Dataset Papers in Science The latest articles from Hindawi Publishing Corporation © 2014 , Hindawi Publishing Corporation . All rights reserved. FTIR Spectra of n-Octanol in Liquid and Solid States Wed, 23 Apr 2014 13:50:59 +0000 The investigation of the temperature dependence of FTIR spectrum of n-octanol in the temperature range from −150°C to 50°C is presented. The observed changes in the registered spectra during gradual heating of the sample were analysed. The structure transformation at the phase transition from solid to liquid phase is detected. A. Vasileva, P. Golub, I. Doroshenko, V. Pogorelov, V. Sablinskas, V. Balevicius, and J. Ceponkus Copyright © 2014 A. Vasileva et al. All rights reserved. Morphological Characterisation of Some Important Indian Garcinia Species Wed, 23 Apr 2014 13:45:38 +0000 The genus Garcinia has over 200 species distributed in the tropics of the world. About 35 species occur in India, many of which are endemic and economically important with immense medicinal properties. However, lack of awareness, coupled with habitat destruction, leads to genetic erosion of this forest resource and many species are threatened. The Indian Institute of Spices Research (IISR), Calicut, has Garcinia genetic resources’ collection of 15 species of Western Ghats and Eastern Himalaya species. The morphological characterisation of the species of these two different eco systems indicates that there are variations within the species of the same ecosystem while there are similarities in the species of two different ecosystems. Utpala Parthasarathy and O. P. Nandakishore Copyright © 2014 Utpala Parthasarathy and O. P. Nandakishore. All rights reserved. DNA Microarray Assay Helps to Identify Functional Genes Specific for Leukemia Stem Cells Wed, 04 Sep 2013 08:35:57 +0000 Chronic myeloid leukemia (CML) is a myeloproliferative disease derived from an abnormal hematopoietic stem cell (HSC) and is consistently associated with the formation of Philadelphia (Ph) chromosome. Tyrosine kinase inhibitors (TKIs) are highly effective in treating chronic phase CML but do not eliminate leukemia stem cells (LSCs), which are believed to be related to disease relapse. Therefore, one major challenge in the current CML research is to understand the biology of LSCs and to identify the molecular difference between LSCs and its normal stem cell counterparts. Comparing the gene expression profiles between LSCs and normal HSCs by DNA microarray assay is a systematic and unbiased approach to address this issue. In this paper, we present a DNA microarray dataset for CML LSCs and normal HSCs to show that the microarray assay will benefit the current and future studies of the biology of CML stem cells. Haojian Zhang and Shaoguang Li Copyright © 2013 Haojian Zhang and Shaoguang Li. All rights reserved. Molecular Data for the Sea Turtle Population in Brazil Thu, 22 Aug 2013 08:00:21 +0000 We report here a dataset comprising nine nuclear markers for the Brazilian population of Cheloniidae turtles: hawksbills (Eretmochelys imbricata), loggerheads (Caretta caretta), olive ridleys (Lepidochelys olivacea), and green turtles (Chelonia mydas). Because hybridization is a common phenomenon between the four Cheloniidae species nesting on the Brazilian coast, we also report molecular markers for the hybrids E. imbricata × C. caretta, C. caretta × L. olivacea, and E. imbricata × L. olivacea and for one hybrid E. imbricata × C. mydas and one between three species C. mydas × E. imbricata × C. caretta. The data was used in previous studies concerning (1) the description of frequent hybrids C. caretta × E. imbricata in Brazil, (2) the report of introgression in some of these hybrids, and (3) population genetics. As a next step for the study of these hybrids and their evolution, genome-wide studies will be performed in the Brazilian population of E. imbricata, C. caretta, and their hybrids. Sibelle Torres Vilaça and Fabricio Rodrigues dos Santos Copyright © 2013 Sibelle Torres Vilaça and Fabricio Rodrigues dos Santos. All rights reserved. Investigation of the Working Parameters of a Single Magnetron of a Multiple Ion Cluster Source: Determination of the Relative Influence of the Parameters on the Size and Density of Nanoparticles Sun, 18 Aug 2013 10:51:35 +0000 Multiple Ion Cluster Source (MICS) is the new optimized route of a standard technique based on a sputtering gas aggregation source, the Ion Cluster Source. The single magnetron used in the standard Ion Cluster Source is replaced by three magnetrons inside the aggregation zone, and they are controlled individually in order to fabricate nanoparticles with the desired and tunable chemical composition. Apart from the working parameters of each magnetron, it is also reported that the relation between the working parameters of individual magnetrons is of prime importance for the control of both the size and density of the nanoparticles. The influences of fluxes of the sputtering gas applied to each magnetron, the total gas flux in the aggregation zone, the position in the aggregation zone of Ag magnetron, and the relative position of the magnetrons in the aggregation zone have been studied through the operation of one of the magnetrons loaded with a silver target. Manuel Ruano, Lidia Martínez, and Yves Huttel Copyright © 2013 Manuel Ruano et al. All rights reserved. Rainfall, Soil Water Content, and Groundwater Levels at the Riverlands Nature Reserve (South Africa) Sun, 16 Jun 2013 08:05:43 +0000 Quantified medium- and long-term hydrological datasets are scarce in South Africa, yet they are essential to gain understanding of natural systems, contribute to ecosystem conservation, and ultimately quantify water balance processes accurately. A hydrological experiment was carried out at Riverlands Nature Reserve (Western Cape, South Africa) in order to quantify the components of the soil water balance at experimental sites occupied by endemic and invasive vegetation. In two separate follow-up projects, five-year time series were collected in three treatments, namely, endemic fynbos vegetation, bare soil, and land invaded by Acacia saligna. Rainfall was recorded daily with a manual rain gauge. Groundwater levels were logged hourly at 14 boreholes. Volumetric soil water contents and soil temperatures were logged hourly at different depths in the soil profile. Groundwater levels and soil water contents responded to rainfall with very clear seasonal trends. The data can be applied in water balance and evapotranspiration studies, unsaturated flux studies, soil temperature profile studies, and rainfall-groundwater level response analysis and for calibrating and validating a wide range of hydrological models. Nebo Jovanovic, Richard D. H. Bugan, and Sumaya Israel Copyright © 2013 Nebo Jovanovic et al. All rights reserved. Temperature Evolution of Cluster Structures in Ethanol Sun, 02 Jun 2013 09:30:42 +0000 The dependence of FTIR spectrum of pure ethanol on the temperature was investigated. The measurements were performed for frozen (the minimum temperature −180°C) and liquid ethanol (the maximum temperature 40°C). All changes in IR spectrum of ethanol during gradual warming were detected and analyzed. On the bases of preset observations, the conclusions concerning the evolution of cluster structures in ethanol during transition from solid (frozen) state to liquid state were made. P. Golub, I. Doroshenko, V. Pogorelov, V. Sablinskas, V. Balevicius, and J. Ceponkus Copyright © 2013 P. Golub et al. All rights reserved. A Benchmark Dataset Comprising Partition and Distribution Coefficients of Linear Peptides Thu, 16 May 2013 11:30:17 +0000 Peptides have a dominant role in biology; yet the study of their physical properties is at best sporadic. Peptide quantitative structure-activity relationship (QSAR) lags far behind the QSAR analysis of drug-like organic small molecules. Traditionally, QSAR has focussed on experimentally determined partition coefficients as the main descriptor of hydrophobicity. A partition coefficient () is the ratio between the concentrations of an uncharged chemical substance in two immiscible phases: most typically water and an organic solvent, usually 1-octanol. A distribution coefficient () is the equivalent ratio for charged molecules. We report here a compilation of partition and distribution coefficients for linear peptides compiled from literature reports, suitable for the development and benchmarking of peptide and prediction algorithms. Matthew N. Davies and Darren R. Flower Copyright © 2013 Matthew N. Davies and Darren R. Flower. All rights reserved. Judd-Ofelt Calculations for Nd3+-Doped Fluorozirconate-Based Glasses and Glass Ceramics Thu, 11 Apr 2013 09:04:44 +0000 A Judd-Ofelt analysis is performed to calculate the optical properties of Nd3+ ions embedded in a fluorozirconate glass matrix. The changes in the Judd-Ofelt parameters were determined as a function of the size of BaCl2 nanocrystals grown inside the matrix. From these data, the radiative decay rates and the branching ratios of every transition in the energy range from 25.000 cm−1 to the ground state are calculated. This was accomplished for samples containing nanocrystals with average sizes ranging from 10 to 40 nm. U. Skrzypczak, C. Pfau, C. Bohley, G. Seifert, and S. Schweizer Copyright © 2013 U. Skrzypczak et al. All rights reserved. Bending Angle and Temperature Climatologies from Global Positioning System Radio Occultations Wed, 27 Mar 2013 12:19:15 +0000 The Global Positioning System (GPS) Radio Occultation (OR) technique provides estimates of atmospheric density, temperature, and water vapour content with high vertical resolution, global coverage, and high accuracy. We have used data acquired using this technique in the period 1995–2009 to create a reference climatology of radio occultation bending angle and atmospheric temperature which are used for meteorological studies. The bending angle is interesting because it is a direct measurement and independent of models. It is given with one-degree spatial resolution and 50-meter vertical sampling. In addition, we give the temperature climatology with one-degree spatial resolution and 100-meter vertical sampling. This dataset can be used for several applications including weather forecast, physics of atmosphere, and climate changes. Since the GPS signal is not affected by clouds and the acquisitions are evenly distributed in the globe, the dataset is well suited for studying extreme events (such as convective systems and tropical cyclones) and remote areas. R. Biondi and T. Neubert Copyright © 2013 R. Biondi and T. Neubert. All rights reserved. Global Speleothem Oxygen Isotope Measurements Since the Last Glacial Maximum Tue, 26 Mar 2013 08:45:53 +0000 This synthesis of thirty-six sites (sixty cores with over 27 000 measurements) located around the world facilitates scientific research on the climate of the last 21 000 years ago obtained from oxygen isotope ( or delta-O-18) measurements. Oxygen isotopes in speleothem calcite record the influence of ambient temperature and the isotopic composition of the source water, the latter providing evidence of hydrologic variability and change. Compared to paleoclimate proxies from sedimentary archives, the age uncertainty is unusually small, around +/−100 years for the last 21 000-year interval. Using data contributed to the World Data Center (WDC) for Paleoclimatology, we have created consistently formatted data files for individual sites as well as composite dataset of annual to millennial resolution. These individual files also contain the chronology information about the sites. The data are useful in understanding hydrologic variability at local and regional scales, such as the Asian summer monsoon and the Intertropical Convergence Zone (as discussed in the underlying source publications), and should also be useful in understanding large-scale aspects of hydrologic change since the Last Glacial Maximum (LGM). A. M. Shah, C. Morrill, E. P. Gille, W. S. Gross, D. M. Anderson, B. A. Bauer, R. Buckner, and M. Hartman Copyright © 2013 A. M. Shah et al. All rights reserved. Optical Constants of - and -Zinc(II)-Phthalocyanine Films Sun, 24 Feb 2013 15:00:01 +0000 We present a dataset of the optical constants of α- and β-zinc(II)-phthalocyanine (ZnPc). They were determined accurately from transmission and differential reflectance spectra, with the surface roughness taken into account. For this purpose, thin films were prepared on quartz glass substrates via physical vapor deposition and characterized by ultraviolet-visible (UV-Vis) spectroscopy before as well as after a well-defined annealing process. Kramers-Kronig consistency of the optical constants obtained was checked by means of a numerical algorithm. Michael Kozlik, Sören Paulke, Marco Gruenewald, Roman Forker, and Torsten Fritz Copyright © 2013 Michael Kozlik et al. All rights reserved. Extending MapMan Ontology to Tobacco for Visualization of Gene Expression Wed, 20 Feb 2013 15:31:22 +0000 Microarrays are a large-scale expression profiling method which has been used to study the transcriptome of plants under various environmental conditions. However, manual inspection of microarray data is difficult at the genome level because of the large number of genes (normally at least 30 000) and the many different processes that occur within any given plant. MapMan software, which was initially developed to visualize microarray data for Arabidopsis, has been adapted to other plant species by mapping other species onto MapMan ontology. This paper provides a detailed procedure and the relevant computing codes to generate a MapMan ontology mapping file for tobacco (Nicotiana tabacum L.) using potato and Arabidopsis as intermediates. The mapping file can be used directly with our custom-made NimbleGen oligoarray, which contains gene sequences from both the tobacco gene space sequence and the tobacco gene index 4 (NTGI4) collection of ESTs. The generated dataset will be informative for scientists working on tobacco as their model plant by providing a MapMan ontology mapping file to tobacco, homology between tobacco coding sequences and that of potato and Arabidopsis, as well as adapting our procedure and codes for other plant species where the complete genome is not yet available. Maurice H. T. Ling, Roel C. Rabara, Prateek Tripathi, Paul J. Rushton, and Xijin Ge Copyright © 2013 Maurice H. T. Ling et al. All rights reserved. First Y-Short Tandem Repeat Categorical Dataset for Clustering Applications Sun, 17 Feb 2013 11:58:13 +0000 The Y-chromosome short tandem repeat (Y-STR) data are mainly collected for a performance benchmarking result in clustering methods. There are six Y-STR dataset items, divided into two categories: Y-STR surname and Y-haplogroup data presented here. The Y-STR data are categorical, unique, and different from the other categorical data. They are composed of a lot of similar and almost similar objects. This characteristic of the Y-STR data has caused certain problems of the existing clustering algorithms in clustering them. Ali Seman, Zainab Abu Bakar, and Mohamed Nizam Isa Copyright © 2013 Ali Seman et al. All rights reserved. A Microarray Dataset of Genes Expressed by the R28 Retinal Precursor Cell Line Thu, 14 Feb 2013 15:34:11 +0000 The R28 rat retinal progenitor cell line was developed from postnatal day six rat retina immortalized with the 12S E1A gene of adenovirus. R28 cells have been distributed to over 100 laboratories worldwide, with over 60 publications on topics that include in vitro toxicology, cellular physiology, gene expression analysis, and experimental transplantation. In this paper, we present a microarray dataset of R28 cells that describes the presence or absence of 8799 genes and ESTs that may be relevant to current and future studies of R28 retinal precursor cells. Gail M. Seigel and Richard J. Salvi Copyright © 2013 Gail M. Seigel and Richard J. Salvi. All rights reserved. Long-Term Aerosol Climate Data Record Derived from Operational AVHRR Satellite Observations Thu, 14 Feb 2013 15:08:50 +0000 Aerosol optical thickness (AOT) was retrieved using the Advanced Very High Resolution Radiometer (AVHRR) PATMOS-x Level-2b gridded radiances and the two-channel algorithm of the National Climatic Data Center (NCDC). The primary retrieval product is AOT at 0.63 μm channel. AOT is also retrieved at 0.83 μm or 1.61 μm channel for consistent check. The retrieval was made during day time, under clear sky and snow-free conditions, and over the global oceans. The spatial resolution is degree grid and the temporal resolution is both daily and monthly. The resultant AVHRR AOT climate data record (CDR) spans from August 1981 to December 2009 and provides the longest aerosol CDR currently available from operational satellites. This dataset is useful in studying aerosol climate forcing, monitoring long-term aerosol trends, and evaluating global air pollution and aerosol transport models over the global ocean. P. K. Chan, X.-P. Zhao, and A. K. Heidinger Copyright © 2013 P. K. Chan et al. All rights reserved. Detection of Introns in Eukaryotic Small Subunit Ribosomal RNA Gene Sequences Wed, 06 Feb 2013 16:19:26 +0000 The gene encoding SSU-rRNA sequences is the tool of choice for phylogenetic analyses and environmental biodiversity analyses of bacteria, Archaea but also unicellular Eukaryota. In Eukaryota, gene sequences may often be interrupted by long or several introns. Searching in GenBank release 188, we found descriptions of 3638 such sequences. Using a database of 180 000 SSU-rRNA sequences well annotated for taxonomy and a C++ program written for that purpose, we computed the presence of 18 691 introns (among which the 3638 described introns). Filtering on length and sequence quality, 3646 sequences were retained. These introns were clustered; clusters were analyzed for the presence of single or multiple clades at various levels of taxonomic depth, allowing future analyses of horizontal transfers. Various analyses of the results are provided as tabulated files as well as FASTA files of described or computed introns. Each sequence is annotated for cellular location (nuclear, chloroplast, and mitochondria), positions at which they were found in the SSU-rRNA sequences and taxonomy as provided by GenBank. Dipankar Bachar, Laure Guillou, and Richard Christen Copyright © 2013 Dipankar Bachar et al. All rights reserved. Rodent Carcinogenicity Dataset Thu, 17 Jan 2013 09:49:18 +0000 The rodent carcinogenicity dataset was compiled from the Carcinogenic Potency Database (CPDBAS) and was applied for the classification of quantitative structure-activity relationship (QSAR) models for the prediction of carcinogenicity based on the counter-propagation artificial neural network (CP ANN) algorithm. The models were developed within EU-funded project CAESAR for regulatory use. The dataset contains the following information: common information about chemicals (ID, chemical name, and their CASRN), molecular structure information (SDF files and SMILES), and carcinogenic (toxicological) properties information: carcinogenic potency (TD50_Rat_mg; carcinogen/noncarcinogen) and structural alert (SA) for carcinogenicity based on mechanistic data. Molecular structure information was used to get chemometrics information to calculate molecular descriptors (254 MDL and 784 Dragon descriptors), which were further used in predictive QSAR modeling. The dataset presented in the paper can be used in future research in oncology, ecology, or chemicals' risk assessment. Natalja Fjodorova and Marjana Novič Copyright © 2013 Natalja Fjodorova and Marjana Novič. All rights reserved. Efficacy and Safety of Botulinum Toxin A for Treating Bladder Hyperactivity in Children and Adolescents with Neuropathic Bladder Secondary to Myelomeningocele Thu, 17 Jan 2013 08:10:23 +0000 We verified the efficacy and safety of botulinum toxin A (BTX-A) in treating bladder overactivity in children with neurogenic bladder (NB) secondary to myelomeningocele (MMC). Forty-seven patients (22, females; 25, males; age range, 5–17 years; mean age, 10.7 years) with poorly compliant/overactive neurogenic bladder on clean intermittent catheterization (CIC) and resistance or noncompliant to anticholinergics were injected with 200 IU of BTX-A intradetrusor. All patients experienced a significant 66.45% average increase of leak point volume (Wilcoxon paired rank test = 7.169 e-10) and a significant 118.57% average increase of specific bladder capacity at 20 cm H2O (Wilcoxon paired rank test = 2.466 e-12). Ten patients who presented with concomitant uni/bilateral grade II–IV vesicoureteral reflux were treated at the same time with Deflux. No patient presented with major perioperative or postoperative problems. Twenty-two patients needed a second and 18 a third injection of BTX-A after 6–9 months for the reappearance of symptoms. After a mean follow-up of 5.7 years, 38 out of 47 patients achieved dryness between CICs, and 9 patients improved their incontinence but still need pads. Our conclusion is that BTX-A represents a viable alternative to more invasive procedure in treatment of overactive NB secondary to MMC. Antonio Marte, Micaela Borrelli, Maurizio Prezioso, Lucia Pintozzi, and Pio Parmeggiani Copyright © 2013 Antonio Marte et al. All rights reserved. Alterations of Hormone-Sensitive Adenylyl Cyclase System in the Tissues of Rats with Long-Term Streptozotocin Diabetes and the Influence of Intranasal Insulin Thu, 27 Dec 2012 08:20:17 +0000 One of the causes of complications in type 1 diabetes mellitus (T1DM) is the changes in adenylyl cyclase (AC) signaling system, identified on the early stages of the disease. However, the most significant disturbances in this system occur on the later stages of T1DM, which ultimately leads to severe complications, but functional state of the AC system in late T1DM is poorly understood. The aim of this work was to study alterations in AC system sensitive to biogenic amines and polypeptide hormones in the heart, brain, and testes of male rats with long-term, 7-month, streptozotocin T1DM and to assess the influence on them of 135-day therapy with intranasal insulin. It was shown that AC effects of -adrenergic agonists in the heart, serotonin receptor agonists and PACAP-38 in the brain, chorionic gonadotropin and PACAP-38 in the testes, and somatostatin in all investigated tissues in long-term T1DM were drastically decreased. The treatment with intranasal insulin (0.48 IU/day) significantly restored these effects. The results were obtained suggesting that long-term T1DM induces significant alterations in hormone-sensitive AC system in the heart, brain, and testes that are much more pronounced, compared with short-term T1DM, and include a large number of hormonal regulations. Alexander O. Shpakov, Kira V. Derkach, Irina V. Moyseyuk, and Oksana V. Chistyakova Copyright © 2013 Alexander O. Shpakov et al. All rights reserved. Solubility Data of Comonomer Pairs Relevant to Aqueous-Phase Study in the Emulsion Copolymerization Wed, 12 Dec 2012 11:37:25 +0000 In emulsion copolymerizations, the two monomers might not be equally incorporated in the copolymers. Besides copolymerization in the particles, also copolymerization in the aqueous phase can take place which affects the formation of oligomeric radicals responsible for the entry of radicals into the particles. In describing copolymerization in emulsion polymerization, one can use the normal reactivity ratios in combination with the monomer feed ratios in the phase at hand (either water phase or particle phase). Most of the research works done were focused on the feed ratio of the monomers in the particle phase. This is because of the interest in the final product. But in case of water-soluble monomers, where significant amount of polymerization already occurs in the water phase, feed ratios of monomers in the water phase have to be known. Even for less water-soluble monomers, the feed ratios in the aqueous phase are important to know, related to entry of radicals. Therefore, to calculate feed ratios in water phase, solubilities of mixtures of monomers in this phase have been measured by using a UV-Vis technique. It is shown that the solubility of one monomer is influenced by the presence of another monomer. Pooja Daswani and Alex van Herk Copyright © 2013 Pooja Daswani and Alex van Herk. All rights reserved. A 10-Year Dataset of Basic Meteorology and Soil Properties in Central Sudan Wed, 07 Nov 2012 10:24:59 +0000 Meteorological data and soil data have been collected at a site in the central Sudan from 2002 to 2012. The site is a sparse savanna in the semiarid region of Sudan. In addition to basic meteorological variables, soil properties (temperature, water content, and heat flux) and radiation (global radiation, net radiation, and photosynthetic active radiation) were measured. The dataset has a temporal resolution of 30 minutes and provides general data for calibration and validation of ecosystem models and remote-sensing-based assessments, and it is relevant for studies of ecosystem properties and processes. Jonas Ardö Copyright © 2013 Jonas Ardö. All rights reserved. First Records of Potamic Leech Fauna of Eastern Siberia, Russia Wed, 24 Oct 2012 11:05:39 +0000 We studied the fauna of leech and leech-like species inhabiting main water streams of Eastern Siberia and its tributaries, which are attributed to Lake Baikal basin and Lena River basin. Here we present their list for the first time. This study was mainly aimed for free-living parasitic and carnivorous leeches whereas piscine parasites were not included specially. In total, the potamic leech fauna of Eastern Siberia includes 12 described species belonging to 10 genera. Representatives of three unidentified species of two genera Erpobdella and Barbronia have been also recorded. Irina A. Kaygorodova, Elena V. Dzyuba, and Natalya V. Sorokovikova Copyright © 2013 Irina A. Kaygorodova et al. All rights reserved. Infrared Absorption Spectra of Monohydric Alcohols Wed, 24 Oct 2012 08:48:18 +0000 FTIR spectra of homologous series of monohydric alcohols which belong to the class of partly ordered liquids were registered. The molecules of monohydric alcohols containing hydroxyl group are able to form hydrogen-bonded clusters in the condensed phase. The existence of clusters is clearly observed from the position and the contour of the stretch OH band in the vibrational spectra of liquid alcohols. In this work, the experimentally registered FTIR spectra of liquid n-alcohols from methanol to decanol are presented as well as the same spectra of methanol, ethanol, propanol, butanol, pentanol, and hexanol in gas phase. Irina Doroshenko, Valeriy Pogorelov, and Valdas Sablinskas Copyright © 2013 Irina Doroshenko et al. All rights reserved. Detailed Food Web Networks of Three Greater Antillean Coral Reef Systems: The Cayman Islands, Cuba, and Jamaica Thu, 27 Sep 2012 15:03:02 +0000 Food webs represent one of the most complex aspects of community biotic interactions. Complex food webs are represented as networks of interspecific interactions, where nodes represent species or groups of species, and links are predator-prey interactions. This paper presents reconstructions of coral reef food webs in three Greater Antillean regions of the Caribbean: the Cayman Islands, Cuba, and Jamaica. Though not taxonomically comprehensive, each food web nevertheless comprises producers and consumers, single-celled and multicellular organisms, and species foraging on reefs and adjacent seagrass beds. Species are grouped into trophic guilds if their prey and predator links are indistinguishable. The data list guilds, taxonomic composition, prey guilds/species, and predators. Primary producer and invertebrate richness are regionally uniform, but vertebrate richness varies on the basis of more detailed occurrence data. Each region comprises 169 primary producers, 513 protistan and invertebrate consumer species, and 159, 178, and 170 vertebrate species in the Cayman Islands, Cuba, and Jamaica, respectively. Caribbean coral reefs are among the world's most endangered by anthropogenic activities. The datasets presented here will facilitate comparisons of historical and regional variation, the assessment of impacts of species loss and invasion, and the application of food webs to ecosystem analyses. Peter D. Roopnarine and Rachel Hertog Copyright © 2013 Peter D. Roopnarine and Rachel Hertog. All rights reserved. Neurogenomics of the Sympathetic Neurotransmitter Switch Indicates That Different Mechanisms Steer Cholinergic Differentiation in Rat and Chicken Models Wed, 26 Sep 2012 12:09:03 +0000 Vertebrate sympathetic neurons have the remarkable potential to switch their neurotransmitter phenotype from noradrenergic to cholinergic—a phenomenon that has been intensively studied in rat and chicken models. In both species, loss of noradrenergic markers and concomitant upregulation of cholinergic markers occurs in response to neuropoietic cytokines such as ciliary neurotrophic factor (CNTF). However, other aspects of the neurotransmitter switch including developmental timing, target tissues of cholinergic neurons, and dependence on neurotrophic factors differ between the two species. Here we compare CNTF-triggered transcriptome changes in both species by using DNA microarrays. CNTF induced changes in 1130 out of 16084 analyzed genomic loci in rat sympathetic neurons. When this set of genes was compared to CNTF-induced changes in the chicken transcriptome, a surprisingly small overlap was found—only 94 genes were regulated in the same direction in chicken and rat. The differential responses of the transcriptome to neuropoietic cytokines provide additional evidence that the cholinergic switch, although conserved during vertebrate evolution, is a heterogeneous phenomenon and may result from differential cellular mechanisms. Roland Dorn, Bernhard Loy, Georg Dechant, and Galina Apostolova Copyright © 2013 Roland Dorn et al. All rights reserved. Longitudinal Observation of Japanese Lancelet, Branchiostoma japonicum, Metamorphosis Sun, 23 Sep 2012 13:19:40 +0000 The lancelet (amphioxus) performs metamorphosis and produces minute and ciliate pelagic larvae commonly found in other metamorphic marine invertebrates. During larval life and metamorphosis, however, the animal displays interesting combination of features not found in other animals such as long coexistence of ciliate and muscular locomotion and no change in feeding behavior. The uniqueness of lancelet metamorphosis can provide important data to understand the evolutionary history of this animal as well as the metamorphosis broadly appeared in metazoans. Although lancelet metamorphosis has been studied, all previous studies depended on cross-sectional observations. To get serial data on metamorphic events, we performed longitudinal observations on the Japanese lancelet under the culture condition and confirmed the following: (1) there were individual variations of the duration of metamorphosis from 15 to 27 days; (2) growth was arrested for a month and the maximum reduction of the body length (2.2%–3.2%) occurred when gill slits became paired; (3) during rather long duration of metamorphosis, the oral transformation and the division of the gill pores by tongue bar were completed within two to four days. Our observations suggest that the duration and mode of lancelet metamorphosis depend mainly on intrinsic requirements rather than on extrinsic selective pressures. Takao Kaji, Yoichi Hoshino, Yasuhisa Henmi, and Kinya Yasui Copyright © 2013 Takao Kaji et al. All rights reserved. Long-Term Data from Fields Recovering after Sugarcane, Banana, and Pasture Cultivation in Ecuador Mon, 17 Sep 2012 13:48:08 +0000 I report here on an ongoing permanent plot study in areas recovering from agriculture in Ecuador. These plots were set up in 1995 at Maquipucuna Reserve where the forest is tropical lower montane. The study consists of replicate fields in three past crop types (Sugarcane, Banana, and Pasture) for a total of six fields. Each field was first divided into 25 continuous 2 m × 5 m subplots which together form a 10 m × 25 m plot with the longest side bordering the adjacent forest. Then starting in 1996, and continuing annually every year since, each subplot has been sampled for percent cover of all plants and diameter at breast height (dbh) for all trees whose dbh is greater than or equal to 1 cm. I have used that data in these published studies: (1) species composition and life form, richness, and basal area trends, (2) computation of all positive and negative pairwise species associations, (3) relationships between richness and productivity over time, (4) dominance-diversity curves, and (5) definition and quantification of old field plant communities. Finally with the help of the LTER program in Puerto Rico, this sampling continues, with 2012 marking the sixteenth year of continuous annual sampling. Randall W. Myster Copyright © 2013 Randall W. Myster. All rights reserved. Adaptation of Escherichia coli ATCC 8739 to 11% NaCl Thu, 13 Sep 2012 14:29:44 +0000 Escherichia coli (E. coli) is a nonhalophilic microbe and used to indicate faecal contamination. Salt (sodium chloride, NaCl) is a common food additive and is used in preservatives to encounter microbial growth. The effect of how E. coli interacts with the salt present in the human diet is unclear. Thus, it is important to investigate this relationship. In order to adapt and survive the changes in the environment, E. coli may undergo halophilization. In this study, we observed the genetic changes and growth kinetics of E. coli ATCC 8739 under 3%–11% NaCl over 80 passages. Our results suggest that E. coli adapted to 1% increase in NaCl every month with a successful adaptation to 11% NaCl. Gram staining and PCR/RFLP showed that the cultures are Gram negative and the DNA profiles of all 4 replicates to be similar, suggesting that the cultures had not been contaminated. Jian Ann How, Joshua Z. R. Lim, Desmond J. W. Goh, Wei Chuan Ng, Jack S. H. Oon, Kun Cheng Lee, Chin How Lee, and Maurice H. T. Ling Copyright © 2013 Jian Ann How et al. All rights reserved. An Illustrated Checklist of Leech Species from Lake Baikal (Eastern Siberia, Russia) Thu, 30 Aug 2012 11:53:54 +0000 New data on Lake Baikal fauna of Hirudinida (Annelida, Clitellata) are presented. The species composition of Baikal leeches extends to 20 species belonging to two orders, four families, and 12 genera. An updated checklist includes information on five species recorded in Eastern Siberia for the first time. All specimens from author’s collection are provided with illustration. Irina Kaygorodova Copyright © 2013 Irina Kaygorodova. All rights reserved.