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1.
Palliat Med Rep ; 4(1): 208-213, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37637761

RESUMO

Background: Social distancing during the COVID-19 pandemic limited how family, friends, and clinicians physically interacted with people who were dying and decreased communal opportunities for processing grief. These barriers can cause or exacerbate suffering due to loneliness while grieving. Purpose: In this article, we describe the protocol for a brief storytelling intervention designed to reduce loneliness among families, friends, and clinicians grieving the death of a person during the time of COVID-19. Methods: We trained four StoryListening doulas (SLDs) to hold a welcoming space and listen to stories with curiosity and openness. The intervention included a video StoryListening session and two brief questionnaires, filled out before and two weeks after the encounter, assessing loneliness and quality of life. During sessions, SLDs invited participants to share their story of loss in their own words and in as much detail as preferred. When participants felt a sense of story completion, SLDs shared validating statements and expressed gratitude to the participant for sharing. The video and audio for each participant's StoryListening encounter were recorded and the participant was offered an audio copy of their session.

2.
FEBS J ; 290(20): 4966-4983, 2023 10.
Artigo em Inglês | MEDLINE | ID: mdl-37437000

RESUMO

Fluorine forms the strongest single bond to carbon with the highest bond dissociation energy among natural products. However, fluoroacetate dehalogenases (FADs) have been shown to hydrolyze this bond in fluoroacetate under mild reaction conditions. Furthermore, two recent studies demonstrated that the FAD RPA1163 from Rhodopseudomonas palustris can also accept bulkier substrates. In this study, we explored the substrate promiscuity of microbial FADs and their ability to defluorinate polyfluorinated organic acids. Enzymatic screening of eight purified dehalogenases with reported fluoroacetate defluorination activity revealed significant hydrolytic activity against difluoroacetate in three proteins. Product analysis using liquid chromatography-mass spectrometry identified glyoxylic acid as the final product of enzymatic DFA defluorination. The crystal structures of DAR3835 from Dechloromonas aromatica and NOS0089 from Nostoc sp. were determined in the apo-state along with the DAR3835 H274N glycolyl intermediate. Structure-based site-directed mutagenesis of DAR3835 demonstrated a key role for the catalytic triad and other active site residues in the defluorination of both fluoroacetate and difluoroacetate. Computational analysis of the dimer structures of DAR3835, NOS0089, and RPA1163 indicated the presence of one substrate access tunnel in each protomer. Moreover, protein-ligand docking simulations suggested similar catalytic mechanisms for the defluorination of both fluoroacetate and difluoroacetate, with difluoroacetate being defluorinated via two consecutive defluorination reactions producing glyoxylate as the final product. Thus, our findings provide molecular insights into substrate promiscuity and catalytic mechanism of FADs, which are promising biocatalysts for applications in synthetic chemistry and bioremediation of fluorochemicals.


Assuntos
Fluoracetatos , Hidrolases , Hidrólise , Fluoracetatos/metabolismo , Hidrolases/química
3.
J Vis Exp ; (195)2023 05 26.
Artigo em Inglês | MEDLINE | ID: mdl-37306421

RESUMO

Echocardiography uses ultrasonic waves to non-invasively assess cardiac structure and function and is the standard of care for cardiac assessment and monitoring. The miniature pig, or minipig, is increasingly being used as a model of cardiac disease in medical research. Pigs are notoriously difficult to restrain and handle safely, and, therefore, research echocardiography in this species is almost always performed under anesthesia or heavy sedation. Anesthetics and sedatives universally affect cardiovascular function and may cause the depression of cardiac output and blood pressure, increases or decreases in heart rate and systemic vascular resistance, changes in the electrical rhythm, and altered coronary blood flow. Therefore, sedated or anesthetized echocardiography may not accurately depict the progression of cardiac disease in large animal models, thereby limiting the translational value of these important studies. This paper describes a novel device that allows for standing awake echocardiography in minipigs. In addition, training techniques used to teach pigs to tolerate this painless and non-invasive procedure without the need for hemodynamic-altering anesthetics are described. Standing awake echocardiography represents a safe and feasible way to perform the most common cardiac monitoring test in minipigs for cardiovascular research.


Assuntos
Cardiopatias , Vigília , Suínos , Animais , Porco Miniatura , Ecocardiografia , Frequência Cardíaca
4.
mBio ; 13(4): e0163022, 2022 08 30.
Artigo em Inglês | MEDLINE | ID: mdl-35862786

RESUMO

Analysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes known to have such functions were identified and experimentally validated, including 5-formyltetrahydrofolate cycloligase, coenzyme A (CoA) disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal. IMPORTANCE Metabolite damage and repair mechanisms are being increasingly recognized. We present here compelling genetic and biochemical evidence for the universal importance of these mechanisms by demonstrating that stripping a genome down to its barest essentials leaves metabolite damage control systems in place. Furthermore, our metabolomic and cheminformatic results point to the existence of a network of metabolite damage and damage control reactions that extends far beyond the corners of it that have been characterized so far. In sum, there can be little room left to doubt that metabolite damage and the systems that counter it are mainstream metabolic processes that cannot be separated from life itself.


Assuntos
Genoma Bacteriano , Metabolômica , Metabolômica/métodos , Oxirredutases
5.
J Environ Manage ; 316: 115174, 2022 Aug 15.
Artigo em Inglês | MEDLINE | ID: mdl-35658267

RESUMO

Land-use conflicts can be costly and time-consuming and cause social burden to all parties. In this study, we developed an approach for mapping synergy and conflict potential between land uses and tested it on nature protection, nature-based tourism, forestry and mining. First, we calculated the ecological and socio-cultural values for the study area, and further the economic values related to forestry and mining. Second, we conducted an integrated spatial assessment of these values and used it jointly with a variant of a value compatibility analysis to locate areas with possible synergistic and conflicting land uses. This study was carried out in Finnish Lapland where land use conflicts have occurred due to the need to develop forestry and mining in areas that are also important for nature-based tourism. The method operated well as it identified sites with ongoing land-use disputes. Synergy potential between biodiversity and socio-cultural values was identified in protected areas and other sites of natural beauty, and conflict potential concerning forestry near tourist resorts and concerning mining at proposed mining project sites. The developed framework can assist in locating sites that may need proactive measurements to avoid conflicts, and sites that would benefit from multi-purpose management thereby supporting sustainable and adaptive land-use planning.


Assuntos
Biodiversidade , Agricultura Florestal , Conservação dos Recursos Naturais , Ecossistema , Finlândia , Mineração
6.
Am J Disaster Med ; 16(3): 203-205, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34904704

RESUMO

BACKGROUND: State Health Departments are at the helm of addressing the myriad needs during the COVID-19 pandemic, including those of vulnerable populations who do not have a place to self-isolate or quarantine to prevent the spread. An estimated 5,000 Arkansas residents face homelessness and are at increased risk of contracting and spreading COVID-19. Additionally, those living in multigenerational families face similar challenges. OBJECTIVE: We share our experiences and lessons learned in planning, executing, and maintaining a quarantine and isolation facility for vulnerable population during the COVID-19 pandemic. SETTING AND PATIENTS: A 29-bed quarantine and isolation facility was instituted and maintained by the Arkansas Department of Health to meet the quarantine and isolation needs of vulnerable populations. Outcomes and conclusions: As the COVID-19 pandemic persists, need for a facility to meet quarantine and isolation requirements of vulnerable population is not just a critical mitigation strategy but is an ethical imperative.


Assuntos
COVID-19 , Quarentena , Humanos , Pandemias , SARS-CoV-2 , Populações Vulneráveis
7.
Front Psychiatry ; 12: 769034, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34966306

RESUMO

Background: Numerous validation studies support the use of the interRAI Mental Health (MH) assessment system for inpatient mental health assessment, triage, treatment planning, and outcome measurement. However, there have been suggestions that the interRAI MH does not include sufficient content relevant to forensic mental health. We address this potential deficiency through the development of a Forensic Supplement (FS) to the interRAI MH system. Using three forensic risk assessment instruments (PCL-R; HCR-20; VRAG) that had a record of independent cross validation in the forensic literature, we identified forensic content domains that were missing in the interRAI MH. We then independently developed items to provide forensic coverage. The resulting FS is a single-page, 19-item supplementary document that can be scored along with the interRAI MH, adding approximately 10-15 min to administration time. We constructed the Problem Behavior Scale (PBS) using 11 items from the interRAI MH and FS. The Developmental Sample, 168 forensic mental health inpatients from two large mental health specialty hospitals, was assessed with both an earlier version of the interRAI MH and FS. This sample also provided us access to scores on the PCL-R, the HCR-20 and the VRAG. To validate our initial findings, we sought additional samples where scoring of the interRAI MH and the FS had been done. The first, the Forensic Sample (N = 587), consisted of forensic inpatients in other mental health units/hospitals. The second, the Correctional Sample (N = 618) was a random, representative sample of inmates in prisons, and the third, the Youth Sample (N = 90) comprised a group of youth in police custody. Results: The PBS ranged from 0 to 11, was positively skewed with most scores below 3, and had good internal consistency (Cronbach's Alpha = 0.80). In a test of concurrent validity, correlations between PBS scores and forensic risk scores were moderate to high (i.e., r with PCL-R Factor two of 0.317; with HCR-20 Clinical of 0.46; and with HCR-20 Risk of 0.39). In a test of convergent validity, we used Binary Logistic Regression to demonstrate that the PBS was related to three negative patient experiences (recent verbal abuse, use of a seclusion room, and failure to attain an unaccompanied leave). For each of these three samples, we conducted the same convergent validity statistical analyses as we had for the Developmental Sample and the earlier findings were replicated. Finally, we examined the relationship between PBS scores and care planning triggers, part of the interRAI systems Clinical Assessment Protocols (CAPs). In all three validity samples, the PBS was significantly related to the following CAPs being triggered: Harm to Others, Interpersonal Conflict, Traumatic Life Events, and Control Interventions. These additional validations generalize our findings across age groups (adult, youth) and across health care and correctional settings. Conclusions: The FS improves the interRAI MH's ability to identify risk for negative patient experiences and assess clinical needs in hospitalized/incarcerated forensic patients. These results generalize across age groups and across health care and correctional settings.

8.
J Biol Chem ; 297(5): 101251, 2021 11.
Artigo em Inglês | MEDLINE | ID: mdl-34592310

RESUMO

The cariogenic pathogen Streptococcus mutans contains two CRISPR systems (type I-C and type II-A) with the Cas5c protein (SmuCas5c) involved in processing of long CRISPR RNA transcripts (pre-crRNA) containing repeats and spacers to mature crRNA guides. In this study, we determined the crystal structure of SmuCas5c at a resolution of 1.72 Å, which revealed the presence of an N-terminal modified RNA recognition motif and a C-terminal twisted ß-sheet domain with four bound sulphate molecules. Analysis of surface charge and residue conservation of the SmuCas5c structure suggested the location of an RNA-binding site in a shallow groove formed by the RNA recognition motif domain with several conserved positively charged residues (Arg39, Lys52, Arg109, Arg127, and Arg134). Purified SmuCas5c exhibited metal-independent ribonuclease activity against single-stranded pre-CRISPR RNAs containing a stem-loop structure with a seven-nucleotide stem and a pentaloop. We found SmuCas5c cleaves substrate RNA within the repeat sequence at a single cleavage site located at the 3'-base of the stem but shows significant tolerance to substrate sequence variations downstream of the cleavage site. Structure-based mutational analysis revealed that the conserved residues Tyr50, Lys120, and His121 comprise the SmuCas5c catalytic residues. In addition, site-directed mutagenesis of positively charged residues Lys52, Arg109, and Arg134 located near the catalytic triad had strong negative effects on the RNase activity of this protein, suggesting that these residues are involved in RNA binding. Taken together, our results reveal functional diversity of Cas5c ribonucleases and provide further insight into the molecular mechanisms of substrate selectivity and activity of these enzymes.


Assuntos
Proteínas de Bactérias/química , Sistemas CRISPR-Cas , Repetições Palindrômicas Curtas Agrupadas e Regularmente Espaçadas , Modelos Moleculares , Processamento Pós-Transcricional do RNA , RNA Bacteriano/química , Ribonucleases/química , Streptococcus mutans/química , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , RNA Bacteriano/metabolismo , Ribonucleases/genética , Ribonucleases/metabolismo , Streptococcus mutans/genética , Streptococcus mutans/metabolismo
9.
Diagnostics (Basel) ; 11(3)2021 Mar 19.
Artigo em Inglês | MEDLINE | ID: mdl-33808677

RESUMO

Research into machine learning (ML) for clinical vascular analysis, such as those useful for stroke and coronary artery disease, varies greatly between imaging modalities and vascular regions. Limited accessibility to large diverse patient imaging datasets, as well as a lack of transparency in specific methods, are obstacles to further development. This paper reviews the current status of quantitative vascular ML, identifying advantages and disadvantages common to all imaging modalities. Literature from the past 8 years was systematically collected from MEDLINE® and Scopus database searches in January 2021. Papers satisfying all search criteria, including a minimum of 50 patients, were further analysed and extracted of relevant data, for a total of 47 publications. Current ML image segmentation, disease risk prediction, and pathology quantitation methods have shown sensitivities and specificities over 70%, compared to expert manual analysis or invasive quantitation. Despite this, inconsistencies in methodology and the reporting of results have prevented inter-model comparison, impeding the identification of approaches with the greatest potential. The clinical potential of this technology has been well demonstrated in Computed Tomography of coronary artery disease, but remains practically limited in other modalities and body regions, particularly due to a lack of routine invasive reference measurements and patient datasets.

10.
Int J Obes (Lond) ; 45(6): 1357-1361, 2021 06.
Artigo em Inglês | MEDLINE | ID: mdl-33637948

RESUMO

This study examined whether the neighborhood built environment moderated gestational weight gain (GWG) in LIFE-Moms clinical trials. Participants were 790 pregnant women (13.9 weeks' gestation) with overweight or obesity randomized within four clinical centers to standard care or lifestyle intervention to reduce GWG. Geographic information system (GIS) was used to map the neighborhood built environment. The intervention relative to standard care significantly reduced GWG (coefficient = 0.05; p = 0.005) and this effect remained significant (p < 0.03) after adjusting for built environment variables. An interaction was observed for presence of fast food restaurants (coefficient = -0.007; p = 0.003). Post hoc tests based on a median split showed that the intervention relative to standard care reduced GWG in participants living in neighborhoods with lower fast food density 0.08 [95% CI, 0.03,0.12] kg/week (p = 0.001) but not in those living in areas with higher fast food density (0.02 [-0.04, 0.08] kg/week; p = 0.55). Interaction effects suggested less intervention efficacy among women living in neighborhoods with more grocery/convenience stores (coefficient = -0.005; p = 0.0001), more walkability (coefficient -0.012; p = 0.007) and less crime (coefficient = 0.001; p = 0.007), but post-hoc tests were not significant. No intervention x environment interaction effects were observed for total number of eating establishments or tree canopy. Lifestyle interventions during pregnancy were effective across diverse physical environments. Living in environments with easy access to fast food restaurants may limit efficacy of prenatal lifestyle interventions, but future research is needed to replicate these findings.


Assuntos
Ambiente Construído/estatística & dados numéricos , Ganho de Peso na Gestação/fisiologia , Estilo de Vida , Complicações na Gravidez/epidemiologia , Adulto , Feminino , Humanos , Obesidade/epidemiologia , Sobrepeso/epidemiologia , Gravidez , Características de Residência , Caminhada/estatística & dados numéricos
11.
Contemp Clin Trials ; 94: 106003, 2020 07.
Artigo em Inglês | MEDLINE | ID: mdl-32304829

RESUMO

PURPOSE: This article describes the protocol for a randomized effectiveness and cost-effectiveness trial of Stanley and Brown's Safety Planning Intervention (SPI) during pretrial jail detention to reduce post-release suicide events (suicide attempts, suicide behaviors, and suicide-related hospitalizations). BACKGROUND: With 10 million admissions per year and short stays (often days), U.S. jails touch many individuals at risk for suicide, providing an important opportunity for suicide prevention that is currently being missed. This study (N = 800) is the first randomized evaluation of an intervention to reduce suicide risk in the vulnerable year after jail release. Given that roughly 10% of all suicides in the U.S. with known circumstances occur in the context of a criminal legal stressor, reducing suicide risk in the year after arrest and jail detention could have a noticeable impact on national suicide rates. DESIGN: Pretrial jail detainees at risk for suicide were randomized to SPI during jail detention plus post-release phone follow-up or to enhanced Standard Care. Outcomes assessed through 12 months post-release include suicide events, suicide attempts, weeks of active suicide ideation, severity of suicide ideation, time to first event, psychiatric symptoms, functioning, and cost-effectiveness. Methods accommodate short jail stays and maximize trial safety and follow-up in a large sample with severe suicide risk, access to lethal means including substances and firearms, high rates of psychiatric illness, and unstable circumstances. CONCLUSION: Adequate funding was important to create the infrastructure needed to run this large trial cleanly. We encourage funders to provide adequate resources to ensure clean, well-run trials.


Assuntos
Prisões Locais , Transtornos Mentais , Humanos , Ensaios Clínicos Controlados Aleatórios como Assunto , Comportamento de Redução do Risco , Ideação Suicida , Tentativa de Suicídio
12.
Oecologia ; 189(2): 307-316, 2019 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-30535812

RESUMO

The invasion of habitats with novel environmental challenges may require physiological tolerances not seen in conspecifics from the native range. We used a combination of field and laboratory-based experiments to assess physiological tolerance to limited water access at four sites distributed across the historical invasion path of cane toads (Rhinella marina) in Australia that, from east to west, alternated between mesic and seasonally xeric habitats. Toads from all locations were well hydrated at the time of capture. However, experimental dehydration caused greater mass loss, higher plasma osmolality, and inhibition of lytic ability in toads from xeric compared to mesic locations. These results suggest somewhat surprisingly that toads from xeric environments are physiologically more vulnerable to water loss. In contrast, bactericidal ability was not sensitive to hydric state and was greater in toads from eastern (long-colonized) areas. Similar patterns in lytic ability in hydrated toads and agglutination ability in wild toads suggest that toads along the invasion front face a tradeoff between enhanced dispersal ability and physiological responses to dehydration. The ability of this invasive species to spread into drier environments may be underpinned by a combination of phenotypic plasticity and evolved (heritable) traits.


Assuntos
Espécies Introduzidas , Água , Animais , Austrália , Bufo marinus , Ecossistema
13.
Environ Sci Technol ; 52(21): 12388-12401, 2018 11 06.
Artigo em Inglês | MEDLINE | ID: mdl-30284819

RESUMO

The continuous growth of global plastics production, including polyesters, has resulted in increasing plastic pollution and subsequent negative environmental impacts. Therefore, enzyme-catalyzed depolymerization of synthetic polyesters as a plastics recycling approach has become a focus of research. In this study, we screened over 200 purified uncharacterized hydrolases from environmental metagenomes and sequenced microbial genomes and identified at least 10 proteins with high hydrolytic activity against synthetic polyesters. These include the metagenomic esterases MGS0156 and GEN0105, which hydrolyzed polylactic acid (PLA), polycaprolactone, as well as bis(benzoyloxyethyl)-terephthalate. With solid PLA as a substrate, both enzymes produced a mixture of lactic acid monomers, dimers, and higher oligomers as products. The crystal structure of MGS0156 was determined at 1.95 Å resolution and revealed a modified α/ß hydrolase fold, with a lid domain and highly hydrophobic active site. Mutational studies of MGS0156 identified the residues critical for hydrolytic activity against both polyester and monoester substrates, with two-times higher polyesterase activity in the MGS0156 L169A mutant protein. Thus, our work identified novel, highly active polyesterases in environmental metagenomes and provided molecular insights into their activity, thereby augmenting our understanding of enzymatic polyester hydrolysis.


Assuntos
Metagenoma , Poliésteres , Esterases , Hidrolases , Hidrólise
14.
ACS Chem Biol ; 13(10): 3011-3020, 2018 10 19.
Artigo em Inglês | MEDLINE | ID: mdl-30240188

RESUMO

Sugar alcohols (polyols) exist widely in nature. While some specific sugar alcohol phosphatases are known, there is no known phosphatase for some important sugar alcohols (e.g., sorbitol-6-phosphate). Using liquid chromatography-mass spectrometry-based metabolomics, we screened yeast strains with putative phosphatases of unknown function deleted. We show that the yeast gene YNL010W, which has close homologues in all fungi species and some plants, encodes a sugar alcohol phosphatase. We term this enzyme, which hydrolyzes sorbitol-6-phosphate, ribitol-5-phosphate, and (d)-glycerol-3-phosphate, polyol phosphatase 1 or PYP1. Polyol phosphates are structural analogs of the enediol intermediate of phosphoglucose isomerase (Pgi). We find that sorbitol-6-phosphate and ribitol-5-phosphate inhibit Pgi and that Pyp1 activity is important for yeast to maintain Pgi activity in the presence of environmental sugar alcohols. Pyp1 expression is strongly positively correlated with yeast growth rate, presumably because faster growth requires greater glycolytic and accordingly Pgi flux. Thus, yeast express the previously uncharacterized enzyme Pyp1 to prevent inhibition of glycolysis by sugar alcohol phosphates. Pyp1 may be useful for engineering sugar alcohol production.


Assuntos
Monoéster Fosfórico Hidrolases/metabolismo , Proteínas de Saccharomyces cerevisiae/metabolismo , Saccharomyces cerevisiae/enzimologia , Fosfatos Açúcares/metabolismo , Deleção de Genes , Glucose-6-Fosfato Isomerase/antagonistas & inibidores , Hidrólise , Monoéster Fosfórico Hidrolases/genética , Proteínas de Saccharomyces cerevisiae/genética , Fosfatos Açúcares/química
15.
Suicidologi ; 23(1): 22-30, 2018.
Artigo em Inglês | MEDLINE | ID: mdl-29970972

RESUMO

Suicide is a serious public health concern in the US, especially for those served in outpatient behavioral health. Over the past decade, there has been a dramatic increase in US suicide rates, and a significant proportion of those dying by or attempting suicide were treated in outpatient behavioral healthcare within the prior year. In response, the US Action Alliance released the National Strategy for Suicide Prevention in 2012, a key tenet of which is the "Zero Suicide" (ZS) model. ZS provides resources for administrators and providers to create a systematic approach to quality improvement for suicide prevention in healthcare systems via seven essential elements (Lead, Train, Identify, Engage, Treat, Transition, Improve). In this paper, we describe the ZS model, as well as our operationalization of the model in an NIMH-funded study in ~170 free-standing New York State outpatient behavioral health clinics, serving >80,000 patients. This study is the largest implementation and evaluation of the ZS approach ever conducted in outpatient behavioral health. Evaluation of ZS implementation in "real-world" clinical settings will provide crucial insight regarding broader dissemination and inform how to best adopt empirically-supported care for suicidal patients in outpatient behavioral health, thereby reducing tragic and preventable loss of life.

16.
Cell Chem Biol ; 25(5): 560-570.e6, 2018 05 17.
Artigo em Inglês | MEDLINE | ID: mdl-29551348

RESUMO

Prenylated flavin mononucleotide (prFMN) is a recently discovered cofactor required by the UbiD family of reversible decarboxylases involved in ubiquinone biosynthesis, biological decomposition of lignin, and biotransformation of aromatic compounds. This cofactor is synthesized by UbiX-like prenyltransferases catalyzing the transfer of the dimethylallyl moiety of dimethylallyl-monophosphate (DMAP) to FMN. The origin of DMAP for prFMN biosynthesis and the biochemical properties of free prFMN are unknown. We show that in Escherichia coli cells, DMAP can be produced by phosphorylating prenol using ThiM or dephosphorylating DMAPP using Nudix hydrolases. We produced 14 active prenyltransferases whose properties enabled the purification and characterization of protein-free forms of prFMN. In vitro assays revealed that the UbiD-like ferulate decarboxylase (Fdc1) can be activated by free prFMNiminium or C2'-hydroxylated prFMNiminium under both oxidized and reduced conditions. These insights into the biosynthesis and properties of prFMN will facilitate further elucidation of the biochemical diversity of reversible UbiD (de)carboxylases.


Assuntos
Vias Biossintéticas , Escherichia coli/metabolismo , Mononucleotídeo de Flavina/metabolismo , Carboxiliases/metabolismo , Escherichia coli/enzimologia , Proteínas de Escherichia coli/metabolismo , Hemiterpenos/metabolismo , Compostos Organofosforados/metabolismo , Pentanóis/metabolismo , Prenilação
17.
ACS Chem Biol ; 13(1): 225-234, 2018 01 19.
Artigo em Inglês | MEDLINE | ID: mdl-29182315

RESUMO

Esterases receive special attention because of their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases' substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here, we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps rank (classify) the promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence data sets.


Assuntos
Esterases/química , Esterases/metabolismo , Filogenia , Domínio Catalítico , Especificidade por Substrato
18.
Biotechnol J ; 12(11)2017 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-28762640

RESUMO

Carboxylic acid reductases (CARs) selectively reduce carboxylic acids to aldehydes using ATP and NADPH as cofactors under mild conditions. Although CARs attracts significant interest, only a few enzymes have been characterized to date, whereas the vast majority of CARs have yet to be examined. Herein the authors report that 12 bacterial CARs reduces a broad range of bifunctional carboxylic acids containing oxo-, hydroxy-, amino-, or second carboxyl groups with several enzymes showing activity toward 4-hydroxybutanoic (4-HB) and adipic acids. These CARs exhibits significant reductase activity against substrates whose second functional group is separated from the carboxylate by at least three carbons with both carboxylate groups being reduced in dicarboxylic acids. Purified CARs supplemented with cofactor regenerating systems (for ATP and NADPH), an inorganic pyrophosphatase, and an aldo-keto reductase catalyzes a high conversion (50-76%) of 4-HB to 1,4-butanediol (1,4-BDO) and adipic acid to 1,6-hexanediol (1,6-HDO). Likewise, Escherichia coli strains expressing eight different CARs efficiently reduces 4-HB to 1,4-BDO with 50-95% conversion, whereas adipic acid is reduced to a mixture of 6-hydroxyhexanoic acid (6-HHA) and 1,6-HDO. Thus, our results illustrate the broad biochemical diversity of bacterial CARs and their compatibility with other enzymes for applications in biocatalysis.


Assuntos
Proteínas de Bactérias , Engenharia Metabólica/métodos , Oxirredutases , Trifosfato de Adenosina/metabolismo , Adipatos , Proteínas de Bactérias/genética , Proteínas de Bactérias/metabolismo , Ácidos Carboxílicos/metabolismo , Escherichia coli/enzimologia , Escherichia coli/genética , Escherichia coli/metabolismo , Hidroxibutiratos , NADP/metabolismo , Oxirredutases/genética , Oxirredutases/metabolismo
19.
J Environ Manage ; 197: 706-718, 2017 Jul 15.
Artigo em Inglês | MEDLINE | ID: mdl-28448808

RESUMO

Planning for coastal and marine environments is often characterized by conflict over current and proposed uses. Marine spatial planning has been proposed as a way forward, however, social data are often missing impeding decision-making. Participatory mapping, a technique useful for providing social data and predict conflict potential, is being used in an increasing number of terrestrial applications to inform planning, but has been little used in the marine realm. This study collected social data for an extensive coastline in northwestern Australia via 167 in-depth face-to-face interviews including participant mapping of place values. From the transcribed interviews and digitized maps, we inductively identified 17 values, with biodiversity, the physical landscape, and Aboriginal culture being most valued. To spatially identify conflict potential, values were classified in matrices as consumptive or non-consumptive with the former assumed to be less compatible with other values. Pairwise comparisons of value compatibilities informed a spatial GIS determination of conflict potential. The results were overlaid with the boundaries of nine marine protected areas in the region to illustrate the application of this method for marine spatial planning. The three near shore marine protected areas had at least one third of their area exhibiting conflict potential. Participatory mapping accompanied by conflict potential mapping provides important insights for spatial planning in these often-highly contested marine environments.


Assuntos
Biodiversidade , Conservação dos Recursos Naturais , Austrália , Humanos , Havaiano Nativo ou Outro Ilhéu do Pacífico , Resolução de Problemas
20.
Conserv Biol ; 31(6): 1439-1449, 2017 12.
Artigo em Inglês | MEDLINE | ID: mdl-28425128

RESUMO

Conservation success is contingent on assessing social and environmental factors so that cost-effective implementation of strategies and actions can be placed in a broad social-ecological context. Until now, the focus has been on how to include spatially explicit social data in conservation planning, whereas the value of different kinds of social data has received limited attention. In a regional systematic conservation planning case study in Australia, we examined the spatial concurrence of a range of spatially explicit social values and land-use preferences collected using a public participation geographic information system and biological data. We used Zonation to integrate the social data with the biological data in a series of spatial-prioritization scenarios to determine the effect of the different types of social data on spatial prioritization compared with biological data alone. The type of social data (i.e., conservation opportunities or constraints) significantly affected spatial prioritization outcomes. The integration of social values and land-use preferences under different scenarios was highly variable and generated spatial prioritizations 1.2-51% different from those based on biological data alone. The inclusion of conservation-compatible values and preferences added relatively few new areas to conservation priorities, whereas including noncompatible economic values and development preferences as costs significantly changed conservation priority areas (48.2% and 47.4%, respectively). Based on our results, a multifaceted conservation prioritization approach that combines spatially explicit social data with biological data can help conservation planners identify the type of social data to collect for more effective and feasible conservation actions.


Assuntos
Conservação dos Recursos Naturais , Sistemas de Informação Geográfica , Valores Sociais , Agricultura , Participação da Comunidade , Agricultura Florestal , Queensland , Urbanização
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