Isolation and characterization of nine microsatellite loci for the tropical understory tree Miconia affinis Wurdack (Melastomataceae)

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/75161/1/j.1755-0998.2008.02428.x.pd

Systematics of Bromelioideae (Bromeliaceae)—Evidence from Molecular and Anatomical Studies

A reconstruction of the phylogeny of Bromeliaceae based on sequence data from three noncoding chloroplast DNA markers (trnL intron, trnT–trnL, and trnT–trnF intergenic spacer [IGS]) is presented, including 26 genera and 33 species. Relationships of Bromelioideae and phylogeny within this subfamily were analyzed in more detail on the basis of two of these markers (trnL intron and trnL–trnF IGS) using a set of 37 genera/74 species of Bromeliaceae, including 28 genera/60 species of Bromelioideae. Sister group relationships of Bromelioideae were not resolved with sufficient reliability, but the most likely candidates are the genera Fosterella and Puya. The basal phylogeny of Bromelioideae also was not resolved. Greigia, Ochagavia/Fascicularia/Fernseea, Deinacanthon, Bromelia, and a ‘‘core group’’ of the remaining Bromelioideae formed a basal polytomy. Within Bromelioideae, the AFLP technique was applied to assess relationships among selected groups of genera. In the Ochagavia/Fascicularia group (5 species and subspecies/16 accessions), AFLP data fully confirmed the systematic relationships based on morphological and anatomical characters. Investigation of 30 Aechmea species (33 accessions), including all subgenera and one species each from the related genera Ursulaea, Portea, Chevaliera, and Streptocalyx produced no resolution for several of the species. Clades that received good bootstrap support generally did not correspond with the delimitation of subgenera of Aechmea. Additionally, leaf blade anatomy of these species was investigated. The results corresponded partly with those of the AFLP analysis. Generic rank for Ursulaea and Portea was not supported

A set of variable plastid SSR markers for the genus Cryptanthus (Bromeliaceae)

The genus Cryptanthus (Bromeliaceae) is endemic to Brazil. Many of its currentlyrecognized 66 species are narrow endemics that are threatened by habitat destruction.Molecular markers are needed to evaluate the extent and distribution of genetic diversityin rare Cryptanthus species, which would be a prerequisite for taking appropriateconservation measures. Here we describe the development of plastid microsatellitemarkers (cpSSRs) for Cryptanthus. PCR primers specific for 34 cpSSR loci in Dyckiamarnier-lapostollei were initially tested for their functionality in Cryptanthus schwackeanus. PCR was successful for 29 loci, and 13 loci were shown to harbour extended stretches of mononucleotide repeats. Seven loci were further characterized bygenotyping Cryptanthus samples at the level of populations and species, and six lociproved to be polymorphic among 30 individuals of each of the two endangered species C. schwackeanus and C. warren-loosei, respectively. All primers cross-amplified in other genera from three subfamilies of Bromeliaceae

Phylogeography of three closely related myrmecophytic pioneer tree species in SE Asia: implications for species delimitation

Members of the Euphorbiaceae are ecologically important elements of Southeast Asian forests. Species of the pioneer tree genus Macaranga, which is also known for its association with ants, are often abundant in disturbed areas. Phylogenetic studies suggested a recent radiation of section Pachystemon which comprises the majority of obligate myrmecophytes within Macaranga. In the present study, we analyzed the genetic structure of three closely related species of this section (M. constricta, M. griffithiana, and M. motleyana) with the aim of resolving their controversial taxonomy and historical biogeography. Chloroplast DNA haplotypes proved to be species-specific and showed a strong phylogeographic pattern. Nuclear microsatellite data supported the taxonomic distinctness of M. griffithiana and M. motleyana, but gave ambiguous results for M. constricta. Genetic differentiation was stronger each within M. griffithiana and M. motleyana than between M. constricta and M. griffithiana, highlighting problems of defining species boundaries. We found no indication for introgression or hybridization events. The high intraspecific morphological variation of the Bornean endemic M. motleyana was partly reflected by similar patterns of genetic variation. The pronounced genetic structure indicates a comparatively long diversification for this species. In contrast, the weak genetic differentiation within M. griffithiana, as well as the widespread distribution of its most common chloroplast haplotype from peninsular Malaysia up to Indochina, indicates a recent expansion in this area. Despite their morphological similarity and close relatedness, all species possess their own specific ant-partners with a corresponding distribution pattern

Biogeography of the Sunda Shelf revisited: Insights from Macaranga section Pruinosae (Euphorbiaceae)

The Southeast Asian region of Sundaland is among the world’s major biodiversity hotspots. The region’s biodiversity coupled with its complex and dynamic geographic and climatic histories makes it an ideal region to study the various factors that determine the diversification and distribution patterns of tropical biota. Here we investigate the biogeographic patterns in the partly myrmecophytic Macaranga section Pruinosae to reveal some of the factors that play a role in determining the distribution of biota in Sundaland. We used single nucleotide polymorphisms (SNP) data derived from GBS, a next generation sequencing technique, in maximum likelihood and cluster analyses to determine phylogenetic relationships and population structures within this taxonomic section. Bayesian inference based on secondary calibration points and ancestral area reconstruction analyses were performed to infer spatial–temporal origins of the major lineages in the section. The results from these analyses were further substantiated using nuclear microsatellite data obtained from a broader sample set of two widely distributed species within the section: Macaranga gigantea and Macaranga pruinosa. Phylogenetic and cluster analyses reveal four well-defined, discrete species groups within section Pruinosae, all of which but one originated in Borneo with the crown node dated at 3.58 mya. Biogeographic patterns within the species reveal a biogeographic barrier between east and west Sundaland besides bringing to light the role played by various geological factors, especially the Crocker Range, on Borneo. Patterns also reveal a biogeographic barrier between the Bangka/Belitung islands and Sumatra for ant-free, swamp-adapted species. This study provides evidence that geographic barriers, edaphic conditions, and ecological adaptations are tightly linked and that their mutual interaction determines the diversification and distribution of species

SAMHD1 enhances nucleosideanalogue efficacy against HIV-1 in myeloid cells

SAMHD1 is an intracellular enzyme that specifically degrades deoxynucleoside triphosphates into component nucleoside and inorganic triphosphate. In myeloid-derived dendritic cells and macrophages as well as resting T-cells, SAMHD1 blocks HIV-1 infection through this dNTP triphosphohydrolase activity by reducing the cellular dNTP pool to a level that cannot support productive reverse transcription. We now show that, in addition to this direct effect on virus replication, manipulating cellular SAMHD1 activity can significantly enhance or decrease the anti-HIV-1 efficacy of nucleotide analogue reverse transcription inhibitors presumably as a result of modulating dNTP pools that compete for recruitment by viral polymerases. Further, a variety of other nucleotide-based analogues, not normally considered antiretrovirals, such as the anti-herpes drugs Aciclovir and Ganciclovir and the anti-cancer drug Clofarabine are now revealed as potent anti-HIV-1 agents, under conditions of low dNTPs. This in turn suggests novel uses for nucleotide analogues to inhibit HIV-1 in differentiated cells low in dNTPs.This work was supported by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC001042, FC001162, FC001178), the UK Medical Research Council (FC001042, FC001162, FC001178), and the Wellcome Trust (FC001042, FC001162, FC001178); and by the Wellcome Trust (108014/Z/15/Z and 108012/Z/15/Z)

An Optimized Protocol for DNA Extraction from Wheat Seeds and Loop-Mediated Isothermal Amplification (LAMP) to Detect Fusarium graminearum Contamination of Wheat Grain

A simple, rapid, and efficient method for isolating genomic DNA from germinated seeds of wheat that is free from polysaccharides and polyphenols is reported. DNA was extracted, treated with RNase, measured and tested for completeness using agarose gel electrophoresis. DNA purification from wheat grains yielded abundant, amplifiable DNA with yields typically between 100 and 200 ng DNA/mg. The effectiveness and reliability of the method was tested by assessing quantity and quality of the isolated DNA using three PCR-based markers. Inter-simple sequence repeats (ISSRs) were used to assess the genetic diversity between different wheat varieties. Specific PCR primer pair Tox5-1/Tox5-2 and a loop-mediated isothermal amplification (LAMP) procedure were used to detect genomic DNA of Fusarium graminearum in contaminated wheat seeds. In this method there is no need to use liquid nitrogen for crushing germinated seedlings. The protocol takes approximately one hour to prepare high quality DNA. In combination with the LAMP assay it is a fast and cost-effective alternative to traditional diagnostic methods for the early detection of toxigenic fusaria in cereals