DNA barcoding involves sequencing a standard region of DNA as a tool for species identification. However, there has been no agreement on which region(s) should be used for barcoding land plants. To provide a community recommendation on a standard plant barcode, we have compared the performance of 7 leading candidate plastid DNA regions (atpF-atpH spacer, matK gene, rbcL gene, rpoB gene, rpoC1 gene, psbK-psbI spacer, and trnH-psbA spacer). Based on assessments of recoverability, sequence quality, and levels of species discrimination, we recommend the 2-locus combination of rbcL؉matK as the plant barcode. This core 2-locus barcode will provide a universal framework for the routine use of DNA sequence data to identify specimens and contribute toward the discovery of overlooked species of land plants.matK ͉ rbcL ͉ species identification L arge-scale standardized sequencing of the mitochondrial gene CO1 has made DNA barcoding an efficient species identification tool in many animal groups (1). In plants, however, low substitution rates of mitochondrial DNA have led to the search for alternative barcoding regions. From initial investigations of plastid regions (2-4), 7 leading candidates have emerged (5, 6). Four are portions of coding genes (matK, rbcL, rpoB, and rpoC1), and 3 are noncoding spacers (atpF-atpH, trnH-psbA, and psbK-psbI). Different research groups have proposed various combinations of these loci as their preferred plant barcodes, but no consensus has emerged (5-12). This lack of an agreed standard has impeded progress in plant barcoding.Our aim here is to identify a standard DNA barcode for land plants. To achieve this goal, we have pooled data across laboratories including sequence data from 907 samples, representing 445 angiosperm, 38 gymnosperm, and 67 cryptogam species. Using various subsets of these data, we evaluated the 7 candidate loci using criteria in the Consortium for the Barcode of Life's (CBOL) data standards and guidelines for locus selection (http:// www.barcoding.si.edu/protocols.html). Universality: Which loci can be routinely sequenced across the land plants? Sequence quality and coverage: Which loci are most amenable to the production of bidirectional sequences with few or no ambiguous base calls? Discrimination: Which loci enable most species to be distinguished? ResultsUniversality. Direct universality assessments using a single primer pair for each locus in angiosperms resulted in 90%-98% PCR and sequencing success for 6/7 regions. Success for the seventh region, psbK-psbI, was 77% (Fig. 1A). Greater problems were encountered in other land plant groups, with rpoB, matK, atpF-atpH, and psbK-psbI all showing Ͻ50% success in gymnosperms and/or cryptogams based on data compiled from several laboratories (Fig. 1 A).Sequence Quality. Evaluation of sequence quality and coverage from the candidate loci demonstrated that high quality bidirectional sequences were routinely obtained from rbcL, rpoC1, and rpoB (Fig. 1B, x axis). The remaining 4 loci required more manual editing and produced f...

ClpXP is a protein machine composed of the ClpX ATPase, a member of the Clp/Hsp100 family of remodeling enzymes, and the ClpP peptidase. Here, ClpX and ClpXP are shown to catalyze denaturation of GFP modified with an ssrA degradation tag. ClpX translocates this denatured protein into the proteolytic chamber of ClpP and, when proteolysis is blocked, also catalyzes release of denatured GFP-ssrA from ClpP in a reaction that requires ATP and additional substrate. Kinetic experiments reveal that multiple reaction steps require collaboration between ClpX and ClpP and that denaturation is the rate-determining step in degradation. These insights into the mechanism of ClpXP explain how it executes efficient degradation in a manner that is highly specific for tagged proteins, irrespective of their intrinsic stabilities.

The intensity ratio between two major Raman bands in graphene is one of the most important information for physics of graphene and has been believed to represent various intrinsic properties of graphene without critical assessment of extrinsic effects. We report a micro Raman spectroscopy study on the Raman intensity ratio of the 2D band to the G Raman band of graphene varying the thickness of dielectric layers (SiO 2 ) underneath it. The ratio is shown to change by almost 370% when the thickness is varied by 60%. The large variation in the ratio is well explained by theoretical calculations considering multiple Raman scattering events at the interfaces. Our analysis shows that the interference effect is critical in extracting the intrinsic 2D to G intensity ratio and therefore must be taken into account in extracting various physical properties of graphene from Raman measurements.

Cytoplasmic chloroplast (cp) genomes and nuclear ribosomal DNA (nR) are the primary sequences used to understand plant diversity and evolution. We introduce a high-throughput method to simultaneously obtain complete cp and nR sequences using Illumina platform whole-genome sequence. We applied the method to 30 rice specimens belonging to nine Oryza species. Concurrent phylogenomic analysis using cp and nR of several of specimens of the same Oryza AA genome species provides insight into the evolution and domestication of cultivated rice, clarifying three ambiguous but important issues in the evolution of wild Oryza species. First, cp-based trees clearly classify each lineage but can be biased by inter-subspecies cross-hybridization events during speciation. Second, O. glumaepatula, a South American wild rice, includes two cytoplasm types, one of which is derived from a recent interspecies hybridization with O. longistminata. Third, the Australian O. rufipogan-type rice is a perennial form of O. meridionalis.

The aim of this study is to compare the time-course changes in neurologic impairments (trunk control, motor function, sensory, and cognition) and recovery in functional impairments (activity of daily livings and gait) simultaneously from initiating rehabilitation to 6 months after stroke. Consecutive stroke patients were recruited from the department of nervous surgery, and transferred into the department of rehabilitation medicine and continued on treatment during the acute stage. Outcome measures were examined at the initial rehabilitation baseline, 1, 2, and 4 weeks after rehabilitation treatment, and 3, 4, 5, and 6 months after stroke. Patients were assessed using the Trunk Impairment Scale, the Fugl-Meyer Motor and Sensory Assessments for the upper and lower limbs, Mini-Mental State Examination, Functional Ambulation Category, and Modified Barthel Index. Twenty consecutive patients were analyzed in the study with complete assessments. The recovery was relatively rapid during the 4 weeks after treatment (P value ranges from <0.001 to <0.007) and then to a lesser extent decelerated between 3 and 6 months after stroke (P value between <0.001 and 0.080). Statistical comparison by repeated measures analysis showed a significant interaction between time points and measures of all recovery variables (P<0.001). Significant differences in level of impairments and functional recovery were found at the different time points. In comparison with the lower leg and trunk control, the upper arm showed less recovery, with a significant difference. All variables except for leg motor function improved continuously over 6 months after stroke. Nevertheless, this study confirms the importance of the period within 3 months for recovery after stroke, during which most of the recovery occurred, ranging from 48 to 91%. Therefore, intensive treatment targeting motor and sensory functions early after stroke may be beneficial for recovery of impairments and functional performance.

Background Ethiopia is one of the species-rich countries in the world and the center of origin with regard to the diversity of many plant species. Ethnobotanical studies are vital to investigate these diverse biological resources for medicinal purposes. The aim of this study was to document the indigenous knowledge of the Sidama people regarding the use of medicinal plants to treat human and livestock diseases in the Hawassa Zuria district of Southern Ethiopia. Methods A total of 150 informants (118 men and 32 women) were selected to collect ethnobotanical information from ten kebeles by means of a stratified purposive sampling method. Among the informants, 30 key informants were selected purposefully. Ethnobotanical data were collected through semi-structured interviews and group discussions and were analyzed by descriptive statistics, informant consensus factor (ICF), fidelity level (FL), and ranking methods. Results A total of 105 medicinal plants distributed across 52 families and 96 genera were collected. Fabaceae (11 species) was represented by the highest number of plant species, followed by Lamiaceae (7 species). Herbs (34%) were the dominant growth habits, followed by trees (33%). Leaves (56%) were the dominant plant part used in the preparation of remedies, followed by fruit (15%). The most common method of remedy preparation was grinding (39%) followed by chewing and boiling (11% each). Oral (74%) was the major routes of administration, followed by dermal (20%). There was a significant knowledge difference ( p < 0.05) between social groups regarding the use of traditional medicinal plants. Insects and ectoparasites disease category (0.95) had higher informant consensus factor value followed by fever disease category (0.91). Eucalyptus globulus Labill. (100%) had a higher fidelity level to treat stomachache, followed by Ensete ventricosum (Welw.) Cheesman. (87.27%) to treat placenta delay. Ensete ventricosum (total score = 73) was ranked highest as the most preferable medicinal plant for various purposes by local people, followed by Olea welwitschii (Knobl.) Gilg (total score = 72). Conclusion The present study revealed the existence of indigenous knowledge of medicinal plants to treat human and livestock ailments. However, agricultural expansion, firewood collection, environmental degradation, and deforestation are the main threats to medicinal plants. Therefore, there should be mentoring for the local people in the study area to conserve their indigenous knowledge resources and prevent the extinction of medicinal plants. Electronic supplementary material The online version of this article (10.1186/s13002-019-0302-7) contains supplementary material, which is available to authorized users.

Convolutional Neural Networks (CNNs) provide excellent performance when used for image classification. The classical method of training CNNs is by labeling images in a supervised manner as in "input image belongs to this label" (Positive Learning; PL), which is a fast and accurate method if the labels are assigned correctly to all images. However, if inaccurate labels, or noisy labels, exist, training with PL will provide wrong information, thus severely degrading performance. To address this issue, we start with an indirect learning method called Negative Learning (NL), in which the CNNs are trained using a complementary label as in "input image does not belong to this complementary label." Because the chances of selecting a true label as a complementary label are low, NL decreases the risk of providing incorrect information. Furthermore, to improve convergence, we extend our method by adopting PL selectively, termed as Selective Negative Learning and Positive Learning (SelNLPL). PL is used selectively to train upon expected-to-be-clean data, whose choices become possible as NL progresses, thus resulting in superior performance of filtering out noisy data. With simple semi-supervised training technique, our method achieves state-of-the-art accuracy for noisy data classification, proving the superiority of SelNLPL's noisy data filtering ability.

The Clp/Hsp100 ATPases are hexameric protein machines that catalyze the unfolding, disassembly and disaggregation of specific protein substrates in bacteria, plants and animals. Many family members also interact with peptidases to form ATP-dependent proteases. In Escherichia coli, for instance, the ClpXP protease is assembled from the ClpX ATPase and the ClpP peptidase. Here, we have used multiple sequence alignments to identify a tripeptide 'IGF' in E. coli ClpX that is essential for ClpP recognition. Mutations in this IGF sequence, which appears to be part of a surface loop, disrupt ClpXP complex formation and prevent protease function but have no effect on other ClpX activities. Homologous tripeptides are found only in a subset of Clp/Hsp100 ATPases and are a good predictor of family members that have a ClpP partner. Mapping of the IGF loop onto a homolog of known structure suggests a model for ClpX-ClpP docking.