RIL-StEp: epistasis analysis of rice recombinant inbred lines (RILs) reveals candidate interacting genes that control seed hull color and leaf chlorophyll content

Characterizing epistatic gene interactions is fundamental for understanding the genetic architecture of complex traits. However, due to the large number of potential gene combinations, detecting epistatic gene interactions is computationally demanding. A simple, easy-to-perform method for sensitive detection of epistasis is required. Due to their homozygous nature, use of recombinant inbred lines excludes the dominance effect of alleles and interactions involving heterozygous genotypes, thereby allowing detection of epistasis in a simple and interpretable model. Here, we present an approach called RIL-StEp (recombinant inbred lines stepwise epistasis detection) to detect epistasis using single-nucleotide polymorphisms in the genome. We applied the method to reveal epistasis affecting rice (Oryza sativa) seed hull color and leaf chlorophyll content and successfully identified pairs of genomic regions that presumably control these phenotypes. This method has the potential to improve our understanding of the genetic architecture of various traits of crops and other organisms

Combined use of an epidural cooling catheter and systemic moderate hypothermia enhances spinal cord protection against ischemic injury in rabbits

BackgroundEpidural placement of a cooling catheter can protect against ischemic spinal cord injury. With the use of rabbits, we investigated whether this epidural cooling technique, when combined with systemic moderate hypothermia, can protect the spinal cord against ischemic metabolic stress.MethodsNew Zealand white rabbits (n = 28) were assigned to 1 of 4 different groups. Animals underwent abdominal aortic occlusion for 30 minutes using a 3F balloon catheter. Group 1 (n = 7) underwent epidural cooling by the catheter and systemic moderate hypothermia (35°C) induced with a cooling blanket. Group 2 (n = 7) underwent epidural cooling under systemic normothermia (38.5°C). Group 3 (n = 7) underwent systemic moderate hypothermia (35°C) without epidural cooling. Group 4 (n = 7) underwent neither epidural nor blanket cooling as a negative control. Neurologic status of their hind limbs was graded according to the modified Tarlov scale at 1, 2, and 7 days after surgery.ResultsDuring infrarenal aortic ischemia, epidural temperature was significantly lower in group 1 (18.5°C ± 0.8°C) than in group 2 (28.6°C ± 1.0°C; P = .0001), group 3 (34.2°C ± 0.06°C; P = .0001), or group 4 (38.5°C ± 0.2°C; P = .0001). Hind limb function recovery was greater in group 1 (mean Tarlov score, 4.9 ± 0.057) than in group 2 (2.6 ± 0.3; P = .0028), group 3 (2.1 ± 0.34; P = .0088), or group 4 (0.0 ± 0.0; P = .0003).ConclusionsEpidural cooling catheter combined with systemic moderate hypothermia produced additive cooling ability and protected the spinal cord against ischemia in rabbits more effectively than either intervention alone

Cuticular Hydrocarbon Content that Affects Male Mate Preference of Drosophila melanogaster from West Africa

Intraspecific variation in mating signals and preferences can be a potential source of incipient speciation. Variable crossability between Drosophila melanogaster and D. simulans among different strains suggested the abundance of such variations. A particular focus on one combination of D. melanogaster strains, TW1(G23) and Mel6(G59), that showed different crossabilities to D. simulans, revealed that the mating between females from the former and males from the latter occurs at low frequency. The cuticular hydrocarbon transfer experiment indicated that cuticular hydrocarbons of TW1 females have an inhibitory effect on courtship by Mel6 males. A candidate component, a C25 diene, was inferred from the gas chromatography analyses. The intensity of male refusal of TW1 females was variable among different strains of D. melanogaster, which suggested the presence of variation in sensitivity to different chemicals on the cuticle. Such variation could be a potential factor for the establishment of premating isolation under some conditions

A Comparison of Physical vs. Nonphysical Wedge Modalities in Radiotherapy

This chapter discusses the clinical application and implementation of wedge techniques in radiation therapy. Coverage of the target region with a curative dose is critical for treating several cancer types; to that end, wedge filters are commonly used to improve dose uniformity to the target volume. Initially, wedges designed for this purpose were physical and were made of high-density materials such as lead or steel. Subsequently, nonphysical wedges were introduced; these improved the dose uniformity using computer systems in lieu of physical materials. As wedge systems evolve, however, they each continue to have their advantages and disadvantages. When using physical wedges, it is difficult to control the generation of secondary radiation resulting from the collision of the radiation beam with the wedge body; conversely, nonphysical wedges do not create any secondary radiation because there is no physical interference with the beam. On the other hand, nonphysical wedges are less suitable for treating moving tumors, such as those in the lung, and physical wedges have better dose coverage to the target volume than nonphysical wedges. This chapter aims to guide decision-making regarding the choice of wedge types in various clinical situations

Hinode Calibration for Precise Image Co-alignment between SOT and XRT (November 2006 -- April 2007)

To understand the physical mechanisms for activity and heating in the solar atmosphere, the magnetic coupling from the photosphere to the corona is an important piece of information from the Hinode observations, and therefore precise positional alignment is required among the data acquired by different telescopes. The Hinode spacecraft and its onboard telescopes were developed to allow us to investigate magnetic coupling with co-alignment accuracy better than 1 arcsec. Using the Mercury transit observed on 8 November 2006 and co-alignment measurements regularly performed on a weekly basis, we have determined the information necessary for precise image co-alignment and have confirmed that co-alignment better than 1 arcsec can be realized between Solar Optical Telescope (SOT) and X-Ray Telescope (XRT) with our baseline co-alignment method. This paper presents results from the calibration for precise co-alignment of CCD images from SOT and XRT.Comment: 8 pages, 9 figures, accepted for publication in PASJ (Hinode Special issue

Genome Analysis Revives a Forgotten Hybrid Crop Edo-dokoro in the Genus Dioscorea

忘れられた作物「えどどころ」の起原 --ゲノム解析が明らかにする青森県三八上北地域に残る栽培イモの歴史--. 京都大学プレスリリース. 2022-08-10.A rhizomatous Dioscorea crop “Edo-dokoro” was described in old records of Japan, but its botanical identify has not been characterized. We found that Edo-dokoro is still produced by four farmers in Tohoku-machi of Aomori Prefecture, Japan. Rhizomes of Edo-dokoro are a delicacy to the local people and are sold in the markets. Morphological characters of Edo-dokoro suggest its hybrid origin between the two species, D. tokoro and D. tenuipes. Genome analysis revealed that Edo-dokoro is likely originated by hybridization of a male D. tokoro to a female D. tenuipes, followed by a backcross with a male plant of D. tokoro. Edo-dokoro is a typical minor crop possibly maintained for more than 300 years but now almost forgotten from the public. We hypothesize that there are many such uncharacterized genetic heritages passed over generations by small scale farmers that await serious scientific investigation for future use and improvement by using modern genomics information