Complete genome sequences and characteristics of mycobacteriophages Diminimus, Dulcita, Glaske16, and Koreni.

Complete genome sequences of four novel mycobacteriophages, Diminimus, Dulcita, Glaske16, and Koreni, isolated from soil are presented. All these bacteriophages belong to subcluster M1, except Koreni that belongs to subcluster A4. Moreover, all have siphovirus morphologies, with genome sizes ranging from 51,055 to 81,156 bp.

The effect of non-oncology drugs on clinical and genomic risk in early luminal breast cancer.

BACKGROUND: An effect of non-oncology medications on cancer outcome has been proposed. In this study, we aimed to systematically examine the impact of commonly prescribed non-oncology drugs on clinical risk and on the genomic risk [based on the Oncotype DX recurrence score (RS)] in early breast cancer (BC). EXPERIMENTAL DESIGN: We collected data on clinical risk (stage and grade), genomic risk (Oncotype DX RS), and on non-oncology medications administered to 1423 patients with estrogen receptor-positive human epidermal growth factor receptor 2-negative BC during the month of their surgery. The influence of various medications on clinical and genomic risks was evaluated by statistical analysis. RESULTS: Out of the multiple drugs we examined, levothyroxine was significantly associated with a high Oncotype DX RS (mean 24.78; P < 0.0001) and metformin with a low Oncotype DX RS (mean 14.87; P < 0.01) compared with patients not receiving other non-oncology drugs (mean 18.7). By contrast, there were no differences in the clinical risk between patients receiving metformin, levothyroxine, or no other non-oncology drugs. Notably, there was no association between the consumption of levothyroxine and metformin and proliferation marker (Ki67) levels, but both drugs were significantly associated with progesterone-related features, suggesting that they influence genomic risk through estrogen-dependent signaling. CONCLUSIONS: The results of this study indicate a significant impact of metformin and levothyroxine on clinical decisions in luminal BC, with potential impact on the clinical course of these patients.

The complex impact of five years of stress related to life-threatening events on pregnancy outcomes: a preliminary retrospective study.

OBJECTIVE: To study the impact of chronic, life-threatening stressors in the form of daily missile attacks, for five consecutive years, on pregnancy outcomes. METHOD: Charts of deliveries from two neighboring towns in the south of Israel, covering the years 2000 and 2003-2008, were reviewed retrospectively. One city had been exposed to missile attacks, while the other was not. For each year, 100 charts were chosen at random. RESULTS: Significant association was found between exposure to stress and frequency of pregnancy complications (P=0.047) and premature membrane rupture (P=0.029). A more detailed analysis, based on dividing the stressful years into three distinct periods: early (2003-2004), intermediate (2005-2006) and late (2007-2008), revealed that preterm deliveries were significantly more frequent (P=0.044) during the intermediate period, as was premature membrane rupture during the late period (P=0.014). CONCLUSION: Exposure to chronic life-threatening stress resulted in more pregnancy complications and in particular more premature membrane ruptures. The impact was most significant during the middle period of the 5-year-exposure to the stressor. Hence it seems that factors of duration and habituation may play a role in the impact of chronic, life-threatening stressors on pregnancy.

Inhibition of Photosystem II activity by saturating single turnover flashes in calcium-depleted and active Photosystem II.

Inhibition of Photosystem II (PS II) activity induced by continuous light or by saturating single turnover flashes was investigated in Ca(2+)-depleted, Mn-depleted and active PS II enriched membrane fragments. While Ca(2+)- and Mn-depleted PS II were more damaged under continuous illumination, active PS II was more susceptible to flash-induced photoinhibition. The extent of photoinactivation as a function of the duration of the dark interval between the saturating single turnover flashes was investigated. The active centres showed the most photodamage when the time interval between the flashes was long enough (32 s) to allow for charge recombination between the S(2) or S(3) and Q(B) (-) to occur. Illumination with groups of consecutive flashes (spacing between the flashes 0.1 s followed by 32 s dark interval) resulted in a binary oscillation of the loss of PS II-activity in active samples as has been shown previously (Keren N, Gong H, Ohad I (1995), J Biol Chem 270: 806-814). Ca(2+)- and Mn-depleted PS II did not show this effect. The data are explained by assuming that charge recombination in active PS II results in a back reaction that generates P(680) triplet and thence singlet oxygen, while in Ca(2+)- and Mn-depleted PS II charge recombination occurs through a different pathway, that does not involve triplet generation. This correlates with an up-shift of the midpoint potential of Q(A) in samples lacking Ca(2+) or Mn that, in term, is predicted to result in the triplet generating pathway becoming thermodynamically less favourable (G.N. Johnson, A.W. Rutherford, A. Krieger, 1995, Biochim. Biophys. Acta 1229, 201-207). The diminished susceptibility to flash-induced photoinhibition in Ca(2+)- and Mn-depleted PS II is attributed at least in part to this mechanism.

Photosystem II activity and turnover of the D1 protein are impaired in the psbA Y112L mutant of Synechocystis PCC6803 sp.

Site-directed psbA mutants at the tyrosine Y112 position have been generated in Synechocystis PCC6803 cells. The mutation Y112F does not affect photosystem II (PSII) activity as compared with control 4 delta 1K cells. However, the Y112L mutant exhibits a photosynthetically impaired phenotype. PSII activity is not detectable in this mutant when grown at 30 mumol photons m-2 s-1, while low levels of the D1 and D2 proteins and oxygen evolution activity are present in the mutant cells grown at a low light intensity (0.5-1 mumol m-2 s-1). The recombination of the QB-/S2,3 states of PSII in the Y112L mutant cells as detected by thermoluminescence (TL) is altered. The TL signal emission maximum of these cells due to charge recombination of the S2,3/QB- occurs at 20 degrees C as compared to 35-40 degrees C for the wild-type cells, indicating a possible change in the S2,3/Yz equilibrium. The Y112L mutant cells are rapidly photoinactivated and impaired in the recovery of the PSII activity. These results suggest that replacement of the aromatic residue at position Y112 by a hydrophobic amino acid may alter the function of the donor-side activity and affects the degradation and replacement of the PSII core proteins.

Use of failure rate databases and process safety performance measurements to improve process safety.

Employing equipment reliability databases can generate a process of continual improvement. This paper suggests a methodology that uses equipment reliability databases, and a process of benchmarking to establish a continual improvement procedure by learning "how others are doing it". A simple decision-making procedure is suggested too, to assist in prioritizing the processes/equipment that are considered to be improved as well as a methodology to measure the improvement.

Development of a safety decision-making scenario to measure worker safety in agriculture.

Human factors play an important role in the management of occupational safety, especially in high-hazard workplaces such as commercial grain-handling facilities. Employee decision-making patterns represent an essential component of the safety system within a work environment. This research describes the process used to create a safety decision-making scenario to measure the process that grain-handling employees used to make choices in a safety-related work task. A sample of 160 employees completed safety decision-making simulations based on a hypothetical but realistic scenario in a grain-handling environment. Their choices and the information they used to make their choices were recorded. Although the employees emphasized safety information in their decision-making process, not all of their choices were safe choices. Factors influencing their choices are discussed, and implications for industry, management, and workers are shared.

Measurement of worker perceptions of trust and safety climate in managers and supervisors at commercial grain elevators.

The safety climate of an agricultural workplace may be affected by several things, including the level of trust that workers have in their work group supervisor and organizational management. Safety climate has been used by previous safety researchers as a measure of worker perceptions of the relative importance of safety as compared with other operational goals. Trust has been linked to several positive safety outcomes, particularly in hazardous work environments, but has not been examined relative to safety climate in the perennially hazardous work environment of a commercial grain elevator. In this study, 177 workers at three Midwest grain elevator companies completed online surveys measuring their perceptions of trust and safety at two administrative levels: organizational management and work group supervisors. Positive and significant relationships were noted between trust and safety climate perceptions for organizational managers and for work group supervisors. Results from this research suggest that worker trust in organizational management and work group supervisors has a positive influence on the employees' perceptions of safety climate at the organizational and work group levels in an agricultural workplace.

Management of safety and quality and the relationship with employee decisions in country grain elevators.

Human factors play an important role in the management of safety and quality in an agricultural work environment. Although employee actions and decisions have been identified as a key component of successful occupational safety programs and quality management programs, little attention has been given to the employees' role in these types of programs. This research explored two safety relationships that have theoretical connections but little previous research: the relationship between safety climate and quality climate, and the relationship of the safety and quality climates between the organizational level and the group level within a workplace. Survey data were collected at three commercial grain handling facilities from 177 employees. Employees also participated in safety and quality decision-making simulations. Significant positive predictions were noted for safety and quality climate. Decision-making predictions are also discussed. This research suggests that organizational safety is an important predictor of group safety. In addition, recognizing the larger role that supervisors play in group workplace behavior, more should be done to increase employee perceptions of group-level involvement in quality climate to promote more quality-oriented decision-making by employees.

Oscillations of reaction center II-D1 protein degradation in vivo induced by repetitive light flashes. Correlation between the level of RCII-QB- and protein degradation in low light.

The D1 protein subunit of the photochemical reaction center II (RCII) turns over rapidly in oxygenic photosynthetic organisms exposed to the light. At high photon flux densities (PFD), photoinactivation of RCII precedes the degradation of the D1 protein. We found that the apparent quantum yield for the D1 protein degradation in Chlamydomonas cells is severalfold higher at low PFDs (10-100 mumol m-2 s-1) as compared to that observed at PFDs which induce photoinactivation of RCII (1.5-3 x 10(3) mumol m-2 s-1). Relative high levels of reduced RCII secondary plastoquinone acceptor, QB-, are induced in cells exposed to low PFDs as determined by thermoluminescence measurements. The probability of generating elevated levels of QB- which may recombine with the S2,3 oxidized states of the oxygen evolving complex decreases with increase in the light intensities at which consecutive double reduction of QB and exchange with the plastoquinone pool prevail. We have used light flashes to test if a correlation exists between the degradation of D1 protein and the relative level of QB-. D1 protein degradation could be induced in dark-incubated cells exposed to a series of 1.4 x 10(3) single light flashes given at intervals compatible with generation of elevated levels of QB- and its decay by charge recombination. Oscillations of the QB- level in cells exposed to 960-1440 series of 1 to several flashes correlated with oscillations of the D1 protein degradation in Chlamydomonas cells and in the Scenedesmus wild type but not in the LF-1 mutant lacking photosystem II donor side activity. In this mutant the "S state cycle" and QB- oscillations are abolished. We propose that the process of recombination of long lived RCII-QB- with the S2,3 states may involve damaging events related to the D1 protein degradation induced by light flashes or continuous low light in vivo.

Mechanism of photosystem II photoinactivation and D1 protein degradation at low light: the role of back electron flow.

Light intensities that limit electron flow induce rapid degradation of the photosystem II (PSII) reaction center D1 protein. The mechanism of this phenomenon is not known. We propose that at low excitation rates back electron flow and charge recombination between the QB*- or QA*- semiquinone acceptors and the oxidized S(2,3) states of the PSII donor side may cause oxidative damage via generation of active oxygen species. Therefore, damage per photochemical event should increase with decreasing rates of PSII excitation. To test this hypothesis, the effect of the dark interval between single turnover flashes on the inactivation of water oxidation, charge separation and recombination, and the degradation of D1 protein were determined in spinach thylakoids. PSII inactivation per flash increases as the dark interval between the flashes increases, and a plateau is reached at dark intervals, allowing complete charge recombination of the QB*-/S2,3 or QA*-/S2 states (about 200 and 40 s, respectively). At these excitation rates: (i) 0.7% and 0.4% of PSII is inactivated and 0.4% and 0.2% of the D1 protein is degraded per flash, respectively, and (ii) the damage per flash is about 2 orders of magnitude higher than that induced by equal amount of energy delivered by excess continuous light. No PSII damage occurs if flashes are given in anaerobic conditions. These results demonstrate that charge recombination in active PSII is promoted by low rates of excitation and may account for a the high quantum efficiency of the rapid turnover of the D1 protein induced by limiting light.

The PsbY protein is not essential for oxygenic photosynthesis in the cyanobacterium Synechocystis sp. PCC 6803.

A tetra-manganese cluster in the photosystem II (PSII) pigment-protein complex plays a critical role in the photosynthetic oxygen evolution process. PsbY, a small membrane-spanning polypeptide, has recently been suggested to provide a ligand for manganese in PSII (A.E. Gau, H.H. Thole, A. Sokolenko, L. Altschmied, R.G. Herrmann, E.K. Pistorius [1998] Mol Gen Genet 260: 56-68). We have constructed a mutant strain of the cyanobacterium Synechocystis sp. PCC 6803 with an inactivated psbY gene (sml0007). Southern-blot and polymerase chain reaction analysis showed that the mutant had completely segregated. However, the DeltapsbY mutant cells grew normally under photoautotrophic conditions. Moreover, growth of the wild-type and mutant cells were similar under high-light photoinhibition conditions, as well as in media without any added manganese, calcium, or chloride, three required inorganic cofactors for the oxygen-evolving complex of PSII. Analysis of steady-state and flash-induced oxygen evolution, fluorescence induction, and decay kinetics, and thermoluminescence profiles demonstrated that the DeltapsbY mutant cells have normal photosynthetic activities. We conclude that the PsbY protein in Synechocystis 6803 is not essential for oxygenic photosynthesis and does not provide an important binding site for manganese in the oxygen-evolving complex of PSII.

GTP enhances the degradation of the photosystem II D1 protein irrespective of its conformational heterogeneity at the Q(B) site.

The light exposure history and/or binding of different herbicides at the Q(B) site may induce heterogeneity of photosystem II acceptor side conformation that affects D1 protein degradation under photoinhibitory conditions. GTP was recently found to stimulate the D1 protein degradation of photoinactivated photosystem II (Spetea, C. , Hundal, T., Lohmann, F., and Andersson, B. (1999) Proc. Natl. Acad. Sci. U. S. A. 96, 6547-6552). Here we report that GTP enhances the cleavage of the D1 protein D-E loop following exposure of thylakoid membranes to either high light, low light, or repetitive single turnover flashes but not to trypsin. GTP does not stimulate D1 protein degradation in the presence of herbicides known to affect the accessibility of the cleavage site to proteolysis. However, GTP stimulates degradation that can be induced even in darkness in some photosystem II conformers following binding of the PNO8 herbicide (Nakajima, Y., Yoshida, S., Inoue, Y., Yoneyama, K., and Ono, T. (1995) Biochim. Biophys. Acta 1230, 38-44). Both the PNO8- and the light-induced primary cleavage of the D1 protein occur in the grana membrane domains. The subsequent migration of photosytem II containing the D1 protein fragments to the stroma domains for secondary proteolysis is light-activated. We conclude that the GTP effect is not confined to a specific photoinactivation pathway nor to the conformational state of the photosystem II acceptor side. Consequently, GTP does not interact with the site of D1 protein cleavage but rather enhances the activity of the endogenous proteolytic system.

Passive entry of CO2 and its energy-dependent intracellular conversion to HCO3- in cyanobacteria are driven by a photosystem I-generated deltamuH+.

CO(2) entry into Synechococcus sp. PCC7942 cells was drastically inhibited by the water channel blocker p-chloromercuriphenylsulfonic acid suggesting that CO(2) uptake is, for the most part, passive via aquaporins with subsequent energy-dependent conversion to HCO3(-). Dependence of CO(2) uptake on photosynthetic electron transport via photosystem I (PSI) was confirmed by experiments with electron transport inhibitors, electron donors and acceptors, and a mutant lacking PSI activity. CO(2) uptake was drastically inhibited by the uncouplers carbonyl cyanide m-chlorophenylhydrazone (CCCP) and ammonia but substantially less so by the inhibitors of ATP formation arsenate and N, N,-dicyclohexylcarbodiimide (DCCD). Thus a DeltamuH(+) generated by photosynthetic PSI electron transport apparently serves as the direct source of energy for CO(2) uptake. Under low light intensity, the rate of CO(2) uptake by a high-CO(2)-requiring mutant of Synechococcus sp. PCC7942, at a CO(2) concentration below its threshold for CO(2) fixation, was higher than that of the wild type. At saturating light intensity, net CO(2) uptake was similar in the wild type and in the mutant IL-3 suggesting common limitation by the rate of conversion of CO(2) to HCO3(-). These findings are consistent with a model postulating that electron transport-dependent formation of alkaline domains on the thylakoid membrane energizes intracellular conversion of CO(2) to HCO3(-).

Regulation of thylakoid protein phosphorylation at the substrate level: reversible light-induced conformational changes expose the phosphorylation site of the light-harvesting complex II.

Light-dependent activation of thylakoid protein phosphorylation regulates the energy distribution between photosystems I and II of oxygen-evolving photosynthetic eukaryotes as well as the turnover of photosystem II proteins. So far the only known effect of light on the phosphorylation process is the redox-dependent regulation of the membrane-bound protein kinase(s) activity via plastoquinol bound to the cytochrome bf complex and the redox state of thylakoid dithiols. By using a partially purified thylakoid protein kinase and isolated native chlorophyll (chl) a/b light-harvesting complex II (LHCII), as well as recombinant LHCII, we find that illumination of the chl-protein substrate exposes the phosphorylation site to the kinase. Light does not activate the phosphorylation of the LHCII apoprotein nor the recombinant pigment-reconstituted complex lacking the N-terminal domain that contains the phosphothreonine site. The suggested light-induced conformational change exposing the N-terminal domain of LHCII to the kinase is evidenced also by an increase in its accessibility to tryptic cleavage after light exposure. Light activates preferentially the trimeric form of LHCII, and the process is paralleled by chl fluorescence quenching. Both phenomena are slowly reversible in darkness. Light-induced exposure of the LHCII N-terminal domain to the endogenous protein kinase(s) and tryptic cleavage occurs also in thylakoid membranes. These results demonstrate that light may regulate thylakoid protein phosphorylation not only via the signal transduction chain connecting redox reactions to the protein kinase activation, but also by affecting the conformation of the chl-protein substrate.