Reliability-oriented bioinformatic networks visualization

SUMMARY: We present our protein-protein interaction (PPI) network visualization system RobinViz (reliability-oriented bioinformatic networks visualization). Clustering the PPI network based on gene ontology (GO) annotations or biclustered gene expression data, providing a clustered visualization model based on a central/peripheral duality, computing layouts with algorithms specialized for interaction reliabilities represented as weights, completely automated data acquisition, processing are notable features of the system. AVAILABILITY: RobinViz is a free, open-source software protected under GPL. It is written in C++ and Python, and consists of almost 30 000 lines of code, excluding the employed libraries. Source code, user manual and other Supplementary Material are available for download at http://code.google.com/p/robinviz/.     

Effect of 1-(1-Naphtylmethyl)-piperazine,an Efflux Pump Inhibitor,on Antimicrobial Drug Susceptibilities of Clinical <Emphasis Type="Italic">Acinetobacter baumannii</Emphasis> Isolates

In this study, the effects of 1-(1-naphtylmethyl)-piperazine (NMP), an efflux pump inhibitor, on antimicrobial drug susceptibilities of 42 clinical Acinetobacter baumannii isolates were investigated by the disc diffusion method. The inhibition zone diameters of antibiotic discs were tested in the presence and absence of NMP and then these zone diameters were compared. Presence of NMP restored ciprofloxacin susceptibility in 15 intermediate and 2 resistant isolates. One ciprofloxacin resistant isolate became intermediate in the presence of NMP. One isolate resistant to gentamicin became intermediate with NMP. Interestingly, one isolate susceptible to meropenem became resistant in the presence of NMP. Although NMP increased the inhibition zone diameters of some of the tested antibiotics against the resistant isolates, the increase was not enough to restore susceptibility. In conclusion, the presence of NMP increases the zone diameters of ciprofloxacin and levofloxacin. Intermediate strains become susceptible but the resistant isolates do not.     

Cytomegalovirus induces interferon-stimulated gene expression and is attenuated by interferon in the developing brain

Cytomegalovirus (CMV) is considered the most common infectious agent causing permanent neurological dysfunction in the developing brain. We have previously shown that CMV infects developing brain cells more easily than it infects mature brain cells and that this preference is independent of the host B- and T-cell responses. In the present study, we examined the innate antiviral defenses against mouse (m) and human (h) CMVs in developing and mature brain and brain cells. mCMV infection induced interferon (IFN)-stimulated gene expression by 10- to 100-fold in both glia- and neuron-enriched cultures. Treatment of primary brain cultures with IFN-alpha, -beta, and -gamma or a synthetic RNA, poly(I:C), reduced the number of mCMV-infected cells, both in older cells and in fresh cultures from embryonic mouse brains. When a viral dose that killed almost all unprotected cells was used, IFN-protected cells had a natural appearance, and when they were tested with whole-cell patch clamp recording, they appeared physiologically normal with typical resting membrane potentials and action potentials. mCMV infection increased expression of representative IFN-stimulated genes (IFIT3, OAS, LMP2, TGTP, and USP18) in both neonatal and adult brains to similarly large degrees. The robust upregulation of gene expression in the neonatal brain was associated with a much higher degree of viral replication at this stage of development. In contrast to the case for downstream gene induction, CMV upregulated IFN-alpha/beta expression to a greater degree in the adult brain than in the neonatal brain. Similar to the case with cultured brain cells, IFN treatment of the developing brain in vivo depressed mCMV replication. In parallel work with cultured primary human brain cells, IFN and poly(I:C) treatment reduced hCMV infection and prevented virus-mediated cell death. These results suggest that coupling IFN administration with current treatments may reduce CMV infections in the developing brain.     

Lipid peroxidation and total antioxidant status in patients with breast cancer

Oxidative stress is considered to be involved in the pathophysiology of all cancers. The aim of this study is to examine oxidative stress and antioxidant status in patients with breast cancer by evaluation of the serum levels of total antioxidant capacity (TAC) and lipid peroxidation products as malondialdehyde (MDA) and lipid hydroperoxide and to investigate the relationship between these parameters, oxidative stress and serum lipids and lipoproteins. In our study, serum TAC, MDA, lipid hydroperoxide, HDL-cholesterol, VLDL-cholesterol, LDL-cholesterol, total cholesterol, triacylglycerol (TAG), albumin and uric acid levels of 56-breast cancer patients in different clinical stages and 18 healthy women were determined. Significantly lower-levels of TAC were detected in patients with breast cancer in comparison to controls (2.01 +/- 0.01 mmol/l and 2.07 +/- 0.03 mmol/l, respectively, p < 0.05). Serum MDA levels of the patients were higher compared to the controls (3.64 +/- 0.25 microM and 2.72 +/- 0.22 microM, respectively, p < 0.05). No significant difference between lipid hydroperoxide levels of patients and controls was found (0.33 +/- 0.05 microM and 0.32 +/- 0.01 microM, respectively, p > 0.05). These data show that lower TAC and higher MDA levels i.e. increased oxidative stress may be related to breast cancer.     

Fine needle aspiration biopsy features with histologic correlation in mediastinal hepatoid yolk sac tumor presenting with sternum metastasis: a case report

BACKGROUND: The hepatoid variant of yolk sac tumor (H-YST) is an exceedingly rare and highly malignant neoplasm. We present and discuss our experience with cytologic and histopathologic features of a mediastinal H-YST presenting with sternum metastasis, which to the best of our knowledge has not been previously reported. CASE: A 38-year-old man presented with a large mass on the sternum. Computed tomography of the thorax showed a large anterior mediastinal mass with sternum metastsis and multiple lung metastases. Laboratory examination revealed elevated serum alpha-fetoprotein (60,000 IU/mL). No tumor was found in the other organ systems. A percutaneous fine needle aspiration biopsy and subsequent open surgical biopsy were performed on the sternum metastasis. Cytologically, the tumor was composed of monotonous, large, round to polygonal hepatoid cells forming solid sheets and trabeculae entrapped with endothelial cells resembling hepatocellular carcinoma. Histopathologic sections of tumor showed tumor cells with eosinophilic to clear cytoplasm arranged in a solid, trabecular growth pattern, with some acinar formations. Immunohistochemical study supported the hepatoid origin. CONCLUSION: Fine needle aspiration cytology, together with the characteristic clinical presentations and specific tumor markers, is crucial to the initial diagnosis of H-YST.     

Novel short peptides isolated from phage display library inhibit vascular endothelial growth factor activity

Signal transduction through the vascular endothelial growth factor (VEGF)-VEGF receptor (VEGFR) pathway has a pivotal importance in angiogenesis, and has therefore become a prime target in antitumor therapy. In search for peptides antagonizing VEGF binding to its receptors, we screened a random heptamer library displayed on phage for peptides that bind the whole VEGF₁₆₅ molecule and inhibit VEGF dependent human umbilical vein endothelial cell (HUVEC) proliferation. Two selected peptides with sequences WHLPFKC and WHKPFRF were synthesized. Biacore and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry analysis indicated that these peptides bind the VEGF homodimer in a concentration-dependent manner, with micromolar affinity, and with a 2:1 peptide: VEGF stoichiometry. They inhibited HUVEC proliferation in vitro by 77 and 55%, respectively. Taken together, our results indicate that these peptides could be potent inhibitors of angiogenesis. Furthermore, we show that the peptide-VEGF binding properties can be quantified, a prerequisite for the further optimization of binders.     

Regulatory NK cells suppress antigen-specific T cell responses

The immune system has a variety of regulatory/suppressive processes, which are decisive for the development of a healthy or an allergic immune response to allergens. NK1 and NK2 subsets have been demonstrated to display counterregulatory and provocative roles in immune responses, similar to Th1 and Th2 cells. T regulatory cells suppressing both Th1 and Th2 responses have been the focus of intensive research during the last decade. In this study, we aimed to investigate regulatory NK cells in humans, by characterization of NK cell subsets according to their IL-10 secretion property. Freshly purified IL-10-secreting NK cells expressed up to 40-fold increase in IL-10, but not in the FoxP3 and TGF-beta mRNAs. PHA and IL-2 stimulation as well as vitamin D3/dexamethasone and anti-CD2/CD16 mAbs are demonstrated to induce IL-10 expression in NK cells. The effect of IL-10+ NK cells on Ag-specific T cell proliferation has been examined in bee venom major allergen, phospholipase A2- and purified protein derivative of Mycobecterium bovis-induced T cell proliferation. IL-10+ NK cells significantly suppressed both allergen/Ag-induced T cell proliferation and secretion of IL-13 and IFN-gamma, particularly due to secreted IL-10 as demonstrated by blocking of the IL-10 receptor. These results demonstrate that a distinct small fraction of NK cells display regulatory functions in humans.