Genome-wide identification of functional enhancers and their potential roles in pig breeding

Background:The pig is an economically important livestock species and is a widely applied large animal model in medical research.Enhancers are critical regulatory elements that have fundamental functions in evolution,development and disease.Genome-wide quantification of functional enhancers in the pig is needed.Results:We performed self-transcribing active regulatory region sequencing(STARR-seq)in the porcine kidney epithelial PK15 and testicular ST cell lines,and reliably identified 2576 functional enhancers.Most of these enhancers were located in repetitive sequences and were enriched within silent and lowly expressed genes.Enhancers poorly overlapped with chromatin accessibility regions and were highly enriched in chromatin with the repressive histone modification H3K9me3,which is different from predicted pig enhancers detected using ChIP-seq for H3K27ac or/and H3K4me1 modified histones.This suggests that most pig enhancers identified with STARR-seq are endogenously repressed at the chromatin level and may function during cell type-specific development or at specific developmental stages.Additionally,the PPP3CA gene is associated with the loin muscle area trait and the QKI gene is associated with alkaline phosphatase activity that may be regulated by distal functional enhancers.Conclusions:In summary,we generated the first functional enhancer map in PK15 and ST cells for the pig genome and highlight its potential roles in pig breeding.

Simultaneous Extraction of Carboxylated Celulose Nanocrystals and Nanofibrils via Citric Acid Hydrolysis--A Sustainable Route

In this study, cellulose nanocrystals(CNC) with surface carboxylic groups were prepared from bleached softwood pulp by hydrolysis with concentrated citric acid at concentrations of 60 wt%~80 wt%. The solid residues from acid hydrolysis were collected for producing cellulose nanofibrils(CNF) via post high-pressure homogenization. Citric acid could be easily recovered after hydrolysis reactions through crystallization due to its low water solubility or through precipitation as a calcium salt followed by acidification. Several important properties of CNC and CNF, such as dimension, crystallinity, surface chemistry, thermal stability, were evaluated. Results showed that the obtained CNC and CNF surfaces contained carboxylic acid groups that facilitated functionalization and dispersion in aqueous processing. The recyclability of citric acid and the carboxylated CNC/CNF give the renewable cellulose nanomaterial huge potential for a wide range of industrial applications. Furthermore, the resultant CNC and CNF were used as reinforcing agents to make sodium carboxymethyl cellulose(CMC) films. Both CNC and CNF showed reinforcing effects in CMC composite films. The tensile strength of CMC films increased by 54.3% and 85.7% with 10 wt% inclusion of CNC and CNF, respectively. This study provides detailed information on carboxylated nanocellulose prepared by critic acid hydrolysis; a sustainable approach for the preparation of CNC/CNF is of significant importance for their various uses.

Multi-modes control method for spacecraft formation establishment and reconfiguration near the libration points

This paper studies Multi-modes control method for libration points formation establishment and reconfiguration. Firstly, relations between optimal impulse control and Floquet modes are investigated. Method of generating modes is proposed. Characteristics of the mode coefficients stimulated at different time are also given. Studies show that coefficients of controlled modes can be classified into four types, and formation establishment and reeonfiguration can be achieved by multi-impulse control with the presented method of generating modes. Then, since libration points formation is generally unstable, mutli-modes keeping control method which can stabilize five Floquet modes simultaneously is proposed. Finally, simulation on formation establishment and reconfiguration are carried out by using method of generating modes and mutli-modes keeping control method. Results show that the proposed control method is effective and practical.

抗胰岛素样生长因子1受体单链抗体复性研究

[目的]建立抗人胰岛素样生长因子1受体单链抗体包涵体复性方法。[方法]首先,在96孔板上进行稀释复性,从72种复性液中筛选最佳条件。每孔复性液2 m L,滴入起始浓度1. 5 mg/m L的包涵体溶解液100μL过夜复性。然后,选择最佳复性液与变性液混合在Superdex 75柱上形成1 cm柱长下降5%的变性液梯度,样品按5%柱体积上样进行柱上复性。[结果]最适稀释复性液为C8(50 mmol/L Tris-Cl,GSH/GSSG=5/0. 5 mmol/L,0. 4 mol/L精氨酸,p H 9.0),对应复性率约为78%;以该复性液为基础通过柱上复性,目标蛋白复性率提高到95%,复性样品抗原结合活性良好。[结论]建立了目标蛋白包涵体柱上复性方法,复性率达到95%,产量达到384 mg/L。

Global Quantitative Mapping of Enhancers in Rice by STARR-seq

Enhancers activate transcription in a distance-,orientation-,and position-independent manner,which makes them difficult to be identified. Self-transcribing active regulatory region sequencing (STARR-seq) measures the enhancer activity of millions of DNA fragments in parallel. Here we used STARR-seq to generate a quantitative global map of rice enhancers. Most enhancers were mapped within genes,especially at the 5' untranslated regions (5'UTR) and in coding sequences. Enhancers were also frequently mapped proximal to silent and lowly-expressed genes in transposable element (TE)-rich regions. Analysis of the epigenetic features of enhancers at their endogenous loci revealed that most enhancers do not co-localize with DNase I hypersensitive sites (DHSs) and lack the enhancer mark of histone modification H3K4me1. Clustering analysis of enhancers according to their epigenetic marks revealed that about 40%of identified enhancers car-ried one or more epigenetic marks. Repressive H3K27me3 was frequently enriched with positive marks,H3K4me3 and/or H3K27ac,which together label enhancers. Intergenic enhancers were also predicted based on the location of DHS regions relative to genes,which overlap poorly with STARR-seq enhancers. In summary,we quantitatively identified enhancers by functional analysis in the genome of rice,an important model plant. This work provides a valuable resource for further mechanistic studies in different biological contexts.

Sustainable preparation and characterization of thermally stable and functional cellulose nanocrystals and nanofibrils via formic acid hydrolysis

In this work,a sustainable method to prepare functional cellulose nanocrystals(CNCs)and cellulose nanofibrils(CNFs)using formic acid(FA)(a recoverable organic acid)was established.After FA hydrolysis,the obtained CNCs could be well dispersed in DMAC.Thus,the CNC products and fibrous cellulosic solid residue(FCSR)in DMAC could be easily separated by a conventional centrifugal process,and the collected FCSR could be further fibrillated to CNFs with relatively low-intensity mechanical fibrillation process.The isolated CNC products showed high crystallinity index(about 75%)and excellent thermal stability(with onset thermal degradation temperature of 325℃).Both the resultant CNCs and CNFs showed better dispersibility in DMSO,DMF and DMAC respectively because of the introduction of ester groups on the surface of the products.The presence of surface ester groups could increase the interface compatibility of nanocelluloses with polymeric matrices and enable their applications in reinforcing polymeric matrix materials(e.g.the composite films like PHVB+CNFs).

Ameliorated enzymatic saccharification of corn stover with a novel modified alkali pretreatment

Enzymatic saccharification/hydrolysis is one of the key steps for the bioconversion of lignocelluloses into sustainable biofuels.In this work,corn stover was pretreated with a novel modified alkali process(NaOH+anthraquinone(AQ)+sodium lignosulfonate(SLS)),and then enzymatically hydrolyzed with an enzyme cocktail(cellulase(Celluclast 1.5L),β-glucosidase(Novozyme 188)and xylanase(from thermomyceslanuginosus))in the pH range of 4.0-6.5.It was found that the suitable pH for the enzymatic saccharification process to achieve a high glucan yield was between 4.2 and 5.7,while the appropriate pH to obtain a high xylan yield was in the range of 4.0-4.7.The best pH for the enzymatic saccharification process was found to be 4.4 in terms of the final total sugar yield,as xylanase worked most efficiently in the pH range of 4.0-4.7,under the conditions in the study.The addition of xylanase in the enzymatic saccharification process could hydrolyze xylan in the substrates and reduce the nonspecific binding of cellulase,thus improving the total sugar yields.

Recent progress on the pretreatment and fractionation of lignocelluloses for biorefinery at QIBEBT

Pretreatment and fractionation are amongst the key steps for the conversion of lignocelluloses to sustainable biofuels,biomaterials or biochemicals,as pretreatment/fractionation can break the natural recalcitrance of lignocelluloses,improving the conversion efficiency of downstream processes.This paper reviews the recent progress on the pretreatment and fractionation of lignocelluloses for biorefinery at the Chinese Academy of Sciences-Qingdao Institute of Bioenergy and Bioprocess Technology(QIBEBT).The main technologies developed at the QIBEBT in recent years include alkaline twin-screw extrusion pretreatment,modified alkali pretreatment,hydrogen peroxide-assisted sodium carbonate pretreatment,fractionation with formic acid,as well as the two-step fractionation by hot water treatment coupling ammonium sulfite treatment.With the development of these technologies,a pilot scale platform for the pretreatment and saccharification of biomass has been established in the pilot plant of QIBEBT.