Cohesin's concatenation of sister DNAs maintains their intertwining

The contribution of DNA catenation to sister chromatid cohesion is unclear partly because it has never been observed directly within mitotic chromosomes. Differential sedimentation-velocity and gel electrophoresis reveal that sisters of 26 kb circular minichromosomes are held together by catenation as well as by cohesin. The finding that chemical crosslinking of cohesin's three subunit interfaces entraps sister DNAs of circular but not linear minichromosomes implies that cohesin functions using a topological principle. Importantly, cohesin holds both catenated and uncatenated DNAs together in this manner. In the vicinity of centromeres, catenanes are resolved by spindle forces, but linkages mediated directly by cohesin resist these forces even after complete decatenation. Crucially, persistence of catenation after S phase depends on cohesin. We conclude that by retarding Topo II-driven decatenation, cohesin mediates sister chromatid cohesion by an indirect mechanism as well as one involving entrapment of sister DNAs inside its tripartite ring.     

Meeting Report: Hackathon-Workshop on Darwin Core and MIxS Standards Alignment (February 2012)

The Global Biodiversity Information Facility and the Genomic Standards Consortium convened a joint workshop at the University of Oxford, 27-29 February 2012, with a small group of experts from Europe, USA, China and Japan, to continue the alignment of the Darwin Core with the MIxS and related genomics standards. Several reference mappings were produced as well as test expressions of MIxS in RDF. The use and management of controlled vocabulary terms was considered in relation to both GBIF and the GSC, and tools for working with terms were reviewed. Extensions for publishing genomic biodiversity data to the GBIF network via a Darwin Core Archive were prototyped and work begun on preparing translations of the Darwin Core to Japanese and Chinese. Five genomic repositories were identified for engagement to begin the process of testing the publishing of genomic data to the GBIF network commencing with the SILVA rRNA database.     

In vitro and histological investigation of antitumor effect of some triazole compounds in colon cancer cell line

1,2,4-Triazoles are used as antifungal, antibacterial, antimicrobial, and antioxidant against some oxidative radical species. Recently, many 1,2,4-triazoles continue to be synthesized. In this study, the effect of the 1,2,4-triazole derivatives on human colon cancer (HT29) was investigated in vitro and in vivo in rats. MTT test was applied to in in vitro experiments. For in vivo study, rats were divided into seven groups as follows: Control group (negative control), azoxymethane (AOM), AOM + cisplatin 15, AOM + L1, AOM + L2, AOM + L3, and AOM + L4. To create colon cancer, the AOM injection was injected subcutaneously at a dose of 15 mg/kg, three times (once weekly). The in vivo studies were completed at 28 weeks. It was found that the 1,2,4-triazole derivatives reduced the cell viability (P < 0.05). In all animals in the experimental groups, mild dysplasia was detected in 100% of the colon mucosal epithelium. Severe dysplasia and adenocarcinoma were observed in L1 groups. As a result, this study determined that the 1,2,4-triazole derivatives exhibit antitumor activity.     

Induced pluripotent stem cells for therapy personalization in pediatric patients:Focus on drug-induced adverse events

Adverse drug reactions(ADRs) are major clinical problems, particularly in special populations such as pediatric patients. Indeed, ADRs may be caused by a plethora of different drugs leading, in some cases, to hospitalization, disability or even death. In addition, pediatric patients may respond differently to drugs with respect to adults and may be prone to developing different kinds of ADRs,leading, in some cases, to more severe consequences. To improve the comprehension, and thus the prevention, of ADRs, the set-up of sensitive and personalized assays is urgently needed. Important progress is represented by the possibility of setting up groundbreaking patient-specific assays. This goal has been powerfully achieved using induced pluripotent stem cells(iPSCs). Due to their genetic and physiological species-specific differences and their ability to be differentiated ideally into all tissues of the human body, this model may be accurate in predicting drug toxicity, especially when this toxicity is related to individual genetic differences. This review is an up-to-date summary of the employment of iPSCs as a model to study ADRs, with particular attention to drugs used in the pediatric field. We especially focused on the intestinal, hepatic,pancreatic, renal, cardiac, and neuronal levels, also discussing progress in organoids creation. The latter are three-dimensional in vitro culture systems derived from pluripotent or adult stem cells simulating the architecture and functionality of native organs such as the intestine, liver, pancreas, kidney, heart,and brain. Based on the existing knowledge, these models are powerful and promising tools in multiple clinical applications including toxicity screening,disease modeling, personalized and regenerative medicine.     

Targeted label‐free quantification of interleukin‐8 in PMA‐activated U937 cell secretome by nanoLC‐ESI‐MS/MS‐sSRM

Monocytes are a part of the innate immune system. Their differentiation into macrophages changes their cellular proteome and secretome. Particularly secretome components such as cytokines are crucial for immune response and inflammation in many diseases. Differentiation of human lymphoma cell line U937 can be triggered by phorbol 12‐myristate 13‐acetate (PMA). Screening of the cytokine release in U937 upon PMA stimulation by cytometric bead array almost exclusively showed interleukin‐8 (IL‐8). Next, a label‐free nanoLC‐ESI‐MS/MS‐sSRM method for quantification of IL‐8 in the cell secretome was established and applied to monitor the time kinetics of PMA treatment in different concentrations. Targeted secretome analysis was achieved by scheduled SRM‐MS using one proteotypic peptide as precursor ion and four mass transitions. Label‐free quantification was performed by external calibration using IL‐8 standard. Validation results indicated that the method was suited for the quantification of IL‐8 in the secretome. The maximal IL‐8 release of 62.4 ng/mL was observed after incubating cells treated by 50 ng/mL PMA for 48 h. The method can now be used for quantification of IL‐8 release from different cells under various conditions. Furthermore, it can be easily expanded to other secreted proteins detected by untargeted screening methods.     

Small-World Communication of Residues and Significance for Protein Dynamics

It is not merely the position of residues that is critically important for a protein's function and stability, but also their interactions. We illustrate, by using a network construction on a set of 595 nonhomologous proteins, that regular packing is preserved in short-range interactions, but short average path lengths are achieved through some long-range contacts. Thus, lying between the two extremes of regularity and randomness, residues in folded proteins are distributed according to a “small-world” topology. Using this topology, we show that the core residues have the same local packing arrangements irrespective of protein size. Furthermore, we find that the average shortest path lengths are highly correlated with residue fluctuations, providing a link between the spatial arrangement of the residues and protein dynamics.     

Zinc treatment affects superoxide dismutase activity in growth retardation

Children with growth dysfunction present complex diagnostic challenges. The purpose of this study was to determine the effects of oral zinc treatment on red cell copper/zinc superoxide dismutase (Cu/Zn-SOD) activity and copper and zinc concentrations in children with “growth retardation.” Twenty-nine patients, average age of 11 yr, whose percentile was under 3% of the National Center of Health Statistics parameters were selected. For the control group, 10 children whose average age was 10 yr were included. Red cell Cu/Zn-SOD activity was determined by spectrophotometer. Red cell copper and zinc concentrations were measured by atomic absorption spectrophotometer. Red cell Cu/Zn-SOD activity was higher than the control group before zinc treatment (p<0.001). There was a decrease in the Cu/Zn-SOD activity after zinc treatment, but the mean value of the Cu/Zn-SOD activity of patients was still higher than the control values (p<0.001). After zinc treatment, there was an increase in red cell zinc concentration (p<0.01) and a decrease in copper concentration (p<0.001), which were statistically significant. The results of this study suggested that Cu/Zn-SOD activity was increased significantly during growth retardation and zinc treatment appeared to ameliorate the enzyme activity. There were also insignificant alterations in red cell copper and zinc concentrations. Presented at the 23rd Congress of Endocrinology and Metabolic Diseases of Turkey Joint Meeting with the European Federation of Endocrine Societies, Bilkent Hotel, Ankara, 7–9 September, 2000.     

Hydrogen sulfide can inhibit and enhance oxygenic photosynthesis in a cyanobacterium from sulfidic springs

We used microsensors to investigate the combinatory effect of hydrogen sulfide (H₂S) and light on oxygenic photosynthesis in biofilms formed by a cyanobacterium from sulfidic springs. We found that photosynthesis was both positively and negatively affected by H₂S: (i) H₂S accelerated the recovery of photosynthesis after prolonged exposure to darkness and anoxia. We suggest that this is possibly due to regulatory effects of H₂S on photosystem I components and/or on the Calvin cycle. (ii) H₂S concentrations of up to 210 μM temporarily enhanced the photosynthetic rates at low irradiance. Modelling showed that this enhancement is plausibly based on changes in the light‐harvesting efficiency. (iii) Above a certain light‐dependent concentration threshold H₂S also acted as an inhibitor. Intriguingly, this inhibition was not instant but occurred only after a specific time interval that decreased with increasing light intensity. That photosynthesis is most sensitive to inhibition at high light intensities suggests that H₂S inactivates an intermediate of the oxygen evolving complex that accumulates with increasing light intensity. We discuss the implications of these three effects of H₂S in the context of cyanobacterial photosynthesis under conditions with diurnally fluctuating light and H₂S concentrations, such as those occurring in microbial mats and biofilms.     

Resveratrol: Is There Any Effect on Healthy Subject?

This preliminary study was planned to investigate the effects of resveratrol on oxidative–nitrosative stress markers and on trace element concentrations in blood and on circulatory system parameters in rats. Twenty-five Sprague–Dawley male rats, 10–12 weeks old, with mean body weight of 295 g were used in the study. Administration of resveratrol (0.5 ml/day) was performed in experimental group in 10 days. In control (n = 10) and in experimental groups (n = 15), after 1 week training period, systolic arterial blood pressures and heart rates were recorded daily. At the end of the tenth day, blood samples of control and experimental groups were drawn. Total nitrite, nitrite, nitrate, malondialdehyde, copper, zinc concentrations in plasma, superoxide dismutase, and catalase activities and copper, zinc concentrations in red cell were determined both in control and experimental groups. Alterations in oxidative and nitrosative stress markers, trace element concentrations, and circulatory system parameters in experimental group compared to controls were observed. The results of this study were discussed according to the effect of resveratrol. This study was presented at “The 5th International Congress of Pathophysiology (ISP2006)” June 28–July 1, 2006 Beijing, China.