One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT)

Ohtsuka, M., Miura, H., Mochida, K. et al. One-step generation of multiple transgenic mouse lines using an improved Pronuclear Injection-based Targeted Transgenesis (i-PITT). BMC Genomics 16, 274 (2015). https://doi.org/10.1186/s12864-015-1432-

A new unifying heuristic algorithm for the undirected minimum cut problems using minimum range cut algorithms

AbstractGiven a connected undirected multigraph with n vertices and m edges, we first propose a new unifying heuristic approach to approximately solving the minimum cut and the s-t minimum cut problems by using efficient algorithms for the corresponding minimum range cut problems. Our method is based on the association of the range value of a cut and its cut value when each edge weight is chosen uniformly randomly from the fixed interval. Our computational experiments demonstrate that this approach produces very good approximate solutions. We shall also propose an O(log2 n) time parallel algorithm using O(n2) processors on an arbitrary CRCW PRAM model for the minimum range cut problems, by which we can efficiently obtain approximate minimum cuts in poly-log time using a polynomial number of processors

Comparison of Targeted vs Random Biopsies for Surveillance of Ulcerative Colitis-Associated Colorectal Cancer

Background & AimsA random biopsy is recommended for surveillance of ulcerative colitis (UC)-associated colorectal cancer. However, a targeted biopsy might be more effective. We conducted a randomized controlled trial to compare rates of neoplasia detection by targeted vs random biopsies in patients with UC.MethodsWe performed a study of 246 patients with UC for 7 years or more, seen at 52 institutions in Japan from October 1, 2008 through December 31, 2010. Patients were randomly assigned to the random group (4 random biopsies collected every 10 cm in addition to targeted biopsies, n = 122) or the target group (biopsies collected from locations of suspected neoplasia, n = 124). The primary end point was the number of neoplastic lesions detected in a single surveillance colonoscopy. We estimated the ratio and difference in the mean number of neoplastic lesions between the groups. We also evaluated the non-inferiority between the groups as an exploratory study. A non-inferiority margin of 0.65 (0.13 of 0.20) was considered for the ratio of the mean number of neoplastic lesions between groups.ResultsThe mean number of biopsies found to contain neoplastic tissue per colonoscopy was 0.211 (24 of 114) in the target group and 0.168 (18 of 107) in the random group (ratio of 1.251; 95% confidence interval, 0.679–2.306). The lower limit was above the non-inferiority margin of 0.65. Neoplasias were detected in 11.4% of patients in the target group and 9.3% of patients in the random group (P = .617). Larger numbers of biopsy samples per colonoscopy were collected in the random group (34.8 vs 3.1 in the target group; P < .001), and the total examination time was longer (41.7 vs 26.6 minutes in the target group; P < .001). In the random group, all neoplastic tissues found in random biopsies were collected from areas of the mucosa with a history or presence of inflammation.ConclusionsIn a randomized controlled trial, we found that targeted and random biopsies detect similar proportions of neoplasias. However, a targeted biopsy appears to be a more cost-effective method. Random biopsies from areas without any signs of present or past inflammation were not found to contain neoplastic tissues. Clinical Trial Registry: UMIN000001608

Plankton introduction via ship ballast water : A review

Introduction of marine plankton via ship ballast water and cultured fish and shellfish has hitherto caused serious social problems, and has greatly influenced native ecosystems. The present paper briefly reviews previous data concerning newly introduced plankton. At least 25 marine benthic species have been introduced to Japan since the early 1900's, whereas alien plankters have never been confirmed in Japan. This may be partly due to the relatively a small volume of ballast water discharged into Japanese ports. In contrast, the eastern Pacific coasts of North and South America are one of the main receiver areas for brackish and coastal zooplankters such as copepods from East Asia. Some East Asian copepods are so invasive in the USA that they appear to have highly changed the ecosystems into alien-dependent ones, and eliminated native copepods. These copepods could have been introduced either as (resting) eggs or as post-embryonic stages. When many benthic and planktonic invertebrates are simultaneously introduced, more complex ecological changes have occurred than were expected. Since introduction is mainly caused by economic activities, distinct patterns can be recognized, considering the intensity of international trade leading to intensive introduction. Fourteen major routes of transoceanic invasion are identified in the Pacific, in which the main receiver areas are Hawaii, the Pacific coasts of North and South America, and Australia, while donor areas are East Asia. In particular the San Francisco estuary has been already dominated by East Asian copepods, the Origin and evolutionary history of alien species also seems to affect their establishment. The major donor area in East Asia is a special area with a remarkably high diversity of brackish organisms that have evolved as the phylogenetically young "East Asian Initial Element" during the Miocene to Pleistocene. Hence East Asian species may potentially become strong competitors against American indigenous ones. Abundance and taxon numbers of both zoo- and phytoplankters generally declined sharply in ballast tanks within a few days after departure. However some detritus-feeding, semiplanktonic copepods propagated in the tanks to become approximately 100 times as high as the initial density at the end of the cruise. Ballast tanks can be incubators for some invertebrates rather than coffins. Some phytoplankton groups, such as dinoflagellates, diatoms and raphidophytes, are known to produce resting cysts. They are resistant and can survive during the transportation within the ship's ballast water tanks. Three main, complementary hypotheses have been proposed concerning introduction: "Propagule Supply Hypothesis", "Invasion Resistance Hypothesis", and "Enemy Release Hypothesis". Introduction is determined by density, frequency and duration of inoculation, by the condition of propagules, and by different donor areas. Establishment of introduced species is facilitated or prevented by physico-chemical and biological factors in the receiver area. Loss of predators and parasites in a newly introduced area is considered to facilitate establishment of the alien species greatly. Recently the release from parasite pressure has arthered in creasing attention to explain why alien species flourish in an introduced area. In fact zooplankters harbor many parasites and parasitoids, some of which greatly influence the host population dynamics. Many physical and chemical treatments of ballast water are applied to remove plankton in the ballast tanks, all of which are still incomplete in consideration of cost and environmental contamination. Since the rate of invasion is enhanced by increases in size and speed of modern vessels, improvement of effective sterilization methods and the issue of relevant laws is urgent. In addition the ecology of potentially invasive brackish and coastal invertebrates and algae should be studied prior to introduction in order to minimize their invasion. Long-term monitoring and assessment of ecological niches of introduced species are needed to detect changes in the ecosystem

A new unifying heuristic algorithm for the undirected minimum cut problems using minimum range cut algorithms

AbstractGiven a connected undirected multigraph with n vertices and m edges, we first propose a new unifying heuristic approach to approximately solving the minimum cut and the s-t minimum cut problems by using efficient algorithms for the corresponding minimum range cut problems. Our method is based on the association of the range value of a cut and its cut value when each edge weight is chosen uniformly randomly from the fixed interval. Our computational experiments demonstrate that this approach produces very good approximate solutions. We shall also propose an O(log2 n) time parallel algorithm using O(n2) processors on an arbitrary CRCW PRAM model for the minimum range cut problems, by which we can efficiently obtain approximate minimum cuts in poly-log time using a polynomial number of processors