bluuebunny/crossref_metadata_2025_split huggingface dataset:
Juvenile Hormone Extraction, Purification, and Quantification in Ants
Authors: Brent Colin , Dolezal Adam 
Published: July 2009

INTRODUCTIONJuvenile hormone (JH) is an important insect hormone known to have many effects on development, reproduction, and behavior in both solitary and social insects. A number of questions using ants as a model involve JH. This procedure allows for quantification of circulating levels of JH III, which can be an important factor in many questions relating to insect research. The JH III is extracted from a subject, purified, and converted to a d3-methoxyhydrin derivative that can be quantified by gas chromatography-mass spectrometry (GC-MS). The major advantages of this protocol are its high resolution, and its ability to quantify significant differences between relatively small quantities of the hormone. Its major limitations are the time necessary to process samples, its relatively high cost, and maintaining the sensitivity of the equipment.
Ant Ecdysteroid Extraction and Radioimmunoassay
Authors: Brent Colin , Dolezal Adam 
Published: July 2009

INTRODUCTIONEcdysteroids are a group of steroid compounds present in many plant and invertebrate species. In arthropods, they function primarily as hormones involved in the regulation of molting. This protocol describes how to extract ecdysteroid hormones from ant specimens and subsequently quantify circulating levels of the hormone. The hormone can be extracted from hemolymph or from whole-body homogenates of insects and quantified by radioimmunoassay.
Phase-Unknown Linkage Mapping in Ants: Figure 1.
Authors: Gadau Jürgen 
Published: July 2009

INTRODUCTIONTo create a genetic linkage map of an ant genome, the phase of a marker (i.e., which marker/allele came from the grandmother and which came from the grandfather of the individuals used for linkage mapping) must be known. However, field colonies contain only two generations: the queen(s) and their offspring. Normally, virgin queens disperse from their nest, mate with one or multiple males who die after mating, and start a new colony. A new reproductive brood (i.e., virgin queens and males) is usually produced after colony establishment, which can take from 6 mo to 3-5 yr. Hence, determining the phase of markers from field samples is impossible because the grandparents of a reproductive queen are no longer available for genetic analysis. Ants raised in the laboratory are likewise unsuitable for such analyses, because most ants cannot be bred regularly in the laboratory, and attempts to inseminate ant queens artificially have not been successful. However, three features facilitate “phase-unknown” linkage mapping for any ant (or other social hymenopteran) species, which is described here: (1) Mature colonies usually produce many reproductive offspring during a short period of time, which allows for the collection of a good-sized mapping population (>100 males) from a field colony; (2) Ants have a haplodiploid sex determination system (i.e., males are haploid and females diploid); (3) Queens produce males parthenogenetically. Thus, because they have no father, only those markers for which the queen is heterozygous are expected to segregate 1:1 in her male offspring.
Preparation of High-Molecular-Weight DNA from Drosophila Embryos: Figure 1.
Authors: Karpen Gary H. 
Published: July 2009

INTRODUCTIONStandard methods for extracting DNA from cells or organisms (e.g., phenol extraction and ethanol precipitation) produce fragments with an average size of 50-200 kb under optimal conditions. The shearing forces that are applied to DNA in solution during mechanical vortexing or mixing and pipetting produce frequent double-stranded breaks. To prepare high-molecular-weight (HMW) DNA, it is necessary to guard against such damaging forces by performing all extractions and manipulations on DNA that is embedded within a protective matrix. Preparation of HMW DNA from Drosophila embryos is described in detail here because, in our hands, it is the simplest and most reliable protocol and can be used for large- or small-scale preparations. The overall strategy is to purify nuclei, gently embed them in molten agarose, and then extract proteins and perform other enzymatic reactions by transferring the solidified agarose block into the appropriate solutions. Salts, soaps, and enzymes act on the DNA by diffusing through the agarose matrix, while the matrix protects the DNA from shearing forces.
Using Hidden Markov Models to Align Multiple Sequences
Authors: Mount David W. 
Published: July 2009

INTRODUCTIONA hidden Markov model (HMM) is a probabilistic model of a multiple sequence alignment (msa) of proteins. In the model, each column of symbols in the alignment is represented by a frequency distribution of the symbols (called a “state”), and insertions and deletions are represented by other states. One moves through the model along a particular path from state to state in a Markov chain (i.e., random choice of next move), trying to match a given sequence. The next matching symbol is chosen from each state, recording its probability (frequency) and also the probability of going to that state from a previous one (the transition probability). State and transition probabilities are multiplied to obtain a probability of the given sequence. The hidden nature of the HMM is due to the lack of information about the value of a specific state, which is instead represented by a probability distribution over all possible values. This article discusses the advantages and disadvantages of HMMs in msa and presents algorithms for calculating an HMM and the conditions for producing the best HMM.
Using Multiple Sequence Alignment Editors and Formatters: Figure 1.
Authors: Mount David W. 
Published: July 2009

INTRODUCTIONSequence alignment editors enable the user to manually edit a multiple sequence alignment (msa) in order to obtain a more reasonable or expected alignment. Editors allow sequences to be reordered and/or modified using the computer’s cut and paste commands. They are designed to accept various msa formats and to provide the output file in a suitable user-designated format. Sequence formatters provide various output formatting options, such as color and shading schemes to enhance visualization of residue alignments. The formatters can output files in Postscript, EPS, RTF, and other widely recognized formats, while accepting the standard input formats, such as MSF, ALN, and FASTA. This article introduces a number of sequence alignment editors and formatters, and provides links to sites where they can be found.
The PLASTID DIVISION1 and 2 Components of the Chloroplast Division Machinery Determine the Rate of Chloroplast Division in Land Plant Cell Differentiation
Authors: Okazaki Kumiko , Kabeya Yukihiro , Suzuki Kenji , Mori Toshiyuki , Ichikawa Takanari , Matsui Minami , Nakanishi Hiromitsu , Miyagishima Shin-ya 
Published: July 2009

AbstractIn most algae, the chloroplast division rate is held constant to maintain the proper number of chloroplasts per cell. By contrast, land plants evolved cell and chloroplast differentiation systems in which the size and number of chloroplasts change along with their respective cellular function by regulation of the division rate. Here, we show that PLASTID DIVISION (PDV) proteins, land plant–specific components of the division apparatus, determine the rate of chloroplast division. Overexpression of PDV proteins in the angiosperm Arabidopsis thaliana and the moss Physcomitrella patens increased the number but decreased the size of chloroplasts; reduction of PDV levels resulted in the opposite effect. The level of PDV proteins, but not other division components, decreased during leaf development, during which the chloroplast division rate also decreased. Exogenous cytokinins or overexpression of the cytokinin-responsive transcription factor CYTOKININ RESPONSE FACTOR2 increased the chloroplast division rate, where PDV proteins, but not other components of the division apparatus, were upregulated. These results suggest that the integration of PDV proteins into the division machinery enabled land plant cells to change chloroplast size and number in accord with the fate of cell differentiation.
Prognostic impact of immunohistochemical biomarkers in diffuse large B‐cell lymphoma in the rituximab era
Authors: Seki Ritsuko , Ohshima Koichi , Fujisaki Tomoaki , Uike Naokuni , Kawano Fumio , Gondo Hisashi , Makino Shigeyoshi , Eto Tetsuya , Moriuchi Yukiyoshi , Taguchi Fumihiro , Kamimura Tomohiko , Tsuda Hiroyuki , Ogawa Ryosuke , Shimoda Kazuya , Yamashita Kiyoshi , Suzuki Keiko , Suzushima Hitoshi , Tsukazaki Kunihiro , Higuchi Masakazu , Utsunomiya Atae , Iwahashi Masahiro , Imamura Yutaka , Tamura Kazuo , Suzumiya Junji , Yoshida Minoru , Abe Yasunobu , Matsumoto Tadashi , Okamura Takashi 
Published: July 2009

We evaluated the usefulness of prognostic markers in patients with diffuse large B‐cell lymphoma (DLBCL) treated with cyclophosphamide, vincristine, doxorubicin, and prednisolone (CHOP) ± rituximab (R‐CHOP) in Japan. We studied 730 patients with DLBCL; 451 received CHOP and 279 R‐CHOP. We analyzed biopsy samples immunohistochemically for markers of germinal center B cells (CD10, Bcl‐6), postgerminal center B cells (Multiple myeloma‐1), and apoptosis (Bcl‐2). The median follow‐up period for surviving patients was 56.4 months for the CHOP group and 25.2 months for the R‐CHOP group. DLBCL were categorized as germinal center B (GCB) subtype (352/730; 48.2%) or non‐GCB subtype (378/730; 51.8%). In the CHOP group, the high expression of CD10 (P = 0.022) or Bcl‐6 (P = 0.021), or GCB subtype (P = 0.05) was associated with better overall survival, whereas the high expression of Bcl‐2 (P = 0.001) or MUM1 (P = 0.011), or non‐GCB subtype (P = 0.05) was associated with worse overall survival. In the R‐CHOP group, however, these biomarkers except Bcl‐6 were not significant prognostic factors. The patients with non‐GCB subtype showed improved survival in the R‐CHOP group (P = 0.756). The International Prognostic Index was a useful clinical marker of survival in the CHOP group (P < 0.001) and also in the R‐CHOP group (P < 0.001). Results of improved survival with rituximab addition indicate that the relevance of previously recognized prognostic factors should be re‐evaluated. (Cancer Sci 2009; 100: 1842–1847)
Heat shock protein 70‐binding protein 1 is highly expressed in high‐grade gliomas, interacts with multiple heat shock protein 70 family members, and specifically binds brain tumor cell surfaces
Authors: Graner Michael W. , Raynes Deborah A. , Bigner Darell D. , Guerriero Vince 
Published: July 2009

Chaperone proteins and heat shock proteins (HSP) are essential components of cellular protein folding systems under normal conditions; their expression and activities are upregulated during stress. Chronically stressed tumors frequently exhibit high chaperone protein levels, exploiting their anti‐apoptotic mechanisms and general proteome homeostasis amidst a background of genetic instability. Co‐chaperones interact with chaperones as malleable regulatory components of protein folding activity and may represent a conduit for modification of chaperone activity to the detriment of the tumor. We have initially characterized one such co‐chaperone, heat shock protein 70‐binding protein (HspBP) 1 from human brain tumors, their xenografts grown in immune‐compromised mice, and in syngeneic murine models in immune‐competent mice. Immunohistochemical analyses show HspBP1 overexpression (with unusual subcellular localizations) in patient brain tumors relative to normal brain tissue. This holds true for the xenograft and syngeneic murine tumor models. In biochemical affinity chromatography assays, HspBP1 interacts with members of the HSP70 family from brain tumor lysates and from surface‐derived samples, including HSP70, glucose regulated protein (GRP)75, GRP78, and HSP110. From normal brain lysates, only heat shock cognate (HSC)70, GRP75, and HSP110 bind to HspBP1. FACS analyses indicate that HspBP1 binds to brain tumor cell surfaces, possibly via HSP70 family members, and internalizes into cells. This has implications for HspBP1 biology as well as its utility as a tumor‐targeting agent. Our results suggest that HspBP1 may play a role in tumor (dys)regulation of chaperone proteins, and that HspBP1 may have extracellular roles with therapeutic implications. (Cancer Sci 2009; 100: 1870–1879)
Immunotherapy of ovarian cancer with cell wall skeleton of Mycobacterium bovis Bacillus Calmette‐Guérin: Effect of lymphadenectomy
Authors: Hayashi Akira , Nishida Yuichi , Yoshii Saiji , Kim Seo Young , Uda Hirotsugu , Hamasaki Toshimitsu 
Published: July 2009

The significance of lymphadenectomy in surgery for various kinds of cancer has been widely debated, particularly in the gynecological field. The cell wall skeleton of Mycobacterium bovis Bacillus Calmette‐Guérin (BCG‐CWS) has been used as an effective adjuvant for immunotherapy of a variety of cancer patients. Here we tested the immunological importance of lymph nodes in treatment of ovarian cancer patients with BCG‐CWS. After surgical removal of tumors, 73 ovarian cancer patients were intracutaneously inoculated with BCG‐CWS in the antigen‐unloaded state in the upper arm at 4‐week intervals at a dosage of 2–200 µg. Significant correlation of lymphadenectomy and reduced survival of patients was observed (stages I, II, III, IV; hazard ratio 2.38, 95% confidence interval 1.02–5.12, Cox regression model). Lymphadenectomy also compromised with induction of interferon‐γ. In view of the importance of the role of lymph nodes in stimulation of Toll‐like receptors by BCG‐CWS, it is suggested that lymph nodes should be kept as much as possible to preserve the patient's immunity against cancer. Application of these results to surgery for other cancers should be considered. (Cancer Sci 2009; 100: 1991–1995)
Probiotics for the treatment of eczema: a systematic review
Authors: Boyle R. J. , Bath‐Hextall F. J. , Leonardi‐Bee J. , Murrell D. F. , Tang M. L‐K 
Published: July 2009

SummaryBackground
Probiotics have been proposed as a treatment for eczema, but the results of intervention trials have been mixed.Objective
To evaluate the efficacy of probiotics for treating eczema by performing a systematic review of randomized‐controlled trials (RCTs).Design
We searched the Cochrane Skin Group Specialised Register, Cochrane Central Register of Controlled Trials, MEDLINE, EMBASE, PsycINFO, AMED, LILACS, ISI Web of Science, the reference lists of articles, ongoing clinical trial registers and conference proceedings. RCTs of live orally ingested microorganisms for the treatment of eczema were eligible for inclusion.Results
Twelve trials (781 participants) were identified. Meta‐analysis of data from five of these trials showed that there was no significant reduction in eczema symptoms with probiotic treatment compared with placebo (mean difference −0.90 points on a 20‐point visual analogue scale; 95% confidence interval −2.84, 1.04). Meta‐analysis of data from seven trials showed no significant difference in investigator rated eczema severity between probiotic and placebo treatments. Subgroup analysis by eczema severity or presence of atopy did not identify a specific population in which probiotic treatment was effective. There was significant heterogeneity between studies; however, the results of three studies that used the same probiotic strain were concordant. The adverse events search identified case reports of sepsis and bowel ischaemia caused by probiotics.Conclusions
Currently, probiotics cannot be recommended for treating eczema. The heterogeneity between studies may be attributable to probiotic strain‐specific effects, which means that novel probiotic strains may still have a role in eczema management.
Plasticity in vertical behaviour of migrating juvenile southern bluefin tuna (Thunnus maccoyii) in relation to oceanography of the south Indian Ocean
Authors: BESTLEY SOPHIE , GUNN JOHN S. , HINDELL MARK A. 
Published: July 2009

AbstractElectronic tagging provides unprecedented information on the habitat use and behaviour of highly migratory marine predators, but few analyses have developed quantitative links between animal behaviour and their oceanographic context. In this paper we use archival tag data from juvenile southern bluefin tuna (Thunnus maccoyii, SBT) to (i) develop a novel approach characterising the oceanographic habitats used throughout an annual migration cycle on the basis of water column structure (i.e., temperature‐at‐depth data from tags), and (ii) model how the vertical behaviour of SBT altered in relation to habitat type and other factors. Using this approach, we identified eight habitat types occupied by juvenile SBT between the southern margin of the subtropical gyre and the northern edge of the Subantarctic Front in the south Indian Ocean. Although a high degree of variability was evident both within and between fish, mixed‐effect models identified consistent behavioural responses to habitat, lunar phase, migration status and diel period. Our results indicate SBT do not act to maintain preferred depth or temperature ranges, but rather show highly plastic behaviours in response to changes in their environment. This plasticity is discussed in terms of the potential proximate causes (physiological, ecological) and with reference to the challenges posed for habitat‐based standardisation of fishery data used in stock assessments.
Theory, methods and tools for determining environmental flows for riparian vegetation: riparian vegetation‐flow response guilds
Authors: MERRITT DAVID M. , SCOTT MICHAEL L. , LeROY POFF N. , AUBLE GREGOR T. , LYTLE DAVID A. 
Published: July 2009

Summary1. Riparian vegetation composition, structure and abundance are governed to a large degree by river flow regime and flow‐mediated fluvial processes. Streamflow regime exerts selective pressures on riparian vegetation, resulting in adaptations (trait syndromes) to specific flow attributes. Widespread modification of flow regimes by humans has resulted in extensive alteration of riparian vegetation communities. Some of the negative effects of altered flow regimes on vegetation may be reversed by restoring components of the natural flow regime.2. Models have been developed that quantitatively relate components of the flow regime to attributes of riparian vegetation at the individual, population and community levels. Predictive models range from simple statistical relationships, to more complex stochastic matrix population models and dynamic simulation models. Of the dozens of predictive models reviewed here, most treat one or a few species, have many simplifying assumptions such as stable channel form, and do not specify the time‐scale of response. In many cases, these models are very effective in developing alternative streamflow management plans for specific river reaches or segments but are not directly transferable to other rivers or other regions.3. A primary goal in riparian ecology is to develop general frameworks for prediction of vegetation response to changing environmental conditions. The development of riparian vegetation‐flow response guilds offers a framework for transferring information from rivers where flow standards have been developed to maintain desirable vegetation attributes, to rivers with little or no existing information.4. We propose to organise riparian plants into non‐phylogenetic groupings of species with shared traits that are related to components of hydrologic regime: life history, reproductive strategy, morphology, adaptations to fluvial disturbance and adaptations to water availability. Plants from any river or region may be grouped into these guilds and related to hydrologic attributes of a specific class of river using probabilistic response curves.5. Probabilistic models based on riparian response guilds enable prediction of the likelihood of change in each of the response guilds given projected changes in flow, and facilitate examination of trade‐offs and risks associated with various flow management strategies. Riparian response guilds can be decomposed to the species level for individual projects or used to develop flow management guidelines for regional water management plans.
Greenhouse gas fluxes from tropical peatlands in south‐east Asia
Authors: COUWENBERG JOHN , DOMMAIN RENÉ , JOOSTEN HANS 
Published: July 2009

AbstractThe lowland peatlands of south‐east Asia represent an immense reservoir of fossil carbon and are reportedly responsible for 30% of the global carbon dioxide (CO2) emissions from Land Use, Land Use Change and Forestry. This paper provides a review and meta‐analysis of available literature on greenhouse gas fluxes from tropical peat soils in south‐east Asia. As in other parts of the world, water level is the main control on greenhouse gas fluxes from south‐east Asian peat soils. Based on subsidence data we calculate emissions of at least 900 g CO2 m−2 a−1 (∼250 g C m−2 a−1) for each 10 cm of additional drainage depth. This is a conservative estimate as the role of oxidation in subsidence and the increased bulk density of the uppermost drained peat layers are yet insufficiently quantified. The majority of published CO2 flux measurements from south‐east Asian peat soils concerns undifferentiated respiration at floor level, providing inadequate insight on the peat carbon balance. In contrast to previous assumptions, regular peat oxidation after drainage might contribute more to the regional long‐term annual CO2 emissions than peat fires. Methane fluxes are negligible at low water levels and amount to up to 3 mg CH4 m−2 h−1 at high water levels, which is low compared with emissions from boreal and temperate peatlands. The latter emissions may be exceeded by fluxes from rice paddies on tropical peat soil, however. N2O fluxes are erratic with extremely high values upon application of fertilizer to wet peat soils. Current data on CO2 and CH4 fluxes indicate that peatland rewetting in south‐east Asia will lead to substantial reductions of net greenhouse gas emissions. There is, however, an urgent need for further quantitative research on carbon exchange to support the development of consistent policies for climate change mitigation.
The importance of mesophyll conductance in regulating forest ecosystem productivity during drought periods
Authors: KEENAN TREVOR , SABATE SANTI , GRACIA CARLOS 
Published: July 2009

AbstractWater availability is the most limiting factor to global plant productivity, yet photosynthetic responses to seasonal drought cycles are poorly understood, with conflicting reports on which limiting process is the most important during drought. We address the problem using a model‐data synthesis approach to look at canopy level fluxes, integrating twenty years of half hour data gathered by the FLUXNET network across six Mediterranean sites. The measured canopy level, water and carbon fluxes were used, together with an inverse canopy ecophysiological model, to estimate the bulk canopy conductance, bulk mesophyll conductance, and the canopy scale carbon pools in both the intercellular spaces and at the site of carboxylation in the chloroplasts. Thus the roles of stomatal and mesophyll conductance in the regulation of internal carbon pools and photosynthesis could be separated. A quantitative limitation analysis allowed for the relative seasonal responses of stomatal, mesophyll, and biochemical limitations to be gauged. The concentration of carbon in the chloroplast was shown to be a potentially more reliable estimator of assimilation rates than the intercellular carbon concentration. Both stomatal conductance limitations and mesophyll conductance limitations were observed to regulate the response of photosynthesis to water stress in each of the six species studied. The results suggest that mesophyll conductance could bridge the gap between conflicting reports on plant responses to soil water stress, and that the inclusion of mesophyll conductance in biosphere–atmosphere transfer models may improve their performance, in particular their ability to accurately capture the response of terrestrial vegetation productivity to drought.