Global DNA methylation levels in white blood cell DNA from sisters discordant for breast cancer from the New York site of the Breast Cancer Family Registry

Lower global DNA methylation is associated with genomic instability and it is one of the epigenetic mechanisms relevant to carcinogenesis. Emerging evidence for several cancers suggests that lower overall levels of global DNA methylation in blood are associated with different cancer types, although less is known about breast cancer. We examined global DNA methylation levels using a sibling design in 273 sisters affected with breast cancer and 335 unaffected sisters from the New York site of the Breast Cancer Family Registry. We measured global DNA methylation in total white blood cell (WBC) and granulocyte DNA by two different methods, the [³H]-methyl acceptance assay and the luminometric methylation assay (LUMA). Global methylation levels were only modestly correlated between sisters discordant for breast cancer (Spearman correlation coefficients ranged from -0.08 to 0.24 depending on assay and DNA source). Using conditional logistic regression models, women in the quartile with the lowest DNA methylation levels (as measured by the [³H]-methyl acceptance assay) had a 1.8-fold (95% CI = 1.0–3.3) higher relative association with breast cancer than women in the quartile with the highest DNA methylation levels. When we examined the association on a continuous scale, we also observed a positive association (odds ratio, OR = 1.3, 95% CI = 1.0–1.7, for a one unit change in the natural logarithm of the DPM/μg of DNA). We observed no association between measures by the LUMA assay and breast cancer risk. If replicated in prospective studies, this study suggests that global DNA methylation levels measured in WBC may be a potential biomarker of breast cancer risk even within families at higher risk of cancer.     

Human bone marrow mesenchymal cells express NG2: possible increase in discriminative ability of flow cytometry during mesenchymal stromal cell identification

Background aimsMesenchymal stromal cells (MSC) exhibit non-specific hematopoietic cell and/or stromal cell markers (e.g. CD73, CD105 and CD166) that have been used to identify MSC by flow cytometry. Because a neural glial antigen, NG2 (a progenitor cell marker in the central nervous system), is expressed by several tissue cells originating in the mesenchyme but not hematopoietic cells, it might be useful for isolating and identifying MSC. We investigated NG2 expression on culture-expanded MSC by flow cytometry.MethodsHuman bone marrow (BM) samples taken from 12 donors were cultured for MSC to be used in up to nine serial passages. Using flow cytometry, the neural glial antigen NG2 and commonly used MSC markers CD73, CD105 and CD166, were analyzed on the surface of culture-expanded MSC. The multipotential differentiation of the MSC was examined by adipogenic and osteogenic induction.ResultsThe percentage of cells positive for NG2 was similar to the percentages of cells positive for CD73, CD105 and CD166 in all passages of BM samples. The mean fluorescent intensities of NG2 did not change with culture passage. The MSC was successfully differentiated into adipogenic and osteogenic lines. The cells showed no karyotypic abnormalities.ConclusionsNG2 seems to be a promising marker for investigating the biology of MSC.     

A Geometric Buildup Algorithm for the Solution of the Distance Geometry Problem Using Least-Squares Approximation

We propose a new geometric buildup algorithm for the solution of the distance geometry problem in protein modeling, which can prevent the accumulation of the rounding errors in the buildup calculations successfully and also tolerate small errors in given distances. In this algorithm, we use all instead of a subset of available distances for the determination of each unknown atom and obtain the position of the atom by using a least-squares approximation instead of an exact solution to the system of distance equations. We show that the least-squares approximation can be obtained by using a special singular value decomposition method, which not only tolerates and minimizes small distance errors, but also prevents the rounding errors from propagation effectively, especially when the distance data is sparse. We describe the least-squares formulations and their solution methods, and present the test results from applying the new algorithm for the determination of a set of protein structures with varying degrees of availability and accuracy of the distances. We show that the new development of the algorithm increases the modeling ability, and improves stability and robustness of the geometric buildup approach significantly from both theoretical and practical points of view.     

Coupled Plasmonic Cavities on Moire Surfaces

Surface plasmon polariton (SPP) waveguides formed by coupled plasmonic cavities on metallic Moire surfaces have been investigated both experimentally and numerically. The Moire surface, fabricated by interference lithography, contains periodic arrays of one-dimensional cavities. The coupling strength between the cavities has been controlled by changing the periodicities of the Moire surface. The ability to control the coupling strength allows us to tune the dispersion and the group velocity of the plasmonic coupled cavity mode. Reflection measurements and numerical simulation of the array of SPP cavities have shown a coupled resonator type plasmonic waveguide band formation within the band gap. Coupling coefficients of cavities and group velocities of SPPs are calculated for a range of cavity sizes from weakly coupled regime to strongly coupled regime.     

Morphology and function of cryopreserved whole ovine ovaries after heterotopic autotransplantation

Background

The objective of this study was to perform complex characterization of cryopreserved and then autotransplanted ovaries including determination of the ability to respond to in vivo follicle stimulating hormone (FSH)-treatment, fertilizability of retrieved oocytes, and morphology, vascularization, cellular proliferation and apoptosis in sheep.

Methods

Mature crossbred ewes were divided into two groups; an intact (control) group (n = 4), and autotransplanted group (n = 4) in which oophorectomy was performed laparoscopically and ovaries with intact vascular pedicles frozen, thawed and transplanted back into the same animal at a different site. Approximately five months after autotransplantation, estrus was synchronized, ewes were treated with FSH, and ovaries were collected. For all ovaries, number of visible follicles was determined, and collected cumulus oocyte complexes (COC) were matured and fertilized in vitro. Remaining ovarian tissues were fixed for evaluation of morphology, expression of factor VIII (marker of endothelial cells), vascular endothelial growth factor (VEGF; expressed by pericytes and smooth muscle cells), and smooth muscle cell actin (SMCA; marker of pericytes and smooth muscle cells), and cellular proliferation and apoptosis. Two fully functional ovaries were collected from each control ewe (total 8 ovaries).

Results

Out of eight autotransplanted ovaries, a total of two ovaries with developing follicles were found. Control ewes had 10.6 +/- 2.7 follicles/ovary, oocytes were in vitro fertilized and developed to the blastocyst stage. One autotransplanted ewe had 4 visible follicles from which 3 COC were collected, but none of them was fertilized. The morphology of autotransplanted and control ovaries was similar. In control and autotransplanted ovaries, primordial, primary, secondary, antral and preovulatory follicles were found along with fully functional vascularization which was manifested by expression of factor VIII, VEGF and SMCA. Proliferating cells were detected in follicles, and the rate of apoptosis was minimal in ovaries of control and autotransplanted ovaries.

Conclusion

These data demonstrate successful autotransplantation of a portion of frozen/thawed ovaries manifested by restoration of selected ovarian function including in vitro maturation of collected oocytes, presence of follicles from several stages of folliculogenesis and blood vessels expressing specific markers of vascularization, and proliferation and apoptosis of ovarian cells. Thus, heterotopic autotransplantation of a whole frozen/thawed ovary allows for development of preovulatory follicles, oocyte growth, and for restoration of vascularization and cellular function. However, additional improvements are required to enhance the efficiency of autotransplantation of frozen/thawed ovaries to produce more oocytes.     

An alternative supporting electrolyte for enzyme immobilization in conducting polymers

In this study an alternative supporting electrolyte was used in enzyme immobilization. Invertase was studied to observe the effect of the supporting electrolyte. Sulfonated poly(arylene ether sulfone) was used as the supporting electrolyte during the electrolysis of pyrrole. The results show that the polymeric supporting electrolyte can be used instead of sodium dodecyl sulfate.     

Quantitative trait loci associated with soybean seed weight and composition under different phosphorus levels

Seed size and composition are important traits in food crops and can be affected by nutrient availability in the soil. Phosphorus (P) is a non‐renewable, essential macronutrient, and P deficiency limits soybean (Glycine max) yield and quality. To investigate the associations of seed traits in low‐ and high‐P environments, soybean recombinant inbred lines (RILs) from a cross of cultivars Fiskeby III and Mandarin (Ottawa) were grown under contrasting P availability environments. Traits including individual seed weight, seed number, and intact mature pod weight were significantly affected by soil P levels and showed transgressive segregation among the RILs. Surprisingly, P treatments did not affect seed composition or weight, suggesting that soybean maintains sufficient P in seeds even in low‐P soil. Quantitative trait loci (QTLs) were detected for seed weight, intact pods, seed volume, and seed protein, with five significant QTLs identified in low‐P environments and one significant QTL found in the optimal‐P environment. Broad‐sense heritability estimates were 0.78 (individual seed weight), 0.90 (seed protein), 0.34 (seed oil), and 0.98 (seed number). The QTLs identified under low P point to genetic regions that may be useful to improve soybean performance under limiting P conditions.     

Sex-linked variations in the sagittal otolith biometry of Nemipterus randalli (Russell, 1986) from the eastern Mediterranean Sea

Few studies have been conducted on the sagittal otolith shape and morphometry of Nemipterus randalli, and none of these studies has examined the effect of sexual dimorphism on the otolith morphology of this species, therefore this study aimed to contribute to knowledge about the otolith morphology of N. randalli, an invasive fish species for the Mediterranean Sea. For this purpose, a total of 132 samples (51 female and 81 male) were obtained from İskenderun Bay with the help of commercial fishermen in November 2018. Relationships between otolith measurements and fish size were determined. Shape indices and elliptic Fourier coefficients were calculated. Significant differences were detected between males and females in all analysis. The sexes were separated from each other using both shape indices and elliptic Fourier coefficients. However, shape analysis was more effective in distinguishing sexes than traditional morphometric analysis. Asymmetry in the otolith morphology of sexes has been attributed to differences in the growth and sexual maturity of male and female fish. The results of this study indicated that sexual dimorphism in Nemipterus randalli was also reflected in the otolith morphology.     

The expression level of fibulin-2 in the circulating RNA (ctRNA) of epithelial tumor cells of peripheral blood and tumor tissue of patients with metastatic lung cancer

Molecular Biology Reports - The Fibulins are a recently discovered family of extracellular matrix proteins. In this study, expression levels of the fibulin-2 (FBLN2) gene and its role in the...     

Tau pathology reduction with SM07883, a novel,potent, and selective oral DYRK1A inhibitor: A potential therapeutic for Alzheimer's disease

Dual‐specificity tyrosine phosphorylation‐regulated kinase‐1A (DYRK1A) is known to phosphorylate the microtubule‐associated tau protein. Overexpression is correlated with tau hyperphosphorylation and neurofibrillary tangle (NFT) formation in Alzheimer's disease (AD). This study assessed the potential of SM07883, an oral DYRK1A inhibitor, to inhibit tau hyperphosphorylation, aggregation, NFT formation, and associated phenotypes in mouse models. Exploratory neuroinflammatory effects were also studied. SM07883 specificity was tested in a kinase panel screen and showed potent inhibition of DYRK1A (IC₅₀ = 1.6 nM) and GSK‐3β (IC₅₀ = 10.8 nM) kinase activity. Tau phosphorylation measured in cell‐based assays showed a reduction in phosphorylation of multiple tau epitopes, especially the threonine 212 site (EC₅₀ = 16 nM). SM07883 showed good oral bioavailability in multiple species and demonstrated a dose‐dependent reduction of transient hypothermia‐induced phosphorylated tau in the brains of wild‐type mice compared to vehicle (47%, p < 0.001). Long‐term efficacy assessed in aged JNPL3 mice overexpressing the P301L human tau mutation (3 mg/kg, QD, for 3 months) exhibited significant reductions in tau hyperphosphorylation, oligomeric and aggregated tau, and tau‐positive inclusions compared to vehicle in brainstem and spinal cord samples. Reduced gliosis compared to vehicle was further confirmed by ELISA. SM07883 was well tolerated with improved general health, weight gain, and functional improvement in a wire‐hang test compared to vehicle‐treated mice (p = 0.048). SM07883, a potent, orally bioavailable, brain‐penetrant DYRK1A inhibitor, significantly reduced effects of pathological tau overexpression and neuroinflammation, while functional endpoints were improved compared to vehicle in animal models. This small molecule has potential as a treatment for AD.