. The DNA G+C content was 59.7 mol%. Based on its distinctive genotypic and phenotypic characteristics, strain IMMIB L-1656Trepresents a novel species in a novel genus, for which the nameAuritidibacter ignavusgen. nov., sp. nov. is proposed. We also propose that members of the familyYaniellaceaebe transferred to the familyMicrococcaceaewith amendments to the description of the suborderMicrococcineae.The type strain ofAuritidibacter ignavusis IMMIB L-1656T(=DSM 45359T=CCUG 57943T).
Fibrella aestuarina gen. nov., sp. nov., a filamentous bacterium of the family Cytophagaceae isolated from a tidal flat, and emended description of the genus Rudanella Weon et al. 2008
Authors: Filippini Manuela , Svercel Miroslav , Laczko Endre , Kaech Andres , Ziegler Urs , Bagheri Homayoun C.
Published: February 2010

A Gram-staining-negative, pink bacterium, designated strain BUZ 2T, was isolated from coastal mud from the North Sea (Fedderwardersiel, Germany). Cells were rod-shaped and able to form multicellular filaments. Growth after 7 days was observed at 10–40 °C, at pH 6–8 and with 0–0.5 % NaCl. The phylogenetic tree based on 16S rRNA gene sequences indicated that strain BUZ 2T is a member of the family Cytophagaceae, its closest neighbours being Rudanella lutea 5715S-11T, Spirosoma linguale LMG 10896T and Spirosoma panaciterrae Gsoil 1519T (87.8, 86.4 and 86.1 % sequence similarity, respectively). The major fatty acids were summed feature 3 (comprising C16 : 1
ω7c and/or iso-C15 : 0 2-OH), C16 : 1
ω5c and iso-C15 : 0. The predominant respiratory quinone was MK-7 and the major polar lipids were phosphatidylethanolamine and several unidentified aminophospholipids. The DNA G+C content was 56.5 mol%. On the basis of this polyphasic study, we propose that strain BUZ 2T represents a novel genus and species, for which the name Fibrella aestuarina gen. nov., sp. nov. is proposed. The type strain of Fibrella aestuarina is BUZ 2T (=DSM 22563T =CCUG 58136T). An emended description of the genus Rudanella is also proposed.
Haloactinopolyspora alba gen. nov., sp. nov., a halophilic filamentous actinomycete isolated from a salt lake, with proposal of Jiangellaceae fam. nov. and Jiangellineae subord. nov.
Authors: Tang Shu-Kun , Zhi Xiao-Yang , Wang Yun , Shi Rong , Lou Kai , Xu Li-Hua , Li Wen-Jun
Published: February 2010

A halophilic, filamentous actinomycete strain, designated YIM 93246T, was isolated from a salt lake in Xinjiang province, north-west China, and subjected to polyphasic taxonomic characterization. The isolate grew in the presence of 7–23 % (w/v) NaCl, but not in the absence of NaCl. Strain YIM 93246T had particular morphological properties, forming aerial mycelium that had long spore chains and pseudosporangium-like, rhiziform spore aggregates at maturity. ll-DAP was the cell-wall diamino acid and glucosamine, mannose, glucose, arabinose and galactose were the cell-wall sugars. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. MK-9 (H4) was the predominant menaquinone and the genomic DNA G+C content was 70.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain YIM 93246T clustered with the genus Jiangella. The sequence similarities between strain YIM 93246T and Jiangella alba, Jiangella gansuensis and Jiangella alkaliphila were 96.9, 96.9 and 96.6 %, respectively. Based on morphological, physiological and chemotaxonomic differences, and phylogenetic analysis, a novel genus and species, Haloactinopolyspora alba gen. nov., sp. nov., is proposed. The type strain of the species is YIM 93246T (=DSM 45211T=KCTC 19409T). Additionally, phylogenetic analysis placed the genus Jiangella together with strain YIM 93246T within the order Actinomycetales as an independent lineage, clearly distinguished from other described suborders of the class Actinobacteria. Hence, based on phylogenetic characteristics, the genus Jiangella together with the newly proposed genus Haloactinopolyspora are proposed to be classified as Jiangellaceae fam. nov. and Jiangellineae subord. nov.
Paenibacillus xylanisolvens sp. nov., a xylan-degrading bacterium from soil
Authors: Khianngam Saowapar , Tanasupawat Somboon , Akaracharanya Ancharida , Kim Kwang Kyu , Lee Keun Chul , Lee Jung-Sook
Published: February 2010

A xylan-degrading bacterium, strain X11-1T, was isolated from soil collected in Nan province, Thailand. The strain was characterized based on its phenotypic and genotypic characteristics. Strain X11-1Twas a Gram-stain-positive, facultatively anaerobic, spore-forming, rod-shaped bacterium. It containedmeso-diaminopimelic acid in the cell-wall peptidoglycan. The major menaquinone was MK-7, anteiso-C15 : 0(56.6 %) and C16 : 0(14.0 %) were the predominant cellular fatty acids and diphosphatidylglycerol, phosphatidylmonomethylethanolamine, phosphatidylethanolamine and phosphatidylglycerol were the major phospholipids. The DNA G+C content was 51.6 mol%. Phylogenetic analysis using 16S rRNA gene sequences showed that strain X11-1Twas affiliated to the genusPaenibacillusand was closely related toPaenibacillus naphthalenovoransKACC 11505TandPaenibacillus validusCCM 3894T, with 96.5 % sequence similarity. Therefore, the strain represents a novel species of the genusPaenibacillus, for which the namePaenibacillus xylanisolvenssp. nov. is proposed. The type strain is X11-1T(=KCTC 13042T=PCU 311T=TISTR 1829T).
De novo telomere formation is suppressed by the Mec1-dependent inhibition of Cdc13 accumulation at DNA breaks
Authors: Zhang Wei , Durocher Daniel
Published: March 2010

DNA double-strand breaks (DSBs) are a threat to cell survival and genome integrity. In addition to canonical DNA repair systems, DSBs can be converted to telomeres by telomerase. This process, herein termed telomere healing, endangers genome stability, since it usually results in chromosome arm loss. Therefore, cells possess mechanisms that prevent the untimely action of telomerase on DSBs. Here we report that Mec1, the ATR ortholog, couples the detection of DNA ends with the inhibition of telomerase. Mec1 inhibits telomere healing by phosphorylating Cdc13 on its S306 residue, a phosphorylation event that suppresses Cdc13 accumulation at DSBs. Conversely, telomere addition at accidental breaks is promoted by Pph3, the yeast protein phosphatase 4 (PP4). Pph3 is itself modulated by Rrd1, an activator of PP2A family phosphatases. Rrd1 and Pph3 oppose Cdc13 S306 phosphorylation and are necessary for the efficient accumulation of Cdc13 at DNA breaks. These studies therefore identify a mechanism by which the ATR family of kinases enforces genome integrity, and a process that underscores the contribution of Cdc13 to the fate of DNA ends.
Histone deacetylases 1 and 2 act in concert to promote the G1-to-S progression
Authors: Yamaguchi Teppei , Cubizolles Fabien , Zhang Yu , Reichert Nina , Kohler Hubertus , Seiser Christian , Matthias Patrick
Published: March 2010

Histone deacetylases (HDACs) regulate gene expression by deacetylating histones and also modulate the acetylation of a number of nonhistone proteins, thus impinging on various cellular processes. Here, we analyzed the major class I enzymes HDAC1 and HDAC2 in primary mouse fibroblasts and in the B-cell lineage. Fibroblasts lacking both enzymes fail to proliferate in culture and exhibit a strong cell cycle block in the G1 phase that is associated with up-regulation of the CDK inhibitors p21WAF1/CIP1 and p57Kip2 and of the corresponding mRNAs. This regulation is direct, as in wild-type cells HDAC1 and HDAC2 are bound to the promoter regions of the p21 and p57 genes. Furthermore, analysis of the transcriptome and of histone modifications in mutant cells demonstrated that HDAC1 and HDAC2 have only partly overlapping roles. Next, we eliminated HDAC1 and HDAC2 in the B cells of conditionally targeted mice. We found that B-cell development strictly requires the presence of at least one of these enzymes: When both enzymes are ablated, B-cell development is blocked at an early stage, and the rare remaining pre-B cells show a block in G1 accompanied by the induction of apoptosis. In contrast, elimination of HDAC1 and HDAC2 in mature resting B cells has no negative impact, unless these cells are induced to proliferate. These results indicate that HDAC1 and HDAC2, by normally repressing the expression of p21 and p57, regulate the G1-to-S-phase transition of the cell cycle.
Involvement of the lateral septal area in the expression of fear conditioning to context
Authors: Reis Daniel G. , Scopinho América A. , Guimarães Francisco S. , Corrêa Fernando M.A. , Resstel Leonardo B.M.
Published: February 2010

Considering the evidence that the lateral septal area (LSA) modulates defensive responses, the aim of the present study is to verify if this structure is also involved in contextual fear conditioning responses. Neurotransmission in the LSA was reversibly inhibited by bilateral microinjections of cobalt chloride (CoCl2, 1 mM) 10 min before or after conditioning or 10 min before re-exposure to the aversively conditioned chamber. Only those animals that received CoCl2before re-exposure showed a decrease in both cardiovascular and behavioral conditioned responses. These results suggest that the LSA participates in the expression, but not acquisition or consolidation, of contextual fear conditioning.
Post-training reversible inactivation of the hippocampus enhances novel object recognition memory
Authors: Oliveira Ana M.M. , Hawk Joshua D. , Abel Ted , Havekes Robbert
Published: February 2010

Research on the role of the hippocampus in object recognition memory has produced conflicting results. Previous studies have used permanent hippocampal lesions to assess the requirement for the hippocampus in the object recognition task. However, permanent hippocampal lesions may impact performance through effects on processes besides memory consolidation including acquisition, retrieval, and performance. To overcome this limitation, we used an intrahippocampal injection of the GABA agonist muscimol to reversibly inactivate the hippocampus immediately after training mice in two versions of an object recognition task. We found that the inactivation of the dorsal hippocampus after training impairs object-place recognition memory but enhances novel object recognition (NOR) memory. However, inactivation of the dorsal hippocampus after repeated exposure to the training context did not affect object recognition memory. Our findings suggest that object recognition memory formation does not require the hippocampus and, moreover, that activity in the hippocampus can interfere with the consolidation of object recognition memory when object information encoding occurs in an unfamiliar environment.
Emotional memory persists longer than event memory
Authors: Kuriyama Kenichi , Soshi Takahiro , Fujii Takeshi , Kim Yoshiharu
Published: February 2010

The interaction between amygdala-driven and hippocampus-driven activities is expected to explain why emotion enhances episodic memory recognition. However, overwhelming behavioral evidence regarding the emotion-induced enhancement of immediate and delayed episodic memory recognition has not been obtained in humans. We found that the recognition performance for event memory differs from that for emotional memory. Although event recognition deteriorated equally for episodes that were or were not emotionally salient, emotional recognition remained high for only stimuli related to emotional episodes. Recognition performance pertaining to delayed emotional memory is an accurate predictor of the context of past episodes.
The role of amygdala nuclei in the expression of auditory signaled two-way active avoidance in rats
Authors: Choi June-Seek , Cain Christopher K. , LeDoux Joseph E.
Published: February 2010

Using a two-way signaled active avoidance (2-AA) learning procedure, where rats were trained in a shuttle box to avoid a footshock signaled by an auditory stimulus, we tested the contributions of the lateral (LA), basal (B), and central (CE) nuclei of the amygdala to the expression of instrumental active avoidance conditioned responses (CRs). Discrete or combined lesions of the LA and B, performed after the rats had reached an asymptotic level of avoidance performance, produced deficits in the CR, whereas CE lesions had minimal effect. Fiber-sparing excitotoxic lesions of the LA/B produced by infusions ofN-methyl-d-aspartate (NMDA) also impaired avoidance performance, confirming that neurons in the LA/B are involved in mediating avoidance CRs. In a final series of experiments, bilateral electrolytic lesions of the CE were performed on a subgroup of animals that failed to acquire the avoidance CR after 3 d of training. CE lesions led to an immediate rescue of avoidance learning, suggesting that activity in CE was inhibiting the instrumental CR. Taken together, these results indicate that the LA and B are essential for the performance of a 2-AA response. The CE is not required, and may in fact constrain the instrumental avoidance response by mediating the generation of competing Pavlovian responses, such as freezing.
Prefrontal cortex: Role in acquisition of overlapping associations and transitive inference
Authors: DeVito Loren M. , Lykken Christine , Kanter Benjamin R. , Eichenbaum Howard
Published: February 2010

“Transitive inference” refers to the ability to judge from memory the relationships between indirectly related items that compose a hierarchically organized series, and this capacity is considered a fundamental feature of relational memory. Here we explored the role of the prefrontal cortex in transitive inference by examining the performance of mice with selective damage to the medial prefrontal cortex. Damage to the infralimbic and prelimbic regions resulted in significant impairment in the acquisition of a series of overlapping odor discrimination problems, such that animals with prefrontal lesions required twice as many trials to learn compared to sham-operated controls. Following eventually successful acquisition, animals with medial prefrontal lesions were severely impaired on a transitive inference probe test, whereas they performed as well as controls on a test that involved a nontransitive judgment from a novel odor pairing. These results suggest that the prefrontal cortex is part of an integral hippocampal–cortical network essential for relational memory organization.
Using WebGBrowse to Visualize Genome Annotation on GBrowse
Authors: Podicheti Ram , Dong Qunfeng
Published: March 2010

INTRODUCTION

Although GBrowse is popular for visualizing genomic features along a reference sequence, its installation and configuration are difficult for many biologists. WebGBrowse is a web server that takes a user-supplied annotation file, guides users to configure the display of each genomic feature, and allows users to visualize the genome annotation with integrated GBrowse software. This protocol guides the user through each step of using WebGBrowse.
Determination of Recombinant Baculovirus Display Viral Titer
Authors: Mäkelä Anna R. , Ernst Wolfgang , Grabherr Reingard , Oker-Blom Christian
Published: March 2010

INTRODUCTION

The baculovirus expression vector system has been used extensively to produce numerous proteins originating from both prokaryotic and eukaryotic sources. In addition to easy cloning techniques and abundant viral propagation, the system’s insect cell environment provides eukaryotic post-translational modification machinery. The baculovirus display vector system provides a number of advantages over prokaryotic systems, allowing the combination of genotype with phenotype, enabling presentation of foreign peptides or even complex proteins on the baculoviral envelope or capsid. Baculoviruses permit larger gene insertions, are easily propagated, and can be grown to high titers. Furthermore, surface modifications of the viral capsid enable specific targeting. This strategy can be used to enhance viral binding and entry to a wide variety of both dividing and nondividing mammalian cells, as well as to produce antibodies against the displayed antigen. In addition, the technology should enable modifications of intracellular behavior, i.e., trafficking of recombinant “nanoparticles,” a highly relevant feature for studies of targeted gene or protein delivery. Although baculovirus titer can be determined by standard methods such as classical plaque assays or end-point dilution assays, such methods often are tedious and time-consuming. The protocol described here is rapid and can be performed directly using marker genes such as green fluorescent protein or β-galactosidase regulated by baculovirus-specific promoters, or indirectly as an immunoassay with baculovirus-specific antibodies (e.g., anti-gp64).
Combined Transcript and Metabolite Profiling of Arabidopsis Grown under Widely Variant Growth Conditions Facilitates the Identification of Novel Metabolite-Mediated Regulation of Gene Expression
Authors: Hannah Matthew A. , Caldana Camila , Steinhauser Dirk , Balbo Ilse , Fernie Alisdair R. , Willmitzer Lothar
Published: February 2010

Regulation of metabolism at the level of transcription and its corollary metabolite-mediated regulation of transcription are well-documented mechanisms by which plants adapt to circumstance. That said the function of only a minority of transcription factor networks are fully understood and it seems likely that we have only identified a subset of the metabolites that play a mediator function in the regulation of transcription. Here we describe an integrated genomics approach in which we perform combined transcript and metabolite profiling on Arabidopsis (Arabidopsis thaliana) plants challenged by various environmental extremes. We chose this approach to generate a large variance in the levels of all parameters recorded. The data was then statistically evaluated to identify metabolites whose level robustly correlated with those of a particularly large number of transcripts. Since correlation alone provides no proof of causality we subsequently attempted to validate these putative mediators of gene expression via a combination of statistical analysis of data available in publicly available databases and iterative experimental evaluation. Data presented here suggest that, on adoption of appropriate caution, the approach can be used for the identification of metabolite mediators of gene expression. As an exemplary case study we document that in plants, as in yeast (Saccharomyces cerevisiae) and mammals, leucine plays an important role as a regulator of gene expression and provide a leucine response gene regulatory network.
RNA PROCESSING FACTOR2 Is Required for 5′ End Processing of nad9 and cox3 mRNAs in Mitochondria of Arabidopsis thaliana
Authors: Jonietz Christian , Forner Joachim , Hölzle Angela , Thuss Sabine , Binder Stefan
Published: February 2010

In mitochondria of higher plants, the majority of 5′ termini of mature mRNAs are generated posttranscriptionally. To gain insight into this process, we analyzed a natural 5′ end polymorphism in the species Arabidopsis thaliana. This genetic approach identified the nuclear gene At1g62670, encoding a pentatricopeptide repeat protein. The functional importance of this mitochondrial restorer of fertility-like protein, designated RNA PROCESSING FACTOR2 (RPF2), is confirmed by the analysis of a respective T-DNA knockout mutant and its functional restoration by in vivo complementation. RPF2 fulfills two functions: it is required for the generation of a distinct 5′ terminus of transcripts of subunit 9 of the NADH DEHYDROGENASE complex (nad9) and it determines the efficiency of 5′ end formation of the mRNAs for subunit 3 of the CYTOCHROME C OXIDASE (cox3), the latter also being influenced by mitochondrial DNA sequences. Accordingly, recombinant RPF2 protein directly binds to a nad9 mRNA fragment in vitro. Two-dimensional gel electrophoresis and immunodetection analyses reveal that altered 5′ processing does not influence accumulation of the nad9 and cox3 polypeptides. In accessions C24, Oystese-1, and Yosemite-0, different inactive RPF2 alleles exist, demonstrating the variability of this gene in Arabidopsis. The identification of RPF2 is a major step toward the characterization of 5′ mRNA processing in mitochondria of higher plants.