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The present work provides an overview of the different methods used in molecular diversity analysis. Issues like identifying voids in proprietary databases, reducing the number of redundancies present in databases, or designing focused libraries by grouping compounds similar to a template with the aim to fine tune its properties, are potent diversity analysis tools that may be used to optimize molecules based on their properties and specifically, to speed up the process of lead discovery and optimization. The present work describes first methods that are used to describe molecular systems. This is followed by a section devoted to describe different measures of similarity between molecules, to finish with a description of different methods used to select subsets molecules according to the constraints imposed. The final section deals with the validation of these methods, based on different studies available in the literature.

Solanum section Petota, the potato and its wild relatives, contains about 200 wild species distributed from the southwestern United States, to central Argentina and adjacent Chile. Although most species occur in South America, a secondary center of diversity peaks at 20 degrees north in the central Mexican highlands, including diploids (2n = 2x = 24), tetraploids (2n = 4x = 48), hexaploids (2n = 6x = 72), and triploid and pentaploid nothospecies. This treatment covers the wild potatoes of North and Central America (United States to Panama). It is a summary of recent morphological and molecular studies of species limits and their interrelationships. We collected herbarium and germplasm samples from all countries harboring wild potatoes in this region and now have access to germplasm of every species. A comprehensive treatment in 1990 recognized 33 species, 12 subspecies, and five nothospecies from the region, partitioned into eight formal taxonomic series. We recognize 25 species and four nothospecies from the region, partitioned into eleven informal species groups. It provides the first formal typification of many of these names, an extensive list of georeferenced localities, a geographic information systems based diversity analysis, and illustrations and maps of all the species.

Hierarchical diversity analysis of data on fish and aquatic insects showed that the component of diversity contributed by the species level was generally very small compared with the component at the generic level or with the total diversity. Very high rank correlations between generic diversity, in which genera were discriminated but not identified, and species diversity suggested that the purposes of environmental monitoring might best be served by working at the generic level rather than the species level. This is particularly true when an index of diversity is to be used as the major comparative and communicative tool. The savings of time and money could be appreciable.

Bioaerosol charge information is of vital importance for their electrostatic collection. Here, electrostatic means and molecular tools were applied to studying bioaerosol charge dynamics. Positively or negatively charged bioaerosols were collected using an electrostatic sampler operated with a field strength of 1.1 kV cm−1 at a flow rate of 3 L min−1 for 40 min. Those with fewer or no charges bypassing the sampler were also collected using a filter at the downstream of the electrostatic sampler in one environment. The experiments were independently conducted three times in three different environments. The collected bacterial aerosols were cultured directly on agar plates at 26°C, and the colony forming units (CFU) were manually counted. In addition, the CFUs were washed off from the agar plates, and further subjected to polymerase chain reaction (PCR) and denaturing gradient gel electrophoresis (DGGE) for culturable diversity analysis. The results revealed remarkable differences in positively and negatively charged culturable bacterial aerosol concentration and diversity among the studied environments. In the office environment, negatively charged culturable bacterial aerosols appeared to dominate (P = 0.0489), while in outdoor and hotel environments both polarities had similar concentration levels (P = 0.078, P = 0.88, respectively). DGGE patterns for positively charged culturable bacterial aerosols were shown strikingly different from those of negatively charged regardless of the sampling environments. In addition, for each of the environments positively charged culturable bacterial aerosols collected were found to have more band pattern similarity with those positively charged for respective regions of agar plates than those negatively charged, and vice versa. The information developed here is useful for developing efficient electrostatic sampling protocols for bioaerosols.

The use in the literature of statistics and measures derived for the measurement and the analysis of inbreeding from data on gene frequency diversity and applied to data on surname diversity is discussed. To overcome the difficulties encountered with this approach, a simple mathematical model for analysing isonymy data is proposed. Finally some further measures of surname diversity are given based on measures developed for gene diversity analysis and for community diversity analysis in ecology.

Numerous national or international agriculture research institutes are dealing with common bean (Phaseolus vulgaris L.) breeding, in order to develop cultivars with higher and more stable yield. Such breeding programmes reguire the existence of a very wide range of genetic variability from which useful characters can be identified and combined to obtain improved cultivars.

The genetic structure of Pileolaria pseudomilitaris was studied by means of gene-diversity analysis of allozyme frequencies. At an esterase locus, most of the gene diversity was due to subdivision of the population into colonies and subpopulations separated by less than 100 meters. Gene frequencies at a phosphoglucose isomerase locus were similar over many kilometers, but differed between two habitat types. Differences between colonies are attributed to drift and founder effect; similarities over greater distances are attributed to similar selection pressures. A mathematical appendix details the method of gene diversity analysis for a multi-leveled, hierarchically subdivided population.

It is show that Wright's F-statistics can be defined as ratios of gene diversities of heterozygosities rather than as the correlations of uniting gametes. This definition is applicable irrespective of the number of alleles involved or whether there is selection or not. The relationship between F-statistics and Nei's gene diversity analysis is discussed.

Widiastuti A, Sobir, Suhartanto MR. 2010. Diversity analysis of mangosteen (Garcinia mangostana L.) irradiated by gamma-ray based on morphological and anatomical characteristics. Nusantara Bioscience 2: 23-33. The aim of this research was to increase genetic variability of mangosteen (Garcinia mangostana L.) irradiated by gamma rays dosage of 0 Gy, 20 Gy, 25 Gy, 30 Gy,35 Gy, and 40 Gy. Plant materials used were seeds collected from Cengal Sub-village, Karancak Village, Leuwiliang Sub-district, Bogor District, West Java. Data was generated from morphological and anatomical characteristics. The result indicated that increasing gamma-ray dosage had inhibited ability of seed to grow, which needed longer time and decreased seed viability. Morphologically, it also decreased plant height, stem diameter, leaf seizure, and amount of leaf. Anatomically, stomatal density had positive correlation with plant height by correlation was 90% and 74%. Gamma rays irradiation successfully increase morphological variability until 30%. Seed cleavage after irradiation increased variability and survival rate of mangosteen.

Millions of distinct metal-organic frameworks (MOFs) can be made by combining metal nodes and organic linkers. At present, over 90,000 MOFs have been synthesized and over 500,000 predicted. This raises the question whether a new experimental or predicted structure adds new information. For MOF chemists, the chemical design space is a combination of pore geometry, metal nodes, organic linkers, and functional groups, but at present we do not have a formalism to quantify optimal coverage of chemical design space. In this work, we develop a machine learning method to quantify similarities of MOFs to analyse their chemical diversity. This diversity analysis identifies biases in the databases, and we show that such bias can lead to incorrect conclusions. The developed formalism in this study provides a simple and practical guideline to see whether new structures will have the potential for new insights, or constitute a relatively small variation of existing structures. At present there are databases with over 500,000 predicted or synthesized MOF structures, yet a method to establish whether a new material adds new information does not exist. Here the authors propose a machine-learning based approach to quantify the structural and chemical diversity in common MOF databases.

In cooperative communication systems, hierarchical modulation is used to increase systems robustness and to send different information flows simultaneously. In cooperative communication systems which use hierarchical modulation, error propagation is the most important problem that prevents achieving full diversity gain. Thresholds that depend on the signal to noise ratio (SNR) value between the source and the relay can be used to mitigate error propagation. If the instantaneous SNR between the source and the relay is lower than the first threshold, the relay does not transmit. If the SNR is between the first and the second thresholds, the relay demodulates and forwards only the primary bits. If the SNR is higher than the second threshold, the relay demodulates and forwards both the primary and the secondary bits. Mitigating error propagation and achieving full diversity for both primary (high priority) and secondary (low priority) bits depend on setting the thresholds at the relay properly. In this work, the first and the second threshold values are determined so that full diversity gains are attained for both primary and secondary bits. Analytical and simulation results are provided to verify the analysis.

In Eco-Metabolomics interactions are studied of non-model organisms in their natural environment and relations are made between biochemistry and ecological function. Current challenges when processing such metabolomics data involve complex experiment designs which are often carried out in large field campaigns involving multiple study factors, peak detection parameter settings, the high variation of metabolite profiles and the analysis of non-model species with scarcely characterised metabolomes. Here, we present a dataset generated from 108 samples of nine bryophyte species obtained in four seasons using an untargeted liquid chromatography coupled with mass spectrometry acquisition method (LC/MS). Using this dataset we address the current challenges when processing Eco-Metabolomics data. Here, we also present a reproducible and reusable computational workflow implemented in Galaxy focusing on standard formats, data import, technical validation, feature detection, diversity analysis and multivariate statistics. We expect that the representative dataset and the reusable processing pipeline will facilitate future studies in the research field of Eco-Metabolomics.

The experiment was conducted to evaluate black pepper accessions for growth parameters, yield attributing characters and yield. Out of the ten accessions tested, Karimunda recorded the highest fresh (1.61 kg) and dry (508.7 g) yield of berries plant-1. Fresh weight showed significant positive genotypic correlation to dry weight and while negative correlated to 100 berry volume, 100 berry weight and number of berries spike-1. Hence, selection based on number of berries spike-1, 100 berry volume and 100 berry weight may not lead to the high yielding black pepper variety. The results showed that Karimunda is the most suitable black pepper variety for high altitude areas of Idukki district.