ResearchPad - agricultural-and-biological-science https://www.researchpad.co Default RSS Feed en-us © 2020 Newgen KnowledgeWorks <![CDATA[High resolution mass spectral data from the analysis of copper chlorophylls and copper chlorophyll degradation products in bright green table olives]]> https://www.researchpad.co/article/N878854b4-98b0-4384-a129-9ab3a7c7dfeb This publication reports high resolution mass spectral data for copper chlorophyll and copper chlorophyll degradation products extracted from bright green table olives. These data support analyte identifications made in “Quantitation of copper chlorophylls in green table olives by ultra-high-performance liquid chromatography with inductively coupled plasma isotope dilution mass spectrometry” in the Journal of Chromatography A (Petigara Harp et al., 2020 [1]). Table olive pigments, divided into lipophilic and hydrophilic fractions by liquid-liquid repartition, were separated by ultra-high-performance liquid chromatography and detected by visible wavelength absorbance and high resolution mass spectrometry, using an Orbitrap HF with positive electrospray ionization. Full-scan mass spectra were acquired to assign pigment chemical formulae. Fragment-rich higher-energy collisional dissociation tandem mass spectra were acquired to facilitate structural assignments. Extracted ion chromatograms, full-scan, and tandem mass spectra obtained from representative lipophilic and hydrophilic green table olive extracts are presented in Figures 1-6. Annotated mass spectra comparing experimental and calculated isotope distributions, .raw mass spectral data files, and experimental details linking .raw data files to annotated spectra are provided as Supplementary Material. Spectra extracted from these native data files can be added to mass spectral libraries for use in other studies. Access to native data files uniquely enables rigorous data examination (e.g., molecular ion isotopic distribution, effective mass resolution, presence of overlapping ion series) and use in ways that are not possible when spectra are otherwise reported in simple tables listing mono-isotopic peaks and mass errors. Mass spectra reported here can be used to design multiple-reaction monitoring methods to detect these bright green pigments in agricultural food commodities and finished products.

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<![CDATA[Metabolomic data of phenolic compounds from <i>Acer negundo</i> extracts]]> https://www.researchpad.co/article/N6e1cf058-421e-49ec-9e2d-f3b5492bd0c0 Phytochemical and metabolomic data were obtained for the most important phenolic compounds in ethanolic extracts from the endangered Acer negundo tree in Morelia, Michoacan. Samples of leaves and stems were subjected to ethanolic extraction with electric rotavapor. We developed a metabolomic analysis that encompassed the correlation between the leaf and stem extracts through principal component analysis. The data were obtained with an infinity Agilent ultrahigh resolution liquid chromatograph coupled to a Agilent triple quadrupole mass spectrometer. The protocol used was a dynamic MRM (Multiple Reaction Monitoring). Clustering result shown as heatmap (distance measure using euclidean, and clustering algorithm using ward.D).

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<![CDATA[Draft genome sequencing data of a pathogenic <i>Pantoea stewartii</i> subspecies <i>stewartii</i> strain SQT1 causing bronzing disease of jackfruit in Malaysia]]> https://www.researchpad.co/article/N794b69f7-c314-4fed-af1c-4c38c5046cab A Gram-negative bacterium, Pantoea stewartii subspecies stewartii (P. stewartii subsp. stewartii) has been recognized as the causative agent for jackfruit bronzing disease in Malaysia. Here, we report the whole genome sequencing dataset of P. stewartii subsp. stewartii strain SQT1 isolated from local infected jackfruit. The paired-end libraries with an insert size of 350 bp was subjected to the Illumina Hiseq 4000, generating a genome size of 4,783,993 bp with a G+C content of 53.7%. A total protein of 4,671 was identified including virulence factors, resistance factors and secretion systems. Pantoea stewartii subsp. stewartii strain DC283 (NCBI accession no. CP017581.1) was used as a reference genome, where the query hit 72% coverage and average sequencing depth of 68. In total, 28,717 nucleotide polymorphisms, 520 small insertion/deletions and 142 structure variants were identified. The complete genome was deposited at the European Nucleotide Archive under the sample accession number ERP119356 and study accession number PRJEB36196.

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<![CDATA[Dataset supporting description of the new mussel species of genus <i>Gigantidas</i> (Bivalvia: Mytilidae) and metagenomic data of bacterial community in the host mussel gill tissue]]> https://www.researchpad.co/article/N9f042d02-91bf-4c83-acb8-294a9580d965 This article contains supplementary data from the research paper entitled “A newly discovered Gigantidas bivalve mussel from the Onnuri Vent Field on the northern Central Indian Ridge” [1], describes a new mussel species within the subfamily Bathymodiolinae named Gigantidas vrijenhoeki. Data are comprised of two parts: 1) shell image and molecular analyses of G. vrijenhoeki and 2) metagenomic community analyses of gill-associated symbiotic bacteria on G. vrijenhoeki. G. vrijenhoeki data were obtained from type specimens described in Jang et al. 2020 [1]. The molecular analysis was conducted by calculating genetic distance at intra- and inter-specific level within genus Gigantidas based on the sequence data of two mitochondrial genes (COI and ND4). The metagenomic dataset of gill-associated symbionts were generated by Illumina Miseq sequencing of the V3-V4 region of 16S rRNA from 12 specimens of G. vrijenhoeki collected from the same vent site, Onnuri Vent Field.

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<![CDATA[Dataset of the survey on e-registration and geo-referenced of rice value chain actors for the diffusion of technologies: Case of Benin and Côte d'Ivoire]]> https://www.researchpad.co/article/N15449c99-3594-4a53-82ce-572f4cdba9fc The paper presents a dataset of the e-registration of rice value chain actors in Benin and Côte d'Ivoire for assessing the adoption of innovations and the diffusion of new rice technologies. Data were collected from actors after a census conducted in three steps. In the first step, main rice production regions and rice value chain actors were identified. In the second step, we updated the list of actors based on membership of actors’ associations. In third step, we did the census of all individual actors and geo-localized all farmers’ fields and villages using GPS device. Data were collected for the 2018 growing seasons. The dataset contains 17,639 observations (9,000 in Benin and 8,639 in Côte d'Ivoire) with 159 variables divided into six sections: (i) preliminary information on the respondents; (ii) socio-economic characteristics; (iii) information on the rice plots; (iv) knowledge, use and access to rice varieties; (v) knowledge, use and access to agricultural equipment and methods; and (vi) information on post-harvest activities. Six categories of actors were identified: foundation seed producers (420), certified seed producers (1,212), paddy rice producers (14,230), parboilers (1,735), millers (188) and traders (1,429). The dataset is available online at Mendeley data repository. The dataset is valuable for the diffusion at large scale of improved technologies and an effective monitoring of the dissemination. Data can be used by scientists to have better understanding of the rice value chains, rice production systems, the level of knowledge, accessibility and adoption of improved rice varieties and agricultural technologies, for further research regarding rice value chain development, technologies testing and socioeconomics study of rice value chain actors. Because of the large number of observations (17,639), data can be used as sampling frame for further experiment or surveys based on random samples. Moreover, the dataset has the potential of generating descriptive statistics at the most disaggregated level of administrative units or villages for different equipment, methods and varieties adopted by gender and country.

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<![CDATA[Data on leaf structural, physiological and nutritional characteristics of species co-occurring in restinga and semidecidual seasonal forest ecosystems]]> https://www.researchpad.co/article/N70927ea4-376a-4040-955e-ded8c23c514a This paper presents additional data on the leaf structural, physiological and nutritional characteristics of three species (Maytenus obtusifolia, Manilkara subsericea e Inga laurina), co-occurring in restinga and semideciduous seasonal forest (forest). The data of the leaf structural, physiological and nutritional characteristics were obtained from the three species to identify possible adaptive strategies that could explain the co-occurrence of these species in the restinga and forest. In addition, this data can help identify key functional traits in the plant community of restinga and forests that can be employed in the reestablishment of ecological and edaphic processes in these ecosystems. This work presents data complementary to the published article “Acclimatization capacity of leaf traits of species co-occurring in restinga and seasonal semideciduous forest ecosystems” [1]

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<![CDATA[XYZ color data on the visual degradation of vegetables]]> https://www.researchpad.co/article/N2df10ba8-0a96-406c-94e5-18ea656bf722

This data article includes the visual stimuli used to model the freshness perception of four different vegetable textures, namely a cabbage, a carrot, a strawberry and a spinach. All four vegetables were optically measured during their degradation process in a humidity, temperature and light controlled environment. The visual data is in csv format for convenient usage. Each data point represents a pixel value using the hardware independent XYZ color space. The total size of the data can be related to an equivalent image of 1360 × 1024 resolution. Additionally, using the calibration data of an LCD-Display, the respective RGB color space images were derived from the XYZ data as an example. For interpretation and discussion, please see the original article entitled “Model of vegetable freshness perception using luminance cues” [1].

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<![CDATA[Datasets of essential oils from naturally formed and synthetically induced Aquilaria malaccensis agarwoods]]> https://www.researchpad.co/article/N8c4a05b0-5a33-4c26-8418-40c8ea6f0c57

Agarwood is the highly valuable fragrant resin of the wounded Aquilaria spp. trees widely used in fragrances, medicines and incenses. Among the Aquilaria spp., A. malaccensis is the primary producer and is mainly found in Indonesia and Malaysia. In normal condition, agarwood is naturally formed in Aquilaria trees as a defense mechanism upon physical damage or microbial infection on the trees, which is a slow process that occurs over several years. The high demand in agarwood has spurred the development of various artificial inoculation methods where agarwood formation is synthetically induced in a shorter period of time. However, the synthetic induction method produces agarwood with aromas different from the naturally formed agarwood. To understand the changes in the agarwoods produced from different induction conditions, metabolite profiling of agarwood essential oil from A. malaccensis has been performed. The essential oils of healthy undamaged tree trunks and, naturally formed and synthetically induced agarwoods were obtained using hydrodistillation (HS) method and analysed using gas chromatography mass spectrometer (GC-MS). These data will provide valuable resources for chemical components of agarwood produced by the species in the genus Aquilaria.

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<![CDATA[De novo transcriptome datasets of Shorea balangeran leaves and basal stem in waterlogged and dry soil]]> https://www.researchpad.co/article/N741aa60c-b70f-4cf3-940d-b1921c7cc2f9

Shorea balangeran Burk locally known as balangeran has been widely used as recommended species for tropical peat swamp forest restoration, due to the capability of these species to grow in waterlogged and dry areas. However, the information concerning genetic basis of adaptation to ecological condition variation is limited and no transcriptome study has been reported in this context. Here we reported two sets of transcriptome data from a sample of leaf and basal stem that were taken from seedlings growing in potted media containing peat and mineral soil. The raw reads are stored in the DDBJ platform with accession number DRA008633.

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<![CDATA[Dataset of reptiles in fragmented forests at Tasik Kenyir, Hulu Terengganu, Malaysia]]> https://www.researchpad.co/article/Nbc941107-ff8d-48d4-b1b5-a5f3be99f663

This data article is about reptiles (lizard, snake, and skink) captured from fragmented forest within man-made lake of Tasik Kenyir that is situated in Terengganu State, Peninsular Malaysia. Data collection was conducted in January 2019 and sampling methods included drift fenced-pitfall traps and Visual Encounter Survey (VES). All animals were identified, measured snout to vent (SVL) and weighted before their release at the site of capture. The highlights like conservation statuses in the wild, detection type and substrate type are presented with the data to increase its value. A total of 73 individuals from 18 species, 15 generas and seven families of reptiles were recorded. The data comprised of seven reptile family groups Agamidae, Gekkonidae, Scincidae, Colubridae, Elapidae, Viperidae and Homalopsidae. Reptiles like Cyrtodactylus quadrivirgattus (n = 33, 45.2%) and Aphaniotis fusca (n = 7, 9.6%) were most dominant in the checklist and most of the animals were captured using VES. Data of SVL and mass of the animals can be further interpreted by researchers to assess the health condition of animals in the altered habitats.

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<![CDATA[Data on occurrence of miRNA precursors in the Cucurbita maxima phloem sap]]> https://www.researchpad.co/article/N71bdbf39-d6b5-4530-9bb3-eb22efbf6b7e

The phloem sieve elements (SEs), enucleate cells, contain RNAs, which are imported from surrounding tissues and cells, mostly companion cells tightly associated with SEs, and transported via the phloem over the whole plant body. The RNA phloem transport is essential for plant individual development and responses to environmental cues. Recently, we identified primary miRNA (pri-miRNA) sequences in de novo assembled transcriptome of Cucurbita maxima phloem sap and reported 11 most abundant pri-miRNAs [1]. Here, we provide the output of this analysis in complete detail. For the full set of pri-miRNAs identified in the C. maxima phloem sap transcriptome, data on relative abundance are provided along with annotated sequence data.

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<![CDATA[Data on germination, growth and morphological changes of oil palm (Elaeis guineensis Jacq.) zygotic embryos during in vitro culturing]]> https://www.researchpad.co/article/N2d0825d5-3fed-4574-b939-fcaff48290d1

Oil palm (Elaeis guineensis Jacq.) from being almost unknown crop a mere three decades ago is now the most consumed and the most traded edible oil in the world. It is a highest yielding crop producing on an average 4 to 6 tons of oil per ha per year. Due to its innumerable uses in the food, oleochemicals and biofuel industries, cultivation of oil palm has expanded enormously in recent years. Since oil palm is a perennial monocotyledonous species with a single growing apex, the plant cannot be multiplied vegetatively and the conventional propagation through seed is limited by dormancy. Thus in vitro germination has become the key method for multiplication of elite oil palm genotypes. Although there are several reports on in vitro germination of oil palm, still there is a lack of an efficient & repeatable method. Hence an attempt is made to standardize the suitable culture media for direct germination from mature oil palm zygotic embryos. The data presented here represents the effect of genotypes, pretreatments and culture media on Mean Germination Time, Speed of Germination Index, Shoot Formation Index and Root Formation Index during in vitro culturing of oil palm zygotic embryos.

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<![CDATA[Rapid, simplified microscale quantitative analysis of lignin H/G/S composition with GC–MS in glass ampules and glass capillaries]]> https://www.researchpad.co/article/N74d22327-e42b-45eb-a1e2-2208e251019c

Graphical abstract

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<![CDATA[Dataset on interactors of the Arabidopsis thaliana Plant Natriuretic Peptide (AtPNP-A) determined by mass spectrometry]]> https://www.researchpad.co/article/Nf4bac310-62b1-4db3-9cd6-597f903ac35b

Interactors of the plant natriuretic peptide present in Arabidopsis thaliana, termed AtPNP-A, were affinity-based isolated from A. thaliana (Col-0) leaf mesophyll cell protoplasts by incubating the protoplasts with biologically active biotinylated peptide corresponding to amino acid sequence of the active site of AtPNP-A (pAtPNP-A), either in the presence or absence of a cross-linking agent, 3,3′-dithiobis(sulfosuccinimidyl propionate) (DTSSP), or with equimolar amount of biotin with DTSSP (negative control). Upon biotin/streptavidin-based isolation of proteins bound to the pAtPNP-A or biotin, the proteins were separated by sodium dodecyl sulphate – polyacrylamide gel electrophoresis (SDS-PAGE), digested with trypsin and subjected to identification with liquid chromatography tandem mass spectrometry (LC-MS/MS). Label-free quantification of identified proteins allowed identification of binding partners of AtPNP-A, paving the way for pinpointing novel signal transduction pathways AtPNP-A is involved in. The raw and processed LC-MS/MS data reported in this article have been deposited to the ProteomeXchange Consortium with the dataset identifier PXD017925.

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<![CDATA[Data on ectoparasites infestation on small mammals from different habitats in east-coast Peninsular Malaysia]]> https://www.researchpad.co/article/Ncc2344ea-69ab-40ac-917b-f729a528755a

This data article presents on the ectoparasites infestation on small mammals in Peninsular Malaysia. The dataset on ectoparasites infestation is important because it raises a major medical concern regarding the spread of potentially zoonotic disease from wildlife to human. Tick and chigger are the primary ectoparasites as reservoirs of vector-borne diseases found on small mammals in Malaysia. These small mammals that are infested with ectoparasites occupy various types of habitats, including human settlements, could be of community health risks as the carriers of potentially zoonotic diseases. Field samplings were conducted from February 2015 to February 2016 in three different ecological habitats of mixed dipterocarp forest, coastal forest and insular forest, in Terengganu, Malaysia. A total of 35 and 22 species of bats and rodents respectively were captured and examined for ectoparasites. Twenty-three species of bats and 16 species of small mammal were recorded as hosts for at least one species of ectoparasites. These findings show that the highest ectoparasite infestation occurred on bat community.

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<![CDATA[1H NMR metabolic profiling dataset of spiny chicory (Cichorium spinosum L.) exposed to abiotic stresses]]> https://www.researchpad.co/article/Neb55d932-14b6-4bf1-9181-ab33bb2d14f8

The data presented here were derived by 1H NMR metabolic profiling of stamnagathi (Cichorium spinosum L.) plants following treatments with different isosmotic salt solutions; eight saline nutrient solutions with two different levels of total molar concentrations, which were obtained by adding different amounts of NaCl, KCl, Na2SO4 or CaCl2 to the replenishment nutrient solution, were applied. The 1H NMR metabolite profiles of stamnagathi plants’, which are included in this article, were recorded 56 days after transplanting. Since stamnagathi is a niche product combining unique taste and superior phytonutrient content (e.g. vitamins C and K1, lutein, β-carotene, tocopherols, phenolic acids, fatty acids, minerals, and glutathione), the dataset could serve as a reference for future metabolomics studies related to the investigation of the effects of the four salinity sources on the plant's metabolism. Also, the dataset could be a valuable resource for the discovery of validated biomarkers of the plant's tolerance to salinity stress and responses to new plant protection products (e.g. bioelicitors). The dataset support the research article “Salinity source alters mineral composition and metabolism of Cichorium spinosum” authored by Ntatsi et al., (2017) [1].

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<![CDATA[A spatiotemporal database on the energy, macro and micro-nutrients from the Brazilian agricultural production]]> https://www.researchpad.co/article/Nc258d109-2f84-471a-b10d-f35f1b2d400c

To construct this database, we integrate the nutritional content of 62 crops and 5 livestock categories to estimate the amount of 21 macro and micro-nutrients (including energy) that were produced from agriculture in each Brazilian municipality during the last three decades. Additionally, we allocate these nutrients according to their share in the food system (for example, human food, animal feed, export etc.). It is a unique data source on macro and micro-nutrients availability for human consumption and animal feed, but also regarding another aspects of the food system, such as international agricultural trade, energy production (for example, in the form of ethanol) or post-harvest and post-processing losses, from local to national levels, in a wide time frame of 30 years. This database can be used in scientific research regarding food and nutrition security and in the construction of indicators for monitoring food and agricultural programs and policies that aim at the promotion of food and nutritional security. Also, it has the potential to enable broader analysis of the food system as whole in terms of food stability and resilience.

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<![CDATA[Data on the vegetative response of cowpea to fertilizer application on three selected benchmark soils of the Upper West region of Ghana]]> https://www.researchpad.co/article/N772ed10b-705f-4682-a144-46de5472e35b

Declining soil fertility among smallholder farmers in the Savannah zones of Ghana, among other issues, is triggered by continuous cultivation, low fertilizer use and low soil organic matter content. The area is faced with insufficient domestic production, food insecurity and poverty, all of which constitute major constraints to national development. Continuous cultivation leads to low soil organic matter levels. To build up the soil organic matter levels, residue incorporation is a major factor to be considered. Cowpea is grown in these areas for the grain yield while the residue is incorporated into the soil to gain maximum benefits of the nitrogen fixation. We present the physical and chemical properties of three benchmark soils in the Savannah zones of Ghana as well as their vegetative response to NPK fertilizer application. The FAO soil classification also helps in the thorough understanding of the soil and an appropriate management option for optimal productivity is recommended.

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<![CDATA[Enhanced near infrared spectral data to improve prediction accuracy in determining quality parameters of intact mango]]> https://www.researchpad.co/article/N71e4be94-818c-44e8-8220-54dcee9037df

Presented manuscript aimed to describes enhanced near infrared spectral dataset used to improve prediction performances of near infrared models in determining quality parameters of intact mango fruits. The two mentioned quality parameters are total acidity (TA) and vitamin C which corresponds to main inner attributes of fruits. Near infrared (NIR) spectra data were acquired and recorded as absorbance spectral data in wavelength range from 1000 to 2500 nm. These data were then enhanced by means of several algorithms like multiplicative scatter correction (MSC), baseline linear correction (BLC) and combination of them (MSC+BLC). Prediction models, used to determine TA and vitamin C were established using most common approach: partial least square regression (PLS) based on raw and enhanced spectral data respectively. Prediction performances can be evaluated based on prediction accuracy and robustness, by looking statistical indicators presented as coefficient of determination (R2) and correlation (r), root mean square error (RMSE) and residual predictive deviation (RPD). Enhanced NIR spectral dataset can be employed as a rapid, effective and non-destructive method to determine inner quality parameters of intact fruits.

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<![CDATA[Data of feed formulation for Indonesian short-fin eel, Anguilla bicolor McClelland, 1844 elver]]> https://www.researchpad.co/article/N7d97d40f-0cee-4949-87e8-f570f9a78f6f

This article describes the data of raw material compositions for formulating the diet for Indonesian short-fin eel, Anguilla bicolor Anguilla bicolor McClelland, 1844 elver. The data on growth performance, survival and feed utilization of eel elver from the formulated diet test results are also presented here. Four formulated diets and one commercial feed were tested for the eel elver. The formulated diet was formulated from animal and plant based protein sources such as; fish meal, cornmeal, soybean meal, fine bran, ebi-shrimp meal, golden snail meal, bloodmeal, and tapioca flour. Vitamins and minerals were added into the diet. In addition, probiotics and papain enzyme and its combination were also included into the experimental diets to boost the growth performance, survival and feed utilization of the fish. The tested treatments were; (A) commercial diet without probiotic and papain enzyme, (B) experimental diet without probiotic and papain enzyme, (C) experimental diet with probiotic 10 ml kg−1 feed, (D) experimental diet with papain enzyme 10 g kg−1 feed, (E) experimental diet with probiotic 10 ml kg−1 + papain 10 g kg−1 feed, (F) experimental diet with probiotic 5 ml kg−1 + papain 5 g kg−1 feed. Each experimental fish group was fed on an experimental diet twice a day at 08.00 AM and 06.00 PM at feeding level of 10% body weight for 60 days. The results showed that the weight gain ranged between 4.60 g to 5.92 g, daily growth rate between 0.063 g day−1 and 0.098 g per day−1, the specific growth rate varies from 0.72% day−1 to 1.35% day−1, survival rate 50.00% to 73.33%, feed conversion ratio from 2.35 to 4.17, and feed efficiency between 41.82% to 58.98%. The best treatment was found in fish fed on the experimental diet with papain enzyme 10 g kg−1 of feed

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