Article
Biochemical Research Methods
Stefano Camborda, Jan-Niklas Weder, Nadine Toepfer
Summary: CobraMod is a Python package for pathway-centric modification and extension of genome-scale metabolic networks. It integrates data from different metabolic pathway databases and user-curated information, and provides high quality metabolic reconstructions.
Article
Biology
Annette R. Rowe, Farshid Salimijazi, Leah Trutschel, Joshua Sackett, Oluwakemi Adesina, Isao Anzai, Liat H. Kugelmass, Michael H. Baym, Buz Barstow
Summary: Extracellular electron transfer (EET) enables microbial electron uptake for the synthesis of complex organic molecules, but there are significant gaps in understanding the mechanism and genetics of electron uptake.
COMMUNICATIONS BIOLOGY
(2021)
Article
Agriculture, Multidisciplinary
Mengli Li, Yejiao Luo, Miaomiao Hu, Chenchen Li, Zhu Liu, Tao Zhang
Summary: In this study, an efficient E. coli cell factory was engineered to produce 2'/3-fucosyllactose (2'/3-FL), a beneficial compound for infant health. The strategy involved metabolic network remodeling and resulted in high yields of 2'-FL and 3-FL. This work provides a safe chassis for the production of other lactose-independent human milk oligosaccharides (HMOs) using E. coli as the host.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Chemistry, Applied
Miaomiao Hu, Mengli Li, Chenchen Li, Tao Zhang
Summary: In this study, an efficient engineered strain for the biosynthesis of LNFP I was reported by rational design of metabolic pathways in Escherichia coli. The engineered strains produced high yields of LNFP I in fed-batch cultivation, with a conversion rate of lacto-N-tetraose to LNFP I reaching the highest level reported so far. The LNFP I-produced platform established here is broadly suitable for the production of complex and branched oligosaccharides.
CARBOHYDRATE POLYMERS
(2022)
Article
Multidisciplinary Sciences
Seirana Hashemi, Zahra Razaghi-Moghadam, Zoran Nikoloski
Summary: This study introduces the concept of absolute flux trade-offs and presents a constraint-based approach called FluTO for identifying and enumerating flux trade-offs in metabolic networks. The research demonstrates that flux trade-offs are specific to carbon sources and are related to reactions involved in growth processes.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Qiang Yang, Dongbo Cai, Wenshou Chen, Huiying Chen, Wei Luo
Summary: By analyzing the metabolism of an L-threonine over-producing strain, several important target sites were identified, and the example of metabolic regulation confirmed that combined metabolic analysis could improve the production of threonine in E. coli.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2022)
Article
Agricultural Engineering
Lian Wang, Ning Li, Shiqin Yu, Jingwen Zhou
Summary: Caffeic acid, a widely used phenylpropanoid in the medical industry, can be produced through microbial fermentation as a green strategy. To enhance the production of caffeic acid in Escherichia coli, the competing pathways for L-tyrosine synthesis were deactivated and the biosynthesis pathway of the cofactor FAD and the expression of polyphenol transporters were improved. Transcriptomics analysis identified potential transporters that upregulated the production of caffeic acid in engineered E. coli. Overexpression of ycjP, a previously identified sugar ABC transporter permease, significantly increased the titer of caffeic acid to 775.7 mg/L. In a 5-L fermenter, the titer was further improved to 7922.0 mg/L, the highest achieved by microorganisms.
BIORESOURCE TECHNOLOGY
(2023)
Article
Agriculture, Multidisciplinary
Wenxian Liu, Jing Peng, Sini Zou, Liting Xu, Haina Cheng, Yuguang Wang, Zhu Chen, Hongbo Zhou
Summary: This study achieved efficient biosynthesis of colanic acid through fine regulation and also revealed the decrease in saturated fatty acid content in the cell membrane caused by CA accumulation.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Article
Biochemical Research Methods
Joshua A. M. Kaste, Yair Shachar-Hill
Summary: The study demonstrates that integrating relative gene expression levels into metabolic flux predictions improves the accuracy of the predictions in a multi-tissue system.
Article
Biochemistry & Molecular Biology
Harpreet Kaur, Manmohit Kalia, Vikram Singh, Neelam Taneja
Summary: This study utilized computational methods to screen potential inhibitors for Escherichia coli, a significant bacterial pathogen. The results have important implications for combating antibiotic resistance.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Multidisciplinary Sciences
Xinfang Song, Mingyu Dong, Min Liu
Summary: The article introduces a new metabolic pathway design tool called PyMiner, which can effectively simplify metabolic networks, improve search efficiency, and demonstrate excellent performance.
Article
Biochemical Research Methods
Zahra Razaghi-Moghadam, Zoran Nikoloski
Summary: Existing computational approaches often neglect the impact of gene expression regulation on metabolic engineering strategies. This study finds that the association of genes with multiple reactions may render engineering strategies infeasible at the flux level, and proposes a constraint-based approach called GeneReg to facilitate the design of feasible strategies at the gene level.
Article
Biochemical Research Methods
Xianghua Peng, Fang Liu, Ping Liu, Xing Li, Xinguo Lu
Summary: This study introduced a metabolic pathway based driver gene identification method (pathDriver) to distinguish different cancer types/subtypes. By using a protein-protein interaction network combined with metabolic pathways to construct a pathway network, the collaborative impact factor of genes in the pathway network was evaluated using Interaction Frequency (IF) and Inverse Pathway Frequency (IPF) to identify cancer-specific driver genes. The application of this method to 16 types of TCGA cancers for pan-cancer analysis successfully identified biologically significant known cancer genes and potential new candidate genes.
CURRENT BIOINFORMATICS
(2021)
Article
Microbiology
Mitsuko Hayashi-Nishino, Kota Aoki, Akihiro Kishimoto, Yuna Takeuchi, Aiko Fukushima, Kazushi Uchida, Tomio Echigo, Yasushi Yagi, Mika Hirose, Kenji Iwasaki, Eitaro Shin'ya, Takashi Washio, Chikara Furusawa, Kunihiko Nishino
Summary: This study utilizes a computational method to identify antibiotic-resistant bacteria cells without the use of antibiotics. By classifying TEM images of enoxacin-sensitive and enoxacin-resistant Escherichia coli cells using a convolutional neural network, the method accurately identifies resistant cells and distinguishes them based on differences in the envelope. The study also identifies four genes strongly associated with the image features of enoxacin-resistant cells.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Yue Wang, Disheng Zhou, Hongshun Yang
Summary: In recent years, there have been increasing outbreaks of six major Escherichia coli strains linked to wheat flour consumption, highlighting the importance of adopting antimicrobial treatment during flour production. This study evaluated the effectiveness of thermal treatment, a typical sanitizing approach, against these six strains in wheat flour and explored the underlying antimicrobial mechanisms. The findings showed that thermal treatment at 60 and 70 degrees C significantly reduced the loads of all strains in wheat flour. Additionally, activated heat shock protein synthesis, expedited glycolysis, and enhanced osmotic protection were identified as major metabolic alteration patterns in the E. coli strains to cope with heat stress. These findings provide a scientific basis for incorporating a thermal inactivation step in wheat flour production.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Ecology
Derek Ping, Tong Wang, David T. Fraebel, Sergei Maslov, Kim Sneppen, Seppe Kuehn
Article
Physics, Multidisciplinary
Bjarke Frost Nielsen, Lone Simonsen, Kim Sneppen
Summary: Although COVID-19 has caused severe suffering globally, the efficacy of nonpharmaceutical interventions has been greater than typical models have predicted. Evidence is mounting that the pandemic is characterized by superspreading, which requires modeling at the scale of individuals. Using a mathematical model, it is shown that superspreading drastically enhances mitigations which reduce the overall personal contact number, with social clustering further increasing this effect.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Jan Fabio Nickels, Ashleigh Katrine Edwards, Sebastian Jespersen Charlton, Amanda Moller Mortensen, Sif Christine Lykke Hougaard, Ala Trusina, Kim Sneppen, Genevieve Thon
Summary: The study found that heterochromatin establishment shows exponential decays, with establishment periods varying from a few generations to over 200 generations. This indicates individual regions may be silenced in sudden bursts on a chromatin level, potentially suggesting a general mode of heterochromatin propagation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Multidisciplinary Sciences
Kim Sneppen, Bjarke Frost Nielsen, Robert J. Taylor, Lone Simonsen
Summary: The overdispersion of COVID-19 transmission gives the virus a weakness: reducing contacts between people who do not regularly meet would significantly reduce the pandemic, while reducing repeated contacts in defined social groups would be less effective.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Physics, Condensed Matter
Bjarke Frost Nielsen, Kim Sneppen, Lone Simonsen, Joachim Mathiesen
Summary: The study suggests that contact tracing can be significantly effective in reducing the spread of COVID-19 in workplace environments and realistic social networks, highlighting the importance of considering the impact of social network structure and heterogeneous social activities on contact tracing strategies.
EUROPEAN PHYSICAL JOURNAL B
(2021)
Article
Physics, Multidisciplinary
Yeonghoon Kim, Ludvig Lizana, Jae-Hyung Jeon
Summary: The 3D folding and macromolecular size of chromosomes determine their transport characteristics. The fractal globule-like chromosome structure accelerates macromolecular diffusion and target search.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Gustav S. Halvorsen, Lone Simonsen, Kim Sneppen
Summary: This study models the impact of behavior changes on the transmission of Ebola virus and finds that behavior changes can explain why local outbreaks of Ebola recede before substantial international aid is mobilized during the 2014-2016 epidemic.
Article
Multidisciplinary Sciences
Stanley Brown, Namiko Mitarai, Kim Sneppen
Summary: Bacteriophage A is a temperate virus that infects Escherichia coli. The protection provided by A lysogen against A-sensitive bacteria is sensitive to the growth state of the mixed culture and is dependent on bacterial energy metabolism. However, a mutant of the A tail protein, AJ, is not affected by these factors and retains its protective function.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemical Research Methods
Anastasios Marantos, Namiko Mitarai, Kim Sneppen
Summary: This study finds that phages and bacteria can coexist and maintain ecosystems with a high diversity of strains. The kill the winner model, where virulent phages prey on fast-growing bacteria and suppress the competitive exclusion of slower-growing bacteria, can explain this diversity. Additionally, the occasional elimination of even the fastest-growing bacteria strains by phage infections reinforces the kill the winner dynamics and supports diversity.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Infectious Diseases
Bjarke Frost Nielsen, Andreas Eilersen, Lone Simonsen, Kim Sneppen
Summary: The SARS-CoV-2 ancestral strain has led to significant superspreading events, with about 10% of infected individuals causing 80% of infections. Variants of the virus exhibit different levels of person-to-person variability in viral load, with the Alpha (B.1.1.7) variant being more infectious but less prone to superspreading. Non-pharmaceutical interventions such as lockdowns, mask wearing, and social distancing have been employed to reduce transmission risk. A mathematical model shows that the effectiveness of these interventions in curbing the spread of variants depends on the imposed restrictions, with lockdowns favoring variants with lower levels of overdispersion. This suggests that overdispersion is an evolutionarily unstable trait, with more homogeneously spreading variants tending to dominate.
Article
Physics, Multidisciplinary
Lucas Hedstrom, Ludvig Lizana
Summary: The most common gene regulation mechanism involves transcription factor proteins binding to regulatory sequences to regulate RNA transcription. However, transcription factors face challenges in finding these sequences due to their short length and the presence of many similar sequences in the genome. A computational study suggests that considering DNA looping can reduce search times for these sequences. This research explores if this phenomenon occurs over longer distances in chromosomes. A cross-scale computational framework combining basepair-level search models and a network model capturing chromosome-wide leaps was developed and used to analyze Hi-C data sets and binding profiles for over 100 transcription factors. The results indicate that the 3D structure of chromosomes plays a role in guiding essential transcription factors to relevant DNA regions.
NEW JOURNAL OF PHYSICS
(2023)
Article
Multidisciplinary Sciences
Anton Holmgren, Dolores Bernenko, Ludvig Lizana
Summary: To study the folding of DNA in cell nuclei, researchers have used methods like Hi-C to measure contact frequencies between DNA segment pairs across the genome. Hi-C data sets are often massive, so bioinformatics methods are commonly used to group DNA segments into 3D regions with correlated contact patterns. Another research direction treats Hi-C data as a network of 3D contacts and uses community detection algorithms to group nodes into tightly connected communities. However, due to the dense connectivity of Hi-C networks, multiple node partitions may produce feasible solutions, highlighting the need for thoughtful algorithm design or method cross-evaluation.
SCIENTIFIC REPORTS
(2023)
Article
Biochemical Research Methods
Dolores Bernenko, Sang Hoon Lee, Per Stenberg, Ludvig Lizana
Summary: Mammalian DNA folds into 3D structures that regulate genetic processes. Hi-C experiments reveal complex cross-scale organization of DNA interactions, contradicting the Russian-doll-like nested hierarchy model. This study maps out the actual chromosome folding relationships using Hi-C data sets and identifies nested and non-nested community pairs alongside randomness, emphasizing the importance of cross-scale relationships in understanding chromosome folding.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Physics, Multidisciplinary
Andreas Eilersen, Bjarke Frost Nielsen, Kim Sneppen
Summary: The rapid succession of new variants of SARS-CoV-2 highlights the need to understand the factors driving pathogen evolution. Researchers have found a possible tradeoff between the rate of disease progression and its reproductive number. During the exponential growth phase of an epidemic, there is an optimal disease duration that balances the advantage of fast progression with causing many secondary infections. However, the context and mitigation strategies, such as quarantine measures, can influence the evolution of the pathogen.
PHYSICAL REVIEW RESEARCH
(2023)
Article
Physics, Multidisciplinary
Markus Nyberg, Tobias Ambjornsson, Per Stenberg, Ludvig Lizana
Summary: The study finds that the 3D conformation of DNA is crucial for protein search times in vivo, with segments enriched with active gene starts showing higher rates. The research also offers a method for interpreting protein-binding profiles in eukaryotes.
PHYSICAL REVIEW RESEARCH
(2021)