Article
Green & Sustainable Science & Technology
Xiafei Yin, Xuan Shan, Guobin Liang, Quanfa Zhou, Wei Lin
Summary: An acidophilic metal-resistant bacterial strain, Acidomyces acidothermus (A. acidothermus), was identified and optimized for its culture conditions using response surface methodology (RSM). The highest copper leaching rate (39.8%) was achieved at a temperature of 40°C, pH 3 in a 9k medium, and a rotation speed of 140 r/min. Scanning electron microscopy (SEM) images and a heatmap of differential metabolites indicated that A. acidothermus adsorbed on the surface of WPCBs and secreted extracellular polymeric substances (EPS), primarily D-glucuronic acid, suggesting an efficient mechanism for copper recovery from WPCBs.
Article
Genetics & Heredity
Sabrina Marin, Mayra Cortes, Mauricio Acosta, Karla Delgado, Camila Escuti, Diego Ayma, Cecilia Demergasso
Summary: Bioleaching presents potential applications in treating non-profitable reserve marginal resources, but lacks understanding of critical event attributes at the industrial level. By assessing the microbial-mineral interaction environment and quantifying microbial metabolic responses, some limiting factors can be addressed.
Article
Biochemistry & Molecular Biology
Yucui Jiang, Saixing Liu, Qipeng Yuan, Hao Liang
Summary: This study reported Zr-based acid-stable nucleotide coordination polymers for efficient immobilization of acidophilic enzymes, showing promising results in catalytic reactions. Among all tested metal ions, Zr4+/AMP CPs exhibited the highest acid stability and enzyme affinity for Chloroperoxidase immobilization, leading to robust reusability in the asymmetric synthesis with high conversion rate and enantiomeric excess values. The work demonstrated a novel acid-stable bioorganic and inorganic hybrid nanomaterial for immobilizing acidophilic enzymes.
JOURNAL OF INORGANIC BIOCHEMISTRY
(2021)
Article
Biotechnology & Applied Microbiology
Ryutaro Kawai, Yoshihiro Toya, Kenta Miyoshi, Manami Murakami, Teppei Niide, Takaaki Horinouchi, Tomoya Maeda, Atsushi Shibai, Chikara Furusawa, Hiroshi Shimizu
Summary: Co-culture is a promising approach to alleviate metabolic burden by dividing metabolic pathways into multiple modules and sharing conversion processes with different strains. Enhancing intermediate consumption rate is crucial for increasing target productivity. Adaptive laboratory evolution can improve mevalonate consumption in E. coli, leading to increased isoprenol production in a co-culture system.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Biochemistry & Molecular Biology
Andrea G. Marshall, Zer Vue, Heather K. Beasley, Kit Neikirk, Dominique Stephens, Celestine N. Wanjalla, Steven M. Damo, Joann Trejo, Piere Rodriguez-Aliaga, Colwyn Ansel Headley, Haysetta Shuler, Kaihua Liu, Nathan Smith, Edgar Garza-Lopez, Taylor Barongan, Estevao Scudese, Elsie Spencer, Jennifer Heemstra, Arnaldo Diaz Vazquez, Sandra A. Murray, Antentor Hinton Jr
Summary: Building a diverse and equitable laboratory is crucial for talent retention and the personal and professional growth of trainees. In order to enable trainees to achieve their highest success, strategies such as enhancing cultural competency and humility, establishing laboratory values, and developing equitable laboratory structures can create an inclusive laboratory environment.
Article
Engineering, Industrial
Frederico G. P. Moreira, Ana L. F. Ramos, Kewin R. C. Fonseca
Summary: This study evaluated the safety culture maturity in laboratories at the Civil Engineering Department of the Federal University of Para (UFPa), Brazil, and found that the laboratories are in a reactive maturity stage, with information, involvement, and commitment being the main organizational factors directly affecting safety culture maturity. The study results, based on students' perceptions, may advance safety culture maturity theories by incorporating discussions related to functionalist versus interpretive approaches, as well as organizational structure influences.
Article
Engineering, Geological
Reza Ahmadi-Naghadeh, Tingfa Liu, Ken Vinck, Richard J. Jardine, Stavroula Kontoe, Byron W. Byrne, Ross A. McAdam
Summary: This paper investigates the cyclic behavior of chalk and finds that it exhibits stability and elasticity during cyclic loading, with an improvement in stiffness without losing shear strength. However, cyclic failure can occur, leading to brittle collapse due to cracking and displacement-induced pore pressure reductions. The behavior of chalk is similar to the fatigue response of metals, concretes, and rocks.
Article
Engineering, Chemical
Z. Ye, M. Yahyaei, M. M. Hilden, M. S. Powell
Summary: Most mine sites use large coarse ore stockpiles as a buffer between the mine and the processing plant. However, the particle size distribution of the product drawn from these stockpiles can vary significantly over time due to size segregation phenomena. This research aims to develop a laboratory test to quantify the propensity of an ore pile to segregate and correlate these results to industrial stockpiles.
MINERALS ENGINEERING
(2022)
Article
Environmental Sciences
Pietro Fiorentin, Andrea Bertolo, Stefano Cavazzani, Sergio Ortolani
Summary: The use of RGB cameras in photometric applications has grown in various fields such as industrial applications, light engineering, and night sky quality analysis. This study compares the performance of a Sky Quality Meter (SQM) and an RGB camera. The results show that these two instruments have significantly different levels of spectral responsivity, and their outputs need to be corrected based on the spectral distribution of the sky light.
Review
Microbiology
Elizabeth L. Palavecino, Victoria L. Campodonico, Rosemary C. She
Summary: This mini-review provides practical recommendations on elaborating BCC rate reports, defining parameters for pre-set criteria, collecting and interpreting data, and including additional analysis in a BCC report.
JOURNAL OF CLINICAL MICROBIOLOGY
(2023)
Article
Computer Science, Artificial Intelligence
Bo Li, Lv Tang, Senyun Kuang, Mofei Song, Shouhong Ding
Summary: In this paper, a novel model for simultaneous stable co-saliency detection and object co-segmentation is proposed. Inspired by RNN-based models, a multi-path stable recurrent unit (MSRU) and a cross-order contrastive loss (COCL) are introduced to capture inter-image relations and address order-sensitive problem. Experimental results demonstrate the superiority of the proposed approach over state-of-the-art methods.
IEEE TRANSACTIONS ON IMAGE PROCESSING
(2022)
Article
Construction & Building Technology
Mudasir Nazeer, Kanish Kapoor, S. P. Singh
Summary: Pervious concrete is a special type of concrete that can be improved in strength and durability by changing the fine aggregate content. When using 20% of fine aggregates, pervious interlocking pavers have good permeability limits after 28 days, and a significant increase in compressive strength can be achieved by substituting 10% and 20% of fine aggregates.
INTERNATIONAL JOURNAL OF PAVEMENT ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Tatsiana Mikulchyk, Pamela Stoeva, Alicja Kaworek, Mohamed Oubaha, Brian Rogers, Suzanne Martin, Dervil Cody, Izabela Naydenova
Summary: This paper presents the development of a featured application of holographic optical elements (HOEs) with controlled diffraction efficiency and improved environmental stability. The approach is based on the use of a photopolymerisable hybrid sol-gel (PHSG) material, which has shown good recording capability, dimensional stability, and water resistance. The study focuses on the characterization of grating recording in PHSG, providing insights into the mechanisms of refractive index modulation and enhancing the potential for customisable HOEs.
APPLIED SCIENCES-BASEL
(2022)
Article
Evolutionary Biology
Oscar Istas, Marianna Szucs
Summary: Laboratory-selected native parasitoids show improved control of invasive targets, but their performance in natural environments and comparison to co-evolved specialists is unclear. Rearing in artificial diet did not impair the ability of laboratory-selected native parasitoids to locate and attack hosts in natural conditions. Specialist and generalist parasitoids have different biocontrol potentials in nature.
EVOLUTIONARY APPLICATIONS
(2023)
Article
Infectious Diseases
Paul R. Ingram, L. Barrett, E. Raby, P. Boan, G. A. Weaire-Buchanan, H. Darragh, P. Lloyd, I Kay, J. Flexman
Summary: Implementing an overnight laboratory service led to significantly shorter turnaround times for reporting blood culture results, resulting in more prompt initiation of effective antimicrobial therapies for patients, improving sepsis management outcomes.
EUROPEAN JOURNAL OF CLINICAL MICROBIOLOGY & INFECTIOUS DISEASES
(2021)
Article
Biotechnology & Applied Microbiology
Sabrina Gfrerer, Dennis Winkler, Julia Novion Ducassou, Yohann Coute, Reinhard Rachel, Johannes Gescher
Summary: This study demonstrates the existence of an S-layer protein on the cytoplasmic membrane of Candidatus Micrarchaeum harzensis A_DKE, suggesting that the ability to form an S-layer may be a common trait among Micrarchaeota. The research also provides insights into the interaction between Micrarchaeota and their host organisms, shedding light on the limited metabolic capabilities shared by several DPANN archaea.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Edina Klein, Janek Weiler, Michael Wagner, Minja Celikic, Christof M. Niemeyer, Harald Horn, Johannes Gescher
Summary: Aerobic granular sludge has become an increasingly popular method for wastewater treatment due to its ability to remove organic carbon, nitrogen, and phosphorus simultaneously. However, analyzing the processes and microbial population within the granules is challenging due to their microscale. In this study, a small-scale model system for aerobic granular sludge was introduced using a machine-assisted microfluidic cultivation platform. With this setup, it was possible to enrich specific microorganisms and investigate the influence of process parameters on wastewater treatment systems.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2022)
Letter
Multidisciplinary Sciences
Alice C. McHardy
Article
Biochemistry & Molecular Biology
Zhi-Luo Deng, Philipp C. Munch, Rene Mreches, Alice C. McHardy
Summary: This article introduces a novel software called RiboDetector, based on a bi-directional long short-term memory neural network, which can rapidly and accurately identify ribosomal RNA (rRNA) sequences from different types of RNA. The software produces fewer misclassifications compared to current state-of-the-art methods and has the ability to detect novel rRNA sequences. Additionally, RiboDetector has a much faster processing speed than other methods.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemical Research Methods
Fernando Meyer, Adrian Fritz, Zhi-Luo Deng, David Koslicki, Till Robin Lesker, Alexey Gurevich, Gary Robertson, Mohammed Alser, Dmitry Antipov, Francesco Beghini, Denis Bertrand, Jaqueline J. Brito, C. Titus Brown, Jan Buchmann, Aydin Buluc, Bo Chen, Rayan Chikhi, Philip T. L. C. Clausen, Alexandru Cristian, Piotr Wojciech Dabrowski, Aaron E. Darling, Rob Egan, Eleazar Eskin, Evangelos Georganas, Eugene Goltsman, Melissa A. Gray, Lars Hestbjerg Hansen, Steven Hofmeyr, Pingqin Huang, Luiz Irber, Huijue Jia, Tue Sparholt Jorgensen, Silas D. Kieser, Terje Klemetsen, Axel Kola, Mikhail Kolmogorov, Anton Korobeynikov, Jason Kwan, Nathan LaPierre, Claire Lemaitre, Chenhao Li, Antoine Limasset, Fabio Malcher-Miranda, Serghei Mangul, Vanessa R. Marcelino, Camille Marchet, Pierre Marijon, Dmitry Meleshko, Daniel R. Mende, Alessio Milanese, Niranjan Nagarajan, Jakob Nissen, Sergey Nurk, Leonid Oliker, Lucas Paoli, Pierre Peterlongo, Vitor C. Piro, Jacob S. Porter, Simon Rasmussen, Evan R. Rees, Knut Reinert, Bernhard Renard, Espen Mikal Robertsen, Gail L. Rosen, Hans-Joachim Ruscheweyh, Varuni Sarwal, Nicola Segata, Enrico Seiler, Lizhen Shi, Fengzhu Sun, Shinichi Sunagawa, Soren Johannes Sorensen, Ashleigh Thomas, Chengxuan Tong, Mirko Trajkovski, Julien Tremblay, Gherman Uritskiy, Riccardo Vicedomini, Zhengyang Wang, Ziye Wang, Zhong Wang, Andrew Warren, Nils Peder Willassen, Katherine Yelick, Ronghui You, Georg Zeller, Zhengqiao Zhao, Shanfeng Zhu, Jie Zhu, Ruben Garrido-Oter, Petra Gastmeier, Stephane Hacquard, Susanne Haeussler, Ariane Khaledi, Friederike Maechler, Fantin Mesny, Simona Radutoiu, Paul Schulze-Lefert, Nathiana Smit, Till Strowig, Andreas Bremges, Alexander Sczyrba, Alice Carolyn McHardy
Summary: This study presents the results of the second round of the Critical Assessment of Metagenome Interpretation challenges (CAMI II), which is a community-driven effort for comprehensively benchmarking tools for metagenomics data analysis. The results show substantial improvements in assembly, but related strains and assembly quality still pose challenges. Taxon profilers and binners excel at higher bacterial ranks but underperform for viruses and Archaea. The need to improve reproducibility is emphasized by the clinical pathogen detection results.
Article
Immunology
Sven-Kevin Hotop, Susanne Reimering, Aditya Shekhar, Ehsaneddin Asgari, Ulrike Beutling, Christine Dahlke, Anahita Fathi, Fawad Khan, Marc Luetgehetmann, Rico Ballmann, Andreas Gerstner, Werner Tegge, Luka Cicin-Sain, Ursula Bilitewski, Alice C. McHardy, Mark Broenstrup
Summary: This study constructed a microarray capable of capturing the IgA, IgG, and IgM antibody response of individuals infected with SARS-CoV-2. The research identified specific peptides associated with the severity of COVID-19 and highlighted potential viral binding epitopes that could be used as vaccine candidates.
EMERGING MICROBES & INFECTIONS
(2022)
Editorial Material
Genetics & Heredity
Tomislav Cernava, Daria Rybakova, Francois Buscot, Thomas Clavel, Alice Carolyn McHardy, Fernando Meyer, Folker Meyer, Jorg Overmann, Barbel Stecher, Angela Sessitsch, Michael Schloter, Gabriele Berg
Summary: This article introduces the key issues regarding the current system for metadata submission in omics research and proposes the development of a global metadata system. The system should be easy to use, structured in a hierarchical way, and compatible with existing microbiome data repositories. The article also emphasizes the need for greater awareness and engagement of the scientific community in international legal issues related to genetic resource and sequence sharing.
ENVIRONMENTAL MICROBIOME
(2022)
Article
Biotechnology & Applied Microbiology
Carine Poussin, Lusine Khachatryan, Nicolas Sierro, Vijay Kumar Narsapuram, Fernando Meyer, Vinay Kaikala, Vandna Chawla, Usha Muppirala, Sunil Kumar, Vincenzo Belcastro, James N. D. Battey, Elena Scotti, Stephanie Boue, Alice C. McHardy, Manuel C. Peitsch, Nikolai Ivanov, Julia Hoeng
Summary: This research summarizes the results of a challenge designed to evaluate the performance of existing metagenomics software and confirms the robustness of these results through extended analysis. The study finds that kmer-based pipelines using Kraken/Bracken or CLARK-S perform the best across most microbiome datasets. Additionally, the performance of these tools can be further enhanced by removing non-reliably predicted low-abundance species using adaptive filtering thresholds.
Article
Agricultural Engineering
Daniel Haerrer, Ahmed Elreedy, Rowayda Ali, Andrea Hille-Reichel, Johannes Gescher
Summary: This study investigated the impacts of toxic ions/acids in real fermentation-hydrolysate on the model exoelectrogenic G. sulfurreducens. Different concentrations of acetate, butyrate, propionate, Na+, and K+ were tested individually and in combination to understand their effects on planktonic growth. The study found that excess Na+ (>= 100 mM) causes inhibition that can be reduced by K+ replacement, butyrate (>= 10 mM) induces higher toxicity than propionate, and hydrolysate induces synergistic inhibition where organic constituents are more significant than Na+. The research concluded that using G. sulfurreducens in bioelectrochemical systems can effectively recover energy from fermentation-hydrolysate.
BIORESOURCE TECHNOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Edina M. M. Klein, Melanie T. T. Knoll, Johannes Gescher
Summary: Microbial electrochemical systems (MESs) are a versatile platform technology focused on power or energy production, often combined with substrate conversion and value-added compound production. This review provides a brief summary of the terminology and essential biological background of MES technology. Recent research on improvements at the biofilm-electrode interface is discussed, comparing biotic and abiotic approaches. The review concludes with future directions for increasing process efficiency in MES technology.
MICROBIAL BIOTECHNOLOGY
(2023)
Article
Biology
Hueseyin Anil Guenduez, Martin Binder, Xiao-Yin To, Rene Mreches, Bernd Bischl, Alice C. McHardy, Philipp C. Muench, Mina Rezaei
Summary: Deep learning in bioinformatics is often limited by the availability of labeled data. This study introduces Self-GenomeNet, a self-supervised learning technique specialized for genomic data, which leverages reverse-complement sequences and predicts targets of different lengths to effectively learn short- and long-term dependencies. Self-GenomeNet outperforms other self-supervised methods and requires significantly fewer labeled training data compared to standard supervised training. The learned representations of Self-GenomeNet demonstrate good generalization to new datasets and tasks, suggesting its potential to substantially improve the performance of genomic models.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Andrew Dickson, Ehsaneddin Asgari, Alice C. McHardy, Mohammad R. K. Mofrad
Review
Microbiology
Laura-Alina Philipp, Katja Buehler, Roland Ulber, Johannes Gescher
Summary: Biofilm systems are adaptable and offer a wide range of opportunities due to their ability to optimize metabolism and adhere in continuous systems. The field of beneficial biofilms is rapidly evolving, with increasing applications being explored.
NATURE REVIEWS MICROBIOLOGY
(2023)
Review
Microbiology
Curtis Huttenhower, Robert D. Finn, Alice Carolyn Mchardy
Summary: Microbiome data has become large and complex, making it difficult to identify and use the available resources. Following best practices for data deposition requires substantial effort with little obvious reward. There is a gap in microbiome-specific resources for data sharing or reproducibility. This article outlines available best practices and advocates for their enforcement and incentivization.
NATURE MICROBIOLOGY
(2023)
Article
Microbiology
Melanie Tabea Knoll, Emely Fuderer, Johannes Gescher
Summary: The utilization of a synthetic hydrogel matrix with S. oneidensis cells improves anodic processes in BES, leading to a significant increase in current density. This has the potential for higher space-time yields in industrial applications.