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Bird Transcription
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The plant-specific GAI, RGA and SCR (GRAS) family proteins play critical roles in plant development and signalling. Two GRAS proteins, SHORT-ROOT (SHR) and SCARECROW (SCR), cooperatively direct asymmetric cell division and the patterning of root cell types by transcriptional control in conjunction with BIRD/INDETERMINATE DOMAIN (IDD) transcription factors, although precise details of these specific interactions and actions remain unknown. Here, we present the crystal structures of the SHR-SCR binary and JACKDAW (JKD)/IDD10-SHR-SCR ternary complexes. Each GRAS domain comprises one / core subdomain with an -helical cap that mediates heterodimerization by forming an intermolecular helix bundle. The / core subdomain of SHR forms the BIRD binding groove, which specifically recognizes the zinc fingers of JKD. We identified a conserved SHR-binding motif in 13 BIRD/IDD transcription factors. Our results establish a structural basis for GRAS-GRAS and GRAS-BIRD interactions and provide valuable clues towards our understanding of these regulators, which are involved in plant-specific signalling networks.
Vertebrate CpG islands (CGIs) are short interspersed DNA sequences that deviate significantly from the average genomic pattern by being GC-rich, CpG-rich, and predominantly nonmethylated. Most, perhaps all, CGIs are sites of transcription initiation, including thousands that are remote from currently annotated promoters. Shared DNA sequence features adapt CGIs for promoter function by destabilizing nucleosomes and attracting proteins that create a transcriptionally permissive chromatin state. Silencing of CGI promoters is achieved through dense CpG methylation or polycomb recruitment, again using their distinctive DNA sequence composition. CGIs are therefore generically equipped to influence local chromatin structure and simplify regulation of gene activity.
I don't have perfect pitch and badly trained and imprecise relative pitch. I only started two years ago to learn musical notation as a hobby and writing little stuff for myself and friends (For example). I said this just to give a context that I am not a musician and that I certainly ignore many basic things about notation, terminology, and the capabilities of the different musical instruments......................
I imagine there are ways to get a recorded natural occurring sound and somehow make the sound into a MIDI file, for example, and then open the MIDI, let's say in Sibelius and that should give an approximation for how its transcription into the score should look like.
Some composers manage to write down parts for an instrument that makes it resemble a particular natural occurring sound (horse whinnying, bird songs, rain, ...). My aim is to have a technical procedure to help myself in the process of doing that. Something that gives me a first approximation of notes that I can afterwards, by hand, tweak to make it more like the natural sound I wanted, or make it more playable, and then be able to elaborate them into a larger composition.
With brass instruments, it's typically done with a valved instrument, such as a trumpet or a tuba (or valve trombone if you have one.) The sound is typically produced by pressing the valves halfway down and either shaking the instrument (in the case of a trumpet) or by making a very wide vibrato. Using a tuba is less effective as it tends to sound more like a whale.
As far as notation goes, the easiest thing would probably be to just put a note in the score that says "whinny like horse" with perhaps an "x" for a note head; as long as the duration of the sound is clear. In addition to that, you may want to put a note at the front of the score explaining how to produce the sound as well as putting that same note at the bottom of the part for the instrument you write it for.
As for other naturally occurring sounds, you'll want to become more familiar with percussion instruments. For example, a "sea drum" simulates the sound of rolling waves, a "wind machine" generates the sound of wind, an aluminum sheet can mimic thunder, a clipboard can mimic a whip, temple blocks can mimic horse hooves, etc etc.
For bird sounds, you can check out the "Spring" movement of Vivaldi's Four Seasons where he mimics the songs of birds in spring. Also check out work by Olivier Messiaen, who was infatuated with birds and transcribed many of their calls, and even wrote works using his transcriptions.
You may find that, unfortunately, the best technology can do at this point is going to be somewhat below your expectations. Transcription is something even humans struggle with, and the more complicated a piece of music (audio) is, the trickier it is to transcribe--either for human OR computer, but the limit of a computer program is going to be far below that of a capable human. The more polyphonic, the trickier it is to transcribe.
AudioScore is probably the most widely-known tool that does what you are talking about, since a lite version is bundled with Sibelius, but those tools are almost never perfect, and output typically requires a lot of tweaking from the user.
If you're looking at birdsong in particular, though, that's essentially monophonic (single-line) music with no easily quantifiable rhythm. So, I wouldn't put too much faith in the software's ability to notate the rhythm, but it may be fairly successful with the pitches--and even if it's not totally accurate, good transcription software will be able to show you a spectrogram that visually places pitch occurrences over time on an axis (see the first screenshot on the AudioScore link above).
For many years, the U.S. government supported the Bird Migration and Distribution program, but participation gradually declined, and the program closed in 1970. What remained were millions of bird migration records spanning 90 years, a treasure trove of information that we can use today to help us understand how climate change is affecting migratory birds across North America.
The project is helping scientists and the general public understand how climate change is affecting bird migration across North America. After several years of digitizing data, the project now provides researchers with enough information to produce a growing number of scientific publications. The studies examine particular bird species and changes in their geographic locations over time to track the impact of a changing climate on migratory birds.
Well over 400,000 records have been validated and released to the public and scientific community on the project website as well as in other data repositories. The project has a dedicated community of transcribers who spend numerous hours making transcriptions.
Cytochrome P450 1 (CYP1) genes are biomarkers for aryl hydrocarbon receptor (AHR) agonists and may be involved in some of their toxic effects. CYP1s other than the CYP1As are poorly studied in birds. Here we characterize avian CYP1B and CYP1C genes and the expression of the identified CYP1 genes and AHR1, comparing basal and induced levels in chicken and quail embryos.
The apparent absence of CYP1C1 in quail, and weak expression and induction of CYP1C1 in chicken suggest that CYP1Cs have diminishing roles in tetrapods; similar tissue expression suggests that such roles may be met by CYP1B1. Tissue distribution of CYP1B and CYP1C transcripts in birds resembles that previously found in zebrafish, suggesting that these genes serve similar functions in diverse vertebrates. Determining CYP1 catalytic functions in different species should indicate the evolving roles of these duplicated genes in physiological and toxicological processes.
Copyright: 2011 Jnsson et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Funding: Funding to MEJ and BB was from the Carl Tryggers Stiftelse and The Swedish Research Council Formas. Funding for BRW and JJS was from the United States National Institutes of Health (National Institute of Environmental Health Sciences), grants R01ES015912 and P42ES007381 to JJS. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
Members of the cytochrome P450 (CYP) superfamily of enzymes are present in most organisms, including bacteria, archaea, plants, fungi, and animals. They catalyze oxidative metabolism of various endogenous and exogenous compounds. Endogenous substrates include eicosanoids, cholesterol, bile acids, steroids, biogenic amines, vitamin D3, and retinoids [1], [2]. Enzymes in the CYP1, CYP2, CYP3, and CYP4 families also metabolize exogenous compounds, such as plant or fungal secondary metabolites, environmental pollutants, and pharmaceuticals [3], [4]. The CYP1 enzymes have been studied extensively because they can generate reactive and sometimes carcinogenic metabolites from environmental pollutants (e.g., polycyclic aromatic hydrocarbons, PAHs), but the interest in their endogenous functions is growing [e.g., [5]].
Avian species vary substantially in sensitivity to embryo toxicity of halogenated aromatic hydrocarbons that activate the AHR [14], [15]. Chicken embryos are particularly sensitive to these compounds and the effects of exposure in ovo include reduced hatchability, developmental abnormalities, and induction of CYP1A-catalyzed enzyme activity [16], [17], [18]. Japanese quail embryos are considerably less sensitive than chicken embryos to TCDD and PCB126, both in terms of embryo toxicity and ethoxyresorufin O-deethylase (EROD) induction [19], [20], [21]. The difference in sensitivity has been attributed to variations in a few amino acid residues in the AHR [15], [22]. 152ee80cbc
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