SNX25 regulates TGF-β signaling by enhancing the receptor degradation

SNXs (sorting nexin), a family of proteins playing roles in cargo sorting and signaling from compartments within the endocytic network, regulate traffic of membrane proteins including TGF-β receptors. Here we report that the full length human and mouse SNX25, a SNX member with PX, PXA and RGS domains, co-localizes with TGF-β receptors, and forms internalized cytosolic punctae upon treatment with TGF-β. While overexpression of SNX25 inhibits TGF-β induced luciferase reporter activity, knocking down endogenous SNX25 by siRNA in NIH3T3 cells elevates the TGF-β receptor levels and facilitates TGF-β signaling. Immunoprecipitation experiments demonstrate that SNX25 interacts with TβRI. Western blot analyses indicate that SNX25 enhances the degradation of TGF-β receptors. SNX25 induced TGF-β receptor degradation is shown via the clathrin dependent endocytosis pathway into lysosome. We have characterized that PXA domain of SNX25 is required for the degradation of TβRI. Our findings demonstrate that SNX25 negatively regulates TGF-β signaling by enhancing the receptor degradation through lysosome pathway.     

Evaluation of the environmental specificity of Fluorescence In Situ Hybridization (FISH) using Fluorescence-Activated Cell Sorting (FACS) of probe (PSE1284)-positive cells extracted from rhizosphere soil

We explicitly tested for the first time the ‘environmental specificity’ of traditional 16S rRNA-targeted Fluorescence In Situ Hybridization (FISH) through comparison of the bacterial diversity actually targeted in the environment with the diversity that should be exactly targeted (i.e. without mismatches) according to in silico analysis. To do this, we exploited advances in modern Flow Cytometry that enabled improved detection and therefore sorting of sub-micron-sized particles and used probe PSE1284 (designed to target Pseudomonads) applied to Lolium perenne rhizosphere soil as our test system. The 6-carboxyfluorescein (6-FAM)-PSE1284-hybridized population, defined as displaying enhanced green fluorescence in Flow Cytometry, represented 3.51 ± 1.28% of the total detected population when corrected using a nonsense (NON-EUB338) probe control. Analysis of 16S rRNA gene libraries constructed from Fluorescence Activated Cell Sorted-recovered fluorescent populations (n = 3), revealed that 98.5% (Pseudomonas spp. comprised 68.7% and Burkholderia spp. 29.8%) of the total sorted population was specifically targeted as evidenced by the homology of the 16S rRNA sequences to the probe sequence. In silico evaluation of probe PSE1284 with the use of RDP-10 probeMatch justified the existence of Burkholderia spp. among the sorted cells. The lack of novelty in Pseudomonas spp. sequences uncovered was notable, probably reflecting the well-studied nature of this functionally important genus. To judge the diversity recorded within the FACS-sorted population, rarefaction and DGGE analysis were used to evaluate, respectively, the proportion of Pseudomonas diversity uncovered by the sequencing effort and the representativeness of the Nycodenz^® method for the extraction of bacterial cells from soil.     

UBE4B Protein Couples Ubiquitination and Sorting Machineries to Enable Epidermal Growth Factor Receptor (EGFR) Degradation

The signaling of plasma membrane proteins is tuned by internalization and sorting in the endocytic pathway prior to recycling or degradation in lysosomes. Ubiquitin modification allows recognition and association of cargo with endosomally associated protein complexes, enabling sorting of proteins to be degraded from those to be recycled. The mechanism that provides coordination between the cellular machineries that mediate ubiquitination and endosomal sorting is unknown. We report that the ubiquitin ligase UBE4B is recruited to endosomes in response to epidermal growth factor receptor (EGFR) activation by binding to Hrs, a key component of endosomal sorting complex required for transport (ESCRT) 0. We identify the EGFR as a substrate for UBE4B, establish UBE4B as a regulator of EGFR degradation, and describe a mechanism by which UBE4B regulates endosomal sorting, affecting cellular levels of the EGFR and its downstream signaling. We propose a model in which the coordinated action of UBE4B, ESCRT-0, and the deubiquitinating enzyme USP8 enable the endosomal sorting and lysosomal degradation of the EGFR.     

Crystal and Molecular Structure of the Sodium Salt of the Dinucleotide Duplex d(CpG)

Abstract

The crystal and molecular structure of the sodium salt of deoxycytidylyl-{3′ ?5′)-deoxyguanosine has been determined from X-ray diffraction data. The crystals, obtained from an aqueous y- butyrolactone solution at pH = 5.3, are orthorhombic, P2₁2₁2₁, a= 10.640(2), b= 11.184(2) and c=44.618(4) A. The structure was refined to an R = 0.041. The d(CpG) structure is similar to the ammonium salt solved by Cruse et al.(1). Both structures form a parallel self base paired mini-double helix. In d(CpG).Na⁺, one of the two paired cytosines is protonated on N(3). The cytosines form 3 hydrogen bonds while the guanines form only 2. The Na⁺ ion is coordinated with five groups: two water molecules, 0(6) of guanine A, N(7) of guanine B and 0(5′) of cytosine B, forming a square pyramid. The hydration shell around the mini-helix is analysed and compared with that of the ammonium salt. d(CpG).Na⁺ is the second d(CpG) oligonucleotide found with a self base pairing arrangement despite of the fact that the crystallization conditions and counterion were different in both cases. The hypothesis that self base pairing is not only a crystallization artifact but may play a role under physiological conditions as a source of transversion mutations is discussed.     

基于乒乓算法的复杂疾病标志物识别

目的:生物标志物是标识系统、器官、组织等改变或可能发生改变的生化指标,具有非常广泛的临床应用。本文希望从高通量数据出发,提出一种新的研究复杂疾病标志物的方法。方法:以"组学"数据为研究对象,利用乒乓算法构建lnc RNA-mRNA交互网络,通过随机游走算法计算选出复杂疾病的生物标志物,并将其与t检验结果比较。结果:将本文方法运用于食管癌标志物的识别,得出与食管癌发生和发展过程相关的14个lnc RNA(CCAT1、MEG3、Snhg1、MALAT1、HOTAIR、UCA1、PVT1、CASC9、LOC100130476、TUG1、BC200、POU6F2-AS2、TP73-AS1和ZEB1-AS1)和12个mRNA(SPARC、CMTM7、Sph K1、NANOG、LOXL2、HMGCS2、FZD7、PTOV1、CADM1、CTHRC1、MGMT和RECK)。对比显示,识别出t检验未识别出的4个lnc RNA(BC200、POU6F2-AS2、TP73-AS1和ZEB1-AS1)和3个mRNA(CADM1、Sph K1和RECK)。结论:该方法能够更有效的预测复杂疾病相关的标志物。     

Mixed-beam approach for high-risk prostate cancer: Carbon-ion boost followed by photon intensity-modulated radiotherapy. Dosimetric and geometric evaluations (AIRC IG-14300)

Background and purposeThe aim was to evaluate dosimetric uncertainties of a mixed beam approach for patients with high-risk prostate cancer (PCa). The treatment consists of a carbon ion radiotherapy (CIRT) boost followed by whole-pelvis intensity-modulated RT (IMRT).Materials and methodsPatients were treated with a CIRT boost of 16.6 Gy/4 fractions followed by whole-pelvis IMRT of 50 Gy/25 fractions, with consequent long term androgen deprivation therapy. Deformable computed tomography image registration (DIR) was performed and corresponding doses were used for plan sum. A comparative IMRT photon plan was obtained as whole-pelvis IMRT of 50 Gy/25 fractions followed by a boost of 28 Gy/14 fractions. DIR performances were evaluated through structure-related and image characteristics parameters.ResultsUntil now, five patients out of ten total enrolled ended the treatment. Dosimetric parameters were lower in CIRT + IMRT than IMRT-only plans for all organs at risk (OARs) except femoral heads.Regarding DIR evaluation, femoral heads were the less deformed OAR. Penile bulb, bladder and anal canal showed intermediate deformation. Rectum was the most deformed. DIR algorithms were patient (P)-dependent, as performances were the highest for P3 and P4, intermediate for P2 and P5, and the lowest for P1.ConclusionsCIRT allows better OARs sparing while increasing the efficacy due to the higher radio-biological effect of carbon ions. However, a mixed beam approach could introduce DIR problems in multi-centric treatments with different operative protocols. The development of this prospective trial will lead to more mature data concerning the clinical impact of implementing DIR procedures in dose accumulation applications for high-risk PCa treatments.     

Use of the β‐function to estimate the skewness of species responses

Abstract. Response of a species to an environmental variable may be modeled and predicted using a wide spectrum of different functions. Contrary to other functions (Gaussian, polynomial etc), all parameters of the β‐function are interpretable in ecological terms. However, computational difficulties in the determination of the β‐function parameters initiated controversial debates on the applicability and usefulness of this function in vegetation modelling and gradient analysis. We propose a simple algorithm for fitting the β‐function to observed data. Analytic properties of the algorithm (its ability to recover the known species responses along gradients) are tested using a series of simulated data. In most cases the algorithm correctly estimated parameters of the simulated responses.     

A simple method to improve probe set estimates from oligonucleotide arrays

A popular commercially available oligonucleotide microarray technology employs sets of 25 base pair oligonucleotide probes for measurement of gene expression levels. A mathematical algorithm is required to compute an estimate of gene expression from the multiple probes. Previously proposed methods for summarizing gene expression data have either been substantially ad hoc or have relied on model assumptions that may be easily violated. Here we present a new algorithm for calculating gene expression from probe sets. Our approach is functionally related to leave-one-out cross-validation, a non-parametric statistical technique that is often applied in limited data situations. We illustrate this approach using data from our study seeking a molecular fingerprint of STAT3 regulated genes for early detection of human cancer.     

The community structure of human cellular signaling network

Living cell is highly responsive to specific chemicals in its environment, such as hormones and molecules in food or aromas. The reason is ascribed to the existence of widespread and diverse signal transduction pathways, between which crosstalks usually exist, thus constitute a complex signaling network. Evidently, knowledge of topology characteristic of this network could contribute a lot to the understanding of diverse cellular behaviors and life phenomena thus come into being. In this presentation, signal transduction data is extracted from KEGG to construct a cellular signaling network of Homo sapiens, which has 931 nodes and 6798 links in total. Computing the degree distribution, we find it is not a random network, but a scale-free network following a power-law of P(K) approximately K(-gamma), with gamma approximately equal to 2.2. Among three graph partition algorithms, the Guimera's simulated annealing method is chosen to study the details of topology structure and other properties of this cellular signaling network, as it shows the best performance. To reveal the underlying biological implications, further investigation is conducted on ad hoc community and sketch map of individual community is drawn accordingly. The involved experiment data can be found in the supplementary material.