Plant synthetic biology has emerged as a transformative field in agriculture,offering innovative solutions to enhance food security,provide resilience to climate change,and transition to sustainable farming practices....Plant synthetic biology has emerged as a transformative field in agriculture,offering innovative solutions to enhance food security,provide resilience to climate change,and transition to sustainable farming practices.By integrating advanced genetic tools,computational modeling,and systems biology,researchers can precisely modify plant genomes to enhance traits such as yield,stress tolerance,and nutrient use efficiency.The ability to design plants with specific characteristics tailored to diverse environmental conditions and agricultural needs holds great potential to address global food security challenges.Here,we highlight recent advancements and applications of plant synthetic biology in agriculture,focusing on key areas such as photosynthetic efficiency,nitrogen fixation,drought tolerance,pathogen resistance,nutrient use efficiency,biofortification,climate resilience,microbiology engineering,synthetic plant genomes,and the integration of artificial intelligence with synthetic biology.These innovations aim to maximize resource use efficiency,reduce reliance on external inputs,and mitigate environmental impacts associated with conventional agricultural practices.Despite challenges related to regulatory approval and public acceptance,the integration of synthetic biology in agriculture holds immense promise for creating more resilient and sustainable agricultural systems,contributing to global food security and environmental sustainability.Rigorous multi-field testing of these approaches will undoubtedly be required to ensure reproducibility.展开更多
The domesticated silkworm(Bombyx mori)has evolved a highly efficient nitrogen utilization system to support silk production.The silk glands play a pleiotropic role in sequestering nitrogen resources for silk synthesis...The domesticated silkworm(Bombyx mori)has evolved a highly efficient nitrogen utilization system to support silk production.The silk glands play a pleiotropic role in sequestering nitrogen resources for silk synthesis,mitigating aminoacidemia by assimilating free amino acids,and reallocating nitrogen during metamorphosis through programmed cell death.However,the specific functions of nitrogen metabolism-related genes in this process remain unclear.Using CRISPR/Cas9-based gene editing,mutations were generated in glutamine synthetase(GS),glutamate synthetase(GOGAT),asparagine synthetase(AS),glutamate dehydrogenase(GDH)and glutamate oxaloacetate transaminase 1(GOT1).Disruption of GS,GOGAT,and AS consistently reduced silkworm cocoon and pupal weight and significantly down-regulated silk protein gene transcription,whereas GOT1 mutation had no such effect.GOGAT mutants exhibited abnormally enlarged silk glands,whereas GS and AS mutants showed delayed programmed cell death in the silk glands.In contrast,GOT1 mutants displayed normal silk gland morphology but were consistently smaller.Disruption of GS,GOGAT,and AS led to more extensive transcriptional changes,including altered expression of transcription factors in the silk glands,compared with GOT1 mutants.Both GS and GOGAT mutants exhibited up-regulation of AS and GDH,while only GOGAT mutants displayed elevated AS enzymatic activity,suggesting that GOGAT may compete with AS for glutamine in the silk glands to support silk protein synthesis.AS mutants showed significantly elevated GOT activity and up-regulation of several metabolic pathways,indicating that AS may functionally interact with GOT in regulating both silk gland development and programmed cell death during metamorphosis.展开更多
The recognition that neurogenesis does not stop with adolescence has spun off research towards the reduction of brain disorders by enhancing brain regeneration. Adult neurogenesis is one of the tougher problems of dev...The recognition that neurogenesis does not stop with adolescence has spun off research towards the reduction of brain disorders by enhancing brain regeneration. Adult neurogenesis is one of the tougher problems of developmental biology as it requires the generation of complex intracellular and pericellular anatomies, amidst the danger of neuroinflammation. We here review how a multitude of regulatory pathways optimized for early neurogenesis has to be revamped into a new choreography of time dependencies. Distinct pathways need to be regulated, ranging from neural growth factor induced differentiation to mitochondrial bioenergetics, reactive oxygen metabolism, and apoptosis. Requiring much Gibbs energy consumption, brain depends on aerobic energy metabolism, hence on mitochondrial activity. Mitochondrial fission and fusion, movement and perhaps even mitoptosis, thereby come into play. All these network processes are interlinked and involve a plethora of molecules. We recommend a deep thinking approach to adult neurobiology.展开更多
Synthetic biotechnology has led to the widespread application of genetically modified organisms(GMOs)in biochemistry, bioenergy, and therapy. However, the uncontrolled spread of GMOs may lead to genetic contamination ...Synthetic biotechnology has led to the widespread application of genetically modified organisms(GMOs)in biochemistry, bioenergy, and therapy. However, the uncontrolled spread of GMOs may lead to genetic contamination by horizontal gene transfer, resulting in unpredictable biosafety risks. To deal with these challenges, many effective methods have been developed for biocontainment. In this article, we summarize and discuss recent advances in biocontainment strategies from three aspects: DNA replication, transcriptional regulation, and protein translation. We also briefly introduce the efforts in the biocontainment convention, such as the recent publication of the Tianjin Biosecurity Guidelines for the Code of Conduct for Scientists.展开更多
In sub-Saharan Africa, foodborne Salmonella infections cause around 680,000 deaths per year. The evolutionary aspects of the incidence of antibiotic resistance in Salmonella strains no longer seem to attract much inte...In sub-Saharan Africa, foodborne Salmonella infections cause around 680,000 deaths per year. The evolutionary aspects of the incidence of antibiotic resistance in Salmonella strains no longer seem to attract much interest in the Central African Republic (CAR), although salmonellosis remains a health problem requiring national and international surveillance. Methodology: The study conducted at the National Laboratory of Clinical Biology and Public Health, Bangui, Central African Republic (LNBCSP) was a retrospective descriptive study. The study duration was five years (January 2019 to December 2023). The study sample consisted of patients who underwent bacteriological testing of stool, blood and urine samples for Salmonella at the LNBCSP in Bangui during this period. Study variables were age, sex, year and bacteriological test results. Statistical tests were used to compare incidences. Relative risks (RR) were calculated to measure the degree of association. Results: From 2019 to 2023, we recorded 353 Salmonella strains, of which 5% were found in blood, 37% in urine and 58% in stool. Patient age ranged from 1 to 86 years, with a mean of 27 ± 22.05 years and a mode of 5 years. Children aged 0 to 14 years (34%) and females (55.81%) predominated. The highest rate of contamination by Salmonella strains was 1.69% in 2022. The overall incidence of salmonellosis was 6.72 in 2019, 7.05 in 2020, 6.91 in 2021, 16.9 in 2022 and 6.26 in 2023 per 1000 samples. Resistance was 30.47% to β_lactam antibiotics, 24.22% to fluroquinolones and 37.97% to Salmonella spp. For Salmonella arizonae strains, resistance was 20.25% to aminoglycosides, 43.67% to chloramphenicol and 7.59% to imipenem. Conclusion: Laboratory-based surveillance of antibiotic resistance in Salmonella strains is needed in both human and veterinary medicine. Another study based on molecular characterization will identify new antibiotic-resistant variants circulating in CAR.展开更多
China experiences serious agricultural damages from rodents, and, correspondingly, researchers in China are actively studying rodent biology and management. Following the popularization of ecologically-based rodent pe...China experiences serious agricultural damages from rodents, and, correspondingly, researchers in China are actively studying rodent biology and management. Following the popularization of ecologically-based rodent pest management and extension of the basic state policy of Ecological Civilization Construction in China, recent efforts in rodent control technologies are mainly focused on eliminating side effects of rodenticides and developing environmentally friendly techniques. Considering ecological functions of rodents to test their interaction with the environment is a promising design for understanding rodent populations in local ecosystems and for developing ecologically-based rodent management. Using ecological phenotypes and applying advanced techniques of molecular biology, genetics, and epigenetics might be useful for illustrating the deep regulatory mechanisms of fluctuations in rodent populations. However, facing the dual characteristics of rodents as pests and their roles as keystone species in many ecosystems, it is still a challenge to establish reasonable local thresholds to balance rodent management with the negative effects of rodent control on the environment in the future.展开更多
INTRODUCTIONMolecular biology has made a tremendous impact on thediagnosis and treatment of liver diseases.In particular,advances in molecular biology made possible the
Objective:To present an integrated molecular biology dedicated system for tuberculosis diagnosis.Methods:One hundred and five sputum specimens from patients strongly suspected by clinical parameters of tuberculosis we...Objective:To present an integrated molecular biology dedicated system for tuberculosis diagnosis.Methods:One hundred and five sputum specimens from patients strongly suspected by clinical parameters of tuberculosis were studied by Ziehl-Neelsen staining,by cultivation on solid medium and by a balanced hemincsted fluorometric PCR system(Orange C3TB) that could preserve worker safety and produce a rather pure material free of potential inhibitors. DNA amplification was performed in a low cost tuberculosis termocycler-fluorotneter.Produced double stranded DNA was flurometrically detected.The whole reaction was conducted in one single tube which would not be opened after adding the processed sample in order to minimize the risk of cross contamination with amplicons.Results:The assay was able to delect 30 bacillus per sample mL with 99.8%interassay variation coefficient.PCR was positive in 23(21.9%) tested samples(21 of them were smear negative).In our study it showed a preliminary sensitivity of 94.5%for sputum and an overall specificity of 98.7%.Conclusions:Total run time of the test is 4 h with 2.5 real working time.All PCR positive samples are also positive by microbiological culture and clinical criteria.Results show that it could be a very useful tool to increase detection efficiency of tuberculosis disease in low bacilus load samples.Furthermore,its low cost and friendly using make it feasible to run in poor regions.展开更多
BACKGROUND Human Wharton’s jelly-derived mesenchymal stromal/stem cells(hWJ-MSCs)have gained considerable attention in their applications in cell-based therapy due to several advantages offered by them.Recently,we re...BACKGROUND Human Wharton’s jelly-derived mesenchymal stromal/stem cells(hWJ-MSCs)have gained considerable attention in their applications in cell-based therapy due to several advantages offered by them.Recently,we reported that hWJ-MSCs and their conditioned medium have significant therapeutic radioprotective potential.This finding raised an obvious question to identify unique features of hWJ-MSCs over other sources of stem cells for a better understanding of its radioprotective mechanism.AIM To understand the radioprotective mechanism of soluble factors secreted by hWJMSCs and identification of their unique genes.METHODS Propidium iodide staining,endogenous spleen colony-forming assay,and survival study were carried out for radioprotection studies.Homeostasis-driven proliferation assay was performed for in vivo lymphocyte proliferation.Analysis of RNAseq data was performed to find the unique genes of WJ-MSCs by comparing them with bone marrow mesenchymal stem cells,embryonic stem cells,and human fibroblasts.Gene enrichment analysis and protein-protein interaction network were used for pathway analysis.RESULTS Co-culture of irradiated murine splenic lymphocytes with WJ-MSCs offered significant radioprotection to lymphocytes.WJ-MSC transplantation increased the homeostasis-driven proliferation of the lymphocytes.Neutralization of WJ-MSC conditioned medium with granulocyte-colony stimulating factor antibody abolished therapeutic radioprotection.Transcriptome analysis showed that WJ-MSCs share several common genes with bone marrow MSCs and embryonic stem cells and express high levels of unique genes such as interleukin(IL)1-α,IL1-β,IL-6,CXCL3,CXCL5,CXCL8,CXCL2,CCL2,FLT-1,and IL-33.It was also observed that WJ-MSCs preferentially modulate several cellular pathways and processes that handle the repair and regeneration of damaged tissues compared to stem cells from other sources.Cytokine-based network analysis showed that most of the radiosensitive tissues have a more complex network for the elevated cytokines.CONCLUSION Systemic infusion of WJ-MSC conditioned media will have significant potential for treating accidental radiation exposed victims。展开更多
Future agricultural development needs to solve the food security crisis caused by the global food shortage and the environmental demand for green and sustainable technology.The vigorous development of synthetic biolog...Future agricultural development needs to solve the food security crisis caused by the global food shortage and the environmental demand for green and sustainable technology.The vigorous development of synthetic biology has brought new opportunities for modern agriculture.Synthetic biology can transform crops'metabolic pathways and genetic information and involves microorganisms'application in agriculture.Therefore,it has bright prospects in crop breeding and yield increase and ensuring the safety of the agricultural production environment.This perspective summarizes the application status and future development of synthetic biology in agriculture from the aspects of plant breeding,photosynthetic system,nitrogen fixation,and microorganisms.展开更多
The Red Palm Weevil （RPW）, Rhynchophorus ferrugineus （Olivier）, （Coleoptera, Curculionidae, Rhynchophorinae）, is an invasive species that is originated from Southeast Asia. It has.invaded Middle East and several...The Red Palm Weevil （RPW）, Rhynchophorus ferrugineus （Olivier）, （Coleoptera, Curculionidae, Rhynchophorinae）, is an invasive species that is originated from Southeast Asia. It has.invaded Middle East and several countries of the Mediterranean Basin during the last three decades where it attacks palm trees. During the last three decades, multiple introductions of RPW to the Middle East, Europe and Caribbean （Island of Curacao, Netherland Antilles）, Lebanon and United States of America （Laguna Beach, Orange County, California） （USA） have occurred and the RPW is now a serious pest of many palm species. Duration of all life parameters varies significantly where the entire life cycle takes about 45 to 298 days. Different artificial diets were developed and were tested for mass rearing of RPW. Control of RPW is difficult due to the concealed nature of the life cycle of the pest. Integrated Pest Management （IPM） strategy has been applied successfully to deal with RPW problem. The IPM strategy consists of various preventive and curative methods; those methods were categorized in nine categories in this review. The main objective of this work was to review the existing knowledge on RPW＇s different aspects, with an ultimate aim of revealing the actual situation of the research on RPW.展开更多
Chilo iridescent virus (CIV) is the type species for genus Iridovirus, and belongs to the family Iridoviridae. Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure. The v...Chilo iridescent virus (CIV) is the type species for genus Iridovirus, and belongs to the family Iridoviridae. Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure. The virions contain a single linear ds DNA molecule that is circularly permuted and terminally redundant. The genome of CIV has been entirely sequenced. The CIV virion consists of an unusual three-layer structure containing an outer proteinaceous capsid, an intermediate lipid membrane, and a core DNA-protein complex containing the genome. CIV has a broad host spectrum and has, in general, a limited mortality effect on its hosts. Up to now there have been several studies about CIV describing its structure, ecology, and molecular biology. In this review study we present all these studies together to describe the CIV.展开更多
Zonal distribution and population biology of llyoplaxfrater were studied in a mangrove mudflat area of Pakistan. The crabs were collected from Korangi creek through transect and quadrat method from low tide level to h...Zonal distribution and population biology of llyoplaxfrater were studied in a mangrove mudflat area of Pakistan. The crabs were collected from Korangi creek through transect and quadrat method from low tide level to high tide level. Two transects were delimited in a mangrove area of Korangi creek （24°79′N/67°20′E）. On each transect, three 0.25 m quadrats were sampled at three tidal levels on a monthly basis during low tide periods from March 2001 to February 2002. A total of 1124 crabs were obtained, of which 482 were males and 642 were females. Density of crabs varied between 0 and 90/m^2. The density and size distribution varied and showed significant differences from low to high tide level, and were positively correlated with the percent moisture, percent organic matter and sediment grain size. The carapace width （CW） ranged from 2.5 to 11.5 mm for male and 2.5 to 11.0 mm for female and was not significantly different. The overall sex ratio did not differ significantly from the expected 1：1 throughout the year in small crabs but was significantly different in adult crabs （Z2 = 49.73） with more male crabs, Size frequency distribution showed recruitment of juvenile crabs （〈 4 mm） nearly throughout the year except during June and July. Presence of ovigerous females in all months with seasonal peaks in September, October, December and May indicates seasonal continuous breeding. Weight of egg mass increases with weight of ovigerous females and show positive linear relationship. The estimated mean diameter of egg was 2.83±0.25μm, and the average number of eggs was 3065±902.展开更多
Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new...Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new generation of deep sequencing technologies, and faster and better computational and modeling approaches have opened new frontiers for both systems biologists and developmental biologists to reexamine the old developmental biology questions, such as pattern formation, and to tackle new problems, such as stem cell reprogramming. As showcased in the International Developmental Systems Biology Symposium organized by Chinese Academy of Sciences, developmental systems biology is flourishing in many perspectives, from the evolution of developmental systems, to the underlying genetic and molecular pathways and networks, to the genomic, epigenomic and noncoding levels, to the computational analysis and modeling. We believe that the field will continue to reap rewards into the future with these new approaches.展开更多
Safety assessment of genetically modified organisms (GMOs) is a contentious topic. Proponents of GMOs assert that GMOs are safe since the FDA’s policy of substantial equivalence considers GMOs “equivalent” to their...Safety assessment of genetically modified organisms (GMOs) is a contentious topic. Proponents of GMOs assert that GMOs are safe since the FDA’s policy of substantial equivalence considers GMOs “equivalent” to their non-GMO counterparts, and argue that genetic modification (GM) is simply an extension of a “natural” process of plant breeding, a form of “genetic modification”, though done over longer time scales. Anti-GMO activists counter that GMOs are unsafe since substantial equivalence is unscientific and outdated since it originates in the 1970s to assess safety of medical devices, which are not comparable to the complexity of biological systems, and contend that targeted GM is not plant breeding. The heart of the debate appears to be on the methodology used to determine criteria for substantial equivalence. Systems biology, which aims to understand complexity of the whole organism, as a system, rather than just studying its parts in a reductionist manner, may provide a framework to determine appropriate criteria, as it recognizes that GM, small or large, may affect emergent properties of the whole system. Herein, a promising computational systems biology method couples known perturbations on five biomolecules caused by the CP4 EPSPS GM of Glycine max L. (soybean), with an integrative model of C1 metabolism and oxidative stress (two molecular systems critical to plant function). The results predict significant accumulation of formaldehyde and concomitant depletion of glutathione in the GMO, suggesting how a “small” and single GM creates “large” and systemic perturbations to molecular systems equilibria. Regulatory agencies, currently reviewing rules for GMO safety, may wish to adopt a systems biology approach using a combination of in silico, computational methods used herein, and subsequent targeted experimental in vitro and in vivo designs, to develop a systems understanding of “equivalence” using biomarkers, such as formaldehyde and glutathione, which predict metabolic disruptions, towards modernizing the safety assessment of GMOs.展开更多
As a new interdisciplinary field,synthetic biology has led to valuable innovations in the fields of medicine,chemistry,agriculture,energy and environment.In this paper,we systematically review the development status o...As a new interdisciplinary field,synthetic biology has led to valuable innovations in the fields of medicine,chemistry,agriculture,energy and environment.In this paper,we systematically review the development status of global synthetic biology in the past six years,and make an in-depth benchmarking analysis of the field in China.With the aid of Scopus and SciVal,we analyze the scholarly output of synthetic biology in the world and individual countries,including publication distribution,popular journals and eminent institutions.Furthermore,the research focus and concepts,citation impact and collaborations are also examined using numerical index methods such as the field-weighted citation impact(FWCI)and relative activity index(RAI),showing the differences between data more intuitively.This study aims to offer a comprehensive understanding of the research status of synthetic biology in China and the world,offering a benchmarked overview of the results as a reference to guide the development of this field in the future.展开更多
Data on zooplankton from 13 high-mountain lakes of East Siberia have shown that the Holarctic copepod Cyclops scutifer Sars,1863 dominates among crustaceans.In July,its abundance comprised 64%-98%of the total plankton...Data on zooplankton from 13 high-mountain lakes of East Siberia have shown that the Holarctic copepod Cyclops scutifer Sars,1863 dominates among crustaceans.In July,its abundance comprised 64%-98%of the total plankton fauna in the pelagial of these lakes,approximately 30%in the littoral zone and10%in small northern thermokarst lakes.Biometric measurements and morphological descriptions based on scanning microscope images are supplemented by the data on its geographic distribution and phenology.展开更多
The improvements of high-throughput experimental devices such as microarray and mass spectrometry have allowed an effective acquisition of biological comprehensive data which include genome, transcriptome, proteome, a...The improvements of high-throughput experimental devices such as microarray and mass spectrometry have allowed an effective acquisition of biological comprehensive data which include genome, transcriptome, proteome, and metabolome (multi-layered omics data). In Systems Biology, we try to elucidate various dynamical characteristics of biological functions with applying the omics data to detailed mathematical model based on the central dogma. However, such mathematical models possess multi-time-scale properties which are often accompanied by time-scale differences seen among biological layers. The differences cause time stiff problem, and have a grave influence on numerical calculation stability. In the present conventional method, the time stiff problem remained because the calculation of all layers was implemented by adaptive time step sizes of the smallest time-scale layer to ensure stability and maintain calculation accuracy. In this paper, we designed and developed an effective numerical calculation method to improve the time stiff problem. This method consisted of ahead, backward, and cumulative algorithms. Both ahead and cumulative algorithms enhanced calculation efficiency of numerical calculations via adjustments of step sizes of each layer, and reduced the number of numerical calculations required for multi-time-scale models with the time stiff problem. Backward algorithm ensured calculation accuracy in the multi-time-scale models. In case studies which were focused on three layers system with 60 times difference in time-scale order in between layers, a proposed method had almost the same calculation accuracy compared with the conventional method in spite of a reduction of the total amount of the number of numerical calculations. Accordingly, the proposed method is useful in a numerical analysis of multi-time-scale models with time stiff problem.展开更多
This study advances previous efforts towards development of computational systems biology, in silico, methods for biosafety assessment of genetically modified organisms (GMOs). C1 metabolism is a critical molecular sy...This study advances previous efforts towards development of computational systems biology, in silico, methods for biosafety assessment of genetically modified organisms (GMOs). C1 metabolism is a critical molecular system in plants, fungi, and bacteria. In our previous research, critical molecular systems of C1 metabolism were identified and modeled using CytoSolve<sup>?</sup>, a platform for in silico analysis. In addition, multiple exogenous molecular systems affecting C1 metabolism such as oxidative stress, shikimic acid metabolism, glutathione biosynthesis, etc. were identified. Subsequent research expanded the C1 metabolism computational models to integrate oxidative stress, suggesting glutathione (GSH) depletion. Recent integration of data from the EPSPS genetic modification of Soy, also known as Roundup Ready Soy (RRS), with C1 metabolism predicts similar GSH depletion and HCHO accumulation in RRS. The research herein incorporates molecular systems of glutathione biosynthesis and glyphosate catabolism to expand the extant in silico models of C1 metabolism. The in silico results predict that Organic Soy will have a nearly 250% greater ratio of GSH and GSSG, a measure of glutathione levels, than in RRS that are glyphosate-treated glyphosate-resistant Soy versus the Organic Soy. These predictions also concur with in vivo greenhouse results. This concurrence suggests that these in silico models of C1 metabolism may provide a viable and validated platform for biosafety assessment of GMOs, and aid in selecting rational criteria for informing in vitro and in vivo efforts to more accurately decide in the problem formulation phase whose parameters need to be assessed so that conclusion on “substantial equivalence” or material difference of a GMO and its non-GMO counterpart can be drawn on a well-grounded basis.展开更多
基金supported by the Strategic Priority Research Program of the Chinese Academy of Sciences(Category B,XDB1090000).
文摘Plant synthetic biology has emerged as a transformative field in agriculture,offering innovative solutions to enhance food security,provide resilience to climate change,and transition to sustainable farming practices.By integrating advanced genetic tools,computational modeling,and systems biology,researchers can precisely modify plant genomes to enhance traits such as yield,stress tolerance,and nutrient use efficiency.The ability to design plants with specific characteristics tailored to diverse environmental conditions and agricultural needs holds great potential to address global food security challenges.Here,we highlight recent advancements and applications of plant synthetic biology in agriculture,focusing on key areas such as photosynthetic efficiency,nitrogen fixation,drought tolerance,pathogen resistance,nutrient use efficiency,biofortification,climate resilience,microbiology engineering,synthetic plant genomes,and the integration of artificial intelligence with synthetic biology.These innovations aim to maximize resource use efficiency,reduce reliance on external inputs,and mitigate environmental impacts associated with conventional agricultural practices.Despite challenges related to regulatory approval and public acceptance,the integration of synthetic biology in agriculture holds immense promise for creating more resilient and sustainable agricultural systems,contributing to global food security and environmental sustainability.Rigorous multi-field testing of these approaches will undoubtedly be required to ensure reproducibility.
基金supported by the National Natural Science Foundation of China(32270458,32070411,2023A1515010657)State Key Laboratory of Resource Insects(SKLSGB-ORP202209)。
文摘The domesticated silkworm(Bombyx mori)has evolved a highly efficient nitrogen utilization system to support silk production.The silk glands play a pleiotropic role in sequestering nitrogen resources for silk synthesis,mitigating aminoacidemia by assimilating free amino acids,and reallocating nitrogen during metamorphosis through programmed cell death.However,the specific functions of nitrogen metabolism-related genes in this process remain unclear.Using CRISPR/Cas9-based gene editing,mutations were generated in glutamine synthetase(GS),glutamate synthetase(GOGAT),asparagine synthetase(AS),glutamate dehydrogenase(GDH)and glutamate oxaloacetate transaminase 1(GOT1).Disruption of GS,GOGAT,and AS consistently reduced silkworm cocoon and pupal weight and significantly down-regulated silk protein gene transcription,whereas GOT1 mutation had no such effect.GOGAT mutants exhibited abnormally enlarged silk glands,whereas GS and AS mutants showed delayed programmed cell death in the silk glands.In contrast,GOT1 mutants displayed normal silk gland morphology but were consistently smaller.Disruption of GS,GOGAT,and AS led to more extensive transcriptional changes,including altered expression of transcription factors in the silk glands,compared with GOT1 mutants.Both GS and GOGAT mutants exhibited up-regulation of AS and GDH,while only GOGAT mutants displayed elevated AS enzymatic activity,suggesting that GOGAT may compete with AS for glutamine in the silk glands to support silk protein synthesis.AS mutants showed significantly elevated GOT activity and up-regulation of several metabolic pathways,indicating that AS may functionally interact with GOT in regulating both silk gland development and programmed cell death during metamorphosis.
基金supported by grants from the Italian Ministry of University and Research(MIUR)(SYSBIONET-Italian ROADMAP ESFRI Infrastructures to LA,AMC and MP IVASCOMAR-National Cluster to AMC)+5 种基金Netherlands Organization for Scientific Research(NWO)in the integrated program of WOTRO [W01.65.324.00/project 4] Science for Global DevelopmentSynpol:EU-FP7 [KBBE.2012.3.4-02#311815]Corbel:EU-H2020 [NFRADEV-4-2014-2015#654248]Epipredict:EU-H2020 MSCA-ITN-2014-ETN:Marie Sk?odowska-Curie Innovative Training Networks(ITN-ETN)[#642691]BBSRC China [BB/J020060/1] to HVWCorbel:EU-H2020 [PID 2354] to HVW and AMC
文摘The recognition that neurogenesis does not stop with adolescence has spun off research towards the reduction of brain disorders by enhancing brain regeneration. Adult neurogenesis is one of the tougher problems of developmental biology as it requires the generation of complex intracellular and pericellular anatomies, amidst the danger of neuroinflammation. We here review how a multitude of regulatory pathways optimized for early neurogenesis has to be revamped into a new choreography of time dependencies. Distinct pathways need to be regulated, ranging from neural growth factor induced differentiation to mitochondrial bioenergetics, reactive oxygen metabolism, and apoptosis. Requiring much Gibbs energy consumption, brain depends on aerobic energy metabolism, hence on mitochondrial activity. Mitochondrial fission and fusion, movement and perhaps even mitoptosis, thereby come into play. All these network processes are interlinked and involve a plethora of molecules. We recommend a deep thinking approach to adult neurobiology.
基金supported by grants from the National Key Research and Development Program of China (2019YFA0903800)the National Natural Science Foundation of China (31800719 and 21621004)。
文摘Synthetic biotechnology has led to the widespread application of genetically modified organisms(GMOs)in biochemistry, bioenergy, and therapy. However, the uncontrolled spread of GMOs may lead to genetic contamination by horizontal gene transfer, resulting in unpredictable biosafety risks. To deal with these challenges, many effective methods have been developed for biocontainment. In this article, we summarize and discuss recent advances in biocontainment strategies from three aspects: DNA replication, transcriptional regulation, and protein translation. We also briefly introduce the efforts in the biocontainment convention, such as the recent publication of the Tianjin Biosecurity Guidelines for the Code of Conduct for Scientists.
文摘In sub-Saharan Africa, foodborne Salmonella infections cause around 680,000 deaths per year. The evolutionary aspects of the incidence of antibiotic resistance in Salmonella strains no longer seem to attract much interest in the Central African Republic (CAR), although salmonellosis remains a health problem requiring national and international surveillance. Methodology: The study conducted at the National Laboratory of Clinical Biology and Public Health, Bangui, Central African Republic (LNBCSP) was a retrospective descriptive study. The study duration was five years (January 2019 to December 2023). The study sample consisted of patients who underwent bacteriological testing of stool, blood and urine samples for Salmonella at the LNBCSP in Bangui during this period. Study variables were age, sex, year and bacteriological test results. Statistical tests were used to compare incidences. Relative risks (RR) were calculated to measure the degree of association. Results: From 2019 to 2023, we recorded 353 Salmonella strains, of which 5% were found in blood, 37% in urine and 58% in stool. Patient age ranged from 1 to 86 years, with a mean of 27 ± 22.05 years and a mode of 5 years. Children aged 0 to 14 years (34%) and females (55.81%) predominated. The highest rate of contamination by Salmonella strains was 1.69% in 2022. The overall incidence of salmonellosis was 6.72 in 2019, 7.05 in 2020, 6.91 in 2021, 16.9 in 2022 and 6.26 in 2023 per 1000 samples. Resistance was 30.47% to β_lactam antibiotics, 24.22% to fluroquinolones and 37.97% to Salmonella spp. For Salmonella arizonae strains, resistance was 20.25% to aminoglycosides, 43.67% to chloramphenicol and 7.59% to imipenem. Conclusion: Laboratory-based surveillance of antibiotic resistance in Salmonella strains is needed in both human and veterinary medicine. Another study based on molecular characterization will identify new antibiotic-resistant variants circulating in CAR.
基金supported by the National Natural Science Foundation of China(31401761)the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences
文摘China experiences serious agricultural damages from rodents, and, correspondingly, researchers in China are actively studying rodent biology and management. Following the popularization of ecologically-based rodent pest management and extension of the basic state policy of Ecological Civilization Construction in China, recent efforts in rodent control technologies are mainly focused on eliminating side effects of rodenticides and developing environmentally friendly techniques. Considering ecological functions of rodents to test their interaction with the environment is a promising design for understanding rodent populations in local ecosystems and for developing ecologically-based rodent management. Using ecological phenotypes and applying advanced techniques of molecular biology, genetics, and epigenetics might be useful for illustrating the deep regulatory mechanisms of fluctuations in rodent populations. However, facing the dual characteristics of rodents as pests and their roles as keystone species in many ecosystems, it is still a challenge to establish reasonable local thresholds to balance rodent management with the negative effects of rodent control on the environment in the future.
文摘INTRODUCTIONMolecular biology has made a tremendous impact on thediagnosis and treatment of liver diseases.In particular,advances in molecular biology made possible the
文摘Objective:To present an integrated molecular biology dedicated system for tuberculosis diagnosis.Methods:One hundred and five sputum specimens from patients strongly suspected by clinical parameters of tuberculosis were studied by Ziehl-Neelsen staining,by cultivation on solid medium and by a balanced hemincsted fluorometric PCR system(Orange C3TB) that could preserve worker safety and produce a rather pure material free of potential inhibitors. DNA amplification was performed in a low cost tuberculosis termocycler-fluorotneter.Produced double stranded DNA was flurometrically detected.The whole reaction was conducted in one single tube which would not be opened after adding the processed sample in order to minimize the risk of cross contamination with amplicons.Results:The assay was able to delect 30 bacillus per sample mL with 99.8%interassay variation coefficient.PCR was positive in 23(21.9%) tested samples(21 of them were smear negative).In our study it showed a preliminary sensitivity of 94.5%for sputum and an overall specificity of 98.7%.Conclusions:Total run time of the test is 4 h with 2.5 real working time.All PCR positive samples are also positive by microbiological culture and clinical criteria.Results show that it could be a very useful tool to increase detection efficiency of tuberculosis disease in low bacilus load samples.Furthermore,its low cost and friendly using make it feasible to run in poor regions.
文摘BACKGROUND Human Wharton’s jelly-derived mesenchymal stromal/stem cells(hWJ-MSCs)have gained considerable attention in their applications in cell-based therapy due to several advantages offered by them.Recently,we reported that hWJ-MSCs and their conditioned medium have significant therapeutic radioprotective potential.This finding raised an obvious question to identify unique features of hWJ-MSCs over other sources of stem cells for a better understanding of its radioprotective mechanism.AIM To understand the radioprotective mechanism of soluble factors secreted by hWJMSCs and identification of their unique genes.METHODS Propidium iodide staining,endogenous spleen colony-forming assay,and survival study were carried out for radioprotection studies.Homeostasis-driven proliferation assay was performed for in vivo lymphocyte proliferation.Analysis of RNAseq data was performed to find the unique genes of WJ-MSCs by comparing them with bone marrow mesenchymal stem cells,embryonic stem cells,and human fibroblasts.Gene enrichment analysis and protein-protein interaction network were used for pathway analysis.RESULTS Co-culture of irradiated murine splenic lymphocytes with WJ-MSCs offered significant radioprotection to lymphocytes.WJ-MSC transplantation increased the homeostasis-driven proliferation of the lymphocytes.Neutralization of WJ-MSC conditioned medium with granulocyte-colony stimulating factor antibody abolished therapeutic radioprotection.Transcriptome analysis showed that WJ-MSCs share several common genes with bone marrow MSCs and embryonic stem cells and express high levels of unique genes such as interleukin(IL)1-α,IL1-β,IL-6,CXCL3,CXCL5,CXCL8,CXCL2,CCL2,FLT-1,and IL-33.It was also observed that WJ-MSCs preferentially modulate several cellular pathways and processes that handle the repair and regeneration of damaged tissues compared to stem cells from other sources.Cytokine-based network analysis showed that most of the radiosensitive tissues have a more complex network for the elevated cytokines.CONCLUSION Systemic infusion of WJ-MSC conditioned media will have significant potential for treating accidental radiation exposed victims。
基金supported by the National Key Research and Development Program of China[2019YFA09005000 to J.Z.]Shenzhen Science and Technology Program[ZDSYS20210623091810032 to J.Z.].
文摘Future agricultural development needs to solve the food security crisis caused by the global food shortage and the environmental demand for green and sustainable technology.The vigorous development of synthetic biology has brought new opportunities for modern agriculture.Synthetic biology can transform crops'metabolic pathways and genetic information and involves microorganisms'application in agriculture.Therefore,it has bright prospects in crop breeding and yield increase and ensuring the safety of the agricultural production environment.This perspective summarizes the application status and future development of synthetic biology in agriculture from the aspects of plant breeding,photosynthetic system,nitrogen fixation,and microorganisms.
文摘The Red Palm Weevil （RPW）, Rhynchophorus ferrugineus （Olivier）, （Coleoptera, Curculionidae, Rhynchophorinae）, is an invasive species that is originated from Southeast Asia. It has.invaded Middle East and several countries of the Mediterranean Basin during the last three decades where it attacks palm trees. During the last three decades, multiple introductions of RPW to the Middle East, Europe and Caribbean （Island of Curacao, Netherland Antilles）, Lebanon and United States of America （Laguna Beach, Orange County, California） （USA） have occurred and the RPW is now a serious pest of many palm species. Duration of all life parameters varies significantly where the entire life cycle takes about 45 to 298 days. Different artificial diets were developed and were tested for mass rearing of RPW. Control of RPW is difficult due to the concealed nature of the life cycle of the pest. Integrated Pest Management （IPM） strategy has been applied successfully to deal with RPW problem. The IPM strategy consists of various preventive and curative methods; those methods were categorized in nine categories in this review. The main objective of this work was to review the existing knowledge on RPW＇s different aspects, with an ultimate aim of revealing the actual situation of the research on RPW.
文摘Chilo iridescent virus (CIV) is the type species for genus Iridovirus, and belongs to the family Iridoviridae. Since the discovery of CIV in 1966, many attempts were made to elucidate the viral genome structure. The virions contain a single linear ds DNA molecule that is circularly permuted and terminally redundant. The genome of CIV has been entirely sequenced. The CIV virion consists of an unusual three-layer structure containing an outer proteinaceous capsid, an intermediate lipid membrane, and a core DNA-protein complex containing the genome. CIV has a broad host spectrum and has, in general, a limited mortality effect on its hosts. Up to now there have been several studies about CIV describing its structure, ecology, and molecular biology. In this review study we present all these studies together to describe the CIV.
基金funded by the Pakistan Science Foundation project PSF/Res/S-KU/Envr(51) grant to NAQ
文摘Zonal distribution and population biology of llyoplaxfrater were studied in a mangrove mudflat area of Pakistan. The crabs were collected from Korangi creek through transect and quadrat method from low tide level to high tide level. Two transects were delimited in a mangrove area of Korangi creek （24°79′N/67°20′E）. On each transect, three 0.25 m quadrats were sampled at three tidal levels on a monthly basis during low tide periods from March 2001 to February 2002. A total of 1124 crabs were obtained, of which 482 were males and 642 were females. Density of crabs varied between 0 and 90/m^2. The density and size distribution varied and showed significant differences from low to high tide level, and were positively correlated with the percent moisture, percent organic matter and sediment grain size. The carapace width （CW） ranged from 2.5 to 11.5 mm for male and 2.5 to 11.0 mm for female and was not significantly different. The overall sex ratio did not differ significantly from the expected 1：1 throughout the year in small crabs but was significantly different in adult crabs （Z2 = 49.73） with more male crabs, Size frequency distribution showed recruitment of juvenile crabs （〈 4 mm） nearly throughout the year except during June and July. Presence of ovigerous females in all months with seasonal peaks in September, October, December and May indicates seasonal continuous breeding. Weight of egg mass increases with weight of ovigerous females and show positive linear relationship. The estimated mean diameter of egg was 2.83±0.25μm, and the average number of eggs was 3065±902.
基金the China National Science Foundation (NSF) (No. 30588001, 30620120433)National Basic Research Program of China (No. 2006CB910700)funds from the Chinese Acad-emy of Sciences to J.-D.J.H. and NSF fellowship to T.A.
文摘Organism development is a systems level process. It has benefited greatly from the recent technological advances in the field of systems biology. DNA microarray, phenome, interactome and transcriptome mapping, the new generation of deep sequencing technologies, and faster and better computational and modeling approaches have opened new frontiers for both systems biologists and developmental biologists to reexamine the old developmental biology questions, such as pattern formation, and to tackle new problems, such as stem cell reprogramming. As showcased in the International Developmental Systems Biology Symposium organized by Chinese Academy of Sciences, developmental systems biology is flourishing in many perspectives, from the evolution of developmental systems, to the underlying genetic and molecular pathways and networks, to the genomic, epigenomic and noncoding levels, to the computational analysis and modeling. We believe that the field will continue to reap rewards into the future with these new approaches.
文摘Safety assessment of genetically modified organisms (GMOs) is a contentious topic. Proponents of GMOs assert that GMOs are safe since the FDA’s policy of substantial equivalence considers GMOs “equivalent” to their non-GMO counterparts, and argue that genetic modification (GM) is simply an extension of a “natural” process of plant breeding, a form of “genetic modification”, though done over longer time scales. Anti-GMO activists counter that GMOs are unsafe since substantial equivalence is unscientific and outdated since it originates in the 1970s to assess safety of medical devices, which are not comparable to the complexity of biological systems, and contend that targeted GM is not plant breeding. The heart of the debate appears to be on the methodology used to determine criteria for substantial equivalence. Systems biology, which aims to understand complexity of the whole organism, as a system, rather than just studying its parts in a reductionist manner, may provide a framework to determine appropriate criteria, as it recognizes that GM, small or large, may affect emergent properties of the whole system. Herein, a promising computational systems biology method couples known perturbations on five biomolecules caused by the CP4 EPSPS GM of Glycine max L. (soybean), with an integrative model of C1 metabolism and oxidative stress (two molecular systems critical to plant function). The results predict significant accumulation of formaldehyde and concomitant depletion of glutathione in the GMO, suggesting how a “small” and single GM creates “large” and systemic perturbations to molecular systems equilibria. Regulatory agencies, currently reviewing rules for GMO safety, may wish to adopt a systems biology approach using a combination of in silico, computational methods used herein, and subsequent targeted experimental in vitro and in vivo designs, to develop a systems understanding of “equivalence” using biomarkers, such as formaldehyde and glutathione, which predict metabolic disruptions, towards modernizing the safety assessment of GMOs.
基金financially supported by the National Natural Science Foundation of China (21776209, 21621004 and 21776208)Ministry of Education of the People’s Republic of China Humanities and Social Sciences Youth Foundation (21YJCZH232)the Natural Science Foundation of Tianjin City (No. 19JCYBJC21100)
文摘As a new interdisciplinary field,synthetic biology has led to valuable innovations in the fields of medicine,chemistry,agriculture,energy and environment.In this paper,we systematically review the development status of global synthetic biology in the past six years,and make an in-depth benchmarking analysis of the field in China.With the aid of Scopus and SciVal,we analyze the scholarly output of synthetic biology in the world and individual countries,including publication distribution,popular journals and eminent institutions.Furthermore,the research focus and concepts,citation impact and collaborations are also examined using numerical index methods such as the field-weighted citation impact(FWCI)and relative activity index(RAI),showing the differences between data more intuitively.This study aims to offer a comprehensive understanding of the research status of synthetic biology in China and the world,offering a benchmarked overview of the results as a reference to guide the development of this field in the future.
基金Supported by the Projects"Modem state,biodiversity and ecology of the shore zone of Baikal"(VI.51.1.10)(2013-2016)the "Dynamics of natural and natural-human systems to climate change and anthropogenic pressures(for example,Trans-Baikal)"(Ⅷ.79.1.2)(2013-2016)
文摘Data on zooplankton from 13 high-mountain lakes of East Siberia have shown that the Holarctic copepod Cyclops scutifer Sars,1863 dominates among crustaceans.In July,its abundance comprised 64%-98%of the total plankton fauna in the pelagial of these lakes,approximately 30%in the littoral zone and10%in small northern thermokarst lakes.Biometric measurements and morphological descriptions based on scanning microscope images are supplemented by the data on its geographic distribution and phenology.
文摘The improvements of high-throughput experimental devices such as microarray and mass spectrometry have allowed an effective acquisition of biological comprehensive data which include genome, transcriptome, proteome, and metabolome (multi-layered omics data). In Systems Biology, we try to elucidate various dynamical characteristics of biological functions with applying the omics data to detailed mathematical model based on the central dogma. However, such mathematical models possess multi-time-scale properties which are often accompanied by time-scale differences seen among biological layers. The differences cause time stiff problem, and have a grave influence on numerical calculation stability. In the present conventional method, the time stiff problem remained because the calculation of all layers was implemented by adaptive time step sizes of the smallest time-scale layer to ensure stability and maintain calculation accuracy. In this paper, we designed and developed an effective numerical calculation method to improve the time stiff problem. This method consisted of ahead, backward, and cumulative algorithms. Both ahead and cumulative algorithms enhanced calculation efficiency of numerical calculations via adjustments of step sizes of each layer, and reduced the number of numerical calculations required for multi-time-scale models with the time stiff problem. Backward algorithm ensured calculation accuracy in the multi-time-scale models. In case studies which were focused on three layers system with 60 times difference in time-scale order in between layers, a proposed method had almost the same calculation accuracy compared with the conventional method in spite of a reduction of the total amount of the number of numerical calculations. Accordingly, the proposed method is useful in a numerical analysis of multi-time-scale models with time stiff problem.
文摘This study advances previous efforts towards development of computational systems biology, in silico, methods for biosafety assessment of genetically modified organisms (GMOs). C1 metabolism is a critical molecular system in plants, fungi, and bacteria. In our previous research, critical molecular systems of C1 metabolism were identified and modeled using CytoSolve<sup>?</sup>, a platform for in silico analysis. In addition, multiple exogenous molecular systems affecting C1 metabolism such as oxidative stress, shikimic acid metabolism, glutathione biosynthesis, etc. were identified. Subsequent research expanded the C1 metabolism computational models to integrate oxidative stress, suggesting glutathione (GSH) depletion. Recent integration of data from the EPSPS genetic modification of Soy, also known as Roundup Ready Soy (RRS), with C1 metabolism predicts similar GSH depletion and HCHO accumulation in RRS. The research herein incorporates molecular systems of glutathione biosynthesis and glyphosate catabolism to expand the extant in silico models of C1 metabolism. The in silico results predict that Organic Soy will have a nearly 250% greater ratio of GSH and GSSG, a measure of glutathione levels, than in RRS that are glyphosate-treated glyphosate-resistant Soy versus the Organic Soy. These predictions also concur with in vivo greenhouse results. This concurrence suggests that these in silico models of C1 metabolism may provide a viable and validated platform for biosafety assessment of GMOs, and aid in selecting rational criteria for informing in vitro and in vivo efforts to more accurately decide in the problem formulation phase whose parameters need to be assessed so that conclusion on “substantial equivalence” or material difference of a GMO and its non-GMO counterpart can be drawn on a well-grounded basis.
