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Identific tion of quantitative trait loci and associated candidate genes for pregnancy success in Angus–Brahman crossbred heifers

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Journal of Animal Science and Biotechnology 2024年第1期15卷 162-170页

作者： Quinn A.Hoorn Gabriel A.Zayas Eduardo E.Rodriguez Laura M.Jensen Raluca G.Mateescu Peter J.Hansen Department of Animal Sciences Donald Henry Barron Reproductive and Perinatal Biology Research Programand the Genetics InstituteUniversity of FloridaGainesvilleFLUSA School of Applied systems biology La Trobe UniversityBundooraVIC 3083Australia

Background In beef cattle, more than 50% of the energy input to produce a unit of beef is consumed by the female that produced the calf. Development of genomic tools to identify females with high genetic merit for reproductive function could increase the profitability and sustainability of beef *** Genome-wide association studies(GWAS) were performed using a single-step genomic best linear unbiased prediction approach on pregnancy outcome traits from a population of Angus–Brahman crossbred heifers. Furthermore, a validation GWAS was performed using data from another farm. Heifers were genotyped with the Bovine GGP F250 array that contains 221,077 SNPs. In the discovery population, heifers were bred in winter breeding seasons involving a single round of timed artificial insemination(AI) followed by natural mating for 3 months. Two phenotypes were analyzed: pregnancy outcome to first-service AI(PAI;n = 1,481) and pregnancy status at the end of the breeding season(PEBS;n = 1,725). The heritability was estimated as 0.149 and 0.122 for PAI and PEBS, respectively. In the PAI model, one quantitative trait locus(QTL), located between 52.3 and 52.5 Mb on BTA7, explained about 3% of the genetic variation, in a region containing a cluster of γ-protocadherin genes and SLC25A2. Other QTLs explaining between 0.5% and 1% of the genetic variation were found on BTA12 and 25. In the PEBS model, a large QTL on BTA7 was synonymous with the QTL for PAI, with minor QTLs located on BTA5, 9, 10, 11, 19, and 20. The validation population for pregnancy status at the end of the breeding season were Angus–Brahman crossbred heifers bred by natural mating. In concordance with the discovery population, the large QTL on BTA7 and QTLs on BTA10 and 12 were *** In summary, QTLs and candidate SNPs identified were associated with pregnancy outcomes in beef heifers, including a large QTL associated with a group of protocadherin genes. Confirmation of these associations

关键词： Beef cattle Fertility GWAS QTL

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Brain-inspired chaotic spiking backpropagation

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National Science Review 2024年第6期11卷 169-179页

作者： Zijian Wang Peng Tao Luonan Chen Key Laboratory of systems Health Science of Zhejiang Province School of Life ScienceHangzhou Institute for Advanced StudyUniversity of Chinese Academy of Sciences Key Laboratory of systems biology Shanghai Institute of Biochemistry and Cell Biology Center for Excellence in Molecular Cell Science Chinese Academy of Sciences Guangdong Institute of Intelligence Science and Technology Pazhou Laboratory(Huangpu)

Spiking neural networks(SNNs) have superior energy efficiency due to their spiking signal transmission,which mimics biological nervous systems, but they are difficult to train effectively. Although surrogate gradient-based methods offer a workable solution, trained SNNs frequently fall into local minima because they are still primarily based on gradient dynamics. Inspired by the chaotic dynamics in animal brain learning, we propose a chaotic spiking backpropagation(CSBP) method that introduces a loss function to generate brain-like chaotic dynamics and further takes advantage of the ergodic and pseudo-random nature to make SNN learning effective and robust. From a computational viewpoint, we found that CSBP significantly outperforms current state-of-the-art methods on both neuromorphic data sets(***-CIFAR10 and DVS-Gesture) and large-scale static data sets(e.g. CIFAR100 and Image Net) in terms of accuracy and robustness. From a theoretical viewpoint, we show that the learning process of CSBP is initially chaotic, then subject to various bifurcations and eventually converges to gradient dynamics,consistently with the observation of animal brain activity. Our work provides a superior core tool for direct SNN training and offers new insights into understanding the learning process of a biological brain.

关键词： spiking neural networks surrogate gradient local minima backpropagation brain-inspired learning chaos

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Inter-chromosomal insertions into wild-type chromosomes induced by SCRaMbLE

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Frontiers of Chemical Science and Engineering 2024年第9期18卷 125-135页

作者： Sijie Zhou Junyanrui Li Xichen Cui Ying Wang Ying-Jin Yuan Frontiers Science Center for Synthetic biology and Key Laboratory of systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin 300072China Frontiers Research Institute for Synthetic biology Tianjin UniversityTianjin 300072China

Genomic rearrangements play a crucial role in shaping biological phenotypic diversity and driving species *** chromosome rearrangement and modification by LoxP-mediated evolution(SCRaMbLE)has been applied to explore large-scale genomic rearrangements,yet it has been observed that these rearrangements occur exclusively in genomic regions containing loxPsym ***,we found that SCRaMbLE of synthetic yeast harboring synthetic chromosome V and X can generate a variety of synthetic segment insertions into wild-type chromosomes,ranging from 1 to 300 ***,it was revealed that the novel insertions impacted the transcriptional level of neighboring regions and affected the production of exemplar pathway of ***,our results improve the understanding of the ability of SCRaMbLE to generate complex structural variations in nonsynthetic regions and provide a potential model to explore genomic transposable events.

关键词： genomic rearrangements synthetic yeast genome SCRaMbLE inter-chromosomal insertions synthetic biology

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A sphingolipid message promotes neuronal health across generations

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Neural Regeneration Research 2024年第11期19卷 2325-2326页

作者： Wenyue Wang Roger Pocock Development and Stem Cells program Monash Biomedicine Discovery Institute and Department of Anatomy and Developmental BiologyMonash UniversityMelbourneVICAustralia

Maternal nutrition can affect brain function of offspring in later life(Fitzgerald et al.,2020).Emerging studies have also shown that the maternal environment can modify susceptibility to neurodegenerative disease(Boots et al.,2023).Transmission of environmental information from mother to offspring depends on maternal nutrient *** the nematode Caenorhabditis elegans,maternal yolk,which is synthesized in the intestine and transferred to nourish oocytes and early embryos,can provide extranuclear inheritance factors to mediate phenotypic plasticity across ***,the molecular mechanisms of regulating such intergenerational effects remain largely unknown.

关键词： mother intestine transferred

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Identification of crucial roles of transcription factor IhfA on high production of free fatty acids in Escherichia coli

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Synthetic and systems Biotechnology 2024年第1期9卷 144-151页

作者： Lixia Fang Ziyi Han Xueru Feng Xueyan Hao Mengxiao Liu Hao Song Yingxiu Cao Frontiers Science Center for Synthetic biology and Key Laboratory of systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China Frontiers Research Institute for Synthetic biology Tianjin UniversityChina

Transcription factor engineering has unique advantages in improving the performance of microbial cell factories due to the global regulation of gene *** analyses and reverse engineering enable learning and subsequent incorporation of novel design strategies for further ***,we identify the role of the global regulator IhfA for overproduction of free fatty acids(FFAs)using CRISPRi-facilitated reverse engineering and cellular physiological *** the differentially expressed genes in the ihfAL􀀀strain,a total of 14 beneficial targets that enhance FFAs production by above 20% are identified,which involve membrane function,oxidative stress,and *** membrane-related genes,the engineered strains obtain lower cell surface hydrophobicity and increased average length of membrane lipid *** oxidative stress-related genes,the engineered strains present decreased reactive oxygen species(ROS)*** gene modulations enhance cellular robustness and save cellular resources,contributing to FFAs *** study provides novel targets and strategies for engineering microbial cell factories with improved FFAs bioproduction.

关键词： Free fatty acids CRISPRi ihfA Cell membrane ROS

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Recent progress in MOFs-based nanozymes for biosensing

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Nano Research 2024年第1期17卷 39-64页

作者： Imamdin Chandio Yongjian Ai Lei Wu Qionglin Liang MOE Key Laboratory of Bioorganic Phosphorus Chemistry&Chemical biology Department of ChemistryLaboratory of Flexible Electronics TechnologyCenter for Synthetic and Systems BiologyTsinghua University-Peking University Joint Centre for Life SciencesTsinghua UniversityBeijing 100084China

Nanozymes are nanomaterials with enzyme-mimicking catalytic *** to natural enzymes,nanozymes show various properties such as easy to manufacture,stable,adjustable,and *** play key roles in biosensing,biocatalysis,and disease *** an important kind of nanozymes,metal-organic framework(MOF)-based nanozymes are receiving a lot of attention due to their structural properties and *** developing MOF with enzymes-like catalytic properties has opened new perspectives in *** review summarizes the up-to-date developments in synthesizing two-dimensional and three-dimensional MOF-based nanozymes and their applications in ***,classification of nanozymes obtained by MOFs is categorized,and different properties of MOF-based nanozymes are ***,the distinctive applications of MOF-based nanozymes in identifying various analytes are thoroughly ***,the recent challenges and progressive directions in this area are highlighted.

关键词： metal-organic frameworks nanozymes metal-organic framework (MOF)-based nanozymes biosensing analytes

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Biotransformation of ethylene glycol by engineered Escherichia coli

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Synthetic and systems Biotechnology 2024年第3期9卷 531-539页

作者： Wenlong Yan Xinhua Qi Zhibei Cao Mingdong Yao Mingzhu Ding Yingjin Yuan Frontiers Science Center for Synthetic biology and Key Laboratory of systems Bioengineering(Ministry of Education) School of Chemical Engineering and TechnologyTianjin UniversityTianjin300072China Frontiers Research Institute for Synthetic biology Tianjin UniversityTianjin300072China

There has been extensive research on the biological recycling of PET waste to address the issue of plastic waste pollution,with ethylene glycol(EG)being one of the main components recovered from this ***,finding ways to convert PET monomer EG into high-value products is crucial for effective PET waste *** this study,we successfully engineered Escherichia coli to utilize EG and produce glycolic acid(GA),expecting to facilitate the biological recycling of PET *** engineered ***,able to utilize 10 g/L EG to produce 1.38 g/L GA within 96 h,was initially ***,strategies based on overexpression of key enzymes and knock-out of the competing pathways are employed to enhance EG utilization along with GA *** engineered ***,characterized by the highest GA production titer and substrate conversion rate,was *** GA titer increased to 5.1 g/L with a yield of 0.75 g/g EG,which is the highest level in the shake flake *** level analysis and metabolomic analysis were then conducted,revealing that overexpression of key enzymes and knock-out of the competing pathways improved the metabolic flow in the EG *** improved metabolic flow also leads to accelerated synthesis and metabolism of amino acids.

关键词： PET biological recycling Ethylene glycol utilization Glycolic acid production Escherichia coli Synthetic biology Metabolomics analysis

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Bringing CAM photosynthesis to the table:Paving the way for resilient and productive agricultural systems in a changing climate

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Plant Communications 2024年第3期5卷 17-30页

作者： Noe´Perron Matias Kirst Sixue Chen Plant Molecular and Cellular biology program University of FloridaGainesvilleFL 32608USA School of Forest Fisheries and Geomatics SciencesUniversity of FloridaGainesvilleFL 32603USA Department of biology University of MississippiOxfordMS 38677-1848USA

Modern agricultural systems are directly threatened by global climate change and the resulting freshwater crisis.A considerable challenge in the coming years will be to develop crops that can cope with the conse-quences of declining freshwater resources and changing *** approach to meeting this chal-lenge may lie in our understanding of plant photosynthetic adaptations and water use *** from various taxa have evolved crassulacean acid metabolism(CAM),a water-conserving adaptation of photosynthetic carbon dioxidexation that enables plants to thrive under semi-arid or seasonally drought-prone *** past research on CAM has led to a better understanding of the inner workings of plant resilience and adaptation to stress,successful introduction of this pathway into C3 or C4 plants has not been *** recent revolution in molecular,systems,and synthetic biology,as well as innovations in high-throughput data generation and mining,creates new opportunities to uncover the minimum genetic tool kit required to introduce CAM traits into drought-sensitive ***,we pro-pose four complementary research avenues to uncover this tool ***,genomes and computational methods should be used to improve understanding of the nature of variations that drive CAM ***,single-cell’omics technologies offer the possibility for in-depth characterization of the mecha-nisms that trigger environmentally controlled CAM ***,the rapid increase in new’omics data enables a comprehensive,multimodal exploration of ***,the expansion of functional geno-mics methods is paving the way for integration of CAM into farming systems.

关键词： CAM photosynthesis single-cell genomics phylogenetics crop engineering synthetic biology stress resilience

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Rational surface charge engineering of haloalkane dehalogenase for boosting the enzymatic performance in organic solvent solutions

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Chinese Journal of Chemical Engineering 2024年第1期65卷 276-285页

作者： Yin Wu Yan Sun Department of Biochemical Engineering School of Chemical Engineering and Technology and Key Laboratory of Systems Bioengineering and Frontiers Science Center for Synthetic Biology(Ministry of Education)Tianjin UniversityTianjin 300350China

Biocatalysis in organic solvents(OSs)has numerous important applications,but native enzymes in OSs often exhibit limited catalytic ***,we proposed a computation-aided surface charge engineering strategy to improve the catalytic performance of haloalkane dehalogenase DhaA in OSs based on the energetic analysis of substrate binding to the DhaA *** variants with enhanced OS resistance were obtained by replacing negative charged residues on the surface with positive charged residue(Arg).Particularly,a four-substitution variant E16R/E93R/E121R/E257R exhibited the best catalytic performance(five-fold improvement in OS resistance and seven-fold half-life increase in 40%(vol)dimethylsulfoxide).As a result,the overall catalytic performance of the variant could be at least 26 times higher than the wild-type *** spectroscopy and molecular dynamics simulation studies revealed that the residue substitution mainly enhanced OS resistance from four aspects:(a)improved the overall structural stability,(b)increased the hydrophobicity of the local microenvironment around the catalytic triad,(c)enriched the hydrophobic substrate around the enzyme molecule,and(d)lowered the contact frequency between OS molecules and the catalytic *** findings validate that computationaided surface charge engineering is an effective and ingenious rational strategy for tailoring enzyme performance in OSs.

关键词： Surface charge engineering Organic solvent resistance Molecular dynamics simulation Haloalkane dehalogenase

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Refining biome labeling for large-scale microbial community samples:Leveraging neural networks and transfer learning

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Environmental Science and Ecotechnology 2024年第1期17卷 128-137页

作者： Nan Wang Teng Wang Kang Ning Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imagingCenter of AI BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan430074HubeiChina

Microbiome research has generated an extensive amount of data,resulting in a wealth of publicly accessible *** annotation of these samples is crucial for effectively utilizing microbiome data across scientific ***,a notable challenge arises from the lack of essential annotations,particularly regarding collection location and sample biome information,which significantly hinders environmental microbiome *** this study,we introduce Meta-Sorter,a novel approach utilizing neural networks and transfer learning,to enhance biome labeling for thousands of microbiome samples in the MGnify database that have incomplete *** findings demonstrate that Meta-Sorter achieved a remarkable accuracy rate of 96.7%in classifying samples among the 16,507 lacking detailed biome ***,Meta-Sorter provides precise classifications for representative environmental samples that were previously ambiguously labeled as“Marine”in MGnify,thereby elucidating their specific origins in benthic and water column ***,Meta-Sorter effectively distinguishes samples derived from human-environment interactions,enabling clear differentiation between environmental and human-related *** improving the completeness of biome label information for numerous microbial community samples,our research facilitates more accurate knowledge discovery across diverse disciplines,with particular implications for environmental research.

关键词： Microbial community Transfer learning Sample classification Environmental scientific research Novel knowledge discovery

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