Biological collections in an ever changing world: Herbaria as tools for biogeographical and environmental studies

Plant specimens stored in herbaria are being used as never before to document the impacts of global change on humans and nature. However, published statistics on the use of biological collections are rare, and ecologists lack quantitative data demonstrating the relevance to science of herbarium specimens. I found 382 studies with original data that used herbarium specimens to document biogeographical patterns or environmental changes. Most studies are less than 10 years old, and only 1.4% of the herbarium specimens worldwide have been used to answer biogeographical or environmental questions. The vast majority (82%) of papers dealt with vascular plants, but some studies also used bryophytes, lichens, seaweeds and fungi. The herbarium specimens were collected from all continents, but most of the studies used specimens from North America (40% of studies) or Europe (28%). Many types of researches (conservation, plant disease, plant invasion, pollution, etc.) can be conducted using herbarium specimens. Climate change, and especially phenological reconstructions, are clearly emerging research topics. By group, small herbaria (<100,000 specimens) are consulted as often as very large herbaria (>1,000,000 specimens) for biogeographical and environmental research, but in most cases, only large facilities provide specimens collected worldwide. The median number of specimens per study in papers using computerized collections (15,295) was much higher than for papers that did not include electronic data (226). The use of molecular analyses to investigate herbarium specimens is still relatively unexplored, at least from biogeographical and environmental points of view. Combined with recently developed procedures to correct biases, herbarium specimens might provide in the near future exciting additional spatio-temporal insights that are currently unimaginable.     

Use of Medicinal Plants Among Thai Ethnic Groups: A Comparison

Economic Botany - Use of Medicinal Plants Among Thai Ethnic Groups: A Comparison. Thailand has a large rural population that uses traditional medicinal plants extensively. The country is also the...     

Impact of Inclusion of Industry Trial Results Registries as an Information Source for Systematic Reviews

Background

Clinical trial results registries may contain relevant unpublished information. Our main aim was to investigate the potential impact of the inclusion of reports from industry results registries on systematic reviews (SRs).

Methods

We identified a sample of 150 eligible SRs in PubMed via backward selection. Eligible SRs investigated randomized controlled trials of drugs and included at least 2 bibliographic databases (original search date: 11/2009). We checked whether results registries of manufacturers and/or industry associations had also been searched. If not, we searched these registries for additional trials not considered in the SRs, as well as for additional data on trials already considered. We reanalysed the primary outcome and harm outcomes reported in the SRs and determined whether results had changed. A “change” was defined as either a new relevant result or a change in the statistical significance of an existing result. We performed a search update in 8/2013 and identified a sample of 20 eligible SRs to determine whether mandatory results registration from 9/2008 onwards in the public trial and results registry ClinicalTrials.gov had led to its inclusion as a standard information source in SRs, and whether the inclusion rate of industry results registries had changed.

Results

133 of the 150 SRs (89%) in the original analysis did not search industry results registries. For 23 (17%) of these SRs we found 25 additional trials and additional data on 31 trials already included in the SRs. This additional information was found for more than twice as many SRs of drugs approved from 2000 as approved beforehand. The inclusion of the additional trials and data yielded changes in existing results or the addition of new results for 6 of the 23 SRs. Of the 20 SRs retrieved in the search update, 8 considered ClinicalTrials.gov or a meta-registry linking to ClinicalTrials.gov, and 1 considered an industry results registry.

Conclusion

The inclusion of industry and public results registries as an information source in SRs is still insufficient and may result in publication and outcome reporting bias. In addition to an essential search in ClinicalTrials.gov, authors of SRs should consider searching industry results registries.     

The Potential Use of a Silicon Source as a Component of an Ecological Management of Coffee Plants

Coffee is one of the most important agricultural export commodities in the world and it represents the main export from some developing countries. Therefore, the development of new methods of coffee management that improves production without causing any damage to the environment is an attractive alternative for producers. Much effort has been invested towards understanding the mode of action of compounds that can induce resistance against several pathogens without injuring the environment. Many researches have considered silicon efficient in avoiding plant pathogen penetration and development. Our aim was to verify the effect of potassium silicate and calcium/magnesium silicate in the development of coffee seedlings ( Coffea arabica cv. Mundo Novo ) as well as to evaluate the incidence of coffee leaf rust development under greenhouse conditions. The experiment was a completely randomized design with 12 treatments with 10 plants per treatment. The treatments were 0, 0.25, 1.25, 2.5, 4 and 5  μ m of Si for each source of silicon incorporated into the soil. The seedlings were inoculated with a urediniospores suspension of Hemileia vastatrix (2 mg/ml) at the seventh month after planting (six pair of leaves). Evaluations were performed by counting the number of lesions per leaf. The statistical analysis showed that the number of lesions reduced by up to 66% at the highest silicon dose when compared to the number of lesions in control plants. Infected plants were found to have a linear decrease of lesions with the increase of silicate concentration. The lowest number of lesions per leaf area was observed in plants that received 5  μ m of Si from potassium silicate. This result indicates the use of silicon as an alternative for an ecological management system for coffee disease protection.     

In Vivo and In Vitro Localization of Leishmania within Macrophage Phagolysosomes: Use of Colloidal Gold as a Lysosomal Label1

The interaction of Leishmania with lysosomes within macrophages in vivo has been investigated. Lysosomes labeled with colloidal gold in vivo fused with phagocytic vacuoles containing Leishmania amastigotes within the macrophages of infected footpad tissue of BALB/c mice. This localization of Leishmania within macrophage phagolysosomes in vivo is the first confirmation for any obligate intracellulaire protozoon that parasite-lysosome interactions in vitro occur in vivo.     

Population Genetics and Reproductive Strategies of African Trypanosomes: Revisiting Available Published Data

Trypanosomatidae are a dangerous family of Euglenobionta parasites that threaten the health and economy of millions of people around the world. More precisely describing the population biology and reproductive mode of such pests is not only a matter of pure science, but can also be useful for understanding parasite adaptation, as well as how parasitism, specialization (parasite specificity), and complex life cycles evolve over time. Studying this parasite’s reproductive strategies and population structure can also contribute key information to the understanding of the epidemiology of associated diseases; it can also provide clues for elaborating control programs and predicting the probability of success for control campaigns (such as vaccines and drug therapies), along with emergence or re-emergence risks. Population genetics tools, if appropriately used, can provide precise and useful information in these investigations. In this paper, we revisit recent data collected during population genetics surveys of different Trypanosoma species in sub-Saharan Africa. Reproductive modes and population structure depend not only on the taxon but also on the geographical location and data quality (absence or presence of DNA amplification failures). We conclude on issues regarding future directions of research, in particular vis-à-vis genotyping and sampling strategies, which are still relevant yet, too often, neglected issues.     

Ethnobotanical Knowledge Transmission and Evolution: The Case of Medicinal Markets in Tanga,Tanzania<Superscript>1</Superscript>

Ethnobotanical Knowledge Transmission and Evolution: The Case of Medicinal Markets in Tanga, Tanzania. This paper explores the range and distribution of local ecological knowledge (LEK) of popular medicinal plants by means of a case study in the medicinal markets of Tanga, Tanzania. Seventy–four medicinal plant harvesters, healers, and vendors were surveyed to test if knowledge differed based on their role in the market system, age, years of experience, and level of formal education. These results diverge from previous studies that explain variation in plant knowledge based on sociodemographic variables. It also questions the assumption that markets inevitably erode local or traditional knowledge. This study contributes to an understanding of the dynamics of ethnobotanical knowledge transmission and evolution by showing how particular contexts, in this case medicinal plant markets, can influence this process.     

Comparison of the Equine Reference Sequence with Its Sanger Source Data and New Illumina Reads

The reference assembly for the domestic horse, EquCab2, published in 2009, was built using approximately 30 million Sanger reads from a Thoroughbred mare named Twilight. Contiguity in the assembly was facilitated using nearly 315 thousand BAC end sequences from Twilight’s half brother Bravo. Since then, it has served as the foundation for many genome-wide analyses that include not only the modern horse, but ancient horses and other equid species as well. As data mapped to this reference has accumulated, consistent variation between mapped datasets and the reference, in terms of regions with no read coverage, single nucleotide variants, and small insertions/deletions have become apparent. In many cases, it is not clear whether these differences are the result of true sequence variation between the research subjects’ and Twilight’s genome or due to errors in the reference. EquCab2 is regarded as “The Twilight Assembly.” The objective of this study was to identify inconsistencies between the EquCab2 assembly and the source Twilight Sanger data used to build it. To that end, the original Sanger and BAC end reads have been mapped back to this equine reference and assessed with the addition of approximately 40X coverage of new Illumina Paired-End sequence data. The resulting mapped datasets identify those regions with low Sanger read coverage, as well as variation in genomic content that is not consistent with either the original Twilight Sanger data or the new genomic sequence data generated from Twilight on the Illumina platform. As the haploid EquCab2 reference assembly was created using Sanger reads derived largely from a single individual, the vast majority of variation detected in a mapped dataset comprised of those same Sanger reads should be heterozygous. In contrast, homozygous variations would represent either errors in the reference or contributions from Bravo''s BAC end sequences. Our analysis identifies 720,843 homozygous discrepancies between new, high throughput genomic sequence data generated for Twilight and the EquCab2 reference assembly. Most of these represent errors in the assembly, while approximately 10,000 are demonstrated to be contributions from another horse. Other results are presented that include the binary alignment map file of the mapped Sanger reads, a list of variants identified as discrepancies between the source data and resulting reference, and a BED annotation file that lists the regions of the genome whose consensus was likely derived from low coverage alignments.     

The genus Laggera (Asteraceae) – Ethnobotanical and Ethnopharmacological Information,Chemical Composition as well as Biological Activities of Its Essential Oils and Extracts: A Review

Most species of the genus Laggera are often used in traditional and folk medicines for the treatment of jaundice, inflammation, leukemia, removing phlegm, bronchitis and bacterial diseases. The essential oils obtained from Laggera plants are rich sources of oxygenated monoterpenes and sesquiterpenes. Among oxygenated monoterpenes, aromatic ether 2,5‐dimethoxy‐p‐cymene is the most abundant and dominant compound of many essential oils of the Laggera species. Till today, to the best of our knowledge, chemical compounds of the essential oils and/or extracts of only eight Laggera species were reported from different countries. Thus, this review presents the chemical compositions and biological activities of the essential oils of these plants studied in thirteen countries. In addition, it discusses the reported ethnobotanical and ethnopharmacological information as well as biological activities of the extracts and some of the isolated compounds of Laggera plants species.     

Amphibian Anomalies as a Source of Information on the Adaptive and Evolutionary Potential

Long-term data on the morphological anomalies of four anuran species (family Ranidae) and two tailed amphibian species (families Hynobiidae and Salamandridae), inhabiting forest and urbanized areas in the eastern slope of the Middle Urals, have been studied. The morphological deviations of amphibians were investigated in terms of the module principle, which predetermines the similarity of evolutionary transformations in different taxa and limit the number of possible directions of diversification in morphogenesis. The definitive spectra and frequencies of morphological anomalies in juvenile and adult individuals are compared in the urbanization gradient. Original methodological and methodical approaches to using the potential and implemented spectra of deviation are proposed for assessing the role of the ecological component in their formation. The possibility of using deviant forms of variability for assessing the evolutionary and adaptive potentials of the species is discussed.     

A Review and Comparison of Methods for Recreating Individual Patient Data from Published Kaplan-Meier Survival Curves for Economic Evaluations: A Simulation Study

Background

In general, the individual patient-level data (IPD) collected in clinical trials are not available to independent researchers to conduct economic evaluations; researchers only have access to published survival curves and summary statistics. Thus, methods that use published survival curves and summary statistics to reproduce statistics for economic evaluations are essential. Four methods have been identified: two traditional methods 1) least squares method, 2) graphical method; and two recently proposed methods by 3) Hoyle and Henley, 4) Guyot et al. The four methods were first individually reviewed and subsequently assessed regarding their abilities to estimate mean survival through a simulation study.

Methods

A number of different scenarios were developed that comprised combinations of various sample sizes, censoring rates and parametric survival distributions. One thousand simulated survival datasets were generated for each scenario, and all methods were applied to actual IPD. The uncertainty in the estimate of mean survival time was also captured.

Results

All methods provided accurate estimates of the mean survival time when the sample size was 500 and a Weibull distribution was used. When the sample size was 100 and the Weibull distribution was used, the Guyot et al. method was almost as accurate as the Hoyle and Henley method; however, more biases were identified in the traditional methods. When a lognormal distribution was used, the Guyot et al. method generated noticeably less bias and a more accurate uncertainty compared with the Hoyle and Henley method.

Conclusions

The traditional methods should not be preferred because of their remarkable overestimation. When the Weibull distribution was used for a fitted model, the Guyot et al. method was almost as accurate as the Hoyle and Henley method. However, if the lognormal distribution was used, the Guyot et al. method was less biased compared with the Hoyle and Henley method.     

Overall Survival Benefits for Combining Targeted Therapy as Second-Line Treatment for Advanced Non-Small-Cell-Lung Cancer: A Meta-Analysis of Published Data

Background

Combining targeted therapy has been extensively investigated in previously treated advanced non-small-cell lung cancer (NSCLC), but it is still unclear whether combining targeted therapy might offer any benefits against standard monotherapy with erlotinib. We thus performed a meta-analysis of randomized controlled trials to compare the efficacy and safety of combining targeted therapy versus erlotinib alone as second-line treatment for advanced NSCLC.

Methods

Several databases were searched, including Pubmed, Embase and Cochrane databases. The endpoints were overall survival (OS), progression-free survival (PFS), overall response rate (ORR) and grade 3 or 4 adverse event (AEs). The pooled hazard ratio (HR) or odds ratio (OR), and 95% confidence intervals (CI) were calculated employing fixed- or random-effects models depending on the heterogeneity of the included trials.

Results

Eight eligible trials involved 2417 patients were ultimately identified. The intention to treatment (ITT) analysis demonstrated that combining targeted therapy significantly improved OS (HR 0.90, 95%CI: 0.82–0.99, p = 0.024), PFS (HR 0.83, 95%CI: 0.72–0.97, p = 0.018), and ORR (OR 1.35, 95%CI 1.01–1.80, P = 0.04). Sub-group analysis based on phases of trials, EGFR-status and KRAS status also showed that there was a tendency to improve PFS and OS in combining targeted therapy, except that PFS for patients with EGFR-mutation or wild type KRAS favored erlotinib monotherapy. Additionally, more incidence of grade 3 or 4 rash, fatigue and hypertension were observed in combining targeted therapy.

Conclusions

With the available evidence, combining targeted therapy seems superior over erlotinib monotherapy as second-line treatment for advanced NSCLC. More studies are still needed to identify patients who will most likely benefit from the appropriate combining targeted therapy.     

Toward an Information Tool for Integrated Product Policy: Requirements for Data and Computation

Integrated product policy, according to the European Union, requires reliable data on the impact of consumer products along their life cycles. We argue that this necessarily requires the development of an information tool for hybrid analysis, combining aspects of life-cycle assessment and input-output analysis. A number of requirements in the development of such a hybrid information tool are identified, mainly concerning data and computational structure. For the former, some important points of attention are discussed, whereas for the latter, operational formulas are developed.     

Nematode Autofluorescence and Its Use as an Indicator of Viability

Representatives of 15 nematode genera were viewed with 450-490-nm epi-illumination and found to autofluoresce. The autofluorescence was limited to 1-5-μm-d globules in the intestinal cells of live nematodes. When adult Pratylenchus penetrans or Caenorhabditis elegans were killed with formaldehyde, freezing, or heat, autofluorescence dispersed throughout the body. Mixed stages of P. penetrans were killed by freezing at several different temperatures. Estimates of survival based on autofluorescence dispersal matched estimates based on mobility more closely than did estimates based on the vital stain, eosin-y.     

Mixtures of UK Wheat as an Efficient and Environmentally Friendly Source for Bioethanol

Concerns about access to oil supplies have encouraged the exploration of renewable fuel and energy sources. Industrial ecology offers tools to compare the energy implications and benefits of differing strategies, but using botanical sources of raw materials to replace nonrenewable ones also requires appreciation of plant science, especially the variation in genetic potential within species. Whereas cultivation methods determine whether genetic potential is realized, different methods impact the environment to varying degrees. Experience with barley variety mixtures, aimed at reducing chemical input, has shown them to improve yield and reduce disease, while maintaining or even enhancing quality. Yield improvements still occurred in the absence of disease and increased in proportion to the number of component varieties. Because other research showed mixtures to be similarly effective in wheat, a protocol to grow and exploit a complex mixture of soft wheat is proposed, offering a cost‐effective and energy efficient feedstock for a possible bioethanol industry in the United Kingdom. Ethanol would be produced initially from grain, with the straw used for heating or electricity generation. Fertilizer production and use and vehicle fuels have been shown as the main forms of energy consumption in growing a crop, and targets for enhancing the energy balance, by growing mixtures under an integrated farming system, are postulated. A close but negative association between grain protein and alcohol yield is demonstrated and a mixture giving comparable grain yield, but superior alcohol yield, to its best component is identified. Mixing varieties differing in plant morphology may also increase total biomass yield and, therefore, the energy generated from the crop. Pesticide reduction has another positive, though small, effect on the energy balance, from using mixtures. Eliminating prophylactic spraying also reduces vehicle fuel consumption, and may provide the low‐toxicity benefits of organic agriculture without the yield penalty. A range of alternative uses for straw and other by‐products is also discussed.