Article
Chemistry, Multidisciplinary
Yi-Tsao Chen, Haw Yang, Jhih-Wei Chu
Summary: In gene transcription, certain dsDNA sequences are important for nucleosome positioning and expression initiation. We used statistical machine learning to determine the rigidity between DNA chemical moieties and found a unique trigram that represents the mechanical strengths between bases and along the backbone. This sequence-dependent mechanical code sheds light on DNA allostery and DNA-binding drugs.
Article
Computer Science, Artificial Intelligence
Penghang Liu, Valerio Guarrasi, A. Erdem Sariyuce
Summary: Investigating the frequency and distribution of motifs, or small subgraphs with a few nodes/edges, is a valuable analysis method for both static and temporal networks. However, designing a temporal motif model that considers all aspects of temporality is challenging due to the variety of motifs. This work compares existing temporal motif models and evaluates the overlooked facets of temporal networks in the literature. Through this comparative survey and extensive evaluation, it aims to catalyze further research on temporal network motif models.
IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING
(2023)
Article
Agriculture, Multidisciplinary
Ruiqin Zhang, Dongxia Lin, Liang Zhang, Ruoting Zhan, Sidi Wang, Kui Wang
Summary: A novel trifunctional enzyme Bi76 with endoxylanase, endoglucanase, and feruloyl esterase activities was identified. It exhibited hydrolysis ability towards various substrates and showed great potential in agricultural residue utilization.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Review
Neurosciences
Darian Hadjiabadi, Ivan Soltesz
Summary: The convergence of advanced single-cell in vivo functional imaging techniques, computational modelling tools and graph-based network analytics has opened up new opportunities for studying single-cell dynamics across large-scale networks. Hub cells, identified as richly connected neurons, play an important role in network communication and dysfunction. Higher-order graph analytics can uncover repeating subgraph patterns and reveal new functional cell types, such as the superhub, which regulates network dynamics.
JOURNAL OF PHYSIOLOGY-LONDON
(2023)
Article
Endocrinology & Metabolism
Fei Liao, Muhammad Yousif, Ruya Huang, Yanlong Qiao, Yanchun Hu
Summary: Here, network pharmacology was used to identify the active components in Ilex kudingcha and common hypertension-related targets. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were conducted, and molecular docking was performed to verify molecular dynamic simulations. The study identified six active components in Ilex kudingcha and 123 target genes common to hypertension, suggesting their potential role in hypertension treatment.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Multidisciplinary Sciences
Joyce Odeke Akello, Richard Kamgang, Maria Teresa Barbani, Franziska Suter-Riniker, Christoph Aebi, Christian Beuret, Daniel H. Paris, Stephen L. Leib, Alban Ramette
Summary: This study used whole-genome sequencing to compare circulating HAdV strains associated with severe and mild infections among pediatric patients in Bern, Switzerland, finding that HAdV species C were the main cause of severe infections. Recombination events occurred more frequently in severe cases, highlighting the importance of further research on HAdVs for public health preparedness.
SCIENTIFIC REPORTS
(2021)
Article
Biochemical Research Methods
Vinod Kumar Singh, Rohan Misra, Steven C. Almo, Ulrich G. Steidl, Hannes E. Bulow, Deyou Zheng
Summary: A new method has been proposed to search for motifs in biopolymer sequences that exist in non-single-letter contexts. The modified sequence elements are converted to representative single-letter codes and a modified Gibbs-sampling algorithm is used to define the position specific scoring matrix representing the motifs.
Article
Engineering, Environmental
Han Wang, Yufei Fan, Mingda Zhou, Weigang Wang, Xiang Li, Yayi Wang
Summary: This study found that Fe(III) minerals play an important role in the anaerobic ammonium oxidation (anammox) process. They increase the activity of granule formation, nitrogen removal, and enhance the resistance of microbial communities to environmental disturbances. However, the extra addition of Fe(III) minerals has limited promotion on anammox central metabolism in the presence of sufficient Fe(II).
Article
Biochemistry & Molecular Biology
Gabriela de Lima Menezes, Marielena Vogel Saivish, Mauricio Lacerda Nogueira, Roosevelt Alves da Silva
Summary: Diseases caused by flaviviruses, such as dengue, yellow fever, and Zika viruses, are a serious global public health problem. The NS1 protein, encoded by these viruses, plays crucial roles in their pathogenesis and RNA replication. This study aimed to identify compounds that can inhibit the formation of NS1 protein dimers from DENV, YFV, and ZIKV. Molecular dynamics simulations and virtual screening were performed, and two compounds were found to have high affinity for all three virus species. These findings highlight the potential of these compounds for multitarget therapy.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Biochemistry & Molecular Biology
Nilesh Kumar, Bharat K. Mishra, Jinbao Liu, Binoop Mohan, Doni Thingujam, Karolina M. Pajerowska-Mukhtar, M. Shahid Mukhtar
Summary: Drought is a serious stressor in the environment that reduces plant growth and agricultural productivity. To understand its effects on plants, a systems biology approach was used to study the transcriptome of Arabidopsis during drought. Co-expression network analysis identified 117 transcription factors (TFs) with important properties. Mathematical modeling and simulations revealed major transcriptional events and the involvement of TFs. Experimental evidence validated the predictions, showcasing the potential of these TFs in crop engineering programs.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemical Research Methods
Rong Li, Yu Li, Xiao Liang, Lu Yang, Min Su, Keng Po Lai
Summary: Niacin may have potential therapeutic effects for CRC/COVID-19 by exerting cytoprotection, enhancing immunologic functions, inhibiting inflammatory reactions, and regulating the cellular microenvironment. Five core pharmacological targets of niacin in CRC/COVID-19 were identified.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Biochemistry & Molecular Biology
Kirill Sergeevich Nikolsky, Liudmila Ivanovna Kulikova, Denis Vitalievich Petrovskiy, Vladimir Removich Rudnev, Tatiana Vladimirovna Butkova, Kristina Akhmedovna Malsagova, Arthur Tigranovich Kopylov, Anna Leonidovna Kaysheva
Summary: In this study, we investigated the autonomous stability of three-helix bundle and SH3-type barrels outside the protein environment. Through molecular experiments and comparative analysis, we demonstrated the potential for reducing computational time and improving performance without significant loss of information.
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS
(2023)
Article
Polymer Science
Francis Joy, Aatika Nizam, Yamuna Nair, Renjith. S. Pillai, Jyothis Devasia, Praveen Nagella
Summary: This review focuses on the design and synthetic strategy adopted in driving the macrocycle to the molecular axle using hydrogen bonding interactions in [2]rotaxanes. It also provides a detailed description and mechanistic insights about the utilization of hydrogen bonding [2]rotaxanes in applications such as molecular motors, organic synthesis, and catalysis.
EUROPEAN POLYMER JOURNAL
(2022)
Review
Cell Biology
Caroline Jane Ross, Igor Ulitsky
Summary: This review outlines the development and limitations of methods for discovering functional elements in long noncoding RNAs (lncRNAs), and discusses the main challenges in this field.
WILEY INTERDISCIPLINARY REVIEWS-RNA
(2022)
Article
Chemistry, Physical
Vinicius Wilian D. Cruzeiro, Andrew Wildman, Xiaosong Li, Francesco Paesani
Summary: The splitting of the 1b(1) peak in liquid water has been a subject of intense research, with a novel theoretical/computational approach combining simulations and calculations predicting this split. The analysis shows that multiple hydrogen-bonding motifs contribute to the XE line shape in liquid water, indicating that the split of the 1b(1) peak cannot be attributed to just two specific structural arrangements.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2021)
Article
Neurosciences
Zhiting Cai, Curtis L. Neveu, Douglas A. Baxter, John H. Byrne, Behnaam Aazhang
JOURNAL OF NEUROPHYSIOLOGY
(2017)
Article
Neurosciences
Lian Zhou, Douglas A. Baxter, John H. Byrne
JOURNAL OF NEUROPHYSIOLOGY
(2014)
Article
Neurosciences
Rong-Yu Liu, Yili Zhang, Douglas A. Baxter, Paul Smolen, Leonard J. Cleary, John H. Byrne
JOURNAL OF NEUROSCIENCE
(2013)
Article
Biology
Paul Smolen, Douglas A. Baxter, John H. Byrne
JOURNAL OF THEORETICAL BIOLOGY
(2014)
Article
Biology
Paul Smolen, Douglas A. Baxter, John H. Byrne
JOURNAL OF THEORETICAL BIOLOGY
(2018)
Article
Mathematical & Computational Biology
Paul Smolen, Douglas A. Baxter, John H. Byrne
FRONTIERS IN COMPUTATIONAL NEUROSCIENCE
(2020)
Article
Rehabilitation
Danielle A. Baxter, Johannah L. Shergis, Catherine J. Hill, Christopher Worsnop, Meaghan E. Coyle
Summary: The study showed that manual therapy intervention, specifically the Muscle Energy Technique (MET), was well received by participants in a clinical trial setting for COPD. Participants found MET to be a gentle and comfortable form of stretching that helped them breathe easier and prepare for pulmonary rehabilitation. Some participants reported mild discomfort during MET, but this was short-lasting and not bothersome. Participants expressed a preference for longer and more frequent MET sessions, as well as requested "homework" stretching exercises.
CHIROPRACTIC & MANUAL THERAPIES
(2021)
Article
Neurosciences
Yuto Momohara, Curtis L. Neveu, Hsin-Mei Chen, Douglas A. Baxter, John H. Byrne
Summary: In this study, the researchers used an in vitro analog of operant conditioning (OC) to investigate the effects of OC on the excitability of the inhibitory neuron B4 and its inhibitory connection to the decision-making neuron B51 in a feeding neural circuit. They found that OC decreased the excitability of B4 and weakened its inhibitory connection to B51. These changes were specific and did not affect other neurons critical for feeding behavior. Additionally, the researchers demonstrated that reducing the B4-to-B51 synapse or increasing B51 excitability mediated the OC phenotype more effectively than decreasing B4 excitability alone. Furthermore, they found that combinations of these modifications synergistically enhanced feeding behavior. These results suggest that diverse loci work together to mediate OC and that certain neurons are well suited to work synergistically with plasticity in other loci.
JOURNAL OF NEUROSCIENCE
(2022)
Article
Biology
Renan M. Costa, Douglas A. Baxter, John H. Byrne
Summary: The study identifies two low-dimensional motor modules in the neuronal population underlying Aplysia feeding using single-neuron resolution voltage imaging. The findings highlight a temporal shift in module recruitment as the primary signature of operant learning.
COMMUNICATIONS BIOLOGY
(2022)
Article
Neurosciences
Renan M. Costa, Douglas A. Baxter, John H. Byrne
Review
Rehabilitation
Danielle A. Baxter, Johannah L. Shergis, Azharuddin Fazalbhoy, Meaghan E. Coyle
CHIROPRACTIC & MANUAL THERAPIES
(2019)
Article
Neurosciences
Curtis L. Neveu, Renan M. Costa, Ryota Homma, Shin Nagayama, Douglas A. Baxter, John H. Byrne
Article
Neurosciences
Yili Zhang, Paul Smolen, Douglas A. Baxter, John H. Byrne
Article
Neurosciences
Yili Zhang, Paul Smolen, Cristina M. Alberini, Douglas A. Baxter, John H. Byrne