LncRNA MALAT1 Modulates TGF-ß1-Induced EMT in Keratinocyte.

One of the major complications in diabetes is impaired wound healing. Unfortunately, effective therapies are currently lacking. Epithelial to mesenchymal transition (EMT) is a critical process involved in cutaneous wound healing. In response to injury, EMT is required to activate and mobilize stationary keratinocytes in the skin toward the wound bed, which allows for re-epithelialization. This process is stalled in diabetic wounds. In this study, we investigate the role of long non-coding RNA (lncRNA), MALAT1, in transforming growth factor beta 1(TGF-ß1)-induced EMT of human keratinocyte (HaCaT) cells. Initially, we detected MALAT1 and TGF-ß1 expression in non-diabetic and diabetic wounds and found that these expression are significantly up-regulated in diabetic wounds. Then, HaCaT cells were cultured and exposed to TGF-ß1. The EMT of HaCaT cells were confirmed by the increased expression of CDH2, KRT10, and ACTA2, in addition to the down-regulation of CDH1. Knockdown of MALAT1 was achieved by transfecting a small interfering RNA (SiRNA). MALAT1 silencing attenuates TGFß1-induced EMT. Mechanistically, MALAT1 is involved in TGF-ß1 mediated EMT through significantly induced ZEB1 expression, a critical transcription factor for EMT. In summary, lncRNA MALAT1 is involved in TGFß1-induced EMT of human HaCaT cells and provides new understanding for the pathogenesis of diabetic wounds.

Comparison of Descemet stripping under continuous air flow, manual air injection and balanced salt solution for DMEK: a pilot study.

BACKGROUND: Descemet's membrane endothelial keratoplasty (DMEK) involves removal of the recipient's Descemet membrane (DM) prior to transplanting the donor's DM. When using balanced salt solution (BSS) or ophthalmic viscosurgical devices (OVDs), visualization of the host's DM during its stripping may be inadequate and may result in Descemet remnants and could lead to sub-optimal surgical results. Previous articles described excellent visualization when utilizing air injection but this requires repeated air injection into the anterior chamber (AC). We present a pilot study that compares different techniques under which DM stripping can be performed: with continuous automated air infusion, with manual air infusion, and with BSS. METHODS: We retrospectively compared video footage of DM stripping with BSS, with continuous air and with manual injection of air into the AC to determine DM stripping duration and the number of times the surgeon had to insert and retrieve a surgical instrument from the AC. RESULTS: Thirty videos of 10 consecutive cases of the three DM stripping techniques were evaluated. DM stripping duration was 3.26 (±1.32), 3.92 (±1.2) and 12.9 (±3.98) minutes for BSS, continuous air flow, and manual air injection, respectively. Frequency of instrument retrieval (FIR) was 3.6 (±1.71), 1.5 (±0.71) and 15.1 (±3.28) for BSS, continuous air flow, and manual air injection, respectively. Continuous air flow and BSS were both statistically different than manual air injection into the AC (p < 0.05), but did not differ from one another statistically. CONCLUSION: DM stripping during posterior lamellar surgery is imperative for favorable post-operative results and prevention of complications. Performing this step under air in the AC contributes to better visualization and an efficient surgery.

[Galleria mellonella larva model in evaluating the effects of biofilm in Candida albicans]. / Candida albicans biyofilm etkilerinin degerlendirilmesinde Galleria mellonella larvasi modeli.

Biofilm-related infections are chronic infections that cause serious increase in morbidity and mortality as well as significant economic loss. Galleria mellonella larva is shown as a reliable animal model for in vivo toxicology and pathogenicity tests due to its large size, ease of practice, ability to survive at 15-37°C and its similarity to mammals' natural immune system. The aim of this study was to evaluate the effects biofilm activity of Candida albicans in a G.mellonella larva model. Two C.albicans strains isolated as a disease agent were used for the model, where one was positive (BP), and the other one was negative (BN) for biofilm production. Eighty healthy G.mellonella larvae, all in the last larval stage and 2-2.5 cm long, were divided into 4 groups of equal size. Group 1 was set as the control group. Group 2 was injected with sterile phosphate buffer (PBS) group. Group 3 was injected with BP C.albicans strain and group 4 with BN C.albicans strain. A 5 µL volume of C.albicans prepared at 5 × 105 cfu/ml concentration with PBS was injected into the last left rear-legs of the larvae. The larvae were kept in sterile petri dishes at 37°C. They were observed for a total of 96 hours, for 4 hours in the first 24 hours, then in 12 hours intervals. Melanization, survival, total hemocyte count and fungal burden were evaluated as infection indicators. Melanization and death were not observed throughout the study period in group 1. One larva died in group 2. Small melanization spots (dark spots) and subsequent progressive melanization were observed from 3rd hour in the larvae infected with C.albicans. When compared with the BN C.albicans infected group, survival rate was 20% for BP C.albicans infected larvae at the end of 24 hours. Total hemocyte count was very low in the infected groups compared to groups 1 and 2, also significantly lower in group 3 than in group 4. In quantitative cultures, growth of C.albicans was detected in groups 3 and 4 while not in groups 1 and 2. Fungal load was significantly higher in BP C.albicans infected group than BN C.albicans infected group. In this study, G.mellonella larvae were used as live hosts to demonstrate the effects of biofilm activity of C.albicans. Our results suggest that larval models can be used to investigate the effects of fungal infections and biofilm like virulence factors on host cells, and invertebrate animal models can be widely used and can bridge between in vitro studies and mammalian models.

Validation of the EORTC QLQ-BIL21 questionnaire for measuring quality of life in patients with cholangiocarcinoma and cancer of the gallbladder.

BACKGROUND: There is no specific quality of life (QoL) measurement tool to quantify QoL in patients with biliary tract cancer. Quality of life measurement is an increasingly crucial trial end point and is now being incorporated into clinical practice. METHODS: This International Multicentre Phase IV Validation Study assessed the QLQ-BIL21 module in 172 patients with cholangiocarcinoma and 91 patients with cancer of the gallbladder. Patients completed the questionnaire at baseline pretherapy and subsequently at 2 months. Following this, the psychometric properties of reliability, validity, scale structure and responsiveness to change were analysed. RESULTS: Analysis of the QLQ-BIL21 scales showed appropriate reliability with Cronbach's α-coefficients >0.70 for all scales overall. Intraclass correlations exceeded 0.80 for all scales. Convergent validity >0.40 was demonstrated for all items within scales, and discriminant validity was confirmed with values <0.70 for all scales compared with each other. Scale scores changed in accordance with Karnofsky performance status and in response to clinical change. CONCLUSIONS: The QLQ-BIL21 is a valid tool for the assessment of QoL in patients with cholangiocarcinoma and cancer of the gallbladder.

Global motions exhibited by proteins in micro- to milliseconds simulations concur with anisotropic network model predictions.

The Anton supercomputing technology recently developed for efficient molecular dynamics simulations permits us to examine micro- to milli-second events at full atomic resolution for proteins in explicit water and lipid bilayer. It also permits us to investigate to what extent the collective motions predicted by network models (that have found broad use in molecular biophysics) agree with those exhibited by full-atomic long simulations. The present study focuses on Anton trajectories generated for two systems: the bovine pancreatic trypsin inhibitor, and an archaeal aspartate transporter, GltPh. The former, a thoroughly studied system, helps benchmark the method of comparative analysis, and the latter provides new insights into the mechanism of function of glutamate transporters. The principal modes of motion derived from both simulations closely overlap with those predicted for each system by the anisotropic network model (ANM). Notably, the ANM modes define the collective mechanisms, or the pathways on conformational energy landscape, that underlie the passage between the crystal structure and substates visited in simulations. In particular, the lowest frequency ANM modes facilitate the conversion between the most probable substates, lending support to the view that easy access to functional substates is a robust determinant of evolutionarily selected native contact topology.

[Evaluation of the Relationship Between Microenvironment and Biofilm and Coagulase Responses of Staphylococcus aureus Strains Under the Effect of Gentamicin]. / Gentamisin Etkisi Altindaki Staphylococcus aureus Suslarinin Biyofilm ve Koagülaz Yanitlari ile Mikroçevre Iliskisinin Degerlendirilmesi.

The frequency of infections caused by Staphylococcus aureus strains and the rate of antibiotic resistance among these strains are gradually increasing. Accordingly, serious problems emerge in the treatment of community or hospital acquired S.aureus infections. This study was aimed to determine the role of MIC and sub-MIC concentrations of gentamicin on biofilm and coagulase forming effects of S.aureus in in vitro test systems and cell cultures. A standard S.aureus ATCC 25923 strain and two clinical S.aureus strains isolated from blood cultures (C1 and C2) were included in the study. Gentamicin MIC values of the strains were determined with microdilution method at the cation-adjusted Mueller Hinton broth according to CLSI standards. For each strain, MIC, 50% MIC and 25% MIC values of gentamicin were determined separately. At the determined MIC values, biofilm formations of strains were determined with crystal violet method spectrophotometrically. Also, coagulase activities of the strains were evaluated in glass tubes. Human origin epithelial cell cultures namely HEp-2 cell lines, were infected with the standard and clinical S.aureus strains (Multiplicity of infection: 50/1) and left for incubation for two hours. After all, MIC, 50% MIC and 25% MIC values of gentamicin, were added to infected cell lines and incubated for 18 hours. Cells were blown up with distilled water and then bacteria were collected. Biofilm formation and coagulase production of these bacteria were evaluated. When S.aureus ATCC 25923 strain and C1 strains' biofilm formation was evaluated before (in vitro) and after incubation in cell culture, no difference was observed. However in C2 strain, under the effect of MIC level gentamicin, biofilm formation was occurred after interaction with the cell. In the same way, when coagulase responses were evaluated, after interaction with the cell, coagulase production of C2 strain was inhibited. These results indicated that, phenotypic characteristics such as biofilm formation and coagulase production might change during the process of bacterial adaptation to microenvironment. Further advanced experimental modelling designed with different combinations of antibiotics and different cell lines may provide data about the causes and timing of these phenotypic changes and shed light on the development of new treatment policies.

Cellular and Molecular Mechanisms of Pathogenesis Underlying Inherited Retinal Dystrophies.

Inherited retinal dystrophies (IRDs) are congenital retinal degenerative diseases that have various inheritance patterns, including dominant, recessive, X-linked, and mitochondrial. These diseases are most often the result of defects in rod and/or cone photoreceptor and retinal pigment epithelium function, development, or both. The genes associated with these diseases, when mutated, produce altered protein products that have downstream effects in pathways critical to vision, including phototransduction, the visual cycle, photoreceptor development, cellular respiration, and retinal homeostasis. The aim of this manuscript is to provide a comprehensive review of the underlying molecular mechanisms of pathogenesis of IRDs by delving into many of the genes associated with IRD development, their protein products, and the pathways interrupted by genetic mutation.

Formation of protein adducts with Hydroperoxy-PE electrophilic cleavage products during ferroptosis.

Ferroptosis is an iron dependent form of cell death, that is triggered by the discoordination of iron, lipids, and thiols. Its unique signature that distinguishes it from other forms of cell death is the formation and accumulation of lipid hydroperoxides, particularly oxidized forms of polyunsaturated phosphatidylethanolamines (PEs), which drives cell death. These readily undergo iron-catalyzed secondary free radical reactions leading to truncated products which retain the signature PE headgroup and which can readily react with nucleophilic moieties in proteins via their truncated electrophilic acyl chains. Using a redox lipidomics approach, we have identified oxidatively-truncated PE species (trPEox) in enzymatic and non-enzymatic model systems. Further, using a model peptide we demonstrate adduct formation with Cys as the preferred nucleophilic residue and PE(26:2) +2 oxygens, as one of the most reactive truncated PE-electrophiles produced. In cells stimulated to undergo ferroptosis we identified PE-truncated species with sn-2 truncations ranging from 5 to 9 carbons. Taking advantage of the free PE headgroup, we have developed a new technology using the lantibiotic duramycin, to enrich and identify the PE-lipoxidated proteins. Our results indicate that several dozens of proteins for each cell type, are PE-lipoxidated in HT-22, MLE, and H9c2 cells and M2 macrophages after they were induced to undergo ferroptosis. Pretreatment of cells with the strong nucleophile, 2-mercaptoethanol, prevented the formation of PE-lipoxidated proteins and blocked ferroptotic death. Finally, our docking simulations showed that the truncated PE species bound at least as good to several of the lantibiotic-identified proteins, as compared to the non-truncated parent molecule, stearoyl-arachidonoyl PE (SAPE), indicating that these oxidatively-truncated species favor/promote the formation of PEox-protein adducts. The identification of PEox-protein adducts during ferroptosis suggests that they are participants in the ferroptotic process preventable by 2-mercaptoethanol and may contribute to a point of no return in the ferroptotic death process.

[Experimental oral candidiasis in healthy and immunocompromised BALB/c mice]. / Saglikli ve Immün Sistemi Baskilanmis BALB/c Farelerde Deneysel Oral Kandidiyaz.

Oral candidiasis which is the most common type of Candida infections affecting humans, is most frequently caused by C.albicans. Immune response of the host, as well as a variety of virulence factors of the causative agent, play important roles in the development of Candida infections. The colonization rate of Candida in the oral cavity of healthy individuals, is between 25-30%, however, this rate is reported to be increased in immunosuppressive subjects. In our study, we established an oral candidiasis model with C.albicans in healthy and experimentally immunocompromised mice and aimed to compare Candida colonization rates and histopathological changes occurred in the tongue and esophagus tissues of the animal groups. A total of 21 BALB/c mice were grouped as control (Group 1; n= 7), healthy (Group 2; n= 7) and immunocompromised (Group 3; n= 7) groups. Immunosuppression in mice was performed by subcutaneous injection of prednisolone. For experimental oral candidiasis, cotton swab impregnated with C.albicans strains which did not have acid proteinase and phospholipase enzyme activity, no biofilm production, and sensitive to fluconazole and amphotericin B, were used. In the control group, physiological saline solution was used instead of C.albicans strain. In the forth day of experimental oral candidiasis model swab samples taken from the dorsal tongue surface of mice were evaluated by quantitative cultivation method. No yeast colonies were detected in Group 1 while more significant number of yeast colonies were observed in Group 3 compared to Group 2 (p= 0.002). Tongue and esophagus tissues of mice were stained with hematoxylin-eosin and periodic acid schiff staining and evaluated in terms of inflammatory response, abscess formation, vascular congestion, vasodilation and for the presence of yeast and hyphae. When the inflammation in esophagus was considered, statistically significant difference was determined between group 1 and group 3 (p= 0.023), however, no difference was detected between group 2 and 3 (p= 0.107). The level of inflammation in tongue tissue exhibited no difference between groups 2 and 3 (p= 0.317) while the difference was significant when these groups were compared to the control group (p= 0.00, p= 0.002, respectively). Similarly, the level of congestion in tongue tissue exhibited no difference between groups 2 and 3, however, the difference was significant when compared to the control group. To enlighten the relation between host immune status and oral candidiasis caused by C. albicans, further larger-scale studies also concerning the various virulence factors of the infectious agent, should be conducted by the use of experimental animal models which may successfully guide us in this regard.

[Comparison of different antifungal treatment regimens for experimental Candida endophthalmitis in rabbit models]. / Tavsanlarda olusturulan deneysel Candida endoftalmisinde farkli tedavi seçeneklerinin karsilastirilmasi.

The aim of this study was to evaluate the treatment options of experimental in-vivo Candida endophthalmitis. For inoculation, a 0.1 ml of suspension of Candida albicans was injected into the vitreous of the right eye of each New Zealand rabbit. On the 15th day, the clinical evaluation for the resultant endophthalmitis was noted, and vitreous samples were obtained. On the 21st day, culture positive eyes were divided into four groups in terms of treatment modalities. Group 1 (n = 7) received intravitreal amphotericin B injection, group 2 (n = 8) received both intravitreal dexamethasone and amphotericin B injections, group 3 (n = 8) underwent pars plana vitrectomy (PPV) and amphotericin B injection, and group 4 (n = 8) underwent PPV and both amphotericin B and silicone oil injections. The vitreous samples obtained from right eyes of the rabbits on the 15th day, were all culture positive for Candida albicans. On the 35th day, the least colony counts (colony forming unit) were present in eyes that received only intravitreal amphotericin B injection in group 1, followed by group 4 that underwent PPV and both amphotericin B and silicone oil injections. In Candida endophthalmitis, intravitreal injection of amphotericin B without steroid appears to be the primary choice of therapy. In cases who fail to respond to this regimen alone, PPV in combination with silicone oil injection may be considered. Benefit-risk ratio should be cautiously interpreted for application of intravitreal steroid injection.

Iron catalysis of lipid peroxidation in ferroptosis: Regulated enzymatic or random free radical reaction?

Duality of iron as an essential cofactor of many enzymatic metabolic processes and as a catalyst of poorly controlled redox-cycling reactions defines its possible biological beneficial and hazardous role in the body. In this review, we discuss these two "faces" of iron in a newly conceptualized program of regulated cell death, ferroptosis. Ferroptosis is a genetically programmed iron-dependent form of regulated cell death driven by enhanced lipid peroxidation and insufficient capacity of thiol-dependent mechanisms (glutathione peroxidase 4, GPX4) to eliminate hydroperoxy-lipids. We present arguments favoring the enzymatic mechanisms of ferroptotically engaged non-heme iron of 15-lipoxygenases (15-LOX) in complexes with phosphatidylethanolamine binding protein 1 (PEBP1) as a catalyst of highly selective and specific oxidation reactions of arachidonoyl- (AA) and adrenoyl-phosphatidylethanolamines (PE). We discuss possible role of iron chaperons as control mechanisms for guided iron delivery directly to their "protein clients" thus limiting non-enzymatic redox-cycling reactions. We also consider opportunities of loosely-bound iron to contribute to the production of pro-ferroptotic lipid oxidation products. Finally, we propose a two-stage iron-dependent mechanism for iron in ferroptosis by combining its catalytic role in the 15-LOX-driven production of 15-hydroperoxy-AA-PE (HOO-AA-PE) as well as possible involvement of loosely-bound iron in oxidative cleavage of HOO-AA-PE to oxidatively truncated electrophiles capable of attacking nucleophilic targets in yet to be identified proteins leading to cell demise.

Survey of the analysis of continuous conformational variability of biological macromolecules by electron microscopy.

Single-particle analysis by electron microscopy is a well established technique for analyzing the three-dimensional structures of biological macromolecules. Besides its ability to produce high-resolution structures, it also provides insights into the dynamic behavior of the structures by elucidating their conformational variability. Here, the different image-processing methods currently available to study continuous conformational changes are reviewed.

Structure-derived potentials and protein simulations.

There has recently been an explosion in the number of structure-derived potential functions that are based on the increasing number of high-resolution protein crystal structures. These functions differ principally in their reference states; the usual two classes correspond either to initial solvent exposure or to residue exposure of residues. Reference states are critically important for applications of these potentials functions. Inspection of the potential functions and their derivation can tell us not only about protein interaction strengths themselves, but can also provide suggestions for the design of better folding simulations. An appropriate goal in this field is achieving self-consistency between the details in the derivation of potentials and the applied simulations.

Serum cytokine levels in active uveitis and remission.

Serum levels of interleukin(IL)-8, IL-6, and (TNF)-alpha were measured in 25 patients during active uveitis and uveitis in remission and compared to age-matched controls. Levels of IL-8 and IL-6 were significantly elevated in patients with active disease and were decreased during remission. IL-8 levels were highest in patients with anterior uveitis, with greatest difference between active disease and remission. No consistent pattern was observed for TNF-alpha. In conclusion, serum cytokine levels are elevated in active noninfectious uveitis. The rise in IL-8 may suggest innate immune mechanisms in the acute disease, while IL-6 participates in modulation of inflammation in the chronic disease.

Allosteric changes in protein structure computed by a simple mechanical model: hemoglobin T<-->R2 transition.

Information on protein dynamics has been usually inferred from spectroscopic studies of parts of the proteins, or indirectly from the comparison of the conformations assumed in the presence of different substrates or ligands. While molecular simulations also provide information on protein dynamics, they usually suffer from incomplete sampling of conformational space, and become prohibitively expensive when exploring the collective dynamics of large macromolecular structures. Here, we explore the dynamics of a well-studied allosteric protein, hemoglobin (Hb), to show that a simple mechanical model based on Gaussian fluctuations of residues can efficiently predict the transition between the tense (T, unliganded) and relaxed (R or R2, O(2) or CO-bound) forms of Hb. The passage from T into R2 is shown to be favored by the global mode of motion, which, in turn is driven by entropic effects. The major difference between the dynamics of the T and R2 forms is the loss of the hinge-bending role of alpha(1)-beta(2) (or alpha(2)-beta(1)) interfacial residues at alpha Phe36-His45 and beta Thr87-Asn102 in the R2 form, which implies a decreased cooperativity in the higher affinity (R2) form of Hb, consistent with many experimental studies. The involvement of the proximal histidine beta His92 in this hinge region suggests that the allosteric propagation of the local structural changes (induced upon O(2) binding) into global ones occur via hinge regions. This is the first demonstration that there is an intrinsic tendency of Hb to undergo T-->R2 transition, induced by purely elastic forces of entropic origin that are uniquely defined for the particular contact topology of the T form.

Inter-residue potentials in globular proteins and the dominance of highly specific hydrophilic interactions at close separation.

Residue-specific potentials between pairs of side-chains and pairs of side-chain-backbone interaction sites have been generated by collecting radial distribution data for 302 protein structures. Multiple atomic interactions have been utilized to enhance the specificity and smooth the distance-dependence of the potentials. The potentials are demonstrated to successfully discriminate correct sequences in inverse folding experiments. Many specific effects are observable in the non-bonded potentials; grouping of residue types is inappropriate, since each residue type manifests some unique behavior. Only a weak dependence is seen on protein size and composition. Effective contact potentials operating in three different environments (self, solvent-exposed and residue-exposed) and over any distance range are presented. The effective contact potentials obtained from the integration of radial distributions over the distance interval r < or = 6.4 A are in excellent agreement with published values. The hydrophobic interactions are verified to be dominantly strong in this range. Comparison of these with a newly derived set of effective contact potentials for closer inter-residue separations (r < or = 4.0 A) demonstrates drastic changes in the most favorable interactions. In the closer approach case, where the number of pairs with a given residue is approximately one, the highly specific interactions between charged and polar side-chains predominate. These closer approach values could be utilized to select successively the relative positions and directions of residue side-chains in protein simulations, following a hierarchical algorithm optimizing side-chain-side-chain interactions over the two successively closer distance ranges. The homogeneous contribution to stability is stronger than the specific contribution by about a factor of 5. Overall, the total non-bonded interaction energy calculated for individual proteins follows a dependence on the number of residues of the form of n1.28, indicating an enhanced stability for larger proteins.

Vibrational dynamics of transfer RNAs: comparison of the free and synthetase-bound forms.

The vibrational dynamics of transfer RNAs, both free, and complexed with the cognate synthetase, are analyzed using a model (Gaussian network model) which recently proved to satisfactorily describe the collective motions of folded proteins. The approach is similar to a normal mode analysis, with the major simplification that no residue specificity is taken into consideration, which permits us (i) to cast the problem into an analytical form applicable to biomolecular systems including about 10(3 )residues, and (ii) to acquire information on the essential dynamics of such large systems within computational times at least two orders of magnitude shorter than conventional simulations. On a local scale, the fluctuations calculated for yeast tRNAPhe and tRNAAsp in the free state, and for tRNAGln complexed with glutaminyl-tRNA synthetase (GlnRS) are in good agreement with the corresponding crystallographic B factors. On a global scale, a hinge-bending region comprising nucleotides U8 to C12 in the D arm, G20 to G22 in the D loop, and m7G46 to C48 in the variable loop (for tRNAPhe), is identified in the free tRNA, conforming with previous observations. The two regions subject to the largest amplitude anticorrelated fluctuations in the free form, i.e. the anticodon region and the acceptor arm are, at the same time, the regions that experience the most severe suppression in their flexibilities upon binding to synthetase, suggesting that their sampling of the conformational space facilitates their recognition by the synthetase. Likewise, examination of the global mode of motion of GlnRS in the complex indicates that residues 40 to 45, 260 to 270, 306 to 314, 320 to 327 and 478 to 485, all of which cluster near the ATP binding site, form a hinge-bending region controlling the cooperative motion, and thereby the catalytic function, of the enzyme. The distal beta-barrel and the tRNA acceptor binding domain, on the other hand, are distinguished by their high mobilities in the global modes of motion, a feature typical of recognition sites, also observed for other proteins. Most of the conserved bases and residues of tRNA and GlnRS are severely constrained in the global motions of the molecules, suggesting their having a role in stabilizing and modulating the global motion.

Collective motions in HIV-1 reverse transcriptase: examination of flexibility and enzyme function.

In order to study the inferences of structure for mechanism, the collective motions of the retroviral reverse transcriptase HIV-1 RT (RT) are examined using the Gaussian network model (GNM) of proteins. This model is particularly suitable for elucidating the global dynamic characteristics of large proteins such as the presently investigated heterodimeric RT comprising a total of 982 residues. Local packing density and coordination order of amino acid residues is inspected by the GNM to determine the type and range of motions, both at the residue level and on a global scale, such as the correlated movements of entire subdomains. Of the two subunits, p66 and p51, forming the RT, only p66 has a DNA-binding cleft and a functional polymerase active site. This difference in the structure of the two subunits is shown here to be reflected in their dynamic characteristics: only p66 has the potential to undergo large-scale cooperative motions in the heterodimer, while p51 is essentially rigid. Taken together, the global motion of the RT heterodimer is comprised of movements of the p66 thumb subdomain perpendicular to those of the p66 fingers, accompanied by anticorrelated fluctuations of the RNase H domain and p51 thumb, thus providing information about the details of one processivity mechanism. A few clusters of residues, generally distant in sequence but close in space, are identified in the p66 palm and connection subdomains, which form the hinge-bending regions that control the highly concerted motion of the subdomains. These regions include the catalytically active site and the non-nucleoside inhibitor binding pocket of p66 polymerase, as well as sites whose mutations have been shown to impair enzyme activity. It is easily conceivable that this hinge region, indicated by GNM analysis to play a critical role in modulating the global motion, is locked into an inactive conformation upon binding of an inhibitor. Comparative analysis of the dynamic characteristics of the unliganded and liganded dimers indicates severe repression of the mobility of the p66 thumb in RT's global mode, upon binding of non-nucleoside inhibitors.

Molecular characterization of TEM- and SHV-derived extended-spectrum beta-lactamases in hospital-based Enterobacteriaceae in Turkey.

TEM- and SHV-derived extended-spectrum beta-lactamases (ESBLs) producing Enterobacteriaceae have been reported from throughout the world, but there has been limited data for the molecular characterization of these enzymes in Turkey. The aim of this study was to investigate and to type the TEM- and SHV-derived ESBLs in 63 ESBL-producing clinical isolates of Enterobacteriaceae, and it included further analysis; transfer experiments, isoelectric focusing, PCR, PCR-restriction fragment length polymorphism, and DNA sequencing. According to PCR results the transconjugant strains included 52.7% TEM, 74.3% SHV, and 32.4% of both the TEM and SHV genes. Using PCR/NheI restriction analysis, 45 of the 46 ESBL detected in transconjugants were determined to be SHV-derived. DNA sequencing was performed for the identification of TEM- and SHV-derived ESBLs for 18 selected transconjugants. SHV-2, SHV-5, and SHV-12 were detected in five, seven, and five samples, respectively. This is the first description of SHV-12 in Turkey.

Effects of non toxic doses of acyclovir on nitric oxide and cellular death responses in herpesvirus types 1 and 2 infected hep-2 cells.

Herpes simplex virus type-1 (HSV-1) and type-2 (HSV-2) are among the most "successful" pathogens and code for a variety of proteins to direct the apoptosis/necrosis responses of the cells they infect. Nitric oxide (NO) is an important intracellular signaling molecule in pathological processes. Acyclovir (ACV) is a chain terminator that targets the viral DNA polymerase as an antiviral agent. In this study, NO signals, and apoptosis/necrosis responses of HEp-2 cells were compared when infected by HSV-1 and -2 for 24 hours against non toxic doses (starting from 48.8, 24.4, 12.2, 6.1, 3 to 1.5 microg/mL) of ACV. In 48.8, 24.4 and 12.2 microg/mL of ACV, HSV-1 had an "upregulating effect" whereas HSV-2 had a "downregulating effect" on NO production, and in 6.1, 3 and 1.5 microg/mL of ACV HSV-1 had a "down-regulating effect" whereas HSV-2 had an "upregulating effect" on NO responses (HSV-1 had a "downregulating effect" on NO production whereas HSV-2 had an "upregulating effect" on NO production without any ACV). In 48.8, 24.4 and 12.2 microg/mL of ACV, HSV-1 had an "anti-apoptotic effect" whereas HSV-2 had a stimulation on "apoptotic effect", and in 6.1, 3 and 1.5 microg/mL of ACV HSV-1 had an "apoptotic effect" and HSV-2 turned to "its natural viral apoptotic effect level" (HSV-1 had an "natural viral apoptotic effect" whereas HSV-2 had a "natural viral apoptotic effect" on apoptosis response without any ACV). In 48.8, and 24.4 microg/mL of ACV, HSV-1 had significant "necrotic effect" on necrotic cellular death, "necrosis" increased in 12.2, 6.1, 3 and 1.5 microg/mL of ACV (HSV-1 had a negligible "necrotic effect" on HEp-2 cells alone), and HSV-2 had a "natural viral necrotic effect" alone; and also in all non toxic ACV concentrations. These results showed that HSV-1 and -2 had different "strategies" on apoptosis/necrosis and NO with and without non toxic ACV. These differences deserve further studies in order to explain the interactions between apoptotic/anti apoptotic, necrotic genes and NO, and ACV in HSV-1 and HSV-2 infections respectively.