Frequent Patterns Algorithm of Biological Sequences based on Pattern Prefix-tree

In the application of bioinformatics, the existing algorithms cannot be directly and efficiently implement sequence pattern mining. Two fast and efficient biological sequence pattern mining algorithms for biological single sequence and multiple sequences are proposed in this paper. The concept of the basic pattern is proposed, and on the basis of mining frequent basic patterns, the frequent pattern is excavated by constructing prefix trees for frequent basic patterns. The proposed algorithms implement rapid mining of frequent patterns of biological sequences based on pattern prefix trees. In experiment the family sequence data in the pfam protein database is used to verify the performance of the proposed algorithm. The prediction results confirm that the proposed algorithms can’t only obtain the mining results with effective biological significance, but also improve the running time efficiency of the biological sequence pattern mining

Complete genome sequence of biocontrol strain Bacillus velezensis YC89 and its biocontrol potential against sugarcane red rot

IntroductionSugarcane is one of the most important sugar crops worldwide, however, sugarcane production is seriously limited by sugarcane red rot, a soil-borne disease caused by Colletotrichum falcatum. Bacillus velezensis YC89 was isolated from sugarcane leaves and can significantly inhibited red rot disease caused by C. falcatum.MethodsIn this study, the genome of YC89 strain was sequenced, its genome structure and function were analyzed using various bioinformatics software, and its genome was compared with those of other homologous strains. In addition, the effectiveness of YC89 against sugarcane red rot and the evaluation of sugarcane plant growth promotion were also investigated by pot experiments.ResultsHere, we present the complete genome sequence of YC89, which consists of a 3.95 Mb circular chromosome with an average GC content of 46.62%. The phylogenetic tree indicated that YC89 is closely related to B. velezensis GS-1. Comparative genome analysis of YC89 with other published strains (B. velezensis FZB42, B. velezensis CC09, B. velezensis SQR9, B. velezensis GS-1, and B. amyloliquefaciens DSM7) revealed that the strains had a part common coding sequences (CDS) in whereas 42 coding were unique of strain YC89. Whole-genome sequencing revealed 547 carbohydrate-active enzymes and identified 12 gene clusters encoding secondary metabolites. Additionally, functional analysis of the genome revealed numerous gene/gene clusters involved in plant growth promotion, antibiotic resistance, and resistance inducer synthesis. In vitro pot tests indicated that YC89 strain controlled sugarcane red rot and promoted the growth of sugarcane plants. Additionally, it increased the activity of enzymes involved in plant defense, such as superoxide dismutase, peroxidase, polyphenol oxidase, chitinase, and β-1,3-glucanase.DiscussionThese findings will be helpful for further studies on the mechanisms of plant growth promotion and biocontrol by B. velezensis and provide an effective strategy for controlling red rot in sugarcane plants

Phase selection controlled by sodium ions in the synthesis of FAU/LTA composite zeolite

Zeolite faujasite (FAU), Linde type A (LTA) and FAU/LTA composite have been synthesized using tetramethylammonium cation (TMA +) as template, by adjusting only the concentration of Na + ions in the initial solution (1.00 Al2 O3 4.36 SiO2 : 2.39 (TMA)2 O : β Na2 O : 249.00H2 O). Na + ions alter the phase composition of the product more than TMA+ or OH− ions. When Na2 O concentration [Na2 O] increases from 0.024 to 0.168, the product gradually changes from pure FAU to pure LTA via the formation of FAU/LTA composite with increasing LTA fraction. Interestingly, the induction periods of FAU and LTA in the FAU/LTA composite zeolite ([Na2 O] is 0.072) are both 13 h, quite different from the induction periods of their individual pure phases—45 h for FAU and 4 h for LTA. During the crystallization, the LTA/(FAU + LTA) fraction in the composite zeolite decreases in a nearly linear fashion. Scanning electron microscopy, thermogravimetry and differential thermal analysis indicate some difference between the properties of the FAU/LTA composite zeolite and of the mechanical mixture

Influence of natural polysaccharides on intestinal microbiota in inflammatory bowel diseases : an overview

The incidence of inflammatory bowel disease (IBD) has increased in recent years. Considering the potential side effects of conventional drugs, safe and efficient treatment methods for IBD are required urgently. Natural polysaccharides (NPs) have attracted considerable attention as potential therapeutic agents for IBD owing to their high efficiency, low toxicity, and wide range of biological activities. Intestinal microbiota and their fermentative products, mainly short-chain fatty acids (SCFAs), are thought to mediate the effect of NPs in IBDs. This review explores the beneficial effects of NPs on IBD, with a special focus on the role of intestinal microbes. Intestinal microbiota exert alleviation effects via various mechanisms, such as increasing the intestinal immunity, anti-inflammatory activities, and intestinal barrier protection via microbiota-dependent and microbiota-independent strategies. The aim of this paper was to document evidence of NP-intestinal microbiota-associated IBD prevention, which would be helpful for guidance in the treatment and management of IBD

Rapamycin Prevents cyclophosphamide-induced Over-activation of Primordial Follicle pool through PI3K/Akt/mTOR Signaling Pathway in vivo

Abstract Background Primordial follicular depletion has thought to be a common adverse effect of chemotherapy especially for female of reproductive age. The study aimed to evaluate the protective effect of rapamycin on the primordial follicles and its potential mechanism for patients receiving chemotherapy. Methods 8-week old BALB/c female mice were randomly assigned into four groups (control; rapamycin; cyclophosphamide; and rapamycin combined with cyclophosphamide). Hematoxylin staining, immunohistochemical, TUNEL, western blotting and ELISA were employed to assess inter-group differences using Student’s t-test and Mann-Whitney test. Results Cyclophosphamide depleted the follicular reserve and induced the phosphorylation of the key proteins of PI3K/Akt/mTOR pathway in mice in a dose-dependent manner. Co-treatment with rapamycin significantly reduced primordial follicle loss at all cyclophosphamide dose groups and prevent the follicle growth wave caused by cyclophosphamide treatment (P < 0.05). TUNEL staining showed that no apoptosis occured in the primordial follicles in all groups and fewer apoptosis in large growing follicles were observed in ovaries from rapamycin + cyclophosphamide group compared to that received cyclophosphamide alone. Serum anti-Müllerian hormone (AMH) was significantly reduced in cyclophosphamide alone group, in contrast to the normal level in rapamycin + cyclophosphamide group. Compared to p-Akt/Akt and p-mtor/mtor, p-rps6/rps6 was significantly decreased in rapamycin + cyclophosphamide group (P < 0.05), indicating that rapamycin attenuated the increased level of phosphorylation of rpS6 after cyclophosphamide treatment. Conclusions Rapamycin can prevent the primordial follicle activation induced by cyclophosphamide through PI3K/Akt/mTOR signaling pathway and thus plays a role in preserving the follicle pool. These results suggest that rapamycin may be an effective protection for ovarian function during chemotherapy, which means a new nonsurgical application for protection of ovarian reserve and prevention of POF

Prediction of superconductivity in pressure-induced new silicon boride phases

The crystal structures and properties of boron-silicon (B-Si) compounds under pressure have been systematically explored using particle swarm optimization structure prediction method in combination with first-principles calculations. Three new stoichiometries, B2Si, BSi, and BSi2, are predicted to be stable gradually under pressure, where increasing pressure favors the formation of silicon rich B-Si compounds. In the boron-rich compounds, the network of boron atoms changes from B12 icosahedron in the ambient phases to the similar buckled graphenelike layers in the high-pressure phases, which crystalize in the same P¯3m1 symmetry but with different numbers of boron layers between adjacent silicon layers. Phonon calculations show that these structures might be retained to ambient conditions as metastable phases. Further electron-phonon coupling calculations indicate that the high-pressure phases of boron-rich compounds might superconduct at 1 atm, with the highest Tc value of 21 K from the Allen-Dynes equation in P¯3m1 B2Si, which is much higher than the one observed in boron doped diamond-type silicon. Moreover, further fully anisotropic Migdal-Eliashberg calculations indicate that B2Si is a two-gap anisotropic superconductor and the estimated Tc might reach up to 30 K at 1 atm. On the silicon-rich side, BSi2 is predicted to be stable in the CuAl2-type structure. Our current results significantly enrich the phase diagram of the B-Si system and will stimulate further experimental study.The work was supported by Fostering Program of Major Research Plan of NSFC (91963115), National Key R & D Program of China (2018YFA0703400), National Natural Science Foundation of China (No. 51732010, 11674176, 11874224), Funding Program for Recruited Oversea Scholars of Hebei Province (Grant No. CL201729), and the Ph.D. Foundation by Yanshan University (Grant No. B970). A.B. acknowledges financial support from the Spanish Ministry of Economy and Competitiveness (Grant No. FIS2016-76617-P) and the Department of Education, Universities and Research of the Basque Government and the University of the Basque Country (Grant No. IT756-13).Peer reviewe

A Comparative Identification of Ochratoxin A in Longan Fruit Pulp by High Performance Liquid Chromatography-Fluorescence Detection and Electron Spray Ionization-Mass Spectrometry

Harvested longan (Dimocarpus longan Lour.) fruit are susceptible to decay caused by both bacterial and fungal infections. Ochratoxin A (OTA) is a kind of mycotoxin produced by a number of fungi. In this study, OTA was extracted from longan fruit pulp by 80% methanol and then loaded on C-18 solid-phase extraction columns. The extract solution was then analyzed by high-performance liquid chromatography - fluorescence detection (HPLC-FD) and an electron spray ionization-mass spectrometry (ESI-MS), respectively. The HPLC-FD analysis showed that a compound similar to OTA might exist in longan fruit pulp, but further analysis by the ESI-MS method demonstrated that OTA was not present in the longan pulp, indicating that the presence of OTA in longan fruit pulp detected by the HPLC-FD analysis needed to be confirmed by the ESI-MS method