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JOURNAL ARTICLE
Maninderjeet Singh, Wenjie Wu, Vinay Nuka, Joseph Strzalka, Jack F Douglas, Alamgir Karim
Block copolymer (BCP) phase separation dynamics can be expected to differ significantly from that of the polymer blends due to the constraint of chain connectivity. BCP phase separation dynamics has been studied theoretically, but there has been little experimental evidence to confirm the BCP domain growth scaling laws put forward theoretically. Here, we investigate the dynamics of late-stage lamellar BCP domain coarsening and find that the scaling exponent for lamellar domain growth is ≈1/6 (0.17), irrespective of the annealing temperature, a value close to the scaling exponent of 0...
June 15, 2021: ACS Macro Letters
#22
REVIEW
Victor V Dyakin, Nuka V Dyakina-Fagnano, Laura B Mcintire, Vladimir N Uversky
In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirality, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP ), and non-equilibrium phase transitions...
December 28, 2021: International Journal of Molecular Sciences
#23
JOURNAL ARTICLE
Sascha Hein, Nuka Ivalu Benz, Jonathan Eisert, Marie-Luise Herrlein, Doris Oberle, Michael Dreher, Julia C Stingl, Christoph Hildt, Eberhard Hildt
Many of the approved SARS-CoV-2 vaccines are based on a stabilized variant of the spike protein. This raises the question of whether the immune response against the stabilized spike is identical to the immune response that is elicited by the native spike in the case of a SARS-CoV-2 infection. Using a peptide array-based approach, we analysed the binding of antibodies from Comirnaty-elicited, convalescent, and control sera to the peptides covering the spike protein. A total of 37 linear epitopes were identified...
December 1, 2021: Vaccines
#24
JOURNAL ARTICLE
Sascha Hein, Marie-Luise Herrlein, Ines Mhedhbi, Daniela Bender, Vanessa Haberger, Nuka Benz, Jonathan Eisert, Julia Stingl, Michael Dreher, Doris Oberle, Jessica Schulze, Christin Mache, Matthias Budt, Christoph Hildt, Thorsten Wolff, Eberhard Hildt
BACKGROUND: The mRNA vaccine BNT162b2 (Comirnaty, BioNTech/Pfizer) and the vaccine candidate CVnCoV (Curevac) each encode a stabilized spike protein of SARS-CoV2 as antigen but differ with respect to the nature of the mRNA (modified versus unmodified nucleotides) and the mRNA amount (30 μg versus 12 μg RNA). This study characterizes antisera elicited by these two vaccines in comparison to convalescent sera. METHODS: Sera from BNT162b2 vaccinated healthcare workers, and sera from participants of a phase I trial vaccinated with 2, 4, 6, 8, or 12 μg CVnCoV and convalescent sera from hospitalized patients were analyzed by ELISA, neutralization tests, surface plasmon resonance (SPR), and peptide arrays...
November 25, 2021: Allergy
#25
JOURNAL ARTICLE
Henry T Mwakalinga, Yamikani M Nuka, Patrick C Banda, Thuy D Bui
Background: Type 2 diabetes is a major health concern worldwide and requires urgent attention from health care providers and policy makers. Due to shortage of health care workers in low-income countries, peer support programs have been viewed as a viable option in management of diabetes and have shown to be effective in sub-Saharan Africa. Objective: The aim of this study is to assess and evaluate the Kamuzu Central Hospital (KCH) diabetic peer support program's (DPSP) impact 4 years after its establishment by assessing knowledge, self-efficacy and behaviours of DPSP members compared to non-members...
June 2021: Malawi Medical Journal: the Journal of Medical Association of Malawi
#26
JOURNAL ARTICLE
Matthias Blum, Hsin-Yu Chang, Sara Chuguransky, Tiago Grego, Swaathi Kandasaamy, Alex Mitchell, Gift Nuka, Typhaine Paysan-Lafosse, Matloob Qureshi, Shriya Raj, Lorna Richardson, Gustavo A Salazar, Lowri Williams, Peer Bork, Alan Bridge, Julian Gough, Daniel H Haft, Ivica Letunic, Aron Marchler-Bauer, Huaiyu Mi, Darren A Natale, Marco Necci, Christine A Orengo, Arun P Pandurangan, Catherine Rivoire, Christian J A Sigrist, Ian Sillitoe, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Alex Bateman, Robert D Finn
The InterPro database (https://www.ebi.ac.uk/interpro/) provides an integrative classification of protein sequences into families, and identifies functionally important domains and conserved sites. InterProScan is the underlying software that allows protein and nucleic acid sequences to be searched against InterPro's signatures. Signatures are predictive models which describe protein families, domains or sites, and are provided by multiple databases. InterPro combines signatures representing equivalent families, domains or sites, and provides additional information such as descriptions, literature references and Gene Ontology (GO) terms, to produce a comprehensive resource for protein classification...
November 6, 2020: Nucleic Acids Research
#27
JOURNAL ARTICLE
Kristina Volkenborn, Laura Kuschmierz, Nuka Benz, Patrick Lenz, Andreas Knapp, Karl-Erich Jaeger
BACKGROUND: Bacillus subtilis is widely used for the industrial production of recombinant proteins, mainly due to its high secretion capacity, but higher production yields can be achieved only if bottlenecks are removed. To this end, a crucial process is translation initiation which takes place at the ribosome binding site enclosing the Shine Dalgarno sequence, the start codon of the target gene and a short spacer sequence in between. Here, we have studied the effects of varying spacer sequence lengths in vivo on the production yield of different intra- and extracellular proteins...
July 29, 2020: Microbial Cell Factories
#28
JOURNAL ARTICLE
Kousuke Shiwaku, Atsushi Teramoto, Satoshi Nuka, Takashi Matsumura, Kota Watanabe, Toshihiko Yamashita
BACKGROUND: The aim of the study was to investigate the effects of navigation-based varus or axial rotational alignment through knee flexion on patient reported outcomes or the maximum flexion angle of unicompartmental knee arthroplasty (UKA). METHODS: Data were retrospectively collected from 46 knees that underwent UKA for medial unicompartmental knee osteoarthritis. An image-free knee navigation system was used in all cases, and intraoperative varus and axial rotational alignment at every knee flexion angle were recorded before and after implantation...
April 2020: Asia-Pacific Journal of Sports Medicine, Arthroscopy, Rehabilitation and Technology
#29
JOURNAL ARTICLE
Shinichiro Okimura, Atsushi Teramoto, Kota Watanabe, Satoshi Nuka, Tomoaki Kamiya, Toshihiko Yamashita
We developed a new internal fixator: a rigid T: -shaped plate with locking screws and wedge-shaped spacer block for high tibial osteotomy. The purpose of the present study was to evaluate the radiographic outcome of opening-wedge high tibial osteotomy (OWHTO) using this new internal fixator. Sixty OWHTOs were performed in patients with medial compartment osteoarthritis and varus deformity (28 males and 23 females). Patients' mean age was 60.4 years. Preoperative and postoperative radiographs were obtained. The paired t -test was used to evaluate the differences over time with respect to radiographic variables...
January 13, 2020: Journal of Knee Surgery
#30
REVIEW
Robin J Bullock, Robert A Perkins, Srijan Aggarwal
With increased oil exploration and marine activity in the warming Arctic, there is an increased risk of future oil spills in the Arctic region. In-situ burning (ISB), along with the use of chemical herders (to thicken the slick of spilled oil) has emerged as a potentially viable oil-spill response technique for various Arctic scenarios. The purpose of this research review is to document the field use, research, and analysis regarding the use of ISB to address an offshore oil spill response in the Arctic, with a specific focus on the use of chemical herders to aid ISB in Arctic waters...
July 20, 2019: Science of the Total Environment
#31
JOURNAL ARTICLE
Samane Rahmdel, Seyed Shahram Shekarforoush, Saeid Hosseinzadeh, Sandra Torriani, Veronica Gatto
Bacteriocins have attracted great attention as potential alternatives to antibiotics and chemical food additives. In the present study, 243 Staphylococcus isolates from milk samples (n = 110) of goat and sheep herds located in Fars province, Iran, were screened for antimicrobial substance production. Twenty-eight isolates showed an antagonistic activity against the indicator strain Micrococcus luteus ATCC 4698. The susceptibility of all antimicrobial substances to proteolytic enzymes allowed us to consider them as bacteriocin-like inhibitory substances (BLIS)...
April 2019: Journal of Dairy Science
#32
JOURNAL ARTICLE
Alex L Mitchell, Teresa K Attwood, Patricia C Babbitt, Matthias Blum, Peer Bork, Alan Bridge, Shoshana D Brown, Hsin-Yu Chang, Sara El-Gebali, Matthew I Fraser, Julian Gough, David R Haft, Hongzhan Huang, Ivica Letunic, Rodrigo Lopez, Aurélien Luciani, Fabio Madeira, Aron Marchler-Bauer, Huaiyu Mi, Darren A Natale, Marco Necci, Gift Nuka, Christine Orengo, Arun P Pandurangan, Typhaine Paysan-Lafosse, Sebastien Pesseat, Simon C Potter, Matloob A Qureshi, Neil D Rawlings, Nicole Redaschi, Lorna J Richardson, Catherine Rivoire, Gustavo A Salazar, Amaia Sangrador-Vegas, Christian J A Sigrist, Ian Sillitoe, Granger G Sutton, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Siew-Yit Yong, Robert D Finn
The InterPro database (https://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic interface and website...
January 8, 2019: Nucleic Acids Research
#33
JOURNAL ARTICLE
Cailyn Lingwall, Eric Nehl, Marina Topuridze, Lela Sturua, Nuka Maglakelidze, Carla J Berg
Background : While pictorial health warning labels (HWLs) are evidence-based, the different messaging strategies are understudied. Methods : We analyzed 2014 national survey data from 1163 Georgian adults to examine: (1) perceived effectiveness of pictorial vs. text-only HWLs; (2) pictorial HWL themes; and (3) correlates of perceived effectiveness of different pictorial themes. Participants were randomized to evaluate the effectiveness of either Set A or Set B of HWLs (each contained half pictorial, half text-only)...
October 11, 2018: International Journal of Environmental Research and Public Health
#34
JOURNAL ARTICLE
Erika Nuka, Kohta Ohnishi, Junji Terao, Yoshichika Kawai
Innate immune cells, such as macrophages, respond to pathogen-associated molecular patterns, such as a lipopolysaccharide (LPS), to secrete various inflammatory mediators. Recent studies have suggested that damage-associated molecular patterns (DAMPs), released extracellularly from damaged or immune cells, also play a role in the activation of inflammatory responses. In this study, to prevent excess inflammation, we focused on DAMPs-mediated signaling that promotes LPS-stimulated inflammatory responses, especially adenosine 5'-triphosphate (ATP)-triggered signaling through the ionotropic purinergic receptor 7 (P2X7R), as a potential new anti-inflammatory target of natural polyphenols...
2018: PloS One
#35
JOURNAL ARTICLE
Kota Watanabe, Atsushi Teramoto, Takuma Kobayashi, Yuzuru Sakakibara, Hiroaki Shoji, Shinichiro Okimura, Satoshi Nuka, Toshihiko Yamashita
BACKGROUND: Low tibial osteotomy is an effective joint-preserving surgery for ankle arthritis. However, poor postoperative wound healing, infection, and delayed or non-union of bones remain significant concerns. We describe a modified distal tibial oblique osteotomy procedure and report preliminary results for varus ankle arthritis. METHODS: The osteotomy path consisted of an oblique doglegged line from the lateral end of the distal tibia to a proximal point about one-third from the lateral edge and continuing along an arc defined by virtual coronal-plane rotation of the doglegged line to the medial edge...
September 21, 2018: Journal of Orthopaedic Science: Official Journal of the Japanese Orthopaedic Association
#36
REVIEW
Abundance of DNA adducts of 4-oxo-2-alkenals, lipid peroxidation-derived highly reactive genotoxins.
Yoshichika Kawai, Erika Nuka
Reactive oxygen species and their reaction products can damage DNA to form mutagenic lesions. Among the reactive species, lipid peroxidation-derived aldehydes react with nucleobases and form bulky exocyclic adducts. Many types of aldehyde-derived DNA adducts have been characterized, identified and detected in vitro and in vivo , whereas relative quantitative and pathophysiological contributions of each adduct still remain unclear. In recent years, an abundant class of DNA adducts derived from 4-oxo-2-alkenals have been identified, in addition to classic aldehyde-derived adducts...
January 2018: Journal of Clinical Biochemistry and Nutrition
#37
JOURNAL ARTICLE
Sen Zheng, Jun-Ichi Nagao, Mami Nishie, Takeshi Zendo, Kenji Sonomoto
Lantibiotic nukacin ISK-1 is produced by Staphylococcus warneri ISK-1. The dual functional transporter NukT, an ABC transporter maturation and secretion protein, contributes to cleavage of the leader peptide from the prepeptide (modified NukA) and the final transport of nukacin ISK-1. NukT consists of an N-terminal peptidase domain (PEP), a C-terminal nucleotide-binding domain (NBD), and a transmembrane domain (TMD). In this study, NukT and its peptidase-inactive mutant were expressed, purified, and reconstituted into liposomes for analysis of their peptidase and ATPase activities...
January 2018: Applied Microbiology and Biotechnology
#38
JOURNAL ARTICLE
Robert D Finn, Teresa K Attwood, Patricia C Babbitt, Alex Bateman, Peer Bork, Alan J Bridge, Hsin-Yu Chang, Zsuzsanna Dosztányi, Sara El-Gebali, Matthew Fraser, Julian Gough, David Haft, Gemma L Holliday, Hongzhan Huang, Xiaosong Huang, Ivica Letunic, Rodrigo Lopez, Shennan Lu, Aron Marchler-Bauer, Huaiyu Mi, Jaina Mistry, Darren A Natale, Marco Necci, Gift Nuka, Christine A Orengo, Youngmi Park, Sebastien Pesseat, Damiano Piovesan, Simon C Potter, Neil D Rawlings, Nicole Redaschi, Lorna Richardson, Catherine Rivoire, Amaia Sangrador-Vegas, Christian Sigrist, Ian Sillitoe, Ben Smithers, Silvano Squizzato, Granger Sutton, Narmada Thanki, Paul D Thomas, Silvio C E Tosatto, Cathy H Wu, Ioannis Xenarios, Lai-Su Yeh, Siew-Yit Young, Alex L Mitchell
InterPro (https://www.ebi.ac.uk/interpro/) is a freely available database used to classify protein sequences into families and to predict the presence of important domains and sites. InterProScan is the underlying software that allows both protein and nucleic acid sequences to be searched against InterPro's predictive models, which are provided by its member databases. Here, we report recent developments with InterPro and its associated software, including the addition of two new databases (SFLD and CDD), and the functionality to include residue-level annotation and prediction of intrinsic disorder...
January 4, 2017: Nucleic Acids Research
#39
JOURNAL ARTICLE
Dai Inoue, Norihide Yoneda, Kotaro Yoshida, Hiromi Nuka, Jun Kinoshita, Sachio Fushida, Fumihito Toshima, Tetsuya Minami, Masayuki Takahira, Shoko Hamaoka, Hiroko Ikeda, Toshifumi Gabata, Mitsuhiro Kawano
We describe a 67-year-old man with immunoglobulin G4-related disease (IgG4-RD) presenting with optic neuropathy, dacryoadenitis, periaortitis, retroperitoneal fibrosis, and a gastric mass-like lesion. A mass-like lesion measuring 52 × 40 mm in the antrum of the stomach was found incidentally through whole-body screening for other organ involvement of IgG4-RD using contrast-enhanced computed tomography (CT). Histology of the stomach revealed that the lesion was also IgG4-related and was located in the submucosal layer extending to the subserosal region...
March 2019: Modern Rheumatology
#40
JOURNAL ARTICLE
Erika Nuka, Susumu Tomono, Akari Ishisaka, Yoji Kato, Noriyuki Miyoshi, Yoshichika Kawai
Lipid peroxidation products react with cellular molecules, such as DNA bases, to form covalent adducts, which are associated with aging and disease processes. Since lipid peroxidation is a complex process and occurs in multiple stages, there might be yet unknown reaction pathways. Here, we analyzed comprehensively 2'-deoxyguanosine (dG) adducts with oxidized arachidonic acid using liquid chromatography-tandem mass spectrometry and found the formation of 7-(2-oxo-hexyl)-etheno-dG as one of the major unidentified adducts...
October 2016: Bioscience, Biotechnology, and Biochemistry
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