Academic literature on the topic '059999 Environmental Sciences not elsewhere classified'

SummaryThe family registration records from a village population in a small island of Japan are used to assess the effect of demographic differentiation within a population on genetic measures. When the couples studied are classified by birth cohorts and origins, wives of the couples where one spouse came from elsewhere were older at marriage and had a shorter duration of marriage or registration than wives where both spouses were natives of the village. The mean number of offspring is statistically smaller in the former except for the latest cohort, due mainly to out-migration during the reproductive ages which also resulted in low rates of marriage among the offspring within the village. This leads to a small effective population size and an increased likelihood of genetic drift in the overall population.

Signet-ring cell carcinoma of the prostate gland (SRCCP) an uncommon and aggressive malignant tumour of the prostate gland which is characterized by histopathology examination features of compression of the nucleus into the form of a crescent by a large cytoplasmic vacuole. SRCCPs that have so far been reported have been either (a) primary tumours, metastatic tumours with the primary tumour elsewhere with the gastro-intestinal tract being the site of the primary tumour but the primary tumour could originate elsewhere, and additionally some reported SRCCPs have been classified as carcinoma of unknown primary. SRCCP could be a pure tumour or a tumour that is contemporaneously associated with other types of tumour including various variants of adenocarcinoma. SRCCP can manifest in various ways including: Incidental finding following prostatectomy that has been undertaken for a presumed benign prostatic hyperplasia, lower urinary tract symptoms, visible and non-visible haematuria, raised levels of serum PSA but some SRCCPs have been diagnosed with normal / low levels of serum PSA, there may be a history of dyspepsia in cases of metastatic signet-ring cell carcinoma in association with contemporaneous primary signet-ring cell carcinoma of the stomach or there may be a past history of surgical treatment for signet-ring cell carcinoma of the gastrointestinal tract, or bleeding from the gastrointestinal tract in cases of upper gastrointestinal tract and rectal bleeding as well as change in bowel habit for primary tumours of the anorectal region, retention of urine, and rarely a rectal mass in the case of SRCCP with an anorectal primary tumour. In order to exclude a primary signet ring cell carcinoma elsewhere, a detailed past medical history is required as well as radiology imaging including contrast – enhanced computed tomography (CECT) scan and contrast-enhanced magnetic resonance imaging (CEMRI) scan as well as upper gastrointestinal endoscopy and colonoscopy to exclude a primary lesion within the gastrointestinal tract. Diagnosis of SRCCP requires utilization of the histopathology and immunohistochemistry examination features of prostate biopsy, prostatic chips obtained from trans-urethral resection of prostate specimen or radical prostatectomy specimen. SRCCPs upon immunohistochemistry staining studies tend to show tumour that tend to exhibit positive staining for the following tumour markers as follows: PSA – positive staining for PSA has been variable in some studies, AE1/AE3, CAM 5.2, Ki-67 with a mean of 8%, PAS-diastase, Mucicarmine (50%), Alcian blue (60%), Alpha-methyl-acyl coenzyme A racemase (P504S), and Cytokeratin 5/6. SRCCPs also tend to exhibit negative staining for: Bcl2 (rare positive), and CEA (80%). Traditionally the treatment of Primary Signet-Ring Cell Carcinoma of the Prostate Gland has tended to be similar to the treatment of the traditional adenocarcinoma of the prostate gland which does include: hormonal treatment, radiotherapy, and surgery. Nevertheless, considering that primary SRCCPs and metastatic SRCCPs that have been reported in the literature have generally tended to be associated with an aggressive biological behaviour, even though there is no consensus opinion on the treatment of the disease it would be strongly recommended that these tumours that tend to be associated with rapid progress of the disease and poor survival there is an urgent need to treat all these tumours with aggressive surgery including radical prostatectomy plus adjuvant therapies including: radical radiotherapy, combination chemotherapy, selective prostatic angiography and super-selective embolization of the artery feeding the tumour including intra-arterial infusion of chemotherapy agents directly to the tumour, radiofrequency ablation of the tumour as well as irreversible electroporation of the tumour which should form part of a global multicentre study of various treatment options. With regard to metastatic signet-ring cell carcinomas of the prostate gland with a contemporaneous primary tumour elsewhere the primary tumour should also be treated by radical and complete excision of the primary tumour plus radical surgery and aggressive adjuvant therapy. Considering that SRCCPs have tendered not to respond well to available chemotherapy agents, there is need for urologists, oncologists, and pharmacotherapy research workers to identify new chemotherapy medicaments that would more effectively and safely destroy signet-ring cell tumours in order to improve upon the prognosis.

Environments containing significant concentration of NaCl such as salt lakes harbor extremophiles microorganisms which have a great biotechnology interest. To explore the diversity of Bacteria in Chott Tinsilt (Algeria), an isolation program was performed. Water samples were collected from the saltern during the pre-salt harvesting phase. This Chott is high in salt (22.47% (w/v). Seven halophiles Bacteria were selected for further characterization. The isolated strains were able to grow optimally in media with 10–25% (w/v) total salts. Molecular identification of the isolates was performed by sequencing the 16S rRNA gene. It showed that these cultured isolates included members belonging to the Halomonas, Staphylococcus, Salinivibrio, Planococcus and Halobacillus genera with less than 98% of similarity with their closest phylogenetic relative. The halophilic bacterial isolates were also characterized for the production of biosurfactant and industrially important enzymes. Most isolates produced hydrolases and biosurfactants at high salt concentration. In fact, this is the first report on bacterial strains (A4 and B4) which were a good biosurfactant and coagulase producer at 20% and 25% ((w/v)) NaCl. In addition, the biosurfactant produced by the strain B4 at high salinity (25%) was also stable at high temperature (30-100°C) and high alkalinity (pH 11).Key word: Salt Lake, Bacteria, biosurfactant, Chott, halophiles, hydrolases, 16S rRNAINTRODUCTIONSaline lakes cover approximately 10% of the Earth’s surface area. The microbial populations of many hypersaline environments have already been studied in different geographical regions such as Great Salt Lake (USA), Dead Sea (Israel), Wadi Natrun Lake (Egypt), Lake Magadi (Kenya), Soda Lake (Antarctica) and Big Soda Lake and Mono Lake (California). Hypersaline regions differ from each other in terms of geographical location, salt concentration and chemical composition, which determine the nature of inhabitant microorganisms (Gupta et al., 2015). Then low taxonomic diversity is common to all these saline environments (Oren et al., 1993). Halophiles are found in nearly all major microbial clades, including prokaryotic (Bacteria and Archaea) and eukaryotic forms (DasSarma and Arora, 2001). They are classified as slight halophiles when they grow optimally at 0.2–0.85 M (2–5%) NaCl, as moderate halophiles when they grow at 0.85–3.4 M (5–20%) NaCl, and as extreme halophiles when they grow at 3.4–5.1 M (20–30%) NaCl. Hyper saline environments are inhabited by extremely halophilic and halotolerant microorganisms such as Halobacillus sp, Halobacterium sp., Haloarcula sp., Salinibacter ruber , Haloferax sp and Bacillus spp. (Solomon and Viswalingam, 2013). There is a tremendous demand for halophilic bacteria due to their biotechnological importance as sources of halophilic enzymes. Enzymes derived from halophiles are endowed with unique structural features and catalytic power to sustain the metabolic and physiological processes under high salt conditions. Some of these enzymes have been reported to be active and stable under more than one extreme condition (Karan and Khare, 2010). Applications are being considered in a range of industries such as food processing, washing, biosynthetic processes and environmental bioremediation. Halophilic proteases are widely used in the detergent and food industries (DasSarma and Arora, 2001). However, esterases and lipases have also been useful in laundry detergents for the removal of oil stains and are widely used as biocatalysts because of their ability to produce pure compounds. Likewise, amylases are used industrially in the first step of the production of high fructose corn syrup (hydrolysis of corn starch). They are also used in the textile industry in the de-sizing process and added to laundry detergents. Furthermore, for the environmental applications, the use of halophiles for bioremediation and biodegradation of various materials from industrial effluents to soil contaminants and accidental spills are being widely explored. In addition to enzymes, halophilic / halotolerants microorganisms living in saline environments, offer another potential applications in various fields of biotechnology like the production of biosurfactant. Biosurfactants are amphiphilic compounds synthesized from plants and microorganisms. They reduce surface tension and interfacial tension between individual molecules at the surface and interface respectively (Akbari et al., 2018). Comparing to the chemical surfactant, biosurfactant are promising alternative molecules due to their low toxicity, high biodegradability, environmental capability, mild production conditions, lower critical micelle concentration, higher selectivity, availability of resources and ability to function in wide ranges of pH, temperature and salinity (Rocha et al., 1992). They are used in various industries which include pharmaceuticals, petroleum, food, detergents, cosmetics, paints, paper products and water treatment (Akbari et al., 2018). The search for biosurfactants in extremophiles is particularly promising since these biomolecules can adapt and be stable in the harsh environments in which they are to be applied in biotechnology.OBJECTIVESEastern Algeria features numerous ecosystems including hypersaline environments, which are an important source of salt for food. The microbial diversity in Chott Tinsilt, a shallow Salt Lake with more than 200g/L salt concentration and a superficies of 2.154 Ha, has never yet been studied. The purpose of this research was to chemically analyse water samples collected from the Chott, isolate novel extremely or moderate halophilic Bacteria, and examine their phenotypic and phylogenetic characteristics with a view to screening for biosurfactants and enzymes of industrial interest.MATERIALS AND METHODSStudy area: The area is at 5 km of the Commune of Souk-Naâmane and 17 km in the South of the town of Aïn-Melila. This area skirts the trunk road 3 serving Constantine and Batna and the railway Constantine-Biskra. It is part the administrative jurisdiction of the Wilaya of Oum El Bouaghi. The Chott belongs to the wetlands of the High Plains of Constantine with a depth varying rather regularly without never exceeding 0.5 meter. Its length extends on 4 km with a width of 2.5 km (figure 1).Water samples and physico-chemical analysis: In February 2013, water samples were collected from various places at the Chott Tinsilt using Global Positioning System (GPS) coordinates of 35°53’14” N lat. and 06°28’44”E long. Samples were collected randomly in sterile polythene bags and transported immediately to the laboratory for isolation of halophilic microorganisms. All samples were treated within 24 h after collection. Temperature, pH and salinity were measured in situ using a multi-parameter probe (Hanna Instruments, Smithfield, RI, USA). The analytical methods used in this study to measure ions concentration (Ca2+, Mg2+, Fe2+, Na+, K+, Cl−, HCO3−, SO42−) were based on 4500-S-2 F standard methods described elsewhere (Association et al., 1920).Isolation of halophilic bacteria from water sample: The media (M1) used in the present study contain (g/L): 2.0 g of KCl, 100.0/200.0 g of NaCl, 1.0 g of MgSO4.7HO2, 3.0 g of Sodium Citrate, 0.36 g of MnCl2, 10.0 g of yeast extract and 15.0 g agar. The pH was adjusted to 8.0. Different dilutions of water samples were added to the above medium and incubated at 30°C during 2–7 days or more depending on growth. Appearance and growth of halophilic bacteria were monitored regularly. The growth was diluted 10 times and plated on complete medium agar (g/L): glucose 10.0; peptone 5.0; yeast extract 5.0; KH2PO4 5.0; agar 30.0; and NaCl 100.0/200.0. Resultant colonies were purified by repeated streaking on complete media agar. The pure cultures were preserved in 20% glycerol vials and stored at −80°C for long-term preservation.Biochemical characterisation of halophilic bacterial isolates: Bacterial isolates were studied for Gram’s reaction, cell morphology and pigmentation. Enzymatic assays (catalase, oxidase, nitrate reductase and urease), and assays for fermentation of lactose and mannitol were done as described by Smibert (1994).Optimization of growth conditions: Temperature, pH, and salt concentration were optimized for the growth of halophilic bacterial isolates. These growth parameters were studied quantitatively by growing the bacterial isolates in M1 medium with shaking at 200 rpm and measuring the cell density at 600 nm after 8 days of incubation. To study the effect of NaCl on the growth, bacterial isolates were inoculated on M1 medium supplemented with different concentration of NaCl: 1%-35% (w/v). The effect of pH on the growth of halophilic bacterial strains was studied by inoculating isolates on above described growth media containing NaCl and adjusted to acidic pH of 5 and 6 by using 1N HCl and alkaline pH of 8, 9, 10, 11 and 12 using 5N NaOH. The effect of temperature was studied by culturing the bacterial isolates in M1 medium at different temperatures of incubation (4°C–55°C).Screening of halophilic bacteria for hydrolytic enzymes: Hydrolase producing bacteria among the isolates were screened by plate assay on starch, tributyrin, gelatin and DNA agar plates respectively for amylase, lipase, protease and DNAse activities. Amylolytic activity of the cultures was screened on starch nutrient agar plates containing g/L: starch 10.0; peptone 5.0; yeast extract 3.0; agar 30.0; NaCl 100.0/250.0. The pH was 7.0. After incubation at 30 ºC for 7 days, the zone of clearance was determined by flooding the plates with iodine solution. The potential amylase producers were selected based on ratio of zone of clearance diameter to colony diameter. Lipase activity of the cultures was screened on tributyrin nutrient agar plates containing 1% (v/v) of tributyrin. Isolates that showed clear zones of tributyrin hydrolysis were identified as lipase producing bacteria. Proteolytic activity of the isolates was similarly screened on gelatin nutrient agar plates containing 10.0 g/L of gelatin. The isolates showing zones of gelatin clearance upon treatment with acidic mercuric chloride were selected and designated as protease producing bacteria. The presence of DNAse activity on plates was determined on DNAse test agar (BBL) containing 10%-25% (w/v) total salt. After incubation for 7days, the plates were flooded with 1N HCl solution. Clear halos around the colonies indicated DNAse activity (Jeffries et al., 1957).Milk clotting activity (coagulase activity) of the isolates was also determined following the procedure described (Berridge, 1952). Skim milk powder was reconstituted in 10 mM aqueous CaCl2 (pH 6.5) to a final concentration of 0.12 kg/L. Enzyme extracts were added at a rate of 0.1 mL per mL of milk. The coagulation point was determined by manual rotating of the test tube periodically, at short time intervals, and checking for visible clot formation.Screening of halophilic bacteria for biosurfactant production. Oil spread Assay: The Petridis base was filled with 50 mL of distilled water. On the water surface, 20μL of diesel and 10μl of culture were added respectively. The culture was introduced at different spots on the diesel, which is coated on the water surface. The occurrence of a clear zone was an indicator of positive result (Morikawa et al., 2000). The diameter of the oil expelling circles was measured by slide caliber (with a degree of accuracy of 0.02 mm).Surface tension and emulsification index (E24): Isolates were cultivated at 30 °C for 7 days on the enrichment medium containing 10-25% NaCl and diesel oil as the sole carbon source. The medium was centrifuged (7000 rpm for 20 min) and the surface tension of the cell-free culture broth was measured with a TS90000 surface tensiometer (Nima, Coventry, England) as a qualitative indicator of biosurfactant production. The culture broth was collected with a Pasteur pipette to remove the non-emulsified hydrocarbons. The emulsifying capacity was evaluated by an emulsification index (E24). The E24 of culture samples was determined by adding 2 mL of diesel oil to the same amount of culture, mixed for 2 min with a vortex, and allowed to stand for 24 h. E24 index is defined as the percentage of height of emulsified layer (mm) divided by the total height of the liquid column (mm).Biosurfactant stability studies : After growth on diesel oil as sole source of carbone, cultures supernatant obtained after centrifugation at 6,000 rpm for 15 min were considered as the source of crude biosurfactant. Its stability was determined by subjecting the culture supernatant to various temperature ranges (30, 40, 50, 60, 70, 80 and 100 °C) for 30 min then cooled to room temperature. Similarly, the effect of different pH (2–11) on the activity of the biosurfactant was tested. The activity of the biosurfactant was investigated by measuring the emulsification index (El-Sersy, 2012).Molecular identification of potential strains. DNA extraction and PCR amplification of 16S rDNA: Total cellular DNA was extracted from strains and purified as described by Sambrook et al. (1989). DNA was purified using Geneclean® Turbo (Q-BIO gene, Carlsbad, CA, USA) before use as a template in polymerase chain reaction (PCR) amplification. For the 16S rDNA gene sequence, the purified DNA was amplified using a universal primer set, forward primer (27f; 5′-AGA GTT TGA TCM TGG CTC AG) and a reverse primer (1492r; 5′-TAC GGY TAC CTT GTT ACG ACT T) (Lane, 1991). Agarose gel electrophoresis confirmed the amplification product as a 1400-bp DNA fragment.16S rDNA sequencing and Phylogenic analysis: Amplicons generated using primer pair 27f-1492r was sequenced using an automatic sequencer system at Macrogene Company (Seoul, Korea). The sequences were compared with those of the NCBI BLAST GenBank nucleotide sequence databases. Phylogenetic trees were constructed by the neighbor-joining method using MEGA version 5.05 software (Tamura et al., 2011). Bootstrap resembling analysis for 1,000 replicates was performed to estimate the confidence of tree topologies.Nucleotide sequence accession numbers: The nucleotide sequences reported in this work have been deposited in the EMBL Nucleotide Sequence Database. The accession numbers are represented in table 5.Statistics: All experiments were conducted in triplicates. Results were evaluated for statistical significance using ANOVA.RESULTSPhysico-chemical parameters of the collected water samples: The physicochemical properties of the collected water samples are reported in table 1. At the time of sampling, the temperature was 10.6°C and pH 7.89. The salinity of the sample, as determined in situ, was 224.70 g/L (22,47% (w/v)). Chemical analysis of water sample indicated that Na +and Cl- were the most abundant ions (table 1). SO4-2 and Mg+2 was present in much smaller amounts compared to Na +and Cl- concentration. Low levels of calcium, potassium and bicarbonate were also detected, often at less than 1 g/L.Characterization of isolates. Morphological and biochemical characteristic feature of halophilic bacterial isolates: Among 52 strains isolated from water of Chott Tinsilt, seven distinct bacteria (A1, A2, A3, A4, B1, B4 and B5) were chosen for further characterization (table 2). The colour of the isolates varied from beige, pale yellow, yellowish and orange. The bacterial isolates A1, A2, A4, B1 and B5 were rod shaped and gram negative (except B5), whereas A3 and B4 were cocci and gram positive. All strains were oxidase and catalase positive except for B1. Nitrate reductase and urease activities were observed in all the bacterial isolates, except B4. All the bacterial isolates were negative for H2S formation. B5 was the only strain positive for mannitol fermentation (table 2).We isolated halophilic bacteria on growth medium with NaCl supplementation at pH 7 and temperature of 30°C. We studied the effect of NaCl, temperature and pH on the growth of bacterial isolates. All the isolates exhibited growth only in the presence of NaCl indicating that these strains are halophilic. The optimum growth of isolates A3 and B1 was observed in the presence of 10% NaCl, whereas it was 15% NaCl for A1, A2 and B5. A4 and B4 showed optimum growth in the presence of 20% and 25% NaCl respectively. A4, B4 and B5 strains can tolerate up to 35% NaCl.The isolate B1 showed growth in medium supplemented with 10% NaCl and pH range of 7–10. The optimum pH for the growth B1 was 9 and they did not show any detectable growth at or below pH 6 (table 2), which indicates the alkaliphilic nature of B1 isolate. The bacterial isolates A1, A2 and A4 exhibited growth in the range of pH 6–10, while A3 and B4 did not show any growth at pH greater than 8. The optimum pH for growth of all strains (except B1) was pH 7.0 (table 2). These results indicate that A1, A2, A3, A4, B4 and B5 are neutrophilic in nature. All the bacterial isolates exhibited optimal growth at 30°C and no detectable growth at 55°C. Also, detectable growth of isolates A1, A2 and A4 was observed at 4°C. However, none of the bacterial strains could grow below 4°C and above 50°C (table 2).Screening of the halophilic enzymes: To characterize the diversity of halophiles able to produce hydrolytic enzymes among the population of microorganisms inhabiting the hypersaline habitats of East Algeria (Chott Tinsilt), a screening was performed. As described in Materials and Methods, samples were plated on solid media containing 10%-25% (w/v) of total salts and different substrates for the detection of amylase, protease, lipase and DNAse activities. However, coagulase activity was determined in liquid medium using milk as substrate (figure 3). Distributions of hydrolytic activity among the isolates are summarized in table 4.From the seven bacterial isolates, four strains A1, A2, A4 and B5 showed combined hydrolytic activities. They were positive for gelatinase, lipase and coagulase. A3 strain showed gelatinase and lipase activities. DNAse activities were detected with A1, A4, B1 and B5 isolates. B4 presented lipase and coagulase activity. Surprisingly, no amylase activity was detected among all the isolates.Screening for biosurfactant producing isolates: Oil spread assay: The results showed that all the strains could produce notable (>4 cm diameter) oil expelling circles (ranging from 4.11 cm to 4.67 cm). The average diameter for strain B5 was 4.67 cm, significantly (P < 0.05) higher than for the other strains.Surface tension and emulsification index (E24): The assimilation of hydrocarbons as the sole sources of carbon by the isolate strains led to the production of biosurfactants indicated by the emulsification index and the lowering of the surface tension of cell-free supernatant. Based on rapid growth on media containing diesel oil as sole carbon source, the seven isolates were tested for biosurfactant production and emulsification activity. The obtained values of the surface tension measurements as well as the emulsification index (E24) are shown in table 3. The highest reduction of surface tension was achieved with B5 and A3 isolates with values of 25.3 mN m−1 and 28.1 mN m−1 respectively. The emulsifying capacity evaluated by the E24 emulsification index was highest in the culture of isolate B4 (78%), B5 (77%) and A3 (76%) as shown in table 3 and figure 2. These emulsions were stable even after 4 months. The bacteria with emulsification indices higher than 50 % and/or reduction in the surface tension (under 30 mN/m) have been defined as potential biosurfactant producers. Based on surface tension and the E24 index results, isolates B5, B4, A3 and A4 are the best candidates for biosurfactant production. It is important to note that, strains B4 and A4 produce biosurfactant in medium containing respectively 25% and 20% (w/v) NaCl.Stability of biosurfactant activities: The applicability of biosurfactants in several biotechnological fields depends on their stability at different environmental conditions (temperatures, pH and NaCl). For this study, the strain B4 appear very interesting (It can produce biosurfactant at 25 % NaCl) and was choosen for futher analysis for biosurfactant stability. The effects of temperature and pH on the biosurfactant production by the strain B4 are shown in figure 4.biosurfactant in medium containing respectively 25% and 20% (w/v) NaCl.Stability of biosurfactant activities: The applicability of biosurfactants in several biotechnological fields depends on their stability at different environmental conditions (temperatures, pH and NaCl). For this study, the strain B4 appear very interesting (It can produce biosurfactant at 25 % NaCl) and was chosen for further analysis for biosurfactant stability. The effects of temperature and pH on the biosurfactant production by the strain B4 are shown in figure 4. The biosurfactant produced by this strain was shown to be thermostable giving an E-24 Index value greater than 78% (figure 4A). Heating of the biosurfactant to 100 °C caused no significant effect on the biosurfactant performance. Therefore, the surface activity of the crude biosurfactant supernatant remained relatively stable to pH changes between pH 6 and 11. At pH 11, the value of E24 showed almost 76% activity, whereas below pH 6 the activity was decreased up to 40% (figure 4A). The decreases of the emulsification activity by decreasing the pH value from basic to an acidic region; may be due to partial precipitation of the biosurfactant. This result indicated that biosurfactant produced by strain B4 show higher stability at alkaline than in acidic conditions.Molecular identification and phylogenies of potential isolates: To identify halophilic bacterial isolates, the 16S rDNA gene was amplified using gene-specific primers. A PCR product of ≈ 1.3 kb was detected in all the seven isolates. The 16S rDNA amplicons of each bacterial isolate was sequenced on both strands using 27F and 1492R primers. The complete nucleotide sequence of 1336,1374, 1377,1313, 1305,1308 and 1273 bp sequences were obtained from A1, A2, A3, A4, B1, B4 and B5 isolates respectively, and subjected to BLAST analysis. The 16S rDNA sequence analysis showed that the isolated strains belong to the genera Halomonas, Staphylococcus, Salinivibrio, Planococcus and Halobacillus as shown in table 5. The halophilic isolates A2 and A4 showed 97% similarity with the Halomonas variabilis strain GSP3 (accession no. AY505527) and the Halomonas sp. M59 (accession no. AM229319), respectively. As for A1, it showed 96% similarity with the Halomonas venusta strain GSP24 (accession no. AY553074). B1 and B4 showed for their part 96% similarity with the Salinivibrio costicola subsp. alcaliphilus strain 18AG DSM4743 (accession no. NR_042255) and the Planococcus citreus (accession no. JX122551), respectively. The bacterial isolate B5 showed 98% sequence similarity with the Halobacillus trueperi (accession no. HG931926), As for A3, it showed only 95% similarity with the Staphylococcus arlettae (accession no. KR047785). The 16S rDNA nucleotide sequences of all the seven halophilic bacterial strains have been submitted to the NCBI GenBank database under the accession number presented in table 5. The phylogenetic association of the isolates is shown in figure 5.DICUSSIONThe physicochemical properties of the collected water samples indicated that this water was relatively neutral (pH 7.89) similar to the Dead Sea and the Great Salt Lake (USA) and in contrast to the more basic lakes such as Lake Wadi Natrun (Egypt) (pH 11) and El Golea Salt Lake (Algeria) (pH 9). The salinity of the sample was 224.70 g/L (22,47% (w/v). This range of salinity (20-30%) for Chott Tinsilt is comparable to a number of well characterized hypersaline ecosystems including both natural and man-made habitats, such as the Great Salt Lake (USA) and solar salterns of Puerto Rico. Thus, Chott Tinsilt is a hypersaline environment, i.e. environments with salt concentrations well above that of seawater. Chemical analysis of water sample indicated that Na +and Cl- were the most abundant ions, as in most hypersaline ecosystems (with some exceptions such as the Dead Sea). These chemical water characteristics were consistent with the previously reported data in other hypersaline ecosystems (DasSarma and Arora, 2001; Oren, 2002; Hacěne et al., 2004). Among 52 strains isolated from this Chott, seven distinct bacteria (A1, A2, A3, A4, B1, B4 and B5) were chosen for phenotypique, genotypique and phylogenetique characterization.The 16S rDNA sequence analysis showed that the isolated strains belong to the genera Halomonas, Staphylococcus, Salinivibrio, Planococcus and Halobacillus. Genera obtained in the present study are commonly occurring in various saline habitats across the globe. Staphylococci have the ability to grow in a wide range of salt concentrations (Graham and Wilkinson, 1992; Morikawa et al., 2009; Roohi et al., 2014). For example, in Pakistan, Staphylococcus strains were isolated from various salt samples during the study conducted by Roohi et al. (2014) and these results agreed with previous reports. Halomonas, halophilic and/or halotolerant Gram-negative bacteria are typically found in saline environments (Kim et al., 2013). The presence of Planococcus and Halobacillus has been reported in studies about hypersaline lakes; like La Sal del Rey (USA) (Phillips et al., 2012) and Great Salt Lake (Spring et al., 1996), respectively. The Salinivibrio costicola was a representative model for studies on osmoregulatory and other physiological mechanisms of moderately halophilic bacteria (Oren, 2006).However, it is interesting to note that all strains shared less than 98.7% identity (the usual species cut-off proposed by Yarza et al. (2014) with their closest phylogenetic relative, suggesting that they could be considered as new species. Phenotypic, genetic and phylogenetic analyses have been suggested for the complete identification of these strains. Theses bacterial strains were tested for the production of industrially important enzymes (Amylase, protease, lipase, DNAse and coagulase). These isolates are good candidates as sources of novel enzymes with biotechnological potential as they can be used in different industrial processes at high salt concentration (up to 25% NaCl for B4). Prominent amylase, lipase, protease and DNAase activities have been reported from different hypersaline environments across the globe; e.g., Spain (Sánchez‐Porro et al., 2003), Iran (Rohban et al., 2009), Tunisia (Baati et al., 2010) and India (Gupta et al., 2016). However, to the best of our knowledge, the coagulase activity has never been detected in extreme halophilic bacteria. Isolation and characterization of crude enzymes (especially coagulase) to investigate their properties and stability are in progress.The finding of novel enzymes with optimal activities at various ranges of salt concentrations is of great importance. Besides being intrinsically stable and active at high salt concentrations, halophilic and halotolerant enzymes offer great opportunities in biotechnological applications, such as environmental bioremediation (marine, oilfiel) and food processing. The bacterial isolates were also characterized for production of biosurfactants by oil-spread assay, measurement of surface tension and emulsification index (E24). There are few reports on biosurfactant producers in hypersaline environments and in recent years, there has been a greater increase in interest and importance in halophilic bacteria for biomolecules (Donio et al., 2013; Sarafin et al., 2014). Halophiles, which have a unique lipid composition, may have an important role to play as surface-active agents. The archae bacterial ether-linked phytanyl membrane lipid of the extremely halophilic bacteria has been shown to have surfactant properties (Post and Collins, 1982). Yakimov et al. (1995) reported the production of biosurfactant by a halotolerant Bacillus licheniformis strain BAS 50 which was able to produce a lipopeptide surfactant when cultured at salinities up to 13% NaCl. From solar salt, Halomonas sp. BS4 and Kocuria marina BS-15 were found to be able to produce biosurfactant when cultured at salinities of 8% and 10% NaCl respectively (Donio et al., 2013; Sarafin et al., 2014). In the present work, strains B4 and A4 produce biosurfactant in medium containing respectively 25% and 20% NaCl. To our knowledge, this is the first report on biosurfactant production by bacteria under such salt concentration. Biosurfactants have a wide variety of industrial and environmental applications (Akbari et al., 2018) but their applicability depends on their stability at different environmental conditions. The strain B4 which can produce biosurfactant at 25% NaCl showed good stability in alkaline pH and at a temperature range of 30°C-100°C. Due to the enormous utilization of biosurfactant in detergent manufacture the choice of alkaline biosurfactant is researched (Elazzazy et al., 2015). On the other hand, the interesting finding was the thermostability of the produced biosurfactant even after heat treatment (100°C for 30 min) which suggests the use of this biosurfactant in industries where heating is of a paramount importance (Khopade et al., 2012). To date, more attention has been focused on biosurfactant producing bacteria under extreme conditions for industrial and commercial usefulness. In fact, the biosurfactant produce by strain B4 have promising usefulness in pharmaceutical, cosmetics and food industries and for bioremediation in marine environment and Microbial enhanced oil recovery (MEOR) where the salinity, temperature and pH are high.CONCLUSIONThis is the first study on the culturable halophilic bacteria community inhabiting Chott Tinsilt in Eastern Algeria. Different genera of halotolerant bacteria with different phylogeneticaly characteristics have been isolated from this Chott. Culturing of bacteria and their molecular analysis provides an opportunity to have a wide range of cultured microorganisms from extreme habitats like hypersaline environments. Enzymes produced by halophilic bacteria show interesting properties like their ability to remain functional in extreme conditions, such as high temperatures, wide range of pH, and high salt concentrations. These enzymes have great economical potential in industrial, agricultural, chemical, pharmaceutical, and biotechnological applications. Thus, the halophiles isolated from Chott Tinsilt offer an important potential for application in microbial and enzyme biotechnology. In addition, these halo bacterial biosurfactants producers isolated from this Chott will help to develop more valuable eco-friendly products to the pharmacological and food industries and will be usefulness for bioremediation in marine environment and petroleum industry.ACKNOWLEDGMENTSOur thanks to Professor Abdelhamid Zoubir for proofreading the English composition of the present paper.CONFLICT OF INTERESTThe authors declare that they have no conflict of interest.Akbari, S., N. H. Abdurahman, R. M. Yunus, F. Fayaz and O. R. Alara, 2018. Biosurfactants—a new frontier for social and environmental safety: A mini review. Biotechnology research innovation, 2(1): 81-90.Association, A. P. H., A. W. W. Association, W. P. C. 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Roman biotechnol lett, 17(2): 7049-7064.Elazzazy, A. M., T. Abdelmoneim and O. Almaghrabi, 2015. Isolation and characterization of biosurfactant production under extreme environmental conditions by alkali-halo-thermophilic bacteria from Saudi Arabia. Saudi journal of biological Sciences, 22(4): 466-475.Graham, J. E. and B. Wilkinson, 1992. Staphylococcus aureus osmoregulation: Roles for choline, glycine betaine, proline, and taurine. Journal of bacteriology, 174(8): 2711-2716.Gupta, S., P. Sharma, K. Dev and A. Sourirajan, 2016. Halophilic bacteria of lunsu produce an array of industrially important enzymes with salt tolerant activity. Biochemistry research international, 1: 1-10.Gupta, S., P. Sharma, K. Dev, M. Srivastava and A. Sourirajan, 2015. A diverse group of halophilic bacteria exist in lunsu, a natural salt water body of Himachal Pradesh, India. SpringerPlus 4(1): 274.Hacěne, H., F. Rafa, N. Chebhouni, S. Boutaiba, T. Bhatnagar, J. C. Baratti and B. Ollivier, 2004. 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Ohta, Y. Tanaka, K. Takeyasu and T. Msadek, 2009. Adaptation beyond the stress response: Cell structure dynamics and population heterogeneity in Staphylococcus aureus. Microbes environments, 25: 75-82.Morikawa, M., Y. Hirata and T. J. B. e. B. A.-M. Imanaka, 2000. A study on the structure–function relationship of lipopeptide biosurfactants. Biochimica et biophysica acta, 1488(3): 211-218.Oren, A., 2002. Diversity of halophilic microorganisms: Environments, phylogeny, physiology, and applications. Journal of industrial microbiology biotechnology, 28(1): 56-63.Oren, A., 2006. Halophilic microorganisms and their environments. Springer science & business media.Oren, A., R. Vreeland and L. Hochstein, 1993. Ecology of extremely halophilic microorganisms. The biology of halophilic bacteria, 2(1): 1-8.Phillips, K., F. Zaidan, O. R. Elizondo and K. L. Lowe, 2012. Phenotypic characterization and 16s rDNA identification of culturable non-obligate halophilic bacterial communities from a hypersaline lake, la sal del rey, in extreme south texas (USA). Aquatic biosystems, 8(1): 1-5.Post, F. and N. Collins, 1982. A preliminary investigation of the membrane lipid of Halobacterium halobium as a food additive 1. Journal of food biochemistry, 6(1): 25-38.Rocha, C., F. San-Blas, G. San-Blas and L. Vierma, 1992. Biosurfactant production by two isolates of Pseudomonas aeruginosa. World Journal of microbiology biotechnology, 8(2): 125-128.Rohban, R., M. A. Amoozegar and A. Ventosa, 2009. Screening and isolation of halophilic bacteria producing extracellular hydrolyses from howz soltan lake, Iran. Journal of industrial microbiology biotechnology, 36(3): 333-340.Roohi, A., I. Ahmed, N. Khalid, M. Iqbal and M. Jamil, 2014. Isolation and phylogenetic identification of halotolerant/halophilic bacteria from the salt mines of Karak, Pakistan. 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Background: Reperfusion following ischemia can lead to more injuries than ischemia itself especially in diabetic patients. The aim of this study was to evaluate the effect of dexmedetomidine on ischemia-reperfusion injury (IRI) in rats with have hepatic IRI and diabetes mellitus. Methodology: Twenty-eight Wistar Albino rats were randomised into four groups as control (C), diabetic (DC), diabetic with hepatic ischemia-reperfusion injury (DIR), and diabetic but administered dexmedetomidine followed by hepatic IRI (DIRD) groups. Hepatic tissue samples were evaluated histopathologically by semiquantitative methods. Malondialdehyde (MDA), superoxide dismutase (SOD), glutathion s-transpherase (GST), and catalase (CAT) enzyme levels were investigated in liver and kidney tissues as oxidative state parameters. Results: In Group DIR; hepatocyte degeneration, sinusoidal dilatation, pycnotic nucleus, and necrotic cells were found to be more in rat hepatic tissue; while mononuclear cell infiltration was higher in the parenchyme. MDA levels were significantly lower; but SOD levels were significantly higher in Group DIRD with regard to Group DIR. In the IRI induced diabetic rats’ hepatic and nephrotic tissues MDA levels, showing oxidative injury, were found to be lower. SOD levels, showing early antioxidant activity, were higher. Conclusion: The enzymatic findings of our study together with the hepatic histopathology indicate that dexmedetomidine has a potential role to decrease IRI. Key words: Hepatic ischemia reperfusion injury; Diabetes mellitus; Dexmedetomidine; Rat; MDA; SOD Citation: Sezen SC, Işık B, Bilge M, Arslan M, Çomu FM, Öztürk L, Kesimci E, Kavutçu M. Effect of dexmedetomidine on ischemia-reperfusion injury of liver and kidney tissues in experimental diabetes and hepatic ischemia-reperfusion injury induced rats. Anaesth Pain & Intensive Care 2016;20(2):143-149 Received: 21 November 2015; Reviewed: 10, 24 December 2015, 9, 10 June 2016; Corrected: 12 December 2015; Accepted: 10 June 2016 INTRODUCTİON Perioperative acute tissue injury induced by ischemia-reperfusion is a comman clinical event caused by reduced blood supply to the tissue being compromised during major surgery. Ischemia leads to cellular injury by depleting cellular energy deposits and resulting in accumulation of toxic metabolites. The reperfusion of tissues that have remained in ischemic conditions causes even more damage.1 Furthermore hepatic ischemia-reperfusion injury (IRI) demonstrates a strong relationship with peri-operative acute kidney injury.2 The etiology of diabetic complications is strongly associated with increased oxidative stress (OS). Diabetic patients are known to have a high risk of developing OS or IRI which results with tissue failure.3 The most important role in ischemia and reperfusion is played by free oxygen radicals.1 In diabetes, characterized by hyperglycemia, even more free oxygen radicals are produced due to oxidation of glucose and glycosylation of proteins.3 The structures which are most sensitive to free oxygen radicals in the cells are membrane lipids, proteins, nucleic acids and deoxyribonucleic acids.1 It has been reported that endogenous antioxidant enzymes [superoxide dismutase (SOD), glutathion s-transpherase (GST), catalase (CAT)] play an important role to alleviate IRI.4-8 Also some pharmacological agents have certain effects on IRI.1 The anesthetic agents influence endogenous antioxidant systems and free oxygen radical formation.9-12 Dexmedetomidine is a selective α-2 adrenoceptor agonist agent. It has been described as a useful and safe adjunct in many clinical applications. It has been found that it may increase urine output by considerably redistributing cardiac output, inhibiting vasopressin secretion and maintaining renal blood flow and glomerular filtration. Previous studies demonstrated that dexmedetomidine provides protection against renal, focal cerebral, cardiac, testicular, and tourniquet-induced IRI.13-18 Arslan et al observed that dexmedetomidine protected against lipid peroxidation and cellular membrane alterations in hepatic IRI, when given before induction of ischemia.17 Si et al18 demonstrated that dexmedetomidine treatment results in a partial but significant attenuation of renal demage induced by IRI through the inactivation of JAK/STAT signaling pathway in an in vivo model. The efficacy of the dexmedetomidine for IRI in diabetic patient is not resarched yet. The purpose of this experimental study was to evaluate the biochemical and histological effects of dexmedetomidine on hepatic IRI in diabetic rat’s hepatic and renal tissue. METHODOLOGY Animals and Experimental Protocol: This study was conducted in the Physiology Laboratory of Kirikkale University upon the consent of the Experimental Animals Ethics Committee of Kirikkale University. All of the procedures were performed according to the accepted standards of the Guide for the Care and Use of Laboratory Animals. In the study, 28 male Wistar Albino rats, weighing between 250 and 300 g, raised under the same environmental conditions, were used. The rats were kept under 20-21 oC at cycles of 12-hour daylight and 12-hour darkness and had free access to food until 2 hours before the anesthesia procedure. The animals were randomly separated into four groups, each containing 7 rats. Diabetes was induced by a single intraperitoneal injection of streptozotocin (Sigma Chemical, St. Louis, MO, USA) at a dose of 65 mg/kg body weight. The blood glucose levels were measured at 72 hrs following this injection. Rats were classified as diabetic if their fasting blood glucose (FBG) levels exceeded 250 mg/dl, and only animals with FBGs of > 250 mg/dl were included in the diabetic groups (dia­betes only, diabetes plus ischemia-reperfusion and diabetes plus dexmedetomidine-ischemia-reperfusion). The rats were kept alive 4 weeks after streptozotocin injection to allow development of chronic dia­betes before they were exposed to ischemia-reperfusion.(19) The rats were weighed before the study. Rats were anesthetized with intraperitoneal ketamine 100 mg/kg. The chest and abdomen were shaved and each animal was fixed in a supine position on the operating table. The abdomen was cleaned with 1% polyvinyl iodine and when dry, the operating field was covered with a sterile drape and median laparotomy was performed. There were four experimental groups (Group C (sham-control; n = 7), (Group DC (diabetes-sham-control; n = 7), Group DIR (diabetes-ischemia-reperfusion; n = 7), and Group DIRD (diabetes-ischemia-reperfusion-dexmedetomidine; n = 7). Sham operation was performed on the rats in Group C and Group DC. The sham operation consisted of mobilization of the hepatic pedicle only. The rats in this group were sacrificed 90 min after the procedure. Hepatic I/R injury was induced in Groups DIR and DIRD respectively with hepatic pedicle clamping using a vascular clamp as in the previous study of Arslan et al.(17) After an ischemic period of 45 min, the vascular clamp was removed. A reperfusion period was maintained for 45 min. In Group DIRD, dexmedetomidine hydrochloride 100 μg/kg, (Precedex 100 μg/2 ml, Abbott®, Abbott Laboratory, North Chicago, Illinois, USA) was administrated via intraperitoneal route 30 minutes before surgery. All the rats were given ketamine 100 mg/kg intraperitoneally and intracardiac blood samples were obtained. Preserving the tissue integrity by avoiding trauma, liver and renal biopsy samples were obtained. Biochemical Analysis: The liver and renal tissues were first washed with cold deionized water to discard blood contamination and then homogenized in a homogenizer. Measurements on cell contest require an initial preparation of the tissues. The preparation procedure may involve grinding of the tissue in a ground glass tissue blender using a rotor driven by a simple electric motor. The homogenizer as a tissue blender similar to the typical kitchen blender is used to emulsify and pulverize the tissue (Heidolph Instruments GMBH & CO KGDiax 900 Germany®) at 1000 U for about 3 min. After centrifugation at 10,000 g for about 60 min, the upper clear layer was taken. MDA levels were determined using the method of Van Ye et al,(20) based on the reaction of MDA with thiobarbituric acid (TBA). In the TBA test reaction, MDA and TBA react in acid pH to form a pink pigment with an absorption maximum at 532 nm. Arbitrary values obtained were compared with a series of standard solutions (1,1,3,3-tetraethoxypropane). Results were expressed as nmol/mg.protein. Part of the homogenate was extracted in ethanol/chloroform mixture (5/3 v/v) to discard the lipid fraction, which caused interferences in the activity measurements of T-SOD, CAT and GST activities. After centrifugation at 10.000 x g for 60 min, the upper clear layer was removed and used for the T-SOD, CAT, GST enzyme activity measurement by methods as described by Durak et al21, Aebi22 and Habig et al23 respectively. One unit of SOD activity was defined as the enzyme protein amount causing 50% inhibition in NBTH2 reduction rate and result were expressed in U/mg protein. The CAT activity method is based on the measurement of absorbance decrease due to H2O2 consumption at 240 nm. The GST activity method is based on the measurement of absorbance changes at 340 nm due to formation of GSH-CDNB complex. Histological determinations: Semiquantitative evaluation technique used by Abdel-Wahhab et al(24) was applied for interpreting the structural changes investigated in hepatic tissues of control and research groups. According to this, (-) (negative point) represents no structural change, while (+) (one positive point) represents mild, (++) (two positive points) medium and (+++) (three positive points) represents severe structural changes. Statistical analysis: The Statistical Package for the Social Sciences (SPSS, Chicago, IL, USA) 20.0 softwre was used for the statistical analysis. Variations in oxidative state parameters, and histopathological examination between study groups were assessed using the Kruskal-Wallis test. The Bonferroni-adjusted Mann-Whitney U-test was used after significant Kruskal-Wallis to determine which groups differed from the others. Results were expressed as mean ± standard deviation (Mean ± SD). Statistical significance was set at a p value < 0.05 for all analyses. RESULTS There was statistically significant difference observed between the groups with respect to findings from the histological changes in the rat liver tissue (hepatocyte degeneration, sinüsoidal dilatation, pycnotic nucleus, prenecrotic cell) determined by light microscopy according to semiquantitative evaluation techniques (p < 0.0001). In Group DIR, hepatocyte degeneration was significantly high compared to Group C, Group DC and Group DIRD (p < 0.0001, p < 0.0001, p = 0.002, respectively), (Table 1, Figure 1-4). Similarly, sinüsoidal dilatation was significantly higher in Group DIR (p < 0.0001, p = 0.004, p = 0.015, respectively). Although, pcynotic nucleus was decreased in Group DIRD, it did not make a significant difference in comparison to Group DIR (p = 0.053), (Table 1, Figure 1-4). The prenecrotic cells were significantly increased in Group DIR, with respect to Group C, Group DC and Group DIRD (p < 0.0001, p = 0.004, p < 0.0001, respectively), (Table 1, Figure 1-4). Table 1. The comparison of histological changes in rat hepatic tissue [Mean ± SD)] p**: Statistical significance was set at a p value < 0.05 for Kruskal-Wallis test *p < 0.05: When compared with Group DIR Figure 1: Light microscopic view of hepatic tissue of Group C (control). VC: vena centralis, *: sinusoids. ®: hepatocytes, k: Kupffer cells, G: glycogen granules, mc: minimal cellular changes, Hematoxilen & Eosin x 40 Figure 2: Light-microscopic view of hepatic tissue of Group DC (diabetes mellitus control) (G: Glycogen granules increased in number, (VC: vena centralis, *:sinusoids. ®:hepatocytes, k:Kupffer cells, G: glycogen granules, mc: minimal cellular changes; Hematoxylin & Eosin x 40) Figure 3: Light-microscopic view of hepatic tissue of Group DIR (Diabetes Mellitus and ischemia-reperfusion) (VC: vena centralis, (H) degenerative and hydrophic hepatocytes, (dej) vena centralis degeneration (centrolobar injury) (*): sinusoid dilatation. (←) pycnotic and hyperchromatic nuclei, MNL: mononuclear cell infiltration, (¯) congestion, K: Kupffer cell hyperplasia, (­) vacuolar degeneration (Hematoxylin & Eosin x 40) Figure 4: Light-microscopic view of hepatic tissue of Group DIRD (Diabetes Mellitus and ischemia-reperfusion together with dexmedetomidine applied group) (VC: vena centralis, (MNL) mononuclear cell infiltration, (dej) hydrophilic degeneration in hepatocytes around vena centralis, (conj) congestion, G: glycogen granules, (←) pycnotic and hyperchromatic nuclei, sinusoid dilatation (*) (Hematoxylin & Eosin x 40) Besides, in liver tissue parenchyma, MN cellular infiltration was a light microscopic finding; and showed significant changes among the groups (p < 0.0001). This was significantly higher in Group DIR, compared to Group C, DC, and DIRD (p < 0.0001, p=0.007, p = 0.007, respectively), (Table 1, Figure 1-4). The enzymatic activity of MDA, SOD and GST in hepatic tissues showed significant differences among the groups [(p = 0.019), (p = 0.034). (p = 0.008) respectively]. MDA enzyme activity was significantly incresed in Group DIR, according to Group C and Group DIRD (p = 0.011, p = 0.016, respectively), (Table 2). In Group DIR SOD enzyme activity was lower with respect to Group C and Group DIRD (p = 0.010, p = 0.038, respectively), (Table 2). The GST enzyme activity was significantly higher in Group DIR, when compared to Group C, DC and DIRD (p = 0.007, p = 0.038, p = 0.039, respectively), (Table 2). Table 2. Oxidative state parameters in rat hepatic tissue [Mean ± SD] p**: Statistical significance was set at a p value < 0.05 for Kruskal-Wallis test *p < 0.05: When compared with Group DIR The enzymatic activity of MDA, SOD in renal tissues, showed significant differences among the groups [(p < 0.0001), (p = 0.008) respectively ]. MDA enzyme activity was significantly incresed in Group DIR, according to Group C and Group DIRD (p < 0.0001, p < 0.0001, respectively). Also MDA enzyme activity level was significantly increased in Group DC, in comparison to Group C and Group DIRD (p = 0.003, p = 0.001, respectively), (Table 3). In Group DIR SOD enzyme activity was lower with respect to Group C and Group DIRD (p = 0.032, p = 0.013, respectively), (Table 3). The GST enzyme activity was significantly higher in Group DIR than the other three groups, however; CAT levels were similar among the groups (Table 3). Table 3: Oxidative state parameters in rat nephrotic tissue [Mean ± SD)] p**: Statistical significance was set at a p value < 0.05 for Kruskal-Wallis test *p < 0.05: When compared with Group DIR DISCUSSION In this study, we have reported the protective effect of dexmedetomidine in experimental hepatic and renal IRI model in the rat by investigating the MDA and SOD levels biochemically. Besides, hepatic histopathological findings also supported our report. Ischemic damage may occur with trauma, hemorrhagic shock, and some surgical interventions, mainly hepatic and renal resections. Reperfusion following ischemia results in even more injury than ischemia itself. IRI is an inflammatory response accompanied by free radical formation, leucocyte migration and activation, sinusoidal endothelial cellular damage, deteoriated microcirculation and coagulation and complement system activation.1 We also detected injury in hepatic and renal tissue caused by reperfusion following ischemia in liver. Experimental and clinical evidence indicates that OS is involved in both the pathogenesis and the complications of diabetes mellitus.25,26 Diabetes mellitus is a serious risk factor for the development of renal and cardiovascular disease. It is also related to fatty changes in the liver.27 Diabetes-related organ damage seems to be the result of multiple mechanisms. Diabetes has been associated with increased free radical reactions and oxidant tissue damage in STZ-induced diabetic rats and also in patients.26Oxidative stress has been implicated in the destruction of pancreatic β-cells28 and could largely contribute to the oxidant tissue damage associated with chronic hyperglycemia.29 A number of reports have shown that antioxidants can attenuate the complications of diabetes in patients30 and in experimental models.28,31 This study demonstrated that diabetes causes a tendency to increase the IRI. There is a lot of investigations related to the pharmacological agents or food supplements applied for decreasing OS and IRI. Antioxidant agents paly an important role in IRI by effecting antioxidant system or lessening the formation of ROS. It has been reported that anesthetic agents too, are effective in oxidative stress.1 During surgical interventions, it seems rational to get benefit from anesthetic agents in prevention of OS caused by IRI instead of using other agents. It has been declared that; dexmedetomidine; as an α-2 agonist with sedative, hypnotic properties; is important in prevention of renal, focal, cerebral, cardiac, testicular and tourniquet-induced IRI.13-18 On the other hand Bostankolu et al. concluded that dexmedetomidine did not have an additional protective role for tournique induced IRI during routine general anesthesia.32 In this study; we have shown that dexmedetomidine has a reducing effect in IRI in diabetic rats. Some biochemical tests and histopathological evaluations are applied for bringing up oxidative stress and IRI in the tissues. Reactive oxygen species (ROS) that appear with reperfusion injury damage cellular structures through the process of the lipid peroxidation of cellular membranes and yield toxic metabolites such as MDA.33 As an important intermidiate product in lipid peroxidation, MDA is used as a sensitive marker of IRI.34 ROS-induced tissue injury is triggered by various defense mechanisms.35 The first defence mechanisms include the antioxidant enzymes of SOD, CAT, and GPx. These endogenous antioxidants are the first lines of defence against oxidative stres and act by scavenging potentially damaging free radical moieties.36 There is a balance between ROS and the scavenging capacity of antioxidant enzymes.1-8 In this study, for evaluation of oxidative damage and antioxidant activity, MDS, SOD, GST and CAT levels were determined in liver and kidney tissues. MDA levels in hepatic and renal tissues were higher in Group DIR compared to Group C and Group DIRD. GST levels were higher in Group DIR compared to all the other three groups. When the groups were arranged from highest to lowest order, with respect to CAT levels, the order was; Group DIR, Group DIRD, Group DC and Group C. However, the difference was not significant. The acute phase reactant MDA, as a marker of OS, was found to be high in Group DIR and low in Group DIRD. This could be interpreted as the presence of protective effect of dexmedetomidine in IRI. IRI developing in splanchnic area causes injury also in the other organs.35 Leithead et al showed that clinically significant hepatic IRI demonstrates a strong relationship with peri-operative acute kidney injury.2 In our experimental research that showed correlation to that of research by Leithead et al. After hepatic IRI in diabetic rats renal OS marker MDA levels were significantly more in Group DIR than Group DIRD. In our study, we observed histopathological changes in the ischemic liver tissue and alterations in the level of MDA, SOD, GST and CAT levels which are OS markers. Histopathological changes of the liver tissues are hepatocyt degeneration, sinusoidal dilatation, nuclear picnosis, celluler necrosis, mononuclear cell infiltrationat paranchimal tissue. These histopathological injury scores were significantly lower in the Group DIRD than those in group DIR. LIMITATION Study limitation is there was no negative control group, as this type of surgical intervention is not possible in rats without anesthesia. CONCLUSION The enzymatic findings of our study together with the hepatic histopathology indicate that dexmedetomidine has a potential role to decrease ischemia-reperfusion injury. Conflict of interest and funding: The authors have not received any funding or benefits from industry or elsewhere to conduct this study. 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An environmentally-based systems approach to sustainability analyses of organic fruit production systems in New Zealand. This research introduces an approach for the assessment of the sustainability of farming systems. It is based on the premises that sustainability has an environmental bottom line and that there is very limited substitutability between natural capital and other forms of capital. Sustainability assessment is undertaken through analyses of energy and material flows of the system and their impacts on the environment. The proposed sustainability assessment approach is based on two high level criteria for sustainability: efficient use of energy and non-degradation of the environment from energy and material use. Sustainability assessment of organic orchard systems in New Zealand was undertaken to demonstrate this approach. Five indicators which address the two criteria for the sustainability of the orchard systems are the energy ratio, the CO2 ratio, changes in the soil carbon level, nutrient balances, and the leaching of nitrogen. Organic kiwifruit and organic apple systems are modelled based on their key energy and material flows and their interactions with the natural environment. The energy and material flows are converted into appropriate energy and matter equivalents based on coefficients taken from the published literature. Sustainability indicators are estimated over one growing season using two computer modelling tools, Overseer® and Stella®, in a life cycle approach. Sustainability assessment of the organic orchard systems suggests that the approach is useful for evaluating energy use and key environmental impacts that occur in soil, water and atmosphere. The results indicate that the model organic orchard systems are sustainable in terms of energy use and are a net sink of CO2-equivalent emissions. The implication of this result is that organic orchard systems potentially could trade carbon credits under the Kyoto Protocol. The findings also suggest that the sustainability assessment approach is capable of identifying the trade-offs within the sustainability indicators associated with particular management practices. Further research to improve and validate the proposed approach is essential, before it can be practically used for decision making at the orchard level and for policy making at the national level.

The health of the environment is integral to the health and wellbeing of the people. When the balance between Atua, whenua and tangata is disrupted, desecrated, disturbed or violated, it can have a detrimental impact on these relationships. This research study explored alternative indigenous paradigms for conceptualizing an environmental health framework that would improve the potency and health of all living things. A key question of the research study was to explore how Ngati Kuri sought to strengthen their relationship and connection with the natural world. The Hapu established Te Tai O Marokura health and social services as a vehicle to improve potency: healthy environments, healthy people. The specificity of Ngati Kuri experiences provided a broader context for researching and theorizing about restorative models that utilized traditional knowledge localized to a particular area. Another key question was to examine how Maori cultural values that were embedded within a worldview, could offer insights and constructs for new ways of being and thinking in the modern world. Kaupapa Maori philosophical positioning and theorizing informed the approaches and practices underpinning the study. The key aspects of the methodology were constructed around the tikanga principles of tinorangatiratanga, whakapapa and kaitiakitanga to provide a rationale for the collaboration formed with the Hapu. At the heart of the thesis is the validity given to the collective ownership of indigenous knowledge which challenges the fictional notion of a singular, temporally bound authorship. The thesis reflects the whakawhanaungatanga (reciprocal understanding) relationship between the Tuakana represented by Miriama Kahu and the Teina, Benita Wakefield working collaboratively with the Kaitiaki construct group formed to ensure that the use of indigenous knowledge and its transmission processes had honest transparency. The Tuakana was responsible for providing guidance, wisdom and mentoring to the Teina, the enrolled academic student responsible for producing the written thesis. These innovative collaborative Kaupapa Maori methods and practices in the study have tested the boundaries of conventional doctoral processes, breaking university academic regulations and challenging the western academy in the political nature of collective knowledge production and validity of indigenous knowledge. Qualitative and quantitative processes, approaches and methods were also utilized to inform the study and to ensure reflexivity of research practices. The key findings of the study were: • Improving potency requires a depth of intimacy and connection with all living things that involves a reciprocal understanding of the relationship between Atua, whenua and tangata. • Indigenous knowledge is localized to a spatial area and embedded within a worldview that validates and affirms cultural values and beliefs which continue to have relevance in more contemporary times. • The transformative nature of alternative indigenous paradigms must encompass the totality of creation, humanity and their genealogical and inter-generational linkages to all life. A major contribution of this PhD has been to create new knowledge, ways of thinking and meaning for restoring potency through the environmental health conceptual framework grounded in cultural and spiritual values. The specific focus on Ngati Kuri traditional knowledge authentic to the Hapu and their application, has significantly contributed towards constructing alternative indigenous approaches for meeting the challenges within the modern world.

Irish agriculture is becoming increasingly regulated, with restrictions on fertiliser application rates and stocking rates to reduce nitrate (NO₀⁻) leaching losses. However these regulations have been, to date, based on minimal field research. The purpose of this study was to determine the actual leaching losses of nitrate from Irish dairy pasture at a range of stocking rates, and to investigate the effectiveness of the nitrification inhibitor DCD at reducing nitrate leaching losses where these are deemed excessive. In grazed pastures, a major source of leached nitrate is the urine patch, where a high rate of N is applied in one application. This trial recorded the losses from urine and non-urine areas of pasture separately. Nitrate leaching losses from three soils were recorded using lysimeters at Johnstown Castle, Co. Wexford, over two years. Total nitrate losses were higher from the freely drained Clonakilty and Elton soils than from the heavy Rathangan soil. Mean nitrate losses from urine patches ranged from 16 - 233 kg nitrate-N / ha⁻¹, and were reduced by up to 53% when DCD was applied. DCD also reduced peak and mean nitrate-N concentrations in many cases. In addition, DCD halved the nitrous oxide (N₂O) emission factor on the Rathangan soil, caused increases in pasture N content, and increased herbage yield in some treatments. The distribution of urine patches under dairy grazing was recorded using GPS at Kilworth, Co. Cork. Cows were also found to deposit 0.359 urine patches per grazing hour. A model was produced to predict field-scale nitrate leaching losses from dairy pasture at a range of stocking rates. At 2.94 cows per hectare, the highest stocking rate, annual field N loss was below 34 kg nitrate-N ha⁻¹, mean drainage N concentrations were below 5.65 mg nitrate-N L⁻¹ (the EU drinking water guideline value), and the worst-case-scenario autumn peak concentration did not exceed 21.55 mg nitrate-N L⁻¹ (above the EU Maximum Allowable Concentration (MAC) but below the World Health Organisation (WHO) drinking water limit). DCD reduced total annual field N loss by 21% (a conservative estimate), and also reduced mean and peak nitrate concentrations. Provided fertiliser application rates are at or below 291 kg N ha⁻¹, and based on current legislative values for drinking water quality, this trial does not support any blanket restrictions on the stocking rate of Irish dairy farms. However where particularly high water quality is required, DCD shows potential as a useful tool to achieve low nitrate concentrations.

Despite the importance of a high white clover (Trifolium repens) content in temperate pastoral systems in terms of livestock performance and nitrogen fixation, the proportion of white clover in grass-clover pastures is often low (<20%). This thesis examined in two experiments whether the white clover content of pastures could be improved by sowing white clover with alternative grass species to diploid perennial ryegrass (Lolium perenne L.). In a pasture experiment, DM production, pasture composition and morphology of grass-clover mixtures was measured over the establishment year (January 2007 to January 2008) where white clover was sown in fine mixtures with diploid perennial ryegrass, tetraploid perennial ryegrass, timothy (Phleum pratense L.) and cocksfoot (Dactylis glomerata L.). Pastures were irrigated and rotationally grazed with on-off grazing with Coopworth ewe hoggets. Total annual DM production of pasture was more than 20% higher in tetraploid (12521 kg DM ha⁻¹) and diploid (11733 kg DM ha⁻¹) perennial ryegrass than timothy (9751 kg DM ha⁻¹) and cocksfoot (9654 kg DM ha⁻¹). However, timothy (5936 kg DM ha⁻¹) and cocksfoot (5311 kg DM ha⁻¹) had more than four times higher white clover annual DM production than tetraploid (1310 kg DM ha⁻¹) and diploid (818 kg DM ha⁻¹) ryegrass. Pasture growth rate at the first three harvests in autumn was significantly greater in tetraploid and diploid ryegrass than timothy and cocksfoot. Timothy and cocksfoot had a higher proportion of white clover than tetraploid and diploid perennial ryegrass throughout the entire year. This was due to more and larger white clover plants in timothy and cocksfoot plots. In a grazing preference experiment, the partial preference of sheep for white clover offered in combination with the same grass species as in the pasture experiment was measured in five grazing tests in May, September, October, November and December 2007. Pastures were sown in January 2007. Paired plots (grass and clover both 4.2 m x 10 m) were grazed by three Coopworth ewe hoggets between 9am and 5pm, and preference was recorded by decline in pasture mass and visual scan sampling for grazing time. Grazing preference for clover was generally low throughout these tests (e.g. average apparent DM intake from clover = 47%; average grazing time from clover = 44%). Several explanations are proposed for this low preference including a high N content and intake rate of the grass relative to the clover. No significant differences were found among the grass treatments in total grass grazing time, total clover grazing time, ruminating time, the proportion of grazing time on clover, selective coefficient for clover and DM intake percentage from clover at any date. There was no significant change in overall sward surface height (SSH) decline among grass treatments throughout all the tests except December 2007 when the overall SSH decline for cocksfoot was significantly lower than the other species. The study indicated that the rapid growth rate of perennial ryegrass in the early phase of pasture establishment, rather than differences in partial preference, was the key factor limiting white clover content in the mixed swards relative to cocksfoot and timothy pastures. It is concluded that high clover-containing pastures capable of delivering high per head performance can be established through the use of slow establishing pasture species such as timothy and cocksfoot.

Utilizing environmental DNA (eDNA) for the detection of species in the field is a potentially cost-effective and time-saving technology that may be useful in understanding the distribution and abundance of threatened or endangered species such as the Eastern Massasauga (Sistrurus catenatus). I describe the development of an eDNA assay for the species and evaluate its ability to detect eDNA in laboratory and field conditions. In the field samples, I also investigated the potential for abiotic conditions to influence eDNA detection. Species-specific primers and probe were designed to amplify a 152 bp segment of the massasauga COI gene. Target eDNA could be detected in samples containing as little as 100 copies of target DNA/μL. Water samples collected from laboratory housed snakes indicated that eDNA can be detected in water 56 days after massasauga removal. Field samples were taken from crayfish burrows, known overwintering habitat for the species, from four sites that vary in snake use as ascertained by traditional visual surveys. Of the 60 burrows sampled, seven had a positive detection for massasauga eDNA with no difference in detection rate between DNA extracted from burrow water and burrow sediment. Occupancy models fitted to burrow water indicated that larger amounts of total DNA in a sample may increase the probability of detection of a massasauga eDNA. Large confidence intervals in site occupancy (ѱ) and burrow detection (Θ) values suggest that a larger sample size is needed for more reliable occupancy models. Abiotic conditions within crayfish burrows varied among sites but correlation with eDNA detection was not supported. Estimates of qPCR detection within a burrow with eDNA (ρ) suggest that up to 10 qPCR replicates per burrow sample may be necessary. Further studies need to examine eDNA degradation in the field, improve upon the limit of detection, and sample a larger number of sites for eDNA sampling to be a stand-alone survey method for Eastern Massasaugas.

Many animal species invest in extended parental care for their offspring. Parental care is costly, and natural selection favors investment strategies which maximize reproductive success. Biparental care is relatively rare, but when it does occur it has been found to increase success in terms of offspring survival and growth and in terms of future reproductive opportunities. In burying beetles (Nicrophorus spp.), both male and female participate in extended parental care. However, the fitness benefits of biparental care in burying beetles have been difficult to establish, with some studies reporting significantly smaller broods produced when both male and female are present. Variation in environmental conditions, such as temperature, is an important part of the context in which biparental care evolves. I hypothesize that biparental care acts as a buffer against environmental variation. This hypothesis predicts that biparental care will lead to greater reproductive success compared to uniparental care when temperature is increased during a reproductive attempt. I also tested the load-lightening hypothesis, which holds that biparental care benefits future reproduction by lowering the costs of reproduction. This predicts that the additional care by the other parent will allow females to rear higher quality second broods. I conducted a male removal experiment at two temperature treatments, using the species Nicrophorus orbicollis. I measured reproductive success during manipulated first brood and during second broods which females reared without a male, regardless of prior experience. I found that, contrary to my hypothesis, biparental care at the higher temperature resulted in reduced reproductive success compared to uniparental care. I found no effect of biparental care on the success of second broods. Instead, I found evidence of reproductive restraint associated with the higher temperature treatment in delayed egg-laying and increased feeding during second broods.

Effective enrichments for farm animals are increasingly important to address public concerns about farm animal welfare and improve the welfare of the animals we raise. The public’s concern has increased in recent years as the management and care that farmers give their animals has become more apparent to them. Some of the conditions in which animals are kept are emotionally not appealing to the public. One such condition is farrowing crates for sows and piglets. The sows are confined in a small space with no social contact and cannot perform nesting behaviors. Farrowing crates are widely used though, as they allow farmers to handle piglets without fear of sow aggression, meet individual sow nutritional needs, and personalize care. Piglet mortality due to crushing is also decreased with crate use. Sow welfare in farrowing crates can be improved through environmental enrichments. Enrichments improve welfare by increasing species-specific behaviors, creating a more complex environment, reducing abnormal behaviors, and increasing an animal’s ability to cope with stressful situations. For pigs, different enrichments have been shown to decrease stereotypies, like sham chewing and bar biting, decrease harmful redirected behavior towards pen mates, like tail biting and belly nosing, increased exploratory behavior, and increase positive affect. Straw has been found to be the best enrichment for pigs because it allows them to perform motivational behaviors such as rooting, foraging, and nest building. It is also complex, manipulatable, destructible, and ingestible, which are important attributes of effective enrichments. Unfortunately, straw cannot be used in farms that have slurry systems, as the straw will fall through the slats into the pit below and cause drainage issues. This includes farrowing crates. There have been a few studies on alternative enrichments for sows in crates, like cloth tassels, but they are not as effective as straw and are rarely used on farm.

Most enrichments target pigs’ motivations to forage, root, graze, or build nests. Pigs perform other behaviors and may have other motivations that enrichments have not targeted yet. One such behavior is scratching. In a semi-natural environment, pigs will rub against trees and bushes. In confinement, pigs rub on fences, walls, and even allow people to scratch them with their hands. There have been no recorded studies done on scratching enrichment for pigs. Many studies have been done in the dairy industry exploring rotating brushes. These brushes have been implemented successfully on commercial farms and are used by cows to groom and scratch themselves. A similar device may allow pigs to also satisfy their itch. Our aim is to provide scratching enrichment to sows in farrowing crates. Since there have been no studies recorded on scratching enrichment or scratching in pigs in general, several steps had to take place before addressing the topic for sows in crates. The first project’s aim was to see what materials pigs prefer to scratch on and their willingness to use such an enrichment.

The first project consisted of 2 experiments. Exp. 1 was a pilot study where 5 different materials on scratch posts were presented to a pen of gestating sows. The scratch posts were constructed from polyvinyl chloride (PVC) pipes, boards, and a gate post. Five different materials were attached to the boards: white, soft, long-bristled brushes (White Brush), red, hard, short-bristled brush (Red Brush), black, short-bristled, astro-turf-like mat (Plastic Mat), colorful coir, hard, short-bristled mat (Fiber Mat), and blue, plastic, large-round-bristled combs (Plastic Combs). The 8 sows received all 5 scratch posts in their pen for a habituation day and then 7 d of testing. During testing, video was continuously recorded from which 2 behaviors were collected; scratching and interacting. Sows scratched the most on Plastic Mat followed by Fiber Mat, Plastic Combs, and Red Brush. The White Brush was scratched on the least. The top 3 preferences were chosen to proceed to Exp. 2.

Experiment 2 for sow preference was performed on several pens (N=14) of sows and gilts with Plastic Mat, Fiber Mat, and Plastic Combs to narrow the preference down to 2 materials to proceed to the farrowing crates. The experiment was carried out in repetitions. Each repetition tested 4 pens at a time. The scratch posts were modified from Exp. 1 and each material was placed in a pen. Due to material destruction only 2 repetitions were carried out, both ending a little early (N=8). During the first repetition (Rep 1), sows ate and destroyed all the Plastic Combs within 2 d. The Plastic Comb scratch posts were pulled from the study and the second repetition (Rep 2) only had the Plastic Mat and Fiber Mat represented. An observation was made that one of the pens in Rep1 had extra feed on their floor and were not destroying their materials as fast as the other pens. So for Rep 2, more modifications to the scratch posts were made and the sows were given a little extra feed. The scratch posts were still destroyed in Rep 2 proving that the sows’ hunger and motivation to perform oral manipulations overwhelmed scratching behaviors. However, from the data that was collected sows spent more time and more frequently interacted with the Fiber Mat compared to the Plastic Mat. They more frequently and spent more time interacting than scratching with the enrichments but scratched on both enrichments the same amount of time and frequency (Durations: F_1,112.6 = 13.63, P = 0.0003; Frequencies: F_1,111.9 = 19.72, P < 0.0001).

The plastic and fiber mats were presented to sows in farrowing crates for the second project by default. Sows (N=18) of parities 2 (P2) and 3 (P3) were housed for 25 d and assigned no enrichment (Control) or to a scratch pad treatment of plastic mats (Plastic) or fiber mats (Fiber). All were assessed for lesions, abnormal behaviors, eating and scratching behaviors, and time spent in different postures and behaviors. Scratching bouts occurred in short durations and were intermittent throughout the day. Parity 2 Plastic sows scratched for a longer total duration than P2 and P3 Fiber sows, P3 Plastic sows, and P2 Control sows (F_2,11 = 11.94, P = 0.002). Parity 2 Plastic sows also displayed scratching bouts more frequently than all except P3 Control sows (F_2,11 = 18.46, P = 0.0003). There were no body lesion differences between treatments (P > 0.05). Abnormal behaviors (P > 0.05) and proportion of time spent in different postures (F_2,94 = 0.0003, P = 0.999) did not differ among treatments.

In conclusion, if a sow is experiencing hunger while in gestation pens this motivation may be overwhelming any other behavior needs. Scratch posts were destroyed and eaten. In this sort of environment, focusing on an enrichment that meets the need to forage and root would be more successful. Sows still scratched on the posts, so their preference and scratching use was still recorded to an extent to proceed to the experiment in farrowing crates. In farrowing crates, plastic scratch pads may be a suitable enrichment as they increased the natural behavior of scratching and did not increase abnormal behaviors. More research is needed to refine the scratch pad design and identify additional measures needed to examine the suitability of scratch pads as a form of environmental enrichment for sows in farrowing crates. In addition, the behavioral characteristics and sows’ underlying motivation for scratching need to be studied because very little is known about scratching behavior of sows. If sows are motivated to scratch, and scratching helps improve their welfare, then scratching enrichment may be beneficial to sows and farmers.

The aim of this thesis is to enquire into genetic approaches for improving milk yield from dairy cattle in order to overcome the milk shortage in Bangladesh. Survey work on the dairy industry was carried out to reveal its current status. The collected data of different genotypes (Pabna cattle, Australian-Friesian-Sahiwal Pabna, Holstein Pabna, Jersey Pabna, and Sahiwal Pabna) from 1999 to 2001, and in two seasons, were used to predict model parameters, fit-statistics and total lactation yields, by fitting ten lactation curve models. Best fitting model(s) were chosen on the basis of fit-statistics. The input parameters from best fiting model(s) were used for: developing a deterministic model; estimating the profitability of individual cows; estimating whole farm profitability; and for developing a profit function to estimate the economic values of traits in breeding objectives. The individual cow performances for different traits were stochastically simulated in respect of additive genetic, permanent and temporary error, herd and age effects, and mendelian sampling under progeny and parent-average testing breeding schemes based on three selection objectives applied over on 20 year period. Genetic gains in different traits were calculated from the regression of trait values on the selection index. The estimated lactation curves model parameters, and predicted lactation milk yield were significantly different between breeds, years and seasons. From four fit-statistics values, the CCC value was considered superior, and this value indicated that the Nelder model best represented the test day records. The net annual income for Holstein Pabna cattle was the highest (US$229) and was lowest (US$115) for Pabna cattle, while all other genotypes were intermediate. The economic values (EVs) of milk yield for all genotypes were similar (US$0.32), and due to payment for milk volume only, the EVs of fat and protein were negative. EVs of liveweight, calving intervals and calving rate were negative, but survivability was positive in all genotypes. The parent-average testing selection scheme showed higher genetic gains than progeny testing. The highest (US$15.80) genetic gain was obtained for milk yield when selection was for milk merit only. The study will assist in undertaking a genetic improvement programme for the increase of milk production in Bangladesh and thereby enhance food security. (Key words: Dairy cattle, genetic improvements, models, stochastic).