A new method for the determination of cerium subgroup rare earths was studied and reported ill this paper. It was found that cerium subgroup rare earth elements react with DBMCSA in 0.6 mol/L hydrochloric acid medium ...A new method for the determination of cerium subgroup rare earths was studied and reported ill this paper. It was found that cerium subgroup rare earth elements react with DBMCSA in 0.6 mol/L hydrochloric acid medium to form stable blue complexes. The absorbances of equal amounts of cerium subgroup rare earths are close to each other at their maximum adsorptive wavelength (641 nm). Beer's law is obeyed for 0-20 mu g of I ars earths in 25 mi of solution. The method has been applied to the determination of the total amount of cerium subgroup rare earths in steel and cast iron samples with satisfactory results.展开更多
Human action recognition has gained popularity because of its worldwide applications such as video surveillance, video retrieval and human– computer interaction. This paper provides a comprehensive overview of notabl...Human action recognition has gained popularity because of its worldwide applications such as video surveillance, video retrieval and human– computer interaction. This paper provides a comprehensive overview of notable advances made by deep neural networks in this field. Firstly, the basic conception of action recognition and its common applications were introduced. Secondly, action recognition was categorized as action classification and action detection according to its respective research goals. And various deep learning frameworks for recognition tasks were discussed in detail and the most challenging datasets and taxonomies were briefly reviewed. Finally, the limitations of the state-of-the-art and promising directions of the research were briefly outlined.展开更多
Kenaf is considered to have great potential for remediation of heavy metals in ecosystems.However,studies on molecular mechanisms of root Cd accumulation and tolerance are still inadequate.In this study,two differentl...Kenaf is considered to have great potential for remediation of heavy metals in ecosystems.However,studies on molecular mechanisms of root Cd accumulation and tolerance are still inadequate.In this study,two differently tolerant kenaf cultivars were selected as materials and the physiological and transcriptomic effects were evaluated under Cd stress.This study showed that 200μmol/L CdCl_(2) treatment triggered the reactive oxygen species(ROS)explosion and membrane lipid peroxidation.Compared with the Cd-sensitive cultivar‘Z',the Cd-tolerant cultivar‘F'was able to resist oxidative stress in cells by producing higher antioxidant enzyme activities and increasing the contents of ascorbic acid(AsA)and glutathione(GSH).The root cell wall of‘F'exhibited higher polysaccharide contents under Cd treatment,providing more Cd-binding sites.There were 3,439 differentially expressed genes(DEGs)that were co-regulated by Cd treatment in two cultivars.Phenylpropanoid biosynthesis and plant hormone signal transduction pathways were significantly enriched by functional annotation analysis.DEGs associated with pectin,cellulose,and hemi-cellulose metabolism were involved in Cd chelation of root cell wall;V-ATPases,ABCC3 and Narmp3 could participated in vacuolar compartmentalization of Cd;PDR1 was responsible for Cd effux;the organic acid transporters contributed to the absorption of Cd in soil.These genes might have played key roles in kenaf Cd tolerance and Cd accumulation.Moreover,HcZIP2 was identified to be involved in Cd uptake and transport in kenaf.Our findings provide a deeper understanding of the molecular pathways underlying Cd accumulation and detoxification mechanisms in kenaf.展开更多
Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic stability.However,our study of the wild-type Streptococcus pneumoniae D39,a pathogen resp...Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic stability.However,our study of the wild-type Streptococcus pneumoniae D39,a pathogen responsible for many common diseases,revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation(MA)lines.This rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T direction.The high mutation rate may have resulted from a reduction in the overall efficiency of selection,conferred by the tiny effective population size in nature.In line with this,S.pneumoniae D39 also exhibited the lowest DNA mismatch-repair(MMR)efficiency among bacteria.Treatment with the antibiotic penicillin did not elevate the mutation rate,as penicillin did not induce DNA damage and S.pneumoniae lacks a stress response pathway.Our findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution.展开更多
Antibiotic-resistant bacteria severely threaten human health.Besides spontaneous mutations generated by endogenous factors,the resistance might also originate from mutations induced by certain antibiotics,such as the ...Antibiotic-resistant bacteria severely threaten human health.Besides spontaneous mutations generated by endogenous factors,the resistance might also originate from mutations induced by certain antibiotics,such as the fluoroquinolones.Such antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair systems.However,the relative contributions of these molecular mechanisms remain unclear,hindering understanding of the generation of resistant pathogens.Here,using newly-accumulated mutations of wild-type and SOS-uninducible Escherichia coli strains,as well as those of the strains deficient for the mismatch repair(MMR)and the oxidative damage repair pathways,we find that the SOS response is the major mutagenesis contributor in mutation elevation,responsible for~30–50%of the total base-pair substitution(BPS)mutation-rate elevation upon treatment with sublethal levels of norfloxacin(0~50 ng/mL).We further estimate the significance of the effects on other mutational features of these mechanisms(i.e.,transversions,structural variations,and mutation spectrum)in E.coli using linear models.The SOS response plays a positive role in all three mutational features(mutation rates of BPSs,transversions,structural variations)and affects the mutational spectrum.The repair systems significantly reduce the BPS mutation rate and the transversion rate,regardless of whether antibiotics are present,while significantly increasing the structural variation rate in E.coli.Our results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis.展开更多
High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of ...High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of complex samples,especially those involving environmental and pathogen-monitoring ones.Commercial library preparation kits for amplicon sequencing,which generally require multiple steps,including adapter ligation and indexing,are expensive and time-consuming,especially for applications at a large scale.To overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion primers.However,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed.To tackle these,we present an integrative protocol for one-step PCR amplicon library construction(OSPALC).High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples.With this protocol,the amplicon library is constructed through one regular PCR with long primers,and the total cost per DNA/cDNA sample decreases to just 7%of the typical cost via the multi-step PCR approach.Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study.Tools to design primers targeting at any genomic regions are also presented.In principle,OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples,and will facilitate research in numerous fields.展开更多
Mutation is a primary source of genetic variation that is used to power evolution.Many studies,however,have shown that most mutations are deleterious and,as a result,extremely low mutation rates might be benefcial for...Mutation is a primary source of genetic variation that is used to power evolution.Many studies,however,have shown that most mutations are deleterious and,as a result,extremely low mutation rates might be benefcial for survival.Using a mutation accumulation experiment,an unbiased method for mutation study,we found an extremely low base-substitution mutation rate of 5.94×10^(-11) per nucleotide site per cell division(95%Poisson confdence intervals:4.65×10^(-11),7.48×10^(-11))and indel mutation rate of 8.25×10^(-12) per site per cell division(95%confdence intervals:3.96×10^(-12),1.52×10^(-11))in the bacterium Photorhabdus luminescens ATCC29999.The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction.It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the efective population size(drift-barrier hypothesis)and we found that the efective population size of this bacterium is signifcantly greater than most other bacteria.This fnding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fdelity can evolve within organisms that maintain large efective population sizes.展开更多
Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although persamplecosts have dramatically decreased, the total budget for such massive genome sequencing constitut...Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although persamplecosts have dramatically decreased, the total budget for such massive genome sequencing constitutes a significantbarrier for poorly funded labs. The costly lab tools required for genomics experiments further hinder such studies. Here, weshare two strategies for extensively reducing the costs of massive genomics experiments, including miniaturization of theNEBNext Ultra II FS DNA Library Prep Kit for Illumina (reducing the per-sample total costs to ~ 1/6 of that charged byservice providers) and in-lab 3D model-designing of genomics tools. These strategies not only dramatically release fundingpressure for labs, but also provide students with additional training in hands-on genomics and 3D-model-designing skills,demonstrating the high potential for their application in genomics experiments and science education.展开更多
Building a rainwater system based on the idea of low-impact development (LID) is an important aspect of the current "sponge city" construction in China. The "sponge city" concept emphasizes that the runoff can p...Building a rainwater system based on the idea of low-impact development (LID) is an important aspect of the current "sponge city" construction in China. The "sponge city" concept emphasizes that the runoff can permeate the soil or be stored temporarily, and rainwater could be used again when it is needed. Beijing is one of the earliest cities to study rainwater harvesting and LID techniques in China.Through long-terua monitoring of rainfall, runoff flow, and water quality of a campus demonstration project in Beijing, the runoff quantity and pollutant concentration variations have been analyzed. Furthermore, the runoffreduction effects of single LID measure, such as green roof, filtration chamber, and permeable pavement, have been investigated. Additionally, the overall reduction effectiveness of the LID system on the average annual rainfall runoff and pollution load has been discussed.展开更多
文摘A new method for the determination of cerium subgroup rare earths was studied and reported ill this paper. It was found that cerium subgroup rare earth elements react with DBMCSA in 0.6 mol/L hydrochloric acid medium to form stable blue complexes. The absorbances of equal amounts of cerium subgroup rare earths are close to each other at their maximum adsorptive wavelength (641 nm). Beer's law is obeyed for 0-20 mu g of I ars earths in 25 mi of solution. The method has been applied to the determination of the total amount of cerium subgroup rare earths in steel and cast iron samples with satisfactory results.
基金The National Science Foundation of China (#61763007)The Nature Science Foundation of Guangxi in China (#2017JJD160017)The Science and Technology Project of Guilin City (20170113-6).
文摘Human action recognition has gained popularity because of its worldwide applications such as video surveillance, video retrieval and human– computer interaction. This paper provides a comprehensive overview of notable advances made by deep neural networks in this field. Firstly, the basic conception of action recognition and its common applications were introduced. Secondly, action recognition was categorized as action classification and action detection according to its respective research goals. And various deep learning frameworks for recognition tasks were discussed in detail and the most challenging datasets and taxonomies were briefly reviewed. Finally, the limitations of the state-of-the-art and promising directions of the research were briefly outlined.
基金supported by the China Agriculture Research System of MOF and MARA (No.CARS-16-E14)。
文摘Kenaf is considered to have great potential for remediation of heavy metals in ecosystems.However,studies on molecular mechanisms of root Cd accumulation and tolerance are still inadequate.In this study,two differently tolerant kenaf cultivars were selected as materials and the physiological and transcriptomic effects were evaluated under Cd stress.This study showed that 200μmol/L CdCl_(2) treatment triggered the reactive oxygen species(ROS)explosion and membrane lipid peroxidation.Compared with the Cd-sensitive cultivar‘Z',the Cd-tolerant cultivar‘F'was able to resist oxidative stress in cells by producing higher antioxidant enzyme activities and increasing the contents of ascorbic acid(AsA)and glutathione(GSH).The root cell wall of‘F'exhibited higher polysaccharide contents under Cd treatment,providing more Cd-binding sites.There were 3,439 differentially expressed genes(DEGs)that were co-regulated by Cd treatment in two cultivars.Phenylpropanoid biosynthesis and plant hormone signal transduction pathways were significantly enriched by functional annotation analysis.DEGs associated with pectin,cellulose,and hemi-cellulose metabolism were involved in Cd chelation of root cell wall;V-ATPases,ABCC3 and Narmp3 could participated in vacuolar compartmentalization of Cd;PDR1 was responsible for Cd effux;the organic acid transporters contributed to the absorption of Cd in soil.These genes might have played key roles in kenaf Cd tolerance and Cd accumulation.Moreover,HcZIP2 was identified to be involved in Cd uptake and transport in kenaf.Our findings provide a deeper understanding of the molecular pathways underlying Cd accumulation and detoxification mechanisms in kenaf.
基金financially supported by Laoshan Laboratory(LSKJ202203203)the National Natural Science Founda-tion of China(31961123002,32270435)+4 种基金the Fundamental Research Funds for the Central Universities of China(202041001)the Shan-dong Provincial Natural Science Foundation(ZR2023QC191)the Postdoctoral Fellowship Program of CPSF under Grant Number GZC20232504the Multidisciplinary University Research Initiative Award from the US Army Research Office(W911NF-09-1-0444)National Institutes of Health award(R35-GM122566 to ML)and(R35-GM131767 to MEW).
文摘Bacteria with functional DNA repair systems are expected to have low mutation rates due to strong natural selection for genomic stability.However,our study of the wild-type Streptococcus pneumoniae D39,a pathogen responsible for many common diseases,revealed a high spontaneous mutation rate of 0.02 per genome per cell division in mutation-accumulation(MA)lines.This rate is orders of magnitude higher than that of other non-mutator bacteria and is characterized by a high mutation bias in the A/T direction.The high mutation rate may have resulted from a reduction in the overall efficiency of selection,conferred by the tiny effective population size in nature.In line with this,S.pneumoniae D39 also exhibited the lowest DNA mismatch-repair(MMR)efficiency among bacteria.Treatment with the antibiotic penicillin did not elevate the mutation rate,as penicillin did not induce DNA damage and S.pneumoniae lacks a stress response pathway.Our findings suggested that the MA results are applicable to within-host scenarios and provide insights into pathogen evolution.
基金supported by Laoshan Laboratory(LSKJ202203203)the National Natural Science Foundation of China(31961123002,32270435)+3 种基金the Fundamental Research Funds for the Central Universities(202161064)the Young Taishan Scholars Program of Shandong Province(tsqn201812024)the Natural Science Foundation of Shandong Province(ZR2023QC191)the National Institutes of Health award(R35-GM122566).
文摘Antibiotic-resistant bacteria severely threaten human health.Besides spontaneous mutations generated by endogenous factors,the resistance might also originate from mutations induced by certain antibiotics,such as the fluoroquinolones.Such antibiotics increase the genome-wide mutation rate by introducing replication errors from the SOS response pathway or decreasing the efficiency of the DNA repair systems.However,the relative contributions of these molecular mechanisms remain unclear,hindering understanding of the generation of resistant pathogens.Here,using newly-accumulated mutations of wild-type and SOS-uninducible Escherichia coli strains,as well as those of the strains deficient for the mismatch repair(MMR)and the oxidative damage repair pathways,we find that the SOS response is the major mutagenesis contributor in mutation elevation,responsible for~30–50%of the total base-pair substitution(BPS)mutation-rate elevation upon treatment with sublethal levels of norfloxacin(0~50 ng/mL).We further estimate the significance of the effects on other mutational features of these mechanisms(i.e.,transversions,structural variations,and mutation spectrum)in E.coli using linear models.The SOS response plays a positive role in all three mutational features(mutation rates of BPSs,transversions,structural variations)and affects the mutational spectrum.The repair systems significantly reduce the BPS mutation rate and the transversion rate,regardless of whether antibiotics are present,while significantly increasing the structural variation rate in E.coli.Our results quantitatively disentangle the contributions of the SOS response and DNA repair systems in antibiotic-induced mutagenesis.
基金supported by the National Natural Science Foundation of China(31961123002,31872228)the Fundamental Research Funds for the Central Universities of China(202041001)+1 种基金the Young Taishan Scholars Program of Shandong Province(tsqn201812024)the National Science Foundation(DEB-1927159).
文摘High-throughput sequencing of amplicons has been widely used to precisely and efficiently identify species compositions and analyze community structures,greatly promoting biological studies involving large amounts of complex samples,especially those involving environmental and pathogen-monitoring ones.Commercial library preparation kits for amplicon sequencing,which generally require multiple steps,including adapter ligation and indexing,are expensive and time-consuming,especially for applications at a large scale.To overcome these limitations,a“one-step PCR approach”has been previously proposed for constructions of amplicon libraries using long fusion primers.However,efficient amplifications of target genes and accurate demultiplexing of pooled sequencing data remain to be addressed.To tackle these,we present an integrative protocol for one-step PCR amplicon library construction(OSPALC).High-quality reads have been generated by this approach to reliably identify species compositions of mock bacterial communities and environmental samples.With this protocol,the amplicon library is constructed through one regular PCR with long primers,and the total cost per DNA/cDNA sample decreases to just 7%of the typical cost via the multi-step PCR approach.Empirically tested primers and optimized PCR conditions to construct OSPALC libraries for 16S rDNA V4 regions are demonstrated as a case study.Tools to design primers targeting at any genomic regions are also presented.In principle,OSPALC can be readily applied to construct amplicon libraries of any target genes using DNA or RNA samples,and will facilitate research in numerous fields.
基金This work is supported by the Young Taishan Scholars Program of Shandong Province(tsqn201812024)the Fundamental Research Funds for the Central Universities of China(201822020)to H.L.+1 种基金the Multidisciplinary University Research Initiative Award from the US Army Research Ofce(W911NF-09-1-0444 and W911NF-09-1-0411)National Institutes of Health award(R35-GM122566)to M.L.
文摘Mutation is a primary source of genetic variation that is used to power evolution.Many studies,however,have shown that most mutations are deleterious and,as a result,extremely low mutation rates might be benefcial for survival.Using a mutation accumulation experiment,an unbiased method for mutation study,we found an extremely low base-substitution mutation rate of 5.94×10^(-11) per nucleotide site per cell division(95%Poisson confdence intervals:4.65×10^(-11),7.48×10^(-11))and indel mutation rate of 8.25×10^(-12) per site per cell division(95%confdence intervals:3.96×10^(-12),1.52×10^(-11))in the bacterium Photorhabdus luminescens ATCC29999.The mutations are strongly A/T-biased with a mutation bias of 10.28 in the A/T direction.It has been hypothesized that the ability for selection to lower mutation rates is inversely proportional to the efective population size(drift-barrier hypothesis)and we found that the efective population size of this bacterium is signifcantly greater than most other bacteria.This fnding further decreases the lower-bounds of bacterial mutation rates and provides evidence that extreme levels of replication fdelity can evolve within organisms that maintain large efective population sizes.
基金by the National NaturalScience Foundation of China (3187222& 31961123002)DistinguishedScholars Support Program of Laboratory for Marine Biology and Biotechnology,Qingdao Pilot National Laboratory for Marine Scienceand Technology (YJ2019N004)+1 种基金the Taishan Scholars Program forEarly Career Experts of Shandong Province (tsqn201812024)theFundamental Research Funds for the Central Universities of China(201822020).
文摘Many modern biology studies require deep, whole-genome sequencing of hundreds to thousands of samples. Although persamplecosts have dramatically decreased, the total budget for such massive genome sequencing constitutes a significantbarrier for poorly funded labs. The costly lab tools required for genomics experiments further hinder such studies. Here, weshare two strategies for extensively reducing the costs of massive genomics experiments, including miniaturization of theNEBNext Ultra II FS DNA Library Prep Kit for Illumina (reducing the per-sample total costs to ~ 1/6 of that charged byservice providers) and in-lab 3D model-designing of genomics tools. These strategies not only dramatically release fundingpressure for labs, but also provide students with additional training in hands-on genomics and 3D-model-designing skills,demonstrating the high potential for their application in genomics experiments and science education.
基金This work was supported by the National Major Science and Technology Program (Grant No. 2013ZX07304-001) and the National Science Foundation of Beijing (Grant No. 8161002).
文摘Building a rainwater system based on the idea of low-impact development (LID) is an important aspect of the current "sponge city" construction in China. The "sponge city" concept emphasizes that the runoff can permeate the soil or be stored temporarily, and rainwater could be used again when it is needed. Beijing is one of the earliest cities to study rainwater harvesting and LID techniques in China.Through long-terua monitoring of rainfall, runoff flow, and water quality of a campus demonstration project in Beijing, the runoff quantity and pollutant concentration variations have been analyzed. Furthermore, the runoffreduction effects of single LID measure, such as green roof, filtration chamber, and permeable pavement, have been investigated. Additionally, the overall reduction effectiveness of the LID system on the average annual rainfall runoff and pollution load has been discussed.