Article
Biochemical Research Methods
Ryan R. Wick, Kathryn E. Holt
Summary: Polypolish is a new short-read polisher that uses all-per-read alignments to fix errors in repeat sequences that other polishers cannot. It performed well in benchmarking tests and introduced minimal errors during the polishing process.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ryan R. Wick, Louise M. Judd, Louise T. Cerdeira, Jane Hawkey, Guillaume Meric, Ben Vezina, Kelly L. Wyres, Kathryn E. Holt
Summary: Trycycler is a tool that produces a consensus assembly from multiple input assemblies to reduce errors in long-read sequencing. Post-assembly polishing further improves accuracy. Multiple users converge on similar assemblies that are more accurate than those produced by automated assembly tools.
Article
Biotechnology & Applied Microbiology
Amanda T. S. Albanaz, Mark Carrington, Alexander O. Frolov, Anna I. Ganyukova, Evgeny S. Gerasimov, Alexei Y. Kostygov, Julius Lukes, Marina N. Malysheva, Jan Votypka, Alexandra Zakharova, Kristina Zahonova, Sara L. Zimmer, Vyacheslav Yurchenko, Anzhelika Butenko
Summary: This study conducted genome sequencing and analysis on previously overlooked trypanosomatid species, revealing their genomic diversity and chromosomal variations. The findings provide a solid foundation for future research on the genetic basis of life cycle changes and adaptation to different hosts in this species.
Article
Microbiology
David A. Yarmosh, Juan G. Lopera, Nikhita P. Puthuveetil, Patrick Ford Combs, Amy L. Reese, Corina Tabron, Amanda E. Pierola, James Duncan, Samuel R. Greenfield, Robert Marlow, Stephen King, Marco A. Riojas, John Bagnoli, Briana Benton, Jonathan L. Jacobs
Summary: The quality, traceability, and curation of public genomics data have significant impacts on microbial genomics research. Issues with NCBI's RefSeq bacterial genome assemblies, such as completeness, mutations, and gaps in traceability, were identified. Improving accountability for data depositors and raising expectations for quality among researchers are essential for addressing these issues.
Article
Materials Science, Ceramics
Fu Jiajun, Shen Tao, Wu Jia, Wang Chen
Summary: This article reviews the antimicrobial mechanism and recent progress of nanozymes as a new generation of artificial enzymes with unique physical and chemical properties in antibacterial research, and provides prospects for future research.
JOURNAL OF INORGANIC MATERIALS
(2021)
Article
Plant Sciences
William G. Voelker, Krittika Krishnan, Kapeel Chougule, Louie C. Alexander, Zhenyuan Lu, Andrew Olson, Doreen Ware, Kittikun Songsomboon, Cristian Ponce, Zachary W. Brenton, J. Lucas Boatwright, Elizabeth A. Cooper
Summary: To enhance the potential of sorghum as a bioenergy feedstock, researchers analyzed the genomic mechanisms and identified a large number of structural variations and single nucleotide polymorphisms. These resources can be used to study the genetic differences between sweet and cellulosic genotypes and their associated phenotypes.
FRONTIERS IN PLANT SCIENCE
(2023)
Article
Plant Sciences
Jonathan Bramsiepe, Anders K. Krabberod, Katrine N. Bjerkan, Renate M. Alling, Ida M. Johannessen, Karina S. Hornslien, Jason R. Miller, Anne K. Brysting, Paul E. Grini
Summary: Arabidopsis thaliana diverged from A. arenosa and A. lyrata at least 6 million years ago. The species differ in genome-wide polymorphisms and morphological traits. Hybridization barriers, particularly those based on the triploid endosperm, contribute to reproductive isolation. The MADS-box type I gene family, which is expressed in the endosperm, likely plays a role in these barriers.
Article
Chemistry, Multidisciplinary
Antonella Schiavone, Nicola Pugliese, Rossella Samarelli, Cosimo Cumbo, Crescenzio Francesco Minervini, Francesco Albano, Antonio Camarda
Summary: The study demonstrates the importance of tailored bioinformatic analysis in achieving successful assembly of Salmonella enterica ser. Bovismorbificans genome by modifying adjustable parameters in Canu.
APPLIED SCIENCES-BASEL
(2022)
Article
Biochemical Research Methods
Jeremie S. Kim, Can Firtina, Meryem Banu Cavlak, Damla Senol Cali, Can Alkan, Onur Mutlu
Summary: Motivation: A fast and efficient tool called FastRemap is introduced for remapping reads between genome assemblies. It provides a 7.82x speedup (6.47x on average) and consumes as low as 61.7% of peak memory compared to the state-of-the-art tool CrossMap.
Article
Microbiology
Arthur W. Pightling, Hugh Rand, James Pettengill
Summary: Whole-genome sequence databases are expanding, posing challenges in comparing recent data to historical samples but also offering opportunities for evolutionary analyses. The evolutionary rates for 22 Salmonella enterica serotypes were measured, and a rate of 1.97 single-nucleotide polymorphisms (SNPs) per year is proposed for determining genome sequence matches.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biology
Sergio Arredondo-Alonso, Anna K. Pontinen, Francois Cleon, Rebecca A. Gladstone, Anita C. Schurch, Pal J. Johnsen, Orjan Samuelsen, Jukka Corander
Summary: The introduction of long-read sequencing technologies allows for bridging contiguous sequences into complete genomes, although the higher costs limit the number of bacterial isolates that can be long-read sequenced. The 96 barcoding kit from Oxford Nanopore Technologies successfully generated near-complete chromosomal sequences for 96 Escherichia coli isolates. The combination of ONT sequencing data with short-read sequencing data is still highly desirable to achieve optimal genome accuracy and completeness.
Article
Plant Sciences
Cheng Zou, Surya Sapkota, Rosa Figueroa-Balderas, Jeff Glaubitz, Dario Cantu, Brewster F. Kingham, Qi Sun, Lance Cadle-Davidson
Summary: Fine mapping of quantitative trait loci (QTL) is essential in modern breeding practice. This study presents a multitiered haplotypic marker system that improves fine mapping accuracy and successfully identifies a grapevine downy mildew resistance locus. The strategy combines different resolutions of genome sequencing and integrates high-density genetic information to pinpoint the genetic basis of QTLs.
Article
Chemistry, Multidisciplinary
Swati Kaushik, Jijo Thomas, Vineeta Panwar, Preethi Murugesan, Vianni Chopra, Navita Salaria, Rupali Singh, Himadri Shekar Roy, Rajesh Kumar, Vikas Gautam, Deepa Ghosh
Summary: During the COVID-19 pandemic, the excessive use of antibiotics could lead to an increase in multi-drug resistant bacteria. Magnetic nanoparticle-mediated hyperthermia-induced antimicrobial therapy has shown potential as an antibiotic-free approach for combating bacterial infections.
Article
Biochemical Research Methods
Xiaotao Wang, Feng Yue
Summary: HiCLift is a fast and efficient tool for converting genomic coordinates of chromatin interaction data from one assembly to another, including the latest T2T-CHM13 genome. Compared to directly remapping raw reads to a different genome, HiCLift runs on average 42 times faster (hours vs. days), while producing nearly identical contact matrices. Importantly, HiCLift can directly convert human patient sample data, where raw sequencing reads may be hard to acquire or unavailable.
Article
Agronomy
Pan-Pan Liu, En-Ping Yu, Zong-Jian Tan, Hong-Mei Sun, Wei-Guang Zhu, Zheng-Feng Wang, Hong-Lin Cao
Summary: This study reports the genome assemblies of two common Ormosia species in South China, providing important data for genetic and biogeographic research on Ormosia species and serving as a reference for species breeding.
Article
Biochemistry & Molecular Biology
Diogo Henrique Kita, Gisele Alves de Andrade, Juliana Morais Missina, Kahoana Postal, Viktor Kalbermatter Boell, Francielli Sousa Santana, Ingrid Fatima Zattoni, Isadora da Silva Zanzarini, Vivian Rotuno Moure, Fabiane Gomes de Moraes Rego, Geraldo Picheth, Emanuel Maltempi de Souza, David A. Mitchell, Suresh Ambudkar, Giovana Gioppo Nunes, Glaucio Valdameri
Summary: The study found that polyoxovanadates can serve as inhibitors of ABC drug transporters, selectively inhibiting P-glycoprotein with V-10 and V-18 being the most promising compounds.
Article
Soil Science
Eliane Cristina Gruszka Vendruscolo, Dany Mesa, Emanuel Maltempi de Souza
Summary: The study evaluated the impact of no-tillage and fallow systems on soil microbiota. It found that the rhizosphere microbial community diversity was significantly lower in the no-tillage system compared to the fallow system, with each having unique microbial populations.
APPLIED SOIL ECOLOGY
(2022)
Article
Virology
Douglas Adamoski, Valter Antonio de Baura, Ana Carolina Rodrigues, Carla Adriane Royer, Mateus Nobrega Aoki, Marcel Kruchelski Tscha, Ana Claudia Bonatto, Roseli Wassem, Meri Bordignon Nogueira, Sonia Mara Raboni, Bernardo Montesanti Machado de Almeida, Edvaldo da Silva Trindade, Daniela Fiori Gradia, Emanuel Maltempi Souza, Jaqueline Carvalho de Oliveira
Summary: Screening efforts and genomic surveillance are crucial for evaluating the progress of the COVID-19 pandemic. A study in Curitiba, Brazil analyzed COVID-19 cases, conducted diagnosis and genotyping, and found that the Omicron variant quickly became dominant. Vaccination was associated with reduced mortality rates.
Article
Biochemistry & Molecular Biology
Cleiton de Paula Soares, Michelle Zibetti Trada-Sfeir, Leonardo Araujo Terra, Jessica de Paula Ferreira, Carlos Magno Dos-Santos, Izamara Gesiele Bezerra de Oliveira, Jean Luiz Simoes Araujo, Carlos Henrique Salvino Gadelha Meneses, Emanuel Maltempi de Souza, Jose Ivo Baldani, Marcia Soares Vidal
Summary: This study provides a comprehensive analysis of the early transcriptional response of Gluconacetobacter diazotrophicus to iron limitations, revealing the regulatory mechanisms of genes related to iron homeostasis and identifying genes that are overexpressed under iron-limited conditions. Additionally, the study demonstrates that the fur protein of G. diazotrophicus can complement an E. coli fur mutant.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Anahi Coniglio, Giovanni Larama, Romina Molina, Veronica Mora, Daniela Torres, Anelis Marin, Andres Ignacio Avila, Coline Lede NoirCarlan, Leonardo Erijman, Eva Lucia Figuerola, Emanuel Maltempi de Souza, Fabricio Cassan
Summary: Azospirillum is a crucial plant growth promoting rhizobacteria used in global agriculture. This study reveals that Azospirillum inoculation can alter the microbial community structure in maize rhizosphere, resulting in an increase in the relative abundance of beneficial bacterial genera.
JOURNAL OF SOIL SCIENCE AND PLANT NUTRITION
(2022)
Article
Chemistry, Analytical
Gustavo Martins, Jeferson L. Gogola, Lucas H. Budni, Mauricio A. Papi, Maritza A. T. Bom, Maria L. T. Budel, Emanuel M. de Souza, Marcelo Muller-Santos, Breno C. B. Beirao, Craig E. Banks, Luiz H. Marcolino-Junior, Marcio F. Bergamini
Summary: The present work reports an innovative approach for constructing immunosensors using graphene quantum dots and polyhydroxybutyric acid modified carbon electrodes. This approach allows for the detection of anti-S antibodies, showing promising results in terms of selectivity and sensitivity. The proposed sensor has the potential to be developed into a single-drop immunosensor.
ANALYTICA CHIMICA ACTA
(2022)
Article
Multidisciplinary Sciences
Regis Goulart Rosa, Julia Spinardi, Kristen E. Allen, Joselia Manfio, Cintia Laura Pereira de Araujo, Mirian Cohen, Caroline Cabral Robinson, Daniel Sganzerla, Diogo Ferreira, Emanuel Maltempi de Souza, Jaqueline Carvalho de Oliveira, Daniela Fiori Gradia, Ana Paula Carneiro Brandalize, Gabriela Almeida Kucharski, Fernando Pedrotti, Cristina de Oliveira Rodrigues, Moe H. Kyaw, Graciela Del Carmen Morales Castillo, Amit Srivastava, John M. McLaughlin, Maicon Falavigna
Summary: This study aims to evaluate the effectiveness of the Pfizer-BioNTech BNT162b2 vaccine against symptomatic COVID-19 and related complications in a real-world setting in Brazil. A case-control study is being conducted among patients seeking care in the public health system, with follow-up and regular telephone interviews. The study findings will be disseminated through peer-reviewed publications and conference presentations.
Article
Biochemical Research Methods
Erick Parize, Edileusa C. M. Gerhardt, Ana C. M. Oliveira, Fabio O. Pedrosa, Emanuel M. Souza, Luciano F. Huergo, Maria B. R. Steffens
Summary: The study successfully heterologously expressed and purified the Rho protein from the diazotrophic environmental bacterium Azospirillum brasilense, showing its similarity to the E. coli orthologue. The purified AbRho protein exhibited correctly folded and active characteristics, indicating it is a RNA-dependent NTPase enzyme.
PROTEIN EXPRESSION AND PURIFICATION
(2022)
Article
Microbiology
Camila P. Perico, Camilla R. De Pierri, Giuseppe Pasqualato Neto, Danrley R. Fernandes, Fabio O. Pedrosa, Emanuel M. de Souza, Roberto T. Raittz
Summary: This study tracked the development of the COVID-19 pandemic in Brazil from a genomic/proteomic perspective and analyzed the comparative and evolutionary panorama of the lineages in the country. The study found two different genetic profiles of the epidemics in Brazil, with the emergence of the more aggressive P.1 lineages in the second wave. The unbalanced sequencing among Brazilian states may have facilitated the silent entry and dissemination of P.1 and other dangerous variants.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Mycology
Nickolas Menezes da Silva, Guilherme Fonseca Reis, Flavia de Fatima Costa, Maria Eduarda Grisolia, Marlon Roger Geraldo, Bruno Paulo Rodrigues Lustosa, Bruna Jacomel Favoreto de Souza Lima, Vinicius Almir Weiss, Emanuel Maltempi de Souza, Ruoyu Li, Yinggai Song, Mariana Machado Fidelis Nascimento, Diogo Robl, Renata Rodrigues Gomes, G. Sybren de Hoog, Vania Aparecida Vicente
Summary: This study focused on the sequencing, assembly, and description of the whole genome of Cladophialophora exuberans, a black yeast related fungus, with an emphasis on genes and pathways related to carbon and toxin management, tolerance and bioremediation of lead and copper, and metal homeostasis. The results showed that the strain exhibited growth inhibition at minimum inhibitory and fungicidal concentrations of copper and lead, and could grow at higher concentrations in agar tests. In addition, the strain demonstrated uptake capacities of copper and lead in heavy metal bioremediation assays. This study contributed to the annotation of genes involved in heavy metal homeostasis and provided insights into the mechanisms of tolerance and adaptation to extreme conditions.
Article
Chemistry, Analytical
Gustavo Martins, Helena R. Galeski, Gabrielle A. Andrade, Marcia G. P. Valenga, Maria K. Ramos, Aldo J. G. Zarbin, Bruno C. Janegitz, Marcelo Mueller-Santos, Emanuel M. de Souza, Luiz Humberto Marcolino-Junior, Marcio F. Bergamini
Summary: Researchers proposed a new method for assembling an electrochemical immunosensor based on a one-step approach for selective layer formation, which is crucial for rapid and reliable diagnostic tests for new viruses and diseases. This method successfully detected SARS-CoV-2 nucleocapsid protein in different matrices with low detectable values, and demonstrated selectivity against interferents. The proposed assembly strategy reduces cost, analysis time, and waste generation, making it a suitable and reliable alternative for healthcare diagnostics.
ANALYTICA CHIMICA ACTA
(2023)
Article
Soil Science
Jessica Pereira de Souza, Fabiane Machado Vezzani, Tatiana Suzin Lazeris, Glaciela Kaschuk, Emanuel Maltempi de Souza, Eduardo Balsanelli, Deborah Pinheiro Dick, Helio Antonio Wood Joris, Cimelio Bayer
Summary: Crop system plays a crucial role in shaping soil microbial communities and organic matter content. This study investigates the long-term effects of different crop systems on soil composition and microbial diversity in subtropical soil. The results show that the current crop species significantly influence microbial community structure and diversity, while the long-term history of crop rotation has a relatively smaller impact. Crop rotation increases the proportion of carbohydrate-derived organic matter, while crop succession increases the proportion of alkyl-C and N/O alkyl-C. Crop species richness in rotation maintains soil functions and enhances the formation of biochemically labile organic matter, contributing to soil ecosystem functioning.
SOIL & TILLAGE RESEARCH
(2023)
Article
Environmental Sciences
Ricardo Belmonte-Lopes, Carlos E. R. Barquilha, Caroline Kozak, Demian S. Barcellos, Barbara Z. Leite, Fernanda J. O. Gomes da Costa, William L. Martins, Pamela E. Oliveira, Edy H. R. A. Pereira, Cesar R. Mota Filho, Emanuel M. de Souza, Gustavo R. C. Possetti, Vania A. Vicente, Ramiro G. Etchepare
Summary: The COVID-19 pandemic led to the collapse of healthcare systems and the emergence of wastewater-based epidemiology. This study conducted SARS-CoV-2 wastewater surveillance in Curitiba, Brazil, and found a correlation between viral loads and reported cases. The approach used proved to be a robust early warning system that can aid public decision-making and health interventions.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Biology
Flavia de Fatima Costa, Renata Carolini Souza, Morgana Ferreira Voidaleski, Amanda Bombassaro, Giovanna Zuzarte Candido, Nickolas Menezes da Silva, Diogo Robl, Leandro Ferreira Moreno, Vinicius Almir Weiss, Roberto Tadeu Raittz, Mauro Antonio Castro, Renata Rodrigues Gomes, Juliana Vitoria Messias Bittencourt, Gerrit Sybren de Hoog, Mariangela Hungria, Vania Aparecida Vicente
Summary: This study analyzed the abundance of pathogenic fungi in Cerrado soils using metagenomic sequences. The results showed that the fungal abundance was lower in soils under no-tillage and conventional tillage treatments compared to native soils.
BRAZILIAN ARCHIVES OF BIOLOGY AND TECHNOLOGY
(2022)
