Improved Method for Isolation of Microbial RNA from Biofuel Feedstock for Metatranscriptomics

Metatranscriptomics—gene express profiling via DNA sequencing—is a powerful tool to identify genes that are actively expressed and might contribute to the phenotype of individual organisms or the phenome (the sum of several phenotypes) of a microbial community. Furthermore, metatranscriptome studies can result in extensive catalogues of genes that encode for enzymes of industrial relevance. In both cases, a major challenge for generating a high quality metatranscriptome is the extreme lability of RNA and its susceptibility to ubiquitous RNAses. The microbial community (the microbiome) of the cow rumen efficiently degrades lignocelullosic biomass, generates significant amounts of methane, a greenhouse gas twenty times more potent than carbon dioxide, and is of general importance for the physiological wellbeing of the host animal. Metatranscriptomes of the rumen microbiome from animals kept under different conditions and from various types of rumen-incubated biomass can be expected to provide new insights into these highly interesting phenotypes and subsequently provide the framework for an enhanced understanding of this socioeconomically important ecosystem. The ability to isolate large amounts of intact RNA will significantly facilitate accurate transcript annotation and expression profiling. Here we report a method that combines mechanical disruption with chemical homogenization of the sample material and consistently yields 1 mg of intact RNA from 1 g of rumen-incubated biofuel feedstock. The yield of total RNA obtained with our method exceeds the RNA yield achieved with previously reported isolation techniques, which renders RNA isolated with the method presented here as an ideal starting material for metatranscriptomic analyses and other molecular biology applications that require significant amounts of starting material.

Building biological foundries for next-generation synthetic biology

Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries.

Residual feed intake divergence during the preweaning period is associated with unique hindgut microbiome and metabolome profiles in neonatal Holstein heifer calves

Background:Recent studies underscored that divergence in residual feed intake(RFI)in mature beef and dairy cattle is associated with changes in ruminal microbiome and metabolome profiles which may contribute,at least in part,to better feed efficiency.Because the rumen in neonatal calves during the preweaning period is underdeveloped until close to weaning,they rely on hindgut microbial fermentation to breakdown undigested diet components.This leads to production of key metabolites such as volatile fatty acids(VFA),amino acids,and vitamins that could potentially be absorbed in the hind-gut and help drive growth and development.Whether RFI divergence in neonatal calves is associated with changes in hindgut microbial communities and metabolites is largely unknown.Therefore,the objective of the current study was to determine differences in hindgut microbiome and metabolome in neonatal Holstein heifer calves retrospectively-grouped based on feed efficiency as mostefficient(M-eff)or least-efficient(L-eff)calves using RFI divergence during the preweaning period.Methods:Twenty-six Holstein heifer calves received 3.8 L of first-milking colostrum from their respective dams within 6 h after birth.Calves were housed in individual outdoor hutches bedded with straw,fed twice daily with a milk replacer,and had ad libitum access to a starter grain mix from birth to weaning at 42 d of age.Calves were classified into M-eff[n=13;RFI coefficient=−5.72±0.94 kg DMI(milk replacer+starter grain)/d]and L-eff[n=13;RFI coefficient=5.61±0.94 kg DMI(milk replacer+starter grain)/d]based on a linear regression model including the combined starter grain mix and milk replacer DMI,average daily gain(ADG),and metabolic body weight(MBW).A deep sterile rectal swab exposed only to the rectum was collected immediately at birth before colostrum feeding(i.e.,d 0),and fecal samples at d 14,28,and 42(prior to weaning)for microbiome and untargeted metabolome analyses using 16S rRNA gene sequencing and LC-MS.Microbiome data were analyzed with the QIIME 2 platform and metabolome data with the MetaboAnalyst 4.0 pipeline.Results:No differences(P>0.05)in body measurements including body weight(BW),body length(BL),hip height(HH),hip width(HW),and wither height(WH)were detected between M-eff and L-eff calves at birth and during preweaning.Although milk replacer intake did not differ between groups,compared with L-eff,M-eff heifers had lower starter intake(P<0.01)between d 18 to 42 of age,whereas no differences(P>0.05)for ADG,cumulative BWG,or body measurements were observed between RFI groups during the preweaning period.Microbiome and metabolome profiles through the first 42 d of age indicated greater hindgut capacity for the production of energy-generating substrates(butyrate and propionate)and essential nutrients(vitamins and amino acids)in heifers with greater estimated feed efficiency.Conclusion:Despite consuming approximately 54.6%less solid feed(cumulative intake,10.90 vs.19.98±1.66 kg)from birth to weaning,the microbiome-metabolome changes in the hindgut of most-efficient heifers might have helped them maintain the same level of growth as the least-efficient heifers.

Distinct mechanisms of FAK mechanoactivation by different extracellular matrix proteins

Introduction Cells can sense and respond to the mechanical microenvironment by converting forces into biochemical signals inside the cells,i.e.mechanotransduction[1-3].Focal adhesions are the major sites of interaction between a cell and its extracellular matrix（ECM）microenvironment,thus outside mechanical signals can be sensed at focal adhesions through transmembrane receptor integrins.In particular,it has been shown that matrix elasticity can control the cell fate[4]by modulating the interactions between ECM proteins and their receptor integrins[5,6].For example,different rigidity of polyacrylamide（PA）gels can lead to different density of ECM ancho-

Genomic insights into the ESBL and MCR-l-producing ST648 Escherichia coli with multi-drug resistance

多粘菌素由 multidrug 抵抗的克否定的病原体对严重感染充当避难处的一根最终的线。这个常规想法被活动 colistin 抵抗基因(mcr-1 ) 的最近的发现戏剧性地质问在食物动物和世界范围的人是流行的。更重要地， mcr-1 基因被发现与另外的抗菌素抵抗基因 co 局部性，提起可能性与平底锅药抵抗超级臭虫正在出现。然而，很少在 mcr-1-positive 的染色体上被报导细菌的主人水库。这里，我们报导三个人定序的染色体 mcr-1-positive Escherichia coli (E15004， E15015 和 E15017 ) 孤立并且通过细菌的比较 genomics 的分析定义一般特征。和顺序打字的进一步的 genomic 采矿允许我们阐明 MCR-1-carrying E。coli E15017 属于顺序类型 ST648 和 coproduces 扩大光谱的 -lactamase (ESBL ) 。给 ST648 与任何一个新德里 metallo 为伙伴所知的事实 -- lactamase 1 或 ESBL，我们的结果与 multidrug 电阻作为流行克隆加亮 ST648 的可能性。

Optimizing photorespiration for improved crop productivity

In C3 plants, photorespiration is an energyexpensive process, including the oxygenation of ribulose-1,5-bisphosphate(RuBP) by ribulose 1,5-bisphosphate carboxylase/oxygenase(Rubisco) and the ensuing multiorganellar photorespiratory pathway required to recycle the toxic byproducts and recapture a portion of the fixed carbon. Photorespiration significantly impacts crop productivity through reducing yields in C3 crops by as much as 50%under severe conditions. Thus, reducing the flux through, or weive R improving the efficiency of photorespiration has the potential of large improvements in C3 crop productivity.Here, we review an array of approaches intended to engineer photorespiration in a range of plant systems with the goal of increasing crop productivity. Approaches include optimizing flux through the native photorespiratory pathway, installing non-native alternative photorespiratory pathways, and lowering or even eliminating Rubiscocatalyzed oxygenation of RuBP to reduce substrate entrance into the photorespiratory cycle. Some proposed designs have been successful at the proof of concept level.A plant systems-engineering approach, based on new opportunities available from synthetic biology to implement in silico designs, holds promise for further progress toward delivering more productive crops to farmer’s fields.

A brief overview of synthetic biology research programs and roadmap studies in the United States

The United States is a leading nation in the development of synthetic biology,an emerging engineering discipline to create,control and reprogram biological systems.With strategic investment from its government agencies,the U.S.has established numerous research centers and programs in synthetic biology,enabling significant advances in foundational tool development and practical applications ranging from bioenergy,biomanufacturing,to biomedicine.To maintain its leadership in synthetic biology,U.S,has conducted several roadmap studies to provide strategic visions and action recommendations.Here we will provide a brief overview of the major research programs and roadmap studies of synthetic biology in the U.S.

Unleashing the power of energy storage: Engineering β-oxidation pathways for polyketide production

Overproduction of polyketides has been a challenge for metabolic engineering for decades.However,recent studies have demonstrated that in both native host and heterologous host,engineeringβ-oxidation pathways can lead to dramatic improvement of polyketide production.

构建合成生物学制造厂

合成生物学是一个"自上而下",以设计-构建-测试循环为研究模式、以工程化组装构建为特征的新兴跨学科领域.近年来在此新兴领域的众多研究成果使该研究循环获得了极大的成功,特别是在基于计算机的生物系统设计、DNA从头合成、组装及验证,以及代谢产物分析等方面为建立未来高通量生物系统加工生产线打下了坚实的基础.本文旨在总结当前合成生物学的技术发展水平,并对建立自动化生物产品制造厂需要应对的挑战展开讨论.

Leaf and Ecosystem Gas Exchange Responses of Buffel Grass-Dominated Grassland to Summer Precipitation

Sporadic rain events that occur during summer play an important role in the initiation of biological activity of semi-arid grasslands.To understand how ecosystem processes of a buffel grass(Cenchrus ciliaris L.)-dominated grassland respond to summer rain events,an LI 6 400 gas exchange system was used to measure the leaf gas exchange and plant canopy chambers were used to measure net ecosystem CO2exchange(NEE) and ecosystem respiration(Reco), which were made sequentially during periods before rain(dry) and after rain(wet). Gross ecosystem photosynthesis(GEP) was estimated from NEE and Reco fluxes, and light use efficiency parameters were estimated using a rectangular hyperbola model. Prior to the monsoon rain, grassland biomass was non-green and dry exhibiting positive NEE(carbon source) and low GEP values during which the soil water became increasingly scarce. An initial rain pulse(60 mm) increased the NEE from pre-monsoon levels to negative NEE(carbon gain) with markedly higher GEP and increased green biomass. The leaf photosynthesis and leaf stomatal conductance were also improved substantially. The maximum net CO2uptake(i.e.,negative NEE) was sustained in the subsequent period due to multiple rain events. As a result, the grassland acted as a net carbon sink for 20 d after first rain. With cessation of rain(drying cycle), net CO2 uptake was reduced to lower values. High sensitivity of this grassland to rain suggests that any decrease in precipitation in summer may likely affect the carbon sequestration of the semiarid ecosystem.

Direct laser writing of volumetric gradient index lenses and waveguides

Direct laser writing(DLW)has been shown to render 3D polymeric optical components,including lenses,beam expanders,and mirrors,with submicrometer precision.However,these printed structures are limited to the refractive index and dispersive properties of the photopolymer.Here,we present the subsurface controllable refractive index via beam exposure(SCRIBE)method,a lithographic approach that enables the tuning of the refractive index over a range of greater than 0.3 by performing DLW inside photoresist-filled nanoporous silicon and silica scaffolds.Adjusting the laser exposure during printing enables 3D submicron control of the polymer infilling and thus the refractive index and chromatic dispersion.Combining SCRIBE’s unprecedented index range and 3D writing accuracy has realized the world’s smallest(15μm diameter)spherical Luneburg lens operating at visible wavelengths.SCRIBE’s ability to tune the chromatic dispersion alongside the refractive index was leveraged to render achromatic doublets in a single printing step,eliminating the need for multiple photoresins and writing sequences.SCRIBE also has the potential to form multicomponent optics by cascading optical elements within a scaffold.As a demonstration,stacked focusing structures that generate photonic nanojets were fabricated inside porous silicon.Finally,an all-pass ring resonator was coupled to a subsurface 3D waveguide.The measured quality factor of 4600 at 1550 nm suggests the possibility of compact photonic systems with optical interconnects that traverse multiple planes.SCRIBE is uniquely suited for constructing such photonic integrated circuits due to its ability to integrate multiple optical components,including lenses and waveguides,without additional printed supports.

Here comes the sun:How optimization of photosynthetic light reactions can boost crop yields

Photosynthesis started to evolve some 3.5 billion years ago CO;is the substrate for photosynthesis and in the past 200-250 years,atmospheric levels have approximately doubled due to human industrial activities.However,this time span is not sufficient for adaptation mechanisms of photosynthesis to be evolutionarily manifested.Steep increases in human population,shortage of arable land and food,and climate change call for actions,now.Thanks to substantial research efforts and advances in the last century,basic knowledge of photosynthetic and primary metabolic processes can now be translated into strategies to optimize photosynthesis to its full potential in order to improve crop yields and food supply for the future.Many different approaches have been proposed in recent years,some of which have already proven successful in different crop species.Here,we summarize recent advances on modifications of the complex network of photosynthetic light reactions.These are the starting point of all biomass production and supply the energy equivalents necessary for downstream processes as well as the oxygen we breathe.

Origin, dissemination and entry of the pandemic Zika viruses

Zika 病毒(ZIKV ) 是打扫了大多数西方的半球的以前忽视，却最新新兴的 zoonotic 病原体。意外注意在新生儿在在 2015 ZIKV 散布到巴西和美国的炸药和它的稀罕关联引起了世界范围的谎言到头小畸型，提起对公共健康的严肃的挑战。我们证明起源和这些流行 ZIKA 的快传播孤立。种系发生的分析表明最新新兴的 ZIKV 孤立的所有属于亚洲美国人的系。ZIKV E 表面蛋白质的结构的分析建议它可能采用类似的入口机制到另外的 Flavi 病毒相似登革热病毒和韦斯特尼罗河病毒的。

Mineralized collagen scaffolds fabricated with amniotic membrane matrix increase osteogenesis under inflammatory conditions

Defects in craniofacial bones occur congenitally,after high-energy impacts,and during the course of treatment for stroke and cancer.These injuries are difficult to heal due to the overwhelming size of the injury area and the inflammatory environment surrounding the injury.Significant inflammatory response after injury may greatly inhibit regenerative healing.We have developed mineralized collagen scaffolds that can induce osteogenic differentiation and matrix biosynthesis in the absence of osteogenic media or supplemental proteins.The amniotic membrane is derived from placentas and has been recently investigated as an extracellular matrix to prevent chronic inflammation.Herein,we hypothesized that a mineralized collagen-amnion composite scaffold could increase osteogenic activity in the presence of inflammatory cytokines.We report mechanical properties of a mineralized collagen-amnion scaffold and investigated osteogenic differentiation and mineral deposition of porcine adipose-derived stem cells within these scaffolds as a function of inflammatory challenge.Incorporation of amniotic membrane matrix promotes osteogenesis similarly to un-modified mineralized collagen scaffolds,and increases in mineralized collagen-amnion scaffolds under inflammatory challenge.Together,these findings suggest that a mineralized collagen-amnion scaffold may provide a beneficial environment to aid craniomaxillofacial bone repair,especially in the course of defects presenting significant inflammatory complications.

SynV and SynX： A story more than DNA synthesis

Genomes have been studied by biologists for decades with a goal to decipher the origin,evolution,and nature of life on earth.These studies often rely on genetic manipulations such as deletions and insertions(a top-down approach),but recent advances in DNA synthesis provide a new option—whole genome synthesis(a bottom-up approach).While several bacterial and viral genomes have been

Ethanol production from corn stover pretreated by electrolyzed water and a two-step pretreatment method

Pretreatment is one of the most important unit operations for ethanol production from biomass feedstocks.In this study,corn stover was used as a feedstock to examine the effectiveness of two pretreatments:electrolyzed water pretreatment and a two-step pretreatment.Electrolyzed water was employed as a catalyst to conduct one-step pretreatment of corn stover at three temperatures(165,180 and 195°C) and three treatment times(10,20 and 30 min).During the two-step pretreatment process,an organic alkaline solution of 1%(w/w) NaOH in 70%(w/w) ethanol was used for lignin removal in the first step,followed by a second step using hot water.No furfural or 5-hydroxymethyl furfural was detected in the hydrolysates from both pretreatment methods when the detection limit of the HPLC was 0.2 g/L.The highest glucan conversion yields were 83% obtained at 195°C for 30 min with acidic electrolyzed water and 83% by the two-step process,where the second step of the pretreatment was at 135°C for 30 min.The hydrolyzates from the two pretreatment methods showed good performance in Saccharomyces cerevisiae fermentation tests.The two new methods may provide promising alternatives for the pretreatment of biomass for ethanol production.

Quantitative analysis of focal adhesion dynamics using photonic resonator outcoupler microscopy (PROM)

Focal adhesions are critical cell membrane components that regulate adhesion and migration and have cluster dimensions that correlate closely with adhesion engagement and migration speed.We utilized a label-free approach for dynamic,long-term,quantitative imaging of cell–surface interactions called photonic resonator outcoupler microscopy(PROM)in which membrane-associated protein aggregates outcoupled photons from the resonant evanescent field of a photonic crystal biosensor,resulting in a highly localized reduction of the reflected light intensity.By mapping the changes in the resonant reflected peak intensity from the biosensor surface,we demonstrate the ability of PROM to detect focal adhesion dimensions.Similar spatial distributions can be observed between PROM images and fluorescence-labeled images of focal adhesion areas in dental epithelial stem cells.In particular,we demonstrate that cell–surface contacts and focal adhesion formation can be imaged by two orthogonal label-free modalities in PROM simultaneously,providing a general-purpose tool for kinetic,high axial-resolution monitoring of cell interactions with basement membranes.

Behavioral strategies to prevent and mitigate COVID-19 infection

The single stranded RNA virus SARS-CoV-2 has caused a massive addition to the already leading global cause of mortality,viral respiratory tract infections.Characterized by and associated with early and deleteriously enhanced production of pro-inflammatory cytokines by respiratory epithelial cells,severe COVID-19 illness has the potential to inflict acute respiratory distress syndrome and even death.Due to the fast spreading nature of COVID-19 and the current lack of a vaccine or specific pharmaceutical treatments,understanding of viral pathogenesis,behavioral prophylaxis,and mitigation tactics are of great public health concern.This review article outlines the immune response to viral pathogens,and due to the novelty of COVID-19 and the large body of evidence suggesting the respiratory and immune benefits from regular moderate intensity exercise,provides observational and mechanistic evidence from research on other viral infections that suggests strategically planned exercise regimens may help reduce susceptibility to infection,while also mitigating severe immune responses to infection commonly associated with poor COVID-19 prognosis.We propose that regular moderate intensity exercise should be considered as part of a combinatorial approach including widespread hygiene initiatives,properly planned and well-executed social distancing policies,and use of efficacious facial coverings like N95 respirators.Studies discerning COVID-19 pathogenesis mechanisms,transfer dynamics,and individual responses to pharmaceutical and adjunct treatments are needed to reduce viral transmission and bring an end to the COVID-19 pandemic.