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The Application of Nicotiana benthamiana as a Transient Expression Host to Clone the Coding Sequences of Plant Genes
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作者 Jianzhong Huang Peng Jia +3 位作者 Xiaoju Zhong Xiuying Guan Hongbin Zhang Honglei Ruan 《American Journal of Molecular Biology》 CAS 2024年第2期54-65,共12页
Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using co... Coding sequences (CDS) are commonly used for transient gene expression, in yeast two-hybrid screening, to verify protein interactions and in prokaryotic gene expression studies. CDS are most commonly obtained using complementary DNA (cDNA) derived from messenger RNA (mRNA) extracted from plant tissues and generated by reverse transcription. However, some CDS are difficult to acquire through this process as they are expressed at extremely low levels or have specific spatial and/or temporal expression patterns in vivo. These challenges require the development of alternative CDS cloning technologies. In this study, we found that the genomic intron-containing gene coding sequences (gDNA) from Arabidopsis thaliana, Oryza sativa, Brassica napus, and Glycine max can be correctly transcribed and spliced into mRNA in Nicotiana benthamiana. In contrast, gDNAs from Triticum aestivum and Sorghum bicolor did not function correctly. In transient expression experiments, the target DNA sequence is driven by a constitutive promoter. Theoretically, a sufficient amount of mRNA can be extracted from the N. benthamiana leaves, making it conducive to the cloning of CDS target genes. Our data demonstrate that N. benthamiana can be used as an effective host for the cloning CDS of plant genes. 展开更多
关键词 Coding sequence Genomic sequence Nicotiana benthamiana Plant Genes
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The Upper Jurassic sediments,Marib-Shabwa Basin,Yemen:Lithofacies aspects and sequence stratigraphic analysis
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作者 Mohammed Albaroot Mohamed M.Elhossainy +2 位作者 Nabil M.Al-Areeq Emad A.Abdullah Abdelhamid M.Salman 《Energy Geoscience》 EI 2024年第1期342-357,共16页
The present study is devoted to understanding the evolution of the Upper Jurassic Sab'atayn Formation in the Marib-Shabwa Basin,Yemen,through a sequence stratigraphic analysis based on integrating datasets of sedi... The present study is devoted to understanding the evolution of the Upper Jurassic Sab'atayn Formation in the Marib-Shabwa Basin,Yemen,through a sequence stratigraphic analysis based on integrating datasets of sedimentology,seismic sections,and well logs.The Sab'atayn Formation(Tithonian age)is represented by a series of clastic and evaporites that were deposited under fluvio-deltaic to prodeltaic settings.It is divided into four members including Yah(at the base),upwards to Seen,Alif,and Safir at the top.Two third-order depositional sequences were determined for the Tithonian succession which were separated by three sequence boundaries.These sequences were classified into their systems tracts signifying several sedimentation patterns of progradational,aggradational,and retrogradational parasequence sets.The first depositional sequence corresponds to the early-middle Tithonian Yah and Seen units that can be classified into lowstand,transgressive,and highstand systems tracts.The second sequence comprises the late Tithonian Alif unit that can be subdivided into transgressive and highstand systems tracts.The sandy deposits of the Alif Member(highstand deposits)represent the most productive hydrocarbon reservoir in the basin.The Upper Jurassic sediments in the study area were resulted from a combination of eustatic and tectonic effects. 展开更多
关键词 sequence stratigraphy Sandstone reservoir Well logs Upper Jurassic Marib-Shabwa Basin Yemen
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Innovative Methods of Synthesis and Characterization for Molecularly Imprinted Polymers
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作者 Youyao Luo 《Open Journal of Applied Sciences》 2024年第9期2559-2579,共21页
The characterization of these molecularly imprinted polymers is essential to understanding their binding dynamics and structural properties. Through the analysis of the current research, it is found that there are ove... The characterization of these molecularly imprinted polymers is essential to understanding their binding dynamics and structural properties. Through the analysis of the current research, it is found that there are overlaps in the methods used by scholars. The Langmuir equation is frequently applied to model the adsorption isotherms of MIPs, providing critical insight into the capacity and affinity of the binding sites. Infrared Spectroscopy (IR) plays a crucial role in identifying the functional groups involved in the imprinting process and confirming the successful formation of specific binding sites. UV-visible spectrophotometry is employed to monitor the absorption characteristics of the polymers, offering data on the interactions between the template molecules and the polymer matrix. Transmission Electron Microscopy (TEM) provides detailed visualization of the internal structure of MIPs at the nanoscale, revealing the morphology and size of the imprinted cavities. Thermogravimetric Analysis (TGA) assesses the thermal stability and composition of the polymers, identifying decomposition patterns that are indicative of the material’s robustness under different conditions. Finally, the Laser Particle Size Analyzer is used to measure the size distribution of the polymer particles, which is critical for determining the uniformity and efficiency of the imprinting process. The six characterization methods discussed in this paper provide a comprehensive understanding of MIP, and it is hoped that in the future, more optimized design solutions will emerge and their applications in various fields will be enhanced. 展开更多
关键词 Molecularly imprinted Polymers Langmuir Equation Infrared Spectroscopy UV Visible Spectrophotometry Transmission Electron Microscopy
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Mitochondrial targeting sequence of magnetoreceptor MagR:More than just targeting 被引量:2
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作者 Yanqi Zhang Peng Zhang +10 位作者 Junjun Wang Jing Zhang Tianyang Tong Xiujuan Zhou Yajie Zhou Mengke Wei Chuanlin Feng Jinqian Li Xin Zhang Can Xie Tiantian Cai 《Zoological Research》 SCIE CSCD 2024年第3期468-477,共10页
Iron-sulfur clusters(ISC)are essential cofactors for proteins involved in various biological processes,such as electron transport,biosynthetic reactions,DNA repair,and gene expression regulation.ISC assembly protein I... Iron-sulfur clusters(ISC)are essential cofactors for proteins involved in various biological processes,such as electron transport,biosynthetic reactions,DNA repair,and gene expression regulation.ISC assembly protein IscA1(or MagR)is found within the mitochondria of most eukaryotes.Magnetoreceptor(MagR)is a highly conserved A-type iron and iron-sulfur cluster-binding protein,characterized by two distinct types of iron-sulfur clusters,[2Fe-2S]and[3Fe-4S],each conferring unique magnetic properties.MagR forms a rod-like polymer structure in complex with photoreceptive cryptochrome(Cry)and serves as a putative magnetoreceptor for retrieving geomagnetic information in animal navigation.Although the N-terminal sequences of MagR vary among species,their specific function remains unknown.In the present study,we found that the N-terminal sequences of pigeon MagR,previously thought to serve as a mitochondrial targeting signal(MTS),were not cleaved following mitochondrial entry but instead modulated the efficiency with which iron-sulfur clusters and irons are bound.Moreover,the N-terminal region of MagR was required for the formation of a stable MagR/Cry complex.Thus,the N-terminal sequences in pigeon MagR fulfil more important functional roles than just mitochondrial targeting.These results further extend our understanding of the function of MagR and provide new insights into the origin of magnetoreception from an evolutionary perspective. 展开更多
关键词 Magnetoreceptor(MagR) N-terminal sequence Mitochondrial targeting signal Iron-sulfur cluster
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The evolution of cancer genomic medicine in Japan and the role of the National Cancer Center Japan 被引量:1
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作者 Teruhiko Yoshida Yasushi Yatabe +6 位作者 Ken Kato Genichiro Ishii Akinobu Hamada Hiroyuki Mano Kuniko Sunami Noboru Yamamoto Takashi Kohno 《Cancer Biology & Medicine》 SCIE CAS CSCD 2024年第1期29-44,共16页
The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer research.At the time,a variety of activating oncogenic alteration... The journey to implement cancer genomic medicine(CGM)in oncology practice began in the 1980s,which is considered the dawn of genetic and genomic cancer research.At the time,a variety of activating oncogenic alterations and their functional significance were unveiled in cancer cells,which led to the development of molecular targeted therapies in the 2000s and beyond.Although CGM is still a relatively new discipline and it is difficult to predict to what extent CGM will benefit the diverse pool of cancer patients,the National Cancer Center(NCC)of Japan has already contributed considerably to CGM advancement for the conquest of cancer.Looking back at these past achievements of the NCC,we predict that the future of CGM will involve the following:1)A biobank of paired cancerous and non-cancerous tissues and cells from various cancer types and stages will be developed.The quantity and quality of these samples will be compatible with omics analyses.All biobank samples will be linked to longitudinal clinical information.2)New technologies,such as whole-genome sequencing and artificial intelligence,will be introduced and new bioresources for functional and pharmacologic analyses(e.g.,a patient-derived xenograft library)will be systematically deployed.3)Fast and bidirectional translational research(bench-to-bedside and bedside-to-bench)performed by basic researchers and clinical investigators,preferably working alongside each other at the same institution,will be implemented;4)Close collaborations between academia,industry,regulatory bodies,and funding agencies will be established.5)There will be an investment in the other branch of CGM,personalized preventive medicine,based on the individual's genetic predisposition to cancer. 展开更多
关键词 Cancer genomic medicine BIOBANK patient-derived xenograft multi-gene panel test whole genome sequencing
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On the relationship between imprint and reliability in Hf_(0.5)Zr_(0.5)O_(2) based ferroelectric random access memory
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作者 Peng Yuan Yuting Chen +9 位作者 Liguo Chai Zhengying Jiao Qingjie Luan Yongqing Shen Ying Zhang Jibin Leng Xueli Ma Jinjuan Xiang Guilei Wang Chao Zhao 《Journal of Semiconductors》 EI CAS CSCD 2024年第4期42-47,共6页
The detrimental effect of imprint,which can cause misreading problem,has hindered the application of ferroelectric HfO_(2).In this work,we present results of a comprehensive reliability evaluation of Hf_(0.5)Zr_(0.5)O... The detrimental effect of imprint,which can cause misreading problem,has hindered the application of ferroelectric HfO_(2).In this work,we present results of a comprehensive reliability evaluation of Hf_(0.5)Zr_(0.5)O_(2)-based ferroelectric random access memory.The influence of imprint on the retention and endurance is demonstrated.Furthermore,a solution in circuity is pro-posed to effectively solve the misreading problem caused by imprint. 展开更多
关键词 FERAM HZO imprint RELIABILITY
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Genetic screening of liver cancer:State of the art 被引量:1
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作者 Milena Peruhova Sonya Banova-Chakarova +1 位作者 Dimitrina Georgieva Miteva Tsvetelina Velikova 《World Journal of Hepatology》 2024年第5期716-730,共15页
Liver cancer,primarily hepatocellular carcinoma,remains a global health challenge with rising incidence and limited therapeutic options.Genetic factors play a pivotal role in the development and progression of liver c... Liver cancer,primarily hepatocellular carcinoma,remains a global health challenge with rising incidence and limited therapeutic options.Genetic factors play a pivotal role in the development and progression of liver cancer.This state-of-the-art paper provides a comprehensive review of the current landscape of genetic screening strategies for liver cancer.We discuss the genetic underpinnings of liver cancer,emphasizing the critical role of risk-associated genetic variants,somatic mutations,and epigenetic alterations.We also explore the intricate interplay between environmental factors and genetics,highlighting how genetic screening can aid in risk stratification and early detection via using liquid biopsy,and advancements in high-throughput sequencing technologies.By synthesizing the latest research findings,we aim to provide a comprehensive overview of the state-of-the-art genetic screening methods for liver cancer,shedding light on their potential to revolutionize early detection,risk assessment,and targeted therapies in the fight against this devastating disease. 展开更多
关键词 Hepatocellular carcinoma Liver cancer Genetic screening Risk-associated genetic variants Epigenetic alterations Genetic biomarkers Circulating tumor DNA Next-generation sequencing
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Transcriptomic and bioinformatics analysis of the mechanism by which erythropoietin promotes recovery from traumatic brain injury in mice 被引量:1
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作者 Weilin Tan Jun Ma +9 位作者 Jiayuanyuan Fu Biying Wu Ziyu Zhu Xuekang Huang Mengran Du Chenrui Wu Ehab Balawi Qiang Zhou Jie Zhang Zhengbu Liao 《Neural Regeneration Research》 SCIE CAS CSCD 2024年第1期171-179,共9页
Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate trau... Recent studies have found that erythropoietin promotes the recovery of neurological function after traumatic brain injury.However,the precise mechanism of action remains unclea r.In this study,we induced moderate traumatic brain injury in mice by intrape ritoneal injection of erythro poietin for 3 consecutive days.RNA sequencing detected a total of 4065 differentially expressed RNAs,including 1059 mRNAs,92 microRNAs,799 long non-coding RNAs,and 2115circular RNAs.Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analyses revealed that the coding and non-coding RNAs that were differentially expressed after traumatic brain injury and treatment with erythropoietin play roles in the axon guidance pathway,Wnt pathway,and MAPK pathway.Constructing competing endogenous RNA networks showed that regulatory relationship between the differentially expressed non-coding RNAs and mRNAs.Because the axon guidance pathway was repeatedly enriched,the expression of Wnt5a and Ephb6,key factors in the axonal guidance pathway,was assessed.Ephb6 expression decreased and Wnt5a expression increased after traumatic brain injury,and these effects were reversed by treatment with erythro poietin.These findings suggest that erythro poietin can promote recove ry of nerve function after traumatic brain injury through the axon guidance pathway. 展开更多
关键词 axon guidance bioinformatics analysis competing endogenous RNA ERYTHROPOIETIN Gene Ontology Kyoto Encyclopedia of Genes and Genomes non-coding RNA RNA sequencing transcriptomics traumatic brain injury
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Imprinting at the KBTBD6 locus involves species-specific m ternal methylation and monoallelic expression in livestock animals
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作者 Jinsoo Ahn In-Sul Hwang +2 位作者 Mi-Ryung Park Seongsoo Hwang Kichoon Lee 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2024年第1期127-145,共19页
Background The primary differentially methylated regions(DMRs) which are maternally hypermethylated serve as imprinting control regions(ICRs) that drive monoallelic gene expression, and these ICRs have been investigat... Background The primary differentially methylated regions(DMRs) which are maternally hypermethylated serve as imprinting control regions(ICRs) that drive monoallelic gene expression, and these ICRs have been investigated due to their implications in mammalian development. Although a subset of genes has been identified as imprinted, in-depth comparative approach needs to be developed for identification of species-specific imprinted genes. Here, we examined DNA methylation status and allelic expression at the KBTBD6 locus across species and tissues and explored potential mechanisms of imprinting.Results Using whole-genome bisulfite sequencing and RNA-sequencing on parthenogenetic and normal porcine embryos, we identified a maternally hypermethylated DMR between the embryos at the KBTBD6 promoter Cp G island and paternal monoallelic expression of KBTBD6. Also, in analyzed domesticated mammals but not in humans, non-human primates and mice, the KBTBD6 promoter Cp G islands were methylated in oocytes and/or allelically methyl-ated in tissues, and monoallelic KBTBD6 expression was observed, indicating livestock-specific imprinting. Further analysis revealed that these Cp G islands were embedded within transcripts in porcine and bovine oocytes which coexisted with an active transcription mark and DNA methylation, implying the presence of transcription-dependent imprinting.Conclusions In this study, our comparative approach revealed an imprinted expression of the KBTBD6 gene in domesticated mammals, but not in humans, non-human primates, and mice which implicates species-specific evolution of genomic imprinting. 展开更多
关键词 Differentially methylated region Domesticated mammal imprintING KBTBD6 PARtheNOGENETIC
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A Transparent Photoresist Made of Titanium Dioxide Nanoparticle-Embedded Acrylic Resin with a Tunable Refractive Index for UV-Imprint Lithography
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作者 Yinglu Liu Dan Wang +7 位作者 Changlin Liu Qianqian Hao Jian Li Jie-Xin Wang Xiuyun Chen Peng Zhong Xibin Shao Jian-Feng Chen 《Engineering》 SCIE EI CAS CSCD 2024年第6期96-104,共9页
Transparent photoresists with a high refractive index(RI)and high transmittance in visible wavelengths have promising functionalities in optical fields.This work reports a kind of tunable optical material composed of ... Transparent photoresists with a high refractive index(RI)and high transmittance in visible wavelengths have promising functionalities in optical fields.This work reports a kind of tunable optical material composed of titanium dioxide nanoparticles embedded in acrylic resin with a high RI for ultraviolet(UV)-imprint lithography.The hybrid film exhibits a tunable RI of up to 1.67(589 nm)after being cured by UV light,while maintaining both a high transparency of over 98%in the visible light range and a low haze of less than 0.05%.The precision machining of optical microstructures can be imprinted easily and efficiently using the hybrid resin,which acts as a light guide plate(LGP)to guide the light from the side to the top in order to conserve the energy of the display device.These preliminary studies based on both laboratory and commercial experiments pave the way for exploiting the unparalleled optical properties of nanocomposite resins and promoting their industrial application. 展开更多
关键词 PHOTORESIST Tunable refractive index Hanson solubility Ultraviolet imprint Organic-inorganic composites
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Periodic Addition of Glucose Suppressed Cyanobacterial Abundance in Additive Lake Water Samples during the Entire Bloom Season
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作者 David Linz Ian Struewing +6 位作者 Nathan Sienkiewicz Alan David Steinman Charlyn Gwen Partridge Kyle McIntosh Joel Allen Jingrang Lu Stephen Vesper 《Journal of Water Resource and Protection》 CAS 2024年第2期140-155,共16页
Previously, we showed that prophylactic addition of glucose to Harsha Lake water samples could inhibit cyanobacteria growth, at least for a short period of time. The current study tested cyanobacterial control with gl... Previously, we showed that prophylactic addition of glucose to Harsha Lake water samples could inhibit cyanobacteria growth, at least for a short period of time. The current study tested cyanobacterial control with glucose for the entire Harsha Lake bloom season. Water samples (1000 ml) were collected weekly from Harsha Lake during the algal-bloom season starting June 9 and lasting until August 24, 2022. To each of two 7-liter polypropylene containers, 500 ml of Harsha Lake water was added, and the containers were placed in a controlled environment chamber. To one container labeled “Treated,” 0.15 g of glucose was added, and nothing was added to the container labeled “Control.” After that, three 25 ml samples from each container were collected and used for 16S rRNA gene sequencing each week. Then 1000 ml of Harsha Lake water was newly collected each week, with 500 ml added to each container, along with the addition of 0.15 g glucose to the “Treated” container. Sequencing data were used to examine differences in the composition of bacterial communities between Treated and Control containers. Treatment with glucose altered the microbial communities by 1) reducing taxonomic diversity, 2) largely eliminating cyanobacterial taxa, and 3) increasing the relative abundance of subsets of non-cyanobacterial taxa (such as Proteobacteria and Actinobacteriota). These effects were observed across time despite weekly inputs derived directly from Lake water. The addition of glucose to a container receiving weekly additions of Lake water suppressed the cyanobacterial populations during the entire summer bloom season. The glucose appears to stimulate the diversity of certain bacterial taxa at the expense of the cyanobacteria. 展开更多
关键词 GLUCOSE CYANOBACTERIA 16S Amplicon Sequencing Microbial Community
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To Analyze the Sensitivity of RT-PCR Assays Employing S Gene Target Failure with Whole Genome Sequencing Data during Third Wave by SARS-CoV-2 Omicron Variant
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作者 Pooja Patel Yogita Mistry +1 位作者 Monika Patel Summaiya Mullan 《Advances in Microbiology》 CAS 2024年第5期247-255,共9页
Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the... Introduction: Omicron is a highly divergent variant of concern (VOCs) of a severe acute respiratory syndrome SARS-CoV-2. It carries a high number of mutations in its spike protein hence;it is more transmissible in the community by immune evasion mechanisms. Due to mutation within S gene, most Omicron variants have reported S gene target failure (SGTF) with some commercially available PCR kits. Such diagnostic features can be used as markers to screen Omicron. However, Whole Genome Sequencing (WGS) is the only gold standard approach to confirm novel microorganisms at genetically level as similar mutations can also be found in other variants that are circulating at low frequencies worldwide. This Retrospective study is aimed to assess RT-PCR sensitivity in the detection of S gene target failure in comparison with whole genome sequencing to detect variants of Omicron. Methods: We have analysed retrospective data of SARS-CoV-2 positive RT-PCR samples for S gene target failure (SGTF) with TaqPath COVID-19 RT-PCR Combo Kit (ThermoFisher) and combined with sequencing technologies to study the emerged pattern of SARS-CoV-2 variants during third wave at the tertiary care centre, Surat. Results: From the first day of December 2021 till the end of February 2022, a total of 321,803 diagnostic RT-PCR tests for SARS-CoV-2 were performed, of which 20,566 positive cases were reported at our tertiary care centre with an average cumulative positivity of 6.39% over a period of three months. In the month of December 21 samples characterized by the SGTF (70/129) were suggestive of being infected by the Omicron variant and identified as Omicron (B.1.1.529 lineage) when sequence. In the month of January, we analysed a subset of samples (n = 618) with SGTF (24%) and without SGTF (76%) with Ct values Conclusions: During the COVID-19 pandemic, it took almost more than 15 days to diagnose infection and identify pathogen by sequencing technology. In contrast to that molecular assay provided quick identification with the help of SGTF phenomenon within 5 hours of duration. This strategy helps scientists and health policymakers for the quick isolation and identification of clusters. That ultimately results in a decreased transmission of pathogen among the community. 展开更多
关键词 SARS-CoV-2 S Gene Target Failure Whole Genome Sequencing Omicron
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Clinical manifestations and the prenatal diagnosis of trisomy 7 mosaicism:Two case reports
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作者 Fei Hou Yan Li Hua Jin 《World Journal of Clinical Cases》 SCIE 2024年第8期1544-1548,共5页
BACKGROUND The clinical manifestations of trisomy 7 mosaicism are diverse and nonspecific,so prenatal diagnosis is very difficult.CASE SUMMARY Two pregnant women with abnormal prenatal screening results were included.... BACKGROUND The clinical manifestations of trisomy 7 mosaicism are diverse and nonspecific,so prenatal diagnosis is very difficult.CASE SUMMARY Two pregnant women with abnormal prenatal screening results were included.One was a 22-year-old woman(G1P0).At 31st week of gestation,ultrasound revealed that the posterior horn of the left lateral ventricle was 10 mm and the right renal pelvis had a separation of 7 mm.The other pregnant woman was 33 years old(G2P1L1A0),and her fetus was found to have a cardiac malformation at the 24th week of gestation.Copy number variation sequencing,whole-exome sequencing and karyotype analysis were carried out after amniocentesis,and both fetuses were diagnosed with trisomy 7 mosaicism.After parental counseling,one woman continued the pregnancy,and the other woman terminated the pregnancy.CONCLUSION In trisomy 7 mosaicism,the low proportion of trisomy does not lead to abortion,but can result in abnormal fetal development,which can be detected via ultrasound.Therefore,clinicians need to pay more attention to various aspects of fetal growth and development,combining with imaging,cellular,molecular genetics and other methods to perform comprehensive evaluations of fetuses to provide more reliable genetic counseling for pregnant women. 展开更多
关键词 Trisomy 7 mosaicism Copy number variation sequencing Whole-exome sequencing Karyotype analysis Prenatal diagnosis Case report
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Hydrolytic and Antimicrobial Activities of Bacteria Isolated from Fermented Peppers Sold in Markets at Brazzaville, Republic of the Congo
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作者 Faly Armel Soloka Mabika Elgie Viennechie Gatsé +3 位作者 Ngo Itsouhou Tarcisse Baloki Ngoulou Mérite Berthelie Mouanda Nzoussi Nguimbi Etienne 《Journal of Biosciences and Medicines》 2024年第9期215-234,共20页
Microorganisms are omnipresent in all environments and play mainly the role of transformers, thanks to the multiple enzymes they are able to produce. In order to valorize fermented foods in the Republic of the Congo, ... Microorganisms are omnipresent in all environments and play mainly the role of transformers, thanks to the multiple enzymes they are able to produce. In order to valorize fermented foods in the Republic of the Congo, this work aimed to characterize and study some properties of microorganisms isolated from samples of peppers sold in three markets of Brazzaville. A numeration of the total aerobic mesophilic flora (TAMF) was made in a solid medium, allowing the evaluation of each sample’s microbial concentration. The microbial mass varied from 2.8 × 105 CFU/g for the Ouénzé sample to 1.8 × 104 CFU/g for the Total sample and 2 × 104 CFU/g for the Moungali market sample. The evaluation of the enzymatic properties of the Bacillus isolates showed that 68.42% were capable of producing cellulases and 78.94% were capable of producing amylases and proteases. Antimicrobial activities revealed that 63.15% of the isolates were able to secrete inhibitory substances against E. coli and Staphylococcus aureus. Molecular analysis by PCR amplification, sequencing of the 16S rRNA gene and BLAST bioinformatics analysis provides newly identified bacteria strains with new accession numbers in GenBank: Bacillus thuringiensis MBCBR322 (OP474008), Bacillus megaterium MBCBJ1822 (OP476493), Bacillus thuringiensis MBCBR222 (OP476494), Priestia megaterium MBCBJ2022 (OP476495) and Lactobacillus paraplantarum MBCBR1522 (OP476496). Multiple sequences alignment of identified sequences with their homologs of GenBank has shown high similarities. The phylogenetic inference assay has provided the two groups of strains observed in this study, and the two groups are very coherent with the phylogeny of the reference. 展开更多
关键词 Antimicrobial Activity Hydrolytic Activity Sequencing PEPPER BRAZZAVILLE
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Pig pangenome graph reveals functional features of non‑reference sequences
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作者 Jian Miao Xingyu Wei +6 位作者 Caiyun Cao Jiabao Sun Yuejin Xu Zhe Zhang Qishan Wang Yuchun Pan Zhen Wang 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2024年第3期956-970,共15页
Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in animals.This constraint is particularly pronounced for non... Background The reliance on a solitary linear reference genome has imposed a significant constraint on our compre-hensive understanding of genetic variation in animals.This constraint is particularly pronounced for non-reference sequences(NRSs),which have not been extensively studied.Results In this study,we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb.Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome.Furthermore,we observed that NRSs were rarely found within coding sequences,while NRS insertions were enriched in immune-related Gene Ontology terms.Notably,our investigation also unveiled a close association between novel genes and the immune capacity of pigs.We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs,and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X.Additionally,we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in South-ern Chinese pigs.Conclusions Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations. 展开更多
关键词 Heat tolerance Immune ability Non-reference sequences Pig pangenome
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Phylogenetic, phylogeographic and divergence time analysis of Anopheles subpictus species complex using ITS2 and COI sequences
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作者 Lihini Sandaleka Muthukumarana Methsala Madurangi Wedage +1 位作者 Samanthika Rathnayake Nissanka Kolitha De Silva 《Asian Pacific Journal of Tropical Medicine》 SCIE CAS 2024年第5期214-225,I0004-I0038,共47页
Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Tran... Objective:To address the phylogenetic and phylogeographic relationship between different lineages of Anopheles(An.)subpictus species complex in most parts of the Asian continent by maximum utilization of Internal Transcriber Spacer 2(ITS2)and cytochrome C oxidase I(COI)sequences deposited at the GenBank.Methods:Seventy-five ITS2,210 COI and 26 concatenated sequences available in the NCBI database were used.Phylogenetic analysis was performed using Bayesian likelihood trees,whereas median-joining haplotype networks and time-scale divergence trees were generated for phylogeographic analysis.Genetic diversity indices and genetic differentiation were also calculated.Results:Two genetically divergent molecular forms of An.subpictus species complex corresponding to sibling species A and B are established.Species A evolved around 37-82 million years ago in Sri Lanka,India,and the Netherlands,and species B evolved around 22-79 million years ago in Sri Lanka,India,and Myanmar.Vietnam,Thailand,and Cambodia have two molecular forms:one is phylogenetically similar to species B.Other forms differ from species A and B and evolved recently in the above mentioned countries,Indonesia and the Philippines.Genetic subdivision among Sri Lanka,India,and the Netherlands is almost absent.A substantial genetic differentiation was obtained for some populations due to isolation by large geographical distances.Genetic diversity indices reveal the presence of a long-established stable mosquito population,at mutation-drift equilibrium,regardless of population fluctuations.Conclusions:An.subpictus species complex consists of more than two genetically divergent molecular forms.Species A is highly divergent from the rest.Sri Lanka and India contain only species A and B. 展开更多
关键词 Molecular systematics ITS2 COI DNA sequences Phylogeny PHYLOGEOGRAPHY
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Diet and monensin influence the temporal dynamics of the rumen microbiome in stocker and finishing cattle
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作者 Jianmin Chai Caleb P.Weiss +3 位作者 Paul A.Beck Wei Zhao Ying Li Jiangchao Zhao 《Journal of Animal Science and Biotechnology》 SCIE CAS CSCD 2024年第2期733-748,共16页
Background Stocker cattle diet and management influence beef cattle performance during the finishing stage,but knowledge of the dynamics of the rumen microbiome associated with the host are lacking.A longitudinal stud... Background Stocker cattle diet and management influence beef cattle performance during the finishing stage,but knowledge of the dynamics of the rumen microbiome associated with the host are lacking.A longitudinal study was conducted to determine how the feeding strategy from the stocker to the finishing stages of production affects the temporal dynamics of rumen microbiota.During the stocker phase,either dry hay or wheat pasture were provided,and three levels of monensin were administrated.All calves were then transported to a feedlot and received similar finishing diets with or without monensin.Rumen microbial samples were collected on d 0,28,85 during the stocker stage(S0,S28 and S85)and d 0,14,28,56,30 d before slaughter and the end of the trial during the finishing stage(F0,F14,F28,F56,Pre-Ba,and Final).The V4 region of the bacterial 16S rRNA gene of 263 rumen samples was sequenced.Results Higher alpha diversity,including the number of observed bacterial features and the Shannon index,was observed in the stocker phase compared to the finishing phase.The bacterial amplicon sequence variants(ASVs)differentiating different sampling time points were identified.Dietary treatments during the stocker stage temporally impact the dynamics of rumen microbiota.For example,shared bacteria,including Bacteroidales(ASV19)and Streptococcus infantarius(ASV94),were significantly higher in hay rumen on S28,S85,and F0,while Bacteroidaceae(ASV11)and Limivicinus(ASV15)were more abundant in wheat.Monensin affected rumen microbial composition at a specific time.Transportation to feedlot significantly influenced microbiome structure and diversity in hay-fed calves.Bacterial taxa associated with body weight were classified,and core microbiotas interacted with each other during the trial.Conclusions In summary,the temporal dynamics of the rumen microbiome in cattle at the stocker and finishing stage are influenced by multiple factors of the feeding strategy.Diet at the stocker phase may temporarily affect the microbial composition during this stage.Modulating the rumen microbiome in the steers at the stocker stage affects the microbial interactions and performance in the finishing stage. 展开更多
关键词 Beef cattle DIET Feedlot phase MONENSIN Next-generation sequencing Rumen microbiota Stocker
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Investigation of the cell composition and gene expression in the delayed-type hypersensitivity tuberculin skin test
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作者 Hui-Juan Duan Hong-Qian Chu +4 位作者 Ting-Ming Cao Guang-Ming Dai Na Tian Gang Sheng Zhao-Gang Sun 《Military Medical Research》 SCIE CAS CSCD 2024年第1期148-151,共4页
Dear Editor,The tuberculin skin test(TST)reagents have continuously improved,with the ESAT6-CFP10(EC)test having recently been introduced,but are seldom based on the direction of the delayed-type hypersensitivity(DTH)... Dear Editor,The tuberculin skin test(TST)reagents have continuously improved,with the ESAT6-CFP10(EC)test having recently been introduced,but are seldom based on the direction of the delayed-type hypersensitivity(DTH)mechanism.Previous studies only partially showed the infiltration and activation of immune cells and the production of cytokines of the skin induration[1,2],and lack the detailed measurements of cell proportions and gene expression in the DTH response.Therefore,in this study,we revealed the comprehensive characteristics of DTH by single-cell RNA sequencing(scRNA-seq)in the guinea pig tuberculosis(TB)model[Experimental Animal Welfare Ethics Committee,Beijing Tuberculosis and Thoracic Tumor Research Institute(2021-064)]. 展开更多
关键词 Tuberculin skin test Delayed-type hypersensitivity Single-cell RNA sequencing
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On power series statistical convergence and new uniform integrability of double sequences
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作者 Sevda Y■ld■z Kamil Demirci 《Applied Mathematics(A Journal of Chinese Universities)》 SCIE CSCD 2024年第3期519-532,共14页
In the present paper,we mostly focus on P_(p)^(2)-statistical convergence.We will look into the uniform integrability via the power series method and its characterizations for double sequences.Also,the notions of P_(p... In the present paper,we mostly focus on P_(p)^(2)-statistical convergence.We will look into the uniform integrability via the power series method and its characterizations for double sequences.Also,the notions of P_(p)^(2)-statistically Cauchy sequence,P_(p)^(2)-statistical boundedness and core for double sequences will be described in addition to these findings. 展开更多
关键词 power series methods statistical convergence uniform integrability double sequences
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The modulatory effect of oolong tea polyphenols on intestinal flora and hypothalamus gene expression in a circadian rhythm disturbance mouse model
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作者 Ruonan Yan Chi-Tang Ho +3 位作者 Yanan Liu Shengnan Zhan Zufang Wu Xin Zhang 《Food Science and Human Wellness》 SCIE CSCD 2024年第2期748-764,共17页
The interaction between host circadian rhythm and gut microbes through the gut-brain axis provides new clues for tea polyphenols to improve host health.Our present research showed that oolong tea polyphenols(OTP)impro... The interaction between host circadian rhythm and gut microbes through the gut-brain axis provides new clues for tea polyphenols to improve host health.Our present research showed that oolong tea polyphenols(OTP)improved the structural disorder of the intestinal flora caused by continuous darkness,thereby modulating the production of metabolites related to pyruvate metabolism,glycolysis/gluconeogenesis,and tryptophan metabolism to alleviate the steady-state imbalance.After fecal microbiota transplantation from the OTP group,the single-cell transcriptomic analysis revealed that OTP significantly increased the number of hypothalamus cell clusters,up-regulated the number of astrocytes and fibroblasts,and enhanced the expression of circadian rhythm genes Cry2,Per3,Bhlhe41,Nr1d1,Nr1d2,Dbp and Rorb in hypothalamic cells.Our results confirmed that OTP can actively improve the intestinal environmental state as well as internal/peripheral circadian rhythm disorders and cognitive impairment,with potential prebiotic functional characteristics to notably contribute to host health. 展开更多
关键词 Gut microbiota Circadian rhythm Oolong tea polyphenols Single-cell sequencing Metabolism
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