SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets

Background  

Array comparative genome hybridization (aCGH) provides information about genomic aberrations. Alterations in the DNA copy number may cause the cell to malfunction, leading to cancer. Therefore, the identification of DNA amplifications or deletions across tumors may reveal key genes involved in cancer and improve our understanding of the underlying biological processes associated with the disease.     

SA-hIL2双功能融合蛋白的研制及其生物学鉴定

目的：制备链亲和素标记的人白细胞介素-2(SA-hIL2)融合蛋白,并研究其生物学功能。方法：构建SA-L-IL2-pET24重组表达质粒,在大肠杆菌中表达SA-hIL2融合蛋白,对表达的SA-hIL2融合蛋白采用镍金属螯合（Ni-NTA）层析柱进行纯化,透析复性。CCK-8法检测SA-hIL2融合蛋白对PHA刺激的人外周血淋巴细胞的增值活性,流式细胞仪分析SA-hIL2融合蛋白对生物素化的B16.F10肿瘤细胞表面锚定修饰效率。结果：SA-hIL2在大肠杆菌中实现了高效表达,约占菌体总蛋白的20％,制备的SA-hIL2融合蛋白纯度达到95％,并具有双重活性,即hIL-2促进PHA刺激的人外周血淋巴细胞的增值活性和SA介导的高效结合至已生物素化的B16.F10肿瘤细胞表面的功能（表面锚定修饰效率约95％）。结论：研制的SA-hIL2融合蛋白具有双重活性,可为研制表面修饰的新型肿瘤细胞疫苗提供基础。     

Contamination of commercial preparations of calmodulin by phospholipase A2

In the course of studies of the possible regulation of cellular phospholipase A2 activities by calcium and calmodulin, it was observed that some of the commercial preparations of calmodulin contained significant phospholipase A2 activity. Six commercially available calmodulin sources were compared for the presence of contaminating phospholipase A2 activity, relative purity by SDS-gel electrophoresis, and relative biological activity in stimulating calmodulin-deficient phosphodiesterase. One of the commercial calmodulin sources contained a relatively high specific phospholipase A2 activity (1.30 +/- 0.11 nmol [1-14C]arachidonic acid released/mg protein per h) and yielded two major bands in SDS-gel electrophoresis. Two of the calmodulin sources tested were relatively free of phospholipase A2 activity, were quite pure (one band on SDS-gel) and had high biological activity in stimulating calmodulin-deficient phosphodiesterase. Thus, investigators using commercially available preparations of calmodulin should be aware of the contamination of some of these sources by phospholipase A2 activity. These findings may be of importance to investigators considering the role of calmodulin in activating a variety of calcium-dependent enzymes, including phospholipase A2.     

Analogs of arachidonic acid methylated at C-7 and C-10 inhibit leukotriene biosynthesis and phospholipase A2 activity

The ability of (all Z)-7,7-dimethyl-5,8,11,14-eico-satetraenoic acid, (all Z)-7,7-dimethyl-5,8,11-eicosatrienoic acid, (Z,Z)-7,7-dimethyl-5,8-eicosadienoic acid, (all Z)-10,10-dimethyl-5,8,11,14-eicosatetraenoic acid, (all Z)-10,10-dimethyl-5,8,11-eicosatrienoic acid, and rac-(Z,Z)-15-hydroxy-7,7-dimethyl-5,8-eicosadienoic acid to inhibit ionophore-induced slow-reacting substance of anaphylaxis (SRS-A) biosynthesis in rat peritoneal cells was studied. It was thought that compounds such as these might inhibit proton abstractions at the 7 or 10 carbon positions on arachidonic acid which are thought to be important in the mechanism of catalysis of Δ⁵-lipoxygenase(Δ⁵-LO). All compounds were found to be potent inhibitors of SRS-A biosynthesis in the in vitro rat peritoneal cell system (IC₅₀ < 10 μM). In fact they were more potent inhibitors in the test system than standard Δ⁵-LO inhibitors such as NDGA and quercetin. To determine if the mechanism of inhibition of the dimethyl arachidonic acid analogs did involve gD⁵-LO inhibition these compounds were evaluated in an assay system utilizing the Δ⁵-LO from rat basophilic leukemia (RBL^?1_cells. It was found, however, that these compounds were much less potent inhibitors of this enzyme (IC₅₀ ～ 100 μM) than standard compounds such as NDGA (IC₅₀ 0.14 μM) and quercetin (IC₅₀, 0.2 μM). The arachidonic acid analogs were subsequently found to be potent inhibitors of phospholipase A₂ (PLA₂) enzymes with IC₅₀'s between 10–20 μM as inhibitors of a snake venom enzyme. In fact these compounds are among the most potent inhibitors of PLA₂ yet studied, having potencies better than standards such as p-bromophenacyl bromide (IC₅₀, 87 μM) and U-10029A (IC₅₀, 36 μM). These results suggest that the methylated arachidonic acid analogs may inhibit SRS-A biosynthesis through inhibiting PLA₂.     

Isolation of Shigellae: VIII. Comparison of Xylose Lysine Deoxycholate Agar, Hektoen Enteric Agar, Salmonella-Shigella Agar, and Eosin Methylene Blue Agar with Stool Specimens

Two enrichment broths and four plating media were compared for efficiency of detection of enteric pathogens from 1,597 stool specimens. Of 170 salmonellae isolated from the composite of all methods, direct streaking yielded but 54%, whereas enrichment in gram-negative broth found 87% and Selenite-F broth 97%. By contrast, gram-negative broth produced 100% of the 17 shigellae, Selenite-F broth but 77%, and direct streaking only 59%. Thus, enrichment methods produced almost twice the number of both pathogens as direct streaking. Comparison of the plating media revealed xylose lysine deoxycholate agar (XLD) and Hektoen enteric agar to be equal in their abilities to find both pathogens. Both were moderately better than Salmonella-Shigella agar and markedly superior to eosin methylene blue agar. XLD fround 83% of salmonellae produced by the composite of four media and 90% of the shigellae. Hektoen enteric agar found 80% of both. Salmonella-Shigella agar detected 74 and 68%, respectively, and eosin methylene blue agar only 42 and 63%. The numbers of false positives accruing to each medium, however, showed Hektoen enteric and Salmonella-Shigella agars to produce more than twice as many false-positive plates as XLD. Similarly, Selenite-F broth resulted in many more false-positives for all plating media than did gram-negative broth. Consequently, the index of validity, which equates successful isolation of pathogens with total pickings, favored XLD and gram-negative broth as the media of choice, with direct streaking the poorest method by all counts.     

Collagenase production by Achromobacter iophagus.

Achromobacter iophagus produced collagenase (EC 3.4.24.3) when cultured aerobically in buffer containing 5% peptone. The bacterium is non-pathogenic and tests on rabbits indicated that the culture medium was atoxic. The collagenase, which hydrolyzed insoluble and soluble native collagen, was purified by (NH4)2 SO4 precipitation, starch block electrophoresis, and gel filtration. It was shown to be serologically distinct from Clostridium histolyticum collagenase and to have molecular weight and sedimentation coefficient values of approx. 112 000 and 5.3 S, respectively.     

Comparison of Two Methods for the Isolation of Salmonellae From Imported Foods

Two methods for the detection of salmonellae in foods were compared in 179 imported meat and egg samples. The number of positive samples and replications, and the number of strains and kinds of serotypes were statistically comparable by both the direct enrichment method of the Food Hygiene Laboratory in England, and the pre-enrichment method devised for processed foods in the United States. Boneless frozen beef, veal, and horsemeat imported from five countries for consumption in England were found to have salmonellae present in 48 of 116 (41%) samples. Dried egg products imported from three countries were observed to have salmonellae in 10 of 63 (16%) samples. The high incidence of salmonellae isolated from imported foods illustrated the existence of an international health hazard resulting from the continuous introduction of exogenous strains of pathogenic microorganisms on a large scale.     

Physiological Reorganization and Post-Traumatic Regeneration in Stylonychia mytilus: Reflections on Developmental Constraints and the Evolutionary Origin of Alternative Modes of Asexual Morphogenesis

We investigated development of cortical ciliature in Stylonychia mytilus during starvation-induced physiological reorganization, and during regeneration following amputation of the anterior part of the cell. Cortical reorganization in the two processes is generally similar. The posterior part of the adoral zone of membranelles is resorbed and replaced with newly assembled membranelles. The pre-existing set of ventral cirri and dorsal bristles is entirely resorbed and replaced with new ones. Regenerants exhibit posterior displacement of the frontal-ventral-transverse cirri primordium and the undulating membrane primordium, and recruit basal bodies from ectopic locations for the development of these ciliature. This illustrates flexibility in the initiation site of ciliary primordia, and opportunism in utilizing building blocks. Such morphogenetic versatility of hypotrichs provides the basis for the operation of a global control of pattern formation, which governs cortical reorganization in dividers, and additionally, in the absence of the prerequisites for binary fission, alternative modes of cortical development such as physiological reorganization or regeneration. These considerations suggest that the three processes are homologous and that physiological reorganization and regeneration have evolved from binary fission. In physiological reorganization and regeneration, the micro- and macronuclei reorganize to resemble that in binary fission; these nuclear events are considered evolutionary relics of the nuclear development of binary fission. Tetrahymena also exhibits such morphogenetic flexibility; stomatogenesis is under global control, so that asexual cells can replace its oral apparatus without undergoing binary fission. Paramecium , on the other hand, adopts a more rigid strategy in relying heavily on pre-existing structures for morphogenetic cues; this could have imposed constraints in the exploration of alternative modes of asexual development.     

Mitochondrial DNA sequence variation in the spruce budworm species complex (Choristoneura: Lepidoptera)

A combination of polymerase-chain-reaction amplification and automated DNA sequencing was used to survey variation in a species complex of pest insects, the spruce budworms (Choristoneura fumiferana species group), and an outgroup species, C. rosaceana. We sequenced an mtDNA region of 1,573 bp that extends from the middle of cytochrome oxidase subunit I (COI) through tRNA leucine (UUR) to the end of cytochrome oxidase subunit II. In addition, we examined levels of intraspecific variation within a 470-bp region of the COI gene. Choristoneura fumiferana clearly represented the oldest lineage within its species group, with 2.7%-2.9% sequence divergence from the other species. In contrast, the four remaining species (C. pinus, C. biennis, C. occidentalis, and C. orae) had closely related or identical mtDNA, with < 1% divergence among most of their haplotypes. Despite its older lineage and widespread geographic distribution, C. fumiferana showed significantly lower intraspecific genetic diversity than did C. occidentalis. Choristoneura orae shared haplotypes with C. occidentalis and C. biennis, and species-level separation of these three species was not supported. Two divergent, uncommon haplotypes were also found in C. occidentalis and C. biennis. The divergent haplotype in C. biennis had an unusually high number of inferred amino acid replacements, suggesting selective differences between mitochondrial DNA haplotypes. Transition:transversion ratios in Choristoneura paralleled those found in Drosophila; transition:transversion ratios were highest in closely related sequences but decreased with increasing sequence divergence. Nucleotide composition showed an A+T bias that was near the high end of the range known for insects. This work illustrates the potential utility of direct DNA sequencing in assessing population structures, species limits, and phylogenetic relationships among organisms that have not previously been subjected to DNA analysis.