Reconstruction of shale image based on Wasserstein Generative Adversarial Networks with gradient penalty

 Generative Adversarial Networks (GANs), as most popular artificial intelligence models in the current image generation field, have excellent image generation capabilities. Based on Wasserstein GANs with gradient penalty, this paper proposes a novel digital core reconstruction method. First, a convolutional neural network is used as a generative network to learn the distribution of real shale samples, and then a convolutional neural network is constructed as a discriminative network to distinguish reconstructed shale samples from real ones. Through this confrontation training method, realistic digital core samples of shale can be reconstructed. The paper uses two-point covariance function, Frechet Inception Distance and Kernel Inception Distance, to evaluate the quality of digital core samples of shale reconstructed by GANs. The results show that the covariance function can test the similarity between generated and real shale samples, and that GANs can efficiently reconstruct digital core samples of shale with high-quality. Compared with multiple point statistics, the new method does not require prior inference of the probability distribution of the training data, and directly uses noise vector to generate digital core samples of shale without using constraints of "hard data" in advance. It is easy to produce an unlimited number of new samples. Furthermore, the training time is also shorter, only 4 hours in this paper. Therefore, the new method has some good points compared with current methods.Cited as: Zha, W., Li, X., Xing, Y., He, L., Li, D. Reconstruction of shale image based on Wasserstein Generative Adversarial Networks with gradient penalty. Advances in Geo-Energy Research, 2020, 4(1): 107-114, doi: 10.26804/ager.2020.01.1

Research on adjustable intelligent speed retarder

The existing speed bumps can reduce the number of traffi c accidents, but it will reduce the comfort of drivers and reduce the service life of passing vehicles. In order to reduce the number of traffi c accidents at the same ti me, to ensure the driver’s comfort according to the provisions of the driving, to prevent the service life of the vehicle to reduce, put forward a lifting speed belt, the speed belt by measuring subsystem, lifting power subsystem and deceleration plate device composed. The experimental results show that the device can maximize the driver’s comfort while reducing the speed of passing vehicles, reduce the number of traffi c accidents, improve traffi c safety, and protect people’s life and property safety

Functional expression of the nitrogenase Fe protein in transgenic rice

Engineering cereals to express functional nitrogenase is a long-term goal of plant biotechnology and would permit partial or total replacement of synthetic N fertilizers by metabolization of atmospheric N2. Developing this technology is hindered by the genetic and biochemical complexity of nitrogenase biosynthesis. Nitrogenase and many of the accessory proteins involved in its assembly and function are O2 sensitive and only sparingly soluble in non-native hosts. We generated transgenic rice plants expressing the nitrogenase structural component, Fe protein (NifH), which carries a [4Fe-4S] cluster in its active form. NifH from Hydrogenobacter thermophilus was targeted to mitochondria together with the putative peptidyl prolyl cis‐trans isomerase NifM from Azotobacter vinelandii to assist in NifH polypeptide folding. The isolated NifH was partially active in electron transfer to the MoFe protein nitrogenase component (NifDK) and in the biosynthesis of the nitrogenase iron-molybdenum cofactor (FeMo-co), two fundamental roles for NifH in N2 fixation. NifH functionality was, however, limited by poor [4Fe-4S] cluster occupancy, highlighting the importance of in vivo [Fe-S] cluster insertion and stability to achieve biological N2 fixation in planta. Nevertheless, the expression and activity of a nitrogenase component in rice plants represents the first major step to engineer functional nitrogenase in cereal crops

Nitrogenase Cofactor Maturase NifB Isolated from Transgenic Rice is Active in FeMo-co Synthesis

The engineering of nitrogen fixation in plants requires assembly of an active prokaryotic nitrogenase complex, which is yet to be achieved. Nitrogenase biogenesis relies on NifB, which catalyzes the formation of the [8Fe−9S−C] metal cluster NifB-co. This is the first committed step in the biosynthesis of the iron−molybdenum cofactor (FeMo-co) found at the nitrogenase active site. The production of NifB in plants is challenging because this protein is often insoluble in eukaryotic cells, and its [Fe−S] clusters are extremely unstable and sensitive to O2. As a first step to address this challenge, we generated transgenic rice plants expressing NifB from the Archaea Methanocaldococcus infernus and Methanothermobacter thermautotrophicus. The recombinant proteins were targeted to the mitochondria to limit exposure to O2 and to have access to essential [4Fe−4S] clusters required for NifB-co biosynthesis. M. infernus and M. thermautotrophicus NifB accumulated as soluble proteins in planta, and the purified proteins were functional in the in vitro FeMo-co synthesis assay. We thus report NifB protein expression and purification from an engineered staple crop, representing a first step in the biosynthesis of a functional NifDK complex, as required for independent biological nitrogen fixation in cereals

Spatial heterogeneity of peri-tumoural lipid composition in postmenopausal patients with oestrogen receptor positive breast cancer

Funding Information: This project was funded by Friends of Aberdeen and North Centre for Haematology, Oncology and Radiotherapy (ANCHOR) (RS2016 004). Sai Man Cheung’s PhD study was jointly supported by Elphinstone scholarship, Roland Sutton Academic Trust and John Mallard scholarship and is currently funded by Cancer Research UK (C68628/A28312). The funding sources were not involved in the study design, in the collection, analysis and interpretation of data, in the writing of the report nor in the decision to submit the article for publication.Peer reviewe

Inactivation of rice starch branching enzyme IIb triggers broad and unexpected changes in metabolism by transcriptional reprogramming

Starch properties can be modified by mutating genes responsible for the synthesis of amylose and amylopectin in the endosperm. However, little is known about the effects of such targeted modifications on the overall starch biosynthesis pathway and broader metabolism. Here we investigated the effects of mutating the OsSBEIIb gene encoding starch branching enzyme IIb, which is required for amylopectin synthesis in the endosperm. As anticipated, homozygous mutant plants, in which OsSBEIIb was completely inactivated by abolishing the catalytic center and C-terminal regulatory domain, produced opaque seeds with depleted starch reserves. Amylose content in the mutant increased from 19.6 to 27.4% and resistant starch (RS) content increased from 0.2 to 17.2%. Many genes encoding isoforms of AGPase, soluble starch synthase, and other starch branching enzymes were up-regulated, either in their native tissues or in an ectopic manner, whereas genes encoding granule-bound starch synthase, debranching enzymes, pullulanase, and starch phosphorylases were largely down-regulated. There was a general increase in the accumulation of sugars, fatty acids, amino acids, and phytosterols in the mutant endosperm, suggesting that intermediates in the starch biosynthesis pathway increased flux through spillover pathways causing a profound impact on the accumulation of multiple primary and secondary metabolites. Our results provide insights into the broader implications of perturbing starch metabolism in rice endosperm and its impact on the whole plant, which will make it easier to predict the effect of metabolic engineering in cereals for nutritional improvement or the production of valuable metabolites.We would like to acknowledge funding from Ministry of Economy and Competitiveness, Spain (RTI2018-097613-BI00 to C.Z., PGC2018-097655-B-I00 to P.C., and AGL2017-85377-R to T.C.); Generalitat de Catalunya Grant 2017 SGR 828 to the Agricultural Biotechnology and Bioeconomy Unit; and the European Union Framework Program DISCO (from discovery to final products: a next-generation pipeline for the sustainable generation of high-value plant products; Project 613513) to P.D.F

The coordinated upregulated expression of genes involved in MEP, chlorophyll, carotenoid and tocopherol pathways, mirrored the corresponding metabolite contents in rice leaves during de-etiolation

Light is an essential regulator of many developmental processes in higher plants. We investigated the effect of 4-hydroxy-3-methylbut-2-enyl diphosphate reductase 1/2 genes (OsHDR1/2) and isopentenyl diphosphate isomerase 1/2 genes (OsIPPI1/2) on the biosynthesis of chlorophylls, carotenoids, and phytosterols in 14-day-old etiolated rice (Oyza sativa L.) leaves during de-etiolation. However, little is known about the effect of isoprenoid biosynthesis genes on the corresponding metabolites during the de-etiolation of etiolated rice leaves. The results showed that the levels of α-tocopherol were significantly increased in de-etiolated rice leaves. Similar to 1-deoxy-D-xylulose-5-phosphate synthase 3 gene (OsDXS3), both OsDXS1 and OsDXS2 genes encode functional 1-deoxy-D-xylulose-5-phosphate synthase (DXS) activities. Their expression patterns and the synthesis of chlorophyll, carotenoid, and tocopherol metabolites suggested that OsDXS1 is responsible for the biosynthesis of plastidial isoprenoids in de-etiolated rice leaves. The expression analysis of isoprenoid biosynthesis genes revealed that the coordinated expression of the MEP (2-C-methyl-D-erythritol 4-phosphate) pathway, chlorophyll, carotenoid, and tocopherol pathway genes mirrored the changes in the levels of the corresponding metabolites during de-etiolation. The underpinning mechanistic basis of coordinated light-upregulated gene expression was elucidated during the de-etiolation process, specifically the role of light-responsive cis-regulatory motifs in the promoter region of these genes. In silico promoter analysis showed that the light-responsive cis-regulatory elements presented in all the promoter regions of each light-upregulated gene, providing an important link between observed phenotype during de-etiolation and the molecular machinery controlling expression of these genesThis research was funded by Gansu Provincial Key Laboratory of Aridland Crop Science, Gansu Agricultural University (Project No. GSCS-2020-07); The National Natural Science Foundation of China (31870278); the Spanish Ministry of Economy and Competitiveness (MINECO), Spain (RTI2018-097613-B-I00; PGC2018-097655-B-I00); in part by the European Union Framework Pro- gram DISCO (613513) “from DISCOvery to products: a next-generation pipeline for the sustainable generation of high-value plant products”, the European Cooperation in Science and Technology project EUROCAROTEN (OC-2015-1-19780), Generalitat de Catalunya Grant 2017 SGR 828 to the Agricultural Biotechnology and Bioeconomy Unit (ABBU), and the International Science and Technol- ogy Cooperation Project 20190201013JC (from Jilin Provincial Science and Technology Department, China); GAU-KYQD-2019-06, Gansu Agricultural University

Addressing Grand Challenges in Rice Productivity and Sustainability through Biotechnology

Aquesta tesis doctoral està enfocada en donar resposta als grans desafiaments de l’agricultura contemporània, concretament la productivitat i la sostenibilitat del cultivo de l’arròs mitjançant l’aplicació de tècniques biotecnològiques com l’enginyeria genètica. Els objectius generales d’aquesta tesis han estat (a) introduir una via de fixació de nitrogeno heteròloga en arròs per a que aquest sigui capaç de fixar el nitrogen biològic i (b) introduir una via ectòpica de captació d’oxigen per a reduir la fotorespiració i millorar la eficiència fotosintètica de les plantes de arròs. Tots dos objectius son congruents amb la millora de la productivitat i la sostenibilitat de l’arròs d’una forma duradora i respectuosa amb el medi ambient i son coherents amb els principals Objectius de Desenvolupament Sostenible, tal com s’articula en la carta de las Nacions Unides sobre el medi ambient. La fixació de nitrogen biològica esta catalitzada por l’enzim nitrogenasa. Aquest enzim està lligat al complex ferro-molibdè (MoFe), denominada proteïna NifDK i a la ferritina, essent denominada proteïna NifH. La proteïna NifB sintetitza precursors del cofactor del lloc actiu de la nitrogenasa (FeMo-co) que s’uneix al nitrogen reduint-lo. En aquesta tesis doctoral he regenerat plantes d’arròs transgèniques que expressen dues formes diferents de la proteïna NifB, prevenients de les arqueobacteries Methanocaldococcus infernus i Methanothermobacter thermautotrophicus. Aquestes proteïnes han estat combinades amb FdxN de Azotobacter vinelandii; NifH de A. vinelandii juntament amb NifM, NifS i NifU de A. vinelandii; i NifH de Hydrogenobacter thermophilus amb NifM de A. vinelandii; a més a més de tres variants de NifD A (NifDAv-Y99K, NifDAv-Y99Q, NifDAv-Y99QY100T) en experiments detallats en cada capítol. Els resultats que he obtingut han estat que ambdues proteïnes NifB i NifH s’acumulen en forma de proteïna soluble in planta. Les proteïnes NifB purificades son funcionals en l’assaig in vitro de síntesis de FeMo-co. La proteïna NifH de H. thermophilus és capaç de desenvolupar els papers fonamentals que las proteïnes complexades a Fe requereixen per a la funcionalitat de la fixació de nitrogen, inclosa la transferència de electrons a la proteïna MoFe component de la nitrogenasa i per a la biosíntesis de FeMo-co. Les tres variants NifDAv han demostrat ser susceptibles de talls per la peptidasa de processat mitocondrial, resultant únicament en la formació de proteïnes truncades. Estudis posteriors cal que s’enfoquin en elucidar el perquè de la inestabilitat de la proteïna i de cóm produir NifD intacta en arròs. La expressió de components biològicament actius de nitrogenasa en arròs transgènic representa un pas crític cap a aconseguir la fixació de nitrogen biològic in planta i quest representa l’únic informe fins ara que ha aconseguit la regeneració d’un cultivo majoritari amb la presencia de components enzimàtics de la nitrogenasa. La fotorespiració redueix l’eficiència fotosintètica perquè resulta a fins un 50% de pèrdua del carbó fixat durant la fotosíntesis. En conseqüència, la reducció de la fotorespiració pot ser una estratègia potencial per a incrementar l’eficiència fotosintètica. En aquesta tesis doctoral he co-introduit l’enzim lactat oxidasa de Lactobacillus buchneri (LbLOX), l’enzim lactat deshidrogenasa de Escherichia coli (EcLDH) i l’enzim catalasa de Oryza sativa (OsCAT) en arròs, establint una nova ruta de captació de oxigen per a reduir la fotorespiració. La co-expressió dels tres gens va ser confirmada a nivell de ARNm. Però solament l’acumulació de la proteïna EcLDH va ser detectable a nivell de teixit de call i en les plantes regenerades. La detecció de l’acumulació de les proteïnes LbLOX i OsCAT va ser probablement interferida por la tag-detectora de proteïnes utilitzada en l’experiment. S’utilitzarà anàlisis d’activitat enzimàtica per a confirmar l’acumulació de proteïnes en tots dos casos i potser és substitueixin les tags-detectores de proteïnes utilitzades.Esta tesis doctoral está enfocada en dar respuesta a los grandes desafíos de la agricultura contemporánea, concretamente la productividad y la sostenibilidad del cultivo del arroz mediante la aplicación de técnicas biotecnológicas como la ingeniería genética. Los objetivos generales de esta tesis han sido (a) introducir una vía de fijación de nitrógeno heteróloga en arroz para que este sea capaz de fijar el nitrógeno biológico e (b) introducir una vía ectópica de captación de oxígeno para reducir la fotorespiración y mejorar la eficiencia fotosintética de las plantas de arroz. Ambos objetivos son congruentes con la mejora de la productividad y la sostenibilidad del arroz de una manera duradera y respetuosa con el medio ambiente y son coherentes con los principales Objetivos de Desarrollo Sostenible, tal como se articula en la carta de las Naciones Unidas sobre el medio ambiente. La fijación de nitrógeno biología esta catalizada por la enzima nitrogenasa. Esta enzima está ligada al complejo hierro-molibdeno (MoFe), denominado proteína NifDK y a la ferritina, siendo denominado proteína NifH. La proteína NifB sintetiza precursores del cofactor del lugar activo de la nitrogenasa (FeMo-co) que se une al nitrógeno reduciéndolo. En esta tesis doctoral he regenerado plantas de arroz transgénicas que expresan dos formas diferentes de la proteína NifB, provenientes de las arqueobacterias Methanocaldococcus infernus y Methanothermobacter thermautotrophicus. Estas proteínas han sido combinadas con FdxN de Azotobacter vinelandii; NifH de A. vinelandii juntamente con NifM, NifS y NifU de A. vinelandii; y NifH de Hydrogenobacter thermophilus con NifM de A. vinelandii; además de tres variantes de NifD A (NifDAv-Y99K, NifDAv-Y99Q, NifDAv-Y99QY100T) en experimentos detallados en cada capítulo. Los resultados que he obtenido han sido que ambas proteínas NifB y NifH se acumulan en forma de proteína soluble in planta. Las proteínas NifB purificadas son funcionales en el ensayo in vitro de síntesis de FeMo-co. La proteína NifH de H. thermophilus es capaz de desarrollar los papeles fundamentales que las proteínas complejadas a Fe requieren para la funcionalidad de la fijación de nitrógeno, incluida la transferencia de electrones a la proteína MoFe componente de la nitrogenasa y para la biosíntesis de FeMo-co. Las tres variantes NifDAv han demostrado ser susceptibles de cortes por la peptidasa de procesado mitocondrial, resultando solo en la formación de proteínas truncadas. Estudios posteriores se tienen que enfocar en elucidar el porqué de la inestabilidad de la proteína y de cómo producir NifD intacta en arroz. La expresión de componentes biológicamente activos de nitrogenasa en arroz transgénico representa un paso criticó hacia conseguir la fijación de nitrógeno biológico in planta y representa el único informe hasta ahora que ha conseguido la regeneración de un cultivo mayoritario con la presencia de componentes enzimáticos de la nitrogenasa. La fotorespiración reduce la eficiencia fotosintética porque resulta en hasta un 50% de pérdida del carbón fijado durante la fotosíntesis. En consecuencia, la reducción de la fotorespiración puede ser una estrategia potencial para incrementar la eficiencia fotosintética. En esta tesis doctoral he co-introducido la enzima lactato oxidasa de Lactobacillus buchneri (LbLOX), la enzima lactato deshidrogenasa de Escherichia coli (EcLDH) y la catalasa de Oryza sativa (OsCAT) en arroz, estableciendo una nueva ruta de captación de oxígeno para reducir la fotorespiración. La co-expresión de los tres genes fue confirmada a nivel de ARNm. Pero solamente la acumulación de la proteína EcLDH fue detectable a nivel de tejido de callo y en las plantas regeneradas. La detección de la acumulación de las proteínas LbLOX y OsCAT fue probablemente interferida por la tag-detectora de proteínas utilizada en el experimento. Se utilizarán análisis de actividad enzimática para confirmar la acumulación de proteínas en ambos casos y quizás se reemplacen las tags-detectoras de proteínas utilizadas.This thesis focuses on addressing the grand challenges of contemporary agriculture in rice productivity and sustainability through biotechnology. The overall aims of my thesis were to (a) engineer a heterologous biological nitrogen fixation pathway to incorporate biological nitrogen fixation in rice and (b) engineer an ectopic oxygen scavenging pathway to reduce photorespiration and improve photosynthetic efficiency. Both objectives are congruent with improving rice productivity and sustainability in a durable and environmentally friendly manner and are consistent with key major Sustainability Development Goals as articulated by the UN charter on the environment. Biological nitrogen fixation is catalyzed by nitrogenase. This enzyme is composed of molybdenum-iron (MoFe) protein (NifDK) and Fe protein (NifH). NifB synthesizes precursors of the nitrogenase active site cofactor (FeMo-co) that binds to nitrogen and reduces it. I generated transgenic rice plants expressing two different forms of NifB from the archaean Methanocaldococcus infernus and Methanothermobacter thermautotrophicus, together with Azotobacter vinelandii FdxN; NifH from A. vinelandii together with A. vinelandii NifM, NifS and NifU; NifH from Hydrogenobacter thermophilus with A. vinelandii NifM; and three A. vinelandii NifD variants (NifDAv-Y99K, NifDAv-Y99Q, NifDAv-Y99QY100T) in separate sets of experiments as detailed in the subsequent chapter of the thesis. I determined that both NifB and NifH proteins accumulated as soluble proteins in planta. The purified NifB proteins were functional in the in vitro FeMo-co synthesis assay. Purified H. thermophilus NifH proteins were able to carry out the fundamental roles of the Fe protein required to engineer nitrogen fixation, including electron transfer to the nitrogenase component MoFe protein and the biosynthesis of FeMo-co. The three NifDAv variants were susceptible to cleavage by mitochondrial processing peptidase, resulting in the formation of only truncated proteins. Further studies need to focus on understanding the basis of this instability and producing intact NifD in rice. The expression of biologically active nitrogenase components in transgenic rice represents a critical step toward achieving biological nitrogen fixation in planta and represents the only report to date which resulted in the recovery of a stably transformed major crop expressing nitrogenase component enzymes. Photorespiration reduces overall photosynthetic efficiency because it results in up to 50% loss of carbon fixed by photosynthesis. Reducing photorespiration, therefore, is a potential strategy to increase photosynthetic efficiency. I co-introduced Lactobacillus buchneri lactate oxidase (LbLOX), Escherichia coli lactate dehydrogenase (EcLDH) and Oryza sativa catalase (OsCAT) into rice to establish a novel oxygen scavenging pathway to reduce photorespiration. Expression of the three transgenes was confirmed at mRNA levels. Only EcLDH protein accumulation was detectable in callus and regenerated plants. Detection of LbLOX and OsCAT protein accumulation was probably hampered by the detection tag used to identify the protein. Further experiments will be required to confirm the accumulation of both proteins by enzymatic assays and the replacement of the assay tags