RESUMEN
Statistical analyses of homologous protein sequences can identify amino acid residue positions that co-evolve to generate family members with different properties. Based on the hypothesis that the coevolution of residue positions is necessary for maintaining protein structure, coevolutionary traits revealed by statistical models provide insight into residue-residue interactions that are important for understanding protein mechanisms at the molecular level. With the rapid expansion of genome sequencing databases that facilitate statistical analyses, this sequence-based approach has been used to study a broad range of protein families. An emerging application of this approach is to design hybrid transcriptional regulators as modular genetic sensors for novel wiring between input signals and genetic elements to control outputs. Among many allosterically regulated regulator families, the members contain structurally conserved and functionally independent protein domains, including a DNA-binding module (DBM) for interacting with a specific genetic element and a ligand-binding module (LBM) for sensing an input signal. By hybridizing a DBM and an LBM from two different family members, a hybrid regulator can be created with a new combination of signal-detection and DNA-recognition properties not present in natural systems. In this review, we present recent advances in the development of hybrid regulators and their applications in cellular engineering, especially focusing on the use of statistical analyses for characterizing DBM-LBM interactions and hybrid regulator design. Based on these studies, we then discuss the current limitations and potential directions for enhancing the impact of this sequence-based design approach.
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Evolución Molecular , Modelos Estadísticos , Ingeniería de Proteínas/métodos , Humanos , Secuencia de Aminoácidos , Proteínas/genética , Proteínas/química , Proteínas/metabolismoRESUMEN
An 85-year-old Chinese lady presented with a 5-day history of a painless left breast lump. There was no fever, nipple discharge, or history of trauma. She had a past medical history of atrial fibrillation that was managed with an oral anticoagulant. Mammography demonstrated a dense mass in the upper outer quadrant of the left breast. Ultrasound showed an irregular, heterogeneous 4.7 cm lesion containing debris and cystic spaces with raised peripheral vascularity at the 2 o'clock position, 3 cm from nipple. No internal vascularity was detected. This was managed as a haematoma and rivaroxaban was withheld. Follow-up imaging 3-weeks later showed persistence of the lesion. Bedside needle aspiration yielded haemoserous fluid with immediate reduction in size of the lesion. However, 2 weeks after aspiration, there was recurrence of the 'haematoma'. Multidisciplinary review of the clinical history, examination and imaging was sought, and biopsy of the irregularly thickened areas with vascularity along the periphery of the lesion was recommended. Vacuum-assisted biopsy was performed, and histology returned as metaplastic carcinoma. A recurring 'haematoma' should always prompt a search for a secondary cause, with features such as irregular thickened walls and papillary/nodular components requiring further evaluation with biopsy for histopathological correlation.
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Neoplasias de la Mama , Hematoma , Humanos , Femenino , Hematoma/diagnóstico por imagen , Neoplasias de la Mama/diagnóstico , Neoplasias de la Mama/patología , Anciano de 80 o más Años , Diagnóstico Diferencial , Mamografía , Metaplasia , RecurrenciaRESUMEN
The persistence of conventional fossil fuel-derived plastics in marine ecosystems has raised significant environmental concerns. Biodegradable plastics are being explored as an alternative. This study investigates the biodegradation behaviour in two marine environments of melt-extruded sheets of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) bioplastic as well as blends of PHBV with a non-toxic plasticiser (triethyl citrate, TEC) and composites of PHBV with wood flour. Samples were submerged for up to 35 weeks in two subtropical marine conditions: on the sandy seabed in the sublittoral benthic zone and the sandy seabed of an open air mesocosm with pumped seawater. Rates of biodegradation, lag times and times to 95 % mass loss (T95) were determined through mass loss data and Gompertz modelling. Mechanisms of biodegradation were studied through changes in molecular weight, mechanical properties and surface features. Results reveal a rapid biodegradation rate for all PHBV samples, demonstrating a range of specific biodegradation rates relative to exposed surface area of 0.03 ± 0.01 to 0.09 ± 0.04 mg.d-1.cm-2. This rapid rate of biodegradation meant that the subtle variations in biodegradation mechanisms across different sample thicknesses and additive compositions had little effect on overall lifetimes, with the T95 for most samples being around 250-350 days, regardless of site, highlighting the robust biodegradability of PHBV in seawater. It was only the PHBV-wood flour composite that showed faster biodegradation, and that was only in the exposed ocean site. The mesocosm site was otherwise shown to be a good model for the open ocean, with very comparable biodegradation rates and changes in mechanical properties over time.
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Biodegradación Ambiental , Contaminantes Químicos del Agua/metabolismo , Contaminantes Químicos del Agua/análisis , Polihidroxialcanoatos/metabolismo , Agua de Mar/química , Poliésteres/metabolismo , Plásticos Biodegradables/metabolismo , PolihidroxibutiratosRESUMEN
Transcriptional regulators generate connections between biological signals and genetic outputs. They are used robustly for sensing input signals in building genetic circuits. However, each regulator can only generate a fixed connection, which generates constraints in linking multiple signals for more complex processes. Recent studies discovered that a domain swapping strategy can be applied to various regulator families to create modular regulators for new signal-output connections, significantly broadening possibilities in circuit design. Here we review the development of this emerging strategy, the use of resulting modular regulators for creating novel genetic response behaviors, and current limitations and solutions for further advancing the design of modular regulators.
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Redes Reguladoras de Genes , Redes Reguladoras de Genes/genéticaRESUMEN
UDP-glycosyltransferases (UGTs) form a large enzyme family that is found in a wide range of organisms. These enzymes are known for accepting a wide variety of substrates, and they derivatize xenobiotics and metabolites for detoxification. However, most UGT homologs have not been well characterized, and their potential for biomedical and environmental applications is underexplored. In this work, we have used a fluorescent assay for screening substrates of a plant UGT homolog by monitoring the formation of UDP. We optimized the assay such that it could be used for high-throughput screening of substrates of the Medicago truncatula UGT enzyme, UGT71G1, and our results show that 34 of the 159 screened compound samples are potential substrates. With an LC-MS/MS method, we confirmed that three of these candidates indeed were glycosylated by UGT71G1, which includes bisphenol A (BPA) and 7-Ethyl-10-hydroxycamptothecin (SN-38); derivatization of these toxic compounds can lead to new environmental and medical applications. This work suggests that UGT homologs may recognize a substrate profile that is much broader than previously anticipated. Additionally, it demonstrates that this screening method provides a new means to study UDP-glycosyltransferases, facilitating the use of these enzymes to tackle a wide range of problems.
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Glicosiltransferasas , Espectrometría de Masas en Tándem , Glicosiltransferasas/metabolismo , Cromatografía Liquida , Plantas/metabolismo , Uridina DifosfatoRESUMEN
The uridine diphosphate glycosyltransferase (UGT) superfamily plays a key role in the metabolism of xenobiotics and metabolic wastes, which is essential for detoxifying those species. Over the last several decades, a huge effort has been put into studying human and mammalian UGT homologs, but family members in other organisms have been explored much less. Potentially, other UGT homologs can have desirable substrate specificity and biological activities that can be harnessed for detoxification in various medical settings. In this review article, we take a plant UGT homology, UGT71G1, and compare its structural and biochemical properties with the human homologs. These comparisons suggest that even though mammalian and plant UGTs are functional in different environments, they may support similar biochemical activities based on their protein structure and function. The known biological functions of these homologs are discussed so as to provide insights into the use of UGT homologs from other organisms for addressing human diseases related to UGTs.
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Glicosiltransferasas , Uridina Difosfato , Animales , Humanos , Glicosiltransferasas/metabolismo , Plantas/metabolismo , Filogenia , Mamíferos/metabolismoRESUMEN
Polyhydroxyalkanoates (PHAs) are a group of natural polyesters that are synthesised by microorganisms. In general, their thermoplasticity and (in some forms) their elasticity makes them attractive alternatives to petrochemical-derived polymers. However, the high crystallinity of some PHAs - such as poly(3-hydroxybutyrate) (P3HB) - results in brittleness and a narrow processing window for applications such as packaging. The production of copolymeric PHA materials is one approach to improving the mechanical and thermal properties of PHAs. Another solution is the manufacture of PHA-based block copolymers. The incorporation of different polymer and copolymer blocks coupled to PHA, and the resulting tailorable microstructure of these block copolymers, can result in a step-change improvement in PHA-based material properties. A range of production strategies for PHA-based block copolymers has been reported in the literature, including biological production and chemical synthesis. Biological production is typically less controllable, with products of a broad molecular weight and compositional distribution, unless finely controlled using genetically modified organisms. By contrast, chemical synthesis delivers relatively controllable block structures and narrowly defined compositions. This paper reviews current knowledge in the areas of the production and properties of PHA-based block copolymers, and highlights knowledge gaps and future potential areas of research.
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Polihidroxialcanoatos , Poliésteres/química , Fenómenos FísicosRESUMEN
PURPOSE: To report long-term results from a phase 1/2a clinical trial assessment of a scaffold-based human embryonic stem cell-derived retinal pigmented epithelium (RPE) implant in patients with advanced geographic atrophy (GA). DESIGN: A single-arm, open-label phase 1/2a clinical trial approved by the United States Food and Drug Administration. PARTICIPANTS: Patients were 69-85 years of age at the time of enrollment and were legally blind in the treated eye (best-corrected visual acuity [BCVA], ≤ 20/200) as a result of GA involving the fovea. METHODS: The clinical trial enrolled 16 patients, 15 of whom underwent implantation successfully. The implant was administered to the worse-seeing eye with the use of a custom subretinal insertion device. The companion nonimplanted eye served as the control. The primary endpoint was at 1 year; thereafter, patients were followed up at least yearly. MAIN OUTCOME MEASURES: Safety was the primary endpoint of the study. The occurrence and frequency of adverse events (AEs) were determined by scheduled eye examinations, including measurement of BCVA and intraocular pressure and multimodal imaging. Serum antibody titers were collected to monitor systemic humoral immune responses to the implanted cells. RESULTS: At a median follow-up of 3 years, fundus photography revealed no migration of the implant. No unanticipated, severe, implant-related AEs occurred, and the most common anticipated severe AE (severe retinal hemorrhage) was eliminated in the second cohort (9 patients) through improved intraoperative hemostasis. Nonsevere, transient retinal hemorrhages were noted either during or after surgery in all patients as anticipated for a subretinal surgical procedure. Throughout the median 3-year follow-up, results show that implanted eyes were more likely to improve by > 5 letters of BCVA and were less likely to worsen by > 5 letters compared with nonimplanted eyes. CONCLUSIONS: This report details the long-term follow-up of patients with GA to receive a scaffold-based stem cell-derived bioengineered RPE implant. Results show that the implant, at a median 3-year follow-up, is safe and well tolerated in patients with advanced dry age-related macular degeneration. The safety profile, along with the early indication of efficacy, warrants further clinical evaluation of this novel approach for the treatment of GA. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.
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Atrofia Geográfica , Epitelio Pigmentado de la Retina , Agudeza Visual , Humanos , Atrofia Geográfica/cirugía , Atrofia Geográfica/fisiopatología , Epitelio Pigmentado de la Retina/trasplante , Epitelio Pigmentado de la Retina/patología , Anciano , Agudeza Visual/fisiología , Femenino , Anciano de 80 o más Años , Masculino , Estudios de Seguimiento , Tomografía de Coherencia Óptica , Células Madre Embrionarias Humanas/trasplante , Células Madre Embrionarias Humanas/citología , Trasplante de Células Madre , Resultado del TratamientoRESUMEN
Purpose: The purpose of this study was to determine the impact of prophylactic ranibizumab (PR) injections given every 3 months in eyes with intermediate nonexudative age-related macular degeneration (AMD) on drusen volume, macular layer thicknesses, and progression of geographic atrophy (GA) area over 24 months in the PREVENT trial. Methods: This post hoc analysis of the prospective PREVENT trial compared eyes with intermediate AMD randomized to PR versus sham injections to determine rates of conversion to neovascular AMD over 24 months. Drusen area and volume, macular thickness and volume, and retinal layer thicknesses were measured on spectral-domain optical coherence tomography images and analyzed. Masked grading of GA area and subretinal drusenoid deposits (SDDs) using fundus autofluorescence images was performed. Results: There were no statistical differences in drusen area and volumes between groups, and similar reductions in central subfield thickness, mean cube thickness, cube volume, and retinal sublayer thickness from baseline to 24 months (P = 0.018 to < 0.001), with no statistical differences between groups in any of these anatomic parameters. These findings were not impacted by the presence or absence of SDD. Among the 9 eyes with GA in this study, mean GA growth rate from baseline to 24 months was 1.34 +/- 0.79 mm2/year after PR and 1.95 +/- 1.73 mm2/year in sham-treated eyes (P = 0.49), and similarly showed no statistical difference with square root transformation (P = 0.61). Conclusions: Prophylactic ranibizumab given every 3 months did not appear to affect drusen volume, macular thinning, or GA progression in eyes with intermediate AMD. Translational Relevance: This work investigates the impact of PR on progressive retinal degeneration in a clinical trial.
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Atrofia Geográfica , Degeneración Macular Húmeda , Humanos , Preescolar , Ranibizumab/uso terapéutico , Inhibidores de la Angiogénesis/uso terapéutico , Estudios Prospectivos , Factor A de Crecimiento Endotelial Vascular , Agudeza Visual , Degeneración Macular Húmeda/diagnóstico , Degeneración Macular Húmeda/tratamiento farmacológico , Retina/diagnóstico por imagenRESUMEN
Bacterially derived polyhydroxyalkanoates (PHAs) are attractive alternatives to commodity petroleum-derived plastics. The most common forms of the short chain length (scl-) PHAs, including poly(3-hydroxybutyrate) (P3HB) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV), are currently limited in application because they are relatively stiff and brittle. The synthesis of PHA-b-PHA block copolymers could enhance the physical properties of PHAs. Therefore, this work explores the synthesis of PHBV-b-PHBV using relatively high molecular weight hydroxy-functionalised PHBV starting materials, coupled using facile diisocyanate chemistry, delivering industrially relevant high-molecular-weight block copolymeric products. A two-step synthesis approach was compared with a one-step approach, both of which resulted in successful block copolymer production. However, the two-step synthesis was shown to be less effective in building molecular weight. Both synthetic approaches were affected by additional isocyanate reactions resulting in the formation of by-products such as allophanate and likely biuret groups, which delivered partial cross-linking and higher molecular weights in the resulting multi-block products, identified for the first time as likely and significant by-products in such reactions, affecting the product performance.
RESUMEN
Iron is an essential element for various lifeforms but is largely insoluble due to the oxygenation of Earth's atmosphere and oceans during the Proterozoic era. Metazoans evolved iron transport glycoproteins, like transferrin (Tf) and lactoferrin (Lf), to keep iron in a non-toxic, usable form, while maintaining a low free iron concentration in the body that is unable to sustain bacterial growth. To survive on the mucosal surfaces of the human respiratory tract where it exclusively resides, the Gram-negative bacterial pathogen Moraxella catarrhalis utilizes surface receptors for acquiring iron directly from human Tf and Lf. The receptors are comprised of a surface lipoprotein to capture iron-loaded Tf or Lf and deliver it to a TonB-dependent transporter (TBDT) for removal of iron and transport across the outer membrane. The subsequent transport of iron into the cell is normally mediated by a periplasmic iron-binding protein and inner membrane transport complex, which has yet to be determined for Moraxella catarrhalis. We identified two potential periplasm to cytoplasm transport systems and performed structural and functional studies with the periplasmic binding proteins (FbpA and AfeA) to evaluate their role. Growth studies with strains deleted in the fbpA or afeA gene demonstrated that FbpA, but not AfeA, was required for growth on human Tf or Lf. The crystal structure of FbpA with bound iron in the open conformation was obtained, identifying three tyrosine ligands that were required for growth on Tf or Lf. Computational modeling of the YfeA homologue, AfeA, revealed conserved residues involved in metal binding.
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Hierro , Lactoferrina , Moraxella catarrhalis , Transferrina , Humanos , Proteínas Bacterianas/metabolismo , Hierro/metabolismo , Lactoferrina/metabolismo , Transferrina/metabolismoRESUMEN
While new biodegradable materials are being rapidly introduced to address plastic pollution, their end-of-life impacts remain unclear. Biodegradable plastics typically comprise a biopolymer matrix with functional additives and/or solid fillers, which may be toxic. Here, using an established method for continuous biodegradation monitoring, we investigated the impact of a commonly used plasticizer, dibutyl phthalate (DBP), on the biodegradation of poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) in soil. The presence of DBP delayed the initial stage of PHBV biodegradation but then accelerated subsequent rates of biodegradation. Furthermore, it led to significant increases in total bacterial and fungal biomass and altered the composition of microbial communities with significant increases in the relative abundances of Thauera (gammaproteobacterial) and Mucor circinelloides (fungal) populations. It is proposed, with evidence from biodegradation behavior and microbial analysis, that the presence of DBP likely stimulated a microbial community shift, introduced higher proportions of more readily degradable amorphous regions from the plasticizing effect, and facilitated access to the bulk polymer matrix for microorganisms or at least their associated enzymes. These effects in combination overcame the initial inhibition effect of the DBP and resulted in a net increase in the rate of biodegradation of PHBV.
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Ácidos Ftálicos , Polihidroxialcanoatos , Plastificantes , Dibutil Ftalato/metabolismo , Biodegradación AmbientalRESUMEN
Paunch is a fibrous solid residue consisting of partially digested feed from the stomachs of processed cattle. It is the largest untapped solid waste stream from animals at meat processing plants, and potentially a valuable source of fibres for the production of sustainable and potentially higher-value natural biocomposite materials. Paunch was obtained from the waste effluent of a red meat processing plant, and the fibre characteristics of the as-obtained material were studied and benchmarked against wood flour and ground buffel grass, with a view to evaluating the potential of paunch as a fibre for polymer composites. The ground paunch possessed a rough fibrous surface and fibre-like characteristics that were comparable to both wood flour and ground buffel grass, demonstrating their potential for use in composites. Without any pre-treatment or compatibilisation, composites of a representative biopolymer, poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) and ground paunch were successfully produced for the first time via extrusion, with up to 50 wt% paunch content. Mechanical property analysis showed that, at 30 wt% content, PHBV/ground paunch composites yielded mechanical properties that were comparable to those of composites with ground buffel grass.
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Bioplastics are materials that are biobased and/or biodegradable, but not necessarily both. Concerns about environmental plastic pollution are constantly growing with increasing demand for substituting fossil-based plastics with those made using renewable resource feedstocks. For many conventional bioplastics to completely decompose/degrade, they require specific environmental conditions that are rarely met in natural ecosystems, leading to rapid formation of micro-bioplastics. As global bioplastic production and consumption/use continue to increase, there is growing concern regarding the potential for environmental pollution from micro-bioplastics. However, the actual extent of their environmental occurrence and potential impacts remains unclear, and there is insufficient mass concentration-based quantitative data due to the lack of quantitative analytical methods. This study developed and validated an analytical method coupling pressurized liquid extraction and pyrolysis-gas chromatography-mass spectrometry combined with thermochemolysis to simultaneously identify and quantify five targeted micro-bioplastics (i.e., polylactic acid (PLA), polyhydroxyalkanoate, polybutylene succinate, polycaprolactone, and polybutylene adipate terephthalate (PBAT)) in environmental samples on a polymer-specific mass-based concentration. The recovery of spiked micro-bioplastics in environmental samples (biosolids) ranged from 74 to 116%. The limits of quantification for the target micro-bioplastics were between 0.02 and 0.05 mg/g. PLA and PBAT were commonly detected in wastewater, biosolids, and sediment samples at concentrations between 0.07 and 0.18 mg/g. The presented analytical method enables the accurate identification, quantification, and monitoring of micro-bioplastics in environmental samples. This study quantified five micro-bioplastic types in complex environmental samples for the first time, filling in gaps in our knowledge about bioplastic pollution and providing a useful methodology and important reference data for future research.
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Polihidroxialcanoatos , Pirólisis , Adipatos/análisis , Biosólidos , Ecosistema , Cromatografía de Gases y Espectrometría de Masas , Plásticos/química , Poliésteres , Aguas ResidualesRESUMEN
Gut microbial ß-glucuronidase (gmGUS) is involved in the disposition of many endogenous and exogenous compounds. Preclinical studies have shown that inhibiting gmGUS activity affects drug disposition, resulting in reduced toxicity in the gastrointestinal tract (GIT) and enhanced systemic efficacy. Additionally, manipulating gmGUS activity is expected to be effective in preventing/treating local or systemic diseases. Although results from animal studies are promising, challenges remain in developing drugs by targeting gmGUS. Here, we review the role of gmGUS in host health under physiological and pathological conditions, the impact of gmGUS on the disposition of phenolic compounds, models used to study gmGUS activity, and the perspectives and challenges in developing drugs by targeting gmGUS.
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Microbioma Gastrointestinal , Glucuronidasa , Animales , Tracto Gastrointestinal , Glucuronidasa/farmacologíaRESUMEN
Cell-based therapies face challenges, including poor cell survival, immune rejection, and integration into pathologic tissue. We conducted an open-label phase 1/2a clinical trial to assess the safety and preliminary efficacy of a subretinal implant consisting of a polarized monolayer of allogeneic human embryonic stem cell-derived retinal pigmented epithelium (RPE) cells in subjects with geographic atrophy (GA) secondary to dry age-related macular degeneration. Postmortem histology from one subject with very advanced disease shows the presence of donor RPE cells 2 years after implantation by immunoreactivity for RPE65 and donor-specific human leukocyte antigen (HLA) class I molecules. Markers of RPE cell polarity and phagocytosis suggest donor RPE function. Further histologic examination demonstrated CD34+ structures beneath the implant and CD4+, CD68+, and FoxP3+ cells in the tissue. Despite significant donor-host HLA mismatch, no clinical signs of retinitis, vitreitis, vasculitis, choroiditis, or serologic immune response were detected in the deceased subject or any other subject in the study. Subretinally implanted, HLA-mismatched donor RPE cells survive, express functional markers, and do not elicit clinically detectable intraocular inflammation or serologic immune responses even without long-term immunosuppression.