New germline mutations in non-BRCA genes among breast cancer women of Mongoloid origin

Molecular Biology Reports - In accordance with the Asian BRCA Consortium data, there is a significant difference in incidence rate of breast cancer depending on age, as well as spectrum and...     

Mis-Assembled "Segmental Duplications" in Two Versions of the Bos taurus Genome

We analyzed the whole genome sequence coverage in two versions of the Bos taurus genome and identified all regions longer than five kilobases (Kbp) that are duplicated within chromosomes with >99% sequence fidelity in both copies. We call these regions High Fidelity Duplications (HFDs). The two assemblies were Btau 4.2, produced by the Human Genome Sequencing Center at Baylor College of Medicine, and UMD Bos taurus 3.1 (UMD 3.1), produced by our group at the University of Maryland. We found that Btau 4.2 has a far greater number of HFDs, 3111 versus only 69 in UMD 3.1. Read coverage analysis shows that 39 million base pairs (Mbp) of sequence in HFDs in Btau 4.2 appear to be a result of a mis-assembly and therefore cannot be qualified as segmental duplications. UMD 3.1 has only 0.41 Mbp of sequence in HFDs that are due to a mis-assembly.     

Comparative analysis of gene expression level by quantitative real-time PCR has limited application in objects with different morphology

qRT-PCR is a generally acknowledged method for gene expression analysis due to its precision and reproducibility. However, it is well known that the accuracy of qRT-PCR data varies greatly depending on the experimental design and data analysis. Recently, a set of guidelines has been proposed that aims to improve the reliability of qRT-PCR. However, there are additional factors that have not been taken into consideration in these guidelines that can seriously affect the data obtained using this method. In this study, we report the influence that object morphology can have on qRT-PCR data. We have used a number of Arabidopsis thaliana mutants with altered floral morphology as models for this study. These mutants have been well characterised (including in terms of gene expression levels and patterns) by other techniques. This allows us to compare the results from the qRT-PCR with the results inferred from other methods. We demonstrate that the comparison of gene expression levels in objects that differ greatly in their morphology can lead to erroneous results.     

Prognosis of Thyroid Nodules in Individuals Living in the Zhitomir Region of Ukraine

Objective

After the accident at the Chernobyl Nuclear Power Plant (CNPP), the incidence of thyroid cancer increased among children. Recently, a strong relationship between solid thyroid nodules and the incidence of thyroid cancer was shown in atomic bomb survivors. To assess the prognosis of benign thyroid nodules in individuals living in the Zhitomir region of Ukraine, around the CNPP, we conducted a follow-up investigation of screening data from 1991 to 2000 in the Ukraine.

Patients and Methods

Participants of this study were 160 inhabitants with thyroid nodules (nodule group) and 160 inhabitants without thyroid nodules (normal control group) intially identified by ultrasonography from 1991 to 2000. All participants were aged 0 to 10 years old and lived in the same area at the time of the accident. We performed follow-up screening of participants and assessed thyroid nodules by fine needle aspiration biopsy.

Results

Among the nodule group participants, the number and size of nodules were significantly increased at the follow-up screening compared with the initial screening. No thyroid nodules were observed among the normal control group participants. The prevalence of thyroid abnormality, especially nodules that could be cancerous (malignant or suspicious by fine needle aspiration biopsy), was 7.5% in the nodule group and 0% in the normal control group (P<0.001).

Conclusions

Our study indicated that a thyroid nodule in childhood is a prognostic factor associated with an increase in the number and size of nodules in individuals living in the Zhitomir region of Ukraine.     

Polyhydroxybutyrate/Hydroxyapatite Highly Porous Scaffold for Small Bone Defects Replacement in the Nonload-bearing Parts

In the present work,Polyhydroxybutyrate (PHB)/Hydroxyapatite (HA) porous composites (10％,20％,30 ％,40％,50％ weight HA) were obtained by sintering.PHB/20％ HA optimally combines satisfactory mechanical properties with a high content of the bioactive component (HA).Porous PHB/20％ HA scaffolds have shown high mechanical properties (compressive strength of 106 MPa and Young's modulus of 901 MPa).A high volume fraction of interconnected pores (＞ 50 vol.％) was achieved with pore size of 50 μm-500 μm.Biocompatibility of porous pure PHB and PHB/20％HA,as its osseointegration were assessed in vitro and after implantation in laboratory animals.PHB/20％ HA (-5％ ± 0.9％) and pure PHB (-3％ ± 1.4％) samples after 24 hours of incubation with human leucocytes showed no significant level of cytotoxicity when p =0.648 (p-value).In vitro massive adhesion of mouse Multipotent Mesenchymal Stromal Cells (MMSC) to the surface of both porous samples was shown.PHB/20％ HA induced more intensive MMSC proliferation compared to pure PHB,which are 31％ ± 6.1％ and 20％ ± 5.7 ％ respectively when p =0.039.We observed the resorption (implant surface area was reduced by 49 ％) and integration of the porous PHB/20％ HA samples into surrounding tissues after 30 days of implantation.The signs of osteoclasts accumulation,neo-angigenesis and new bone formation were observed,which make PHB/20％ HA promising for bone tissue engineering.     

Monocyte Subset Dynamics in Human Atherosclerosis Can Be Profiled with Magnetic Nano-Sensors

Monocytes are circulating macrophage and dendritic cell precursors that populate healthy and diseased tissue. In humans, monocytes consist of at least two subsets whose proportions in the blood fluctuate in response to coronary artery disease, sepsis, and viral infection. Animal studies have shown that specific shifts in the monocyte subset repertoire either exacerbate or attenuate disease, suggesting a role for monocyte subsets as biomarkers and therapeutic targets. Assays are therefore needed that can selectively and rapidly enumerate monocytes and their subsets. This study shows that two major human monocyte subsets express similar levels of the receptor for macrophage colony stimulating factor (MCSFR) but differ in their phagocytic capacity. We exploit these properties and custom-engineer magnetic nanoparticles for ex vivo sensing of monocytes and their subsets. We present a two-dimensional enumerative mathematical model that simultaneously reports number and proportion of monocyte subsets in a small volume of human blood. Using a recently described diagnostic magnetic resonance (DMR) chip with 1 µl sample size and high throughput capabilities, we then show that application of the model accurately quantifies subset fluctuations that occur in patients with atherosclerosis.     

Improving Phrap-based assembly of the rat using "reliable" overlaps

The assembly methods used for whole-genome shotgun (WGS) data have a major impact on the quality of resulting draft genomes. We present a novel algorithm to generate a set of "reliable" overlaps based on identifying repeat k-mers. To demonstrate the benefits of using reliable overlaps, we have created a version of the Phrap assembly program that uses only overlaps from a specific list. We call this version PhrapUMD. Integrating PhrapUMD and our "reliable-overlap" algorithm with the Baylor College of Medicine assembler, Atlas, we assemble the BACs from the Rattus norvegicus genome project. Starting with the same data as the Nov. 2002 Atlas assembly, we compare our results and the Atlas assembly to the 4.3 Mb of rat sequence in the 21 BACs that have been finished. Our version of the draft assembly of the 21 BACs increases the coverage of finished sequence from 93.4% to 96.3%, while simultaneously reducing the base error rate from 4.5 to 1.1 errors per 10,000 bases. There are a number of ways of assessing the relative merits of assemblies when the finished sequence is available. If one views the overall quality of an assembly as proportional to the inverse of the product of the error rate and sequence missed, then the assembly presented here is seven times better. The UMD Overlapper with options for reliable overlaps is available from the authors at http://www.genome.umd.edu. We also provide the changes to the Phrap source code enabling it to use only the reliable overlaps.