An improved heuristic for haplotype inference

We cloned a gene, kexD, that provides a multidrug-resistant phenotype from multidrug-resistant Klebsiella pneumoniae MGH78578. The deduced amino acid sequence of KexD is similar to that of the inner membrane protein, RND-type multidrug efflux pump. Introduction of the kexD gene into Escherichia coli KAM32 resulted in a MIC that was higher for erythromycin, novobiocin, rhodamine 6G, tetraphenylphosphonium chloride, and ethidium bromide than that of the control. Intracellular ethidium bromide levels in E. coli cells carrying the kexD gene were lower than that in the control cells under energized conditions, suggesting that KexD is a component of an energy-dependent efflux pump. RND-type pumps typically consist of three components: an inner membrane protein, a periplasmic protein, and an outer membrane protein. We discovered that KexD functions with a periplasmic protein, AcrA, from E. coli and K. pneumoniae, but not with the periplasmic proteins KexA and KexG from K. pneumoniae. KexD was able to utilize either TolC of E. coli or KocC of K. pneumoniae as an outer membrane component. kexD mRNA was not detected in K. pneumoniae MGH78578 or ATCC10031. We isolated erythromycin-resistant mutants from K. pneumoniae ATCC10031, and some showed a multidrug-resistant phenotype similar to the drug resistance pattern of KexD. Two strains of multidrug-resistant mutants were investigated for kexD expression; kexD mRNA levels were increased in these strains. We conclude that changing kexD expression can contribute to the occurrence of multidrug-resistant K. pneumoniae.     

Characteristics and seasonal variation in the semen of Markhoz bucks in western Iran

The aims of the present study were to evaluate if seasonality in semen characteristics and plasma testosterone concentrations exist in Markhoz male goats. Ten Markhoz (Angora) bucks were housed and fed according to standard recognized practices. During the observation period, semen was collected monthly with the aid of an electro-ejaculator and examined microscopically immediately after collection. Physical parameters of semen and the semen index were recorded. Blood samples were also taken monthly throughout the observation period and the plasma testosterone concentration monitored. Bucks demonstrated a higher semen quality (P < 0.05) in autumn and summer (semen index of 965 × 10⁶ and 752 × 10⁶ ml⁻¹, respectively), compared to spring and winter (semen index of 606 × 10⁶ and 512 × 10⁶, respectively). This coincided with a higher (P < 0.05) plasma testosterone concentration in autumn and summer (8.1 and 10.1 ng ml⁻¹, respectively), compared to that obtained in spring (3.0 ng ml⁻¹) and winter (2.5 ng ml⁻¹). During autumn and summer, the ejaculate volume (average of 1.2 and 1.0 ml), sperm output (1159 × 10⁶ and 1005 × 10⁶ sperm ml⁻¹), sperm mass motility (4.2 and 4.3), sperm progressive motility (83.9 and 82.0%) and percentage live sperm (90.7 and 88.2%, respectively) of the bucks were higher (P < 0.05) than in the spring (0.6 ml, 880 × 10⁶ sperm ml⁻¹, 3.3, 71.5% and 80.2%) and winter (0.7 ml, 863 × 10⁶ sperm ml⁻¹, 4.0, 71.5% and 84.9%, respectively). During autumn and summer, the percentage of sperm abnormalities (5.0 and 9.2%) was significantly lower than that in spring (12.9%) and winter (11.2%). The semen pH was slightly alkaline being significantly (P < 0.05) lower in the autumn (7.1) than in spring (7.3). Data showed season of the year to influence all semen parameters evaluated—indicating that optimal buck performance may be obtained in late summer and autumn. It can thus be said that Markhoz bucks have distinct seasonal spermatogenic activity, with poorer semen characteristics being recorded during winter and spring. This may be a critical obstacle when implementing an intensive breeding system of three kidding seasons in 2 years, with natural mating being implemented.     

Angiogenesis Is Induced and Wound Size Is Reduced by Electrical Stimulation in an Acute Wound Healing Model in Human Skin

Angiogenesis is critical for wound healing. Insufficient angiogenesis can result in impaired wound healing and chronic wound formation. Electrical stimulation (ES) has been shown to enhance angiogenesis. We previously showed that ES enhanced angiogenesis in acute wounds at one time point (day 14). The aim of this study was to further evaluate the role of ES in affecting angiogenesis during the acute phase of cutaneous wound healing over multiple time points. We compared the angiogenic response to wounding in 40 healthy volunteers (divided into two groups and randomised), treated with ES (post-ES) and compared them to secondary intention wound healing (control). Biopsy time points monitored were days 0, 3, 7, 10, 14. Objective non-invasive measures and H&E analysis were performed in addition to immunohistochemistry (IHC) and Western blotting (WB). Wound volume was significantly reduced on D7, 10 and 14 post-ES (p = 0.003, p = 0.002, p<0.001 respectively), surface area was reduced on days 10 (p = 0.001) and 14 (p<0.001) and wound diameter reduced on days 10 (p = 0.009) and 14 (p = 0.002). Blood flow increased significantly post-ES on D10 (p = 0.002) and 14 (p = 0.001). Angiogenic markers were up-regulated following ES application; protein analysis by IHC showed an increase (p<0.05) in VEGF-A expression by ES treatment on days 7, 10 and 14 (39%, 27% and 35% respectively) and PLGF expression on days 3 and 7 (40% on both days), compared to normal healing. Similarly, WB demonstrated an increase (p<0.05) in PLGF on days 7 and 14 (51% and 35% respectively). WB studies showed a significant increase of 30% (p>0.05) on day 14 in VEGF-A expression post-ES compared to controls. Furthermore, organisation of granulation tissue was improved on day 14 post-ES. This randomised controlled trial has shown that ES enhanced wound healing by reduced wound dimensions and increased VEGF-A and PLGF expression in acute cutaneous wounds, which further substantiates the role of ES in up-regulating angiogenesis as observed over multiple time points. This therapeutic approach may have potential application for clinical management of delayed and chronic wounds.     

Canola quality affects second (<Emphasis Type="Italic">Brevicoryne brassicae</Emphasis>) and third (<Emphasis Type="Italic">Diaeretiella rapae</Emphasis>) trophic levels

Biological control agents can be used as a complementary control measure that can be combined with resistant host plants to control pests. In this study, the effects of different canola cultivars (Karaj-1, Karaj-2, Karaj-3, Licord, Okapi, Opera, RGS₀₀₃, Sarigol, Talaye and Zarfam) on the performance and life table parameters of the cabbage aphid, Brevicoryne brassicae, and its parasitoid, Diaeretiella rapae, were determined under laboratory conditions. Total fecundity of the cabbage aphid differed with cultivar, with the highest value (59.41 nymphs per female) of this parameter observed on Opera and the lowest (1.67) observed on RGS₀₀₃. The highest and lowest intrinsic rates of increase (r) of the cabbage aphid were observed on Opera (0.331 day^?1) and RGS₀₀₃ (? 0.242 day^?1) cultivars, respectively, suggesting these to be the most susceptible and most resistant cultivars to this pest. However, because the aphid did not settle and feed well on RGS₀₀₃, it was not possible to determine demographic parameters for its parasitoid. Consequently, the Okapi cultivar, which was the most resistant cultivar to the cabbage aphid after RGS₀₀₃, was used in this study to assess the parasitoid wasp. The parasitoid’s intrinsic rate of increase (r) varied from 0.426 day^?1 on the susceptible cultivar (Opera) to 0.341 day^?1 on the resistant canola cultivar Okapi. Aphid performance decreased 93% on the resistant canola cultivar, while parasitoid performance decreased only 20% on the resistant cultivar compared to more susceptible cultivar.     

Effective haplotype assembly via maximum Boolean satisfiability

The haplotype assembly problem seeks the haplotypes of an individual from which a set of aligned SNP fragments are available. The problem is important as the haplotypes contain all the SNP information, which is essential to such studies as the analysis of the association between specific diseases and their potential genetic causes. Using Minimum Error Correction as the objective function, the problem is NP-hard, which raises the demand for effective yet affordable solutions. In this paper, we propose a new method to solve the problem by providing a novel Max-2-SAT formulation for the problem. The proposed method is compared with several well-known algorithms proposed for the problem in the literature on a recent extensive benchmark, outperforming them all by achieving solutions of higher average quality.     

Reproductive parameters and life expectancy of Tetranychus urticae (Acari: Tetranychidae) on 12 genotypes of melon and cucumber in laboratory condition

The effect of two host plant species including eight genotypes of melon (Cucumis melo L.) and four genotypes of cucumber (Cucumis sativus L.) was studied on reproductive parameters: life expectancy and mortality of Tetranychus urticae (Koch) at 25?±?1?°C, 60?±?5% rh and a photoperiod of 16L:8D hours. The results indicated that the highest value of the gross fecundity rate of T. urticae was 96.72?±?16.70 (eggs/female) on Mir sultan and the lowest value was 14.33?±?0.88 on Ananasi. The maximum value of gross fertility rate (41.55?±?4.79) was recorded on Sultan, while the minimum value (1.38?±?0.08) was recorded on Ananasi. The net fecundity rate was varied from 0.47?±?0.09 on Ananasi to 23.53?±?3.96 eggs/female on Sultan. The net fertility rate was 12.96?±?2.18 on Sultan and 0.04?±?0.009 on Ananasi, which was the maximum and minimum values, respectively. The range of gross hatch rate on different melon and cucumber genotypes was 9.67% on Ananasi to 72.46% on Super sultan. The cohort reared on Super sultan had the highest mean eggs per day and those on Shah abadi had the lowest mean eggs per day. In addition, the mite demonstrated the maximum value of mean fertile eggs per day with the amount of 1.66?±?0.19 eggs/female when fed on Sultan, and Ananasi demonstrated the minimum value (0.09?±?0.005). The life expectancy of one-day-old adults of T. urticae was estimated to be 16?days on Garmak Isfahan and 26.62 days on Mir sultan which is the maximum and minimum values, respectively. Furthermore, the highest mortality percentage of immature stages of T. urticae was recorded on Ananasi and the lowest was recorded on Super sultan. Comparison of the data collected in this study revealed that the mites had considerably better performance on cucumber genotypes than melon genotypes, so we can assume that cucumber is the preferable host species for T. urticae. The use of preferable and resistant host plants is helpful in crop rotation and it will be one of the beneficial strategies to integrated pest management programmes.     

Expression of Flowering Repressor Gene CsSVP,Carbohydrates, and Antioxidants Affected by Plant Growth Regulators in Saffron

Improving flower yield through lengthening flowering duration is a primary breeding objective in saffron (Crocus sativus L.). Asexual reproduction in saffron limits biodiversity and conventional breeding. Hence, eliciting flowering-related gene expression by plant growth regulators is one way to achieve this aim. The phytohormones methyl jasmonate (MeJA) and 6-benzyl amino purine (BAP) signals are received by the MADs-box gene family. In this study, to elucidate the role of phytohormones on flower development, plant were treated with BAP (0 and 5 mg L^?1), and methyl jasmonate (MeJA) (0, 20, and 100 mM) at three developmental stages of the saffron life cycle. Then, the expression of the SHORT VEGETATIVE PHASE (CsSVP) gene as a MADS-box gene family was assessed in the saffron corm. The activities of antioxidant enzymes, soluble sugar, starch content, and soluble protein content were also measured in corm, leaf, and root tissues. The application of MeJA and BAP treatments resulted in down-regulation of CsSVP expression in the corm during dormancy. At the dormancy stage, catalase, peroxidase activity decreased, and ascorbate peroxidase activity increased following MeJA treatment. In contrast, an increment in catalase and peroxidase activity and reduction of ascorbate peroxidase activity were observed after treatment with MeJA during the flowering stage. This change in enzyme activity is most likely due to flowering, which demands the re-allocation of resources. As flowering is a process heavily influenced by the environment, plants treated with MeJA, which may mimic environmental stress, showed changes in antioxidant enzyme activity. Overall, these results suggested that MeJA and BAP treatments play a significant role in the vegetative-to-reproductive phase change in saffron.

     

Physical map of the Salmonella typhimurium histidine transport operon: correlation with the genetic map.

A detailed restriction map of a 12.4-kilobase EcoRI fragment of Salmonella typhimurium deoxyribonucleic acid (DNA) containing the entire histidine transport operon and the argT gene is presented. Subclones of specific regions of the transport operon of S. typhimurium were constructed in plasmid vectors. An accurate correlation between the restriction map and the location of genetically defined deletions was obtained by hybridizing restriction digests of chromosomal DNA from strains carrying each deletion with cloned transport operon DNA as a probe. These data were used to position the histidine transport genes on the cloned 12.4-kilobase fragment of DNA.     

Activity Patterns of <Emphasis Type="Italic">Brachyteles arachnoides</Emphasis> in the Largest Remaining Fragment of Brazilian Atlantic Forest

Time is an important currency for primate energetics, reproduction, and survival. Here, we describe the activity budgets of a group of southern muriquis (Brachyteles arachnoides) inhabiting the largest continuous fragment of Brazilian Atlantic Forest (210,000 ha) in Parque Estadual Carlos Botelho (24°44´–15´S, 47´46–10 W), in the southern region of São Paulo State. We collected instantaneous scan sampling data to assess monthly, seasonal, and between-year differences in time allocation for the different activities for 2 complete, nonconsecutive years—1995 and 2002—and compare these with measures of food availability. Over the 2 yr, the group rested on average for 48%, fed for 28%, traveled for 22.5%, and socialized for 1.5% of daylight hours. On a monthly basis, resting correlated negatively with traveling in 1995, and strongly negatively correlated with feeding for both years. Feeding correlated negatively with traveling in 2002, with significantly more time spent traveling during periods of higher young leaf availability. Season was a major influence on activity: the group rested more during the hotter, rainy austral summer season, whereas feeding occurred more frequently in the cooler, drier winter season. We found no consistent associations between food availability and the time that southern muriquis spent in most activities. We suggest that these southern muriquis, like many other large-bodied and atelin primates, minimize energy expenditure while maximizing energy intake, which may be associated with their ability to be folivorous when their preferred fruit foods are less available. They thus adopt a flexible energetic strategy for coping with variable climatic conditions rather than being constrained by food availability.