While alternative splicing is known to diversify the functional characteristics of some genes, the extent to which protein isoforms globally contribute to functional complexity on a proteomic scale ...remains unknown. To address this systematically, we cloned full-length open reading frames of alternatively spliced transcripts for a large number of human genes and used protein-protein interaction profiling to functionally compare hundreds of protein isoform pairs. The majority of isoform pairs share less than 50% of their interactions. In the global context of interactome network maps, alternative isoforms tend to behave like distinct proteins rather than minor variants of each other. Interaction partners specific to alternative isoforms tend to be expressed in a highly tissue-specific manner and belong to distinct functional modules. Our strategy, applicable to other functional characteristics, reveals a widespread expansion of protein interaction capabilities through alternative splicing and suggests that many alternative “isoforms” are functionally divergent (i.e., “functional alloforms”).
Display omitted
•Alternative splicing can produce isoforms with vastly different interaction profiles•These differences can be as great as those between proteins encoded by different genes•Isoform-specific partners exhibit distinct expression and functional characteristics
Alternatively spliced isoforms of proteins exhibit strikingly different interaction profiles and thus, in the context of global interactome networks, appear to behave as if encoded by distinct genes rather than as minor variants of each other.
Abstract
Additive manufacturing promises a major transformation of the production of high economic value metallic materials, enabling innovative, geometrically complex designs with minimal material ...waste. The overarching challenge is to design alloys that are compatible with the unique additive processing conditions while maintaining material properties sufficient for the challenging environments encountered in energy, space, and nuclear applications. Here we describe a class of high strength, defect-resistant 3D printable superalloys containing approximately equal parts of Co and Ni along with Al, Cr, Ta and W that possess strengths in excess of 1.1 GPa in as-printed and post-processed forms and tensile ductilities of greater than 13% at room temperature. These alloys are amenable to crack-free 3D printing via electron beam melting (EBM) with preheat as well as selective laser melting (SLM) with limited preheat. Alloy design principles are described along with the structure and properties of EBM and SLM CoNi-base materials.
This study presents the first full annual cycle (2019–2020) of ambient surface aerosol particle number concentration measurements (condensation nuclei > 20 nm, N20) collected at Summit Station ...(Summit), in the centre of the Greenland Ice Sheet (72.58∘ N, −38.45∘ E; 3250 ma.s.l.). The mean surface concentration in 2019 was 129 cm−3, with the 6 h mean ranging between 1 and 1441 cm−3. The highest monthly mean concentrations occurred during the late spring and summer, with the minimum concentrations occurring in February (mean: 18 cm−3). High-N20 events are linked to anomalous anticyclonic circulation over Greenland and the descent of free-tropospheric aerosol down to the surface, whereas low-N20 events are linked to anomalous cyclonic circulation over south-east Greenland that drives upslope flow and enhances precipitation en route to Summit. Fog strongly affects particle number concentrations, on average reducing N20 by 20 % during the first 3 h of fog formation. Extremely-low-N20 events (< 10 cm−3) occur in all seasons, and we suggest that fog, and potentially cloud formation, can be limited by low aerosol particle concentrations over central Greenland.
Several attempts have been made to systematically map protein-protein interaction, or 'interactome', networks. However, it remains difficult to assess the quality and coverage of existing data sets. ...Here we describe a framework that uses an empirically-based approach to rigorously dissect quality parameters of currently available human interactome maps. Our results indicate that high-throughput yeast two-hybrid (HT-Y2H) interactions for human proteins are more precise than literature-curated interactions supported by a single publication, suggesting that HT-Y2H is suitable to map a significant portion of the human interactome. We estimate that the human interactome contains approximately 130,000 binary interactions, most of which remain to be mapped. Similar to estimates of DNA sequence data quality and genome size early in the Human Genome Project, estimates of protein interaction data quality and interactome size are crucial to establish the magnitude of the task of comprehensive human interactome mapping and to elucidate a path toward this goal.
Just as reference genome sequences revolutionized human genetics, reference maps of interactome networks will be critical to fully understand genotype-phenotype relationships. Here, we describe a ...systematic map of ∼14,000 high-quality human binary protein-protein interactions. At equal quality, this map is ∼30% larger than what is available from small-scale studies published in the literature in the last few decades. While currently available information is highly biased and only covers a relatively small portion of the proteome, our systematic map appears strikingly more homogeneous, revealing a “broader” human interactome network than currently appreciated. The map also uncovers significant interconnectivity between known and candidate cancer gene products, providing unbiased evidence for an expanded functional cancer landscape, while demonstrating how high-quality interactome models will help “connect the dots” of the genomic revolution.
Display omitted
•Network map of 14,000 high-quality binary human protein-protein interactions•Uniform coverage of the interactome space overlooked by other approaches•This map allows detection of functional relationships beyond previous knowledge•Unbiased network-based evidence for an expanded cancer landscape
A second-generation systematic binary map provides proteome-wide coverage of the human interactome network, expanding connections among human disease genes beyond previous knowledge.
Communicable respiratory viral infections pose both epidemic and pandemic threats and broad-spectrum antiviral strategies could improve preparedness for these events. To discover host antiviral ...restriction factors that may act as suitable targets for the development of host-directed antiviral therapies, we here conduct a whole-genome CRISPR activation screen with influenza B virus (IBV). A top hit from our screen, beta-1,3-glucuronyltransferase 1 (B3GAT1), effectively blocks IBV infection. Subsequent studies reveal that B3GAT1 activity prevents cell surface sialic acid expression. Due to this mechanism of action, B3GAT1 expression broadly restricts infection with viruses that require sialic acid for entry, including Victoria and Yamagata lineage IBVs, H1N1/H3N2 influenza A viruses (IAVs), and the unrelated enterovirus D68. To understand the potential utility of B3GAT1 induction as an antiviral strategy in vivo, we specifically express B3GAT1 in the murine respiratory epithelium and find that overexpression is not only well-tolerated, but also protects female mice from a lethal viral challenge with multiple influenza viruses, including a pandemic-like H1N1 IAV. Thus, B3GAT1 may represent a host-directed broad-spectrum antiviral target with utility against clinically relevant respiratory viruses.
Oncogenic mutations in the serine/threonine kinase B-RAF (also known as BRAF) are found in 50-70% of malignant melanomas. Pre-clinical studies have demonstrated that the B-RAF(V600E) mutation ...predicts a dependency on the mitogen-activated protein kinase (MAPK) signalling cascade in melanoma-an observation that has been validated by the success of RAF and MEK inhibitors in clinical trials. However, clinical responses to targeted anticancer therapeutics are frequently confounded by de novo or acquired resistance. Identification of resistance mechanisms in a manner that elucidates alternative 'druggable' targets may inform effective long-term treatment strategies. Here we expressed ∼600 kinase and kinase-related open reading frames (ORFs) in parallel to interrogate resistance to a selective RAF kinase inhibitor. We identified MAP3K8 (the gene encoding COT/Tpl2) as a MAPK pathway agonist that drives resistance to RAF inhibition in B-RAF(V600E) cell lines. COT activates ERK primarily through MEK-dependent mechanisms that do not require RAF signalling. Moreover, COT expression is associated with de novo resistance in B-RAF(V600E) cultured cell lines and acquired resistance in melanoma cells and tissue obtained from relapsing patients following treatment with MEK or RAF inhibitors. We further identify combinatorial MAPK pathway inhibition or targeting of COT kinase activity as possible therapeutic strategies for reducing MAPK pathway activation in this setting. Together, these results provide new insights into resistance mechanisms involving the MAPK pathway and articulate an integrative approach through which high-throughput functional screens may inform the development of novel therapeutic strategies.
Celotno besedilo
Dostopno za:
DOBA, IJS, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Functional characterization of the human genome requires tools for systematically modulating gene expression in both loss-of-function and gain-of-function experiments. We describe the production of a ...sequence-confirmed, clonal collection of over 16,100 human open-reading frames (ORFs) encoded in a versatile Gateway vector system. Using this ORFeome resource, we created a genome-scale expression collection in a lentiviral vector, thereby enabling both targeted experiments and high-throughput screens in diverse cell types.
Ice-nucleating particles (INPs) influence cloud radiative properties and climate; however, INP sources and concentrations are poorly constrained, particularly in high-latitude regions. Southern ...Alaska is a known source of high-latitude dust, but its contribution to atmospheric mineral dust and INP concentrations has not been quantified. We show that glacial dust collected in southern Alaska is an effective ice-nucleating material under conditions relevant for mixed-phase clouds and is more active than low-latitude dust because of a biological component that enhances its activity. We use dispersion modeling to show that this source contributes to the regional INP population and that the dust emitted is transported over a broad area of North America, reaching altitudes where it could cause cloud glaciation. Our results highlight the importance of quantifying emissions and ice-nucleating characteristics of high-latitude dusts and suggest that the ice-nucleating ability of emitted dust in these regions should be represented in models using different parametrizations to low-latitude dust.
Current yeast interactome network maps contain several hundred molecular complexes with limited and somewhat controversial representation of direct binary interactions. We carried out a comparative ...quality assessment of current yeast interactome data sets, demonstrating that high-throughput yeast two-hybrid (Y2H) screening provides high-quality binary interaction information. Because a large fraction of the yeast binary interactome remains to be mapped, we developed an empirically controlled mapping framework to produce a "second-generation" high-quality, high-throughput Y2H data set covering ~20% of all yeast binary interactions. Both Y2H and affinity purification followed by mass spectrometry (AP/MS) data are of equally high quality but of a fundamentally different and complementary nature, resulting in networks with different topological and biological properties. Compared to co-complex interactome models, this binary map is enriched for transient signaling interactions and intercomplex connections with a highly significant clustering between essential proteins. Rather than correlating with essentiality, protein connectivity correlates with genetic pleiotropy.
PDF
