Indonesian Institute of Sciences

About: Indonesian Institute of Sciences is a facility organization based out in Jakarta, Indonesia. It is known for research contribution in the topics: Population & Genus. The organization has 4795 authors who have published 10544 publications receiving 76990 citations. The organization is also known as: Indonesian Institute of Sciences Cibinong, Indonesia.

Paralogs and off-target sequences improve phylogenetic resolution in a densely-sampled study of the breadfruit genus (Artocarpus, Moraceae).

Abstract: We present a 517-gene phylogenetic framework for the breadfruit genus Artocarpus (ca. 70 spp., Moraceae), making use of silica-dried leaves from recent fieldwork and herbarium specimens (some up to 106 years old) to achieve 96% taxon sampling. We explore issues relating to assembly, paralogous loci, partitions, and analysis method to reconstruct a phylogeny that is robust to variation in data and available tools. Although codon partitioning did not result in any substantial topological differences, the inclusion of flanking noncoding sequence in analyses significantly increased the resolution of gene trees. We also found that increasing the size of data sets increased convergence between analysis methods but did not reduce gene-tree conflict. We optimized the HybPiper targeted-enrichment sequence assembly pipeline for short sequences derived from degraded DNA extracted from museum specimens. Although the subgenera of Artocarpus were monophyletic, revision is required at finer scales, particularly with respect to widespread species. We expect our results to provide a basis for further studies in Artocarpus and provide guidelines for future analyses of data sets based on target enrichment data, particularly those using sequences from both fresh and museum material, counseling careful attention to the potential of off-target sequences to improve resolution. [Artocarpus; Moraceae; noncoding sequences; phylogenomics; target enrichment.]

$\rm \Lambda_{c}^{+}$ production and baryon-to-meson ratios in pp and p-Pb collisions at $\sqrt{s_\mathrm{NN}} = 5.02$ TeV at the LHC

Abstract: The prompt production of the charm baryon Λ c + and the Λ c + / D 0 production ratios were measured at midrapidity with the ALICE detector in p p and p -Pb collisions at s NN = 5.02 TeV . These new measurements show a clear decrease of the Λ c + / D 0 ratio with increasing transverse momentum ( p T ) in both collision systems in the range 2 p T 12 GeV / c , exhibiting similarities with the light-flavor baryon-to-meson ratios p / π and Λ / K S 0 . At low p T , predictions that include additional color-reconnection mechanisms beyond the leading-color approximation, assume the existence of additional higher-mass charm-baryon states, or include hadronization via coalescence can describe the data, while predictions driven by charm-quark fragmentation processes measured in e + e - and e - p collisions significantly underestimate the data. The results presented in this Letter provide significant evidence that the established assumption of universality (colliding-system independence) of parton-to-hadron fragmentation is not sufficient to describe charm-baryon production in hadronic collisions at LHC energies.

The Most Developmentally Truncated Fishes Show Extensive Hox Gene Loss and Miniaturized Genomes.

Abstract: The world’s smallest fishes belong to the genus Paedocypris. These miniature fishes are endemic to an extreme habitat: the peat swamp forests in SoutheastAsia, characterized by highly acidic blackwater. This threatened habitat is home to a large array of fishes, including a number ofminiaturized but also developmentally truncated species. Especially the genus Paedocypris is characterized by profound, organism-wide developmental truncation, resulting in sexually mature individuals of <8mm in length with a larval phenotype. Here, we report on evolutionary simplification in the genomes of two species of the dwarf minnow genus Paedocypris using whole-genome sequencing. The two species feature unprecedented Hox gene loss and genome reduction in association with their massive developmental truncation. We also show how other genes involved in the development of musculature, nervous system, and skeleton have been lost in Paedocypris,mirroring its highly progenetic phenotype. Further, our analyses suggest two mechanisms responsible for the genome streamlining in Paedocypris in relation to other Cypriniformes: severe intron shortening and reduced repeat content. As the first report on the genomic sequence of a vertebrate species with organism-wide developmental truncation, the results of our work enhance our understanding of genome evolution and how genotypes are translated to phenotypes. In addition, as a naturally simplified systemclosely related to zebrafish, Paedocypris provides novel insights into vertebrate development.

Empowering change for sustainable agriculture: the need for participation

Abstract: Sustainable agricultural development (SAD) requires empowerment and engagement of all actors in the agricultural production and supply chain to enable change. This paper proposes a novel framework for Participatory Sustainable Agricultural Development (PSAD) that distinguishes four main classes of factors that influence participation in SAD: environmental, economic, social and governance-related. The factors in each of these classes are analysed in relation to their effect over time, on the basis of 49 SAD programmes reported in the literature. Findings show that the social factors of engagement and empowerment, not often addressed in existing SAD programmes, are of significant influence to effect over time, as are the environmental factors of food safety, and the economic factors of production and capacity development. As such this paper shows that in in addition to the well-acknowledged need for knowledge and skills related to food safety, production and capacity development, SAD programmes also need to address the social factors of engagement and empowerment to enable sustainable change over time for SAD through participation.