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Mehdi Mirzakhanloo, Mohammad-Reza Alam
It has long been believed that eukaryotic flagellated swimming cells feel solid boundaries through direct ciliary contact. Specifically, based on observations of behavior of green alga Chlamydomonas reinhardtii it has been reported that it is their "flagella [that] prevent the cell body from touching the surface" [Kantsler et al., Proc. Natl. Acad. Sci. USA 110, 1187 (2013)PNASA60027-842410.1073/pnas.1210548110]. Here, via investigation of a model swimmer whose flow field closely resembles that of C...
July 2018: Physical Review. E
H S Battey, D R Cox
Recently, Cox and Battey (2017 Proc. Natl Acad. Sci. USA 114 , 8592-8595 (doi:10.1073/pnas.1703764114)) outlined a procedure for regression analysis when there are a small number of study individuals and a large number of potential explanatory variables, but relatively few of the latter have a real effect. The present paper reports more formal statistical properties. The results are intended primarily to guide the choice of key tuning parameters.
July 2018: Proceedings. Mathematical, Physical, and Engineering Sciences
Jaime I Castillo, Marcin Równicki, Monika Wojciechowska, Joanna Trylska
A combination of antibacterial agents should make the emergence of resistance in bacteria less probable. Thus we have analyzed the synergistic effects between antibacterial antisense peptide nucleic acids (PNA) and conventional antibiotics against Escherichia coli AS19 (lipopolysaccharide defective) strain and a derivative of a pathogenic strain E. coli O157:H7. PNAs were designed to target mRNA transcripts encoding the essential acyl carrier protein (gene acpP) and conjugated to the cell-penetrating peptide (KFF)3 K for cellular uptake...
July 27, 2018: Bioorganic & Medicinal Chemistry Letters
Tao Cheng, Andres Jaramillo-Botero, Qi An, Daniil V Ilyin, Saber Naserifar, William A Goddard
This issue of PNAS features "nonequilibrium transport and mixing across interfaces," with several papers describing the nonequilibrium coupling of transport at interfaces, including mesoscopic and macroscopic dynamics in fluids, plasma, and other materials over scales from microscale to celestial. Most such descriptions describe the materials in terms of the density and equations of state rather than specific atomic structures and chemical processes. It is at interfacial boundaries where such atomistic information is most relevant...
August 3, 2018: Proceedings of the National Academy of Sciences of the United States of America
Gangqiang Qin, Qianyi Cui, Weihua Wang, Ping Li, Aijun Du, Qiao Sun
Developing advanced materials and new technologies for efficient CO2 capture and gas separation can enormously alleviate its impact on global climate change. In this study, we report a comprehensive density functional theory investigation of N2 , CH4 , H2 , and CO2 adsorption on a graphene-like C3 N monolayer. Our calculation results show that the four gas molecules are all physisorbed on the neutral C3 N monolayer. However, the interaction between CO2 and C3 N can be significantly boosted via the strategies of electrochemical methods such as introducing negative charge or applying external electric field to the system...
July 31, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
Itamar Peled, Eylon Yavin
The forced-intercalation peptide nucleic acid (FIT-PNA) concept, introduced by Seitz and co-workers, is based on replacing a nucleobase of the PNA sequence with a cyanine dye (such as thiazole orange). The cyanine dye is thus a surrogate base that is forced to intercalate in the duplex (e.g. , PNA: DNA). This allows single-mismatch sensitivity as the introduction of a mismatch in the vicinity of the dye increases freedom of motion and leads to a significant depletion of its fluorescence because of the free rotation of the monomethine bond separating the two π-systems of the cyanine dye...
April 30, 2018: ACS Omega
Bénédicte Ndeboko, Olivier Hantz, Guy Joseph Lemamy, Lucyna Cova
Alternative therapeutic approaches against chronic hepatitis B virus (HBV) infection need to be urgently developed because current therapies are only virostatic. In this context, cell penetration peptides (CPPs) and their Peptide Nucleic Acids (PNAs) cargoes appear as a promising novel class of biologically active compounds. In this review we summarize different in vitro and in vivo studies, exploring the potential of CPPs as vehicles for intracellular delivery of PNAs targeting hepadnaviral replication. Thus, studies conducted in the duck HBV (DHBV) infection model showed that conjugation of (D-Arg)₈ CPP to PNA targeting viral epsilon (ε) were able to efficiently inhibit viral replication in vivo following intravenous administration to ducklings...
July 16, 2018: Biomolecules
Kiran M Patil, Desiree-Faye Kaixin Toh, Zhen Yuan, Zhenyu Meng, Zhiyu Shu, Haiping Zhang, Alan Ann Lerk Ong, Manchugondanahalli S Krishna, Lanyuan Lu, Yunpeng Lu, Gang Chen
Double-stranded RNA (dsRNA) structures form triplexes and RNA-protein complexes through binding to single-stranded RNA (ssRNA) regions and proteins, respectively, for diverse biological functions. Hence, targeting dsRNAs through major-groove triplex formation is a promising strategy for the development of chemical probes and potential therapeutics. Short (e.g., 6-10 mer) chemically-modified Peptide Nucleic Acids (PNAs) have been developed that bind to dsRNAs sequence specifically at physiological conditions...
July 16, 2018: Nucleic Acids Research
Monique A R Udell
Domestic dogs have become well known for their socio-cognitive successes, so what does it mean when domestic dogs fail to cooperate? A new study by Marshall-Pescini, Schwarz, Kostelnik, Virányi, and Range (PNAS, 114(44) 11793-11798, 2017) highlights the importance of considering socioecological context, learning, and relationship quality when evaluating the social cognition of dogs and wolves.
July 6, 2018: Learning & Behavior
Si-Ying Wang, Jing Lin, Ling Huang, Xing-Mei Liu, Yuan-Yuan Han, Wen-Ping Han, Bang-Quan An, Gui-Fang Li, Sheng-Wen Huang
OBJECTIVE: To investigate the effect of blocking polypyrimidine complex binding to DNA site by using peptide nucleic acid (PNA) on γ-globin gene expression. METHODS: PYR-PNA, β-PNA and RS-PNA (random sequence-PNA) were designed and synthesized, then were transfected into K562 cells with the cationic liposome lipofectamine 2000 used as vector. The expression of γ-globin gene at both the transcriptional and translational level was detected by RT-PCR and the Western blot respectively at 24 h, 48 h and 72 h after transfection with PNAs...
June 2018: Zhongguo Shi Yan Xue Ye Xue za Zhi
Adele S Ricciardi, Raman Bahal, James S Farrelly, Elias Quijano, Anthony H Bianchi, Valerie L Luks, Rachael Putman, Francesc López-Giráldez, Süleyman Coşkun, Eric Song, Yanfeng Liu, Wei-Che Hsieh, Danith H Ly, David H Stitelman, Peter M Glazer, W Mark Saltzman
Genetic diseases can be diagnosed early during pregnancy, but many monogenic disorders continue to cause considerable neonatal and pediatric morbidity and mortality. Early intervention through intrauterine gene editing, however, could correct the genetic defect, potentially allowing for normal organ development, functional disease improvement, or cure. Here we demonstrate safe intravenous and intra-amniotic administration of polymeric nanoparticles to fetal mouse tissues at selected gestational ages with no effect on survival or postnatal growth...
June 26, 2018: Nature Communications
Alessandro Bertucci, Simone Silvestrini, Roberto Corradini, Luisa De Cola
Peptide Nucleic Acids (PNAs) are oligonucleotide mimics that can be used as drugs as they can interact with DNA and RNA targets in organisms. Loading PNAs into inorganic nanocarriers can improve their cellular uptake and co-delivering them together with drugs can improve the therapy efficacy by synergic effects. Furthermore, the functionalization of the carriers with labels allows theranostics, and the possibility to monitor the efficacy of the therapy in real time. The present protocol describes the synthesis of Zeolites-L nanocrystals and mesoporous silica nanoparticles and their loading with cationic PNAs and other smaller molecular weight payloads towards theranostics applications...
2018: Methods in Molecular Biology
Alex Manicardi, Roberto Gambari, Luisa de Cola, Roberto Corradini
Peptide Nucleic Acids (PNAs) are oligonucleotide mimics that can be used to block the biological action of microRNA, thus affecting gene expression post-transcriptionally. PNAs are obtained with solid-phase peptide synthesis, and can be easily conjugated to other peptides. Conjugation with R8-Peptide or modification of the PNA backbone (at C5 or C2 carbon) with arginine side chains allows efficient cellular uptake. The present protocol describes the synthesis of cationic PNAs that can be used alone as drugs or for efficient co-delivery in suitable inorganic nanocarriers...
2018: Methods in Molecular Biology
Ehud Gazit
The formation of ordered nanostructures by molecular self-assembly of proteins and peptides represents one of the principal directions in nanotechnology. Indeed, polyamides provide superior features as materials with diverse physical properties. A reductionist approach allowed the identification of extremely short peptide sequences, as short as dipeptides, which could form well-ordered amyloid-like β-sheet-rich assemblies comparable to supramolecular structures made of much larger proteins. Some of the peptide assemblies show remarkable mechanical, optical, and electrical characteristics...
June 20, 2018: Annual Review of Biochemistry
András Micsonai, Frank Wien, Éva Bulyáki, Judit Kun, Éva Moussong, Young-Ho Lee, Yuji Goto, Matthieu Réfrégiers, József Kardos
Circular dichroism (CD) spectroscopy is a widely used method to study the protein secondary structure. However, for decades, the general opinion was that the correct estimation of β-sheet content is challenging because of the large spectral and structural diversity of β-sheets. Recently, we showed that the orientation and twisting of β-sheets account for the observed spectral diversity, and developed a new method to estimate accurately the secondary structure (PNAS, 112, E3095). BeStSel web server provides the Beta Structure Selection method to analyze the CD spectra recorded by conventional or synchrotron radiation CD equipment...
July 2, 2018: Nucleic Acids Research
Adam van Casteren, Peter W Lucas, David S Strait, Shaji Michael, Nick Bierwisch, Norbert Schwarzer, Khaled J Al-Fadhalah, Abdulwahab S Almusallam, Lidia A Thai, Sreeja Saji, Ali Shekeban, Michael V Swain
Mammalian tooth wear research reveals contrasting patterns seemingly linked to diet: irregularly pitted enamel surfaces, possibly from consuming hard seeds, versus roughly aligned linearly grooved surfaces, associated with eating tough leaves. These patterns are important for assigning diet to fossils, including hominins. However, experiments establishing conditions necessary for such damage challenge this paradigm. Lucas et al . (Lucas et al . 2013 J. R. Soc. Interface 10 , 20120923. (doi:10.1098/rsif.2012...
May 2018: Royal Society Open Science
Edward J Calabrese
This historical analysis indicates that it is highly unlikely that the Nobel Prize winning research of Hermann J. Muller was peer-reviewed. The published paper of Muller lacked a research methods section, cited no references, and failed to acknowledge and discuss the work of Gager and Blakeslee (PNAS 13:75-79, 1927) that claimed to have induced gene mutation via ionizing radiation six months prior to Muller's non-data Science paper (Muller, Science 66(1699):84-87, 1927a). Despite being well acclimated into the scientific world of peer-review, Muller choose to avoid the peer-review process on his most significant publication...
June 6, 2018: Philosophy, Ethics, and Humanities in Medicine: PEHM
Andrei Ciuca, Alina Asandei, Irina Schiopu, Aurelia Apetrei, Loredana Mereuta, Chang Ho Seo, Yoonkyung Park, Tudor Luchian
Peptide nucleic acids (PNAs) are artificial, oligonucleotides analogues, where the sugar-phosphate backbone has been substituted with a peptide-like N-(2-aminoethyl)glycine backbone. Because of their inherent benefits, such as increased stability and enhanced binding affinity toward DNA or RNA substrates, PNAs are intensively studied and considered beneficial for the fields of materials and nanotechnology science. Herein, we designed cationic polypeptide-functionalized, 10-mer PNAs, and demonstrated the feasible detection of hybridization with short, complementary DNA substrates, following analytes interaction with the vestibule entry of an α-hemolysin (α-HL) nanopore...
June 19, 2018: Analytical Chemistry
Motlalepula Pholo, Beatrix Coetzee, Hans J Maree, Philip R Young, James R Lloyd, Jens Kossmann, Paul N Hills
Transcriptomic analysis indicates that the bacterial signalling molecule lumichrome enhances plant growth through a combination of enhanced cell division and cell enlargement, and possibly enhances photosynthesis. Lumichrome (7,8 dimethylalloxazine), a novel multitrophic signal molecule produced by Sinorhizobium meliloti bacteria, has previously been shown to elicit growth promotion in different plant species (Phillips et al. in Proc Natl Acad Sci USA 96:12275-12280, , 1999)...
August 2018: Planta
Hanqing Nan, Long Liang, Guo Chen, Liyu Liu, Ruchuan Liu, Yang Jiao
Three-dimensional (3D) collective cell migration in a collagen-based extracellular matrix (ECM) is among one of the most significant topics in developmental biology, cancer progression, tissue regeneration, and immune response. Recent studies have suggested that collagen-fiber mediated force transmission in cellularized ECM plays an important role in stress homeostasis and regulation of collective cellular behaviors. Motivated by the recent in vitro observation that oriented collagen can significantly enhance the penetration of migrating breast cancer cells into dense Matrigel which mimics the intravasation process in vivo [Han et al...
March 2018: Physical Review. E
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