Article
Multidisciplinary Sciences
P. Z. Sun, W. Q. Xiong, A. Bera, I. Timokhin, Z. F. Wu, A. Mishchenko, M. C. Sellers, B. L. Liu, H. M. Cheng, E. Janzen, J. H. Edgar, I. V. Grigorieva, S. J. Yuan, A. K. Geim
Summary: Defect-free monolayer graphene shows unexpected catalytic activity in splitting molecular hydrogen, attributed to surface nanoripples. This finding may have implications for other chemical reactions involving graphene and is important for two-dimensional materials in general.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Callie R. Chappell, Manpreet K. Dhami, Mark C. Bitter, Lucas Czech, Sur Herrera Paredes, Fatoumata Binta Barrie, Yadira Calderon, Katherine Eritano, Lexi-Ann Golden, Daria Hekmat-Scafe, Veronica Hsu, Clara Kieschnick, Shyamala Malladi, Nicole Rush, Tadashi Fukami
Summary: This study identifies pH as a key factor that influences the interactions between nectar-colonizing microbes, plants, and pollinators, thereby exerting important ecological and evolutionary effects on ecological communities. Field and laboratory experiments demonstrate the significance of pH-driven priority effects in species competition and evolution, and a field experiment reveals the functional consequences of nectar pH for plant reproduction.
Article
Genetics & Heredity
Catherine Njeri, Sharon Pepenella, Tripthi Battapadi, Robert A. Bambara, Lata Balakrishnan
Summary: DNA polymerase delta is acetylated on subunits p125, p68, and p12, and this acetylation enhances the polymerization activity and ability of the polymerase to resolve complex structures. Acetylation also enhances the displacement of downstream DNA fragments, suggesting that it may promote higher-fidelity DNA replication.
Article
Multidisciplinary Sciences
Barbara Steurer, Roel C. Janssens, Marit E. Geijer, Fernando Aprile-Garcia, Bart Geverts, Arjan F. Theil, Barbara Hummel, Martin E. van Royen, Bastiaan Evers, Rene Bernards, Adriaan B. Houtsmuller, Ritwick Sawarkar, Jurgen Marteijn
Summary: DNA damage inhibits RNA polymerase II from elongating, but also triggers genome-wide transcriptional responses. Particularly, promoter-bound Pol II is degraded in a GSK3 signaling-mediated response, which is crucial for cells to cope with DNA damage-induced transcription stress.
NATURE COMMUNICATIONS
(2022)
Article
Biochemistry & Molecular Biology
Kristina Zumer, Kerstin C. Maier, Lucas Farnung, Martin G. Jaeger, Petra Rus, Georg Winter, Patrick Cramer
Summary: Transcription by RNA polymerase II requires elongation factors PAF, RTF1, and SPT6. Depletion of RTF1 reduces RNA Pol II velocity, while depletion of SPT6 impairs RNA Pol II progression through nucleosomes. These findings suggest distinct roles of elongation factors in regulating RNA Pol II activity.
Review
Cell Biology
Melvin Noe Gonzalez, Daniel Blears, Jesper Q. Svejstrup
Summary: Transcript elongation by RNA polymerase II can be perturbed by various barriers and obstacles, which the cell distinguishes between and resolves through different mechanisms to maintain genome stability.
NATURE REVIEWS MOLECULAR CELL BIOLOGY
(2021)
Article
Chemistry, Physical
Jinpeng Du, Yulong Shan, Yu Sun, Meng Gao, Zhongqi Liu, Xiaoyan Shi, Yunbo Yu, Hong He
Summary: The study reveals that after hydrothermal aging, Cu-SSZ-39 showed a remarkable increase in low-temperature NH3-SCR catalytic activity, attributed to the transformation of Cu2+ ions into CuxOy species facilitating the production of nitrate species critical for the catalytic process.
APPLIED CATALYSIS B-ENVIRONMENTAL
(2021)
Article
Chemistry, Applied
Valentina Ferraro, Roberto Sole, Lucia Alvarez-Miguel
Summary: Three neutral Cu(I) complexes with different triatomic pseudohalogen ligands (SCN-, OCN-, and N-3(-)) and 2,6-dimethylphenyl isocyanide (CNXyl) were successfully synthesized and characterized. The solid-state structures were determined through single-crystal X-ray diffraction, revealing unexpected bridging coordination modes in the case of OCN- and N-3(-). All the complexes showed interesting catalytic activity in azide-alkyne cycloaddition reactions, particularly the cyanato and azido Cu(I) complexes, which yielded 1,4-disubstituted-1,2,3-triazoles with high yields and 0.5 mol% of catalyst at 50 & DEG;C for 24 h. The azido Cu(I) complex also induced intramolecular CuAAC reactions in the presence of dimethyl acetylenedicarboxylate and benzyl bromide/phenylacetylene.
APPLIED ORGANOMETALLIC CHEMISTRY
(2023)
Article
Chemistry, Inorganic & Nuclear
Ilker Avan, Ibrahim Kani, Leyla Calikusu
Summary: Homoleptic bis(dipyrrinato)zinc(II) complexes, (Dprm)2-Zn and (EDprm)2-Zn, were synthesized using two different dipyrrinato ligands. X-ray crystal structures revealed that these complexes are four-coordinate with distorted tetrahedral geometry. The catalytic activities of these complexes towards the oxidation of various alcohols were investigated, showing high catalytic activity in acetonitrile at 70 degrees C.
INORGANIC CHEMISTRY COMMUNICATIONS
(2023)
Article
Biochemistry & Molecular Biology
Amit Dubey, Vishal Singh, Pawan Kumar Doharey, Md Palashuddin Sk, Sintu Kumar Samanta, Vijay Nema, Bechan Sharma, Pritish Kumar Varadwaj, Amaresh Kumar Sahoo
Summary: Utilizing ultra-small size gold nanoclusters can effectively inhibit the activity of human Topoisomerase enzyme, potentially serving as a target for anticancer drugs. Molecular dynamics simulation and binding energy analysis reveal the interaction mechanism between the gold nanoclusters and the enzyme.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2021)
Article
Electrochemistry
Jana Kocabova, Milan Sys, Jitka Klikarov, Miroslav Novak, Michaela Bartova, Robert Jirasko, Hana Tarabkova, Romana Sokolova, Toms Mikysek
Summary: The catecholase activity of selected mononuclear copper(II) complexes in aqueous and nonaqueous media was studied. The presence of electron-rich substituents and perchlorate ligands increased the catalytic efficiency towards 3,5-di-tert-butylcatechol. Changes in IR absorption spectrum were observed during the catalysis reaction. UV-Vis spectroelectrochemical study showed reversible electron transfer and the ability to catalyze the oxidation of catecholamines.
ELECTROCHIMICA ACTA
(2023)
Article
Chemistry, Multidisciplinary
Yanlin Zhu, Zhao Wang, Ruoxi Zhao, Yiheng Zhou, Lili Feng, Shili Gai, Piaoping Yang
Summary: By using the two-dimensional ultrathin nano-sheet Ti3C2 as a substrate, Pt artificial nanozymes were decorated to synthesize Ti-based MXene nanocomposites Ti3C2Tx-Pt-PEG. In the tumor microenvironment, Pt nanoparticles exhibited peroxidase-like (POD-like) activity, generating hydroxyl radicals to induce cell apoptosis and necrosis. Meanwhile, the composite showed desirable photothermal effect under NIR-II light. Satisfactory synergistic therapy was achieved, accompanied by photoacoustic imaging capability.
Article
Biochemical Research Methods
Dustin P. Patterson, Christy Hjorth, Andrea Hernandez Irias, Nathasha Hewagama, Jessica Bird
Summary: Encapsulation of enzymes inside protein cage structures, particularly virus-like particles, has the potential to develop new catalytic materials with enhanced properties. In this study, the in vivo encapsulation of enzymes inside bacteriophage P22 derived VLPs was examined, and it was found that some enzymes require a delay in encapsulation for proper folding and maturation. Sequential expression strategy resulted in altered enzymatic activities compared to simultaneous coexpression strategy. These findings provide important considerations and potential solutions for researchers investigating enzyme encapsulation inside confined reaction environments via in vivo routes.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biochemical Research Methods
Dustin P. Patterson, Christy Hjorth, Andrea Hernandez Irias, Nathasha Hewagama, Jessica Bird
Summary: Encapsulation of enzymes inside protein cage structures is a promising approach for the development of catalytic materials. This study focuses on the in vivo encapsulation of enzymes within the bacteriophage P22 derived virus-like particles (VLPs) and shows that some enzymes require a delay in encapsulation to ensure full activity. Sequential expression strategy leads to altered enzymatic activities compared to simultaneous coexpression strategy. These findings provide important insights for researchers investigating enzyme encapsulation and offer a potential solution for obtaining active enzymes.
ACS SYNTHETIC BIOLOGY
(2022)
Article
Biodiversity Conservation
Caleb M. Bryce, Carolyn E. Dunford, Anthony M. Pagano, Yiwei Wang, Bridget L. Borg, Stephen M. Arthur, Terrie M. Williams
Summary: This study used accelerometers and GPS telemetry to investigate the activity and energy expenditure of gray wolves in interior Alaska. The findings suggest that environmental conditions can influence wolf movements and energy allocation, which is important for evaluating the impact of environmental factors on carnivores.
ANIMAL BIOTELEMETRY
(2022)
Article
Biochemistry & Molecular Biology
Benjamin C. Kaster, Kevin C. Knippa, Craig D. Kaplan, David O. Peterson
JOURNAL OF BIOLOGICAL CHEMISTRY
(2016)
Article
Genetics & Heredity
Nairita Maitra, Jayamani Anandhakumar, Heidi M. Blank, Craig D. Kaplan, Michael Polymenis
G3-GENES GENOMES GENETICS
(2019)
Review
Biochemical Research Methods
Chenxi Qiu, Craig D. Kaplan
Article
Biology
Zhijie Chen, Ronen Gabizon, Aidan I. Brown, Antony Lee, Aixin Song, Cesar Diaz-Celis, Craig D. Kaplan, Elena F. Koslover, Tingting Yao, Carlos Bustamante
Article
Biochemistry & Molecular Biology
Xueyuan Leng, Maxim Iyanov, Peter Kindgren, Indranil Malik, Axel Thieffry, Peter Brodersen, Albin Sandelin, Craig D. Kaplan, Sebastian Marquardt
Article
Biochemistry & Molecular Biology
Sarah J. Hainer, Craig D. Kaplan
Article
Biochemistry & Molecular Biology
Natalie M. Garza, Aaron T. Griffin, Mohammad Zulkifli, Chenxi Qiu, Craig D. Kaplan, Vishal M. Gohil
Summary: This study identified novel genetic regulators of mitochondrial copper homeostasis through a genome-wide screen, including subunits of the AP-3 complex and components of the cellular pH-sensing pathway. These genes impact vacuolar acidity, which in turn perturbs mitochondrial copper homeostasis and CcO function. The study provides insights into how vacuolar pH affects mitochondrial respiration through copper homeostasis.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Article
Multidisciplinary Sciences
Trevor van Eeuwen, Yoonjung Shim, Hee Jong Kim, Tingting Zhao, Shrabani Basu, Benjamin A. Garcia, Craig D. Kaplan, Jung-Hyun Min, Kenji Murakami
Summary: The study presents a cryo-EM structure of an NER initiation complex, showing how the XPC-RAD23B-CETN2 complex and TFIIH complex work together to recognize and verify DNA lesions. This interaction allows for unwinding of DNA and delivery of damaged strands for subsequent scanning and verification.
NATURE COMMUNICATIONS
(2021)
Article
Biology
Tingting Zhao, Irina O. Vvedenskaya, William K. M. Lai, Shrabani Basu, B. Franklin Pugh, Bryce E. Nickels, Craig D. Kaplan
Summary: Research has shown that Ssl2 plays a crucial role in promoter scanning by controlling TSS selection through regulating processivity rather than rate, possibly related to its ATPase activity. The study reveals the genetic interaction patterns of ssl2 alleles and their impact on the promoter scanning process and TSS selection.
Letter
Multidisciplinary Sciences
Leonid Kruglyak, Andreas Beyer, Joshua S. Bloom, Jan Grossbach, Tami D. Lieberman, Christopher P. Mancuso, Matthew S. Rich, Gavin Sherlock, Craig D. Kaplan
Article
Biochemical Research Methods
Bercem Dutagaci, Bingbing Duan, Chenxi Qiu, Craig D. Kaplan, Michael Feig
Summary: The trigger loop (TL) is a highly conserved active site domain that plays a crucial role in catalysis and fidelity of multisubunit RNA polymerases. This study used molecular dynamics simulation (MD) and machine learning (ML) techniques to investigate TL mutations in Saccharomyces cerevisiae RNA Polymerase II (Pol II). The results showed that ML could predict the phenotypes of TL mutants with a high correlation. While it was challenging to incorporate MD data into machine learning, a variational auto-encoder model based on the MD data successfully clustered mutants based on structural details.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Genetics & Heredity
Adam W. Hansen, Payal Arora, Michael M. Khayat, Leah J. Smith, Andrea M. Lewis, Linda Z. Rossetti, Joy Jayaseelan, Ingrid Cristian, Devon Haynes, Stephanie DiTroia, Naomi Meeks, Mauricio R. Delgado, Jill A. Rosenfeld, Lynn Pais, Susan M. White, Qingchang Meng, Davut Pehlivan, Pengfei Liu, Marie-Claude Gingras, Michael F. Wangler, Donna M. Muzny, James R. Lupski, Craig D. Kaplan, Richard A. Gibbs
Summary: The study reported 12 individuals with variants in POLR2A, showing phenotypes such as ataxia, joint hypermobility, short stature, skin abnormalities, congenital cardiac abnormalities, immune system abnormalities. Most patients also had epilepsy, while the occurrence of hypotonia was lower.
HUMAN GENETICS AND GENOMICS ADVANCES
(2021)
Article
Biotechnology & Applied Microbiology
Chenxi Qiu, Huiyan Jin, Irina Vvedenskaya, Jordi Abante Llenas, Tingting Zhao, Indranil Malik, Alex M. Visbisky, Scott L. Schwartz, Ping Cui, Pavel Cabart, Kang Hoo Han, William K. M. Lai, Richard P. Metz, Charles D. Johnson, Sing-Hoi Sze, B. Franklin Pugh, Bryce E. Nickels, Craig D. Kaplan
Meeting Abstract
Biochemistry & Molecular Biology
Craig D. Kaplan