Miracle-dz/UniFAR-FTUs huggingface dataset:
10 – ANTI-BIOFILM ACTIVITY OF SUBINHIBITORY POVIDONE-IODINE CONCENTRATIONS AGAINST STAPHYLOCOCCUS EPIDERMIDIS AND STAPHYLOCOCCUS AUREUS

Purpose: Biomaterial-related infections continue to hamper the success of reconstructive and arthroplasty procedures in orthopaedic surgery. Staphylococci are the most common etiologic agents, with biofilm formation representing a major virulence factor. Environmental stress factors and sub-inhibitory concentration of some antibiotics have been identified to trigger staphylococcal biofilm formation through increased icaADBC expression. In staphylococci, production of polysaccharide intercellular adhesin (PIA) by the enzyme products of the icaADBC operon is the best understood mechanism of biofilm development, making the ica genes a potential target for biofilm inhibitors. Aims of the current study were Determine the minimum inhibitory concentration (MIC) of Povidone-iodine. Investigate the effect of Povidone-iodine on icaADBC operon encoded staphylococcal biofilm formation. Investigate wether any observed changes on biofilm by Povidone-iodine is mediated through a change in icaADBC operon. Method: MIC of povidone – iodine for both reference strains and strains isolated from infected orthopaedic implants was determined. Biofilm assay was performed at different Povidone-iodine concentrations using 96-well polystyrene plates. Total RNA for cDNA synthesis was isolated from bacteria at different twofold dilutions of Povidone-iodine concentrations. Real time polymerase chain reaction was used to quantify effects of Povidone-iodine on gene expression pattern of the icaADBC operon using the constitutively expressed gyrB gene as internal control Results: The MIC of povidone-iodine was 1.4% for all bacterial strains. Clinical in-use doses of povidone-iodine prevented biofilm formation. A step-wise reduction of biofilm was observed at increasing sub-inhibitory doses of povidone-iodine (p IcaA expression correlated with biofilm formation in staphylococcal organisms. Decrease in icaA expression was strongly associated with an increase in expression in the biofilm repressor gene, icaR. The repressive effect of povidone-iodine on biofilm formation by Staphylococcal bacteria is by a separate mechanism from its bacteriostatic mechanism of action. Conclusion: This study shows that icaR is a potential therapeutic target through which the ability of Staphylococcal bacterial to form biofilm may be reduced. These data reveal an additional therapeutic benefit of povidone-iodine and suggest that studies to evaluate the suitability of povidone-iodine as biomaterial coating agent to reduce device-related infection rates are merited.
The threat to Eucalyptus plantations from an emerging Tasmanian leaf beetle pest: Paropsisterna selmani (Coleoptera: Chrysomelidae)

ABSTRACT A newly described eucalypt leaf beetle, Paropsisterna selmani Reid and de Little, endemic to Tasmania, Australia, required management in Tasmania for the first time in 2011 to protect Eucalyptus nitens plantations from severe defoliation. This species was discovered following its incursion and subsequent establishment in southern Ireland in 2007. Field monitoring using sticky traps in eight E. nitens plantations around Tasmania was performed to compare the spatial and temporal population distributions of adult P. selmani with adult P. bimaculata and P. agricola over two summer seasons, 2009–2010 and 2010–2011. Populations of all three species were extremely variable between sites and between and within the two seasons. While P. bimaculata dominated at six of the eight sites throughout Tasmania, P. agricola had high populations at the three most northerly sites. Adult P. selmani were trapped at all sites but were the dominant leaf beetles at one site and were relatively common at two other northerly sites. During the longer trapping period in the second season, all three species showed two population peaks: one in spring (November–December) following emergence of adults from overwintering, and a second in late January–February of a second generation of adults. Heavy egg-laying followed the first but not the second adult population peak. At the two sites with the largest P. selmani populations, the peak spring flight of P. selmani adults occurred at least two weeks earlier than that of P. bimaculata and P. agricola, and the second flight peak was at least two weeks later than that of these species. A new pest with a population phenology that differs from that of existing plantation pests could have important implications for the success of an Integrated Pest Management program designed to protect plantations from defoliation. Field records of P. selmani since it was first recorded in 1979 suggest that this species is increasing in abundance in Tasmania. Management of this species has been required since 2011 to prevent economic damage to plantations. This newly emerging plantation pest feeds on a range of Eucalyptus hosts, including the adult-phase foliage of the plantation species E. nitens, and poses new problems for plantation management in Australia, as well as increasing the threat of invasion into overseas eucalypt plantations, as already demonstrated in Ireland.
Panicum spikelets from the Early Holocene Takarkori rockshelter (SW Libya): Archaeo-molecular and -botanical investigations

Abstract This paper deals with the extraction, amplification and sequencing of ancient DNA (aDNA) from spikelets of wild cereals dated at ca. 9000 cal yr BP, representing the most ancient plants with preserved genetic material from the Sahara desert. The sub-fossil records were collected from the archaeological excavation carried out at Takarkori, an archaeological site located in south-western Libya. Morphological and genetic analyses were made on 100 well preserved dried spikelets. Ten DNA extraction protocols were performed to evaluate nucleic acid recovery in terms of DNA yield, purity and amplification success of the chloroplast barcode region matK. The extraction protocol that returned the most suitable DNA to be amplified is the Kistler and Shapiro (2011: J Archaeol Sci 38: 3549-3554) modified protocol. In our study, the results from matK amplification suggested that four specimens are the most appropriate number of spikelets for these analyses. DNA was then used for PCR amplifications of four chloroplast barcode genes: rbcL, matK, trnH-psbA and trnL. A phylogenetic analysis shows the strict relation between the archaeological specimens and modern Panicoideae, supporting the morphological identification. The results indicate that spikelets have a close relation to Panicum laetum Kunth, a wild cereal still collected in tropical Africa.
Comparison of the feeding behaviour and strategy of the Killifish, Aphanius sophiae Heckel, 1847, at two different localities in Iran

Abstract The feeding strategy and behavioural differences of a Killifish, Aphanius sophiae Heckel, 1847, were compared at a freshwater spring (Cheshme-Ali at Damghan) and a salty water river (Shour River) by considering stable and non-stable environmental conditions. The results showed that Killifish were affected by environmental differences. Chironomid larvae were its main food item in Shour River, whilst the species mainly fed on crustaceans and Daphnia at Cheshme-Ali. In Cheshme-Ali, the fish had suitable feeding for almost the whole year in spite of some fluctuations during the period of shortened daylight. In Shour River, however, the case was affected by salinity and thermo period. Therefore suitable and stable conditions allowed more prey selection for Killifish in Cheshme-Ali than in Shour River. The observations demonstrated that Killifish probably preferred to hunt a specific prey that is abundant and easy to capture. Furthermore, the size of both prey and predator can affect their feeding diversity. The results in Shour River showed a higher relative length of gut (RLG) (p<0.05) which means more energy utilization and osmoregulation in the gut. Also the Shour River population shows a relatively benthic, passive behaviour and a low condition factor (p<0.05) that is caused by different and non-stable conditions.
Composite control design for trajectory tracking of a quadrotor in the presence of unknown disturbances

this paper is focused on proposition a nonlinear control protocol for a quadrotor. Dynamic model of the quadrotor which is based on the Newton-Euler equation and the model with external unknown disturbances are developed. The quadrotor is an under-actuated system with strongly coupled characteristics. These properties make the controller designing difficult. In this paper, a nonlinear control method is designed by using combination of PID controller, backstepping and sliding mode controls to stabilize the quadrotor attitude and to carry out the trajectory tracking task. The presented controllers are divided into attitude controller and position controller, and Lyapunov stability theorem is used to show the validity of their stability. Traditional sliding mode controller produces the chattering phenomenon and discontinuousness of control inputs. These faults can be avoided by using combined controllers. The effectiveness of the control approach presented in this paper is shown by the different simulations. The results show that the presented control method not only has a better tracking performance than others, but has better robustness when unknown disturbances exist.
Effects of spotted knapweed invasion and restoration treatments on ground beetle diversity abundance and distribution in Rocky Mountain savannas in Montana

Biological invasions are known to alter native communities, yet evidence on effects of spotted knapweed invasion (a highly invasive exotic forb in western U.S. and Canada) on heterotroph communities is lacking even though bottom-up or indirect effects are likely to result. Here, I examine how spotted knapweed invasion affects carabid species and functional group diversity, community composition and structure (abundance), and relate carabid species assemblages in Rocky Mountain savannas to important abiotic and biotic variables, including the presence of spotted knapweed. Six study sites, three with high levels of spotted knapweed (invaded) and three with trace amounts of spotted knapweed (native), were established in Rocky Mountain savannas in MT. Carabid species abundance and environmental measurements were collected in 1999 and 2000 at 52 pitfall tr£C)s per site. Carabid species richness was similar between invaded and native sites; however evenness was significantly different for both carabid species and functional groups between invaded and native sites. Beta diversity was higher among native sites relative to invaded sites for both indices. Carabid species and functional group composition and structure differed significantly between invaded and native sample units. Carabid species composition and structure was more homogenous among invaded sample units relative to native sample units. Carabid functional group shifts between invaded and native sites were largely responsible for alterations in carabid species assemblages. Polyphagous phytophages and specialist predators were more abundant and indicated invaded sites, and generalist predators were more abundant and indicated native sites. Spotted knapweed invasion simplified carabid functional group evenness and influenced trophic groups differentially. In addition, carabid assemblages were more homogenous among invaded sites relative to native sites, and species distribution was mainly associated with cover of spotted knapweed, soil moisture, and ground structural components. As a result increased spotted knapweed invasion in Rocky Moimtain savannas may lead to homogenous carabid assemblages on a landscape level.
Molecular aspects of catabolic gene evolution in Pseudomonads

Twenty different Pseudomonas strains utilizing m-toluate were isolated from oilcontaminated soil samples near Minsk, Belarus. Seventeen of these isolates carried plasmids ranging in size from 78 to about 200 kb (assigned pSVS plasmids) and encoding the meta cleavage pathway for toluene metabolism. Most plasmids were conjugative, but of unknown incompatibility groups, except for one, which belonged to IncP9 group. The organization of the genes for toluene catabolism was determined by restriction analysis and hybridization with xyl gene probes of pWW0. The majority of the plasmids carried xyl-type genes highly homologous to those of pWW53 and organized in similar manner (Gallegos, M. T., P. A. Williams, and J. L. Ramos. 1998, J. Bacteriol. 179: 5024-5029), with two distinguishable meta pathway operons, one upper pathway operon, and three xylS-homologous regions. All of these plasmids also possessed large areas of homologous DNA outside the catabolic genes, suggesting a common ancestry. Two other pSVS plasmids carried only one meta pathway operon, one upper pathway operon and one copy each of xylS and xylR. The plasmid backbones of these two differed greatly from the others. Whereas the parts of the plasmids carrying xyl genes were mostly conserved between plasmids of each group, the noncatabolic part had undergone intensive DNA rearrangements. DNA sequencing data of specific regions near and within the xylTE and xylA genes of the pSVS-plasmids confirmed the strong homologies to xyl genes of pWW53 and pWW0. However several recombinations were discovered within the upper pathway operons of the pSVS plasmids and pWW0. The main genetic mechanisms which are thought to have resulted in the present day configuration of the xyl operons are discussed in light of the diversity analysis carried out on the pSVS plasmids.
Occurrence of Damping-off Caused by Pythium spinosum on Cucumis melo in Korea

ticultural crop grown throughout the world. Global export of melons produced in Korea has increased in recent years (http:// www.kati.net). The cultivated area of melon increased by 13.1% to 1,500 ha in 2014 compared with 2004 (MAFRA, 2015). In 2010 and 2012, damping-off symptoms were observed on melon seedlings in greenhouses in Yeongam and Suncheon. Approximately 5% to 10% of seedlings showed the symptoms. The affected stems and roots were water-soaked, shriveled, softened, and discolored (Fig. 1A). Longitudinal cracks appeared on the lower parts of some stems (Fig. 1B). In the late stage of the disease, the infected plants collapsed and eventually decayed. A Pythium-like fungus was isolated from the diseased plants using the single hyphal tip method. A total of two pure isolates were obtained (Fig. 2A), and these were deposited in the Korean Agricultural Culture Collection under accession numbers KACC47889 and KACC47890 (Table 1). Morphological features were observed and measured from the isolates grown on water agar for 7 days using the grass blade culture technique. Primary hyphae were up to 7 μm in width, and hyphal swellings were often present (Fig. 2B). Oogonia containing plerotic oospores were globose, terminal or intercalary, and 18 to 21 μm in diameter, with spines on the oogonial walls (Fig. 2C, E). Antheridia were 1(–2) per oogonium, and mostly monoclinous (Fig. 2D). On the basis of the morphological data, the fungal pathogen was identified as Pythium spinosum Sawada (Van der Plaats-Niterink, 1981). Genomic DNA was extracted from mycelia scraped from agar plates. The internal transcribed spacer (ITS) rDNA region was amplified using the primers ITS1 (5’-TCC GTA GGT GAA CCT GCG G-3’) and ITS4 (5’-TCC TCC GCT TAT TGA TAT GC-3’) (White et al., 1990). The cytochrome oxidase II (cox2) gene was also amplified using the primers Cox2-F (5’-GGC AAA TGG GTT TTC AAG ATC C-3’) and Cox2-RC4 (5’-TGA TTW AYN CCA CAA ATT TCR CTA CAT TG-3’) (Choi et al., 2015). The PCR amplicons were purified and directly sequenced. The raw sequence data for P. spinosum were edited using SeqMan (DNASTAR Lasergene, Madison, WI, USA). The resulting sequences of the isolates have been lodged in GenBank, with accession numbers KT006894, KT006895,
Genetic diversity analysis in traditional lowland rice (Oryza sativa L.) of Assam using RAPD and ISSR markers

Genetic variability among 24 rice genotypes from Assam was assessed employing random amplified polymorphic DNA (RAPD) and inter-simple sequence repeat polymerase chain reaction (ISSR-PCR) using ten primers in each case. A total of 81 RAPD and 201 ISSR markers were generated with 92.5 and 98% polymorphism respectively. The average polymorphism information content (PIC) for RAPD was 0.741 and for ISSR markers it was 0.888. The Jaccard's similarity coefficient based on RAPD and ISSR analysis was 0.480 and 0.257 respectively. Cluster analysis and cophenetic correlation value based on the ISSR data discretely separated the accessions, according to farmer's classification. This communication reports genetic variability in rice from Assam using two molecular markers.
ISOLATION AND IDENTIFICATION OF THERMOPHILIC CAMPYLOBACTER SPP. BY PCR-RFLP IN BROILER FLOCKS

Summary. The aim of the present work was to isolate and identify thermophilic Campylobacter spp. in broiler flocks using Polymerase Chain Reaction based Restriction Fragment Length Polymorphism (PCR- RFLP) method. Forty cloacal samples were taken and examined from four randomly selected poultry flocks in different poultry farms in Lithuania. Thermophilic Campylobacter spp. were isolated by both direct inoculation on mCCDA selective medium and by selective enrichment in Bolton enrichment broth. The results of our study showed that all four examined poultry flocks were contaminated with Campylobacter spp. Using PCR assay amplification of 491 bp amplicon of a highly polymorphic part of the 23S rRNA gene out of 40 broiler cloacal samples examined Campylobacter spp. were detected and confirmed in 37 samples (92.5 %). After subsequent digestion of the PCR products with restriction enzymes AluI and TspEI, C. jejuni was identified in 32 (86.5 %) and C. coli in 5 (13.5 %) out of 37 isolates. Three broiler flocks of four examined were contaminated only with C. jejuni and one flock carried out mixed infection with C. jejuni and C. coli. To our knowledge, this is the first report of thermophilic Campylobacter isolation and identification from broilers in Lithuania. The results obtained in present study could serve for future surveillance on Campylobacter bacteria.
Refrigeration of Oyster Shellstock: Conditions Which Minimize the Outgrowth of Vibrio vulnificus.

The multiplication of Vibrio vulnificus in summer harvest oyster shellstock held without refrigeration was followed over a 14 h postharvest period. Mean (n = 7) increases were 0,75, 1.30, 1.74, and 1.94 log units at 3.5 h, 7 h, 10.5 h, and 14 h postharvest, respectively. Aerobic plate counts (spread plates on plate count agar [PCA] containing 1% NaCl, 25°C) but not standard plate counts (pour plates, PCA, 35°C) showed a similar trend in increase. Reducing the time oyster shellstock remains outside refrigeration can decrease consumer exposure to high numbers of V. vulnificus , but shellstock must be cooled immediately after harvest to eliminate postharvest growth of this bacterium.
The role of impaired de novo Coenzyme A biosynthesis in pantothenate kinase-associated neurodegeneration

Background: Coenzyme A (CoA) is an essential metabolite, synthesized from vitamin B5 by the subsequent action of five enzymes: PANK, PPCS, PPCDC, PPAT and DPCK. Mutations in Drosophila d PPCS disrupt female fecundity and in this study we analyzed the female sterile phenotype of d PPCS mutants in detail. Results: We demonstrate that d PPCS is required for various processes that occur during oogenesis including chorion patterning. Our analysis demonstrates that a mutation in dPPCS disrupts the organization of the somatic and germ line cells, affects F-actin organization and results in abnormal PtdIns(4,5)P2 localization. Improper cell organization coincides with aberrant localization of the membrane molecules Gurken (Grk) and Notch, whose activities are required for specification of the follicle cells that pattern the eggshell. Mutations in d PPCS also induce alterations in scutellar patterning and cause wing vein abnormalities. Interestingly, mutations in dPANK and dPPAT-DPCK result in similar patterning defects. Conclusion: Together, our results demonstrate that de novo CoA biosynthesis is required for proper tissue morphogenesis. cell migration events are not properly synchronized. Together, these data demonstrate that d PPCS is required for F-actin organization and cell migration events during oogenesis.
Prey approaching predators : a cost-benefit perspective

When faced with the presence of a predator, many species of prey initially approach rather than retreat from such a potential threat. Although seemingly paradoxical, this type of approach behaviour has been noted in a wide variety of taxa. We adopt a cost benefit perspective on the question of why prey approach potential predators, and aim to outline what is known about the putative costs and benefits of such behaviour. We identify five major types of costs associated with approach behaviour: (i) increased risk of mortality to the approacher, (ii) increased risk of mortality to relatives of the approacher, (iii) lost opportunity costs associated with approaching a predator, (iv) energetic costs of approach, and (v) potential costs of the approacher being 'exploited' by other group members. Benefits of approach behaviour are categorized as (i) acquiring information about the nature of the potential threat, (ii) informing others of the potential threat, (iii) deterring predator attack, and (iv) advertising one's quality to mates. After reviewing putative costs and benefits, we present a game theory model of prey approaching potential predators. Based on the costs and benefits of approach behaviour and group size, the model predicts the equilibrial frequency of 'approachers' and 'non approachers' and the (relative) mean approach distance (as a function of group size). To date, much of the work on prey approaching predators is either anecdotal or non experimental. We hope that the review of the costs and benefits of approaching predators presented here, in conjunction with our game theory model, will help provide direction for future studies of this interesting, but understudied, behavioural phenom
Exchangeable cations and available phosphorus in soils with variable charge after application of special liming materials

Special liming materials have the potential to control soil acidity and constitute a source of nutrients for plant development. In this study, the efficiency of special liming materials was evaluated. Their effects in soil exchangeable cations and available P concentrations were compared with the ones of dolomitic limestone (DL). Samples of Typic Distrudept and Rhodic Hapludox were collected from 0 to 20 cm layer. Two experiments were conducted in a completely randomized block of 4x4x8 factorial design. Four liming materials were studied: DL, granulated micronized calcite (GMC), granulated micronized dolomite (GMD) and carbonated suspension (CS). The liming materials were added to the soils doses that increase the soil bases saturation (V) to 50, 70 and 90%; and a control treatment. The treated soil samples were incubated at 23 ± 2°C and 60% of soil water retention capacity for eight periods (0, 7, 15, 30, 45, 60, 75 and 90 days). Exchangeable Ca, Mg and K, and available P were determined. All liming materials increase exchangeable Ca and Mg, and available P. However, the most efficient source that increased exchangeable Ca in the studied soils were CS followed by GMC.