Calcineurin sets the bandwidth for discrimination of signals during thymocyte development

At critical times in development, cells are able to convert graded signals into discrete developmental outcomes; however, the mechanisms involved are poorly understood. During thymocyte development, cell fate is determined by signals originating from the alphabeta T-cell receptor. Low-affinity/avidity interactions between the T-cell receptor and peptide-MHC complexes direct differentiation to the single-positive stage (positive selection), whereas high-affinity/avidity interactions induce death by apoptosis (negative selection). Here we show that mice deficient in both calcineurin and nuclear factor of activated T cells (NFAT)c2/c3 lack a population of preselection thymocytes with enhanced ability to activate the mitogen-activated protein kinase (Raf-MEK-ERK) pathway, and fail to undergo positive selection. This defect can be partially rescued with constitutively active Raf, indicating that calcineurin controls MAPK signalling. Analysis of mice deficient in both Bim (which is required for negative selection) and calcineurin revealed that calcineurin-induced ERK (extracellular signal-regulated kinase) sensitization is required for differentiation in response to 'weak' positive selecting signals but not in response to 'strong' negative selecting signals (which normally induce apoptosis). These results indicate that early calcineurin/NFAT signalling produces a developmental period of ERK hypersensitivity, allowing very weak signals to induce positive selection. This mechanism might be generally useful in the discrimination of graded signals that induce different cell fates.     

基于随机森林特征变量优化的湿地植物分类与密度反演

以长江口滨海湿地为研究区域,采用随机森林算法对滨海湿地植被进行分类。在提取Landsat?8 OLI影像植被指数和水体指数的基础上,提出利用植被指数季节差值对模型进行特征变量优化,分析了长江口滨海湿地植物群落分布的空间特征。以所占面积最大的互花米草（入侵物种）为例,采用多元线性回归模型结合实地测量数据,估算了秋季的互花米草植物密度的空间特征。提出的多时相遥感数据结合随机森林特征变量优化方法,可以较为便捷地提取长江口湿地3种优势物种的空间分布特征,与最大似然法相比,分类精度有较大提高,总体分类精度由78.35%提高至87.55%,Kappa系数由0.72提高至0.84。该方法适用于存在“异物同谱”问题的湿地植物群落研究。     

Weighted Graphs with Distances in Given Ranges

Let \( \mathcal{G} \) = (G,w) be a weighted simple finite connected graph, that is, let G be a simple finite connected graph endowed with a function w from the set of the edges of G to the set of real numbers. For any subgraph G′ of G, we define w(G′) to be the sum of the weights of the edges of G′. For any i, j vertices of G, we define D _{i,j}(\( \mathcal{G} \)) to be the minimum of the weights of the simple paths of G joining i and j. The D _{i,j}(\( \mathcal{G} \)) are called 2-weights of \( \mathcal{G} \). Weighted graphs and their reconstruction from 2-weights have applications in several disciplines, such as biology and psychology.Let \( {\left\{{m}_I\right\}}_{I\in \left(\frac{\left\{1,\dots, n\right\}}{2}\right)} \) and \( {\left\{{M}_I\right\}}_{I\in \left(\frac{\left\{1,\dots, n\right\}}{2}\right)} \) be two families of positive real numbers parametrized by the 2-subsets of {1, …, n} with m _I ≤ M _I for any I; we study when there exist a positive-weighted graph G and an n-subset {1, …, n} of the set of its vertices such that D _I (\( \mathcal{G} \)) ∈ [m _I ,M _I ] for any \( I\in \left(\frac{\left\{1,\dots, n\right\}}{2}\right) \). Then we study the analogous problem for trees, both in the case of positive weights and in the case of general weights.     

DNA breaks and chromosome pulverization from errors in mitosis

The involvement of whole-chromosome aneuploidy in tumorigenesis is the subject of debate, in large part because of the lack of insight into underlying mechanisms. Here we identify a mechanism by which errors in mitotic chromosome segregation generate DNA breaks via the formation of structures called micronuclei. Whole-chromosome-containing micronuclei form when mitotic errors produce lagging chromosomes. We tracked the fate of newly generated micronuclei and found that they undergo defective and asynchronous DNA replication, resulting in DNA damage and often extensive fragmentation of the chromosome in the micronucleus. Micronuclei can persist in cells over several generations but the chromosome in the micronucleus can also be distributed to daughter nuclei. Thus, chromosome segregation errors potentially lead to mutations and chromosome rearrangements that can integrate into the genome. Pulverization of chromosomes in micronuclei may also be one explanation for 'chromothripsis' in cancer and developmental disorders, where isolated chromosomes or chromosome arms undergo massive local DNA breakage and rearrangement.     

Melanoma genome sequencing reveals frequent PREX2 mutations

Melanoma is notable for its metastatic propensity, lethality in the advanced setting and association with ultraviolet exposure early in life. To obtain a comprehensive genomic view of melanoma in humans, we sequenced the genomes of 25 metastatic melanomas and matched germline DNA. A wide range of point mutation rates was observed: lowest in melanomas whose primaries arose on non-ultraviolet-exposed hairless skin of the extremities (3 and 14 per megabase (Mb) of genome), intermediate in those originating from hair-bearing skin of the trunk (5-55 per Mb), and highest in a patient with a documented history of chronic sun exposure (111 per Mb). Analysis of whole-genome sequence data identified PREX2 (phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 2)--a PTEN-interacting protein and negative regulator of PTEN in breast cancer--as a significantly mutated gene with a mutation frequency of approximately 14% in an independent extension cohort of 107 human melanomas. PREX2 mutations are biologically relevant, as ectopic expression of mutant PREX2 accelerated tumour formation of immortalized human melanocytes in vivo. Thus, whole-genome sequencing of human melanoma tumours revealed genomic evidence of ultraviolet pathogenesis and discovered a new recurrently mutated gene in melanoma.     

GABA transporter lysine 448: a key residue for tricyclic antidepressants interaction

The effects of three tricyclic antidepressants (TCAs) and two serotonin selective reuptake inhibitors (SSRIs) have been studied with an electrophysiological approach on Xenopus laevis oocytes expressing the rat GABA (γ-Aminobutyric-acid) transporter rGAT1. All tested TCAs and SSRIs inhibit the GABA-associated current in a dose-dependent way with low but comparable efficacy. The pre-steady-state and uncoupled currents appear substantially unaffected. The efficacy of desipramine, but not of the other drugs, is strongly increased in the lysine-glutamate or -aspartate mutants K448E and K448D. Comparison of I _max and K _0.5GABA in the absence and presence of desipramine showed that both parameters are reduced by the drug in the wild-type and in the K448E mutant. This suggests an uncompetitive inhibition, in which the drug can bind only after the substrate, an explanation in agreement with the lack of effects on the pre-steady-state and leak currents, and with the known structural data.     

A potentiator induces conformational changes on the recombinant CFTR nucleotide binding domains in solution

Nucleotide binding domains (NBD1 and NBD2) of the cystic fibrosis transmembrane conductance regulator (CFTR), the defective protein in cystic fibrosis, are responsible for controlling the gating of the chloride channel and are the putative binding sites for several candidate drugs in the disease treatment. We studied the effects of the application of 2-pyrimidin-7,8-benzoflavone (PBF), a strong potentiator of the CFTR, on the properties of recombinant and equimolar NBD1/NBD2 mixture in solution. The results indicate that the potentiator induces significant conformational changes of the NBD1/NBD2 dimer in solution. The potentiator does not modify the ATP binding constant, but reduces the ATP hydrolysis activity of the NBD1/NBD2 mixture. The intrinsic fluorescence and the guanidinium denaturation measurements indicate that the potentiator induces different conformational changes on the NBD1/NBD2 mixture in the presence and absence of ATP. It was confirmed from small-angle X-ray scattering experiments that, in absence of ATP, the NBD1/NBD2 dimer was disrupted by the potentiator, but in the presence of 2?mM ATP, the two NBDs kept dimerised, and a major change in the size and the shape of the structure was observed. We propose that these conformational changes could modify the NBDs–intracellular loop interaction in a way that would facilitate the open state of the channel.     

Human impact on avian diversity in rural Mediterranean areas

Human activities influence the biodiversity of Mediterranean ecosystems and are involved in the transformation of natural habitats into farmland. We surveyed birds using the point count method on 288 plots at a 50-m radius in three altitudinal landscapes with different rural character in spring and autumn. The results showed that bird species richness in the study area was high (74 species). High total species richness was found in the upland rural landscape characterized by mixed land use and high landscape diversity. The applied richness of total, resident and Sylviidae species illustrated a definite preference for villages with a low human population during the breeding season. Positive and significant correlations were found between rural settlements and Fringillidae, Sylviidae and total bird richness at both periods in the three landscapes. Finally, a clear dependence on the land use/land cover type was shown for the five recorded priority species.