Diversity of human copy number variation and multicopy genes

Copy number variants affect both disease and normal phenotypic variation, but those lying within heavily duplicated, highly identical sequence have been difficult to assay. By analyzing short-read mapping depth for 159 human genomes, we demonstrated accurate estimation of absolute copy number for duplications as small as 1.9 kilobase pairs, ranging from 0 to 48 copies. We identified 4.1 million "singly unique nucleotide" positions informative in distinguishing specific copies and used them to genotype the copy and content of specific paralogs within highly duplicated gene families. These data identify human-specific expansions in genes associated with brain development, reveal extensive population genetic diversity, and detect signatures consistent with gene conversion in the human species. Our approach makes ~1000 genes accessible to genetic studies of disease association.     

Sero-epidemiological and pathological studies on enzootic bovine leukosis in Turkey.

The prevalence of enzootic bovine leukosis (EBL) in Turkey was investigated by serological screenings using the agargel immunodiffusion test (AGID). A total of 4,047 blood samples obtained from 2,780 cattle between one and 14 years of age and taken in 6-8 month-intervals in three dairy farms were tested for the presence of EBL-specific antibodies. A high prevalence of EBL-sero-positive animals was found amongst cattle in two of the farms. Furthermore, recommendations based upon the regulation implemented by an expert group of the European Commission and considering the local dairy management conditions were presented.     

Long-term study (2005–2010) on the vaccination with BoHV-1 glycoprotein E-deleted marker vaccine in selected two dairy herds in Turkey

A follow-up study from 2005 to 2010 was carried out in two herds where eradication programme for the bovine herpes virus-1 (BoHV-1) infection depends on the vaccination with inactivated glycoprotein E-deleted vaccine that was started in 2001 following the vaccination with inactivated conventional vaccine between 1999 and 2001. For serological screening, a total of 12,976 sera sampled over several sampling times approximately 6 months of interval during 5 years (2005–2010) were tested for glycoprotein E (gE)- and glycoprotein B-specific antibodies using ELISA. According to the serological evidence, the long-term persistence of BoHV-1 antibodies, success of marker vaccine, first vaccination time of the calves in herds regularly vaccinated, etc. were discussed in this paper. In conclusion, the vaccination programme using gE (?) marker vaccines, with making efforts to prevent the other factors about transmission of infection, was suggested for the eradication of BoHV-1 infection in Turkey as many EU countries. This is the first report on the BoHV-1 eradication programme in some dairy cattle in Turkey.     

Immunohistochemical and qPCR determination of the expression and serum level of anti‐Müllerian hormone in pre‐pubertal,intact and ovarian remnant syndrome detected bitches

The aim of this study was to determine the serum concentrations, ovarian presence and expression of anti‐Müllerian hormone (AMH) in pre‐pubertal, bitches with signs of ovarian remnant syndrome (ORS) and intact bitches. In addition, we aimed to verify the suitability of serum AMH concentrations for diagnostic purposes in sterilized bitches and/or in suspected cases of ORS in the field of veterinary medicine. For this purpose, 36 healthy female dogs divided into six groups: proestrus, oestrus, dioestrus, anoestrus, pre‐pubertal and ORS. Serum AMH concentrations were determined by electrochemiluminescence immunoassay, and ovarian presence and distribution of AMH was confirmed by immunohistochemical and qPCR techniques. According to the results of qPCR, while the expression values of AMH were at the highest concentrations in the proestrus and oestrus, there was a statistically significant decrease in these values at the later stages of the cycle (p < 0.05). According to hormone analysis, the serum AMH values of the ORS group had decreased significantly compared with the proestrus and oestrus (p < 0.05). Although serum AMH levels of ORS group were increased compared with anestrus and pre‐pubertal groups, this increase was statistically non‐significant (p > 0.05). Immunohistochemically, AMH expression was first observed in the granulosa cells of primordial follicles in folliculogenesis. Expression values were the highest in the proestrous and oestrus groups, but values from bitches in later stages of the cycle were statistically significant decrease in comparison with these groups (p < 0.05). As a result, AMH concentration and expression were found to be higher in proestrus and oestrus than in other periods (p < 0.05). In addition, the measurable level of AMH concentration in bitches with ORS is an indication that it can be used in the diagnosis of ORS.     

Reduction and stabilization of hip luxation by the transposition of the ligamentum sacrotuberale in dogs: an in vivo study

OBJECTIVES: To evaluate the effectiveness of transposition of the sacrotuberous ligament (LST) for the treatment of coxofemoral luxation in the dog. STUDY DESIGN: In vivo experimental study. SAMPLE POPULATION: Ten mixed-breed dogs (weighing 12 to 26 kg). METHODS: After general anesthesia, the LST was exposed and released from the sacrum with a sacral bone fragment. Coxofemoral luxation was created by capsulotomy and transection of the ligament of the head of the femur. Suture was passed through 2 small holes in the bone fragment to guide transposition of the LST through a tunnel drilled through the acetabulum and femoral head and neck. The suture material was pulled tight and an interference screw was placed into the femoral tunnel to lock the sacral bone fragment and LST securely in the tunnel. Butorphanol was administered for pain relief and dogs were allowed unrestricted activity. Coxofemoral radiographs were obtained at 15-day intervals. Two dogs were euthanatized for macroscopic and histopathologic examinations at 3 months. RESULTS: Release of the sacral bone was moderately difficult. The transposed ligament and bone fragment were of an appropriate length and were easily and securely fixed by a interference screw method. Visible severe lameness, during the first 7 to 10 days improved to mild lameness within 10 to 21 days. Gait was subjectively normal after 5 weeks. No radiographic abnormalities were observed at any time point. Grossly, the LST was intact and apparently viable and functional. On histopathology, the space in the bone tunnel was filled with new tissue and a hyaline-like layer surrounded the LST. The sacral bone fragment attached to the LST was united with the femoral bone. CONCLUSIONS: Transposition of the LST reduced and stabilized experimentally induced coxofemoral luxation in 10 dogs. Survival of the LST up to 3 months and its adaptation to transposition suggest that this surgical technique could be considered as a permanent treatment option for hip luxations. Transposition and fixation of the LST was easy, but releasing the sacral edge of the LST was difficult because of its deep location and division of the origin into 2 branches in some dogs. CLINICAL RELEVANCE: Results of this experimental study suggest that the technique may be satisfactorily used in dogs with coxofemoral luxation.     

Histologic characteristics and local cellular immunity of the gland of the third eyelid after topical ophthalmic administration of 2% cyclosporine for treatment of dogs with keratoconjunctivitis sicca

OBJECTIVE: To evaluate the efficacy of topical administration of a 2% solution of cyclosporine (CsA) for treatment of dogs with keratoconjunctivitis sicca (KCS) and to correlate results with histopathologic characteristics and local cellular immunity of the gland of the third eyelid. ANIMALS: 24 dogs with bilateral KCS. PROCEDURE: Lacrimal secretion was measured, using Schirmer tear test (STT) strips. Leukocyte and T-lymphocyte subsets were determined in blood samples. Histopathologic changes as well as CD4+, CD8+, and alpha-naphthyl-acetate esterase-positive (ANAE+) lymphocytes were evaluated. RESULTS: Clinical signs resolved at the end of 1 month in conjunction with significantly increased STT values, compared with baseline values. Fifteen and 30 days after discontinuation of CsA treatment, a decrease was observed in STT values in both eyes; however, only values for the right eye were significantly different. There was a significant decrease in the number of lymphocytes and ANAE+ lymphocytes 15 and 30 days after discontinuation of CsA treatment, compared with baseline values. Differences were not observed in number of CD4+ lymphocytes among treatment groups. However, there was a significant decrease in number of CD8+ lymphocytes with reversal of the CD4+:CD8+ in both eyes after CsA treatment for 30 days, compared with the control group. Increased secretory activity and decreased lymphocyte infiltration were characteristic histopathologic findings. CONCLUSIONS AND CLINICAL RELEVANCE: Topical administration of a 2% solution of CsA was effective for the treatment of dogs with KCS. Strict follow-up monitoring is required after the cessation of treatment because of the possibility of recurrence of KCS.     

Effects of recessive white plumage colour mutation on hatchability and growth of quail hatched from breeders of different ages

1. A total of 1200 eggs were obtained from two pure line stocks of 'wild' and 'recessive white' quail of the Pharaoh strain (Coturnix coturnix Pharaoh), with two different breeder ages (17 or 34 weeks). The recessive white line was derived from mutant birds, which appeared spontaneously within the wild-type quail colony. 2. The analysis included plumage colour and breeder age as main effects together with their interaction. There were no significant effects for apparent fertility but hatchability of total and fertile eggs was affected by plumage colour variant and breeder age. 3. Body weight was affected by plumage colour throughout the growing period, whereas the differences attributable to breeder age were significant from 21 to 42 d only. 4. Main effects and their interaction were significant for feed conversion ratio until the end of the growing period, except at the age of 7 d for the effect of breeder age. 5. It was concluded that the hatchability and growth performance of the recessive white-type was not as good as the wild-type. The young breeders (17 weeks old) had the best hatchability and subsequent growth performance.     

Low-Cost Synthesis of Organic–Inorganic Hybrid MSU-3 from Gold Mine Waste for CO<Subscript>2</Subscript> Adsorption

Amine-grafted MSU-3 mesoporous silica samples were synthesized from pure and waste silica sources and their CO₂ adsorption performances were evaluated. The obtained samples were characterized using X-ray diffraction (XRD), thermogravimetric analysis (TGA), N₂ adsorption–desorption isotherm analysis, Fourier transform infrared (FTIR), and transmission electron microscopy (TEM). CO₂ adsorption capacities of the samples at different temperatures were determined by TGA. The amine-modified MSU-3 synthesized from waste exhibited the highest CO₂ adsorption capacity of 1.32 mmol/g at 25 °C and 1 bar, depending essentially on the porous texture and the amine content of the material. The CO₂ adsorption isotherms of the synthesized samples were measured by a static volumetric method. Adsorption isotherm indicated that the amine-modified samples presented significantly higher CO₂ adsorption capacity than the pure samples. The Avrami kinetic model fitted the experimental data well and suggested that complex reaction mechanism or the appearance of multiple reaction pathway occurred in the CO₂ adsorption.

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Graphical Abstract CO₂ uptake capacities and TEM images of the amine modified samples

     

Simultaneous Determination of Phorate and Oxyfluorfen in Well Water Samples with High Accuracy by GC-MS After Binary Dispersive Liquid-Liquid Microextraction

The potential risk of pesticides to cause harm to humans and other organisms even at trace levels calls for sensitive and accurate analytical techniques for their simultaneous qualitative and quantitative determinations. In this study, a sensitive binary dispersive liquid-liquid microextraction (B-DLLME) strategy was developed for the simultaneous determination of phorate and oxyfluorfen by gas chromatography mass spectrometry after extraction/preconcentration from aqueous solution. An experimental design was used to optimize parameters of the B-DLLME method to obtain maximum outcome. Under the optimum conditions of B-DLLME, the limit of detection (LOD) for phorate and oxyfluorfen were found to be 0.41 μg L^?1 and 0.54 μg L^?1, respectively. The detection limits correlate to about 37 and 73 folds enhancement in detection powers when compared to direct GC-MS determination of phorate and oxyfluorfen, respectively. In order to find out the applicability of developed method to real samples, recovery tests were performed for 20 μg L^?1 of phorate and oxyfluorfen spiked in well water samples. Percent recovery values were found to be 94.5% for phorate and 101.9% for oxyfluorfen.