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1.
J Biol Chem ; 300(7): 107451, 2024 Jun 04.
Artículo en Inglés | MEDLINE | ID: mdl-38844131

RESUMEN

Complement receptor 1 (CR1) is a membrane glycoprotein with a highly duplicated domain structure able to bind multiple ligands such as C3b and C4b, the activated fragments of complement components C3 and C4, respectively. We have previously used our knowledge of this domain structure to identify CSL040, a soluble extracellular fragment of CR1 containing the long homologous repeat (LHR) domains A, B, and C. CSL040 retains the ability to bind both C3b and C4b but is also a more potent complement inhibitor than other recombinant CR1-based therapeutics. To generate soluble CR1 variants with increased inhibitory potential across all three complement pathways, or variants with activity skewed to specific pathways, we exploited the domain structure of CR1 further by generating LHR domain duplications. We identified LHR-ABCC, a soluble CR1 variant containing a duplicated C3b-binding C-terminal LHR-C domain that exhibited significantly enhanced alternative pathway inhibitory activity in vitro compared to CSL040. Another variant, LHR-BBCC, containing duplications of both LHR-B and LHR-C with four C3b binding sites, was shown to have reduced classical/lectin pathway inhibitory activity compared to CSL040, but comparable alternative pathway activity. Interestingly, multiplication of the C4b-binding LHR-A domain resulted in only minor increases in classical/lectin pathway inhibitory activity. The CR1 duplication variants characterized in these in vitro potency assays, as well as in affinity in solution C3b and C4b binding assays, not only provides an opportunity to identify new therapeutic molecules but also additional mechanistic insights to the multiple interactions between CR1 and C3b/C4b.

2.
Nucleic Acids Res ; 52(D1): D891-D899, 2024 Jan 05.
Artículo en Inglés | MEDLINE | ID: mdl-37953337

RESUMEN

Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.


Asunto(s)
Bases de Datos Genéticas , Genómica , Animales , Genoma , Anotación de Secuencia Molecular , Filogenia , Programas Informáticos , Humanos
3.
Biomolecules ; 13(10)2023 10 13.
Artículo en Inglés | MEDLINE | ID: mdl-37892204

RESUMEN

Human complement receptor 1 (CR1) is a membrane-bound regulator of complement that has been the subject of recent attempts to generate soluble therapeutic compounds comprising different fragments of its extracellular domain. This review will focus on the extracellular domain of CR1 and detail how its highly duplicated domains work both separately and together to mediate binding to its main ligands C3b and C4b, and to inhibit the classical, lectin, and alternative pathways of the complement cascade via the mechanisms of decay acceleration activity (DAA) and co-factor activity (CFA). Understanding the molecular basis of CR1 activity is made more complicated by the presence not only of multiple ligand binding domains within CR1 but also the fact that C3b and C4b can interact with CR1 as both monomers, dimers, and heterodimers. Evidence for the interaction of CR1 with additional ligands such as C1q will also be reviewed. Finally, we will bring the mechanistic understanding of CR1 activity together to provide an explanation for the differential complement pathway inhibition recently observed with CSL040, a soluble CR1-based therapeutic candidate in pre-clinical development.


Asunto(s)
Activación de Complemento , Receptores de Complemento 3b , Humanos , Proteínas del Sistema Complemento , Receptores de Complemento 3b/metabolismo
4.
Int J Qual Health Care ; 35(4)2023 Oct 20.
Artículo en Inglés | MEDLINE | ID: mdl-37751386

RESUMEN

Protection of the public is the paramount aim for health practitioner regulation, yet there has been growing concern globally on the association between regulatory complaints processes and practitioner mental health and wellbeing. The objective was to understand the experience, particularly distress, of health practitioners involved in a regulatory complaints process to identify potential strategies to minimise future risk of distress. Semi-structured qualitative interviews were conducted with health practitioners in Australia who had recently been through a regulatory complaints process, together with a retrospective analysis of documentation relating to all identified cases of self-harm or suicide of health practitioners who were involved in such a process over 4 years. Data from interviews and the serious incident analysis found there were elements of the regulatory complaints process contributing to practitioner distress. These included poor communication, extended time to close the investigation, and the management of health-related concerns. The study found external personal circumstances and pre-existing conditions could put the practitioner at greater risk of distress. There were found to be key moments in the process-triggers-where the practitioner was at particular risk of severe distress. Strong support networks, both personal and professional, were found to be protective against distress. Through process improvements and, where appropriate, additional support for practitioners, we hope to further minimise the risk of practitioner distress and harm when involved in a regulatory complaints process. The findings also point to the need for improved partnerships between regulators and key stakeholders, such as legal defence organisations, indemnity providers, employers, and those with lived experience of complaints processes. Together they can improve the support for practitioners facing a complaint and address the stigma, shame, and fear associated with regulatory complaints processes. This project provides further evidence that a more compassionate approach to regulation has the potential to be better for all parties and, ultimately, the wider healthcare system.


Asunto(s)
Pesar , Satisfacción del Paciente , Humanos , Estudios Retrospectivos , Australia , Toma de Decisiones
5.
Clin Anat ; 36(5): 742-753, 2023 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-37078437

RESUMEN

Anatomy is the foundation of many physiology and healthcare-related degrees. With limited access to cadavers in many universities, it is essential to investigate techniques that could be utilized to support and enhance the teaching of anatomy. Ultrasound is used clinically to aid the diagnosis of a wide range of conditions by visualizing the anatomy of the patient. While research has investigated the advantages of ultrasound in medical education, the potential benefits of ultrasound in undergraduate bioscience degrees remain to be investigated. The aim of this study was to identify if a portable ultrasound probe that wirelessly attaches to a smartphone or tablet was perceived by students as beneficial for their understanding and learning of anatomy, and to identify if there were any barriers for students partaking in ultrasound sessions. Following five ultrasound-teaching sessions, 107 undergraduate students completed a 5-point likert questionnaire on their perception of the integration of portable ultrasound machines in anatomy education. The data indicated that 93% of students perceived that the ultrasound teaching sessions improved their anatomical understanding, 94% perceived that ultrasound increased their ability to understand the clinical relevance of learning anatomy, 97% enjoyed the sessions, and 95% of students believed that ultrasound should be integrated into anatomy teaching. In this study, we also found several barriers for students taking part in ultrasound sessions, including religious beliefs, and lacking adequate background knowledge. In conclusion, these findings demonstrate, for the first time, that students perceive portable ultrasound to enhance their anatomy studies, demonstrating the potential benefit the integration of ultrasound into the anatomy curriculum may serve within undergraduate bioscience courses.


Asunto(s)
Anatomía , Educación de Pregrado en Medicina , Estudiantes de Medicina , Humanos , Evaluación Educacional , Educación de Pregrado en Medicina/métodos , Ultrasonografía/métodos , Curriculum , Percepción , Anatomía/educación , Enseñanza
6.
Nucleic Acids Res ; 51(D1): D933-D941, 2023 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-36318249

RESUMEN

Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.


Asunto(s)
Bases de Datos Genéticas , Programas Informáticos , Animales , Humanos , Anotación de Secuencia Molecular , Genómica , Genoma
7.
Nucleic Acids Res ; 51(D1): D942-D949, 2023 01 06.
Artículo en Inglés | MEDLINE | ID: mdl-36420896

RESUMEN

GENCODE produces high quality gene and transcript annotation for the human and mouse genomes. All GENCODE annotation is supported by experimental data and serves as a reference for genome biology and clinical genomics. The GENCODE consortium generates targeted experimental data, develops bioinformatic tools and carries out analyses that, along with externally produced data and methods, support the identification and annotation of transcript structures and the determination of their function. Here, we present an update on the annotation of human and mouse genes, including developments in the tools, data, analyses and major collaborations which underpin this progress. For example, we report the creation of a set of non-canonical ORFs identified in GENCODE transcripts, the LRGASP collaboration to assess the use of long transcriptomic data to build transcript models, the progress in collaborations with RefSeq and UniProt to increase convergence in the annotation of human and mouse protein-coding genes, the propagation of GENCODE across the human pan-genome and the development of new tools to support annotation of regulatory features by GENCODE. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.


Asunto(s)
Biología Computacional , Genoma Humano , Humanos , Animales , Ratones , Anotación de Secuencia Molecular , Biología Computacional/métodos , Genoma Humano/genética , Transcriptoma/genética , Perfilación de la Expresión Génica , Bases de Datos Genéticas
8.
Biochem J ; 479(9): 1007-1030, 2022 05 13.
Artículo en Inglés | MEDLINE | ID: mdl-35470373

RESUMEN

Human Complement Receptor 1 (HuCR1) is a potent membrane-bound regulator of complement both in vitro and in vivo, acting via interaction with its ligands C3b and C4b. Soluble versions of HuCR1 have been described such as TP10, the recombinant full-length extracellular domain, and more recently CSL040, a truncated version lacking the C-terminal long homologous repeat domain D (LHR-D). However, the role of N-linked glycosylation in determining its pharmacokinetic (PK) and pharmacodynamic (PD) properties is only partly understood. We demonstrated a relationship between the asialo-N-glycan levels of CSL040 and its PK/PD properties in rats and non-human primates (NHPs), using recombinant CSL040 preparations with varying asialo-N-glycan levels. The clearance mechanism likely involves the asialoglycoprotein receptor (ASGR), as clearance of CSL040 with a high proportion of asialo-N-glycans was attenuated in vivo by co-administration of rats with asialofetuin, which saturates the ASGR. Biodistribution studies also showed CSL040 localization to the liver following systemic administration. Our studies uncovered differential PD effects by CSL040 on complement pathways, with extended inhibition in both rats and NHPs of the alternative pathway compared with the classical and lectin pathways that were not correlated with its PK profile. Further studies showed that this effect was dose dependent and observed with both CSL040 and the full-length extracellular domain of HuCR1. Taken together, our data suggests that sialylation optimization is an important consideration for developing HuCR1-based therapeutic candidates such as CSL040 with improved PK properties and shows that CSL040 has superior PK/PD responses compared with full-length soluble HuCR1.


Asunto(s)
Lectinas , Polisacáridos , Animales , Complemento C3b/metabolismo , Complemento C4b/metabolismo , Glicosilación , Lectinas/metabolismo , Ratas , Receptores de Complemento/metabolismo , Receptores de Complemento 3b/metabolismo , Distribución Tisular
9.
Nature ; 604(7905): 310-315, 2022 04.
Artículo en Inglés | MEDLINE | ID: mdl-35388217

RESUMEN

Comprehensive genome annotation is essential to understand the impact of clinically relevant variants. However, the absence of a standard for clinical reporting and browser display complicates the process of consistent interpretation and reporting. To address these challenges, Ensembl/GENCODE1 and RefSeq2 launched a joint initiative, the Matched Annotation from NCBI and EMBL-EBI (MANE) collaboration, to converge on human gene and transcript annotation and to jointly define a high-value set of transcripts and corresponding proteins. Here, we describe the MANE transcript sets for use as universal standards for variant reporting and browser display. The MANE Select set identifies a representative transcript for each human protein-coding gene, whereas the MANE Plus Clinical set provides additional transcripts at loci where the Select transcripts alone are not sufficient to report all currently known clinical variants. Each MANE transcript represents an exact match between the exonic sequences of an Ensembl/GENCODE transcript and its counterpart in RefSeq such that the identifiers can be used synonymously. We have now released MANE Select transcripts for 97% of human protein-coding genes, including all American College of Medical Genetics and Genomics Secondary Findings list v3.0 (ref. 3) genes. MANE transcripts are accessible from major genome browsers and key resources. Widespread adoption of these transcript sets will increase the consistency of reporting, facilitate the exchange of data regardless of the annotation source and help to streamline clinical interpretation.


Asunto(s)
Biología Computacional , Bases de Datos Genéticas , Genómica , Genoma , Humanos , Difusión de la Información , Anotación de Secuencia Molecular , National Library of Medicine (U.S.) , Estados Unidos
10.
Nucleic Acids Res ; 50(D1): D988-D995, 2022 01 07.
Artículo en Inglés | MEDLINE | ID: mdl-34791404

RESUMEN

Ensembl (https://www.ensembl.org) is unique in its flexible infrastructure for access to genomic data and annotation. It has been designed to efficiently deliver annotation at scale for all eukaryotic life, and it also provides deep comprehensive annotation for key species. Genomes representing a greater diversity of species are increasingly being sequenced. In response, we have focussed our recent efforts on expediting the annotation of new assemblies. Here, we report the release of the greatest annual number of newly annotated genomes in the history of Ensembl via our dedicated Ensembl Rapid Release platform (http://rapid.ensembl.org). We have also developed a new method to generate comparative analyses at scale for these assemblies and, for the first time, we have annotated non-vertebrate eukaryotes. Meanwhile, we continually improve, extend and update the annotation for our high-value reference vertebrate genomes and report the details here. We have a range of specific software tools for specific tasks, such as the Ensembl Variant Effect Predictor (VEP) and the newly developed interface for the Variant Recoder. All Ensembl data, software and tools are freely available for download and are accessible programmatically.


Asunto(s)
Bases de Datos Genéticas , Genoma/genética , Anotación de Secuencia Molecular , Programas Informáticos , Animales , Biología Computacional/clasificación , Humanos
11.
Sci Rep ; 11(1): 21873, 2021 11 08.
Artículo en Inglés | MEDLINE | ID: mdl-34750424

RESUMEN

The complement system is a potent mediator of ischemia-reperfusion injury (IRI), which detrimentally affects the function and survival of transplanted kidneys. Human complement receptor 1 (HuCR1) is an integral membrane protein that inhibits complement activation by blocking the convertases that activate C3 and C5. We have previously reported that CSL040, a truncated form of recombinant soluble HuCR1 (sHuCR1), has enhanced complement inhibitory activity and improved pharmacokinetic properties compared to the parent molecule. Here, we compared the capacity of CSL040 and full-length sHuCR1 to suppress complement-mediated organ damage in a mouse model of warm renal IRI. Mice were treated with two doses of CSL040 or sHuCR1, given 1 h prior to 22 min unilateral renal ischemia and again 3 h later. 24 h after reperfusion, mice treated with CSL040 were protected against warm renal IRI in a dose-dependent manner, with the highest dose of 60 mg/kg significantly reducing renal dysfunction, tubular injury, complement activation, endothelial damage, and leukocyte infiltration. In contrast, treatment with sHuCR1 at a molar equivalent dose to 60 mg/kg CSL040 did not confer significant protection. Our results identify CSL040 as a promising therapeutic candidate to attenuate renal IRI and demonstrate its superior efficacy over full-length sHuCR1 in vivo.


Asunto(s)
Riñón/lesiones , Receptores de Complemento 3b/administración & dosificación , Daño por Reperfusión/prevención & control , Animales , Activación de Complemento/efectos de los fármacos , Modelos Animales de Enfermedad , Humanos , Riñón/efectos de los fármacos , Riñón/inmunología , Trasplante de Riñón/efectos adversos , Masculino , Ratones , Ratones Endogámicos C57BL , Fragmentos de Péptidos/química , Fragmentos de Péptidos/farmacología , Receptores de Complemento 3b/química , Daño por Reperfusión/etiología , Daño por Reperfusión/inmunología , Solubilidad
12.
J Thromb Haemost ; 19(11): 2710-2725, 2021 11.
Artículo en Inglés | MEDLINE | ID: mdl-34333849

RESUMEN

BACKGROUND: We have recently reported on a recombinant von Willebrand factor (VWF) D'D3 albumin fusion protein (rD'D3-FP) developed to extend the half-life of coagulation factor VIII (FVIII) for the treatment of hemophilia A. Based on predictive modelling presented in this study, we hypothesized that modifying rD'D3-FP to improve FVIII interaction would reduce exchange with endogenous VWF and provide additional FVIII half-life benefit. OBJECTIVES: The aim of this study was to identify novel rD'D3-FP variants with enhanced therapeutic efficacy in extending FVIII half-life. METHODS: Through both directed mutagenesis and random mutagenesis using a novel mammalian display platform, we identified novel rD'D3-FP variants with increased affinity for FVIII (rVIII-SingleChain) under both neutral and acidic conditions and assessed their ability to extend FVIII half-life in vitro and in vivo. RESULTS: In rat preclinical studies, rD'D3-FP variants with increased affinity for FVIII displayed enhanced potency, with reduced dose levels required to achieve equivalent rVIII-SingleChain half-life extension. In cell-based imaging studies in vitro, we also demonstrated reduced dissociation of rVIII-SingleChain from the rD'D3-FP variants within acidic endosomes and more efficient co-recycling of the rD'D3-FP/rVIII-SingleChain complex via the FcRn recycling system. CONCLUSIONS: In summary, at potential clinical doses, the rD'D3-FP variants provide marked benefits with respect to dose levels and half-life extension of co-administered FVIII, supporting their development for use in the treatment of hemophilia A.


Asunto(s)
Factor VIII , Hemofilia A , Albúminas , Animales , Factor VIII/genética , Hemofilia A/tratamiento farmacológico , Hemofilia A/genética , Ratas , Proteínas Recombinantes de Fusión , Proteínas Recombinantes/genética , Factor de von Willebrand/genética
13.
Mol Pharm ; 18(8): 3158-3170, 2021 08 02.
Artículo en Inglés | MEDLINE | ID: mdl-34292741

RESUMEN

Cell-free hemoglobin (Hb) is a driver of disease progression in conditions with intravascular or localized hemolysis. Genetic and acquired anemias or emergency medical conditions such as aneurysmal subarachnoid hemorrhage involve tissue Hb exposure. Haptoglobin (Hp) captures Hb in an irreversible protein complex and prevents its pathophysiological contributions to vascular nitric oxide depletion and tissue oxidation. Preclinical proof-of-concept studies suggest that human plasma-derived Hp is a promising therapeutic candidate for several Hb-driven diseases. Optimizing the efficacy and safety of Hb-targeting biotherapeutics may require structural and functional modifications for specific indications. Improved Hp variants could be designed to achieve the desired tissue distribution, metabolism, and elimination to target hemolytic disease states effectively. However, it is critical to ensure that these modifications maintain the function of Hp. Using transient mammalian gene expression of Hp combined with co-transfection of the pro-haptoglobin processing protease C1r-LP, we established a platform for generating recombinant Hp-variants. We designed an Hpß-scaffold, which was expressed in this system at high levels as a monomeric unit (mini-Hp) while maintaining the key protective functions of Hp. We then used this Hpß-scaffold as the basis to develop an initial proof-of-concept Hp fusion protein using human serum albumin as the fusion partner. Next, a hemopexin-Hp fusion protein with bispecific heme and Hb detoxification capacity was generated. Further, we developed a Hb scavenger devoid of CD163 scavenger receptor binding. The functions of these proteins were then characterized for Hb and heme-binding, binding of the Hp-Hb complexes with the clearance receptor CD163, antioxidant properties, and vascular nitric oxide sparing capacity. Our platform is designed to support the generation of innovative Hb scavenger biotherapeutics with novel modes of action and potentially improved formulation characteristics, function, and pharmacokinetics.


Asunto(s)
Productos Biológicos/metabolismo , Diseño de Fármacos/métodos , Haptoglobinas/metabolismo , Hemoglobinas/metabolismo , Hemopexina/metabolismo , Proteínas Recombinantes de Fusión/metabolismo , Proteínas Recombinantes de Fusión/farmacología , Animales , Antígenos CD/metabolismo , Antígenos de Diferenciación Mielomonocítica/metabolismo , Arteria Basilar/efectos de los fármacos , Productos Biológicos/química , Productos Biológicos/farmacología , Células HEK293 , Haptoglobinas/química , Haptoglobinas/genética , Hemo/metabolismo , Hemoglobinas/química , Hemólisis , Hemopexina/química , Hemopexina/genética , Humanos , Unión Proteica , Receptores de Superficie Celular/metabolismo , Receptores Depuradores/metabolismo , Proteínas Recombinantes de Fusión/genética , Albúmina Sérica Humana/química , Albúmina Sérica Humana/genética , Albúmina Sérica Humana/metabolismo , Porcinos , Transfección , Vasodilatación/efectos de los fármacos
14.
J Biol Chem ; 296: 100200, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33334893

RESUMEN

Human complement receptor 1 (HuCR1) is a pivotal regulator of complement activity, acting on all three complement pathways as a membrane-bound receptor of C3b/C4b, C3/C5 convertase decay accelerator, and cofactor for factor I-mediated cleavage of C3b and C4b. In this study, we sought to identify a minimal soluble fragment of HuCR1, which retains the complement regulatory activity of the wildtype protein. To this end, we generated recombinant, soluble, and truncated versions of HuCR1 and compared their ability to inhibit complement activation in vitro using multiple assays. A soluble form of HuCR1, truncated at amino acid 1392 and designated CSL040, was found to be a more potent inhibitor than all other truncation variants tested. CSL040 retained its affinity to both C3b and C4b as well as its cleavage and decay acceleration activity and was found to be stable under a range of buffer conditions. Pharmacokinetic studies in mice demonstrated that the level of sialylation is a major determinant of CSL040 clearance in vivo. CSL040 also showed an improved pharmacokinetic profile compared with the full extracellular domain of HuCR1. The in vivo effects of CSL040 on acute complement-mediated kidney damage were tested in an attenuated passive antiglomerular basement membrane antibody-induced glomerulonephritis model. In this model, CSL040 at 20 and 60 mg/kg significantly attenuated kidney damage at 24 h, with significant reductions in cellular infiltrates and urine albumin, consistent with protection from kidney damage. CSL040 thus represents a potential therapeutic candidate for the treatment of complement-mediated disorders.


Asunto(s)
Activación de Complemento , Receptores de Complemento 3b/inmunología , Animales , Línea Celular , Complemento C3b/inmunología , Complemento C4b/inmunología , Femenino , Glomerulonefritis/inmunología , Glomerulonefritis/terapia , Humanos , Ratones , Ratones Endogámicos C57BL , Receptores de Complemento 3b/química , Receptores de Complemento 3b/uso terapéutico , Proteínas Recombinantes/química , Proteínas Recombinantes/inmunología , Proteínas Recombinantes/uso terapéutico
15.
Nucleic Acids Res ; 49(D1): D916-D923, 2021 01 08.
Artículo en Inglés | MEDLINE | ID: mdl-33270111

RESUMEN

The GENCODE project annotates human and mouse genes and transcripts supported by experimental data with high accuracy, providing a foundational resource that supports genome biology and clinical genomics. GENCODE annotation processes make use of primary data and bioinformatic tools and analysis generated both within the consortium and externally to support the creation of transcript structures and the determination of their function. Here, we present improvements to our annotation infrastructure, bioinformatics tools, and analysis, and the advances they support in the annotation of the human and mouse genomes including: the completion of first pass manual annotation for the mouse reference genome; targeted improvements to the annotation of genes associated with SARS-CoV-2 infection; collaborative projects to achieve convergence across reference annotation databases for the annotation of human and mouse protein-coding genes; and the first GENCODE manually supervised automated annotation of lncRNAs. Our annotation is accessible via Ensembl, the UCSC Genome Browser and https://www.gencodegenes.org.


Asunto(s)
COVID-19/prevención & control , Biología Computacional/métodos , Bases de Datos Genéticas , Genómica/métodos , Anotación de Secuencia Molecular/métodos , SARS-CoV-2/genética , Animales , COVID-19/epidemiología , COVID-19/virología , Epidemias , Humanos , Internet , Ratones , Seudogenes/genética , ARN Largo no Codificante/genética , SARS-CoV-2/metabolismo , SARS-CoV-2/fisiología , Transcripción Genética/genética
16.
ACS Appl Mater Interfaces ; 12(46): 52192-52200, 2020 Nov 18.
Artículo en Inglés | MEDLINE | ID: mdl-33146516

RESUMEN

ScAlN is an emergent ultrawide-band-gap material with both a high piezoresponse and demonstrated ferroelectric polarization switching. Recent demonstration of epitaxial growth of ScAlN on GaN has unlocked prospects for new high-power transistors and nonvolatile memory technologies fabricated from these materials. An understanding of the band alignments between ScAlN and GaN is crucial in order to control the electronic and optical properties of engineered devices. To date, there have been no experimental studies of the band offsets between ScAlN and GaN. This work presents optical characterization of the band gap of molecular beam epitaxy grown ScxAl1-xN using spectroscopic ellipsometry and measurements of the band offsets of ScxAl1-xN with GaN using X-ray photoemission spectroscopy, along with a comparison to first-principles calculations. The band gap is shown to continuously decrease as a function of increasing ScN alloy fraction with a negative bowing parameter. Furthermore, a crossover from straddling (type-I) to staggered (type-II) band offsets is demonstrated as Sc composition increases beyond approximately x = 0.11. These results show that the ScAlN/GaN valence band alignment can be tuned by changing the Sc alloy fraction, which can help guide the design of heterostructures in future ScAlN/GaN-based devices.

17.
BMC Genomics ; 21(1): 196, 2020 Mar 03.
Artículo en Inglés | MEDLINE | ID: mdl-32126975

RESUMEN

BACKGROUND: Olfactory receptor (OR) genes are the largest multi-gene family in the mammalian genome, with 874 in human and 1483 loci in mouse (including pseudogenes). The expansion of the OR gene repertoire has occurred through numerous duplication events followed by diversification, resulting in a large number of highly similar paralogous genes. These characteristics have made the annotation of the complete OR gene repertoire a complex task. Most OR genes have been predicted in silico and are typically annotated as intronless coding sequences. RESULTS: Here we have developed an expert curation pipeline to analyse and annotate every OR gene in the human and mouse reference genomes. By combining evidence from structural features, evolutionary conservation and experimental data, we have unified the annotation of these gene families, and have systematically determined the protein-coding potential of each locus. We have defined the non-coding regions of many OR genes, enabling us to generate full-length transcript models. We found that 13 human and 41 mouse OR loci have coding sequences that are split across two exons. These split OR genes are conserved across mammals, and are expressed at the same level as protein-coding OR genes with an intronless coding region. Our findings challenge the long-standing and widespread notion that the coding region of a vertebrate OR gene is contained within a single exon. CONCLUSIONS: This work provides the most comprehensive curation effort of the human and mouse OR gene repertoires to date. The complete annotation has been integrated into the GENCODE reference gene set, for immediate availability to the research community.


Asunto(s)
Secuencia Conservada , Exones/genética , Sitios de Carácter Cuantitativo , Receptores Odorantes/genética , Animales , Curaduría de Datos/métodos , Bases de Datos Genéticas , Sitios Genéticos , Genoma Humano , Humanos , Ratones , Seudogenes
18.
Anal Biochem ; 596: 113625, 2020 05 01.
Artículo en Inglés | MEDLINE | ID: mdl-32088200

RESUMEN

Polysialylation is the enzymatic addition of a highly negatively charged sialic acid polymer to the non-reducing termini of glycans. Polysialylation plays an important role in development, and is involved in neurological diseases, neural tissue regeneration, and cancer. Polysialic acid (PSA) is also a biodegradable and non-immunogenic conjugate to therapeutic drugs to improve their pharmacokinetics. PSA chains vary in length, composition, and linkages, while the specific sites of polysialylation are important determinants of protein function. However, PSA is difficult to analyse by mass spectrometry (MS) due to its high negative charge and size. Most analytical approaches for analysis of PSA measure its degree of polymerization and monosaccharide composition, but do not address the key questions of site specificity and occupancy. Here, we developed a high-throughput LC-ESI-MS/MS glycoproteomics method to measure site-specific polysialylation of glycoproteins. This method measures site-specific PSA modification by using mild acid hydrolysis to eliminate PSA and sialic acids while leaving the glycan backbone intact, together with protease digestion followed by LC-ESI-MS/MS glycopeptide detection. PSA-modified glycopeptides are not detectable by LC-ESI-MS/MS, but become detectable after desialylation, allowing measurement of site-specific PSA occupancy. This method is an efficient analytical workflow for the study of glycoprotein polysialylation in biological and therapeutic settings.


Asunto(s)
Glicoproteínas/análisis , Proteómica , Ácidos Siálicos/análisis , Glicoproteínas/metabolismo , Humanos , Espectrometría de Masas , Polisacáridos/metabolismo , Ácidos Siálicos/metabolismo , Espectrometría de Masa por Ionización de Electrospray , Espectrometría de Masas en Tándem
19.
ACS Nano ; 13(6): 6730-6741, 2019 Jun 25.
Artículo en Inglés | MEDLINE | ID: mdl-31184132

RESUMEN

Surface phonon polaritons (SPhPs), the surface-bound electromagnetic modes of a polar material resulting from the coupling of light with optic phonons, offer immense technological opportunities for nanophotonics in the infrared (IR) spectral region. However, once a particular material is chosen, the SPhP characteristics are fixed by the spectral positions of the optic phonon frequencies. Here, we provide a demonstration of how the frequency of these optic phonons can be altered by employing atomic-scale superlattices (SLs) of polar semiconductors using AlN/GaN SLs as an example. Using second harmonic generation (SHG) spectroscopy, we show that the optic phonon frequencies of the SLs exhibit a strong dependence on the layer thicknesses of the constituent materials. Furthermore, new vibrational modes emerge that are confined to the layers, while others are centered at the AlN/GaN interfaces. As the IR dielectric function is governed by the optic phonon behavior in polar materials, controlling the optic phonons provides a means to induce and potentially design a dielectric function distinct from the constituent materials and from the effective-medium approximation of the SL. We show that atomic-scale AlN/GaN SLs instead have multiple Reststrahlen bands featuring spectral regions that exhibit either normal or extreme hyperbolic dispersion with both positive and negative permittivities dispersing rapidly with frequency. Apart from the ability to engineer the SPhP properties, SL structures may also lead to multifunctional devices that combine the mechanical, electrical, thermal, or optoelectronic functionality of the constituent layers. We propose that this effort is another step toward realizing user-defined, actively tunable IR optics and sources.

20.
Protein Expr Purif ; 159: 75-82, 2019 07.
Artículo en Inglés | MEDLINE | ID: mdl-30917921

RESUMEN

The ability to engineer monoclonal antibodies (mAbs) with high specificity made mAbs the fastest growing segment in the drug market. mAbs represent 8 of the top 20 selling drugs with combined sales of more than 57 billion US$ per year. The ability to purify large numbers of mAbs with sufficient yields for initial screening campaigns has direct impact on the timelines of a project. Automated liquid handling (ALH)-based mAb purification platforms have been used to facilitate the production of large numbers of mAbs. However, the ongoing pressure to de-risk potential lead molecules at an early development stage by including bio-physical characterization of mAbs has further increased the demand to produce sufficient quantities from limited sample volumes. A bottleneck so far has been the limited dynamic binding capacity of these systems, which is partly due to the binding properties of commonly used Protein A affinity matrices. The present publication suggests that by using a Protein A matrix optimized for continuous chromatography applications the yields of ALH-based but also standard lab-scale mAb purifications can be significantly increased without the need to change established protocols.


Asunto(s)
Anticuerpos Monoclonales/química , Proteínas Recombinantes de Fusión/química , Anticuerpos Monoclonales/genética , Células Cultivadas , Cromatografía de Afinidad , Ensayos Analíticos de Alto Rendimiento/métodos , Humanos , Proteínas Recombinantes de Fusión/genética , Robótica , Proteína Estafilocócica A/química , Transfección
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