scholarly journals Haplotype mapping uncovers unexplored variation in wild and domesticated soybean at the major protein locus cqProt-003

2021 ◽  
Author(s):  
Jacob I Marsh ◽  
Haifei Hu ◽  
Jakob Petereit ◽  
Philipp E Bayer ◽  
Babu Valliyodan ◽  
...  
Keyword(s):  
Tandem Repeats ◽  
High Protein ◽  
Major Protein ◽  
Strongly Correlated ◽  
Genomic Context ◽  
Demographic Groups ◽  
Functional Characterisation ◽  
Protein Locus ◽  
Haplotype Mapping ◽  
Wild Accessions

Here, we present association and linkage analysis of 985 wild, landrace and cultivar soybean accessions in a pan genomic dataset to characterize the major high-protein/low-oil associated locus cqProt-003 located on chromosome 20. A significant trait associated region within a 173 kb linkage block was identified and variants in the region were characterised, identifying 34 high confidence SNPs, 4 insertions, 1 deletion and a larger 304 bp structural variant in the high-protein haplotype. Trinucleotide tandem repeats of variable length present in the third exon of gene 20G085100 are strongly correlated with the high-protein phenotype and likely represent causal variation. Structural variation has previously been found in the same gene, for which we report the global distribution of the 304bp deletion and have identified additional nested variation present in high-protein individuals. Mapping variation at the cqProt-003 locus across demographic groups suggests that the high-protein haplotype is common in wild accessions (94.7%), rare in landraces (10.6%) and near absent in cultivated breeding pools (4.1%), suggesting its decrease in frequency primarily correlates with domestication and continued during subsequent improvement. However, the variation that has persisted in under-utilized wild and landrace populations holds high breeding potential for breeders willing to forego seed oil to maximise protein content. The results of this study include the identification of distinct haplotype structures within the high-protein population, and a broad characterization of the genomic context and linkage patterns of cqProt-003 across global populations, supporting future functional characterisation and modification.

scholarly journals Robustness of Transposable Element regulation but no genomic shock observed in interspecific Arabidopsis hybrids

2018 ◽  
Author(s):  
Ulrike Göbel ◽  
Agustin Arce ◽  
Fei He ◽  
Alain Rico ◽  
Gregor Schmitz ◽  
...  
Keyword(s):  
Arabidopsis Thaliana ◽  
Transposable Elements ◽  
Transposable Element ◽  
Parental Species ◽  
Strongly Correlated ◽  
Severe Dehydration ◽  
Genomic Context ◽  
Small Magnitude ◽  
F1 Hybrid ◽  
Genomic Shock

AbstractThe merging of two divergent genomes in a hybrid is believed to trigger a “genomic shock”, disrupting gene regulation and transposable element (TE) silencing. Here, we tested this expectation by comparing the pattern of expression of transposable elements in their native and hybrid genomic context. For this, we sequenced the transcriptome of the Arabidopsis thaliana genotype Col-0, the A. lyrata genotype MN47 and their F1 hybrid. Contrary to expectations, we observe that the level of TE expression in the hybrid is strongly correlated to levels in the parental species. We detect that at most 1.1% of expressed transposable elements belonging to two specific subfamilies change their expression level upon hybridization. Most of these changes, however, are of small magnitude. We observe that the few hybrid-specific modifications in TE expression are more likely to occur when TE insertions are close to genes. In addition, changes in epigenetic histone marks H3K9me2 and H3K27me3 following hybridization do not coincide with TEs with changed expression. Finally, we further examined TE expression in parents and hybrids exposed to severe dehydration stress. Despite the major reorganization of gene and TE expression by stress, we observe that hybridization does not lead to increased disorganization of TE expression in the hybrid. We conclude that TE expression is globally robust to hybridization and that the term “genomic shock” is no longerappropriate to describe the anticipated consequences of merging divergent genomes in a hybrid.

PTL-1, a microtubule-associated protein with tau-like repeats from the nematode Caenorhabditis elegans

1996 ◽  
Vol 109 (11) ◽  
pp. 2661-2672 ◽  
Author(s):  
M. Goedert ◽  
C.P. Baur ◽  
J. Ahringer ◽  
R. Jakes ◽  
M. Hasegawa ◽  
...  
Keyword(s):  
Amino Acid ◽  
Caenorhabditis Elegans ◽  
Tandem Repeats ◽  
Microtubule Assembly ◽  
Nematode Caenorhabditis Elegans ◽  
Microtubule Associated Proteins ◽  
C Elegans ◽  
Functional Characterisation ◽  
Associated Proteins ◽  
Mammalian Origin

Tau, MAP2 and MAP4 are structural microtubule-associated proteins (MAPs) that promote the assembly and stability of microtubules. They share three or four imperfect tandem repeats of an amino acid motif, which is involved in the binding to microtubules. All sequences to data containing this motif are of mammalian origin. We report here the cloning and functional characterisation of a new member of this family of proteins from the nematode Caenorhabditis elegans. This protein exists as two isoforms of 413 and 453 amino acids with four or five tandem repeats that are 50% identical to the tau/MAP2/MAP4 repeats. Both isoforms bind to microtubules and promote microtubule assembly, with the five-repeat isoform being more effective at promoting assembly than the four-repeat isoform. When expressed in COS cells, the five-repeat isoform co-localises with microtubules and induces the formation of microtubule bundles, whereas its expression in Sf9 cells leads to the extension of long unipolar processes. In view of its length, amino acid sequence and functional characteristics, we have named this invertebrate structural MAP ‘Protein with Tau-Like Repeats’ (PTL-1). In C. elegans PTL-1 is expressed in two places known to require microtubule function. It is first seen in the embryonic epidermis, when circumferentially oriented microtubules help to distribute forces generated during elongation. Later, it is found in mechanosensory neurons which contain unusual 15 protofilament microtubules required for the response to touch. These findings indicate that MAPs of the tau/MAP2/MAP4 family are found throughout much of the animal kingdom, where they may play a role in specialised processes requiring microtubules.

scholarly journals Comparison of Major Protein-Source Foods and Other Food Groups in Meat-Eaters and Non-Meat-Eaters in the EPIC-Oxford Cohort

Nutrients ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 824 ◽  
Author(s):  
Papier ◽  
Tong ◽  
Appleby ◽  
Bradbury ◽  
Fensom ◽  
...  
Keyword(s):  
Health Outcomes ◽  
Food Group ◽  
Diet Group ◽  
High Protein ◽  
Protein Source ◽  
Major Protein ◽  
Dietary Intakes ◽  
Food Groups ◽  
Sweetened Beverages ◽  
Fried Foods

Differences in health outcomes between meat-eaters and non-meat-eaters might relate to differences in dietary intakes between these diet groups. We assessed intakes of major protein-source foods and other food groups in six groups of meat-eaters and non-meat-eaters participating in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Oxford study. The data were from 30,239 participants who answered questions regarding their consumption of meat, fish, dairy or eggs and completed a food frequency questionnaire (FFQ) in 2010. Participants were categorized as regular meat-eaters, low meat-eaters, poultry-eaters, fish-eaters, vegetarians and vegans. FFQ foods were categorized into 45 food groups and analysis of variance was used to test for differences between age-adjusted mean intakes of each food group by diet group. Regular meat-eaters, vegetarians and vegans, respectively, consumed about a third, quarter and a fifth of their total energy intake from high protein-source foods. Compared with regular meat-eaters, low and non-meat-eaters consumed higher amounts of high-protein meat alternatives (soy, legumes, pulses, nuts, seeds) and other plant-based foods (whole grains, vegetables, fruits) and lower amounts of refined grains, fried foods, alcohol and sugar-sweetened beverages. These findings provide insight into potential nutritional explanations for differences in health outcomes between diet groups.

scholarly journals Towards a better understanding of the low recall of insertion variants with short-read based variant callers

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Wesley J. Delage ◽  
Julien Thevenon ◽  
Claire Lemaitre
Keyword(s):  
Tandem Repeats ◽  
Insertion Site ◽  
Mobile Element ◽  
Genomic Context ◽  
Short Read ◽  
Structural Variant ◽  
Depth Analysis ◽  
Long Read ◽  
Repeat Expansions ◽  
The Impact

Abstract Background Since 2009, numerous tools have been developed to detect structural variants using short read technologies. Insertions >50 bp are one of the hardest type to discover and are drastically underrepresented in gold standard variant callsets. The advent of long read technologies has completely changed the situation. In 2019, two independent cross technologies studies have published the most complete variant callsets with sequence resolved insertions in human individuals. Among the reported insertions, only 17 to 28% could be discovered with short-read based tools. Results In this work, we performed an in-depth analysis of these unprecedented insertion callsets in order to investigate the causes of such failures. We have first established a precise classification of insertion variants according to four layers of characterization: the nature and size of the inserted sequence, the genomic context of the insertion site and the breakpoint junction complexity. Because these levels are intertwined, we then used simulations to characterize the impact of each complexity factor on the recall of several structural variant callers. We showed that most reported insertions exhibited characteristics that may interfere with their discovery: 63% were tandem repeat expansions, 38% contained homology larger than 10 bp within their breakpoint junctions and 70% were located in simple repeats. Consequently, the recall of short-read based variant callers was significantly lower for such insertions (6% for tandem repeats vs 56% for mobile element insertions). Simulations showed that the most impacting factor was the insertion type rather than the genomic context, with various difficulties being handled differently among the tested structural variant callers, and they highlighted the lack of sequence resolution for most insertion calls. Conclusions Our results explain the low recall by pointing out several difficulty factors among the observed insertion features and provide avenues for improving SV caller algorithms and their combinations.

scholarly journals Comparison of major protein-source foods and other food groups in meat-eaters and non-meat-eaters in the EPIC-Oxford cohort

2020 ◽  
Vol 79 (OCE2) ◽  
Author(s):  
Keren Papier ◽  
Tammy Tong ◽  
Paul Appleby ◽  
Kathryn Bradbury ◽  
Georgina Fensom ◽  
...  
Keyword(s):  
Health Outcomes ◽  
Food Group ◽  
Diet Group ◽  
High Protein ◽  
Protein Source ◽  
Major Protein ◽  
Dietary Intakes ◽  
Food Groups ◽  
Animal Products ◽  
Fried Foods

IntroductionDifferences in health outcomes between meat-eaters and non-meat-eaters might relate to differences in dietary intakes between these diet groups. We assessed intakes of major protein-source foods and other food groups in six groups of meat-eaters and non-meat-eaters participating in the European Prospective Investigation into Cancer and Nutrition (EPIC)-Oxford study.Materials and methodsData were from 30, 239 participants who answered four questions regarding their consumption of meat, fish, dairy or eggs and completed a food frequency questionnaire (FFQ) in 2010. Participants were categorized as regular meat-eaters (> 50 grams of total/any meat per day: n = 12,997); low meat-eaters (< 50 grams of total/any meat per day: n = 4,650); poultry-eaters (poultry but no red meat: n = 591); fish-eaters (no meat but consumed fish: n = 4,528); vegetarians (no meat or fish: n = 6,672); and vegans (no animal products: n = 801). FFQ foods were categorised into 45 food groups. Analysis of variance was used to test for differences between age-adjusted mean intakes of each food group by diet group.ResultsWe found that regular meat-eaters, vegetarians and vegans, respectively, consumed about a third, quarter and a fifth of their total energy intake from high protein-source foods. Compared with regular meat-eaters, low and non-meat-eaters consumed higher amounts of high-protein meat alternatives (soy, legumes, pulses, nuts, seeds) and other plant-based foods (whole grains, vegetables, fruits) and lower amounts of refined grains, fried foods, alcohol, and sugar-sweetened beverages.DiscussionOverall, our results suggest that there were large differences in the amounts and types of protein-rich and other foods eaten by regular, low and non-meat-eaters. These findings provide insight into potential nutritional explanations for differences in health outcomes between diet groups.

The Nature of Rapidly Extracted Phycocyanin from the Blue-Green Alga Plectonema Boryanum

1971 ◽  
Vol 29 ◽  
pp. 366-367
Author(s):  
M. Kessel ◽  
R. MacColl
Keyword(s):  
Self Assembly ◽  
Analytical Ultracentrifugation ◽  
Uranyl Acetate ◽  
The Self ◽  
Major Protein ◽  
Subunit Structure ◽  
Blue Green Alga ◽  
Thin Sections ◽  
Blue Green Algae ◽  
Cacodylate Buffer

The major protein of the blue-green algae is the biliprotein, C-phycocyanin (Amax = 620 nm), which is presumed to exist in the cell in the form of distinct aggregates called phycobilisomes. The self-assembly of C-phycocyanin from monomer to hexamer has been extensively studied, but the proposed next step in the assembly of a phycobilisome, the formation of 19s subunits, is completely unknown. We have used electron microscopy and analytical ultracentrifugation in combination with a method for rapid and gentle extraction of phycocyanin to study its subunit structure and assembly.To establish the existence of phycobilisomes, cells of P. boryanum in the log phase of growth, growing at a light intensity of 200 foot candles, were fixed in 2% glutaraldehyde in 0.1M cacodylate buffer, pH 7.0, for 3 hours at 4°C. The cells were post-fixed in 1% OsO4 in the same buffer overnight. Material was stained for 1 hour in uranyl acetate (1%), dehydrated and embedded in araldite and examined in thin sections.

Reading the phosphorylation code: binding of the 14-3-3 protein to multivalent client phosphoproteins

2020 ◽  
Vol 477 (7) ◽  
pp. 1219-1225 ◽  
Author(s):  
Nikolai N. Sluchanko
Keyword(s):  
Protein Function ◽  
Intrinsically Disordered Protein ◽  
Structural Basis ◽  
Major Protein ◽  
Post Translational Modifications ◽  
Protein Protein Interaction ◽  
Intrinsically Disordered ◽  
Biochemical Journal ◽  
Multiple Binding ◽  
And Control

Many major protein–protein interaction networks are maintained by ‘hub’ proteins with multiple binding partners, where interactions are often facilitated by intrinsically disordered protein regions that undergo post-translational modifications, such as phosphorylation. Phosphorylation can directly affect protein function and control recognition by proteins that ‘read’ the phosphorylation code, re-wiring the interactome. The eukaryotic 14-3-3 proteins recognizing multiple phosphoproteins nicely exemplify these concepts. Although recent studies established the biochemical and structural basis for the interaction of the 14-3-3 dimers with several phosphorylated clients, understanding their assembly with partners phosphorylated at multiple sites represents a challenge. Suboptimal sequence context around the phosphorylated residue may reduce binding affinity, resulting in quantitative differences for distinct phosphorylation sites, making hierarchy and priority in their binding rather uncertain. Recently, Stevers et al. [Biochemical Journal (2017) 474: 1273–1287] undertook a remarkable attempt to untangle the mechanism of 14-3-3 dimer binding to leucine-rich repeat kinase 2 (LRRK2) that contains multiple candidate 14-3-3-binding sites and is mutated in Parkinson's disease. By using the protein-peptide binding approach, the authors systematically analyzed affinities for a set of LRRK2 phosphopeptides, alone or in combination, to a 14-3-3 protein and determined crystal structures for 14-3-3 complexes with selected phosphopeptides. This study addresses a long-standing question in the 14-3-3 biology, unearthing a range of important details that are relevant for understanding binding mechanisms of other polyvalent proteins.

The Concurrent Validity of the Minnesota Child Development Inventory as a Measure of Young Children's Language Development

1989 ◽  
Vol 54 (1) ◽  
pp. 101-105 ◽  
Author(s):  
J. Bruce Tomblin ◽  
Cynthia M. Shonrock ◽  
James C. Hardy
Keyword(s):  
Child Development ◽  
Language Development ◽  
Expressive Language ◽  
Strong Predictor ◽  
Receptive Language ◽  
Strongly Correlated ◽  
Language Measure ◽  
The Mean ◽  
Child Development Inventory ◽  
Mean Length Of Utterance

The extent to which the Minnesota Child Development Inventory (MCDI), could be used to estimate levels of language development in 2-year-old children was examined. Fifty-seven children between 23 and 28 months were given the Sequenced Inventory of Communication Development (SICD), and at the same time a parent completed the MCDI. In addition the mean length of utterance (MLU) was obtained for each child from a spontaneous speech sample. The MCDI Expressive Language scale was found to be a strong predictor of both the SICD Expressive scale and MLU. The MCDI Comprehension-Conceptual scale, presumably a receptive language measure, was moderately correlated with the SICD Receptive scale; however, it was also strongly correlated with the expressive measures. These results demonstrated that the Expressive Language scale of the MCDI was a valid predictor of expressive language for 2-year-old children. The MCDI Comprehension-Conceptual scale appeared to assess both receptive and expressive language, thus complicating its interpretation.

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