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171 results for “leucine”
PARAGON 1 - KM2112 - Leucine Incorporation In Situ Measurements
<p>This dataset contains measurements of in situ rates of leucine incorporation as a measure of bacterial production collected during the PARAGON 1 expedition (KM2112) in the North Pacific Subtropical Gyre. Measurements come from daily collections of whole seawater at 150 m using trace metal clean techniques. Rates of leucine incorporation were measured by subsampling 1.5 mL aliquots of whole seawater into 2 mL microcentrifuge tubes (Axygen) and spiking with a final concentration of 20 nmol L⁻¹ leucine with a ³H specific activity of 53.3 Ci mmol⁻¹ of leucine (Perkin Elmer). A killed blank measurement was made by spiking an additional 1.5 mL aliquot with 100 µL of 100% (w/v) ice-cold trichloroacetic acid (TCA) prior to spiking with ³H-leucine. All aliquots were then incubated in the dark at in situ temperature for 4-6 hours after which live incubations were terminated with the addition of 100 µL of 100% (w/v) ice-cold TCA. Samples were processed at sea using the centrifugation method of Smith and Azam (1992), and radioactivity incorporated into bacterial protein was measured on a TriCarb 4910TR scintillation counter using Ultima Gold LLT scintillation cocktail (Perkin Elmer). Values reported are the blank-corrected averages of triplicate measurements from each sample. Timestamp is in UTC.</p>
PARAGON 1 - KM2112 - Leucine Incorporation Timecourse Incubations
<p>This dataset contains measurements of rates of leucine incorporation as a measure of bacterial production collected during the PARAGON 1 expedition (KM2112) in the North Pacific Subtropical Gyre. Measurements come from time-course incubation experiments initiated with whole seawater collected at 150 m using trace metal clean techniques and modified with various additions of organic carbon, iron, and/or nitrogen. Rates of leucine incorporation were measured at multiple time points for each experimental biological replicate by subsampling 1.5 mL aliquots from polycarbonate incubation bottles into 2 mL microcentrifuge tubes (Axygen) and spiking with a final concentration of 20 nmol L⁻¹ leucine with a ³H specific activity of 53.3 Ci mmol⁻¹ of leucine (Perkin Elmer). A killed blank measurement was made for each experimental biological replicate by spiking an additional 1.5 mL aliquot with 100 µL of 100% (w/v) ice-cold trichloroacetic acid (TCA) prior to spiking with ³H-leucine. All aliquots were then incubated in the dark at in situ temperature for 4-6 hours after which live incubations were terminated with the addition of 100 µL of 100% (w/v) ice-cold TCA. Samples were processed at sea using the centrifugation method of Smith and Azam (1992), and radioactivity incorporated into bacterial protein was measured on a TriCarb 4910TR scintillation counter using Ultima Gold LLT scintillation cocktail (Perkin Elmer). Values reported are the blank-corrected averages of triplicate measurements from each sample. Timestamp is in UTC. Version 2 corrects formatting errors in the timestamp.</p>
PARAGON 2 - KM2209 - Leucine Incorporation Timecourse Incubations
<p>This dataset contains measurements of rates of leucine incorporation as a measure of bacterial production collected during the PARAGON 2 expedition (KM2209) in the North Pacific Subtropical Gyre. Measurements come from time-course incubation experiments initiated with whole seawater collected at 150 m using trace metal clean techniques and modified with various additions of organic carbon, iron, and/or nitrogen. Rates of leucine incorporation were measured at multiple time points for each experimental biological replicate by subsampling 1 mL aliquots from polycarbonate incubation bottles into 2 mL microcentrifuge tubes (Axygen) and spiking with a final concentration of 20 nmol L⁻¹ leucine with a ³H specific activity of 53.3 Ci mmol⁻¹ of leucine (Perkin Elmer). A killed blank measurement was made for each experimental biological replicate by spiking an additional 1 mL aliquot with 100 µL of 100% (w/v) ice-cold trichloroacetic acid (TCA) prior to spiking with ³H-leucine. All aliquots were then incubated in the dark at in situ temperature for 4-6 hours after which live incubations were terminated with the addition of 100 µL of 100% (w/v) ice-cold TCA. Samples were processed at sea using the centrifugation method of Smith and Azam (1992), and radioactivity incorporated into bacterial protein was measured on a TriCarb 4910TR scintillation counter using Ultima Gold LLT scintillation cocktail (Perkin Elmer). Values reported are the blank-corrected averages of technical triplicate measurements from each sample. Timestamp is in UTC.</p>
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain in Pathogen recognition molecules from hemocytes of Planorbarius corneus molluscs (Planorbidae, Pulmonata)
Рис. 2. Варианты преΑсказанной Αоменной структуры патогенраспознающих моΛекуΛ гемоцитов моΛΛюсков Planorbarius corneus. a — фибриногенпоΑобные беΛки, b — гаΛектины, c — F-Λектины. УсΛовные обозначения и сокращения, зΑесь и ΑаΛее: горизонтаΛьные красные поΛоски — сигнаΛьный пептиΑ, горизонтаΛьные розовые — обΛасть низкой сΛожности, вертикаΛьные синие поΛоски — трансмембранная обΛасть, FBG — фибриногеновый Αомен, FTP — Αомен фукоΛектина, EGF — Αомен эпиΑермаΛьного фактора роста, EGF_CA — каΛьцийсвязывающий EGF-поΑобный Αомен, PAN_AP — APPLE-поΑобный Αомен, SCAN — обΛасть, богатая Λейцином, GLECT — гаΛактозосвязывающий Λектин, CLECT — Λектин C-типа, Gal-bind — гаΛактозиΑ–связывающий Λектин, ML — MD-2- поΑробный Αомен распознавания ΛипиΑов Fig. 2. Variants of the predicted domain structure of pattern recognition molecules from hemocytes of Planorbarius corneus molluscs. a — fibrinogen-related proteins, b — galectins, c — F-lectins. Symbols and abbreviations (here and further): horizontal red stripes — signal peptide, horizontal pink stripes — a low complexity region, vertical blue stripes — transmembrane region, FBG — fibrinogen-related domain, FTP — fucolectin domain, EGF — epidermal growth factor-like domain, EGF_CA — calcium-binding EGF-like domain, PAN_AP — APPLE-like domain, SCAN — leucine rich region, Apple — APPLE domain, GLECT — galactose-binding lectin, CLECT — C-type lectin, Gal-bind — galactoside-binding lectin, ML — MD-2-related lipid-recognition domain
A New Comprehensive Annotation of Leucine-Rich Repeat-Containing Receptors in Rice
<p>Datasets for preprint (https://doi.org/10.1101/2021.01.29.428842) entitled "<strong>A new comprehensive Annotation of Leucine-Rich Repeat-Containing Receptors in Rice</strong>".</p> <p>This paper describes an in-depth manual curation of LRR-CR annotations including genes containing nonsense mutations, tagged as 'non-canonical', by opposition to 'canonical', that have expected gene models.</p> <p> </p> <p>Contains 7 files for each rice cultivar:</p> <p>- domain annotation for each LRR-CR protein (xxx_LRR_domains_filtered.csv)</p> <p>- gff file containing LRR-CR gene model annotations</p> <p>- fasta file (1): the complete genes 'gene' (nucleotide sequence, exons and introns)</p> <p>- fasta file (2): the coding sequences 'CDS' (nucleotide sequence, exons, translatable). Note that for genes experiencing frameshift, the one or two bases that cause the frameshift are avoided in order to have nucleotide sequence that can be translated. Terminal and in frame stop codons are encoded by a '*'.</p> <p>- fasta file (3): protein sequences 'PEP' (amino acid sequence, exons, corresponding to translation of CDS (2) )</p> <p>- fasta file (4): 'cDNA' (nucleotide sequence, exons). Note that for genes experiencing frameshift, the translated protein sequence will not correspond to the one present in the file (3). For all other genes, the files "CDS" and "cDNA" retrieve the same nucleotide sequences.</p> <p>- fasta file (5): 'cDNA_wFrameshit' (nucleotide sequence, exons) : same sequences than in (4) except for genes experiencing frameshift whose sequences are completed with one or two "!" characters at the position of the frameshift in order to conserve the right reading frame (also used by V. Ranwez et al. for the MACSE programs <a href="https://dx.doi.org/10.1093/molbev/msy159">https://dx.doi.org/10.1093/molbev/msy159</a> ).</p> <p> </p>
Oxidation of L-leucine amino acid initiated by HO● radical - Are transition metal ions an enhancement factor?
<p class="MsoNormal"><span><span>Hydroxyl radical (HO<sup>●</sup>) formation initiated by the Fenton-type reactions of Fe and Cu complexes of L-leucine (Leu) amino acid, as well as its oxidation reaction by HO<sup>●</sup> were computationally investigated by using the density functional theory (DFT) method at the M05-2X/6-311++G(3df,2pd)//M05-2X/6-311++G(d,p) level of theory in the aqueous phase. The results showed that dipole-salt is the main form of Leu in the physiological condition. Leu exhibits high chelating potential towards both Fe(III)/Fe(II) and Cu(II)/Cu(I) ions with the most favorable coordinating positions at two oxygen atoms of the –COO functional groups. Furthermore, the Leu-ions complexes show a high risk of HO<sup>●</sup> formation <em><span>via</span></em> Fenton-like reactions, especially when ascorbate anion exists in the environment as a reducing agent. Finally, the oxidation reaction of L-leucine by HO<sup>●</sup> demonstrated a relatively high overall apparent reaction rate – </span><em><span>k<sub>overall</sub></span></em><span><span> being 1.18 × 10<sup>9</sup> M<sup>-1</sup>s<sup>-1</sup>,</span><span> </span><span>in which</span><span> </span><span>formal hydrogen transfer (FHT) reactions of the dipole-salt form occur as the primary mechanism. Consequently, the Leu oxidation by HO<sup>●</sup> radical can be promoted by the Fenton-reaction enhancement of its transition metal complexes.</span></span></span></p>
Data for: Invasive investigation: Uptake and transport of L-leucine in the gill epithelium of crustaceans
<p><span>Many aquatic species are well-known as extremely successful invaders. The green crab (<em>Carcinus</em> <em>maenas</em>) is an arthropod native to European waters; however, it is now known to be a globally invasive species. Recently it was discovered that <em>C. maenas</em> could transport nutrients in the form of amino acids across their gill from the surrounding environment, a feat previously thought to be impossible in arthropods. We compared the ability for branchial amino acid transport of crustaceans native to Canadian Pacific waters to that of the invasive <em>C. maenas</em>, determining if this was a novel pathway in an extremely successful invasive species or a shared trait among crustaceans. Active transport of L-leucine was exhibited in C<em>arcinus maenas, Metacarcinus gracilis, Metacarcinus magister</em>, and <em>Cancer</em> <em>productus</em> across their gill epithelia. <em>C. maenas</em> exhibited the highest maximum rate of branchial L-leucine transport at 53.7 ± 6.24 </span>nmolg<sup>-1</sup>h<sup>-1</sup>, over twice the rate of two native Canadian crustaceans<span>. We also examined the influence of feeding, gill specificity, and organ accumulation of L-leucine. Feeding events displayed a heavy influence on the branchial transport rate of amino acids, increasing L-leucine transport rates by up to 10-fold in <em>C. maenas</em>. L-leucine displayed </span>a significantly higher accumulation rate <span>in the gills of <em>C. maenas</em> </span>compared to the rest of the body <span>at </span>4.15 <span>± 0.78 </span>nmolg<sup>-1</sup>h<sup>-1</sup>, with the stomach, hepatopancreas, eyestalks, muscle tissue, carapace, and heart muscle exhibiting accumulation under 0.15 nmolg<sup>-1</sup>h<sup>-1</sup>. <span>For the first time, the novel transport of amino acids in Canadian native arthropods is described, suggesting that branchial amino acid transport is a shared trait among arthropods, contrary to existing literature. Further investigation is required to determine the influence of environmental temperature and salinity on transport in each species to outline any competitive advantages of the invasive <em>C. maenas</em> in a fluctuating estuarine environment. </span></p>
N-Acetyl-L-Leucine for Ataxia-Telangiectasia (A-T)
ClinicalTrials.gov study NCT03759678. IPD Sharing: NO. Countries: 4. Publications: 3.
Effects of Intragastric Quinine, Alone or Combined With L-leucine, on Postprandial Glycaemic Control
ClinicalTrials.gov study NCT05720390. IPD Sharing: NO. Countries: 1. Publications: 1.
N-Acetyl-L-Leucine for GM2 Gangliosidosis (Tay-Sachs and Sandhoff Disease)
ClinicalTrials.gov study NCT03759665. IPD Sharing: Not stated. Countries: 4. Publications: 3.
Rapid Antidepressant Effects of Leucine
ClinicalTrials.gov study NCT03079297. IPD Sharing: NO. Countries: 1. Publications: 5.
N-Acetyl-L-Leucine for Niemann-Pick Disease, Type C (NPC)
ClinicalTrials.gov study NCT03759639. IPD Sharing: Not stated. Countries: 5. Publications: 3.
Pilot Phase I/II Study of Amino Acid Leucine in Treatment of Patients With Transfusion-Dependent Diamond Blackfan Anemia
ClinicalTrials.gov study NCT01362595. IPD Sharing: NO. Countries: 1. Publications: 50.
Data for: Invasive investigation: Uptake and transport of L-leucine in the gill epithelium of crustaceans
Open the record for dataset details and reuse information.
Oxidation of L-leucine amino acid initiated by HO● radical - Are transition metal ions an enhancement factor?
Open the record for dataset details and reuse information.
Time series measurements of leucine incorporation as a measure of bacterial production in the subtropical North Pacific Ocean
<p>Samples were collected at or in the vicinity of Station ALOHA on 24 different cruises. On each cruise, rates of 3H-Leu incorporation into protein were measured. Seawater samples for measurements of production were collected from pre-dawn vertical hydrocasts at 6 discrete depths (5, 25, 45, 75, 100, 125 m) using polyvinyl chloride sampling bottles affixed to a rosette sampler. Polyethylene amber bottles (125 ml capacity) were subsampled from the CTD rosette bottles, and duplicate acid-cleaned 12 ml polycarbonate centrifuge tubes were filled from each depth. Each polycarbonate tube was inoculated with 20 nmol L-1 (final concentration) 3,4,5-3H-leucine. An additional 1.5 ml per depth was subsampled into 2 ml microcentrifuge tubes containing 100 µl of 100% (w/v) ice-cold trichloroacetic acid (TCA) to serve as a killed blank. The polycarbonate sample tubes were capped and incubated in situ over the photoperiod to measure rates of 3H-Leu incorporation in both dark (through use of black cloth bags) and light on a free-drifting array. At the end of the photoperiod, triplicate 1.5 ml subsamples were removed from each tube and added to 2 ml microcentrifuge tubes containing 100 µl of 100% ice-cold TCA; these tubes were stored frozen until analysis. Samples were processed following a modified method of the microcentrifuge method. </p>
Data from: TAPBPR mediates peptide dissociation from MHC class I using a leucine lever
Tapasin and TAPBPR are known to perform peptide editing on major histocompatibility complex class I (MHC I) molecules, however, the precise molecular mechanism(s) involved in this process remain largely enigmatic. Here, using immunopeptidomics in combination with novel cell-based assays that assess TAPBPR-mediate peptide exchange, we reveal a critical role for the K22-D35 loop of TAPBPR in mediating peptide exchange on MHC I. We identify a specific leucine within this loop that enables TAPBPR to facilitate peptide dissociation from MHC I. Moreover, we delineate the molecular features of the MHC I F pocket required for TAPBPR to promote peptide dissociation in a loop-dependent manner. These data reveal that chaperone-mediated peptide editing of MHC I can occur by different mechanisms dependent on the C-terminal residue that the MHC I accommodates in its F pocket and provide novel insights that may inform the therapeutic potential of TAPBPR manipulation to increase tumour immunogenicity.
The underground life of homeodomain-leucine zipper transcription factors
<p class="western"><span>Roots are the anchorage organs of plants, responsible for water and nutrient uptake, exhibiting high plasticity. Root architecture is driven by the interactions of biomolecules, including transcription factors (TFs) and hormones that are crucial players regulating root plasticity. Multiple TF families are involved in root development; some, such as ARFs and LBDs, have been well characterized, whereas others remain less investigated. In this review, we synthesize the current knowledge about the involvement of the large family of homeodomain-leucine zipper (HD-Zip) TFs in root development. This family is divided into four subfamilies (I to IV), mainly according to structural features, such as additional motifs aside from HD-Zip, as well as their size, gene structure, and expression patterns. We explored and analyzed public databases and the scientific literature regarding HD-Zip TFs in Arabidopsis and other species. Most members of the four HD-Zip subfamilies are expressed in specific cell types and several ones from each group have assigned functions in root development. Notably, a high proportion of the studied proteins are part of intricate regulation pathways involved in primary and lateral root growth and development.</span></p>
Data from crystal of Leucine-Rich Repeat Protein from Leptospira interrogans recorded during routine commissioning on Diamond Light Source beamline I04
<p>Samples as part of ongoing research / collaboration; for more details see https://www.ncbi.nlm.nih.gov/pubmed/26057675</p>
Asymmetric evolution of protein domains in the leucine-rich repeat receptor-like kinase (LRR-RLK) family of plant developmental coordinators
<p><span>The coding sequences of developmental genes are expected to be conserved over deep time, with cis-regulatory change driving the modulation of gene function. In contrast, proteins with roles in defense are expected to evolve rapidly, in molecular arms races with pathogens. However, some gene families include both developmental and defense genes. In these families, do the tempo and mode of evolution differ between developmental and defense genes, despite shared ancestry and structure? The leucine-rich repeat receptor-like kinase (LRR-RLKs) protein family includes many members with roles in plant development and defense, thus providing an ideal system for answering this question. LRR-RLKs are receptors that traverse plasma membranes. LRR domains bind extracellular ligands, RLK domains initiate intracellular signaling cascades in response to ligand binding. In LRR-RLKs with roles in defense, LRR domains evolve faster than RLK domains. To determine whether this asymmetry extends to developmental LRR-RLKs, we assessed evolutionary rates and tested for selection acting on eleven clades of LRR-RLK proteins, using deeply sampled protein trees. To assess functional evolution, we performed heterologous complementation assays using <em>Arabidopsis thaliana</em> (arabidopsis) LRR-RLK mutants. We found that the LRR domains of developmental LRR-RLK proteins evolved faster than their cognate RLK domains. LRR-RLKs with roles in development and defense had strikingly similar patterns of molecular evolution. Heterologous transformation experiments revealed that the evolution of developmental LRR-RLKs likely involves multiple mechanisms, including changes to cis-regulation, coding sequence evolution, and escape from adaptive conflict. Our results indicate similar evolutionary pressures acting on developmental and defense signaling proteins, despite divergent organismal functions. In addition, deep understanding of the molecular evolution of developmental receptors can help guide targeted genome engineering in agriculture.</span></p>
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