Parentage verification and identity test of Ghezel sheep using microsatillate markers

The Ghezel sheep is a fat tail high weight Iranian breed which is raised in the North-west of Iran. To design an efficient improvement program and genetic evaluation system for this indigenous breed, accurate estimates of the population genetic parameters is per-required and all pedigrees and relationships should be correctly recorded. Otherwise, it can produce biased evaluations when pedigrees contain errors and procedures utilize information from relatives. The pedigree and genotype data of Ghezel sheep were examined for errors. Parentage control has been performed by amplification of microsatellites. Mean heterozygosities, mean polymorphism index content (PIC) and mean number of alleles per loci were 0.50, 0.43 and 3.71, respectively. Mendelian errors were found following the pedigree corrections. Alleles at the following seven microsatellite loci were identified: BM4307, CSSM004, BM415, RM029, INRA49, BM3205 and OarFCB5. The pedigree was considered incorrect in 6 (12%) out of all the evaluated progeny, as their genotype did not match their parents. The present findings attest to the usefulness of the investigated microsatellites for parentage control in Ghezel sheep.Key words: Ghezel sheep, microsatellites, genotyping errors, progeny test

General methods for designing single-mode planar photonic crystal waveguides in hexagonal lattice structures

We systematically investigate and compare general methods of designing single mode photonic crystal waveguides in a two-dimensional hexagonal lattice of air holes in a dielectric material. We apply the rather general methods to dielectric-core hexagonal lattice photonic crystals since they have not been widely explored before. We show that it is possible to obtain single mode guiding in a limited portion of the photonic bandgap of hexagonal lattice structures. We also compare the potentials of different photonic crystal lattices for designing single-mode waveguides and conclude that triangular lattice structures are the best choice

Infection of the fishes with Ligula intestinalis and Bothriocephalus acheilognathi in Sattarkhan Dam, northwestern Iran

After an extensive fish mortality in Sattarkhan Dam, in East-Azarbaijan province during the year 2002, we collected 160 specimens of the fish Alburnus filippi and 5 specimens of the fish and Alburnoides bipunctatus to examine the cause of mortality. The samples measured biometrically an examined them for internal and external infections. We found that of the 160 specimens of Alburnus filippi, 131 (81.8%) were infected with Ligula intestinalis and 26 (16.25%) specimens were infected with Bothriocephalus acheilognathi. Of 5 specimens of Alburnoides bipunctatus, 4 (80%) were infected with Ligula intestinalis and no Bothriocephalus acheilognathi observed. This is the first report of the Ligula and Bothriocephalus parasites infecting fishes in the Sattarkhan Dam

Analysis of the Environmental Factors Affecting the Growth Traits of Iran-Black Sheep

A study was conducted to evaluate the effects of non-genetic factors on the growth behavior of Iran-Black sheep. The data of growth performances, birth weight (BW), weaning weight (W3), weight at 6, 9and 12 months of age (W6, W9 and W12, respectively), were taken from 1522 lambs belonging to data bank from Abbas Abad Sheep Breeding Station located at the North-east of Iran during a period of five years. Statistical analyses were performed using a general linear model including non-genetic factors: lamb sex, birth year and litter size as main effects, the lamb's age when weighed as covariate, and the interactions between these factors. Results showed that all traits were significantly (

onlineFDR: an R package to control the false discovery rate for growing data repositories.

SUMMARY: In many areas of biological research, hypotheses are tested in a sequential manner, without having access to future P-values or even the number of hypotheses to be tested. A key setting where this online hypothesis testing occurs is in the context of publicly available data repositories, where the family of hypotheses to be tested is continually growing as new data is accumulated over time. Recently, Javanmard and Montanari proposed the first procedures that control the FDR for online hypothesis testing. We present an R package, onlineFDR, which implements these procedures and provides wrapper functions to apply them to a historic dataset or a growing data repository. AVAILABILITY AND IMPLEMENTATION: The R package is freely available through Bioconductor (http://www.bioconductor.org/packages/onlineFDR). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online

Association between GH encoding gene polymorphism and semen characteristics in Iranian Holstein bulls

The objective of this present study was to investigate relationships between the growth hormone gene restriction fragment length  polymorphism (RFLP) and bull sperm characteristics. A total of 89 bullsfrom two semen evaluation stations were genotyped for the bovine growth hormone (bGH)-AluI polymorphism by polymerase chain reaction and followed by 4% metaphor agaros gel electrophoresis. The overall allele frequencies for two L and V alleles were 0.50, respectively. The relationship between the bGH-AluI polymorphism and semen characteristics was evaluated according 1500 ejaculated records. Five sperm characteristics were analyzed. Sperm characteristics showed significant variabilityin relation to bGH genotypes. LL bulls had a lower ejaculated volume and higher percentage of live sperm, and VV bulls had higher fresh sperm concentration and minimum effect after cryopreservation. This polymorphism could be further used for semen evaluation process in artificial insemination program in Iranian Holstein bulls.Key word: Semen characteristics, growth hormone (GH) polymorphism, Holstein bulls

Numerical and experimental analysis of a hybrid material acoustophoretic device for manipulation of microparticles.

Acoustophoretic microfluidic devices have been developed for accurate, label-free, contactless, and non-invasive manipulation of bioparticles in different biofluids. However, their widespread application is limited due to the need for the use of high quality microchannels made of materials with high specific acoustic impedances relative to the fluid (e.g., silicon or glass with small damping coefficient), manufactured by complex and expensive microfabrication processes. Soft polymers with a lower fabrication cost have been introduced to address the challenges of silicon- or glass-based acoustophoretic microfluidic systems. However, due to their small acoustic impedance, their efficacy for particle manipulation is shown to be limited. Here, we developed a new acoustophoretic microfluid system fabricated by a hybrid sound-hard (aluminum) and sound-soft (polydimethylsiloxane polymer) material. The performance of this hybrid device for manipulation of bead particles and cells was compared to the acoustophoretic devices made of acoustically hard materials. The results show that particles and cells in the hybrid material microchannel travel to a nodal plane with a much smaller energy density than conventional acoustic-hard devices but greater than polymeric microfluidic chips. Against conventional acoustic-hard chips, the nodal line in the hybrid microchannel could be easily tuned to be placed in an off-center position by changing the frequency, effective for particle separation from a host fluid in parallel flow stream models. It is also shown that the hybrid acoustophoretic device deals with smaller temperature rise which is safer for the actuation of bioparticles. This new device eliminates the limitations of each sound-soft and sound-hard materials in terms of cost, adjusting the position of nodal plane, temperature rise, fragility, production cost and disposability, making it desirable for developing the next generation of economically viable acoustophoretic products for ultrasound particle manipulation in bioengineering applications

Comparing high-resolution gridded precipitation data with satellite rainfall estimates of TRMM_3B42 over Iran

To evaluate satellite rainfall estimates of Tropical Rain Measurement Mission (TRMM) level 3 output (3B42) (TRMM_3B42) over Iran (20°–45° N, 40°–65° E), we compared these data with high-resolution gridded precipitation datasets (0.25°×0.25° latitude/longitude) based on rain gauges (Iran Synoptic gauges Version 0902 (IS0902)). Spatial distribution of mean annual and mean seasonal rainfall in both IS0902 and TRMM_3B42 from 1998 to 2006 shows two main rainfall patterns along the Caspian Sea and over the Zagros Mountains. Scatter plots of annual average rainfall from IS0902 versus TRMM_3B42 for each 0.25°×0.25° grid cell over the entire country (25°–40° N, 45°–60° E), along the Caspian Sea (35°–40° N, 48°–56° E), and over the Zagros Mountains (28°–37° N, 46°–55° E) were derived. For the entire country, the Caspian Sea region, and the Zagros Mountains, TRMM_3B42 underestimates mean annual precipitation by 0.17, 0.39, and 0.15 mm day^−1, respectively, and the mean annual rainfall spatial correlation coefficients are 0.77, 0.57, and 0.75, respectively. The mean annual precipitation temporal correlation coefficient for IS0902 and TRMM_3B42 is ~0.8 in the area along the Zagros Mountains, and ~0.6 in the Caspian Sea and desert regions

Digestion of rice straw and oil palm fronds by microflora from rumen and termite bacteria, in vitro.

The digestion and Volatile Fatty Acid (VFA) production from rice straw and oil palm fronds by cellulolytic bacteria isolated from the termite Coptotermes curvignathus were investigated. The bacteria were Acinetobacter strain Raminalimon, Enterobacter aerogenes strain Razmin C, Enterobacter cloacae strain Razmin B, Bacillus cereus strain Razmin A and Chryseobacterium kwangyangense strain Cb. Acinetobacter strain Raminalimon is an aerobic bacterium, while the other species are facultative anaerobes. There were significant differences (p<0.05) among the bacteria for Dry Matter (DM) lost and acetic acid production from rice straw and Acinetobacter strain Raminalimon showed the highest activity. The facultative bacteria C. kwangyangense strain Cb (cfu mL(-1) 231 x 10(-6), OD: 0.5), E. cloacae (cfu mL(-1) 68 x 10(-7), OD: 0.5) and E. aerogenes (cfu mL(-1) 33 x 10(-7), OD: 0.5) were used for digestion study with the rumen fluid microflora. The in vitro gas production technique was applied for the comparative study and the parameters measured were pH, gas (volume), dry matter lost, acetic acid, propionic acid and butyric acid concentrations. pH was not significantly (p<0.05) different among the five treatments. The bacterium C. kwangyangense strain Cb showed the highest activity (p<0.05) for DM lost, acetic acid, propionic acid and butyric acid production from rice straw when compared to the other bacterial activities. There was no significance (p<0.05) difference between the three bacteria for the dry matter lost of oil palm fronds but the production of Volatile Fatty Acids (VFA) was significantly (p<0.05) high in the treatment which was inoculated with C. kwangyangense strain Cb. The Gen Bank NCBI/EMBL accession numbers for the bacterial strains are EU332791, EU305608, EU305609, EU294508 and EU169201