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Development of sorghum mutants with improved in vitro protein digestibility by CRISPR/Cas9 editing of kafirin genes

The Crop Journal 2023年第5期11卷 1411-1418页

作者： Lev A.Elkonin Grigoriy A.Gerashchenkov Natalie V.Borisenko Odyssey A.Kenzhegulov Saule Kh.Sarsenova Natalya A.Rozhnova Valery M.Panin federal centre of agriculture research of south-east region Saratov 410010Russia Institute of Biochemistry and Genetics-Subdivision of the Ufa federal research centre of the Russian Academy of Sciences Ufa 450054Russia

Sorghum(Sorghum bicolor(L.) Moench) is a major world crop that is a reliable source of fodder and food grain in arid regions. However, unlike other cereals, sorghum grain has low nutritional value, owing mainly to the resistance of its storage proteins(kafirins) to protease digestion. Changing the composition of kafirins or their primary structure may address this problem. To induce mutations in kafirin-encoding genes that were expected to disturb their accumulation in endosperm cells, we used a genome-editing approach. By Agrobacterium-mediated genetic transformation of immature embryos of cv. Avans, we obtained 14 transgenic plants with genetic constructs for site-directed mutagenesis of the k1C5 and g KAF1 genes encoding 22 k Da a-and 28 kDa γ-kafirins, respectively. Sequencing of 5 regenerants obtained by using k1C5-addressing vector revealed two plants with mutations. T_1 progeny of these mutants had higher in vitro digestibility of endosperm proteins(86%–92%), in comparison with the donor Avans(63%–67%). The kernels of these plants had a thick vitreous endosperm. A mutant with increased in vitro protein digestibility and vitreous endosperm, carrying a mutation in the target sequence, was also obtained by use of the gKAF1-addressing vector. Thus, using genome editing technology, we have obtained mutants with improved kafirin digestibility that can be used in sorghum breeding.

关键词： Sorghum CRISPR/Cas Kafirins In vitro protein digestibility Vitreous endosperm

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Plasmonic nanoparticles and nucleic acids hybrids for targeted gene delivery,bioimaging,and molecular recognition

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Journal of Innovative Optical Health Sciences 2021年第4期4卷 3-30页

作者： Timofey Pylaev Elena Avdeeva Nikolai Khlebtsov Institute of Biochemistry and Physiology of Plants and Microorganisms Russian Academy of Sciences Saratov 410049Russia Razumovsky Saratov State Medical University Saratov 410012Russia federal Center of agriculture research of the south-east region Saratov 410010Russia Saratov National research State University Saratov 410012Russia

Promising biomedical applications of hybrid materials composed of gold nanoparticles and nucleic acids have attracted strong interest from the nanobiotechnological *** particular interest is owing to the robust and easy-to-make synthetic approaches,to the versatile optical and catalytic properties of gold nanoparticles combined with the molecular recognition and programmable properties of nucleic *** significant progress is made in the develop-ment of DNA-gold nanostructures and their applications,such as molecular recognition,cell and tissue bioimaging,targeted delivery of therapeutic agents,*** review is focused on the critical discussion of the recent applications of the gold nanoparticles-nucleic acids *** effect of particle size,surface,charge and thermal properties on the interactions with functional nucleic acids is *** each of the above topics,the basic principles,recent advances,and current challenges are *** is placed on the systematization of data over the theranostic systems on the basis of the gold nanoparticles-nucleic acids ***,we start our discussion with observation of the recent data on interaction of various gold nano-particles with nucleic *** we describe existing gene delivery systems,nucleic acids detection,and bioimaging ***,we describe the phenomenon of the polymerase chain reaction improvement by gold nanoparticle additives and its potential underlying ***,we provide a short summary of reported data and outline the challenges and perspectives.

关键词： gold nanoparticles delivery DNA detection bioimaging

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Selective footprints and genes relevant to cold adaptation and other phenotypic traits are unscrambled in the genomes of divergently selected chicken breeds

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Journal of Animal Science and Biotechnology 2023年第3期14卷 887-907页

作者： Michael N.Romanov Alexandra S.Abdelmanova Vladimir I.Fisinin Elena A.Gladyr Natalia A.Volkova Olga A.Koshkina Andrey N.Rodionov Anastasia N.Vetokh Igor V.Gusev Dmitry V.Anshakov Olga I.Stanishevskaya Arsen V.Dotsev Darren K.Griffin Natalia A.Zinovieva L.K.Ernst federal research centre for Animal Husbandry DubrovitsyPodolskMoscow RegionRussia School of Biosciences University of KentCanterburyUK federal State Budget Scientific Institution federal research centre“All-Russian Poultry research and Technological Institute”of the Russian Academy of Sciences Sergiev PosadMoscow RegionRussia Breeding and Genetic centre“Zagorsk Experimental Breeding Farm”–Branch of the federal research centre“All-Russian Poultry research and Technological Institute”of the Russian Academy of Sciences Sergiev PosadMoscow RegionRussia Russian research Institute of Farm Animal Genetics and Breeding–Branch of the L.K.Ernst federal research centre for Animal Husbandry St.PetersburgRussia

Background The genomes of worldwide poultry breeds divergently selected for performance and other phenotypic traits may also be affected by,and formed due to,past and current admixture *** to diverse environments,including acclimation to harsh climatic conditions,has also left selection footprints in breed *** Using the Chicken 50K_CobbCons SNP chip,we genotyped four divergently selected breeds:two aboriginal,cold tolerant Ushanka and Orloff Mille Fleur,one egg-type Russian White subjected to artificial selection for cold tolerance,and one meat-type White *** of selective sweeps were determined in the studied breeds using three methods:(1)assessment of runs of homozygosity islands,(2)F_(ST) based population differential analysis,and(3)haplotype differentiation *** regions of true selection signatures were identified by two or more methods or in two or more *** these regions,we detected 540 prioritized candidate genes supplemented them with those that occurred in one breed using one statistic and were suggested in other *** them,SOX5,ME3,ZNF536,WWP1,RIPK2,OSGIN2,DECR1,TPO,PPARGC1A,BDNF,MSTN,and beta-keratin genes can be especially mentioned as candidates for cold *** factors may be involved in regulating some of these important genes(e.g.,TPO and BDNF).Conclusion Based on a genome-wide scan,our findings can help dissect the genetic architecture underlying various phenotypic traits in chicken *** include genes representing the sine qua non for adaptation to harsh *** tolerance in acclimated chicken breeds may be developed following one of few specific gene expression mechanisms or more than one overlapping response known in cold-exposed individuals,and this warrants further investigation.

关键词： Acclimation Adaptation Chicken breeds Cold tolerance Divergent selection Genetic diversity Genomewide scan Phenotypic traits Selective sweeps

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Forecasting the effects of EU policy measures on the nitrate pollution of groundwater and surface waters

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Journal of Environmental Sciences 2010年第6期22卷 872-877页

作者： Ralf Kunkel Peter Kreins Bjrn Tetzlaff Frank Wendland research centre Jülich Institute of Chemistry and Dynamics of the Geosphere Institute of Rural Studies Federal Agricultural Research Centre

We used the interdisciplinary model network REGFLUD to predict the actual mean nitrate concentration in percolation water at the scale of the Weser river basin （Germany） using an area differentiated （100 m × 100 m） approach. REGFLUD combines the agro-economic model RAUMIS for estimating nitrogen surpluses and the hydrological models GROWA/DENUZ for assessing the nitrate leaching from the soil. For areas showing predicted nitrate concentrations in percolation water above the European Union （EU） groundwater quality standard of 50 mg NO3-N/L, effective agri-environmental reduction measures need to be derived and implemented to improve groundwater and surface water quality by 2015. The effects of already implemented agricultural policy are quantified by a baseline scenario projecting the N-surpluses from agricultural sector to 2015. The REGFLUD model is used to estimate the effects of this scenario concerning groundwater and surface water pollution by nitrate. From the results of the model analysis the needs for additional measures can be derived in terms of required additional N-surplus reduction and in terms of regional prioritization of measures. research work will therefore directly support the implementation of the Water Framework Directive of the European Union in the Weser basin.

关键词： catchment management diffuse source pollution mitigation methods river basin management Water Framework Directive

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Assessing Capacity and Implementation Status of the Disaster Risk Management Strategy for Health and Community Disaster Resilience in Malawi

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International Journal of Disaster Risk Science 2021年第5期12卷 673-688页

作者： Ozius Dewa Donald Makoka Olalekan A.Ayo-Yusuf southern Africa Resilience Innovation Lab(SARiLab) School of Health Systems and Public HealthUniversity of PretoriaPretoria 0002GautengSouth Africa centre for Agricultural research and Development Lilongwe University of Agriculture and Natural ResourcesLilongweCentral RegionMalawi

Floods are among the most frequently occurring natural hazards in Malawi,often with public health *** mixed methods study assessed the capacity for and implementation status of the disaster risk management(DRM)strategy for the health sector in Malawi,using flooding in the Nsanje District as a *** were collected using desk review and a workshop methodology involving key officials from government ministries,national and international development partners,and the *** results show that Malawi had recently strengthened its DRM institutional frameworks,with a pronounced policy shift from reactive to proactive management of *** sector personnel and structures were key contributors in the design and implementation of DRM activities at all *** partners played a significant role in strengthening DRM coordination and implementation *** of funding and the limited availability,and often fragmented nature,of vulnerability and risk assessment data were identified as key *** human resource capacity and inadequate planning processes at district level impeded full implementation of DRM *** findings call for community-level interventions for improved coordination,planning,and human resource capacity to strengthen community disaster resilience and improve public *** approach used in this study can serve as a model framework for other districts in Malawi,as well as in other low-and middle-income countries in the context of Sendai Framework implementation.

关键词： Community disaster resilience Disaster risk management Health Malawi Policy

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Residual dynamics of thiacloprid in medical herbs marjoram,thyme,and camomile in soil

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Journal of Environmental Sciences 2007年第2期19卷 205-209页

作者： YU Yun-long WU Jia-lun STAHLER Matthias PESTEMER Wilfried Department of Plant Protection College of Agriculture and Biotechnology Zhejiang University Hangzhou 310029 China Institute for Ecotoxicology and Ecochemistry in Plant Protection Federal Biological Research Centre for Agriculture and Forestry Koenigin-Luise-Strafle 19 D-14195 Berlin Germany

Thiacloprid is a new insecticide of the chloronicotinyl family. To assess its risk after application, residual characteristics of thiacloprid in marjoram, thyme, and camomile and in soil were studied under field conditions. The active ingredient was extracted from the plant material using a mixture of acetone-water. After filtration, the extract was concentrated to the aqueous phase, diluted with water, and portioned against ethyl acetate on a matrix solid phase dispersion column. Thiacloprid was extracted from soil using a mixture of methanol-water, filtered, and *** （clean up） with dichloromethane. The residues were quantified using HPLC-MS-MS. The methods were validated by recovery experiments. Thiacloprid residues in marjoram, thyme, and camomile and in soil persisted beyond 10, 14, 14, and 21 d but no residues were detected after 14, 21, 21, and 28 d, respectively. The data obtained in this study indicated that the biexponential model is more suitable than the first-order function to describe the decline of thiacloprid in fresh marjoram, fresh thyme, and dried camomile flowers with half-life （t1/2） of 1.1, 0.7, and 1.2 d, respectively. However, both the first-order function and biexponential model were found to be applicable for dissipation of thiacloprid in soil with almost the same t1/2 values of 3.5 and 3.6 d. The results indicated that thiacloprid dissipates rapidly and does not accumulate in the tested herbs and in soil.

关键词： thiacloprid marjoram (Majorana hortensis) thyme (Thymus vilgaris) camomile (Matricaria chamomilla) residue

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Suitability mapping for rice cultivation in Benue State,Nigeria using satellite data Fanan Ujoh

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Geo-Spatial Information Science 2019年第4期22卷 332-344,I0009页

作者： Fanan Ujoh Tertsea Igbawua Moses Ogidi Paul centre for Sustainability and Resilient Infrastructure and Communities London South Bank UniversityLondonUK Department of Physics Federal University of AgricultureMakurdiNigeria Department of Geography and Environmental Management University of AbujaAbujaNigeria

With rising population,decline in soil productivity and land-based conflicts,the per-capita land availability for cultivation is rapidly decreasing within Benue State,a largely agrarian and small-holder *** study attempts a local-level support for the actualisation of Sustainable Development Goal Number 2(“end hunger,achieve food security and improved nutrition,and promote sustainable agriculture”)by *** Multi-Criteria Decision Making(MCDM)method,remote sensing data from Climate research Unit(CRU)and in-situ data from Nigeria Meteorological Agency(NIMET)were analyzed by GIS techniques to map the suitability of rice cultivation in the study area,with the integration of Normalized Difference Vegetation Index(NDVI),land cover,slope,temperature,precipitation and soil parameters(cation exchange capacity,pH,bulk density,organic carbon).We apply the various statistical parameters that include mean spatial NDVI;correlation coefficient,standard deviation and Root Mean Square(RMS)between CRU and NIMET *** regression trend analysis is conducted between CRU precipitation and NDVI and between CRU temperature and NDVI from 1985 to *** results reveal that NDVI in highly suitable rice planting regions is higher than marginally suitable regions except in the months of October and November,which shows that the highly suitable regions will yield better than the marginally suitable regions during the dry ***,NDVI is seasonally bimodal in response to precipitation,meaning that vegetation vigor is more dependent on precipitation than ***,the correlation coefficient,standard deviation and RMS between CRU and NIMET precipitation data shows 0.42,108,and 110,respectively,while these three factors between CRU and NIMET temperature data shows 0.88,1.60,and 0.86,*** conclusion,the MCDM approach reveals that upland is more suitable for rice cultivation in Benue State when comparing with the area provided by the Global Land

关键词： CRU data NIMET data rice cultivation suitability mapping Sustainable Development Goals(SDGs) Benue State

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Scenario analysis for reduction of pollutant load discharged from a watershed by recycling of treated water for irrigation

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Journal of Environmental Sciences 2010年第6期22卷 878-884页

作者： Eisaku Shiratani Yoshiyuki Munakata Ikuo Yoshinaga Tomijiro Kubota Koji Hamada Tadayoshi Hitomi National Institute for Rural Engineering Kokusai Kogyo Co.Ltd. National Agricultural research centre for Kyushu Okinawa region

A model in which a river model was layered on a distributed model （double-layered model） was developed to analyse the transport of water and pollutants （nitrogen, phosphorus, and BOD as organic matter） in watersheds and rivers. The model was applied to the watershed of Abragafuchi Lake, Japan, where serious water pollution has occurred over three decades, and the applicability of the model was demonstrated. Scenarios of recycling of sewage treated-water into agriculture to reduce pollutant load discharged into the lake were analysed. The results showed that irrigating paddy fields with the sewage-treated water could contribute to conserving water and reducing pollutant load, with reduction rate in BOD, nitrogen, and phosphorus ranging from 6%-36%, 16%-46%, and 18%-51%, respectively. Particularly, the results indicated that, irrigating paddy fields with the treated water during non-cropping periods and the accompanying reduction in withdrawn water from the river were more effective in reducing pollutant loads discharged into the lake. Further study is required on the effect of recycled water on crop cultivation and soil conditions for safe implementation.

关键词： watershed management paddy field sewage treatment water reuse

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Binary Vector Construction for Site-Directed Mutagenesis of <i>Kafirin</i>Genes in Sorghum

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American Journal of Plant Sciences 2021年第8期12卷 1276-1287页

作者： Grigoriy A. Gerashchenkov Lev A. Elkonin Kirill G. Gerashchenkov Natalia A. Rozhnova Stefan Hiekel Jochen Kumlehn Alexey V. Chemeris Institute of Biochemistry and Genetics Subdivision of the Ufa Federal Research Centre of the Russian Academy of Sciences Ufa Russia federal centre of agriculture research of south-east region Saratov Russia Kazan federal University Institute of Fundamental Medicine and Biology Kazan Russia Leibniz Institute of Plant Genetics and Crop Plant research (IPK) Gatersleben Germany

Sorghum (Sorghum bicolor (L.) Moench) is one of the world’s leading cereal crops in agricultural production, which has a special importance in the arid regions. However, unlike other cereals, sorghum grain has a lower nutritional value, which is caused, inter alia, by the resistance of its seed storage proteins (kafirins) to protease digestion. One of the effective approaches to improve the nutritional value of sorghum grain is to obtain mutants with partially or completely suppressed synthesis or altered amino acid composition of kafirins. The employment of genome editing may allow to solve this problem by introducing mutations into the nucleotide sequences of the α- and γ-kafirin genes. In this study, genomic target motifs (23 bp sequences) were selected for the introduction of mutations into the α- and γ-KAFIRIN genes of sorghum. The design of the gRNAs was conducted using the online tools CRISPROR and CHOPCHOP. Two most suitable targets were chosen for α-KAFIRIN (k1C5) and two for γ-KAFIRIN (gKAF1) genes. The insertion of respective sequences in the generic vector pSH121 was performed at the BsaI (Eco31I) sites. Validation of the cloning procedure was performed by DNA sequencing. Subcloning of the resulting constructs was performed using the SfiI restriction sites into the compatible binary vector B479p7oUZm-LH. The correct assembly of binary vectors was confirmed by restriction analysis using the MluI and SfiI cleavage sites. The four vectors created (1C - 4C) were transferred by electroporation into the Agrobacterium tumefaciens strain AGL0. Currently, this vector series is used for stable

关键词： Sorghum bicolor (L.) Moench CRISPR/Cas Genome Editing α-Kafirin γ-Kafirin Genetic Engineering Grain Quality

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Biochar derived from invasive plants improved the pH,macronutrient availability and biological properties better than liming for acid rain-affected soil

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Biochar 2023年第1期5卷 1029-1044页

作者： Yazheng Li Ahmed I.Abdo Zhaoji Shi Abdel-Rahman M.A.Merwad Jiaen Zhang Department of Ecology College of Natural Resources and EnvironmentSouth China Agricultural UniversityGuangzhou 510642China Guangdong Provincial Key Laboratory of Utilization and Conservation of Food and Medicinal Resources in Northern region Yingdong College of Biology and AgricultureShaoguan UniversityShaoguan 512005China Soil Science Department Faculty of AgricultureZagazig UniversityZagazig 44519Egypt Guangdong Laboratory for Lingnan Modern agriculture Guangdong Provincial Key Laboratory of Eco-Circular AgricultureSouth China Agricultural UniversityGuangzhou 510642China Guangdong Engineering Technology research centre of Modern Eco-agriculture and Circular agriculture Guangzhou 510642China

Rapid development in industrialization and urbanization causes serious environmental issues,of which acid rain is one of the quintessential hazards,negatively affecting soil *** has been investigated for a long time as the most effective amendment to alter the adverse effects of soil acidity resulting from acid ***,this study tested the biochar produced from invasive plants as an alternative amendment and hypothesized that biochar can maintain better availability of macronutrients under acid rain than liming by improving soil chemical and biological ***,a pot experiment was conducted to compare the effects of lime and biochar at two rates(1%and 3%)on soil available nitrogen(N),phosphorous(P)and potassium(K)under simulated acid rain of two pH levels(4.5:pH_(4.5) and 2.5:pH_(2.5))as compared with tap water(pH7.1)as a control *** was produced using different invasive plants,including Blackjack(Biden Pilosa),Wedelia(Wedelia trilobata)and Bitter Vine(Mikania micrantha Kunth).Liming decreased the availability of soil N,P,and K by 36.3%as compared with the control due to the great increment in soil pH and exchangeable calcium(Ca^(2+))by 59%and 16-fold,***,liming reduced the alpha diversity of soil bacteria and fungi by 27%and 11%,*** contrast,biochar at different types and rates resulted in a fourfold increment in the available N,P,and K as an average under acid rain(pH_(4.5) and pH_(2.5))owing to maintaining a neutral pH(6.5-7),which is the most favorable level for soil microbial and enzymatic activites,and the bioavailability of soil ***,biochar caused balanced increments in Ca^(2+)by threefold,cation exchange capacity by 45%,urease activity by 16%,and fungal diversity by 10%,while having a slight reduction in bacterial diversity by 2.5%.Based on the path,correlation,and principal component analyses,the exchangeable aluminum was a moderator for the reductions in macronutrien

关键词： Acidic soil Liming Invasive plants Biochar feedstock Soil chemical properties

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