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1.
We present a new variable-length encoding scheme for sequences of integers, Directly Addressable Codes (DACs), which enables direct access to any element of the encoded sequence without the need of any sampling method. Our proposal is a kind of implicit data structure that introduces synchronism in the encoded sequence without using asymptotically any extra space. We show some experiments demonstrating that the technique is not only simple, but also competitive in time and space with existing solutions in several applications, such as the representation of LCP arrays or high-order entropy-compressed sequences.  相似文献   

2.
Four advantages of storing and retrieving geometric figures and chromosome images through the use of shape-oriented similarity measures are presented. A complemented but not distributive lattice and a distributive but not complemented lattice are found. Answers to triangle related fuzzy queries such as “retrieve the triangles which are very similar to isosceles triangles but not similar to a given triangle Δx”, and chromosome related fuzzy queries such as “retrieve the chromosomes which are more or less similar to median chromosomes and very very similar to a given chromosome A” are presented and illustrated by examples. For shape-oriented storage of triangles, it is proposed to store the angles of each triangle in decreasing order of the magnitude and logically order all the triangles according to the magnitude of the angles. For shape-oriented storage of chromosomes, it is proposed to logically order all the chromosomes individually and independently according to the angular sums of its exterior biangles and interior biangles. The results may have useful applications in information storage and retrieval, artificial intelligence and pattern recognition.  相似文献   

3.
In the era of the targeted therapy identification of EGFR mutation detection in lung cancer is extremely helpful to predict the treatment efficacy of EGFR tyrosine kinase inhibitors (TKIs). Unfortunately, the inadequacy and quality of the biopsy samples are the major obstacles in molecular testing of EGFR mutation in lung cancer. To address this issue, the present study intended to use liquid biopsy as the non-invasive method for EGFR mutation detection. A total of 31 patients with an advanced stage of lung cancer were enrolled in the study from which cell-free DNA (cfDNA) and FFPE tissue DNA was extracted. Extracted DNA samples were analyzed for further EGFR exon specific mutation analysis by ARMS-PCR. Data were analyzed statistically using SPSS software. In cfDNA samples, the prevalence of wild type EGFR was 48% while the prevalence of TKI resistant and TKI sensitive mutations were 3%. Conversely, in tissue DNA samples, the prevalence of wild type, TKI sensitive and TKI resistant mutations were 48%, 19%, and 3%, respectively. The overall concordance of EGFR mutation between cfDNA and tissue DNA was 83%. McNemar’s test revealed that there was no significant difference between EGFR expression of cfDNA and tissue DNA samples. Additionally, the significant-high incidence of TKI resistant mutations was observed in tobacco habituates, indicating the role of carcinogens present in the tobacco in developing resistant mutations. In conclusion, our data suggest that evaluation of EGFR mutation from cfDNA samples is practicable as a non-invasive tool in patients with advanced-stage of lung cancer.  相似文献   

4.
BackgroundAgkistrodon acutus, a traditional Chinese medicine, clinically used in the treatment of rheumatism, tumor, and cardiovascular and cerebrovascular diseases. Due to the unique medicinal value and the difficulty of artificial breeding of Agkistrodon acutus, the supply of Agkistrodon acutus on the market exceeds the demand, and a large number of its adulterants are found on the market. In this study, the cytb gene sequences of Agkistrodon acutus and 9 snakes were compared and analyzed, specific primers were designed, and specific PCR methods were established to detect Agkistrodon acutus medicinal samples on the market.ResultsThis method was successfully applied to distinguish the snake from other adulterated species, and tested 18 Agkistrodon acutus samples randomly purchased from six cities. Twelve samples were counterfeit and six were genuine. The standard reference material of Agkistrodon acutus was cloned by molecular cloning and sequencing, and the gene sequence difference with other species was significant. It shows that the region could be used as the fingerprint region of the target species.ConclusionsThe proposed method can be used as a species-specific marker and can be highly distinguished from other adulterated snake species, which is helpful to effectively avoid the problem of false sale of Agkistrodon acutus.How to cite: Yingnuo L, Yanshuang W, Mingcheng Li, et al. Development of a species-specific PCR assay for authentication of Agkistrodon acutus based on mitochondrial cytochrome b gene. Electron J Biotechnol 2021;49. https://doi.org/10.1016/j.ejbt.2020.07.005  相似文献   

5.
The global demand for data storage is currently outpacing the world''s storage capabilities. DNA, the carrier of natural genetic information, offers a stable, resource- and energy-efficient and sustainable data storage solution. In this review, we summarize the fundamental theory, research history, and technical challenges of DNA storage. From a quantitative perspective, we evaluate the prospect of DNA, and organic polymers in general, as a novel class of data storage medium.  相似文献   

6.
A histological ground-section from a duck-billed dinosaur nestling (Hypacrosaurus stebingeri) revealed microstructures morphologically consistent with nuclei and chromosomes in cells within calcified cartilage. We hypothesized that this exceptional cellular preservation extended to the molecular level and had molecular features in common with extant avian cartilage. Histochemical and immunological evidence supports in situ preservation of extracellular matrix components found in extant cartilage, including glycosaminoglycans and collagen type II. Furthermore, isolated Hypacrosaurus chondrocytes react positively with two DNA intercalating stains. Specific DNA staining is only observed inside the isolated cells, suggesting endogenous nuclear material survived fossilization. Our data support the hypothesis that calcified cartilage is preserved at the molecular level in this Mesozoic material, and suggest that remnants of once-living chondrocytes, including their DNA, may preserve for millions of years.  相似文献   

7.
In the present work we perform compressed pattern matching in binary Huffman encoded texts [Huffman, D. (1952). A method for the construction of minimum redundancy codes, Proc. of the IRE, 40, 1098–1101]. A modified Knuth–Morris–Pratt algorithm is used in order to overcome the problem of false matches, i.e., an occurrence of the encoded pattern in the encoded text that does not correspond to an occurrence of the pattern itself in the original text. We propose a bitwise KMP algorithm that can move one extra bit in the case of a mismatch since the alphabet is binary. To avoid processing any bit of the encoded text more than once, a preprocessed table is used to determine how far to back up when a mismatch is detected, and is defined so that we are always able to align the start of the encoded pattern with the start of a codeword in the encoded text. We combine our KMP algorithm with two practical Huffman decoding schemes which handle more than a single bit per machine operation; skeleton trees defined by Klein [Klein, S. T. (2000). Skeleton trees for efficient decoding of huffman encoded texts. Information Retrieval, 3, 7–23], and numerical comparisons between special canonical values and portions of a sliding window presented in Moffat and Turpin [Moffat, A., & Turpin, A. (1997). On the implementation of minimum redundancy prefix codes. IEEE Transactions on Communications, 45, 1200–1207]. Experiments show rapid search times of our algorithms compared to the “decompress then search” method, therefore, files can be kept in their compressed form, saving memory space. When compression gain is important, these algorithms are better than cgrep [Ferragina, P., Tommasi, A., & Manzini, G. (2004). C Library to search over compressed texts, http://roquefort.di.unipi.it/~ferrax/CompressedSearch], which is only slightly faster than ours.  相似文献   

8.
Nicotine, responsible for the addictive properties of tobacco, is widely used in nicotine replacement therapy for tobacco use cessation. We investigated the time-dependent effect of treatment with nicotine on the tumor suppressor, DNA repair and immune responses. Swiss Albino mice (laca strain) of both sexes received nicotine dissolved at a dose of 100 µg/ml in 2% sucrose for 24 weeks, by oral gavage, while age- and gender-matched controls received only 2% sucrose for the same period. Nicotine-treated and control mice were sacrificed 6, 16 and 24 weeks post-treatment, and their tissues evaluated for alterations in histology, oxidative stress, TNF-α levels, nitric oxide (NO) and myeloperoxidase (MPO) release, tumor suppressor response and DNA repair response. Statistical significance of results was determined using Students’ t test. The tissues of nicotine treated mice exhibited a large number of multinucleated and binucleated cells, enlarged nuclei and non-uniform distribution of cells, significant increase in expression of TNF-α gene and serum TNF-α, and time-dependent significant increase in lipid peroxidation, protein carbonylation, NO and MPO release when compared to age-and gender-matched controls. The mRNA expression of the tumor suppressor gene p53, its primary regulator Mdm2, and the DNA repair genes Brca2 and Ape1 were significantly elevated, but the corresponding protein levels remained largely unaltered. In conclusion, treatment with nicotine caused oxidative stress and inflammation which can cause widespread cellular damage from the very onset of treatment, without subverting the tumor suppressor and DNA repair responses.Electronic supplementary materialThe online version of this article (10.1007/s12291-020-00903-8) contains supplementary material, which is available to authorized users.  相似文献   

9.
BackgroundThe quality of wheat grain depends on several characteristics, among which the composition of high molecular weight glutenin subunits, encoded by Glu-1 loci, are the most important. Application of biotechnological tools to accelerate the attainment of homozygous lines may influence the proportion of segregated genotypes. The objective was to determine, whether the selection pressure generated by the methods based on in vitro cultures, may cause a loss of genotypes with desirable Glu-1 alleles.ResultsHomozygous lines were derived from six winter wheat crosses by pollination with maize (DH-MP), anther culture (DH-AC) and single seed descent (SSD) technique. Androgenetically-derived plants that originated from the same callus were examined before chromosome doubling using allele-specific and microsatellite markers. It was found that segregation distortion in SSD and DH-MP populations occurred only in one case, whereas in anther-derived lines they were observed in five out of six analyzed combinations.ConclusionsSegregation distortion in DH-AC populations was caused by the development of more than one plant of the same genotype from one callus. This distortion was minimized if only one plant per callus was included in the population. Selection of haploid wheat plants before chromosome doubling based on allele-specific markers allows us to choose genotypes that possess desirable Glu-1 alleles and to reduce the number of plants in the next steps of DH production. The SSD technique appeared to be the most advantageous in terms of Mendelian segregation, thus the occurrence of residual heterozygosity can be minimized by continuous selfing beyond the F6 generation.  相似文献   

10.
BackgroundZymomonas mobilis is a Gram-negative microaerophilic bacterium with excellent ethanol-producing capabilities. The RecET recombination system provides an efficient tool for direct targeting of genes in the bacterial chromosome by PCR fragments.ResultsThe plasmids pSUZM2a-RecET and pSUZM2a-RecE588T were first developed to co-express RecE or RecE588 and RecT for homologous recombination. Thereafter, the PCR fragments of the tetracycline resistance marker gene flanked by 60 bp of adhA (alcohol dehydrogenase I) or adhB (alcohol dehydrogenase II) homologous sequences were electroporated directly into ZM4 cells harboring pSUZM2a-RecET or pSUZM2a-RecE588T. Both adhA and adhB were replaced by the tetracycline resistance gene in ZM4, yielding two mutant strains, Z. mobilis ZM4 ΔadhA and Z. mobilis ZM4 ΔadhB. These two mutants showed varying extent of reduction in ethanol production, biomass generation, and glucose metabolism. Furthermore, enzyme activity of alcohol dehydrogenase II in Z. mobilis ZM4 ΔadhB exhibited a significant reduction compared to that of wild-type ZM4.ConclusionThis approach provided a simple and useful method for introducing mutations and heterologous genes in the Z. mobilis genome.  相似文献   

11.
This paper studies vector incremental L2-gain and incremental stability for switched nonlinear systems using individual incremental gains and multiple storage functions. Firstly, a vector incremental L2-gain concept for switched nonlinear systems is proposed. Each subsystem is not required to have incremental L2-gain, but it has its own incremental L2-gain and the related storage function, when it is active. The transformation of “energy” from the active subsystem to each inactive subsystem is characterized by cross-supply rates. Then, we show that a switched nonlinear system who has vector incremental L2-gain can be incrementally stabilized under some constraints on the energy change of inactive subsystems. Secondly, a state-dependent switching law is designed to achieve vector incremental L2-gain, even if each subsystem does not have incremental L2-gain in the classic sense. Thirdly, each switched system is not required to have vector incremental L2-gain, but the feedback interconnection of switched nonlinear systems is incrementally stabilized by the design of a composite switching law. The switching law allows the two switched systems switch asynchronously. Two examples are provided to verify the effectiveness of the proposed method.  相似文献   

12.
Epigenetic mechanisms, such as DNA methylation, DNA hydroxymethylation, post-translational modifications (PTMs) of histone proteins affecting nucleosome remodelling, and regulation by small and large non-coding RNAs (ncRNAs) work in concert with cis and trans acting elements to drive appropriate gene expression. Advances in detection methods and development of dedicated platforms and methylation arrays resulted in an explosion of information on aberrantly methylated sequences linking deviations in epigenetic landscape with the initiation and progression of complex diseases. Here, we consider how DNA methylation changes in malignancies, such as breast, pancreatic, colorectal, and gastric cancer could be exploited for the purpose of developing specific diagnostic tools. DNA methylation changes can be applicable as biomarkers for detection of malignant disease in easily accessible tissues. Methylation signatures are already proving to be an important marker for determination of drug sensitivity. Even more, promoter methylation patterns of some genes, such as MGMT, SHOX2, and SEPT9, have already been translated into commercial clinical assays aiding in patient assessment as adjunct diagnostic tools. In conclusion, the changes in DNA methylation patterns in tumour cells are slowly gaining entrance into routine diagnostic tests as promising biomarkers and as potential therapeutic targets.Key words: biomarkers, CpG islands, DNA methylation, molecular diagnostics, epigenetics  相似文献   

13.
Central precocious puberty (CPP) refers to a human syndrome of early puberty initiation with characteristic increase in hypothalamic production and release of gonadotropin-releasing hormone (GnRH). Previously, loss-of-function mutations in human MKRN3, encoding a putative E3 ubiquitin ligase, were found to contribute to about 30% of cases of familial CPP. MKRN3 was thereby suggested to serve as a ‘brake’ of mammalian puberty onset, but the underlying mechanisms remain as yet unknown. Here, we report that genetic ablation of Mkrn3 did accelerate mouse puberty onset with increased production of hypothalamic GnRH1. MKRN3 interacts with and ubiquitinates MBD3, which epigenetically silences GNRH1 through disrupting the MBD3 binding to the GNRH1 promoter and recruitment of DNA demethylase TET2. Our findings have thus delineated a molecular mechanism through which the MKRN3–MBD3 axis controls the epigenetic switch in the onset of mammalian puberty.  相似文献   

14.
Backgroundβ-Galactosidases catalyze both hydrolytic and transgalactosylation reactions and therefore have many applications in food, medical, and biotechnological fields. Aspergillus niger has been a main source of β-galactosidase, but the properties of this enzyme are incompletely studied.ResultsThree new β-galactosidases belonging to glycosyl hydrolase family 35 from A. niger F0215 were cloned, expressed, and biochemically characterized. In addition to the known activity of LacA encoded by lacA, three putative β-galactosidases, designated as LacB, LacC, and LacE encoded by the genes lacB, lacC, and lacE, respectively, were successfully cloned, sequenced, and expressed and secreted by Pichia pastoris. These three proteins and LacA have N-terminal signal sequences and are therefore predicted to be extracellular enzymes. They have the typical structure of fungal β-galactosidases with defined hydrolytic and transgalactosylation activities on lactose. However, their activity properties differed. In particular, LacB and lacE displayed maximum hydrolytic activity at pH 4–5 and 50°C, while LacC exhibited maximum activity at pH 3.5 and 60°C. All β-galactosidases performed transgalactosylation activity optimally in an acidic environment.ConclusionsThree new β-galactosidases belonging to glycosyl hydrolase family 35 from A. niger F0215 were cloned and biochemically characterized. In addition to the known LacA, A. niger has at least three β-galactosidase family members with remarkably different biochemical properties.  相似文献   

15.
BackgroundA key challenge for manufacturers of pro-health food containing active probiotic microorganisms is to develop a product with attractive sensory features along with maintenance of declared number of microorganisms during storage and transfer by alimentary tract.ResultsThe highest concentration of polyphenols was observed in snacks without an additive of probiotics as well as those with an additive of L. rhamnosus and B. animalis bacteria and concentration of these compounds increased by 9.5% during six months of storage. None of the products distinguished itself in the sensorial assessment although each was assessed positively. The number of microorganisms was stable and comparatively high during six months of storage at a room temperature and in cooling conditions (108 cfu/g). In the digestion model, an influence of aggressive digestion conditions was examined in the alimentary tract on the number of microorganisms, which allowed to arrange strains from the most resistant (S. boulardii) to the most sensitive (B. breve). It must be noted that currently on the market there is no available snack containing probiotic yeast as well as there is no literature data on works on such formulation of food.ConclusionsIn the newly developed snack made of chocolate, in which sugar has been replaced with maltitol, a raw material was added in the form of raspberry, prebiotic in the form of inulin and a strain of probiotic bacteria, including the unprecedented so far S. boulardii, which stands a high chance to occupy a good place on the market of functional food.How to cite: Cielecka-Piontek J, Dziedziński M, Szczepaniak O, et al. Survival of commercial probiotic strains and their effect on dark chocolate synbiotic snack with raspberry content during the storage and after simulated digestion. Electron J Biotechnol 2020;48. https://doi.org/10.1016/j.ejbt.2020.09.005.  相似文献   

16.
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17.
This paper deals with the stability and dissipative problem of a class of stochastic hybrid system. The system under study involves Markovian jump, impulsive effects and time delay, which are often encountered in practice and are the sources of instability. Our attention is focused on analysis of whether the stochastic hybrid system with time-delay is stochastically asymptotically stable and strictly (Q, S, R) dissipative. By introducing an extra artificial time instance, the equivalent system is obtained and the sufficient conditions are derived by using linear matrix inequality (LMI) techniques. The main results of this paper unify the existing results on H∞ control.  相似文献   

18.
Backgroundβ-Glucosidase assay is performed with purified or semipurified enzymes extracted from cell lysis. However, in screening studies, to find bacteria with β-glucosidase activity among many tested bacteria, a fast method without cell lysis is desirable. In that objective, we report an in vivo β-glucosidase assay as a fast method to find a β-glucosidase producer strain.ResultsThe method consists in growing the strains for testing in a medium supplemented with the artificial substrate p-nitrophenyl-β-glucopyranoside (pNPG). The presence of β-glucosidases converts the substrate to p-nitrophenol (pNP), a molecule that can be easily measured in the supernatant spectrophotometrically at 405 nm. The assay was evaluated using two Bifidobacterium strains: Bifidobacterium longum B7254 strain that lacks β-glucosidase activity and Bifidobacterium pseudocatenulatum B7003 strain that shows β-glucosidase activity. The addition of sodium carbonate during pNP measurement increases the sensitivity of pNP detection and avoids the masking of absorbance by the culture medium. Furthermore, we show that pNP is a stable enzymatic product, not metabolized by bacteria, but with an inhibitory effect on cell growth. The β-glucosidase activity was measured as units of enzyme per gram per minute per dry cell weight. This method also allowed the identification of Lactobacillus strains with higher β-glucosidase activity among several lactobacillus species.ConclusionThis in vivo β-glucosidase assay can be used as an enzymatic test on living cells without cell disruption. The method is simple, quantitative, and recommended, especially in studies screening for bacteria not only with β-glucosidase activity but also with high β-glucosidase activity.  相似文献   

19.
基于DNA纳米技术的各种超分子体(功能单元),能实现信息存储、计算、移动和靶向送药等功能,其纳米结构的控制精度达到了原子级。基于DNA纳米技术的信息存储和计算模式,具有高度并行性、高密度和低能耗,天生适用于大量信息的存储和并行处理。面对这种新兴的计算模式,人们研究和开发了各种计算模型,讨论其对传统密码体系的影响和DNA存储信息的安全问题,包括密钥搜索、信息加密、信息隐藏及认证等。文章综述了基于DNA纳米技术的各种计算模型对传统加密算法的影响,概述了利用DNA纳米技术进行加密解密、认证签名的方案和技术,总结了当前基于DNA纳米技术的信息安全领域研究中存在的问题并展望了DNA计算及其在信息安全和存储领域的应用前景。  相似文献   

20.
Multiple mechanisms underlie the human aging process, but interest continues in the role that free radicals and antioxidants may play. The concentrations of lymphocyte free radical generation (O2 −& H2O2), DNA damage and antioxidant enzyme levels (glutathione Stransferase, superoxide dismutase and catalase) were evaluated in 110 healthy individuals with an age range of 20–80 years. The antioxidant enzyme levels were significantly less in very old age when compared to young. Moreover, the levels of free radical concentration and DNA damage were increased in the same age group with respect to younger group. Cigarette smoking had a positive relation with free radicals and DNA damage, and inverse relation with antioxidants. On the other hand, body mass was found to have positive relation with free radical generation only. The data indicate that depletion of antioxidant enzyme levels would render the older people more susceptible to free radical stress and DNA damage.  相似文献   

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