ICRPfinder: a fast pattern design algorithm for coding sequences and its application in finding potential restriction enzyme recognition sites

<p>Abstract</p> <p>Background</p> <p>Restriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-type DNA sequences to express the same wild-type amino acid sequences but with enhanced codons, specific cut sites, unique post-translational modifications, and other engineered-in components for recombinant applications. A fast DNA pattern design algorithm, ICRPfinder, is provided in this paper and applied to find or create potential recognition sites in target coding sequences.</p> <p>Results</p> <p>ICRPfinder is applied to find or create restriction enzyme recognition sites by introducing silent mutations. The algorithm is shown capable of mapping existing cut-sites but importantly it also can generate specified new unique cut-sites within a specified region that are guaranteed not to be present elsewhere in the DNA sequence.</p> <p>Conclusion</p> <p>ICRPfinder is a powerful tool for finding or creating specific DNA patterns in a given target coding sequence. ICRPfinder finds or creates patterns, which can include restriction enzyme recognition sites, without changing the translated protein sequence. ICRPfinder is a browser-based JavaScript application and it can run on any platform, in on-line or off-line mode.</p

Ultra-small topological spin textures with size of 1.3nm at above room temperature in Fe78Si9B13 amorphous alloy

Topologically protected spin textures, such as skyrmions1,2 and vortices3,4, are robust against perturbations, serving as the building blocks for a range of topological devices5-9. In order to implement these topological devices, it is necessary to find ultra-small topological spin textures at room temperature, because small size implies the higher topological charge density, stronger signal of topological transport10,11 and the higher memory density or integration for topological quantum devices5-9. However, finding ultra-small topological spin textures at high temperatures is still a great challenge up to now. Here we find ultra-small topological spin textures in Fe78Si9B13 amorphous alloy. We measured a large topological Hall effect (THE) up to above room temperature, indicating the existence of highly densed and ultra-small topological spin textures in the samples. Further measurements by small-angle neutron scattering (SANS) reveal that the average size of ultra-small magnetic texture is around 1.3nm. Our Monte Carlo simulations show that such ultra-small spin texture is topologically equivalent to skyrmions, which originate from competing frustration and Dzyaloshinskii-Moriya interaction12,13 coming from amorphous structure14-17. Taking a single topological spin texture as one bit and ignoring the distance between them, we evaluated the ideal memory density of Fe78Si9B13, which reaches up to 4.44*104 gigabits (43.4 TB) per in2 and is 2 times of the value of GdRu2Si218 at 5K. More important, such high memory density can be obtained at above room temperature, which is 4 orders of magnitude larger than the value of other materials at the same temperature. These findings provide a unique candidate for magnetic memory devices with ultra-high density.Comment: 26 pages, 4 figure

Ancestry of the Iban Is Predominantly Southeast Asian: Genetic Evidence from Autosomal, Mitochondrial, and Y Chromosomes

Humans reached present-day Island Southeast Asia (ISEA) in one of the first major human migrations out of Africa. Population movements in the millennia following this initial settlement are thought to have greatly influenced the genetic makeup of current inhabitants, yet the extent attributed to different events is not clear. Recent studies suggest that south-to-north gene flow largely influenced present-day patterns of genetic variation in Southeast Asian populations and that late Pleistocene and early Holocene migrations from Southeast Asia are responsible for a substantial proportion of ISEA ancestry. Archaeological and linguistic evidence suggests that the ancestors of present-day inhabitants came mainly from north-to-south migrations from Taiwan and throughout ISEA approximately 4,000 years ago. We report a large-scale genetic analysis of human variation in the Iban population from the Malaysian state of Sarawak in northwestern Borneo, located in the center of ISEA. Genome-wide single-nucleotide polymorphism (SNP) markers analyzed here suggest that the Iban exhibit greatest genetic similarity to Indonesian and mainland Southeast Asian populations. The most common non-recombining Y (NRY) and mitochondrial (mt) DNA haplogroups present in the Iban are associated with populations of Southeast Asia. We conclude that migrations from Southeast Asia made a large contribution to Iban ancestry, although evidence of potential gene flow from Taiwan is also seen in uniparentally inherited marker data

Dynamic Evolution Analysis of Stock Price Fluctuation and Its Control

This paper studies a simple dynamical system of stock price fluctuation time series based on the rule of stock market. When the stock price fluctuation system is disturbed by external excitations, the system exhibits obviously chaotic phenomena, and its basic dynamic properties are analyzed. At the same time, a new fixed-time convergence theorem is proposed for achieving fixed-time control of stock price fluctuation system. Finally, the effectiveness of the method is verified by numerical simulation

Finite-Time Impulsive Control of Financial Risk Dynamic System with Chaotic Characteristics

The control of financial risk has always been one of the important topics in financial research. Based on the theory of finance, this paper proposes a kind of financial risk dynamic system. By analyzing some properties of the dynamic system, the system shows obvious coexisting chaotic oscillations. In order to control the financial risk dynamic system effectively, this paper proposes a finite-time impulse controller to control the financial risk dynamic system. Simulation results show that the finite-time impulse controller has faster convergence speed than the impulse controller

Ammonium Effects on Nitrate Uptake by Roots of Upland and Paddy Rice Seedlings Related to Transmembrane Potential Differences

Nitrate uptake characteristics and ammonium effects were compared between upland rice (Brazilian upland rice) and paddy rice (Wuyujing 3 and Yangdao 6) through the glass microelectrode technique and the concentration gradient method of uptake kinetics. Results indicated that nitrate uptake by rice seedlings and ammonium effects were related to transmembrane potential difference, and upland rice and paddy rice presented obviously different responses. Nitrate induced a rapid depolarization and then a slow repolarization of transmembrane potential in root epidermal cells, and even hyperpolarization was observed when nitrate concentration was low. Resting transmembrane potential of epidermal cells in Brazilian upland rice roots was lower and its response to NO3- was bigger than that of two paddy rice species. Depolarization of membrane potential was amplified when ammonium was simultaneously added with nitrate into the measure medium, but repolarization was reduced, even disappeared. Brazilian upland rice seedlings had high Vmax of nitrate uptake and low Km, furthermore, Vmax and Km were little affected by ammonium, but Vmax of Wuyujing 3 was reduced significantly. Therefore, inhibition of ammonium to nitrate uptake possibly due to decrease of membrane potential and influence of nitrate transporters. Moreover, inhibition of NH4+ differed obviously between upland rice and paddy rice

Ammonium Effects on Nitrate Uptake by Roots of Upland and Paddy Rice Seedlings Related to Transmembrane Potential Differences

Nitrate uptake characteristics and ammonium effects were compared between upland rice (Brazilian upland rice) and paddy rice (Wuyujing 3 and Yangdao 6) through the glass microelectrode technique and the concentration gradient method of uptake kinetics. Results indicated that nitrate uptake by rice seedlings and ammonium effects were related to transmembrane potential difference, and upland rice and paddy rice presented obviously different responses. Nitrate induced a rapid depolarization and then a slow repolarization of transmembrane potential in root epidermal cells, and even hyperpolarization was observed when nitrate concentration was low. Resting transmembrane potential of epidermal cells in Brazilian upland rice roots was lower and its response to NO3- was bigger than that of two paddy rice species. Depolarization of membrane potential was amplified when ammonium was simultaneously added with nitrate into the measure medium, but repolarization was reduced, even disappeared. Brazilian upland rice seedlings had high Vmax of nitrate uptake and low Km, furthermore, Vmax and Km were little affected by ammonium, but Vmax of Wuyujing 3 was reduced significantly. Therefore, inhibition of ammonium to nitrate uptake possibly due to decrease of membrane potential and influence of nitrate transporters. Moreover, inhibition of NH4+ differed obviously between upland rice and paddy rice