Fabrication and Applications of Micro/Nanostructured Devices for Tissue Engineering

Nanotechnology allows the realization of new materials and devices with basic structural unit in the range of1–100 nm and characterized by gaining control at the atomic, molecular, and supramolecular level. Reducing the dimensions of a material into the nanoscale range usually results in the change of its physiochemical properties such as reactivity,crystallinity, and solubility. This review treats the convergence of last research news at the interface of nanostructured biomaterials and tissue engineering for emerging biomedical technologies such as scaffolding and tissue regeneration. The present review is organized into three main sections. The introduction concerns an overview of the increasing utility of nanostructured materials in the field of tissue engineering. It elucidates how nanotechnology, by working in the submicron length scale, assures the realization of a biocompatible interface that is able to reproduce the physiological cell–matrix interaction. The second, more technical section, concerns the design and fabrication of biocompatible surface characterized by micro- and submicroscale features, using microfabrication, nanolithography, and miscellaneous nanolithographic techniques.In the last part, we review the ongoing tissue engineering application of nanostructured materials and scaffolds in different fields such as neurology, cardiology, orthopedics, and skin tissue regeneration.

The chromosome-level genome of double-petal phenotype jasmine provides insights into the biosynthesis of floral scent

Jasmine(Jasminum sambac Aiton)is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and cosmetics.However,the genetic basis of its floral scent is largely unknown.In this study,using PacBio,Illumina,10×Genomics and highthroughput chromosome conformation capture(Hi-C)sequencing technologies,a high-quality chromosome-level reference genome for J.sambac was obtained,exploiting a double-petal phenotype cultivar‘Shuangbanmoli’(JSSB).The results showed that the final assembled genome of JSSB is 580.33 Mb in size(contig N50=1.05 Mb;scaffold N50=45.07 Mb)with a total of 39618 predicted protein-coding genes.Our analyses revealed that the JSSB genome has undergone an ancient whole-genome duplication(WGD)event at 91.68 million years ago(Mya).It was estimated that J.sambac diverged from the lineage leading to Olea europaea and Osmanthus fragrans about 28.8 Mya.On the basis of a combination of genomic,transcriptomic and metabolomic analyses,a range of floral scent volatiles and genes were identified involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis pathways.The results provide new insights into the molecular mechanism of its fragrance biosynthesis in jasmine.

Untargeted metabolomics analysis of four date palm(Phoenix dactylifera L.)cultivars using MS and NMR

Since ancient times,the inhabitants of dry areas have depended on the date palm(Phoenix dactylifera L.)as a staple food and means of economic security.For example,dates have been a staple diet for the inhabitants of the Arabian Peninsula and Sahara Desert in North Africa for millennia and the local culture is rich in knowledge and experience with the benefits of dates,suggesting that dates contain many substances essential for the human body.Madinah dates are considered one of the most important types of dates in the Arabian Peninsula,with Ajwa being one of the most famous types and grown only in Madinah,Saudi Arabia.Date seeds are traditionally used for animal feed,seed oil production,cosmetics,and as a coffee substitute.Phytochemical compounds that have been detected in date fruits and date seeds include phenolic acids,carotenoids,and flavonoids.Phenolic acids are the most prevalent bioactive constituents that contribute to the antioxidant activity of date fruits.The bioactive properties of these phytochemicals are believed to promote human health by reducing the risk of diseases such as chronic inflammation.Ajwa dates especially are thought to have superior bioactivity properties.To investigate these claims,in this study,we compare the metabolic profiles of Ajwa with different types of dates collected from Saudi Arabia and Tunisia.We show by UHPLC-MS that date seeds contain several classes of flavonoids,phenolic acids,and amino acid derivatives,including citric acid,malic acid,lactic acid,and hydroxyadipic acid.Additionally,GC-MS profiling showed that date seeds are richer in metabolite classes,such as hydrocinnamic acids(caffeic,ferulic and sinapic acids),than flesh samples.Deglet N fruit extract(minimum inhibitory concentration:27 MIC/μM)and Sukkari fruit extract(IC_(50):479±0.58μg/mL)have higher levels of antibacterial and antioxidative activity than Ajwa fruits.However,the seed analysis showed that seed extracts have better bioactivity effects than fruit extracts.Specifically,Ajwa extract showed the best MIC and strongest ABTS radical-scavenging activity among examined seed extracts(minimum inhibitory concentration:20μM;IC_(50):54±3.61μg/mL).Our assays are a starting point for more advanced in vitro antibacterial models and investigation into the specific molecules that are responsible for the antioxidative and anti-bacterial activities of dates.

Installing the neurospora carotenoid pathway in plants enables cytosolic formation of provitamin A and its sequestration in lipid droplets

Vitamin A deficiency remains a severe global health issue,which creates a need to biofortify crops with provitamin A carotenoids(PACs).Expanding plant cell capacity for synthesis and storing of PACs outside the plastids is a promising biofortification strategy that has been little explored.Here,we engineered PAC formation and sequestration in the cytosol of Nicotiana benthamiana leaves,Arabidopsis seeds,and citrus callus cells,using a fungal(Neurospora crassa)carotenoid pathway that consists of only three enzymes converting C5 isopentenyl building blocks formed from mevalonic acid into PACs,including β-carotene.This strategy led to the accumulation of significant amounts of phytoene and γ-and β-carotene,in addition to fungal,health-promoting carotenes with 13 conjugated double bonds,such as the PAC torulene,in the cytosol.Increasing the isopentenyl diphosphate pool by adding a truncated Arabidopsis hydroxymethylglutaryl-coenzyme A reductase substantially increased cytosolic carotene production.Engineered carotenes accumulate in cytosolic lipid droplets(CLDs),which represent a novel sequestering sink for storing these pigments in plant cytosol.Importantly,β-carotene accumulated in the cytosol of citrus callus cells was more light stable compared to compared with plastidialβ-carotene.Moreover,engineering cytosolic carotene formation increased the number of large-sized CLDs and the levels of β-apocarotenoids,including retinal,the aldehyde corresponding to vitamin A.Collectively,our study opens up the possibility of exploiting the high-flux mevalonic acid pathway for PAC biosynthesis and enhancing carotenoid sink capacity in green and non-green plant tissues,especially in lipid-storing seeds,and thus paves the way for further optimization of carotenoid biofortification in crops.

Environmental Stress and Pre-mRNA Splicing

Pre-mRNA splicing is an important step for gene expression regulation in plants in response to abiotic stress. In recent years, RNA sequencing （RNA-seq） based on various next-generation sequencing technologies has been used to study dynamic changes of pre-mRNA splicing under conditions of diverse abiotic stress in several plant species. Accumulating results indi- cate that alternative splicing （AS） of pre-mRNA is closely linked with environmental stress response in plants.

Compliant lightweight non-invasive standalone“Marine Skin”tagging system

Current marine research primarily depends on weighty and invasive sensory equipment and telemetric network to understand the marine environment,including the diverse fauna it contains,as a function of animal behavior and size,as well as equipment longevity.To match animal morphology and activity within the surrounding marine environment,here we show a physically flexible and stretchable skin-like and waterproof autonomous multifunctional system,integrating Bluetooth,memory chip,and high performance physical sensors.The sensory tag is mounted on a swimming crab(Portunus pelagicus)and is capable of continuous logging of depth,temperature,and salinity within the harsh ocean environment.The fully packaged,ultra-lightweight(<2.4 g in water),and compliant“Marine Skin”system does not have any wired connection enabling safe and weightless cuttingedge approach to monitor and assess marine life and the ecosystem’s health to support conservation and management of marine ecosystems.

Simultaneous dual-contrast three-dimensional imaging in live cells via optical diffraction tomography and fluorescence

We report a dual-contrast method of simultaneously measuring and visualizing the volumetric structural information in live biological samples in three-dimensional(3D) space. By introducing a direct way of deriving the 3D scattering potential of the object from the synthesized angular spectra, we obtain the quantitative subcellular morphology in refractive indices(RIs) side-by-side with its fluorescence signals. The additional contrast in RI complements the fluorescent signal, providing additional information of the targeted zones. The simultaneous dual-contrast 3D mechanism unveiled interesting information inaccessible with previous methods, as we demonstrated in the human immune cell(T cell) experiment. Further validation has been demonstrated using a Monte Carlo model.

抽油泵固定凡尔球运动规律的数值模拟

固定凡尔是抽油泵的主要部件之一,其中固定凡尔球的运动规律决定了泵内流体的吸入过程。为研究固定凡尔球的运动规律,采用COMSOL Multiphysics数值模拟软件,建立了多物理场耦合模型;运用动网格技术和接触压力方法,解决了固定凡尔球运动、启闭引起的网格质量和触壁反弹的问题。分析了冲次、泵内流体粘度对固定凡尔球运动规律的影响。结果表明:冲次对固定凡尔球上升的稳定性有较大影响,黏度对固定凡尔球升程影响更为显著。

QAUST:Protein Function Prediction Using Structure Similarity,Protein Interaction,and Functional Motifs

The number of available protein sequences in public databases is increasing exponentially.However,a sig-nificant percentage of these sequences lack functional annotation,which is essential for the understanding of how bio-logical systems operate.Here,we propose a novel method,Quantitative Annotation of Unknown STructure(QAUST),to infer protein functions,specifically Gene Ontology(GO)terms and Enzyme Commission(EC)numbers.QAUST uses three sources of information:structure information encoded by global and local structure similarity search,biological network information inferred by protein–protein interaction data,and sequence information extracted from functionally discriminative sequence motifs.These three pieces of information are combined by consensus averaging to make the final prediction.Our approach has been tested on 500 protein targets from the Critical Assessment of Functional Annotation(CAFA)benchmark set.The results show that our method provides accurate functional annotation and outperforms other prediction methods based on sequence similarity search or threading.We further demonstrate that a previously unknown function of human tripartite motif-containing 22(TRIM22)protein predicted by QAUST can be experimentally validated.

ROS and Lipid Droplet accumulation induced by high glucose exposure in healthy colon and Colorectal Cancer Stem Cells

Lipid Droplets(LDs)are emerging as crucial players in colon cancer development and maintenance.Their expression has been associated with high tumorigenicity in Cancer Stem Cells(CSCs),so that they have been proposed as a new functional marker in Colorectal Cancer Stem Cells(CR-CSCs).They are also indirectly involved in the modulation of the tumor microenvironment through the production of pro-inflammatory molecules.There is growing evidence that a possible connection between metabolic alterations and malignant transformation exists,although the effects of nutrients,primarily glucose,on the CSC behavior are still mostly unexplored.Glucose is an essential fuel for cancer cells,and the connections with LDs in the healthy and CSC populations merit to be more deeply investigated.Here,we showed that a high glucose concentration activated the PI3K/AKT pathway and increased the expression of CD133 and CD44v6 CSC markers.Additionally,glucose was responsible for the increased amount of Reactive Oxygen Species(ROS)and LDs in both healthy and CR-CSC samples.We also investigated the gene modulations following the HG treatment and found out that the healthy cell gene profile was the most affected.Lastly,Atorvastatin,a lipidlowering drug,induced the highest mortality on CR-CSCs without affecting the healthy counterpart.

有杆抽油泵固定凡尔球开启时间规律研究

有杆抽油泵的固定凡尔控制抽油泵的吸入过程,其固定凡尔球的打开程度与开启时间对合理调整抽油机工作制度有至关重要的作用。为此建立抽油泵固定凡尔球的流固耦合模型,运用动网格技术和接触压力方法,实现了上冲程阶段固定凡尔球的运动过程,解决了凡尔球在流体域中接触其他固体壁面产生的拓扑结构变化问题,并在此基础上得到了各影响因素下固定凡尔球的打开程度与所需开启时间的变化规律曲线。数值模拟的结果为抽油机工作制度的合理优化提供了理论参考。

Efficient Mimics for Elucidating Zaxinone Biology and Promoting Agricultural Applications

Zaxinone is an apocarotenoid regulatory metabolite required for normal rice growth and development.In addition,zaxinone has a large application potential in agriculture,due to its growth-promoting activity and capability to alleviate infestation by the root parasitic plant Striga through decreasing strigolactone(SL)production.However,zaxinone is poorly accessible to the scientific community because of its laborious organic synthesis that impedes its further investigation and utilization.In this study,we developed easy-to-synthesize and highly efficient mimics of zaxinone(MiZax).We performed a structure-activity relationship study using a series of apocarotenoids distinguished from zaxinone by different structural features.Using the obtained results,we designed several phenyl-based compounds synthesized with a high-yield through a simple method.Activity tests showed that MiZax3 and MiZax5 exert zaxinone activity in rescuing root growth of a zaxinone-deficient rice mutant,promoting growth,and reducing SL content in roots and root exudates of wild-type plants.Moreover,these compounds were at least as efficient as zaxinone in suppressing transcript level of SL biosynthesis genes and in alleviating Striga infestation under greenhouse conditions,and did not negatively impact mycorrhization.Taken together,MiZax are a promising tool for elucidating zaxinone biology and investigating rice development,and suitable candidates for combating Striga and increasing crop growth.

Integration of Droplet Microfluidic Tools for Single-cell Functional Metagenomics:An Engineering Head Start

Droplet microfluidic techniques have shown promising outcome to study single cells at high throughput.However,their adoption in laboratories studying“-omics”sciences is still irrelevant due to the complex and multidisciplinary nature of the field.To facilitate their use,here we provide engineering details and organized protocols for integrating three droplet-based microfluidic technologies into the metagenomic pipeline to enable functional screening of bioproducts at high throughput.First,a device encapsulating single cells in droplets at a rate of~250 Hz is described considering droplet size and cell growth.Then,we expand on previously reported fluorescence-activated droplet sorting systems to integrate the use of 4 independent fluorescence-exciting lasers(i.e.,405,488,561,and 637 nm)in a single platform to make it compatible with different fluorescence-emitting biosensors.For this sorter,both hardware and software are provided and optimized for effortlessly sorting droplets at 60 Hz.Then,a passive droplet merger is also integrated into our pipeline to enable adding new reagents to already-made droplets at a rate of 200 Hz.Finally,we provide an optimized recipe for manufacturing these chips using silicon dry-etching tools.Because of the overall integration and the technical details presented here,our approach allows biologists to quickly use microfluidic technologies and achieve both single-cell resolution and high-throughput capability(>50,000 cells/day)for mining and bioprospecting metagenomic data.

Alkaloids as potential antivirals.A comprehensive review

Alkaloids are a diverse group of natural phytochemicals.These phytochemicals in plants provide them protection against pests,and herbivorous organisms and also control their development.Numerous of these alkaloids have a variety of biological effects,and some have even been developed into medications with different medicinal properties.This review aims to provide a broad overview of the numerous naturally occurring alkaloids(isolated from both terrestrial and aquatic species)along with synthetically produced alkaloid compounds having prominent antiviral properties.Previous reviews on this subject have focused on the biological actions of both natural and synthetic alkaloids,but they have not gone into comprehensive detail about their antiviral properties.We reviewed here several antiviral alkaloids that have been described in the literature in different investigational environments i.e.(in-vivo,in-ovo,in-vitro,and in-silico),and found that these alkaloid compounds have significant antiviral properties against several infectious viruses.These alkaloids repressed and targeted various important stages of viral infection at non-toxic doses while some of the alkaloids reported here also exhibited comparable inhibitory activities to commercially used drugs.Overall,these anti-viral effects of alkaloids point to a high degree of specificity,implying that they could serve as effective and safe antiviral medicines if further pursued in medicinal and pharmacological investigations.

基于多源数据的黄河源区降雪比变化及其影响因素

黄河源区是黄河流域关键产流区域,对气候变化十分敏感。在气候变暖背景下,降水形态转变及其影响因素的研究依然不足。围绕这一重要科学问题,本研究基于地面气象站点观测和多源高分辨率气象数据集[China Meteorological Forcing Dataset(CMFD)、ECWMF ERA5-Land(ERA5-Land)、Multi-Source Weather(MSWX)],采用湿球温度参数化模型对1980—2015年黄河源区降水形态进行区分,并对降雪比长期变化趋势及其影响因素进行了综合研究。结果表明,1980—2015年黄河源区降水量整体呈增加趋势,降水形态向降雨转变,降雪量减少,平均降雪比呈显著下降趋势(P<0.05),四套数据源的降雪比平均下降速率为0.002 a^(-1)(P<0.05)。降雪比呈显著下降趋势(P<0.05)的格点占比分别为98.31%(ERA5-Land)、96.87%(MSWX)、67.62%(CMFD)。黄河源区中西部降雪比下降速率较快,下降速率最大的地区为玛多、达日等地。三套格点产品中CMFD能够较好地呈现降雪比变化趋势的空间差异,MSWX次之,而ERA5-Land降雪比变化趋势空间变异较小。源区降雪比与年平均气温、降水量相关性较高(P<0.05),相关系数r分别为-0.42和-0.48,亦受到西风的影响(r=-0.31,P=0.07)。研究结果有助于加深气候变暖对黄河源区水文气象过程影响的科学认识,为黄河流域区域水资源管理提供理论支撑。

LIBRA:an adaptative integrative tool for paired single-cell multi-omics data

Background:Single-cell multi-omics technologies allow a profound system-level biology understanding of cells and tissues.However,an integrative and possibly systems-based analysis capturing the different modalities is challenging.In response,bioinformatics and machine learning methodologies are being developed for multi-omics single-cell analysis.It is unclear whether current tools can address the dual aspect of modality integration and prediction across modalities without requiring extensive parameter fine-tuning.Methods:We designed LIBRA,a neural network based framework,to learn translation between paired multi-omics profiles so that a shared latent space is constructed.Additionally,we implemented a variation,aLIBRA,that allows automatic fine-tuning by identifying parameter combinations that optimize both the integrative and predictive tasks.All model parameters and evaluation metrics are made available to users with minimal user iteration.Furthermore,aLIBRA allows experienced users to implement custom configurations.The LIBRA toolbox is freely available as R and Python libraries at GitHub(TranslationalBioinformaticsUnit/LIBRA).Results:LIBRA was evaluated in eight multi-omic single-cell data-sets,including three combinations of omics.We observed that LIBRA is a state-of-the-art tool when evaluating the ability to increase cell-type(clustering)resolution in the integrated latent space.Furthermore,when assessing the predictive power across data modalities,such as predictive chromatin accessibility from gene expression,LIBRA outperforms existing tools.As expected,adaptive parameter optimization(aLIBRA)significantly boosted the performance of learning predictive models from paired data-sets.Conclusion:LIBRA is a versatile tool that performs competitively in both“integration”and“prediction”tasks based on single-cell multi-omics data.LIBRA is a data-driven robust platform that includes an adaptive learning scheme.

Nitric Oxide： A Multitasked Signaling Gas in Plants

Nitric oxide （NO） is a gaseous reactive oxygen species （ROS） that has evolved as a signaling hormone in many physiological processes in animals. In plants it has been demonstrated to be a crucial regulator of development, acting as a signaling molecule present at each step of the plant life cycle. NO has also been implicated as a signal in biotic and abiotic responses of plants to the environment. Remarkably, despite this plethora of effects and functional relationships, the fundamental knowledge of NO production, sensing, and transduction in plants remains largely unknown or inadequately characterized. In this review we cover the current understanding of NO production, perception, and action in different physiological sce- narios. We especially address the issues of enzymatic and chemical generation of NO in plants, NO sensing and downstream signaling, namely the putative cGMP and Ca^2＋ pathways, ion-channel activity modulation, gene expression regulation, and the interface with other ROS, which can have a profound effect on both NO accumulation and function. We also focus on the importance of NO in cell-cell communication during developmental processes and sexual reproduction, namely in pollen tube guidance and embryo sac fertilization, pathogen defense, and responses to abiotic stress.

An alternative,zeaxanthin epoxidase-independent abscisic acid biosynthetic pathway in plants

Abscisic acid(ABA)is an important carotenoid-derived phytohormone that plays essential roles in plant response to biotic and abiotic stresses as well as in various physiological and developmental processes.In Arabidopsis,ABA biosynthesis starts with the epoxidation of zeaxanthin by the ABA DEFICIENT 1(ABA1)enzyme,leading to epoxycarotenoids;e.g.,violaxanthin.The oxidative cleavage of 9-cis-epoxycaro-tenoids,a key regulatory step catalyzed by 9-C/S-EPOXYCAROTENOID DIOXYGENASE,forms xanthoxin,which is converted in further rea.ctions mediated by ABA DEFICIENT 2(ABA2),ABA DEFICIENT 3(ABA3),and ABSCISIC ALDEHYDE OXIDASE 3(AAO3)into ABA.By combining genetic and biochemical approaches,we unravel here an ABA1-independent ABA biosynthetic pathway starting upstream of zeaxanthin.We iden-tified the carotenoid cleavage products(i.e.,apocarotenoids,β-apo-11-carotenal,9-cis-β-apo-11-carotenal,3-OH-β-apo-11-carotenal,and 9-cis-3-OH-β-apo-11-carotenal)as intermediates of this ABA1-independent ABA biosynthetic pathway.Using labeled compounds,we showed thatβ-apo-11-carotenal,9-cis-β-apo-11-carotenal,and 3-OH-β-apo-11-carotenal are successively converted into 9-cis-3-OH-β-apo-11-carotenal,xanthoxin,and finally into ABA in both Arabidopsis and rice.When applied to Arabidopsis,theseβ-apo-11-carotenoids exert ABA biological functions,such as maintaining seed dormancy and inducing the expression of ABA-responsive genes.Moreover,the transcdptomic analysis revealed a high overlap of differentially expressed genes regulated byβ-apo-11-carotenoids and ABA,suggesting thatβ-apo-11-carot-enoids exert ABA-independent regulatory activities.Taken together,our study identifies a biological function for the common plant metabolites,β-apo-11-carotenoids,extends our knowledge about ABA biosynthesis,and provides new insights into plant apocarotenoid metabolic networks.

Direct Modulation of the Guard Cell Outward- Rectifying Potassium Channel （CORK） by Abscisic Acid

Dear Editor,Abscisic acid （ABA） induces turgot loss and hence stomatal closure by promoting rapid net K^＋ efflux from guard cells （GCs） through outward-rectifying K^＋ （K^＋out） channels （Schroeder et al., 1987; Blatt, 1990）. The mechanisms of ABA signaling in GCs are detailed elsewhere （see Munemasa et al., 2015; Weiner et al., 2010; Pandey et al., 2007）. Briefly, ABA binds to the PYR/ PYL/RCARs, a family of soluble steroidogenic acute regulatory- related lipid transfer （START） proteins, and, in turn, inactivates the downstream PP2C （type 2C protein phosphatase）, leading to the activation of SnRK2.6 （SNF1 [sucrose non-fermenting-1- related protein kinase]/OST1 [open stomata 1]） protein kinases.