Article
Cell Biology
Bohan Liu, Jun Nan, Xuehui Zu, Xinhui Zhang, Qiliang Xiao
Summary: The study introduced a support vector machine algorithm to achieve rapid identification and prediction of PAOs using bioinformatics data, demonstrating high accuracy and stability.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Microbiology
Wei-shuang Zheng, Sheng-qiang Zhai, Meng-jun Zhang, Yi Huang
Summary: In this study, a poly-beta-hydroxyalkanoate producing bacterium DP3N28-2(T) was isolated from the sediment of Daya Bay, Guangdong, PR China. Based on the morphological, physiological, biochemical, and genetic analyses, it was identified as a novel species of the genus Mameliella, for which the name Mameliella sediminis sp. nov. is proposed.
INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY
(2022)
Article
Engineering, Environmental
Seungdae Oh, Youngjun Kim
Summary: This study advanced the understanding of the diversity and interactions of PAOs and GAOs in EBPR systems using machine learning models, identifying specific species populations strongly correlated with water temperature and validating their positive association in real-scale processes.
JOURNAL OF WATER PROCESS ENGINEERING
(2021)
Review
Engineering, Environmental
Sheila M. Saia, Hunter J. Carrick, Anthony R. Buda, John M. Regan, M. Todd Walter
Summary: Despite advances in wastewater treatment research on phosphorus cycling, there is still limited application in reducing agricultural phosphorus loading. Interdisciplinary research is needed to improve agricultural phosphorus management strategies and achieve water quality goals.
ENVIRONMENTAL SCIENCE & TECHNOLOGY
(2021)
Article
Microbiology
Juliana R. Almeida, Joana C. Fradinho, Gilda Carvalho, Adrian Oehmen, Maria A. M. Reis
Summary: This work evaluates the influence of different operational conditions on the bacterial communities reported in phototrophic mixed culture (PMC) systems with polyhydroxyalkanoates (PHA) production capabilities. Chromatiaceae members were identified as the main phototrophic PHA producers, favored under high carbon concentrations and the permanent feast regime. Increasing the organic loading rate in systems fed with fermented wastewater enriched for other bacteria responsible for PHA storage. High-sugar feedstock impaired PHA production under the permanent feast conditions, but not under feast and famine conditions.
Article
Biochemistry & Molecular Biology
Brett Trost, Bhooma Thiruvahindrapuram, Ada J. S. Chan, Worrawat Engchuan, Edward J. Higginbotham, Jennifer L. Howe, Livia O. Loureiro, Miriam S. Reuter, Delnaz Roshandel, Joe Whitney, Mehdi Zarrei, Matthew Bookman, Cherith Somerville, Rulan Shaath, Mona Abdi, Elbay Aliyev, Rohan Patel, Thomas Nalpathamkalam, Giovanna Pellecchia, Omar Hamdan, Gaganjot Kaur, Zhuozhi Wang, Jeffrey R. MacDonald, John Wei, Wilson W. L. Sung, Sylvia Lamoureux, Ny Hoang, Thanuja Selvanayagam, Nicole Deflaux, Melissa Geng, Siavash Ghaffari, John Bates, Edwin J. Young, Qiliang Ding, Carole Shum, Lia D'Abate, Clarrisa A. Bradley, Annabel Rutherford, Vernie Aguda, Beverly Apresto, Nan Chen, Sachin Desai, Xiaoyan Du, Matthew L. Y. Fong, Sanjeev Pullenayegum, Kozue Samler, Ting Wang, Karen Ho, Tara Paton, Sergio L. Pereira, Jo-Anne Herbrick, Richard F. Wintle, Jonathan Fuerth, Juti Noppornpitak, Heather Ward, Patrick Magee, Ayman Al Baz, Usanthan Kajendirarajah, Sharvari Kapadia, Jim Vlasblom, Monica Valluri, Joseph Green, Vicki Seifer, Morgan Quirbach, Olivia Rennie, Elizabeth Kelley, Nina Masjedi, Catherine Lord, Michael J. Szego, Ma'n H. Zawati, Michael Lang, Lisa J. Strug, Christian R. Marshall, Gregory Costain, Kristina Calli, Alana Iaboni, Afiqah Yusuf, Patricia Ambrozewicz, Louise Gallagher, David G. Amaral, Jessica Brian, Mayada Elsabbagh, Stelios Georgiades, Daniel S. Messinger, Sally Ozonoff, Jonathan Sebat, Calvin Sjaarda, Isabel M. Smith, Peter Szatmari, Lonnie Zwaigenbaum, Azadeh Kushki, Thomas W. Frazier, Jacob A. S. Vorstman, Khalid A. Fakhro, Bridget A. Fernandez, M. E. Suzanne Lewis, Rosanna Weksberg, Marc Fiume, Ryan K. C. Yuen, Evdokia Anagnostou, Neal Sondheimer, David Glazer, Dean M. Hartley, Stephen W. Scherer
Summary: This study identifies rare variants associated with autism spectrum disorder (ASD) through whole-genome sequencing (WGS) and provides a research guide to explore genotype-phenotype correlations in families carrying these rare variants.
Article
Biotechnology & Applied Microbiology
Ali Akbari, ZiJian Wang, Peisheng He, Dongqi Wang, Jangho Lee, I. L. Han, Guangyu Li, April Z. Gu
Summary: The review focuses on current knowledge about PAOs, particularly on bacteria, including their phylogenetic identities, metabolic pathways, and detection methods. The study also discusses the evidence of the ubiquitous presence of PAOs in nature and recognizes the need for further investigation into the unrevealed roles of PAOs.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Microbiology
Olga Karaseva, Georgii Ozhegov, Dilyara Khusnutdinova, Maria Siniagina, Elizaveta Anisimova, Farida Akhatova, Rawil Fakhrullin, Dina Yarullina
Summary: Lactiplantibacillus plantarum is a versatile bacterium widely used as a probiotic. In this study, the probiotic potential of a novel strain called L. plantarum FCa3L, isolated from fermented cabbage, was characterized through genome sequencing. The results showed that FCa3L had comparable properties to the reference strain, L. plantarum 8PA3, in terms of acid and bile tolerance, adhesiveness, H2O2 production, and acidification rate. FCa3L also exhibited superior antibacterial properties, although it had a higher antibiotic resistance gene content. The study provided genomic evidence supporting the adhesive and antibacterial properties, biosynthesis of bioactive metabolites, and safety of FCa3L, suggesting its potential as a probiotic.
Article
Genetics & Heredity
Ulykbek Kairov, Askhat Molkenov, Aigul Sharip, Saule Rakhimova, Madina Seidualy, Arang Rhie, Ulan Kozhamkulov, Maxat Zhabagin, Jong-Il Kim, Joseph H. Lee, Joseph D. Terwilliger, Jeong-Sun Seo, Zhaxybay Zhumadilov, Ainur Akilzhanova
Summary: Kazakhstan, located along the Great Silk Road, has a rich history and a multiethnic population. By sequencing and analyzing the genomes of five ethnic Kazakhs, this study identified genetic variants associated with higher risks of diseases and demonstrated the importance of genotype-phenotype relations at the population level.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Amnon Koren, Dashiell J. Massey, Alexa N. Bracci, Peter Robinson
Summary: TIGER is a computational approach for extracting DNA replication timing information from whole genome sequence data, applicable to any species with a contiguous genome assembly. Replication dynamics can be observed by analyzing DNA copy number along chromosomes, providing a straightforward approach for measuring replication timing.
Article
Microbiology
Jia Hui Wan, Lee-Mei Ng, Soon Zher Neoh, Rei Kajitani, Takehiko Itoh, Susumu Kajiwara, Kumar Sudesh
Summary: Aquitalea sp. USM4, isolated from Malaysia, is a bacteria that produces polyhydroxyalkanoate (PHA) with biodegradability and biocompatibility features. The genome analysis revealed important genes involved in PHA production, and the heterologous expression of phaC1 from Aquitalea sp. USM4 in Cupriavidus necator PHB(-)4 resulted in the incorporation of six different types of PHA monomers. This study provides valuable genomic information for understanding PHA biosynthesis.
ARCHIVES OF MICROBIOLOGY
(2023)
Article
Engineering, Environmental
Timothy Paez-Watson, Mark C. M. van Loosdrecht, S. Aljoscha Wahl
Summary: Understanding microbial communities and their regulation is important for new technologies. Resource allocation and biosynthesis in microbial communities are poorly understood. In this study, metabolic flux analysis was used to study the optimal phenotype of polyphosphate accumulating organisms (PAOs). The results validate limited anaerobic biosynthesis in PAOs and identify temperature-dependent resource allocation strategies.
Article
Environmental Sciences
Vinaya Kumar Katneni, Mudagandur Shashi Shekhar, Ashok Kumar Jangam, Karthic Krishnan, Sudheesh K. Prabhudas, Nimisha Kaikkolante, Dushyant Singh Baghel, Vijayan K. Koyadan, Joykrushna Jena, Trilochan Mohapatra
Summary: The study presents a high-quality genome assembly of Penaeus indicus, meeting reference standards for contigs and scaffolds among crustacean genomes. This assembly has a high number of protein-coding genes, repeat elements, and single nucleotide polymorphisms (SNPs). It provides valuable resources for genetic improvement, evolutionary studies, and stock management in shrimp fisheries and culture.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Agriculture, Dairy & Animal Science
Giulietta Minozzi, Barbara Lazzari, Maria Grazia De Iorio, Cecilia Costa, Emanuele Carpana, Paola Crepaldi, Rita Rizzi, Elena Facchini, Gustavo Gandini, Alessandra Stella, Giulio Pagnacco
Summary: This study aimed to characterize the population structure of Italian honeybees, identifying the genetic originality of Sicula and limited genetic introgression in A.m. ligustica. Through whole-genome sequencing, SNP variants were detected mapping on specific chromosomes.
Article
Microbiology
Qingxian Su, Dennis A. Bazylinski, Marlene Mark Jensen
Summary: Magnetotactic bacteria (MTB) are microorganisms that inhabit aquatic environments and are important in biogeochemical cycling. In this study, the influence of oxygen availability on intracellular storage of carbon and phosphorus in MTB was investigated. Oxygen had a strong effect on the storage of polyhydroxyalkanoate (PHA) and polyphosphate (polyP) granules in MTB cells, with significant changes in granule abundance and composition observed under different oxygen conditions.
FRONTIERS IN MICROBIOLOGY
(2023)