scholarly journals Variant effect predictions capture some aspects of deep mutational scanning experiments

2019 ◽  
Author(s):  
Jonas Reeb ◽  
Theresa Wirth ◽  
Burkhard Rost
Keyword(s):  
Sequence Variation ◽  
Single Amino Acid ◽  
Prediction Methods ◽  
Loss Of Function ◽  
Early Effect ◽  
Beneficial Effects ◽  
Challenges And Opportunities ◽  
Experimental Protocols ◽  
Variant Effect ◽  
Precise Degree

AbstractDeep mutational scanning (DMS) studies exploit the mutational landscape of sequence variation by systematically and comprehensively assaying the effect of single amino acid variants (SAVs) for particular proteins. Different experimental protocols proxy effect through a diversity of measures. We evaluated three early prediction methods trained on traditional variant effect data (PolyPhen-2, SIFT, SNAP2) along with a regression method optimized on DMS data (Envision). On a common subset of 32,981 SAVs, all methods capture some aspects of variant effects, albeit not the same. Early effect prediction methods correlated slightly more with measurements and better classified binary states (effect or neutral), while Envision predicted better the precise degree of effect. Most surprising was that a simple approach predicting residues conserved in families (found and aligned by PSI-BLAST) in many cases outperformed other methods. All methods predicted beneficial effects (gain-of-function) significantly worse than deleterious (loss-of-function). For the few proteins with several DMS measurements, experiments agreed more with each other than predictions with experiments. Our findings highlight challenges and opportunities of DMS for improving variant effect predictions.

scholarly journals Differences in a Single Extracellular Residue Underlie Adhesive Functions of Two Zebrafish Aqp0s

Cells ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 2005
Author(s):  
Irene Vorontsova ◽  
James E. Hall ◽  
Thomas F. Schilling ◽  
Noriaki Nagai ◽  
Yosuke Nakazawa
Keyword(s):  
Cell Adhesion ◽  
Single Amino Acid ◽  
Amino Acid Difference ◽  
Adhesion Assay ◽  
Loss Of Function ◽  
Adhesive Properties ◽  
The Difference ◽  
In Vitro Adhesion ◽  
Cell To Cell Adhesion

Aquaporin 0 (AQP0) is the most abundant lens membrane protein, and loss of function in human and animal models leads to cataract formation. AQP0 has several functions in the lens including water transport and adhesion. Since lens optics rely on strict tissue architecture achieved by compact cell-to-cell adhesion between lens fiber cells, understanding how AQP0 contributes to adhesion would shed light on normal lens physiology and pathophysiology. We show in an in vitro adhesion assay that one of two closely related zebrafish Aqp0s, Aqp0b, has strong auto-adhesive properties while Aqp0a does not. The difference appears to be largely due to a single amino acid difference at residue 110 in the extracellular C-loop, which is T in Aqp0a and N in Aqp0b. Similarly, P110 is the key residue required for adhesion in mammalian AQP0, highlighting the importance of residue 110 in AQP0 cell-to-cell adhesion in vertebrate lenses as well as the divergence of adhesive and water permeability functions in zebrafish duplicates.

scholarly journals Comparison of Predicted Scaffold-Compatible Sequence Variation in the Triple-Hairpin Structure of Human Immunodeficiency Virus Type 1 gp41 with Patient Data

2002 ◽  
Vol 76 (15) ◽  
pp. 7595-7606 ◽  
Author(s):  
Nathalie Boutonnet ◽  
Wouter Janssens ◽  
Carlo Boutton ◽  
Jean-Luc Verschelde ◽  
Leo Heyndrickx ◽  
...  
Keyword(s):  
Human Immunodeficiency Virus ◽  
Human Immunodeficiency Virus Type ◽  
Virus Type ◽  
Sequence Variation ◽  
Single Point ◽  
Point Mutations ◽  
Hairpin Structure ◽  
Single Amino Acid ◽  
Immunodeficiency Virus

ABSTRACT It has been proposed that the ectodomain of human immunodeficiency virus type 1 (HIV-1) gp41 (e-gp41), involved in HIV entry into the target cell, exists in at least two conformations, a pre-hairpin intermediate and a fusion-active hairpin structure. To obtain more information on the structure-sequence relationship in e-gp41, we performed in silico a full single-amino-acid substitution analysis, resulting in a Fold Compatible Database (FCD) for each conformation. The FCD contains for each residue position in a given protein a list of values assessing the energetic compatibility (ECO) of each of the 20 natural amino acids at that position. Our results suggest that FCD predictions are in good agreement with the sequence variation observed for well-validated e-gp41 sequences. The data show that at a minECO threshold value of 5 kcal/mol, about 90% of the observed patient sequence variation is encompassed by the FCD predictions. Some inconsistent FCD predictions at N-helix positions packing against residues of the C helix suggest that packing of both peptides may involve some flexibility and may be attributed to an altered orientation of the C-helical domain versus the N-helical region. The permissiveness of sequence variation in the C helices is in agreement with FCD predictions. Comparison of N-core and triple-hairpin FCDs suggests that the N helices may impose more constraints on sequence variation than the C helices. Although the observed sequences of e-gp41 contain many multiple mutations, our method, which is based on single-point mutations, can predict the natural sequence variability of e-gp41 very well.

scholarly journals The association of microcephaly protein WDR62 with CPAP/IFT88 is required for cilia formation and neocortical development

2019 ◽  
Vol 29 (2) ◽  
pp. 248-263 ◽  
Author(s):  
Belal Shohayeb ◽  
Uda Ho ◽  
Yvonne Y Yeap ◽  
Robert G Parton ◽  
S Sean Millard ◽  
...  
Keyword(s):  
Radial Glia ◽  
Single Amino Acid ◽  
Missense Mutations ◽  
Loss Of Function ◽  
Protein Loss ◽  
Mutant Proteins ◽  
Cilia Formation ◽  
Morphological Defects ◽  
Cell Processes ◽  
Radial Glial

Abstract WDR62 mutations that result in protein loss, truncation or single amino-acid substitutions are causative for human microcephaly, indicating critical roles in cell expansion required for brain development. WDR62 missense mutations that retain protein expression represent partial loss-of-function mutants that may therefore provide specific insights into radial glial cell processes critical for brain growth. Here we utilized CRISPR/Cas9 approaches to generate three strains of WDR62 mutant mice; WDR62 V66M/V66M and WDR62R439H/R439H mice recapitulate conserved missense mutations found in humans with microcephaly, with the third strain being a null allele (WDR62stop/stop). Each of these mutations resulted in embryonic lethality to varying degrees and gross morphological defects consistent with ciliopathies (dwarfism, anophthalmia and microcephaly). We find that WDR62 mutant proteins (V66M and R439H) localize to the basal body but fail to recruit CPAP. As a consequence, we observe deficient recruitment of IFT88, a protein that is required for cilia formation. This underpins the maintenance of radial glia as WDR62 mutations caused premature differentiation of radial glia resulting in reduced generation of neurons and cortical thinning. These findings highlight the important role of the primary cilium in neocortical expansion and implicate ciliary dysfunction as underlying the pathology of MCPH2 patients.

scholarly journals A home run for human NaCT/SLC13A5/INDY: cryo-EM structure and homology model to predict transport mechanisms, inhibitor interactions and mutational defects

2021 ◽  
Vol 478 (11) ◽  
pp. 2051-2057
Author(s):  
Valeria Jaramillo-Martinez ◽  
Vadivel Ganapathy ◽  
Ina L. Urbatsch
Keyword(s):  
3D Structure ◽  
Homology Model ◽  
Brain Dysfunction ◽  
Neurological Dysfunction ◽  
Metabolic Phenotype ◽  
Detailed Knowledge ◽  
Loss Of Function ◽  
Beneficial Effects ◽  
Function Relationship ◽  
The Brain

NaCT (SLC13A5) is a Na+-coupled transporter for citrate, which is expressed in the liver, brain, testes, and bone. It is the mammalian homolog of Drosophila INDY, a cation-independent transporter for citrate, whose partial loss extends lifespan in the organism. In humans, loss-of-function mutations in NaCT cause a disease with severe neurological dysfunction, characterized by neonatal epilepsy and delayed brain development. In contrast with humans, deletion of NaCT in mice results in a beneficial metabolic phenotype with protection against diet-induced obesity and metabolic syndrome; the brain dysfunction is not readily noticeable. The disease-causing mutations are located in different regions of human NaCT protein, suggesting that different mutations might have different mechanisms for the loss of function. The beneficial effects of NaCT loss in the liver versus the detrimental effects of NaCT loss in the brain provide an opportunity to design high-affinity inhibitors for the transporter that do not cross the blood-brain barrier so that only the beneficial effects could be harnessed. To realize these goals, we need a detailed knowledge of the 3D structure of human NaCT. The recent report by Sauer et al. in Nature describing the cryo-EM structure of human NaCT represents such a milestone, paving the way for a better understanding of the structure-function relationship for this interesting and clinically important transporter.

scholarly journals Multiple Beneficial Effects of Using Biochar (as a Great Organic Material) on Tolerance and Productivity of Rice under Abiotic Stress

2019 ◽  
Vol 6 (1) ◽  
pp. 40-51
Author(s):  
Gulaqa Anwari ◽  
Jin Feng ◽  
Abdourazak Alio Moussa
Keyword(s):  
Abiotic Stress ◽  
Plant Growth ◽  
Abiotic Stresses ◽  
Biological Properties ◽  
Breeding Method ◽  
Plant Growth Hormones ◽  
Crop Tolerance ◽  
Beneficial Effects ◽  
Challenges And Opportunities

Rice as a sensitive crop that usually affected by many harmful environmental stresses. Numerous policies are followed to increase plant growth-tolerance under abiotic-stresses in various plant species. The attempts to improve crop tolerance against abiotic stresses via common breeding method are needed to follow a long-term, and may also be non-affordable, these are due to the existing genetic variability of the plant. Current review analysis existing knowledge gaps, challenges, and opportunities in the biochar application as a beneficial and pyrogenic-C, material. Consequently, a review of the literature with a high focusing on the multiple beneficial effects of using biochar on tolerance and productivity of rice in abiotic stresses is needed. This review provides a summary of those efforts that would be beneficial in reducing inconvenienced abiotic-stresses, and also how using biochar could increase rice tolerance and production through the supporting of plant growth regulator's roles. Accordantly, present review findings showed that biochar is a great amendment and consisting of principally organic rich-C matter, which has multiple benefits on improving soil physicochemical and biological properties as well as increasing rice tolerance and its productivity through enhancing plant hormones roles under abiotic stressed conditions (heat/cold temperature, drought, salinity, heavy metal, and climate change stresses). Nevertheless, it is anticipated that further researches on the benefits of biochar will increase the comprehension of interactions between biochar and plant growth hormones, to accelerate our attempts for improving rice tolerance and productivity, under abiotic-stress conditions.

scholarly journals Spontaneous Loss of Virulence in Natural Populations of Listeria monocytogenes

2017 ◽  
Vol 85 (11) ◽  
Author(s):  
Mylène M. Maury ◽  
Viviane Chenal-Francisque ◽  
Hélène Bracq-Dieye ◽  
Lei Han ◽  
Alexandre Leclercq ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Stop Codon ◽  
Premature Stop Codon ◽  
Host Cells ◽  
Single Amino Acid ◽  
Listeriolysin O ◽  
Loss Of Function ◽  
Phenotypic Marker ◽  
Content Type ◽  
Virulence Attenuation

ABSTRACT The pathogenesis of Listeria monocytogenes depends on the ability of this bacterium to escape from the phagosome of the host cells via the action of the pore-forming toxin listeriolysin O (LLO). Expression of the LLO-encoding gene (hly) requires the transcriptional activator PrfA, and both hly and prfA genes are essential for L. monocytogenes virulence. Here, we used the hemolytic activity of LLO as a phenotypic marker to screen for spontaneous virulence-attenuating mutations in L. monocytogenes. Sixty nonhemolytic isolates were identified among a collection of 57,820 confirmed L. monocytogenes strains isolated from a variety of sources (0.1%). In most cases (56/60; 93.3%), the nonhemolytic phenotype resulted from nonsense, missense, or frameshift mutations in prfA. Five strains carried hly mutations leading to a single amino acid substitution (G299V) or a premature stop codon causing strong virulence attenuation in mice. In one strain, both hly and gshF (encoding a glutathione synthase required for full PrfA activity) were missing due to genomic rearrangements likely caused by a transposable element. The PrfA/LLO loss-of-function (PrfA−/LLO−) mutants belonged to phylogenetically diverse clades of L. monocytogenes, and most were identified among nonclinical strains (57/60). Consistent with the rare occurrence of loss-of-virulence mutations, we show that prfA and hly are under purifying selection. Although occurring at a low frequency, PrfA−/LLO− mutational events in L. monocytogenes lead to niche restriction and open an evolutionary path for obligate saprophytism in this facultative intracellular pathogen.

scholarly journals Vupanorsen, an N-acetyl galactosamine-conjugated antisense drug to ANGPTL3 mRNA, lowers triglycerides and atherogenic lipoproteins in patients with diabetes, hepatic steatosis, and hypertriglyceridaemia

2020 ◽  
Vol 41 (40) ◽  
pp. 3936-3945 ◽  
Author(s):  
Daniel Gaudet ◽  
Ewa Karwatowska-Prokopczuk ◽  
Seth J Baum ◽  
Eunju Hurh ◽  
Joyce Kingsbury ◽  
...  
Keyword(s):  
Hepatic Steatosis ◽  
Density Lipoprotein ◽  
Loss Of Function ◽  
Cardiovascular Risk Reduction ◽  
Residual Cardiovascular Risk ◽  
Double Blind ◽  
Beneficial Effects ◽  
Patients With Diabetes ◽  
Remnant Cholesterol ◽  
Clinically Significant

Abstract Aims  Loss-of-function mutations in ANGPTL3 are associated with beneficial effects on lipid and glucose metabolism and reduced risk of coronary artery disease. Vupanorsen (AKCEA-ANGPTL3-L Rx ) is an N-acetyl galactosamine-conjugated antisense oligonucleotide targeted to the liver that selectively inhibits angiopoietin-like 3 (ANGPTL3) protein synthesis. Methods and results  This was a double-blind, placebo-controlled, dose-ranging, Phase 2 study. Patients (N =105) with fasting triglycerides >150 mg/dL (>1.7 mmol/L), type 2 diabetes, and hepatic steatosis were treated for 6 months with 40 or 80 mg every 4 weeks (Q4W), or 20 mg every week (QW) of vupanorsen, or placebo given subcutaneously. The primary efficacy endpoint was per cent change in fasting triglycerides from baseline at 6 months. Median baseline triglycerides were 2.84 mmol/L (252 mg/dL). Significant reductions in triglycerides of 36%, 53%, 47%, and in ANGPTL3 of 41%, 59%, 56%, were observed in the 40 mg Q4W, 80 mg Q4W, and 20 mg QW groups, respectively, compared with 16% reduction in triglycerides and 8% increase in ANGPTL3 in placebo. Compared with placebo, vupanorsen 80 mg Q4W reduced apolipoprotein C-III (58%), remnant cholesterol (38%), total cholesterol (19%), non-high-density lipoprotein cholesterol (HDL-C; 18%), HDL-C (24%), and apolipoprotein B (9%). There was no improvement in glycaemic parameters, or hepatic fat fraction. Treatment with vupanorsen was not associated with clinically significant changes in platelet counts, and the most common adverse events were those at the injection site, which were generally mild. Conclusion  Vupanorsen results in a favourable lipid/lipoprotein profile and provides a potential strategy for residual cardiovascular risk reduction.

scholarly journals Insect Habitat Systems Integrated into Façades-Impact on Building Physics and Awareness of Society

2020 ◽  
Vol 12 (2) ◽  
pp. 570
Author(s):  
Linda Meier ◽  
Johanna Raps ◽  
Philip Leistner
Keyword(s):  
Holistic Approach ◽  
Point Of View ◽  
Special Focus ◽  
Transfer Coefficients ◽  
Wild Bees ◽  
Physical Point ◽  
Beneficial Effects ◽  
Intensive Farming ◽  
Challenges And Opportunities ◽  
Indoor Comfort

Deforestation, intensive farming and the sealing of green spaces are considered to be the main reasons for the global decrease of biodiversity. In this context, the built environment, and in particular vertical surfaces, are still highly underestimated and need to be taken into account. Although it is acknowledged that greened surfaces have beneficial effects, for example, on the microclimate, the vast majority of buildings are still not biodiversity-friendly. Artificial nesting boxes help birds and bats adapt to the change of their habitats. However, insects, with their tremendous significance for insectivorous species and for humans, are mostly neglected or even threatened. The purpose of this holistic approach is to investigate interactions between integrated insect habitat systems in façades and building physical aspects to create test objects. Heat transfer coefficients, thermal bridges, and the risk of condensation inside the buildings were simulated in different arrangements of nesting boxes for wild bees. As a result, conclusions on heat and humidity protection in ventilated façades and external thermal insulation composite systems could be drawn. The following results showed the maintenance of indoor comfort and energy efficiency as well as a low risk of mold. Further investigations analyzed the sound reduction index and fire protection. From a building physical point of view, integrated insect habitat systems could be part of the constructed environment and even link inner-city biotopes. Further challenges and opportunities are identified rather at a socio-ecological and technical level. Without taking into account the civil society and ecological demands of the various species, habitat systems for insects will miss their objectives. Special focus will be put on the skepticism and lack of knowledge of people, as well as on the comfort of the insects.

scholarly journals Carvedilol-responsive microRNAs, miR-199a-3p and -214 protect cardiomyocytes from simulated ischemia-reperfusion injury

2016 ◽  
Vol 311 (2) ◽  
pp. H371-H383 ◽  
Author(s):  
Kyoung-mi Park ◽  
Jian-peng Teoh ◽  
Yongchao Wang ◽  
Zuzana Broskova ◽  
Ahmed S. Bayoumi ◽  
...  
Keyword(s):  
Adrenergic Receptor ◽  
Target Genes ◽  
Ischemia Reperfusion Injury ◽  
Ischemia Reperfusion ◽  
Stem Cell Markers ◽  
Loss Of Function ◽  
Pluripotency Marker ◽  
Beneficial Effects ◽  
Simulated Ischemia ◽  
Underlying Mechanisms

The nonselective β-adrenergic receptor antagonist (β-blocker) carvedilol has been shown to protect against myocardial injury, but the detailed underlying mechanisms are unclear. We recently reported that carvedilol stimulates the processing of microRNA (miR)-199a-3p and miR-214 in the heart via β-arrestin1-biased β1-adrenergic receptor (β1AR) cardioprotective signaling. Here, we investigate whether these β-arrestin1/β1AR-responsive miRs mediate the beneficial effects of carvedilol against simulated ischemia/reperfusion (sI/R). Using cultured cardiomyocyte cell lines and primary cardiomyocytes, we demonstrate that carvedilol upregulates miR-199a-3p and miR-214 in both ventricular and atrial cardiomyocytes subjected to sI/R. Overexpression of the two miRs in cardiomyocytes mimics the effects of carvedilol to activate p-AKT survival signaling and the expression of a downstream pluripotency marker Sox2 in response to sI/R. Moreover, carvedilol-mediated p-AKT activation is abolished by knockdown of either miR-199a-3p or miR-214. Along with previous studies to directly link the cardioprotective actions of carvedilol to upregulation of p-AKT/stem cell markers, our findings suggest that the protective roles of carvedilol during ischemic injury are in part attributed to activation of these two protective miRs. Loss of function of miR-199a-3p and miR-214 also increases cardiomyocyte apoptosis after sI/R. Mechanistically, we demonstrate that miR-199a-3p and miR-214 repress the predictive or known apoptotic target genes ddit4 and ing4, respectively, in cardiomyocytes. These findings suggest pivotal roles for miR-199a-3p and miR-214 as regulators of cardiomyocyte survival and contributors to the functional benefits of carvedilol therapy.

scholarly journals The population genomics of adaptive loss of function

Heredity ◽  
2021 ◽  
Author(s):  
J. Grey Monroe ◽  
John K. McKay ◽  
Detlef Weigel ◽  
Pádraic J. Flood
Keyword(s):  
Population Genetics ◽  
Evolutionary Dynamics ◽  
Population Genomics ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Loss Of Function ◽  
Population Genomic ◽  
Genomic Tools ◽  
Challenges And Opportunities ◽  
Early View

AbstractDiscoveries of adaptive gene knockouts and widespread losses of complete genes have in recent years led to a major rethink of the early view that loss-of-function alleles are almost always deleterious. Today, surveys of population genomic diversity are revealing extensive loss-of-function and gene content variation, yet the adaptive significance of much of this variation remains unknown. Here we examine the evolutionary dynamics of adaptive loss of function through the lens of population genomics and consider the challenges and opportunities of studying adaptive loss-of-function alleles using population genetics models. We discuss how the theoretically expected existence of allelic heterogeneity, defined as multiple functionally analogous mutations at the same locus, has proven consistent with empirical evidence and why this impedes both the detection of selection and causal relationships with phenotypes. We then review technical progress towards new functionally explicit population genomic tools and genotype-phenotype methods to overcome these limitations. More broadly, we discuss how the challenges of studying adaptive loss of function highlight the value of classifying genomic variation in a way consistent with the functional concept of an allele from classical population genetics.

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