A mathematical additive model of the structure—activity relationships of gibberellins

By means of a modified Free—Wilson technique, the individual contributions of 22 different substituents on the growth-promoting activity of 67 gibberellins and their synthetic derivatives were estimated for three bioassay systems (dwarf pea, cucumber and lettuce). Statistically significant correlations between the presence of certain structural elements and potency in a given bioassay were observed. The additive character of the contributions is considered in terms of a structural correspondence between a C₁₉-hormone and a specific receptor.     

Plankton community and the relationship with the environment in saline lakes of Onon-Torey plain,Northeastern Mongolia

The plankton community of sixteen saline lakes located on Onon-Torey plain (Northeastern Mongolia) during the filling phase and the raising of the water level was investigated in July 2011. Thirty-five taxa of phytoplankton and thirty-one species of zooplankton were found. For phytoplankton, blue-green algae (Merismopedia elegans, Anabaenopsis elenkinii, Arthrospora fusiformis, Spirulina major, Lyngbya sp., Oscillatoria sp.) and green algae (Monoraphidium minutum, Tetrastrum komarekii, Ankyra ocellata, Oocystis sp.) were dominant. For zooplankton, Filinia longiseta, Brachionus plicatilis, B. variabilis, Hexarthra mira (Rotifera), Daphnia magna, Moina brachiata, M. mongolica (Cladocera), Arctodiaptomus bacillifer, Mixodiaptomus incrassatus, Metadiaptomus asiaticus (Copepoda) dominated. Mineralization, active hydrogen ratio, dissolved oxygen and water temperature were the main factors influencing the diversity, structure and distribution of plankton organisms in the steppe lakes during low water level. The RDA analysis for phytoplankton and zooplankton from different lakes was carried out for selected two groups which included lakes and a subset related species. The first group is of oligohaline and mesohaline lakes in which mostly green algae, rotifers and copepods inhabit. The second group is of mesohaline and polyhaline lakes with mainly blue-green algae, some crustaceans and rotifers inhabiting. High abundance and biomass of Spirulina major, Oscillatoria sp. and Brachionus variabilis were observed in lakes with high mineralization, pH and temperature.     

Rapid warming accelerates tree growth decline in semi‐arid forests of Inner Asia

Forests around the world are subject to risk of high rates of tree growth decline and increased tree mortality from combinations of climate warming and drought, notably in semi‐arid settings. Here, we assess how climate warming has affected tree growth in one of the world's most extensive zones of semi‐arid forests, in Inner Asia, a region where lack of data limits our understanding of how climate change may impact forests. We show that pervasive tree growth declines since 1994 in Inner Asia have been confined to semi‐arid forests, where growing season water stress has been rising due to warming‐induced increases in atmospheric moisture demand. A causal link between increasing drought and declining growth at semi‐arid sites is corroborated by correlation analyses comparing annual climate data to records of tree‐ring widths. These ring‐width records tend to be substantially more sensitive to drought variability at semi‐arid sites than at semi‐humid sites. Fire occurrence and insect/pathogen attacks have increased in tandem with the most recent (2007–2009) documented episode of tree mortality. If warming in Inner Asia continues, further increases in forest stress and tree mortality could be expected, potentially driving the eventual regional loss of current semi‐arid forests.     

Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips

Illumina’s Infinium HumanMethylation450 BeadChip arrays were used to examine genome-wide DNA methylation profiles in 22 sample pairs from colorectal cancer (CRC) and adjacent tissues and 19 colon tissue samples from cancer-free donors. We show that the methylation profiles of tumors and healthy tissue samples can be clearly distinguished from one another and that the main source of methylation variability is associated with disease status. We used different statistical approaches to evaluate the methylation data. In general, at the CpG-site level, we found that common CRC-specific methylation patterns consist of at least 15,667 CpG sites that were significantly different from either adjacent healthy tissue or tissue from cancer-free subjects. Of these sites, 10,342 were hypermethylated in CRC, and 5,325 were hypomethylated. Hypermethylated sites were common in the maximum number of sample pairs and were mostly located in CpG islands, where they were significantly enriched for differentially methylated regions known to be cancer-specific. In contrast, hypomethylated sites were mostly located in CpG shores and were generally sample-specific. Despite the considerable variability in methylation data, we selected a panel of 14 highly robust candidates showing methylation marks in genes SND1, ADHFE1, OPLAH, TLX2, C1orf70, ZFP64, NR5A2, and COL4A. This set was successfully cross-validated using methylation data from 209 CRC samples and 38 healthy tissue samples from The Cancer Genome Atlas consortium (AUC = 0.981 [95% CI: 0.9677–0.9939], sensitivity = 100% and specificity = 82%). In summary, this study reports a large number of loci with novel differential methylation statuses, some of which may serve as candidate markers for diagnostic purposes.     

Antiproliferative activity of 2,3-disubstituted indoles toward apoptosis-resistant cancers cells

Many types of cancer, including glioma, melanoma, NSCLC, among others, are resistant to apoptosis induction and poorly responsive to current therapies with propaptotic agents. We describe a series of 2,3-disubstituted indoles, which display cytostatic rather than cytotoxic effects in cancer cells, and serve as a new chemical scaffold to develop anticancer agents capable of combating apoptosis-resistant cancers associated with dismal prognoses.     

<Emphasis Type="Italic">Agrobacterium tumefaciens</Emphasis> and <Emphasis Type="Italic">Agrobacterium rhizogenes</Emphasis> transformed roots of the parasitic plant <Emphasis Type="Italic">Triphysaria versicolor</Emphasis> retain parasitic competence

Parasitic plants in the Orobanchaceae invade roots of neighboring plants to rob them of water and nutrients. Triphysaria is facultative parasite that parasitizes a broad range of plant species including maize and Arabidopsis. In this paper we describe transient and stable transformation systems for Triphysaria versicolor Fischer and C. Meyer. Agrobacterium tumefaciens and Agrobacterium rhizogenes were both able to transiently express a GUS reporter in Triphysaria seedlings following vacuum infiltration. There was a correlation between the length of time seedlings were conditioned in the dark prior to infiltration and the tissue type transformed. In optimized experiments, nearly all of the vacuum infiltrated seedlings transiently expressed GUS activity in some tissue. Calluses that developed from transformed tissues were selected using non-destructive GUS staining and after several rounds of in vivo GUS selection, we recovered uniformly staining GUS calluses from which roots were subsequently induced. The presence and expression of the transgene in Triphysaria was verified using genomic PCR, RT PCR and Southern hybridizations. Transgenic roots were also obtained by inoculating A. rhizogenes into wounded Triphysaria seedlings. Stable transformed roots were identified using GUS staining or fluorescent microscopy following transformation with vectors containing GFP, dsRED or EYFP. Transgenic roots derived from both A. tumefaciens and A. rhizogenes transformations were morphologically normal and developed haustoria that attached to and invaded lettuce roots. Transgenic roots also remained competent to form haustoria in response to purified inducing factors. These transformation systems will allow an in planta assessment of genes predicted to function in plant parasitism. Alexey Tomilov and Natalya Tomilova made an equal contribution in the paper.     

DNA conformational effects on the interaction of netropsin with A-tract sequences

The influence of cosolutes and DNA sequence on the interaction of netropsin with three duplexes has been studied by isothermal titration calorimetry. In buffer, netropsin forms two complexes with a net stoichiometry of 1:1 in the minor groove of the oligonucleotide (GCGCGAATTCGCGC)2. One complex has a weaker affinity and is more enthalpically favored relative to the other one, consistent with previous studies [Freyer, M. W., et al. (2006) Biophys. Chem. 126, 186-196]. With the cosolutes betaine and 2-methyl-2,4-pentanediol, the enthalpy and heat capacity changes indicate that the complex with weaker affinity is disfavored relative to the complex with higher affinity. With (CGCGCAATTGCGCG)2, netropsin has one binding mode in buffer, and complex formation is not influenced by the cosolutes. The similarities of the enthalpy and heat capacity changes suggest that netropsin interacts similarly with these two oligonucleotides in the presence of cosolutes. The oligonucleotide (GCGCAAATTTGCGC)2 also forms two complexes with netropsin, and the complex with weaker affinity is again disfavored by the cosolutes. Thus, the interaction of netropsin with these A/T binding sites is influenced both by the bases adjacent to the binding site and by cosolutes. We suggest that these two factors influence the conformation of the minor-groove binding site of DNA.     

Fluorescence microscopy evidence for quasi-permanent attachment of antifreeze proteins to ice surfaces

Many organisms are protected from freezing by the presence of extracellular antifreeze proteins (AFPs), which bind to ice, modify its morphology, and prevent its further growth. These proteins have a wide range of applications including cryopreservation, frost protection, and as models in biomineralization research. However, understanding their mechanism of action remains an outstanding challenge. While the prevailing adsorption-inhibition hypothesis argues that AFPs must bind irreversibly to ice to arrest its growth, other theories suggest that there is exchange between the bound surface proteins and the free proteins in solution. By conjugating green fluorescence protein (GFP) to a fish AFP (Type III), we observed the binding of the AFP to ice. This was accomplished by monitoring the presence of GFP-AFP on the surface of ice crystals several microns in diameter using fluorescence microscopy. The lack of recovery of fluorescence after photobleaching of the GFP component of the surface-bound GFP-AFP shows that there is no equilibrium surface-solution exchange of GFP-AFP and thus supports the adsorption-inhibition mechanism for this type of AFP. Moreover, our study establishes the utility of fluorescently labeled AFPs as a research tool for investigating the mechanisms underlying the activity of this diverse group of proteins.