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1.
ACS Cent Sci ; 7(10): 1707-1717, 2021 Oct 27.
Artigo em Inglês | MEDLINE | ID: mdl-34729414

RESUMO

Direct RNA sequencing for the epitranscriptomic modification pseudouridine (Ψ), an isomer of uridine (U), was conducted with a protein nanopore sensor using a helicase brake to slowly feed the RNA into the sensor. Synthetic RNAs with 100% Ψ or U in 20 different known human sequence contexts identified differences during sequencing in the base-calling, ionic current, and dwell time in the nanopore sensor; however, the signals were found to have a dependency on the context that would result in biases when sequencing unknown samples. A solution to the challenge was the identification that the passage of Ψ through the helicase brake produced a long-range dwell time impact with less context bias that was used for modification identification. The data analysis approach was employed to analyze publicly available direct RNA sequencing data for SARS-CoV-2 RNA taken from cell culture to locate five conserved Ψ sites in the genome. Two sites were found to be substrates for pseudouridine synthase 1 and 7 in an in vitro assay, providing validation of the analysis. Utilization of the helicase as an additional sensor in direct RNA nanopore sequencing provides greater confidence in calling RNA modifications.

2.
Int J Radiat Biol ; : 1-9, 2021 Nov 21.
Artigo em Inglês | MEDLINE | ID: mdl-34747670

RESUMO

PURPOSE: One outcome of DNA damage from hydroxyl radical generated by ionizing radiation (IR) or by the Fenton reaction is oxidation of the nucleobases, especially guanine (G). While 8-oxo-7,8-dihydroguanine (OG) is a commonly studied oxidized lesion, several others are formed in high abundance, including 5-carboxamido-5-formamido-2-iminohydantoin (2Ih), a prevalent product in in vitro chemistry that is challenging to study from cellular sources. In this short review, we have a goal of explaining new insights into hydroxyl radical-induced oxidation chemistry of G in DNA and comparing it to endogenous DNA damage, as well as commenting on the biological outcomes of DNA base damage. CONCLUSIONS: Pathways of oxidation of G are discussed and a comparison is made between IR (hydroxyl radical chemistry) and endogenous oxidative stress that largely forms carbonate radical anion as a reactive intermediate. These pathways overlap with the formation of OG and 2Ih, but other guanine-derived lesions are more pathway specific. The biological consequences of guanine oxidation include both mutagenesis and epigenetics; a new mechanism of gene regulation via the base excision repair pathway is described for OG, whereas the impact of IR in forming guanine modifications may be to confound this process in addition to introduction of mutagenic sites.

3.
Artigo em Inglês | MEDLINE | ID: mdl-34532707

RESUMO

Despite the promise of powered lower limb prostheses, existing controllers do not assist many daily activities that require continuous control of prosthetic joints according to human states and environments. The objective of this case study was to investigate the feasibility of direct, continuous electromyographic (dEMG) control of a powered ankle prosthesis, combined with physical therapist-guided training, for improved standing postural control in an individual with transtibial amputation. Specifically, EMG signals of the residual antagonistic muscles (i.e. lateral gastrocnemius and tibialis anterior) were used to proportionally drive pneumatical artificial muscles to move a prosthetic ankle. Clinical-based activities were used in the training and evaluation protocol of the control paradigm. We quantified the EMG signals in the bilateral shank muscles as well as measures of postural control and stability. Compared to the participant's daily passive prosthesis, the dEMG-controlled ankle, combined with the training, yielded improved clinical balance scores and reduced compensation from intact joints. Cross-correlation coefficient of bilateral center of pressure excursions, a metric for quantifying standing postural control, increased to .83(±.07) when using dEMG ankle control (passive device: .39(±.29)). We observed synchronized activation of homologous muscles, rapid improvement in performance on the first day of the training for load transfer tasks, and further improvement in performance across training days (p = .006). This case study showed the feasibility of this dEMG control paradigm of a powered prosthetic ankle to assist postural control. This study lays the foundation for future study to extend these results through the inclusion of more participants and activities.

4.
NAR Cancer ; 3(3): zcab038, 2021 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-34541539

RESUMO

Many cancer-associated genes are regulated by guanine (G)-rich sequences that are capable of refolding from the canonical duplex structure to an intrastrand G-quadruplex. These same sequences are sensitive to oxidative damage that is repaired by the base excision repair glycosylases OGG1 and NEIL1-3. We describe studies indicating that oxidation of a guanosine base in a gene promoter G-quadruplex can lead to up- and downregulation of gene expression that is location dependent and involves the base excision repair pathway in which the first intermediate, an apurinic (AP) site, plays a key role mediated by AP endonuclease 1 (APE1/REF1). The nuclease activity of APE1 is paused at a G-quadruplex, while the REF1 capacity of this protein engages activating transcription factors such as HIF-1α, AP-1 and p53. The mechanism has been probed by in vitro biophysical studies, whole-genome approaches and reporter plasmids in cellulo. Replacement of promoter elements by a G-quadruplex sequence usually led to upregulation, but depending on the strand and precise location, examples of downregulation were also found. The impact of oxidative stress-mediated lesions in the G-rich sequence enhanced the effect, whether it was positive or negative.

5.
Nature ; 597(7875): 250-255, 2021 09.
Artigo em Inglês | MEDLINE | ID: mdl-34497389

RESUMO

The cellular landscape of the human intestinal tract is dynamic throughout life, developing in utero and changing in response to functional requirements and environmental exposures. Here, to comprehensively map cell lineages, we use single-cell RNA sequencing and antigen receptor analysis of almost half a million cells from up to 5 anatomical regions in the developing and up to 11 distinct anatomical regions in the healthy paediatric and adult human gut. This reveals the existence of transcriptionally distinct BEST4 epithelial cells throughout the human intestinal tract. Furthermore, we implicate IgG sensing as a function of intestinal tuft cells. We describe neural cell populations in the developing enteric nervous system, and predict cell-type-specific expression of genes associated with Hirschsprung's disease. Finally, using a systems approach, we identify key cell players that drive the formation of secondary lymphoid tissue in early human development. We show that these programs are adopted in inflammatory bowel disease to recruit and retain immune cells at the site of inflammation. This catalogue of intestinal cells will provide new insights into cellular programs in development, homeostasis and disease.


Assuntos
Envelhecimento , Sistema Nervoso Entérico/citologia , Feto/citologia , Saúde , Intestinos/citologia , Intestinos/crescimento & desenvolvimento , Linfonodos/citologia , Linfonodos/crescimento & desenvolvimento , Adulto , Animais , Criança , Doença de Crohn/patologia , Conjuntos de Dados como Assunto , Sistema Nervoso Entérico/anatomia & histologia , Sistema Nervoso Entérico/embriologia , Sistema Nervoso Entérico/crescimento & desenvolvimento , Células Epiteliais/citologia , Feminino , Feto/anatomia & histologia , Feto/embriologia , Humanos , Intestinos/embriologia , Intestinos/inervação , Linfonodos/embriologia , Linfonodos/patologia , Camundongos , Camundongos Endogâmicos C57BL , Organogênese , Receptores de IgG/metabolismo , Transdução de Sinais , Análise Espaço-Temporal , Fatores de Tempo
6.
J Neural Eng ; 18(4)2021 07 27.
Artigo em Inglês | MEDLINE | ID: mdl-34229307

RESUMO

Objective.Advanced robotic lower limb prostheses are mainly controlled autonomously. Although the existing control can assist cyclic movements during locomotion of amputee users, the function of these modern devices is still limited due to the lack of neuromuscular control (i.e. control based on human efferent neural signals from the central nervous system to peripheral muscles for movement production). Neuromuscular control signals can be recorded from muscles, called electromyographic (EMG) or myoelectric signals. In fact, using EMG signals for robotic lower limb prostheses control has been an emerging research topic in the field for the past decade to address novel prosthesis functionality and adaptability to different environments and task contexts. The objective of this paper is to review robotic lower limb Prosthesis control via EMG signals recorded from residual muscles in individuals with lower limb amputations.Approach.We performed a literature review on surgical techniques for enhanced EMG interfaces, EMG sensors, decoding algorithms, and control paradigms for robotic lower limb prostheses.Main results.This review highlights the promise of EMG control for enabling new functionalities in robotic lower limb prostheses, as well as the existing challenges, knowledge gaps, and opportunities on this research topic from human motor control and clinical practice perspectives.Significance.This review may guide the future collaborations among researchers in neuromechanics, neural engineering, assistive technologies, and amputee clinics in order to build and translate true bionic lower limbs to individuals with lower limb amputations for improved motor function.


Assuntos
Amputados , Membros Artificiais , Procedimentos Cirúrgicos Robóticos , Eletromiografia , Humanos , Locomoção , Músculo Esquelético
8.
J Eval Clin Pract ; 27(6): 1235-1242, 2021 Dec.
Artigo em Inglês | MEDLINE | ID: mdl-33960593

RESUMO

RATIONALE, AIMS AND OBJECTIVES: Sharing aspects of the traditional medical record with patients has been successful in primary and antenatal care, but has not been investigated in the UK inpatient setting. Our aim was to evaluate the impact on patient and clinician experience of providing patients with a written lay summary of their care-plan in the acute care setting. METHOD: We carried out a qualitative interview study on two acute medicine wards in an NHS University Teaching Hospital for a 4-week period in 2019. A summary record, designed in response to suggestions from doctors and patients from a previous study, was distributed to patients on the first ward round after admission. Eligible participants included all doctors and nurses working on and all patients and their families attending the acute medical units; patients were excluded if they lacked capacity to consent or were under 18. We interviewed 20 patients, 10 relatives, 10 doctors and 7 nurses. RESULTS: Patients felt that the summary improved their ability to remember details about their care so they could more accurately and easily update their relatives. They did not feel that the summary induced anxiety. Patient-doctor communication was improved: patients felt empowered to ask more questions and doctors felt that it solidified their plan and encouraged them to avoid medical jargon. Most patients felt the summary included the 'right' amount of information. Healthcare professionals were more concerned about the risk of breaching confidentiality than patients. Doctors felt that providing summaries was time-consuming; there were differing opinions about whether this was a worthwhile investment of time. Clinicians recognized that the traditional medical record has many roles. CONCLUSIONS: A summary record could empower patients and improve patient-doctor communication but would require additional clinician and administrative time.

9.
IEEE Sens J ; 21(7): 9413-9422, 2021 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-33776594

RESUMO

Amputees are prone to experiencing discomfort when wearing their prosthetic devices. As the amputee population grows this becomes a more prevalent and pressing concern. There is a need for new prosthetic technologies to construct more comfortable and well-fitted liners and sockets. One of the well-recognized impediments to the development of new prosthetic technology is the lack of practical inner socket sensors to monitor the inner socket environment (ISE), or the region between the residual limb and the socket. Here we present a capacitive pressure sensor fabricated through a simple, and scalable sewing process using commercially available conductive yarns and textile materials. This fully-textile sensor provides a soft, flexible, and comfortable sensing system for monitoring the ISE. We provide details of our low-power sensor system capable of high-speed data collection from up to four sensor arrays. Additionally, we demonstrate two custom set-ups to test and validate the textile-based sensors in a simulated prosthetic environment. Finally, we utilize the textile-based sensors to study the ISE of a bilateral transtibial amputee. Results indicate that the textile-based sensors provide a promising potential for seamlessly monitoring the ISE.

10.
Biopolymers ; 112(1): e23389, 2021 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-33098582

RESUMO

In DNA, i-motif (iM) folds occur under slightly acidic conditions when sequences rich in 2'-deoxycytidine (dC) nucleotides adopt consecutive dC self base pairs. The pH stability of an iM is defined by the midpoint in the pH transition (pHT ) between the folded and unfolded states. Two different experiments to determine pHT values via circular dichroism (CD) spectroscopy were performed on poly-dC iMs of length 15, 19, or 23 nucleotides. These experiments demonstrate two points: (1) pHT values were dependent on the titration experiment performed, and (2) pH-induced denaturing or annealing processes produced isothermal hysteresis in the pHT values. These results in tandem with model iMs with judicious mutations of dC to thymidine to favor particular folds found the hysteresis was maximal for the shorter poly-dC iMs and those with an even number of base pairs, while the hysteresis was minimal for longer poly-dC iMs and those with an odd number of base pairs. Experiments to follow the iM folding via thermal changes identified thermal hysteresis between the denaturing and annealing cycles. Similar trends were found to those observed in the CD experiments. The results demonstrate that the method of iM analysis can impact the pHT parameter measured, and hysteresis was observed in the pHT and Tm values.


Assuntos
Poli C/química , Pareamento de Bases , Sequência de Bases , Dicroísmo Circular , Concentração de Íons de Hidrogênio , Conformação de Ácido Nucleico , Poli C/síntese química , Poli C/metabolismo , Temperatura de Transição
11.
Chem Soc Rev ; 49(18): 6524-6528, 2020 Sep 21.
Artigo em Inglês | MEDLINE | ID: mdl-32785348

RESUMO

Contrary to frequent reports in the literature, hydroxyl radical is not a key species participating in endogenous oxidative DNA damage. Instead, carbonate radical anion is formed from the Fenton reaction under cellular conditions and from decomposition of nitrosoperoxycarbonate generated during inflammation. Carbonate radical anion is a potent one-electron oxidant capable of generating base radical cations that can migrate over long distances in duplex DNA, ultimately generating 8-oxo-7,8-dihydroguanine at a redox-sensitive sequence such as GGG. Such a mechanism enables G-quadruplex-forming sequences to act as long-range sensors of oxidative stress, impacting gene expression via the DNA repair mechanism that reads and ultimately erases the oxidized base. With a writing, reading and erasing mechanism in place, oxidative 'damage' to DNA might be relabeled as 'epigenetic' modifications.


Assuntos
Dano ao DNA , Epigenômica , Radical Hidroxila/metabolismo , Estresse Oxidativo , DNA/química , DNA/genética , DNA/metabolismo , Radical Hidroxila/química
12.
Chem Commun (Camb) ; 56(68): 9779-9782, 2020 Aug 25.
Artigo em Inglês | MEDLINE | ID: mdl-32716425

RESUMO

Product analysis from the iron Fenton oxidation of 2'-deoxyguanosine found reactions in bicarbonate buffer yield 8-oxo-2'-deoxyguanosine and spiroiminodihyantoin consistent with CO3˙-. Reactions in phosphate buffer furnished high yields of sugar oxidation products consistent with HO˙. These observations change the view of DNA oxidation products from the iron-Fenton reaction.


Assuntos
Bicarbonatos/química , Carbonatos/química , Desoxiguanosina/química , Radicais Livres/metabolismo , Peróxido de Hidrogênio/química , Ferro/química , Espécies Reativas de Oxigênio/metabolismo , Ânions/química , Desoxiadenosinas/química , Radicais Livres/química , Radical Hidroxila/química , Oxirredução
13.
Cell Rep ; 32(1): 107857, 2020 07 07.
Artigo em Inglês | MEDLINE | ID: mdl-32640223

RESUMO

Macrophages play a central role in intestinal immunity, but inappropriate macrophage activation is associated with inflammatory bowel disease (IBD). Here, we identify granulocyte-macrophage colony stimulating factor (GM-CSF) as a critical regulator of intestinal macrophage activation in patients with IBD and mice with dextran sodium sulfate (DSS)-induced colitis. We find that GM-CSF drives the maturation and polarization of inflammatory intestinal macrophages, promoting anti-microbial functions while suppressing wound-healing transcriptional programs. Group 3 innate lymphoid cells (ILC3s) are a major source of GM-CSF in intestinal inflammation, with a strong positive correlation observed between ILC or CSF2 transcripts and M1 macrophage signatures in IBD mucosal biopsies. Furthermore, GM-CSF-dependent macrophage polarization results in a positive feedback loop that augmented ILC3 activation and type 17 immunity. Together, our data reveal an important role for GM-CSF-mediated ILC-macrophage crosstalk in calibrating intestinal macrophage phenotype to enhance anti-bacterial responses, while inhibiting pro-repair functions associated with fibrosis and stricturing, with important clinical implications.


Assuntos
Infecções por Enterobacteriaceae/patologia , Fator Estimulador de Colônias de Granulócitos e Macrófagos/metabolismo , Inflamação/patologia , Intestinos/patologia , Macrófagos/patologia , Cicatrização , Animais , Polaridade Celular , Citrobacter rodentium/fisiologia , Colite/complicações , Colite/imunologia , Colite/patologia , Humanos , Imunidade Inata , Linfócitos/imunologia , Ativação de Macrófagos , Camundongos Endogâmicos C57BL , Fenótipo
14.
Biochemistry ; 59(28): 2616-2626, 2020 07 21.
Artigo em Inglês | MEDLINE | ID: mdl-32567845

RESUMO

Sequences of DNA typically adopt B-form duplexes in genomes, although noncanonical structures such as G-quadruplexes, i-motifs, Z-DNA, and cruciform structures can occur. A challenge is to determine the functions of these various structures in cellular processes. We and others have hypothesized that G-rich G-quadruplex-forming sequences in human genome promoters serve to sense oxidative damage generated during oxidative stress impacting gene regulation. Herein, chemical tools and a cell-based assay were used to study the oxidation of guanine to 8-oxo-7,8-dihydroguanine (OG) in the context of a cruciform-forming sequence in a gene promoter to determine the impact on transcription. We found that OG in the nontemplate strand in the loop of a cruciform-forming sequence could induce gene expression; conversely when OG was in the same sequence on the template strand, gene expression was inhibited. A model for the transcriptional changes observed is proposed in which OG focuses the DNA repair process on the promoter to impact expression. Our cellular and biophysical studies and literature sources support the idea that removal of OG from duplex DNA by OGG1 yields an abasic site (AP) that triggers a structural shift to the cruciform fold. The AP-bearing cruciform structure is presented to APE1, which functions as a conduit between DNA repair and gene regulation. The significance is enhanced by a bioinformatic study of all human gene promoters and transcription termination sites for inverted repeats (IRs). Comparison of the two regions showed that promoters have stable and G-rich IRs at a low frequency and termination sites have many AT-rich IRs with low stability.


Assuntos
DNA Cruciforme/genética , Desoxiguanosina/metabolismo , Estresse Oxidativo , Regiões Promotoras Genéticas , Transcrição Genética , Linhagem Celular Tumoral , Reparo do DNA , DNA Cruciforme/metabolismo , Quadruplex G , Guanina/análogos & derivados , Guanina/metabolismo , Humanos , Oxirredução
15.
ACS Chem Biol ; 15(6): 1292-1300, 2020 06 19.
Artigo em Inglês | MEDLINE | ID: mdl-32396327

RESUMO

Maturation of mRNA in humans involves modifying the 5' and 3' ends, splicing introns, and installing epitranscriptomic modifications that are essential for mRNA biogenesis. With respect to epitranscriptomic modifications, they are usually installed in specific consensus motifs, although not all sequences are modified suggesting a secondary structural component to site selection. Using bioinformatic analysis of published data, we identify in human mature-mRNA that potential RNA G-quadruplex (rG4) sequences colocalize with the epitranscriptomic modifications N6-methyladenosine (m6A), pseudouridine (Ψ), and inosine (I). Using the only available pre-mRNA data sets from the literature, we demonstrate colocalization of potential rG4s and m6A was greatest overall and occurred in introns near 5' and 3' splice sites. The loop lengths and sequence context of the m6A-bearing potential rG4s exhibited short loops most commonly comprised of single A nucleotides. This observation is consistent with a literature report of intronic m6A found in SAG (S = C or G) consensus motifs that are also recognized by splicing factors. The localization of m6A and potential rG4s in pre-mRNA at intron splice junctions suggests that these features could function together in alternative splicing. A similar analysis for potential rG4s around sites of Ψ installation or A-to-I editing in mRNA also found a colocalization; however, the frequency was less than that observed with m6A. These bioinformatic analyses guide a discussion of future experiments to understand how noncanonical rG4 structures may collaborate with epitranscriptomic modifications in the human cellular context to impact cellular phenotype.


Assuntos
Adenosina/análogos & derivados , Quadruplex G , Íntrons , Precursores de RNA/química , Sítios de Splice de RNA , Adenosina/análise , Adenosina/genética , Humanos , Pseudouridina/análise , Pseudouridina/genética , Precursores de RNA/genética , Splicing de RNA , Transcriptoma
16.
Proc Natl Acad Sci U S A ; 117(17): 9338-9348, 2020 04 28.
Artigo em Inglês | MEDLINE | ID: mdl-32284409

RESUMO

Oxidation of guanine generates several types of DNA lesions, such as 8-oxoguanine (8OG), 5-guanidinohydantoin (Gh), and spiroiminodihydantoin (Sp). These guanine-derived oxidative DNA lesions interfere with both replication and transcription. However, the molecular mechanism of transcription processing of Gh and Sp remains unknown. In this study, by combining biochemical and structural analysis, we revealed distinct transcriptional processing of these chemically related oxidized lesions: 8OG allows both error-free and error-prone bypass, whereas Gh or Sp causes strong stalling and only allows slow error-prone incorporation of purines. Our structural studies provide snapshots of how polymerase II (Pol II) is stalled by a nonbulky Gh lesion in a stepwise manner, including the initial lesion encounter, ATP binding, ATP incorporation, jammed translocation, and arrested states. We show that while Gh can form hydrogen bonds with adenosine monophosphate (AMP) during incorporation, this base pair hydrogen bonding is not sufficient to hold an ATP substrate in the addition site and is not stable during Pol II translocation after the chemistry step. Intriguingly, we reveal a unique structural reconfiguration of the Gh lesion in which the hydantoin ring rotates ∼90° and is perpendicular to the upstream base pair planes. The perpendicular hydantoin ring of Gh is stabilized by noncanonical lone pair-π and CH-π interactions, as well as hydrogen bonds. As a result, the Gh lesion, as a functional mimic of a 1,2-intrastrand crosslink, occupies canonical -1 and +1 template positions and compromises the loading of the downstream template base. Furthermore, we suggest Gh and Sp lesions are potential targets of transcription-coupled repair.


Assuntos
Guanidinas/química , Guanosina/análogos & derivados , Hidantoínas/química , RNA Polimerase II/metabolismo , Compostos de Espiro/química , Pareamento de Bases , DNA/química , DNA/metabolismo , Dano ao DNA/fisiologia , Reparo do DNA/fisiologia , Guanidinas/metabolismo , Guanina/metabolismo , Guanosina/química , Guanosina/metabolismo , Hidantoínas/metabolismo , Oxirredução , Estresse Oxidativo/fisiologia , Purinas/metabolismo , RNA Polimerase II/fisiologia , Saccharomyces cerevisiae/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Compostos de Espiro/metabolismo , Transcrição Genética/fisiologia , Ativação Transcricional/fisiologia
17.
J Neural Eng ; 17(3): 036020, 2020 06 12.
Artigo em Inglês | MEDLINE | ID: mdl-32348977

RESUMO

OBJECTIVE: Evoking haptic sensation on upper limb amputees via peripheral nerve stimulation has been investigated intensively in the past decade, but related studies involving lower limb amputees are limited. This study aimed to evaluate the feasibility of using non-invasive transcutaneous electrical nerve stimulation to evoke haptic sensation along the phantom limb of the amputated foot of transtibial amputees. APPROACH: A high-density electrode grid (4 × 4) was placed over the skin surface above the distal branching of the sciatic, tibial, and common peroneal nerves. We hypothesized that electrical stimulation delivered to distinct electrode pairs created unique electric fields, which can activate selective sets of sensory axons innervating different skin regions of the foot. Five transtibial amputee subjects (three unilateral and two bilateral) and one able-bodied subject were tested by scanning all possible electrode pair combinations. MAIN RESULTS: All subjects reported various haptic percepts at distinct regions along the foot with each corresponding to specific electrode pairs. These results demonstrated the capability of our non-invasive nerve stimulation method to evoke haptic sensations in the foot of transtibial amputees and the able-bodied subject. SIGNIFICANCE: The outcomes contribute important knowledge and evidence regarding missing tactile sensation in the foot of lower limb amputees and might also facilitate future development of strategies to manage phantom pain and enhance embodiment of prosthetic legs in the future.


Assuntos
Amputados , Membros Artificiais , Membro Fantasma , Estimulação Elétrica Nervosa Transcutânea , Humanos , Tato
18.
J Am Chem Soc ; 142(3): 1115-1136, 2020 01 22.
Artigo em Inglês | MEDLINE | ID: mdl-31880930

RESUMO

Living in an oxygen atmosphere demands an ability to thrive in the presence of reactive oxygen species (ROS). Aerobic organisms have successfully found solutions to the oxidative threats imposed by ROS by evolving an elaborate detoxification system, upregulating ROS during inflammation, and utilizing ROS as messenger molecules. In this Perspective, recent studies are discussed that demonstrate ROS as signaling molecules for gene regulation by combining two emergent properties of the guanine (G) heterocycle in DNA, namely, oxidation sensitivity and a propensity for G-quadruplex (G4) folding, both of which depend upon sequence context. In human gene promoters, this results from an elevated 5'-GG-3' dinucleotide frequency and GC enrichment near transcription start sites. Oxidation of DNA by ROS drives conversion of G to 8-oxo-7,8-dihydroguanine (OG) to mark target promoters for base excision repair initiated by OG-glycosylase I (OGG1). Sequence-dependent mechanisms for gene activation are available to OGG1 to induce transcription. Either OGG1 releases OG to yield an abasic site driving formation of a non-canonical fold, such as a G4, to be displayed to apurinic/apyrimidinic 1 (APE1) and stalling on the fold to recruit activating factors, or OGG1 binds OG and facilitates activator protein recruitment. The mechanisms described drive induction of stress response, DNA repair, or estrogen-induced genes, and these pathways are novel potential anticancer targets for therapeutic intervention. Chemical concepts provide a framework to discuss the regulatory or possible epigenetic potential of the OG modification in DNA, in which DNA "damage" and non-canonical folds collaborate to turn on or off gene expression. The next steps for scientific discovery in this growing field are discussed.


Assuntos
Quadruplex G , Guanina/química , Regiões Promotoras Genéticas , Dano ao DNA , DNA Glicosilases/metabolismo , Reparo do DNA , Regulação da Expressão Gênica , Humanos , Oxirredução
19.
J Am Chem Soc ; 141(41): 16450-16460, 2019 10 16.
Artigo em Inglês | MEDLINE | ID: mdl-31538776

RESUMO

The recent report of RBS-Seq to map simultaneously the epitranscriptomic modifications N1-methyladenosine, 5-methylcytosine, and pseudouridine (Ψ) via bisulfite treatment of RNA provides a key advance to locate these important modifications. The locations of Ψ were found by a deletion signature generated during cDNA synthesis after bisulfite treatment for which the chemical details of the reaction are poorly understood. In the present work, the bisulfite reaction with Ψ was explored to identify six isomers of bisulfite adducted to Ψ. We found four of these adducts involved the heterocyclic ring, similar to the reaction with other pyrimidines. The remaining two adducts were bonded to the 1' carbon, which resulted in opening of the ribose ring. The utilization of complementary 1D- and 2D-NMR, Raman, and electronic circular dichroism spectroscopies led to the assignment of the two ribose adducts being the constitutional isomers of an S- and an O-adduct of bisulfite to the ribose, and these are the final products after heating. A mechanistic proposal is provided to rationalize chemically the formation and stereochemistries of all six isomeric bisulfite adducts to Ψ; conversion of intermediate adducts to the two final products is proposed to involve E2, SN2', and [2,3]-sigmatropic shift reactions. Lastly, a synthetic RNA template with Ψ at a known location was treated with bisulfite, leading to a deletion signature after reverse transcription, supporting the RBS-Seq report. This classical bisulfite reaction used for epigenomic and epitranscriptomic sequencing diverges from the C nucleoside Ψ to form stable bisulfite end products that yield signatures for next-generation sequencing.


Assuntos
Pseudouridina/química , RNA/química , Sulfitos/química , Conformação de Ácido Nucleico
20.
IEEE Int Conf Rehabil Robot ; 2019: 899-904, 2019 06.
Artigo em Inglês | MEDLINE | ID: mdl-31374744

RESUMO

In this study we aimed to investigate the potential for antagonistic residual muscles to generate anticipatory and compensatory postural adjustments and their benefit to postural control with proportional myoelectric control of a powered ankle prosthesis. We conducted this investigation using a predictable pendulum drop task with a single transtibial amputee. In two individual testing sessions the participant used his prescribed passive device and a powered device with pneumatic artificial muscles actuated proportionally to the activation of residual Tibialis Anterior (TA) and Lateral Gastrocnemius (GAS) muscles. Results demonstrated the transtibial amputee generated activations from the residual TA significantly earlier in the powered condition $(p=\theta.\theta\theta 7)$. In the powered condition anticipatory center of pressure excursions were significantly higher $(p=\theta.\theta 17)$, and peak center of mass excursions were reduced $(p=\theta.\theta 21)$. Peak medio-lateral center of pressure excursions were also significantly less in the direction of the intact limb for the powered condition $(p\ =\ \theta.\theta\theta 3)$. The results from this pilot study demonstrate the promise for transtibial amputees to generate anticipatory postural adjustments as well as the potential improvement of stability under expected perturbations. This pilot study provides an initial basis for future study using proportional myoelectric control via antagonistic residual muscles for the control of posture under expected perturbations.


Assuntos
Tornozelo/fisiologia , Eletromiografia , Equilíbrio Postural/fisiologia , Desenho de Prótese , Humanos , Masculino , Pessoa de Meia-Idade , Músculos/fisiologia , Projetos Piloto , Pressão , Processamento de Sinais Assistido por Computador , Análise e Desempenho de Tarefas
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