Traditional knowledge and genetic diversity ofopuntia pilifera (cactaceae) in the tehuacán-cuicatlán valley, Mexico

Traditional Knowledge and Genetic Diversity of Opuntia pilifera (Cactaceae) in the Tehuacán-Cuicatlán Valley, Mexico. Economic Botany 59(4)366-376, 2005. Most studies of the genusOpuntia have focused on economically important species, and therefore more knowledge concerning the genetic diversity among wild and locally managedOpuntia species is needed for an expanded use of cacti in the future. The present study is part of ongoing ethnobotanical work in the Tehuacán-Cuicatlán Valley of Mexico and focuses on six traditionally classified forms ofOpuntia pilifera used as food by the indigenous Popoloca people in San Juan Atzingo. Traditional knowledge of how to distinguish these forms based on fruit flavor, color, size, and number of spines on the fruits and cladodes is preserved in the local community. Genetic fingerprinting with 129 AFLPs did not correlate with this traditional morphological classification of 67 cacti. Yet, these AFLPs distinguished the analyzed 67Opuntia pilifera cacti easily from the out-group comprising 17 wildOpuntia velutina.     

(C5Me5)2NbBH4, a new reagent for the synthesis of Ru and Co carbonyl clusters with interstitial boron or carbon

The reaction of Cp*₂NbBH₄ (Cp* = η⁵-C₅Me₅) with Ru₃(CO)₁₂ gave a mixture of compounds, from which only [Cp*₂Nb(CO)₂]₂[Ru₆(CO)₁₆C] (1) could be characterized by spectroscopic and crystallographic methods. ¹¹B NMR spectroscopy proved that interstitial boron may be present in other Ru₆ clusters, but these compounds did not crystallize. The reaction of Cp*₂NbBH₄ with Co₂(CO)₈ gave among others the salts [Cp*₂Nb(CO)₂]₂[Co₆(CO)₁₅C] (4) and [Cp*₂Nb(CO)₂]₃[Co₁₃(CO)₂₄C₂] (5), which were examined by X-ray diffraction studies. The true nature of the interstitial atoms in 5 was deduced from electrochemical investigations, which reveal similar redox properties as for the already known [Co₁₃(CO)₂₄C₂]³⁻ anion.     

Isolation and characterization of new microsatellites at the nm23-H1 and nm23-H2 gene loci and application for loss of heterozygosity (LOH) analysis

 The nm23-H1 gene has been suggested to be a metastasis suppressor gene. Studies about the events of loss of heterozygosity (LOH) at the nm23 locus and its correlation to metastasis are controversially discussed. To optimize detection of LOH at the nm23 locus, we screened two P1 clones for additional microsatellites. Tumor and normal DNA from 37 colorectal, 16 gastric, and 8 germ cancer patients were examined for LOH. We found two new CA repeats, one 5′ to nm23-H1 and another 3′ to nm23-H2. Using these nm23 locus-specific CA repeats and five other chromosome 17 loci (D17S1522, D17S1566, D17S855, D17S515, and TP53), allele loss was observed in 4/32 (12.5%) patients with colon cancer, 2/14 (14.3%) with gastric cancer, and 1/7 (14%) with germ cancer. No isolated LOH of the nm23 region was observed. Received: 5 May 1997 / Accepted: 2 June 1997     

Relaxation spectra of two-step mechanisms as measured by the NADH-binding to glutamate dehydrogenase

Temperature-jump relaxation experiments performed with glutamate dehydrogenase and the reduced coenzyme nicotinamide adenosine dinucleotide show two clearly separated relaxation times. Three of the simplest and most plausible mechanisms attributable to two relaxation times are treated here theoretically and the concentration dependence of the relaxation times is determined in each case with different experimental conditions. This makes it possible to distinguish between the mechanisms and also to determine the rate constants of the different reaction steps.     

Rational design of a pirinixic acid derivative that acts as subtype-selective PPARγ modulator

Peroxisome proliferator-activated receptor γ (PPARγ) is involved in glucose and lipid homeostasis. PPARγ agonists are in clinical use for the treatment of type 2 diabetes. Lately, a new class of selective PPARγ modulators (SPPARγMs) was developed, which are believed to show less side effects than full PPARγ agonists. We have previously shown that α-substitution of pirinixic acid, a moderate agonist of PPARα and PPARγ, leads to low micromolar active balanced dual agonists of PPARα and PPARγ. Herein we present modifications of pirinixic acid leading to subtype-selective PPARγ agonists and furthermore the development of a selective PPARγ modulator guided by molecular docking studies.     

Degradation of 4-aminobenzenesulfonate by a two-species bacterial coculture

The mutualistic interactions in a 4-aminobenzenesulfonate (sulfanilate) degrading mixed bacterial culture were studied. This coculture consisted of Hydrogenophaga palleronii strain S1 and Agrobacterium radiobacter strain S2. In this coculture only strain S1 desaminated sulfanilate to catechol-4-sulfonate, which did not accumulate in the medium but served as growth substrate for strain S2. During growth in batch culture with sulfanilate as sole source of carbon, energy, nitrogen and sulfur, the relative cell numbers (colony forming units) of both strains were almost constant. None of the strains reached a cell number which was more than threefold higher than the cell number of the second strain. A mineral medium with sulfanilate was inoculated with different relative cell numbers of both strains (relative number of colony forming units S1:S2 2200:1 to 1:500). In all cases, growth was found and the proportion of both strains moved towards an about equal value of about 3:1 (strain S1:strain S2). In contrast to the coculture, strain S1 did not grow in a mineral medium in axenic culture with 4-aminobenzenesulfonate or any other simple organic compound tested. A sterile culture supernatant from strain S2 enabled strain S1 to grow with 4-aminobenzenesulfonate. The same growth promoting effect was found after the addition of a combination of 4-aminobenzoate, biotin and vitamin B₁₂. Strain S1 grew with 4-aminobenzenesulfonate plus the three vitamins with about the same growth rate as the mixed culture in a mineral medium. When (resting) cells of strain S1 were incubated in a pure mineral medium with sulfanilate, up to 30% of the oxidized sulfanilate accumulated as catechol-4-sulfonate in the culture medium. In contrast, only minor amounts of catechol-4-sulfonate accumulated when strain S1 was grown with 4ABS in the presence of the vitamins.     

Inhibition of mRNA deadenylation and degradation by different types of cell stress

We have previously observed rapid and strong inhibition of mRNA deadenylation and degradation in response to UV-B light [Gowrishankar et al., Biol. Chem. 386 (2005), pp. 1287-1293]. Expression analysis using a microarray for inflammatory genes showed that UV-B light induces stabilization of all short-lived mRNAs assayed. Stabilization was observed in HeLa cells, as well as in the keratinocyte line HaCaT. It affected constitutively expressed mRNA species, as well as species induced by the inflammatory cytokine IL-1. Many of the latter encode proteins involved in inflammation, suggesting that stress-induced inhibition of mRNA deadenylation contributes to changes in inflammatory gene expression. Deadenylation and degradation of tet-off-expressed mRNAs were also inhibited upon exposure to H2O2. However, scavengers of reactive oxygen species did not interfere with UV-B-induced inhibition of degradation, arguing against the involvement of UV-induced H2O2 in these effects of UV-B light. Heat shock and hyperosmolarity also inhibited mRNA deadenylation and degradation, whereas gamma-radiation did not. Thus, inhibition of mRNA deadenylation and degradation is a cellular response elicited by several but not all inducers of cell stress.     

A multi-split mapping algorithm for circular RNA,splicing, trans-splicing and fusion detection

Numerous high-throughput sequencing studies have focused on detecting conventionally spliced mRNAs in RNA-seq data. However, non-standard RNAs arising through gene fusion, circularization or trans-splicing are often neglected. We introduce a novel, unbiased algorithm to detect splice junctions from single-end cDNA sequences. In contrast to other methods, our approach accommodates multi-junction structures. Our method compares favorably with competing tools for conventionally spliced mRNAs and, with a gain of up to 40% of recall, systematically outperforms them on reads with multiple splits, trans-splicing and circular products. The algorithm is integrated into our mapping tool segemehl (http://www.bioinf.uni-leipzig.de/Software/segemehl/).     

Bridging near and remote Oceania: mtDNA and NRY variation in the Solomon Islands

Although genetic studies have contributed greatly to our understanding of the colonization of Near and Remote Oceania, important gaps still exist. One such gap is the Solomon Islands, which extend between Bougainville and Vanuatu, thereby bridging Near and Remote Oceania, and include both Austronesian-speaking and Papuan-speaking groups. Here, we describe patterns of mitochondrial DNA (mtDNA) and nonrecombining Y chromosome (NRY) variation in over 700 individuals from 18 populations in the Solomons, including 11 Austronesian-speaking groups, 3 Papuan-speaking groups, and 4 Polynesian Outliers (descended via back migration from Polynesia). We find evidence for ancient (pre-Lapita) colonization of the Solomons in old NRY paragroups as well as from M2-M353, which probably arose in the Solomons ～9,200 years ago and is the most frequent NRY haplogroup there. There are no consistent genetic differences between Austronesian-speaking and Papuan-speaking groups, suggesting extensive genetic contact between them. Santa Cruz, which is located in Remote Oceania, shows unusually low frequencies of mtDNA and NRY haplogroups of recent Asian ancestry. This is in apparent contradiction with expectations based on archaeological and linguistic evidence for an early (～3,200 years ago), direct colonization of Santa Cruz by Lapita people from the Bismarck Archipelago, via a migration that "leapfrogged" over the rest of the Solomons. Polynesian Outliers show dramatic island-specific founder events involving various NRY haplogroups. We also find that NRY, but not mtDNA, genetic distance is correlated with the geographic distance between Solomons groups and that historically attested spheres of cultural interaction are associated with the recent genetic structure of Solomons groups, as revealed by mtDNA HV1 sequence and Y-STR haplotype diversity. Our results fill an important lacuna in human genetic studies of Oceania and aid in understanding the colonization and genetic history of this region.