BACKGROUND & AIMS: :Iminodisuccinate (IDS) epimerase catalyzes the epimerisation of R,R-, S,S- and R,S- iminodisuccinate, one step in the biodegradation of the chelating agent iminodisuccinate by Agrobacterium tumefaciens BY6. The enzyme is a member of the MmgE/PrpD protein family, a diverse and little characterized class of proteins of prokaryotic and eukaryotic origin. IDS epimerase does not show significant overall amino acid sequence similarity to any other protein of known three-dimensional structure. The crystal structure of this novel epimerase has been determined by multi-wavelength diffraction to 1.5 A resolution using selenomethionine-substituted enzyme. In the crystal, the enzyme forms a homo-dimer, and the subunit consists of two domains. The larger domain, not consecutive in sequence and comprising residues Met1-Lys266 and Leu400-Pro446, forms a novel all alpha-helical fold with a central six-helical bundle. The second, smaller domain folds into an alpha+beta domain, related in topology to chorismate mutase by a circular permutation. IDS epimerase is thus not related in three-dimensional structure to other known epimerases. The fold of the IDS epimerase is representative for the whole MmgE/PrpD family. The putative active site is located at the interface between the two domains of the subunit, and is characterized by a positively charged surface, consistent with the binding of a highly negatively charged substrate such as iminodisuccinate. Docking experiments suggest a two-base mechanism for the epimerisation reaction.

背景与目标： ：亚氨基二琥珀酸酯（IDS）差向异构酶催化R，R-，S，S-和R，S-亚氨基二琥珀酸酯的差向异构化，这是根癌农杆菌BY6对螯合剂亚氨基二琥珀酸酯的生物降解的一个步骤。该酶是MmgE / PrpD蛋白质家族的成员，MmgE / PrpD蛋白质家族是原核和真核来源的多种多样且鲜为人知的蛋白质。 IDS差向异构酶与已知三维结构的任何其他蛋白质均未显示出明显的总体氨基酸序列相似性。该新型差向异构酶的晶体结构已通过硒代蛋氨酸取代的酶通过多波长衍射确定为1.5 A的分辨率。在晶体中，酶形成同型二聚体，该亚基由两个结构域组成。较大的结构域，顺序不连续，包含残基Met1-Lys266和Leu400-Pro446，形成带有中心六螺旋束的新型全α螺旋折叠。第二个较小的域折叠成一个alpha beta域，该域在拓扑结构上与通过循环排列分支变异酶有关。因此，IDS差向异构酶在三维结构上与其他已知的差向异构酶无关。 IDS差向异构酶的折叠代表整个MmgE / PrpD家族。推定的活性位点位于亚基的两个结构域之间的界面处，其特征是带正电的表面，与带负电的底物（如亚氨基二琥珀酸酯）的结合相一致。对接实验提出了差向异构反应的两碱基机制。

BACKGROUND & AIMS: BACKGROUND:This study was undertaken to obtain differentially expressed genes related to human glioma by cDNA microarray and the characterization of a novel full-length gene. METHODS:Total RNA was extracted form human glioma and normal brain tissue, and mRNA was used as a probe. The results of hybridization procedure were scanned with the computer system. The gene named 507E08 cone was subsequently analyzed by northern blot, bioinformatic approach, and protein expression. RESULTS:Fifteen differentially expressed genes were obtained from human glioma by hybridization and scanning for four times. Northern blot analysis confirmed that the 507E08 clone was low expressed in human brain tissue and over expressed in human glioma tissues. The analysis of BLASTn and BLASTx showed that the 507E08 clone was a novel full-length gene, which codes 203 amino acid of protein and is called human ribosomal protein 14.22 gene. The nucleotide sequence had been submitted to the GenBank with the accession number of AF329277. After expression in E. coli., protein yielded a major band of apparent molecular mass 22 kDa on an SDS-PAGE gel. CONCLUSIONS:cDNA microarray technology can be successfully used to identify differentially expressed genes. The novel full-length gene of human ribosomal protein 13.22 may be correlated with the development of human glioma.

背景与目标： 背景：本研究旨在通过cDNA微阵列技术获得与人神经胶质瘤相关的差异表达基因，并鉴定一个新的全长基因。
方法：从人脑胶质瘤和正常脑组织中提取总RNA，并以mRNA为探针。杂交程序的结果用计算机系统扫描。随后通过Northern印迹，生物信息学方法和蛋白质表达来分析名为507E08视锥细胞的基因。
结果：通过杂交和扫描4次，从人脑胶质瘤中获得了15个差异表达基因。 Northern印迹分析证实507E08克隆在人脑组织中低表达而在人脑胶质瘤组织中高表达。对BLASTn和BLASTx的分析表明，507E08克隆是一个新颖的全长基因，其编码蛋白质的203个氨基酸，被称为人核糖体蛋白质14.22基因。该核苷酸序列已提交给GenBank，登录号为AF329277。在大肠杆菌中表达后，蛋白质在SDS-PAGE凝胶上产生一条表观分子量为22 kDa的主带。
结论：cDNA微阵列技术可成功用于鉴定差异表达的基因。人核糖体蛋白13.22的新的全长基因可能与人脑胶质瘤的发展有关。

BACKGROUND & AIMS: We studied changes in glutamate receptors, expression of immediate early genes, and AP-1 DNA binding activity in the brains of phenobarbital (PB)-dependent and -withdrawn rats to investigate the possible involvement of activation of glutamate receptors in PB withdrawal syndrome. PB-dependent rats were prepared by feeding drug-admixed food for 5 weeks. Autoradiographic analysis showed that binding of [3H(+)-5-methyl-10,11-dihydro-5H-dibenzo[a,d]cyclohepten-5,10-imin e (MK-801), an antagonist of N-methyl-D-aspartic acid (NMDA) receptors, increased significantly in the cerebral cortices of PB-dependent and 24-h-withdrawn rats. However, [3H]MK-801 binding in the hippocampus and [3H]6-cyano-7-nitroquinoxaline-2,3-dione (CNQX) and [3H]kainic acid binding in the hippocampus and cerebral cortex were essentially unchanged in both groups. PB withdrawal seizures were followed by increased expression of c-fos mRNA in the hippocampus and cerebral cortex and of c-jun mRNA in the cerebral cortex. The induction of c-fos and c-jun mRNA was suppressed by administration of MK-801. Furthermore, PB withdrawal enhanced AP-1 DNA binding activity in the brain. The present findings suggest functional enhancement of glutamatergic neurotransmission during the development of PB withdrawal syndrome.

背景与目标： 我们研究了苯巴比妥（PB）依赖和戒断大鼠大脑中谷氨酸受体的变化，立即早期基因的表达以及AP-1 DNA结合活性，以研究谷氨酸受体激活在PB戒断综合征中的可能。通过喂食药物混合的食物5周来制备PB依赖的大鼠。放射自显影分析表明，[3H（）-5-甲基-10,11-二氢-5H-二苯并[a，d]环庚烯-5,10-亚胺e（MK-801）与N-甲基- D-天冬氨酸（NMDA）受体，在PB依赖和24小时戒断大鼠的大脑皮层中显着增加。然而，在海马中的[3H] MK-801结合以及在海马和大脑皮层中的[3H] 6-氰基-7-硝基喹喔啉-2,3-二酮（CNQX）和[3H]海藻酸结合基本上没有变化。组。 PB抽搐发作后，海马和大脑皮层中c-fos mRNA的表达增加，大脑皮层中c-jun mRNA的表达增加。通过施用MK-801抑制了c-fos和c-jun mRNA的诱导。此外，PB撤离可增强大脑中AP-1 DNA的结合活性。目前的发现表明，在PB戒断综合征的发展过程中，谷氨酸能神经传递的功能增强。

BACKGROUND & AIMS: :The extracellular calcium-sensing receptor (CaR) is usually associated with systemic Ca(2+) homeostasis, but the CaR is also expressed in many other tissues, including pancreatic islets of Langerhans. In the present study, we have used human islets and an insulin-secreting cell line (MIN6) to investigate the effects of CaR activation using the calcimimetic R-568, a CaR agonist that activates the CaR at physiological concentrations of extracellular Ca(2+). CaR activation initiated a marked but transient insulin secretory response from both human islets and MIN6 cells at a sub-stimulatory concentration of glucose, and further enhanced glucose-induced insulin secretion. CaR-induced insulin secretion was reduced by inhibitors of phospholipase C or calcium-calmodulin-dependent kinases, but not by a protein kinase C inhibitor. CaR activation was also associated with an activation of p42/44 mitogen-activated protein kinases (MAPK), and CaR-induced insulin secretion was reduced by an inhibitor of p42/44 MAPK activation. We suggest that the beta-cell CaR is activated by divalent cations co-released with insulin, and that this may be an important mechanism of intra-islet communication between beta-cells.

背景与目标： ：细胞外钙敏感受体（CaR）通常与全身性Ca（2）稳态相关，但该CaR在许多其他组织中也表达，包括Langerhans的胰岛。在本研究中，我们已经使用人类胰岛和胰岛素分泌细胞系（MIN6）来研究使用拟钙剂R-568（CaR激动剂在生理浓度的细胞外Ca（2）激活CaR的CaR激活）的作用。 。 CaR激活在葡萄糖的亚刺激浓度下启动了来自人胰岛和MIN6细胞的显着但短暂的胰岛素分泌反应，并进一步增强了葡萄糖诱导的胰岛素分泌。 CaR诱导的胰岛素分泌通过磷脂酶C或钙钙调蛋白依赖性激酶的抑制剂降低，但不通过蛋白激酶C抑制剂降低。 CaR激活还与p42 / 44丝裂原激活的蛋白激酶（MAPK）激活相关，并且CaR诱导的胰岛素分泌被p42 / 44 MAPK激活的抑制剂减少。我们建议β细胞CaR被与胰岛素共释放的二价阳离子激活，这可能是β细胞之间胰岛内通讯的重要机制。

BACKGROUND & AIMS: :Biological mineralization of tissues in living organisms relies on proteins that preferentially nucleate minerals and control their growth. This process is often referred to as "templating," but this term has become generic, denoting various proposed mineral-organic interactions including both chemical and structural affinities. Here, we present an approach using self-assembled networks of elastin and fibronectin fibers, similar to the extracellular matrix. When induced onto negatively charged sulfonated polystyrene surfaces, these proteins form fiber networks of approximately 10-mum spacing, leaving open regions of disorganized protein between them. We introduce an atomic force microscopy-based technique to measure the elastic modulus of both structured and disorganized protein before and during calcium carbonate mineralization. Mineral-induced thickening and stiffening of the protein fibers during early stages of mineralization is clearly demonstrated, well before discrete mineral crystals are large enough to image by atomic force microscopy. Calcium carbonate stiffens the protein fibers selectively without affecting the regions between them, emphasizing interactions between the mineral and the organized protein fibers. Late-stage observations by optical microscopy and secondary ion mass spectroscopy reveal that Ca is concentrated along the protein fibers and that crystals form preferentially on the fiber crossings. We demonstrate that organized versus unstructured proteins can be assembled mere nanometers apart and probed in identical environments, where mineralization is proved to require the structural organization imposed by fibrillogenesis of the extracellular matrix.

背景与目标： ：生物体内组织的生物矿化依赖蛋白质优先使矿物质成核并控制其生长。该过程通常被称为“模板化”，但该术语已变得通用，表示各种提议的矿物-有机相互作用，包括化学亲和力和结构亲和力。在这里，我们提出一种使用弹性蛋白和纤连蛋白纤维自组装网络的方法，类似于细胞外基质。当被诱导到带负电荷的磺化聚苯乙烯表面上时，这些蛋白质形成大约10微米间距的纤维网络，在它们之间留下了杂乱的蛋白质的开放区域。我们引入基于原子力显微镜的技术来测量碳酸钙矿化之前和期间结构化和无组织蛋白的弹性模量。在矿化的早期阶段，很明显地证明了矿物质诱导的蛋白质纤维的增厚和变硬，早在离散的矿物晶体足够大以至于无法通过原子力显微镜成像时。碳酸钙选择性地使蛋白质纤维变硬而不影响它们之间的区域，强调了矿物质和有组织的蛋白质纤维之间的相互作用。通过光学显微镜和二次离子质谱的后期观察显示，Ca沿着蛋白质纤维集中，并且晶体优先在纤维交叉处形成。我们证明有组织的与非结构化的蛋白质可以仅相隔纳米而组装在一起，并在相同的环境中进行探测，在该环境中，矿化被证明需要细胞外基质的原纤维形成所强加的结构组织。

BACKGROUND & AIMS: Tyrosine phosphorylation of the nicotinic acetylcholine receptor (AChR) is associated with an altered rate of receptor desensitization and also may play a role in agrin-induced receptor clustering. We have demonstrated a previously unsuspected interaction between Torpedo AChR and the adaptor protein Grb2. The binding is mediated by the Src homology 2 (SH2) domain of Grb2 and the tyrosine-phosphorylated delta subunit of the AChR. Dephosphorylation of the delta subunit abolishes Grb2 binding. A cytoplasmic domain of the delta subunit contains a binding motif (pYXNX) for the SH2 domain of Grb2. Indeed, a phosphopeptide corresponding to this region of the delta subunit binds to Grb2 SH2 fusion proteins with relatively high affinity, whereas a peptide lacking phosphorylation on tyrosine exhibits no binding. Grb2 is colocalized with the AChR on the innervated face of Torpedo electrocytes. Furthermore, Grb2 specifically copurifies with AChR solubilized from postsynaptic membranes. These data suggest a novel role for tyrosine phosphorylation of the AChR in the initiation of a Grb2-mediated signaling cascade at the postsynaptic membrane.

背景与目标： 烟碱样乙酰胆碱受体（AChR）的酪氨酸磷酸化与受体脱敏率的改变有关，也可能在凝集素诱导的受体簇中起作用。我们已经证明了鱼雷AChR和衔接蛋白Grb2之间以前没有想到的相互作用。结合是由Grb2的Src同源2（SH2）域和AChR的酪氨酸磷酸化的δ亚基介导的。 δ亚基的去磷酸化消除了Grb2结合。 δ亚基的胞质结构域包含Grb2的SH2结构域的结合基序（pYXNX）。实际上，对应于δ亚基的该区域的磷酸肽以相对高的亲和力与Grb2 SH2融合蛋白结合，而在酪氨酸上缺乏磷酸化的肽没有结合。 Grb2与AChR在鱼雷电池的神经支配面上共定位。此外，Grb2与从突触后膜溶解的AChR特异性共纯化。这些数据表明，AChR的酪氨酸磷酸化在突触后膜的Grb2介导的信号级联反应的起始中起着新的作用。

BACKGROUND & AIMS: The GATA family of vertebrate DNA binding regulatory proteins are expressed in diverse tissues and at different times of development. However, the DNA binding regions of these proteins possess considerable homology and recognize a rather similar range of DNA sequence motifs. DNA binding is mediated through two domains, each containing a zinc finger. Previous results have led to the conclusion that although in some cases the N-terminal finger can contribute to specificity and strength of binding, it does not bind independently, whereas the C-terminal finger is both necessary and sufficient for binding. Here we show that although this is true for the N-terminal finger of GATA-1, those of GATA-2 and GATA-3 are capable of strong independent binding with a preference for the motif GATC. Binding requires the presence of two basic regions located on either side of the N-terminal finger. The absence of one of these near the GATA-1 N-terminal finger probably accounts for its inability to bind. The combination of a single finger and two basic regions is a new variant of a motif that has been previously found in the binding domains of other finger proteins. Our results suggest that the DNA binding properties of the N-terminal finger may help distinguish GATA-2 and GATA-3 from GATA-1 and the other GATA family members in their selective regulatory roles in vivo.

背景与目标： GATA家族的脊椎动物DNA结合调节蛋白在不同的组织中以及在不同的发育时期表达。但是，这些蛋白质的DNA结合区具有相当的同源性，可以识别相当相似范围的DNA序列基序。 DNA结合是通过两个结构域介导的，每个结构域都包含一个锌指。先前的结果得出的结论是，尽管在某些情况下N末端指可以有助于结合的特异性和强度，但它不能独立地结合，而C末端指对于结合既是必需的又是足够的。在这里，我们表明，尽管对于GATA-1的N端手指来说确实如此，但GATA-2和GATA-3的手指却能够强烈独立地结合，并优先选择基序GATC。绑定需要在N末端指状体的两侧都存在两个基本区域。在GATA-1 N端手指附近缺少这些手指之一可能是其无法结合的原因。单个手指和两个基本区域的组合是一个基序的新变体，该变体先前已在其他手指蛋白的结合域中发现。我们的结果表明，N末端手指的DNA结合特性可能有助于区分GATA-2和GATA-3与GATA-1和其他GATA家族成员在体内的选择性调节作用。

BACKGROUND & AIMS: :Detergent-solubilized plasma membrane protein of either adult bovine or calf lens and high-performance liquid chromatography-purified major intrinsic protein (MIP) of the lens were reconstituted into unilamellar vesicles and planar lipid bilayers. Freeze-fracture studies showed that the density of intramembrane particles in the vesicles was proportional to the protein/lipid ratio. At high ratios, these particles crystallized into tetragonal arrays as does MIP in lens fibers. Channels induced by either purified MIP or detergent-solubilized protein had essentially identical properties. The conductance of multichannel membranes was maximal near 0 mV and decreased to 0.49 +/- 0.08 of the maximum value at voltages greater than 80 mV. The dependence of the conductance on voltage was well fit by a two-state Boltzmann distribution. Voltage steps greater than 30 mV elicited an ohmic current step followed by a slow (seconds) biexponential decrease. The amplitudes and time constants depended on the magnitude but not the sign of the voltage. Steps from 100 mV to voltages less than 30 mV caused the channels to open exponentially with a millisecond time constant. Analysis of latency to first closure after a voltage step gave nearly the same time constants as multichannel kinetics. Single-channel conductance is proportional to salt concentration from 0.1 to 1.0 M in KCl. In 0.1M KCl, the channel had two preferred conductance states with amplitudes of 380 and 160 pS, as well as three additional substates. Multi- and single-channel data suggest that the channel has two kinetically important open states. The channel is slightly anion selective. The properties of the channel do not vary appreciably from pH 7.4 to 5.8 or from pCa 7 to 2. We propose that a channel with these properties could contribute to maintenance of lens transparency and fluid balance.

背景与目标： ：成年牛或小牛晶状体的去污剂溶解质膜蛋白和高效液相色谱纯化的晶状体主要内在蛋白（MIP）被重构为单层囊泡和平面脂质双层。冷冻断裂研究表明，囊泡中膜内颗粒的密度与蛋白质/脂质比成正比。在高比例下，这些颗粒与透镜纤维中的MIP一样结晶为四边形阵列。纯化的MIP或去污剂溶解的蛋白诱导的通道具有基本相同的特性。多通道膜的电导在0 mV附近最大，并且在大于80 mV的电压下降低到最大值的0.49 /-0.08。电导对电压的依赖性通过两态玻耳兹曼分布很好地拟合。大于30 mV的电压阶跃引起欧姆电流阶跃，然后缓慢（秒）双指数下降。幅度和时间常数取决于幅度，而不取决于电压的符号。从100 mV到低于30 mV的电压阶跃导致通道以毫秒的时间常数呈指数方式打开。电压阶跃后首次闭合的等待时间的分析给出了与多通道动力学几乎相同的时间常数。单通道电导与KCl中0.1至1.0 M的盐浓度成正比。在0.1M KCl中，通道具有两个优选的电导状态，其振幅分别为380和160 pS，以及三个其他子状态。多通道和单通道数据表明该通道具有两个动力学上重要的开放状态。该通道对阴离子具有轻微的选择性。通道的特性在pH 7.4至5.8或pCa 7至2范围内变化不大。我们建议具有这些特性的通道可有助于维持镜片的透明度和流体平衡。

BACKGROUND & AIMS: :The signaling pathways mediating lysophosphatidic acid (LPA)-stimulated PKD(2) activation and the potential contribution of PKD(2) in regulating LPA-induced interleukin 8 (IL-8) secretion in nontransformed, human colonic epithelial NCM460 cells were examined. Treatment of serum-deprived NCM460 cells with LPA led to a rapid and striking activation of PKD(2), as measured by in vitro kinase assay and phosphorylation at the activation loop (Ser706/710) and autophosphorylation site (Ser876). PKD(2) activation induced by LPA was abrogated by preincubation with selective PKC inhibitors GF-I and Ro-31-8220 in a dose-dependent manner. These inhibitors did not have any direct inhibitory effect on PKD(2) activity. LPA induced a striking increase in IL-8 production and stimulated NF-kappaB activation, as measured by NF-kappaB-DNA binding, NF-kappaB-driven luciferase reporter activity, and IkappaBalpha phosphorylation. PKD(2) gene silencing utilizing small interfering RNAs targeting distinct PKD(2) sequences dramatically reduced LPA-stimulated NF-kappaB promoter activity and IL-8 production. PKD(2) activation is a novel early event in the biological action of LPA and mediates LPA-stimulated IL-8 secretion in NCM460 cells through a NF-kappaB-dependent pathway. Our results demonstrate, for the first time, the involvement of a member of the PKD family in the production of IL-8, a potent proinflammatory chemokine, by epithelial cells.

背景与目标： ：审查了介导溶血磷脂酸（LPA）刺激的PKD（2）活化和PKD（2）在调节LPA诱导的非转化型人结肠上皮NCM460细胞中LPA诱导的白介素8（IL-8）分泌中的潜在作用。用体外LPA处理血清缺乏的NCM460细胞会导致PKD（2）迅速而惊人的激活，这是通过体外激酶测定和激活环（Ser706 / 710）和自磷酸化位点（Ser876）的磷酸化测量的。通过与选择性PKC抑制剂GF-1和Ro-31-8220呈剂量依赖性方式进行预孵育，可以消除LPA诱导的PKD（2）激活。这些抑制剂对PKD（2）活性没有任何直接的抑制作用。如通过NF-κB-DNA结合，NF-κB驱动的萤光素酶报道分子活性和IkappaBalpha磷酸化所测量，LPA诱导IL-8产量显着增加并刺激NF-κB活化。 PKD（2）基因沉默利用针对不同的PKD（2）序列的小干扰RNA，大大降低了LPA刺激的NF-κB启动子活性和IL-8的产生。 PKD（2）激活是LPA的生物学作用中的一个新的早期事件，并通过NF-κB依赖性途径介导LCM刺激NCM460细胞中IL-8的分泌。我们的结果首次证明，上皮细胞参与了PKD家族成员参与IL-8（一种有效的促炎趋化因子）的生产。

BACKGROUND & AIMS: :Human class II MHC Ag are a family of cell surface glycoproteins. Their constitutive expression is limited to B lymphocytes and thymic epithelial cells. In many other cells their expression can be induced by IFN-gamma. Conserved upstream promoter sequences regulate this tissue-specific expression of class II genes. In the DRA promoter, one of these cis-acting regulatory motifs is the X2-box to which nuclear factor X2 (NF-X2) binds. Here, we present the isolation and characterization of the full-length cDNA clone encoding NF-X2. This cDNA clone was isolated by expression cDNA cloning, and encodes the human c-Jun protein, which together with c-Fos forms the heterodimeric activator protein-1 transcription complex. Whereas c-Fos/c-Jun heterodimers do not exist in B cells, they form and bind to the X2-box in class II nonexpressing cells. Thus, c-Fos/c-Jun heterodimers might contribute to the repression of DRA gene expression.

背景与目标： ：人类II类MHC Ag是细胞表面糖蛋白家族。它们的组成型表达仅限于B淋巴细胞和胸腺上皮细胞。在许多其他细胞中，它们的表达可以被IFN-γ诱导。保守的上游启动子序列调节II类基因的这种组织特异性表达。在DRA启动子中，这些顺式作用调控基元之一是X2-box，其与核因子X2（NF-X2）结合。在这里，我们介绍了编码NF-X2的全长cDNA克隆的分离和表征。该cDNA克隆通过表达cDNA克隆进行分离，并编码人c-Jun蛋白，该蛋白与c-Fos一起形成异二聚激活蛋白-1转录复合体。尽管B细胞中不存在c-Fos / c-Jun异二聚体，但它们在II类非表达细胞中形成并与X2-box结合。因此，c-Fos / c-Jun异二聚体可能有助于抑制DRA基因表达。

BACKGROUND & AIMS: BACKGROUND:Accurate and automatic gene identification in eukaryotic genomic DNA is more than ever of crucial importance to efficiently exploit the large volume of assembled genome sequences available to the community. Automatic methods have always been considered less reliable than human expertise. This is illustrated in the EGASP project, where reference annotations against which all automatic methods are measured are generated by human annotators and experimentally verified. We hypothesized that replicating the accuracy of human annotators in an automatic method could be achieved by formalizing the rules and decisions that they use, in a mathematical formalism. RESULTS:We have developed Exogean, a flexible framework based on directed acyclic colored multigraphs (DACMs) that can represent biological objects (for example, mRNA, ESTs, protein alignments, exons) and relationships between them. Graphs are analyzed to process the information according to rules that replicate those used by human annotators. Simple individual starting objects given as input to Exogean are thus combined and synthesized into complex objects such as protein coding transcripts. CONCLUSION:We show here, in the context of the EGASP project, that Exogean is currently the method that best reproduces protein coding gene annotations from human experts, in terms of identifying at least one exact coding sequence per gene. We discuss current limitations of the method and several avenues for improvement.

背景与目标： 背景：在真核生物基因组DNA中进行准确，自动的基因鉴定比以往任何时候都更重要，它对于有效利用社区可利用的大量组装基因组序列至关重要。一直以来，人们一直认为自动方法不如人类专业技术可靠。这在EGASP项目中得到了说明，其中由人工注释者生成了针对其测量所有自动方法的参考注释，并对其进行了实验验证。我们假设可以通过以数学形式主义形式化规则和决策来实现以自动方式复制人类注释器的准确性。
结果：我们开发了Exogean，这是一个基于有向无环彩色多图（DACM）的灵活框架，可以表示生物对象（例如，mRNA，EST，蛋白质比对，外显子）及其之间的关系。根据复制人类注释者使用的规则的规则，对图形进行分析以处理信息。因此，作为输入到Exogean的简单单个起始对象将被合并并合成为复杂的对象，例如蛋白质编码转录本。
结论：在EGASP项目的背景下，我们证明了Exogean目前是从人类专家中复制蛋白质编码基因注释的最佳方法，因为每个基因至少可以识别一个确切的编码序列。我们讨论了该方法的当前局限性和改进的几种途径。

BACKGROUND & AIMS: :Related outer membrane proteins, termed secretins, participate in the secretion of macromolecules across the outer membrane of many Gram-negative bacteria. In the pullulanase-secretion system, PulS, an outer membrane-associated lipoprotein, is required both for the integrity and the proper outer membrane localization of the PulD secretin. Here we show that the PulS-binding site is located within the C-terminal 65 residues of PulD. Addition of this domain to the filamentous phage secretin, pIV, or to the unrelated maltose-binding protein rendered both proteins dependent on PulS for stability. A chimeric protein composed of bacteriophage f1 pIV and the C-terminal domain of PuID required properly localized PulS to support phage assembly. An in vivo complex formed between the pIV-PulD65 chimera and PulS was detected by co-immunoprecipitation and by affinity chromatography.

背景与目标： ：相关的外膜蛋白，称为促胰液素，参与许多革兰氏阴性细菌的外膜大分子的分泌。在支链淀粉酶分泌系统中，PulS是一种与外膜相关的脂蛋白，是PulD促胰液素的完整性和正确的外膜定位所必需的。在这里，我们显示PulS结合位点位于PulD的C末端65个残基内。此结构域添加到丝状噬菌体分泌蛋白，pIV或无关的麦芽糖结合蛋白上，使得这两种蛋白都依赖于PulS来保持稳定性。由噬菌体f1 pIV和PuID的C末端结构域组成的嵌合蛋白需要正确定位PulS以支持噬菌体装配。通过共免疫沉淀法和亲和色谱法检测到了pIV-PulD65嵌合体和PulS之间形成的体内复合物。

BACKGROUND & AIMS: :Heat shock protein 90 (HSP90) is required for structural folding and maintenance of conformational integrity of various proteins, including several associated with cellular signaling. Recent studies utilizing 17-allylamino-17-demethoxygeldanamycin (17-AAG), an inhibitor of HSP90, demonstrated an antitumor effect in solid tumors. To test whether HSP90 could be targeted in multiple myeloma (MM) patients, we first investigated expression of HSP90 by immunofluorescence and flow cytometric analysis in a myeloma cell line (U266) and primary myeloma cells. Following demonstration of HSP90 expression in myeloma cells, archival samples of 32 MM patients were analysed by immunoperoxidase staining. Myeloma cells in all patients showed strong cytoplasmic expression of HSP90 in all samples and 55% also demonstrated concurrent nuclear immunopositivity. Treatment of U266 and primary MM cells with 17AAG resulted in significantly increased apoptosis compared to untreated control cells. Analysis of anti-apoptotic BCL2 family proteins and akt in MM cells incubated with 17-AAG revealed down-regulation of BCL-2, BCL-XL, MCL-1 and akt. Furthermore, although a low concentration of bortezomib resulted in no cell death, a combination of 17AAG and bortezomib treatment revealed a synergistic apoptotic effect on the U266 cell line. These data suggest that targeted inhibition of HSP90 may prove to be a valid and innovative strategy for the development of future therapeutic options for MM patients.

背景与目标： ：热休克蛋白90（HSP90）是结构折叠和维持各种蛋白质（包括与细胞信号相关的几种蛋白质）构象完整性的必需。利用HSP90抑制剂17-烯丙基氨基-17-去甲氧基格尔德霉素（17-AAG）的最新研究表明，在实体瘤中具有抗肿瘤作用。为了测试HSP90是否可以靶向于多发性骨髓瘤（MM）患者，我们首先通过免疫荧光和流式细胞术分析了骨髓瘤细胞系（U266）和原发性骨髓瘤细胞中HSP90的表达。在证明HSP90在骨髓瘤细胞中表达后，通过免疫过氧化物酶染色分析了32例MM患者的档案样本。在所有患者中，骨髓瘤细胞在所有样品中均表现出强烈的HSP90细胞质表达，并且55％的患者还表现出并发的核免疫阳性。与未处理的对照细胞相比，用17AAG处理U266细胞和原代MM细胞可导致凋亡明显增加。分析与17-AAG孵育的MM细胞中的抗凋亡BCL2家族蛋白和akt，表明BCL-2，BCL-XL，MCL-1和akt下调。此外，尽管低浓度的硼替佐米不会导致细胞死亡，但是17AAG和硼替佐米治疗的组合显示出对U266细胞系的协同凋亡作用。这些数据表明，针对HSP90的靶向抑制可能被证明是开发MM患者未来治疗选择的有效且创新的策略。

BACKGROUND & AIMS: :In a previous large scale screen for differentially expressed genes in pancreatic cancer, we identified a gene highly overexpressed in cancer encoding a novel protein with four K-homologous (KH) domains. KH-domains are found in a subset of RNA-binding proteins, including pre-mRNA-binding (hnRNP) K protein and the fragile X mental retardation gene product (FMR1). By fluorescence in situ hybridization (FISH) the identified gene named koc (KH domain containing protein overexpressed in cancer) was assigned to chromosome 7p11.5. Two pseudogenes were localised on chromosome 6 and 11. The cloned koc cDNA has a 250 bp 5'-UTR, a 1740 bp ORF and a 2168 bp 3'-UTR. The AU-rich 3'-untranslated region of koc contains eight AUUUA and four AUUUUUA reiterated motifs. The deduced koc protein with 580 amino-acids has a relative molecular mass (Mr) of approximately 65,000 (65 K). The koc transcript is highly overexpressed in pancreatic cancer cell lines and in pancreatic cancer tissue as compared to both, normal pancreas and chronic pancreatitis tissue. High levels of expression were as well found in tissue samples of other human tumours. As the KH domain has been shown to be involved in the regulation of RNA synthesis and metabolism, we speculate that koc may assume a role in the regulation of tumour cell proliferation by interfering with transcriptional and or posttranscriptional processes. However, the precise role of koc in human tumour cells is unknown and remains to be elucidated.

背景与目标： ：在先前针对胰腺癌中差异表达基因的大规模筛选中，我们鉴定了在癌症中高度过表达的基因，该基因编码具有四个K同源（KH）域的新型蛋白质。 KH结构域存在于RNA结合蛋白的子集中，包括前mRNA结合（hnRNP）K蛋白和脆弱的X智力低下基因产物（FMR1）。通过荧光原位杂交（FISH），将鉴定出的名为koc（在癌症中过表达的KH域蛋白）的基因分配给7p11.5染色体。两个假基因位于6号和11号染色体上。克隆的koc cDNA具有250 bp的5'-UTR，1740 bp的ORF和2168 bp的3'-UTR。富含AU的3'非翻译区域的koc包含八个AUUUA和四个AUUUUUA重复的基序。推导的具有580个氨基酸的koc蛋白的相对分子质量（Mr）约为65,000（65 K）。与正常胰腺和慢性胰腺炎组织相比，koc转录本在胰腺癌细胞系和胰腺癌组织中高度过表达。在其他人类肿瘤的组织样本中也发现了高水平的表达。由于已经显示出KH结构域参与RNA合成和代谢的调节，我们推测koc可能通过干扰转录和/或转录后过程而在调节肿瘤细胞增殖中发挥作用。但是，koc在人肿瘤细胞中的确切作用尚不清楚，尚待阐明。

BACKGROUND & AIMS: :Six different secretory proteins of molecular weights (15, 26, 30, 41, 55 and 70 kDa) were isolated from 8-day-old culture filtrate of Mycobacterium tuberculosis H37Ra using different column chromatography techniques. These proteins were further examined for their ability to induce cell mediated (T-cell proliferation assay) and humoral immune response (ELISA) in mice immunized with total culture filtrate proteins. Out of six proteins, three proteins showed good reactivity. However, the activity was at a maximum with 30 kDa antigen. The immune response induced by 30 kDa antigen emulsified in Freund's incomplete adjuvant (FIA) was investigated and was found to be dose dependent. The T-cell response induced by this protein was skewed towards T-helper (Th1) cells as determined by the pronounced secretion of interleukin-2 (IL-2) and gamma-interferon (IFN-gamma). The protective activity of the 30 kDa protein was also evaluated and compared with reference to Bacillus Calmette Guerin (BCG) vaccine in the mice challenged with virulent M. tuberculosis H37Rv. The degree of protection afforded by the 30 kDa antigen on the basis of mortality and the significant decrease in c.f.u.'s recovered from different organs (lung, liver, spleen) after 30 days of challenge with LD50 of M. tuberculosis H37Rv was significantly higher in comparison to BCG vaccinated animals. However, the degree of immunity induced by this antigen decreased with time (when challenged 8 and 12 weeks post-immunization) but it was still comparable with BCG. These findings suggest that 30 kDa secretory protein of M. tuberculosis is the key immunoprotective antigen and may be a suitable candidate for the development of an alternative subunit vaccine against tuberculosis.

背景与目标： ：使用不同的柱色谱技术从结核分枝杆菌H37Ra的8天龄培养滤液中分离出六个分子量分别为15、26、30、41、55和70 kDa的分泌蛋白。在用总培养滤液蛋白免疫的小鼠中，进一步检查了这些蛋白诱导细胞介导的能力（T细胞增殖测定）和体液免疫应答（ELISA）。在六种蛋白质中，三种蛋白质显示出良好的反应性。但是，对于30kDa抗原，活性最大。研究了在弗氏不完全佐剂（FIA）中乳化的30 kDa抗原诱导的免疫反应，发现该反应是剂量依赖性的。该蛋白诱导的T细胞反应偏向T辅助（Th1）细胞，这由白介素2（IL-2）和γ-干扰素（IFN-γ）的明显分泌确定。还评估了30 kDa蛋白的保护活性，并与卡介苗芽孢杆菌（BCG）疫苗进行了比较，比较了在有毒结核分枝杆菌H37Rv攻击的小鼠中的行为。 30 kDa抗原提供的保护程度基于死亡率以及结核分枝杆菌H37Rv的LD50攻击30天后从不同器官（肺，肝，脾）回收的cfu显着降低。与接种卡介苗的动物比较。但是，这种抗原诱导的免疫度随时间降低（在免疫后8周和12周激发时），但仍可与BCG相提并论。这些发现表明，结核分枝杆菌的30kDa分泌蛋白是关键的免疫保护性抗原，并且可能是开发替代性抗结核亚单位疫苗的合适候选者。