Find research datasets worth reusing

opencc-by-4.0Mar 2024View details →

Replication Package: An Empirical Study on the Characteristics of Reusable Code Clones

This is the updated code and datasets with comments to the code.

opencc-zeroApr 2022View details →

Cloning and functional characterization of a Type 3 Diacylglycerol Acyltransferasegene (GmDGAT3-2) from soybean (Glycine max L.)

Diacylglycerol acyltransferases (DGAT) function as the key rate-limiting enzymes in de novo biosynthesis of triacylglycerol (TAG) by transferring an acyl group from acyl-CoA to sn-3 of diacylglycerol (DAG) to form TAG. Here, two members of type 3 DGAT gene family, GmDGAT3-1 and GmDGAT3-2, were identified from soybean (Glycine max) genome. Both of them were predicted to encode soluble cytosolic proteins containing the typical thioredoxin-like ferredoxin domain. Quantitative PCR analysis revealed that GmDGAT3-2 expression was much higher than GmDGAT3-1's in various soybean tissues such as leaves, flowers and seeds. Functional complementation assay using TAG-deficient yeast (Saccharomyces cerevisiae) mutant H1246 demonstrated that GmDGAT3-2 fully restored TAG biosynthesis in the yeast and preferentially incorporated monounsaturated fatty acids (MUFAs), especially oleic acid (C18:1) into TAGs. This substrate specificity was further verified by feeding assays and in vitro enzyme activity characterization. Notably, transgenic tobacco (Nicotiana benthamiana) data showed that heterogeneous expression of GmDGAT3-2 resulted in significant increase of seed oil and C18:1 levels, but little change in contents of protein and starch compared to the EV-transformed tobacco plants. Taken together, GmDGAT3-2 displayed a strong enzymatic activity to catalyze TAG assembly with high substrate specificity for MUFAs, particularly C18:1, playing an important role in the cytosolic pathway of TAG synthesis in soybean. The present findings provide a scientific reference for improving oil yield and FA composition in soybean through gene modification, further expanding our knowledge of TAG biosynthesis and its regulatory mechanism in oilseeds.

opencc-by-4.0May 2022View details →

Cloned 16S sequences (anya project)

Cloned 16S sequences isolated from mud volcano PAH-degrading community.

opencc-zeroAug 2022View details →

Cloning capacity helps seeds of Garcinia xanthochymus counter animal predation

Seed predators have the potential to act as agents of natural selection that influence seed traits and seed fates, which in turn affect the whole plant population dynamic. Accordingly, plants deploy a variety of mechanisms (e.g. resistance and tolerance strategies) to lessen the impact of predation on seed crop or on an individual seed. In this study, we described a novel mechanism, seed cloning strategy, in a tropical plant species in countering animal predation. By conducting field- and laboratory-based germination experiments, we found that both rodent damaged and artificially damaged seed fragments of a large-seeded tree Garcinia xanthochymus (Clusiaceae) could successfully germinate and establish as seedlings. Tissue culture experiments revealed that G. xanthochymus has no endosperm in seeds, and its seed fragments own strong capacity of differentiation and cloning. Seed damage negatively affected seedling growth and germination, but the seed germination rate was remarkably high. Our study suggests that, seed cloning capacity, adopted by the large-seeded tree G. xanthochymus may act as a novel strategy counteract for seed predation, and would play a significant role in stabilizing the mutualism between plant and animals.

Fig. 5 in Molecular cloning of heat shock protein gene HSP90 and effects of abamectin and double-stranded RNA on its expression in Panonychus citri (Trombidiformes: Tetranychidae)

Fig. 5. Relative expressional levels of HSP90 mRNA in P. citri adult females afer treatment at 32 °C with abamectin concentrations of LC25, LC50 and LC75 for the indicated times. Data are shown as means of 3 replicates ± SD. The relative expression level of HSP90 mRNA in the control group is equal to 1.0 and is marked with a dashed line. The asterisk above the bar indicates a significance difference between treatment with abamectin and control group (t-test, P <0.05).

Fig. 3 in Molecular cloning of heat shock protein gene HSP90 and effects of abamectin and double-stranded RNA on its expression in Panonychus citri (Trombidiformes: Tetranychidae)

Fig. 3. Relative expressional levels of HSP90 mRNA in P. citri adult females afer treatment with abamectin at LC25, LC50 and LC75levels for the indicated times at 18 °C.Data are shown as means of 3 replicates ± SD. The relative expression level of HSP90 mRNA in the control group is equal to 1.0 and is marked with a dashed line. The asterisk above the bar indicates a significance difference between treatment with abamectin and control group (t-test, P <0.05).

Fig. 1 in Molecular cloning of heat shock protein gene HSP90 and effects of abamectin and double-stranded RNA on its expression in Panonychus citri (Trombidiformes: Tetranychidae)

Fig. 1. The cDNA and deduced amino acid sequence of HSP90 of Panonychus citri adult females. The start and stop codons are boxed; the numbers on the lef are for the positions of nucleotides and amino acids in the sequences.

Fig. 7 in Molecular cloning of heat shock protein gene HSP90 and effects of abamectin and double-stranded RNA on its expression in Panonychus citri (Trombidiformes: Tetranychidae)

Fig. 7. Relative expressional levels of HSP90 mRNA in adult female P. citri Mc- Gregor afer treatment with dsRNA at concentrations equivalent to 0.1 µg/µL, 0.2 µg/µL and 0.4 µg/µL. Data are shown as means of 3 replicates ± SD. The relative expression level of HSP90 mRNA in the control group is equal to 1.0 and is marked with a dashed line. The asterisk above the bar indicates a significance difference between treatment with dsRNA and control group (t-test, P <0.05).

Fig. 4 in Molecular cloning of heat shock protein gene HSP90 and effects of abamectin and double-stranded RNA on its expression in Panonychus citri (Trombidiformes: Tetranychidae)

Fig. 4. Relative expressional levels of HSP90 mRNA in P. citri adult females afer treatment at 25 °C with abamectin concentrations of LC25, LC50 and LC75 for the indicated times. Data are shown as means of 3 replicates ± SD. The relative expression level of HSP90 mRNA in the control group is equal to 1.0 and is marked with a dashed line. The asterisk above the bar indicates a significance difference between treatment with abamectin and control group (t-test, P <0.05).

Fig. 6 in Molecular cloning of heat shock protein gene HSP90 and effects of abamectin and double-stranded RNA on its expression in Panonychus citri (Trombidiformes: Tetranychidae)

Fig. 6. Relative expressional levels of HSP90 mRNA in P. citri adult females subjected to 18 °C or 32 °C for the length of time indicated. Data are shown as means of 3 replicates ± SD. The relative expression level of HSP90 mRNA in the control group is equal to 1.0 and is marked with a dashed line. The asterisk above the bar indicates a significance difference between treatment with temperature and control group (t-test, P <0.05).

opencc-by-4.0Jun 2015View details →

Fig. 1 in Susceptibility of Eucalyptus spp. (Myrtales: Myrtaceae) and clones to Leptocybe invasa (Hymenoptera: Eulophidae) in Paraná, Brazil

Fig. 1. Percentage of leaves and stems with galls caused by Leptocybe invasa in approx. 2-m-tall Eucalyptus spp. and clones on each sampling date at Umuarama, PR, Brazil, in 2013.

opencc-by-4.0Jul 2024View details →

Lipid data for clone BL21.pLS12.pLS29

Lipid data describing the composition of clone BL21.pLS12.pLS29 in triplicate

opennotspecifiedFeb 2013View details →

Fig. 3 in Molecular cloning of the trypsin inhibitor from the skin secretion of the Madagascan Tomato Frog, Dyscophus guineti (Microhylidae), and insights into its potential defensive role

Fig. 3 MALDI-TOF mass spectrum of the protease inhibitor-containing fraction

opencc-by-4.0Jun 2015View details →

Figure 1 from: Hughes KW, Morris SD, Reboredo-Segovia A (2015) Cloning of ribosomal ITS PCR products creates frequent, non-random chimeric sequences – a test involving heterozygotes between Gymnopus dichrous taxa I and II. MycoKeys 10: 45-56. https://doi.org/10.3897/mycokeys.10.5126

Figure 1 - The ITS2 region of two haplotypes of Gymnopus dichrous: Haplotypes DI (represented by TENN68084) and DII (represented by TENN68078). The TC pair at position 15 and the indel at position 25 were used to determine which the haplotype was represented by the 5' end of a cloned sequence. Bases in red are points where DI and DII haplotypes differ in sequence and were used to determine if template switching had occurred in a cloned PCR product. Eight base pairs at which template switching can be detected are indicated by numbers 1-8. The possible area in which template switching (ts) could have occurred is indicated by vertical arrows and the number of observed template switching events is given above the vertical arrow. Bases that may be involved in intra-strand base pairing as determined by MFOLD are outlined with black boxes. Ambiguity codes indicate intraspecific variation.

opencc-zeroNov 2022View details →

Primary data used to calculate predator-induced morphological changes in two Daphnia species-associated clones

The expression of inducible defences in reaction to an inconsistent predation pressure is especially well investigated in the freshwater keystone filter-feeder Daphnia. Out of their many inducible defences, which increase their fitness, the highest diversity of induced traits is found within their morphology. In recent time the focus of studies on these has switched, from the previously thoroughly covered large-scale defences, e.g., elongated/enlarged tail-spines, helmets and crests, to rather small-scale predator-induced changes. Inconspicuous spinules that cover the dorsal and ventral carapace margins have only rarely been featured in studies. We, therefore, tested two well-studied Daphnia species (D. magna and D. longicephala) for predator-induced changes concerning the spinules, i.e., their area of distribution relative to the body length (relative dorsal/ventral spinules-bearing area, relSBA) and their change in length (mean spinule length of the five central spinules along the dorsal/ventral carapace margin, mean SL). As invertebrate and vertebrate predators display differently built catching structures, those of invertebrate predators being more delicate, the defensive structures against these predator groups might vary accordingly. To test this, we exposed the daphnids to the vertebrate Leucaspius delineatus and a well co-studied predator of the respective Daphnia species, i.e., Triops cancriformis or Notontecta maculata. Our study discovered induced changes of the spinules' lengths and an area they cover. These changes of inconspicuous traits appear not only to be predator-dependent, but also Daphnia-specific. The inconspicuous morphological changes of Daphnia, in combination with the large scale defences, here measured pointers for the expression of inducible defences were the tail spines (relative tail spine length, relTSL) in both species and the crest in D. longicephala, and some ultrastructural defences are suspected to be rather specifically customised collective defences.

opencc-by-4.0Feb 2023View details →

Semantic Clones Dataset for TrainTicket Microservices benchmark

It contains Component Call Graphs pairs for the analysis of TrainTicket benchmark (release 0.1.0). It classifies the pairs into semantic clones and non-clones. It contains 27,222 total CCGs pairs. This dataset is published as part of the paper titled as "Detecting Semantic Clones In Microservices Using Components".   This version contains correction for 6 pairs are classified as clones. (Highlighted in yellow) This correction is detected using our automatic approach. Check it out in the paper.

opencc-zeroFeb 2023View details →

Diploid and haploid assemblies and annotation of monoecious shrub willow (Salix purpurea), clone ID 94003

The Salicaceae are dioecious perennials that utilize different sex determination systems. There is substantial interest in understanding the impacts of hybridization, speciation, and polyploidy on sex chromosome evolution. Here, a rare monoecious S. purpurea genotype, 94003, was assembled. Based on sequence alignments to dioecious and monoecious genomes, a 1.15 Mb sex-linked region on Chr15W was identified as absent in monecious plants. Inheritance of this structural variation is responsible for the loss of a male-suppressing function in what would otherwise be genetic females, resulting in monoecy or lethality, if homozygous.

opencc-zeroApr 2020View details →

FIG. 4 in Morphological description and molecular phylogeny of two diatom clones from the genus Ulnaria (Kützing) Compère isolated from an ultraoligotrophic lake at the Pole of Cold in the Northern Hemisphere, Republic of Sakha (Yakutia), Russia

FIG. 4. — Phylogenetic analysis of rbcL gene fragments, carried out by the maximum likelihood method. In the tree nodes there are bootstrap values obtained for n = 1000 replicas. Evolution distances are determined by the GTR method with Gamma distributed equal to four. ● Marked sequences obtained in this work.