Whole genome detection of signature of positive selection in African cattle reveals selection for thermotolerance

As African indigenous cattle evolved in a hot tropical climate, they have developed an inherent thermotolerance; survival mechanisms include a light‐colored and shiny coat, increased sweating, and cellular and molecular mechanisms to cope with high environmental temperature. Here, we report the positive selection signature of genes in African cattle breeds which contribute for their heat tolerance mechanisms. We compared the genomes of five indigenous African cattle breeds with the genomes of four commercial cattle breeds using cross‐population composite likelihood ratio (XP‐CLR) and cross‐population extended haplotype homozygosity (XP‐EHH) statistical methods. We identified 296 (XP‐EHH) and 327 (XP‐CLR) positively selected genes. Gene ontology analysis resulted in 41 biological process terms and six Kyoto Encyclopedia of Genes and Genomes pathways. Several genes and pathways were found to be involved in oxidative stress response, osmotic stress response, heat shock response, hair and skin properties, sweat gland development and sweating, feed intake and metabolism, and reproduction functions. The genes and pathways identified directly or indirectly contribute to the superior heat tolerance mechanisms in African cattle populations. The result will improve our understanding of the biological mechanisms of heat tolerance in African cattle breeds and opens an avenue for further study.     

Effect of steel-making slag as a soil amendment on arsenic uptake by radish (Raphanus sativa L.) in an upland soil

The steel-making slag (SMS), a by-product of steel manufacturing process with an alkaline pH (11–12) and high amount of iron (Fe) and calcium (Ca) oxides, was used to reduce arsenic (As) phytoextractability. The by-product was selected as an alternative to commercial Fe oxides, which can decrease plant uptake, but they are expensive if used as amendments of contaminated arable soils. SMS was applied at rates 0, 2, 4, and 8 Mg ha⁻¹ to an As (1 N HCl-extractable As 25 mg kg⁻¹) contaminated soil prepared by mixing non-contaminated soil and mine tailings and cropped to radish (Raphanus sativa L.) seeding. Calcium hydroxide (Ca(OH)₂), a common liming material in Korea, was applied at the same rates for comparison. Steel-making slag more effectively suppressed radish As uptake and increased yield than Ca(OH)₂ due to stronger As immobilization because it significantly increased extractable Fe concentration and decreased extractable As. The SMS-treated soil showed an apparent increase in As chemisorbed by Fe and Al oxides and hydroxides of surface soil, As associated at the Fe and Al oxides and hydroxides of internal surfaces of soil aggregates, and Ca-associated As. The steel-making slag can be a good soil amendment to suppress As phytoextractability and improve nutrient balance in As-contaminated soil.     

Optimized protocol for multiplex nested polymerase chain reaction to detect and differentiate Haemophilus parasuis,Streptococcus suis,and Mycoplasma hyorhinis in formalin-fixed,paraffin-embedded tissues from pigs with polyserositis

An optimized protocol was developed for the simultaneous detection and differentiation of Haemophilus parasuis, Streptococcus suis, and Mycoplasma hyorhinis in formalin-fixed, paraffin-embedded (FFPE) tissues with multiplex nested polymerase chain reaction (PCR). This method also determines the prevalence of these bacteria in pigs with polyserositis. DNA extraction with a combination of a commercial reagent and proteinase K resulted in more frequent detection of the pathogens than DNA extraction with proteinase K alone. Among FFPE tissue samples from 312 cases of polyserositis in which at least 1 bacterial species was detected, multiplex nested PCR detected H. parasuis in 239 (77%), S. suis in 124 (40%), and M. hyorhinis in 40 (13%). The disease was caused by a single pathogen in 224 (72%) of the cases and multiple pathogens in 88 (28%). Among the pigs positive for H. parasuis, S. suis, and M. hyorhinis by multiplex nested PCR, the pathogen was isolated from only 11%, 35%, and 28%, respectively. Therefore, the PCR protocol developed in this study is a useful diagnostic method when samples are negative after isolation methods and even for samples in which only 1 pathogen was isolated.     

Antihypertensive effect of angiotensin i converting enzyme-inhibitory peptide from hydrolysates of Bigeye tuna dark muscle, Thunnus obesus

Angiotensin I converting enzyme (ACE) inhibitory peptide was isolated from tuna dark muscle hydrolysate prepared by alcalase, neutrase, pepsin, papain, alpha-chymotrypsin, and trypsin, respectively. Among hydrolysates, the pepsin-derived hydrolysate exhibited the highest ACE I inhibitory activity versus those of other enzyme hydrolysates. The structure of the peptide was identified to be Trp-Pro-Glu-Ala-Ala-Glu-Leu-Met-Met-Glu-Val-Asp-Pro (molecular weight 1581 Da) by time of flight mass spectrometry/mass spectrometry analysis, and the IC 50 value of the peptide was 21.6 microM. The Lineweaver-Burk plots revealed that the peptide acts as a noncompetitive inhibitor, and the inhibitor constant ( K i) was calculated as 26.6 microM using the secondary plots. The peptide had an antihypertensive effect according to the time-course measurement after oral administration to spontaneously hypertensive rats. Maximal reduction was detected 3 h after oral administration at a dose of 10 mg/kg of body weight. These results suggest that the peptide derived from tuna dark muscle would be a beneficial ingredient for functional food or pharmaceuticals against hypertension and its related diseases.     

Phytophthora ramorum Colonizes Tanoak Xylem and Is Associated with Reduced Stem Water Transport

ABSTRACT Isolation, detection with diagnostic polymerase chain reaction (PCR), and microscopy demonstrated the presence of Phytophthora ramorum in the sapwood of mature, naturally infected tanoak (Lithocarpus densiflorus) trees. The pathogen was strongly associated with discolored sapwood (P < 0.001), and was recovered or detected from 83% of discolored sapwood tissue samples. Hyphae were abundant in the xylem vessels, ray parenchyma, and fiber tracheids. Chlamydospores were observed in the vessels. Studies of log inoculation indicated that P. ramorum readily colonized sapwood from inoculum placed in the bark, cambium, or sapwood. After 8 weeks, radial spread of P. ramorum in sapwood averaged 3.0 to 3.3 cm and axial spread averaged 12.4 to 18.8 cm. A field study was conducted to determine if trees with infected xylem had reduced sap flux and reduced specific conductivity relative to noninfected control trees. Sap flux was monitored with heat-diffusion sensors and tissue samples near the sensors were subsequently tested for P. ramorum. Adjacent wood sections were excised and specific conductivity measured. Both midday sap flux and specific conductivity were significantly reduced in infected trees versus noninfected control trees. Vessel diameter distributions did not differ significantly among the two treatments, but tyloses were more abundant in infected than in noninfected trees. Implications for pathogenesis, symptomology, and epidemiology are discussed.     

Synthesis of fluorescently labeled pyrazole derivative induceing a triple response in Arabidopsis seedlings

A fluorescent labeled pyrazole derivative with a dansyl moiety (EH-DF) was synthesized. Design of EH-DF was carried out by using a dansyl moiety to substitute the naphthalene moiety of the parent compound (EH-1). At a concentration of 30 µM, EH-DF displayed biological activity on inducing a triple response in Arabidopsis seedlings. Compared with the non-chemical treated control, the hypocotyl length of EH-DF-treated Arabidopsis seedlings was reduced from approximately 9.2±0.7 mm to 2.4±0.2 mm. The length of the roots was reduced from 1.7±0.1 mm to 1.0±0.1 mm, and the curvature of the hook of Arabidopsis seedlings increased from 60±16 degrees to 245±35 degrees. The maxim excitation wavelength and emission wavelength of EH-DF were 350 and 535 nm, respectively. Data obtained via fluorescent microscope analysis indicated that intensive fluorescent signals of EH-DF were observed in the shoot of Arabidopsis seedlings.     

Taeanamides A and B,Nonribosomal Lipo-Decapeptides Isolated from an Intertidal-Mudflat-Derived Streptomyces sp.

Two new lipo-decapeptides, namely taeanamides A and B (1 and 2), were discovered from the Gram-positive bacterium Streptomyces sp. AMD43, which was isolated from a mudflat sample from Anmyeondo, Korea. The exact molecular masses of 1 and 2 were revealed by high-resolution mass spectrometry, and the planar structures of 1 and 2 were elucidated using NMR spectroscopy. The absolute configurations of 1 and 2 were determined using a combined analysis of ¹H-¹H coupling constants and ROESY correlations, the advanced Marfey’s method, and bioinformatics. The putative nonribosomal peptide synthetase pathway for the taeanamides was identified by analyzing the full genome sequence data of Streptomyces sp. AMD43. We also found that taeanamide A exhibited mild anti-tuberculosis bioactivity, whereas taeanamide B showed significant bioactivity against several cancer cell lines.     

Experimental susceptibility of different life-stages of the giant freshwater prawn, Macrobrachium rosenbergii (de Man), to white spot syndrome virus (WSSV)

Studies were conducted by injecting/feeding white spot syndrome virus (WSSV) derived from infected shrimp, Penaeus monodon (Fabricius), to different life-stages, namely post-larvae, juveniles, sub-adults and adults of Macrobrachium rosenbergii (de Man). The disease was also induced in brood stock, and the eggs and larvae derived from these animals were subsequently tested for WSSV infection. All the stages except egg used for the experiment were found WSSV positive in histopathology, cross infection bioassay and polymerase chain reaction (PCR) analysis. Experimentally infected post-larvae and juveniles showed a high percentage of mortality and an increased rate of cannibalism. The cumulative mortality in post-larvae was up to 28%; with 28–40% cannibalism resulting in a maximum loss of up to 68%. In juveniles, observed mortality and cannibalism were 10–20% and 6.7–30.0%, respectively, and the maximum loss recorded was 50%. In sub-adults, mortality ranged from 2.8 to 6.7%, cannibalism was up to 20% and the total loss was up to 26.7%. Sub-adults and adults were found to be more tolerant to the infection as evidenced by the mortality pattern. A nested (two-step) PCR resulted in a 570-bp product specific to WSSV in all stages, except the eggs.     

Proliferation of kuchijirosho causative agent in a fugu-derived cell line

Kuchijirosho is a fatal disease of commercially cultured fugu, Takifugu rubripes. The transmissible nature of kuchijirosho strongly suggests that an infectious pathogen is the causative agent. Because it is filtrable, the agent is thought to be a virus; however, it has not yet been identified. The lack of a permissive cell line for the putative kuchijirosho-causing agent (KCA) has hindered research on the identification of this pathogen. We inoculated brain extract prepared from kuchijirosho-affected fugu onto an established fugu cell line, fugu eye, and observed that cytopathic effect appeared 7 days after inoculation. Injection of the culture medium of infected fugu eye cells into fugu resulted in the onset of kuchijirosho, indicating that fugu eye cells are able to proliferate KCA. An infectious fraction separated by sodium iottalamate density gradient centrifugation showed a density of 1.15 g mL(-1) equivalent to that of KCA derived from affected fugu brain. To determine whether the genome of KCA is RNA or DNA based, nucleotide synthesis inhibitors were applied to inoculated fugu eye cell line to influence the production of KCA. 5-Fluorouracil but not IUdR showed a concentration-dependent inhibition of KCA yield. These results suggest that KCA is an RNA virus.