Comparison of farm-level greenhouse gas emissions in transhumance and semi-intensive sheep production systems in continental rangelands

Despite their predominance worldwide, few studies have been conducted to look at the impact of sheep production systems relying on transhumance practices in arid and continental conditions, on farm-level greenhouse gas (GHG) emissions. Using Turkey as an example, this paper examines on farm-level GHG emissions calculated for two contrasting sheep production systems under arid and continental climate conditions. Production and management data were obtained through face-to-face interviews carried out on 10 transhumance and 15 semi-intensive meat sheep farms in Turkey. A total of seven GHG emission estimates were then calculated for each farm with the Agricultural Resource Efficiency Calculator (AgRECalc©) tool; i) total Carbon Dioxide (CO2) from energy use (kg CO2e), ii) total Carbon Dioxide equivalent (CO2e) from methane (kg CO2e), iii) total CO₂e from nitrous oxide (kg CO₂e), iv) whole farm and enterprise CO₂e emissions (kg CO₂e), v) net emission from land use (kg CO₂e), vi) whole farm CO₂e emissions per kg of farm output (kg CO₂e/kg output), vii) product CO₂e emissions (meat): kg CO₂e / kg live weight, and viii) farm output (kg of sheep). Multivariate analyses (using R software) were carried out to compare both farm types and their respective carbon emissions. The total farm output per ewe was lower in the transhumance farms (7.4 kg/ewe) than in the semi-intensive farms (7.7 kg/ewe). The kg CO₂e per kg of output was also lower for the transhumance farms (46.2 kg CO₂e) than for the semi-intensive ones (56.5 kg CO₂e). This trend was similar for the amount of CO₂e per kg of live weight produced (20.8 kg and 25.4 kg for the transhumance and the semi-intensive farms, respectively). Despite overall net emissions from land use being greater on average for the transhumance farms, once measured per hectare, they were found to be lower than those for the semi-intensive farms. This study provides a reference point for different sheep production systems’ GHG emission impact in continental rangelands in Turkey.     

Verbascum eskisehirensis sp. nov. (Scrophulariaceae) from central Anatolia, Turkey

Verbascum eskisehirensis Karavel., Ocak & Ekici sp. nov. (sect. Bothrosperma Murb.) is described and illustrated from Turkey. This new species is confined to B3 Eskisehir in central Anatolia. A morphological comparison is made with the closely related species; V. oreophilum K. Koch and V. pyramidatum M. Bieb. In addition, a cluster analysis was conducted and a distribution map of the new species and the related species is also given.     

Caffeic acid phenethyl ester suppresses oxidative stress in Escherichia coli-induced pyelonephritis in rats

Although oxidative damage is known to be involved in inflammatory-mediated tissue destruction, modulation of oxygen free radical production represents a new approach to the treatment of inflammatory diseases. Caffeic acid phenethyl ester (CAPE), an active component of propolis from honeybee hives, has antioxidant, anti-inflammatory and antibacterial properties. For that reason, we aimed to investigate the efficiency of CAPE administration in preventing oxidative damage in pyelonephritis (PYN) caused by Escherichia coli. In this study, 35 Wistar rats were grouped as follows: control, PYN 24 h, PYN 48 h, PYN 72 h, CAPE 24 h, CAPE 48 h and CAPE 72 h. E. coli (1 × 10⁹ c.f.u.) were inoculated into the rats in both PYN and CAPE groups via urethral catheterization. Ten μM/kg-body weight CAPE was injected to the rats in all CAPE groups 24 h before E. coli infection, and injections were repeated at 24-h intervals. Rats were sacrificed 24 h, 48 h and 72 h after infection in both PYN and CAPE groups. Malondialdehyde (MDA) and nitric oxide (NO) levels were significantly increased in kidneys of PYN groups. The activities of the antioxidant enzymes, catalase (CAT), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and xanthine oxidase (XO) were also elevated by E. coli. However, CAPE administration reduced MDA and NO levels, as well as XO activity, although it increased SOD and GSH-Px activities. Histopathological examination showed that CAPE reduced the inflammation grade induced by E. coli. In conclusion, CAPE administrations decrease the oxidative damage occurring in PYN and therefore could be used for medical management of bacterial nephropathy.     

Effects of a selective Rho-kinase inhibitor Y-27632 on oxidative stress parameters in acute dichlorvos poisoning in rats

This study examined the effects of Y-27632, a selective Rho-kinase inhibitor, on organophosphate-induced acute toxicity in rats. Rats were randomly divided into four groups as control (corn oil), dichlorvos (30 mg kg(-1) i.p.), 1 and 10 mg kg(-1) Y-27632 + dichlorvos groups. Cholinergic signs (fatigue, tremor, cyanosis, hyper-secretion, fasciculations) were observed in all the rats in the dichlorvos group and the mortality rate was 50%. No cholinergic findings and deaths were observed in the control and Y-27632 groups. Plasma cholinesterase activities were suppressed with dichlorvos and these reductions were attenuated with Y-27632 pretreatment. There was a marked increase in plasma malondialdehyde level in the dichlorvos group, but Y-27632 pretreatment abolished this elevation. Dichlorvos markedly depressed cardiac paraoxonase activity, but these changes were not markedly modified with Y-27632. Total antioxidant capacities, total oxidant status, oxidative stress index, total free sulfhydryl groups and catalase activities in plasma and cardiac tissues were not markedly different between the groups. No significant changes were observed with cardiac myeloperoxidase activities or plasma arylesterase and ceruloplasmin activities. In conclusion, our results suggest that Rho-kinase pathway is involved in organophosphate intoxication, and a decrease in cardiac paraoxonase activities may play a role in the pathogenesis of acute organophosphate poisoning in rats.     

SYBR green dye-based probe-free SNP genotyping: Introduction of T-Plex real-time PCR assay

Single-nucleotide polymorphism (SNP) genotyping is widely used in genetic association studies to characterize genetic factors underlying inherited traits. Despite many recent advances in high-throughput SNP genotyping, inexpensive and flexible methods with reasonable throughput levels are still needed. Real-time PCR methods for discovering and genotyping SNPs are becoming increasingly important in various fields of biology. In this study, we introduce a new, single-tube strategy that combines the tetra-primer ARMS PCR assay, SYBR Green I-based real-time PCR, and melting-point analysis with primer design strategies to detect the SNP of interest. This assay, T-Plex real-time PCR, is based on the T_m discrimination of the amplified allele-specific amplicons in a single tube. The specificity, sensitivity, and robustness of the assay were evaluated for common mutations in the FV, PII, MTHFR, and FGFR3 genes. We believe that T-Plex real-time PCR would be a useful alternative for either individual genotyping requests or large epidemiological studies.     

Single Nucleotide Variants in the Protein C Pathway and Mortality in Dialysis Patients

Background

The protein C pathway plays an important role in the maintenance of endothelial barrier function and in the inflammatory and coagulant processes that are characteristic of patients on dialysis. We investigated whether common single nucleotide variants (SNV) in genes encoding protein C pathway components were associated with all-cause 5 years mortality risk in dialysis patients.

Methods

Single nucleotides variants in the factor V gene (F5 rs6025; factor V Leiden), the thrombomodulin gene (THBD rs1042580), the protein C gene (PROC rs1799808 and 1799809) and the endothelial protein C receptor gene (PROCR rs867186, rs2069951, and rs2069952) were genotyped in 1070 dialysis patients from the NEtherlands COoperative Study on the Adequacy of Dialysis (NECOSAD) cohort) and in 1243 dialysis patients from the German 4D cohort.

Results

Factor V Leiden was associated with a 1.5-fold (95% CI 1.1–1.9) increased 5-year all-cause mortality risk and carriers of the AG/GG genotypes of the PROC rs1799809 had a 1.2-fold (95% CI 1.0–1.4) increased 5-year all-cause mortality risk. The other SNVs in THBD, PROC, and PROCR were not associated with 5-years mortality.

Conclusion

Our study suggests that factor V Leiden and PROC rs1799809 contributes to an increased mortality risk in dialysis patients.     

The HLA class II Allele DRB1*1501 is over-represented in patients with idiopathic pulmonary fibrosis

Background

Idiopathic pulmonary fibrosis (IPF) is a progressive and medically refractory lung disease with a grim prognosis. Although the etiology of IPF remains perplexing, abnormal adaptive immune responses are evident in many afflicted patients. We hypothesized that perturbations of human leukocyte antigen (HLA) allele frequencies, which are often seen among patients with immunologic diseases, may also be present in IPF patients.

Methods/Principal Findings

HLA alleles were determined in subpopulations of IPF and normal subjects using molecular typing methods. HLA-DRB1*15 was over-represented in a discovery cohort of 79 Caucasian IPF subjects who had lung transplantations at the University of Pittsburgh (36.7%) compared to normal reference populations. These findings were prospectively replicated in a validation cohort of 196 additional IPF subjects from four other U.S. medical centers that included both ambulatory patients and lung transplantation recipients. High-resolution typing was used to further define specific HLA-DRB1*15 alleles. DRB1*1501 prevalence in IPF subjects was similar among the 143 ambulatory patients and 132 transplant recipients (31.5% and 34.8%, respectively, p = 0.55). The aggregate prevalence of DRB1*1501 in IPF patients was significantly greater than among 285 healthy controls (33.1% vs. 20.0%, respectively, OR 2.0; 95%CI 1.3–2.9, p = 0.0004). IPF patients with DRB1*1501 (n = 91) tended to have decreased diffusing capacities for carbon monoxide (DL_CO) compared to the 184 disease subjects who lacked this allele (37.8±1.7% vs. 42.8±1.4%, p = 0.036).

Conclusions/Significance

DRB1*1501 is more prevalent among IPF patients than normal subjects, and may be associated with greater impairment of gas exchange. These data are novel evidence that immunogenetic processes can play a role in the susceptibility to and/or manifestations of IPF. Findings here of a disease association at the HLA-DR locus have broad pathogenic implications, illustrate a specific chromosomal area for incremental, targeted genomic study, and may identify a distinct clinical phenotype among patients with this enigmatic, morbid lung disease.     

Course of Symptoms and Health-Related Quality of Life during Specialized Pre-Dialysis Care

Background

Concerns are present on the limited value of renal function alone in defining the optimal moment to start dialysis. Disease-related symptoms and health-related quality of life (HRQOL) may have additional clinical value in defining this moment, but little is known about how these parameters change during pre-dialysis care. The aims of our study were to describe the course of symptoms and HRQOL during pre-dialysis care and to investigate their association with poor health outcomes.

Methods

In the prospective PREPARE-2 cohort, incident patients starting specialized pre-dialysis care were included when referred to one of the 25 participating Dutch outpatient clinics (2004–2011). In the present analysis, 436 patients with data available on symptoms and HRQOL were included. Clinical data, symptoms (revised illness perception questionnaire), and HRQOL (short form-36 questionnaire; physical and mental summary score) were collected every 6-month interval. A time-dependent Cox proportional hazard model was used to associate symptoms and HRQOL with the combined poor health outcome (i.e. starting dialysis, receiving a kidney transplant, and death).

Results

All symptoms increased, especially fatigue and loss of strength, and both the physical and mental summary score decreased over time, with the most pronounced change during the last 6–12 months of follow-up. Furthermore, each additional symptom (adjusted HR 1.04 (95% CI, 1.00–1.09)) and each 3-point lower physical and mental summary score (adjusted HR 1.04 (1.02–1.06) and 1.04 (1.02–1.06) respectively) were associated with a higher risk of reaching the combined poor health outcome within the subsequent 6 months.

Conclusions

The number of symptoms increased and both the physical and mental HRQOL score decreased during pre-dialysis care and these changes were associated with starting dialysis, receiving a kidney transplant, and death. These results may indicate that symptoms and HRQOL are good markers for the medical condition and disease stage of pre-dialysis patients.     

Palynological investigations on some Hypericum taxa (Hypericaceae) growing naturally in Turkey

This study examined the detailed pollen morphological structures of sixteen Hypericum taxa (four endemic, twelve non endemic) including eight sections showing the natural distribution in Turkey: H. sect. Ascyreia (H. calycinum L.), H. sect. Heterophyllum (H. heterophyllum Vent.), H. Sect. Taeniocarpium (Hypericum confertum Choisy subsp. confertum, H. venustum Fenzl, H. linaroides Bosse), H. sect. Drosocarpium (H. montbretii Spach, H. bithynicum Boiss.), H. sect. Crossophyllum (H. adenotrichum Spach, H. orientale L.), H. sect. Olympia (H. olympicum L. subsp. olympicum), H. sect. Origanifolia (H. origanifolium Willd., H. avicularifolium Jaub and Spach subsp. depilatum (Freyn and Bornm.) Robson var. depilatum, H. avicularifolium Jaub. and Spach subsp. byzantinum) and H. sect. Hypericum (H. tetrapterum Fries, H. perforatum L., H. triquetrifolium Tura). These taxa were studied under light microscope and scanning electron microscope for the first time. Of the taxa studied, H. tetrapterum has the smallest pollen grains (on average 15.85–17.20 × 15.45–16.05 μm); and H. olympicum subsp. olympicum the largest grains (on average 22.90–23.10 × 21.40–22.10 μm). The pollen grains of 15 taxa are subprolate and one taxon is prolate-spheroidal. The regular pollen grains of all 16 taxa are 3-zonocolporate. Ornamentation is microreticulate; lumina regularly spaced in eight taxa, tectum perforatum; tectal perforations regularly spaced in seven taxa and tectum perforatum; and tectal perforations grouped together in one taxon. Endoaperture is cruciform porus, with short lateral and meridional extensions in ten taxa, cruciform porus, transversally elongated, with very small lateral extensions in one taxon and lalongate colpus in five taxa. Basic pollen types are ten taxa in type X, five taxa in type IV and one taxon in type II.     

Centaurea cadmea subsp. pontica subsp. nov. (Asteraceae) from northwest Anatolia,Turkey

Centaurea cadmea Boiss. subsp. pontica Wagenitz ex Y.B. Köse & Ocak (Asteraceae), a new subspecies occuring in north Anatolia, Turkey, is described and illustrated. The new subspecies grows in rocky places in the Zonguldak province. It is closely related to C. cadmea subsp. cadmea, but differs in its involucrum, achen, appendage and radiant flowers. Diagnostic morphological characters are discussed and notes are presented on ecology and conservation status. In addition, the pollen characteristics of both subspecies have been examined by SEM.