Article
Chemistry, Analytical
Liao Chen, Vivek Yadav, Chenguang Zhang, Xiaoye Huo, Ceming Wang, Satyajyoti Senapati, Hsueh-Chia Chang
Summary: The droplet digital PCR (ddPCR) platform reported in this study utilizes a unique flattened pipette tip design to achieve rapid, stable, and highly sensitive quantification of low virus RNA load without the need for bulky lab-bound equipment. The technology allows for fast generation of thousands of monodispersed droplets, which can be easily counted or imaged for accurate quantification of target copies. This platform shows promising potential for rapid virus detection and epidemic control, offering a convenient solution for point-of-care (POC) applications.
ANALYTICAL CHEMISTRY
(2021)
Article
Medicine, General & Internal
Tomasz Kolenda, Marcel Rys, Kacper Guglas, Anna Teresiak, Renata Blizniak, Jacek Mackiewicz, Katarzyna Lamperska
Summary: This study tested the influence of different commercially available cDNA synthesis kits on RNA degradation and found that cDNA synthesized using random hexamer primers preceded by polyA-tailing and adaptor-anchoring steps enhances the specificity and sensitivity of lncRNA quantification. In most cases, RNA degradation does not affect lncRNA quantification, as these molecules have good stability.
ARCHIVES OF MEDICAL SCIENCE
(2021)
Article
Biochemical Research Methods
Sobia Mushtaq, Asima Tayyeb, Firdaus-e-Bareen
Summary: This study optimized a protocol for extracting high-quality RNA from Trichoderma atrobrunneum. The results showed that the modified high salt CTAB method yielded more intact and high-quality RNA compared to other methods.
JOURNAL OF MICROBIOLOGICAL METHODS
(2022)
Article
Biochemistry & Molecular Biology
Yuri D'Alessandra, Vincenza Valerio, Donato Moschetta, Ilaria Massaiu, Michele Bozzi, Maddalena Conte, Valentina Parisi, Michele Ciccarelli, Dario Leosco, Veronika A. Myasoedova, Paolo Poggio
Summary: In this study, a new method for the detection of circulating miRNAs was evaluated. It involves sample lysis followed by direct evaluation using dPCR, without the need for RNA extraction. The results showed that dPCR can accurately detect low-copy-number and highly expressed miRNAs in plasma samples.
Article
Biochemistry & Molecular Biology
Yahui Yang, Huanhuan Yang, Yinxiao Tan, Tingting Zhao, Xiangyang Xu, Jingfu Li, Jingbin Jiang
Summary: Inflorescences play a crucial role in fruit yield, with the quality and quantity of inflorescences closely linked to fruit quality and yield. Transcriptome sequencing of cherry tomato and tomato plants identified new genes involved in compound inflorescence development, enriching our understanding of this process. The study provides a theoretical basis for further research on compound inflorescence development in tomatoes.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Sarah Vanwijnsberghe, Charlotte Peeters, Emmelie De Ridder, Charles Dumolin, Anneleen D. Wieme, Nico Boon, Peter Vandamme
Summary: The study found multiple Paraburkholderia isolates and species in pristine forest soil, capable of degrading aromatic compounds, possibly due to the abundant presence of aromatic compounds in decomposing plant litter, reflecting microbial habitat diversity or synergistic relationships.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Chemistry, Analytical
Juliane Vigano, Monique Martins Strieder, Rodrigo S. Pizani, Leticia S. Contieri, Leonardo M. de Souza Mesquita, Mauricio A. Rostagno
Summary: This study proposes a new integrative system (2D PLE x HPLC-PDA) for the extraction and online quantification of bioactive compounds in solid samples. The system combines pressurized liquid extraction (PLE) with automated extract injection in HPLC, allowing for a single and online step for sample preparation and chemical analysis.
ANALYTICA CHIMICA ACTA
(2023)
Article
Engineering, Chemical
Mohammad Taghi Fouladvand, Javad Asadi, Mohammad Nader Lotfollahi
Summary: Simulation and optimization of aromatic extraction process using furfural as a solvent were conducted by linking Aspen Plus and MATLAB. Increasing the solvent to feed ratio and extraction temperature decreases extraction efficiency and refractive index, while increasing the energy consumption of the process.
CHEMICAL ENGINEERING RESEARCH & DESIGN
(2021)
Article
Microbiology
Joyce Odeke Akello, Erika Bujaki, Alexander G. Shaw, Adnan Khurshid, Yasir Arshad, Catherine Troman, Manasi Majumdar, Aine O'Toole, Andrew Rambaut, Muhammad Masroor Alam, Javier Martin, Nicholas C. Grassly
Summary: This article examines the effects of 11 nucleic acid extraction methods on the detection of poliovirus. The study found that the choice of RNA extraction method is an important factor in nucleic acid amplification-based diagnostics.
MICROBIOLOGY SPECTRUM
(2023)
Article
Agriculture, Dairy & Animal Science
Paul Dawson, Ahmet Buyukyavuz, Claudia Ionita, Julie Northcutt
Summary: The combination of PCR and DNA extraction techniques can be used to enumerate Campylobacter spp. from poultry gastrointestinal tract samples. The study developed a DNA standard curve for Campylobacter spp. DNA primers and a cell/genomic DNA extraction protocol for complex samples. The results showed that qPCR and standard plate count methods were highly correlated for enumerating Campylobacter spp. in the specified range.
Article
Multidisciplinary Sciences
Jianshi Jin, Reiko Yamamoto, Tadashi Takeuchi, Guangwei Cui, Eiji Miyauchi, Nozomi Hojo, Koichi Ikuta, Hiroshi Ohno, Katsuyuki Shiroguchi
Summary: The study develops a method called Barcoding Bacteria for Identification and Quantification (BarBIQ) that allows for the classification and quantification of individual bacterial cells in the microbiota. It is found that BarBIQ reveals location-dependent differences in the microbiota, which cannot be shown by conventional 16S rRNA gene-amplicon sequencing methods.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Samuel Long
Summary: This review uses a model for human HIV infection and the Raindance ddPCR platform as an example to describe the technical aspects that contribute to sensitive viral signal detection in tissue samples. It emphasizes the importance of such detection for predicting disease outcome and treatment efficacy.
Article
Microbiology
Jia Liu, Paul Villanueva, Jinlyung Choi, Santosh Gunturu, Yang Ouyang, Lisa K. Tiemann, James R. Cole, Kathryn R. Glanville, Steven J. Hall, Marshall D. McDaniel, Jaejin Lee, Adina Howe
Summary: MetaFunPrimer is a bioinformatic pipeline developed to design primers for numerous genes of interest, enabling gene target prioritization based on their presence and abundance in defined reference genomes. The primers designed by this tool improve the characterization and quantification of functional genes, allowing for a quick and affordable assessment of functional gene abundance and microbial community dynamics using high-throughput PCR methods.
Article
Pathology
Reena Yadav, Laxmi Kumari, Sumit Goel, Deepinder Kaur, Divya Dahiya, Yashwant Kumar, Pranab Dey, Alka Bhatia
Summary: Touch imprints can improve the quality and concentration of RNA extracted from breast tissue, providing a fast and cost-effective strategy to ensure that the extracted RNA is representative of the tumor.
PATHOLOGY RESEARCH AND PRACTICE
(2023)
Article
Chemistry, Analytical
Shamsunnahar Suchana, Langping Wu, Elodie Passeport
Summary: Compound-specific isotope analysis (CSIA) is a useful tool for studying the fate of legacy groundwater contaminants, but its application to nonconventional contaminants is still emerging. This study validated CSIA methods for nitro- and amino-substituted chlorobenzenes and developed a solid-phase extraction (SPE) method to minimize matrix interferences. The results showed that the SPE-CSIA procedure had negligible isotope fractionation and can be used to track the environmental fate of these contaminants.
ANALYTICAL CHEMISTRY
(2023)
Article
Environmental Sciences
Xingren Liu, Zhanming Tang, Qingwen Zhang, Weidong Kong
Summary: This study evaluated the combined effects of biochar and straw on N2O flux and the community compositions of nitrifiers and denitrifiers in the maize season in an intensively farmed area in northern China. Biochar and straw applications significantly influenced N2O production by changing the soil factors and microbial gene abundances.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2021)
Article
Environmental Sciences
Hao Chen, Fei Wang, Weidong Kong, Hongzeng Jia, Tianqi Zhou, Ri Xu, Guangjian Wu, Junbo Wang, Jinshui Wu
Summary: The study found that soil microbial primary producers contribute significantly to CO2 fixation in a fragile dry grassland on the Tibetan Plateau, with a high proportion of plant gross primary productivity (GPP). Soil microbial GPP exhibited greater interannual variation than plant GPP, suggesting that the uncertainty in interannual GPP could be largely derived from microbial primary producers.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biology
Xin Chen, Xiaodong Liu, Hongzeng Jia, Jing Jin, Weidong Kong, Yongsong Huang
Summary: Recent studies have found long-chain n-alkanes and n-alkanoic acids in sediments of desolate Antarctic ponds without vascular plants, displaying hydrogen isotopic values up to 300 per mil higher than lake water. This strongly inverse isotopic fractionation is believed to be predominantly produced by heterotrophic micro-organisms, based on experimental data. This represents the first clear example of heterotrophic microbial production of long-chain n-alkyl waxes in a natural environment.
Review
Microbiology
Jason Bosch, Gilda Varliero, John E. Hallsworth, Tiffany D. Dallas, David Hopkins, Beat Frey, Weidong Kong, Pedro Lebre, Thulani P. Makhalanyane, Don A. Cowan
Summary: The loss of cellular water and resulting low cytosolic water activity are major stress factors for organisms, leading to molecular and physiological adaptations. While the changes within cells during desiccation and rehydration have been extensively studied, there is still limited knowledge on the metabolic status of organisms in the desiccated state, highlighting significant gaps in our understanding of molecular and biochemical processes in dry cells.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Biodiversity Conservation
Hao Chen, Weidong Kong, Quan Shi, Fei Wang, Chen He, Jianshuang Wu, Qimei Lin, Xianzhou Zhang, Yong-Guan Zhu, Chao Liang, Yu Luo
Summary: The study found that the quantity and weight of DOM in dryland soils decreased, while the degradability of DOM increased with decreasing precipitation. Desert soils showed a 23.4% increase in DOM degradability compared to meadow soils, with a threefold higher ratio of MBC to total organic carbon. The results suggest that labile DOM accelerates microbial growth and SOM decomposition in desert soils.
JOURNAL OF APPLIED ECOLOGY
(2022)
Article
Plant Sciences
Mukan Ji, Weidong Kong, Hongzeng Jia, Chen Ding, Alexandre M. Anesio, Yanfen Wang, Yong-Guan Zhu
Summary: This study used high-throughput sequencing to examine the characteristics of algal, bacterial, and fungal communities in red and green snow in the Antarctic Peninsula, revealing distinct features. The microbiome in red snow exhibited a more stable network and higher complexity compared to green snow, indicating a higher resistance to external disturbances.
Article
Microbiology
Jinbo Liu, Weidong Kong, Pinhua Xia, Chunmao Zhu, Xiangzhen Li
Summary: The study focused on the changes in pioneer prokaryotic communities in rhizosphere and bulk soils along the high-elevation glacier retreat chronosequence in the northern Himalayas, Tibetan Plateau. Rhizosphere soils had higher levels of total organic carbon, total nitrogen, ammonium, and nitrate compared to bulk soils. The dominant prokaryotic phyla included Proteobacteria, Actinobacteria, Acidobacteria, and others, with the community composition and succession influenced by plants, habitat, and glacier retreat chronosequence.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Soil Science
Mukan Ji, Weidong Kong, Hongzeng Jia, Manuel Delgado-Baquerizo, Tianqi Zhou, Xiaodong Liu, Belinda C. Ferrari, Lucie Malard, Chao Liang, Kai Xue, Thulani P. Makhalanyane, Yong-Guan Zhu, Yanfen Wang, David A. Pearce, Don Cowan
Summary: The study reveals unique patterns of soil microbial diversity and taxonomic compositions in polar regions, and highlights the importance of environmental stresses in controlling soil microbial community.
SOIL BIOLOGY & BIOCHEMISTRY
(2022)
Article
Environmental Sciences
Fei Wang, Weidong Kong, Mukan Ji, Kang Zhao, Hao Chen, Linyan Yue, Xiaobin Dong
Summary: Excessive livestock grazing negatively affects the stability of soil cellulolytic fungal abundance and community structure. Grazing treatment resulted in significant changes in the abundance and community structure of soil cellulolytic fungi, while fencing treatment showed no changes. Grazing played a key role in determining the community structure of soil cellulolytic fungi, explaining 8.1% of the variation, while pH and DOC also had explanatory power. This study provides new insights into the responses of organic matter-decomposing microbes in grassland management.
JOURNAL OF ENVIRONMENTAL SCIENCES
(2022)
Article
Biodiversity Conservation
Dandan Fan, Mukan Ji, Jianshuang Wu, Hao Chen, Hongzeng Jia, Xianzhou Zhang, Xuliang Zhuang, Weidong Kong
Summary: Animal grazing has substantial effects on soil arbuscular mycorrhizal fungi (AMF) and plants. However, its effects on AMF-plant interactions are still unclear, especially in dry grasslands where plants heavily rely on AMF for environmental stress tolerance. The Tibetan Plateau is experiencing rapid grassland degradation due to increased animal grazing. This study investigates the AMF-plant interactions and AMF community assembly processes in grazed and non-grazed grasslands on the Tibetan Plateau.
ECOLOGICAL INDICATORS
(2023)
Article
Green & Sustainable Science & Technology
Chunge Li, Ye Deng, Jingguo Wang, Weibin Ruan, Shang Wang, Weidong Kong
Summary: Soil phenolic acids, derived from crop residue and root exudates, can impact crop growth and soil microbial community. The study investigated the effects of p-hydroxyphenylacetic acid (HPA) and p-hydroxybenzoic acid (HBA) on soil microbial community in soybean and corn fields. HPA/HBA amendment significantly influenced soil bacterial and fungal community structures. HPA enriched bacteria like Gemmatimonas, Bacillus, and Acidobacteria, while HBA enriched fungi like Penicillium and Aspergillus. This research enhances understanding of the barriers to agricultural production caused by monoculture.
Article
Microbiology
Yazhou Tang, Dandan Fan, Wei Guo, Weidong Kong
Summary: The core subcommunity in soils has less diversity but high abundance, while the indicative subcommunity is highly diverse but low abundance. The core subcommunity is essential for maintaining ecosystem stability, while the indicative subcommunity plays a vital role in ecosystem functions and is more sensitive to environmental change. However, their responses to environmental factors and human disturbances are not well-defined. In this study, we investigated the distribution patterns of core and indicative soil microbes and their responses to animal grazing in dry grasslands across the Tibetan Plateau using Illumina sequencing of 16S rRNA gene. The results showed that the core subcommunity had lower diversity and richness compared to the indicative subcommunity in soils. The diversity of the indicative subcommunity was strongly correlated with nutrient-associated factors, such as soil organic carbon, nitrogen, and plant biomass. Both the core and indicative microbial subcommunities showed significant variations in different grassland ecosystems, with the indicative subcommunity being more affected by grazing. The analysis revealed that the indicative microbial subcommunity was influenced less by environmental factors but more by grazing compared to the core subcommunity. These findings highlight the sensitivity of indicative microbes to soil nutrient-associated factors and human disturbances in alpine dry grasslands. This study provides insights into the diversity and structure of core and indicative subcommunities in grassland soils and their driving factors.
FEMS MICROBIOLOGY ECOLOGY
(2023)
Correction
Microbiology
Weidong Kong
FEMS MICROBIOLOGY ECOLOGY
(2021)
Article
Microbiology
Linyan Yue, Weidong Kong, Chunge Li, Guibing Zhu, Liping Zhu, Thulani P. Makhalanyane, Don A. Cowan
Summary: Climate change accelerates the shrinkage of inland lakes globally, leading to increased water salinity and DIC. The study found that increased DIC mitigates the constraints of salinity on microbial primary producers and primary production, enhancing primary productivity in lakes. The findings suggest that inland lakes may support higher primary productivity in future climate change scenarios.
FEMS MICROBIOLOGY ECOLOGY
(2021)
Correction
Ecology
Ajmal Khan, Weidong Kong, Mukan Ji, Linyan Yue, Ying Xie, Jinbo Liu, Baiqing Xu
SOIL ECOLOGY LETTERS
(2020)
