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Worm peptidomics

Steven J. Husson, Ank Reumer, Liesbet Temmerman, Wouter De Haes, Liliane Schoofs, Inge Mertens, Geert Baggerman
2014 EuPA Open Proteomics  
FMRFamide-like peptide Neuropeptide-like protein Insulin Neuropeptide Processing enzyme a b s t r a c t Bioactive peptides are present in all metazoan species where they orchestrate diverse functions.  ...  In this respect, it is very likely that nearly all neurons secrete neuropeptides and many roles for peptides in key physiological processes and behaviours have been characterized [4] [5] [6] . http://dx  ...  C. elegans KPC-2 is also named EGL-3 as mutants were initially discovered in a genetic screen for egg-laying deficiency about 30 years ago [97] .  ... 
doi:10.1016/j.euprot.2014.04.005 fatcat:bbbv5cv4rngerk4ophzzcvidey

Lead Modulates trans- and cis-Expression Quantitative Trait Loci (eQTLs) in Drosophila melanogaster Heads

Wen Qu, Katherine Gurdziel, Roger Pique-Regi, Douglas M. Ruden
2018 Frontiers in Genetics  
of genes in a lead-dependent manner.  ...  This trans-eQTL hotspot validates one identified in a previous study using different recombinant inbred lines.  ...  Great thanks to the High Performance Computing Services offered by Wayne State University for making the entire statistical analysis fast and efficient.  ... 
doi:10.3389/fgene.2018.00395 pmid:30294342 pmcid:PMC6158337 fatcat:3fd6p4ylujainmen3cdmev4siy

Predicting the sequence specificities of DNA- and RNA-binding proteins by deep learning

Babak Alipanahi, Andrew Delong, Matthew T Weirauch, Brendan J Frey
2015 Nature Biotechnology  
For a sequence s, DeepBind computes a binding score f (s) using four stages: )) = net pool rect conv The convolution stage (conv M ) scans a set of motif detectors with parameters M across the sequence  ...  bound sequences of varying length, and HT-SELEX 11 generates a set of very high affinity sequences.  ...  Hughes for helpful discussions.  ... 
doi:10.1038/nbt.3300 pmid:26213851 fatcat:6uvobbdnkvgytkybarlksceysi

Deciphering the Retinal Epigenome during Development, Disease and Reprogramming: Advancements, Challenges and Perspectives

Cristina Zibetti
2022 Cells  
This pipeline is virtually applicable to the study of genetic programs and candidate pioneer factors in any developmental context.  ...  Herein, this review presents the state-of-the-art approaches to investigate the retinal epigenome during development, disease, and reprogramming.  ...  A generalized linear mixed model and a two-part hurdle model with a random effect for the individual (MAST with RE) have recently been developed to correct for type 1 error rates, hence false positives  ... 
doi:10.3390/cells11050806 pmid:35269428 pmcid:PMC8908986 fatcat:5pewk6zas5ch7j65hyx7nktpra

Bioinformatics with soft computing

S. Mitra, Y. Hayashi
2006 IEEE Transactions on Systems Man and Cybernetics Part C (Applications and Reviews)  
RSes for modeling ambiguity, searching potential of genetic algorithms for efficiently traversing large search spaces, and the generalization capability of SVMs for minimizing errors.  ...  The major pattern-recognition and data-mining tasks considered here are clustering, classification, feature selection, and rule generation.  ...  The different techniques of soft computing considered include FSs, artificial neural networks (ANNs), GAs, evolutionary programming, RSes, SVMs, and various hybridizations like neuro-fuzzy (NF) models.  ... 
doi:10.1109/tsmcc.2006.879384 fatcat:owim7m6genf6xc7s2bbhjuz7gu

General sessions (1B-01 - 3F-12)

2011 Genes & Genetic Systems  
For a complete graph the dual is Kingman's coalescent. But in general the dual is a random collision model.  ...  Arts and Sci., Univ. of Tokyo, 2 Adv. Sci.  ...  Sci., Univ. of Tokyo) Dual genetic structure of the Japanese population based on autosomal SNPs and haplotypes Although the Japanese population has a rather low genetic diversity, it appears to have a  ... 
doi:10.1266/ggs.86.407 fatcat:wcfsqf2edvffdfqeoz7hqdld5e

Acoustic signatures in cavefish populations inhabiting different caves [article]

Carole Hyacinthe, Joel Attia, Elisa Schutz, Didier Casane, Sylvie RETAUX
2022 bioRxiv   pre-print
The river-dwelling and the Pachon cave-adapted morphs of the fish Astyanax mexicanus share a repertoire of sounds, but their trigger, use and meaning has changed in cavefish after their recent colonization  ...  Acknowledgments Work supported by a Lidex Neuro-Saclay collaborative grant to SR and JA, an Equipe FRM grant (DEQ20150331745) to SR, a prize from Fondation des Treilles to CH, and an Ecos-Nord exchange  ...  We thank Luis Espinasa, Julien Fumey, and Stéphane Père and all other members of the Rétaux's lab for their helpful spirit in the field, and Patricia Ornelas-Garcia for obtaining shared fieldwork permits  ... 
doi:10.1101/2022.03.29.486255 fatcat:bhevjqgok5gs7cdur7b4cuv444

Polymeric biomaterials and nanomedicines

Jiyuan Yang, Jindřich Kopeček
2015 Journal of Drug Delivery Science and Technology  
Then, the lessons learned for the design of watersoluble polymers as drug carriers are highlighted.  ...  The latter is mediated by biorecognition of complementary motifs; no low molecular weight drug is needed.  ...  A new strategy of hybrid hydrogel synthesis entails the non-covalent attachment of genetically engineered coiled-coil protein motifs to hydrophilic synthetic HPMA copolymer backbone.  ... 
doi:10.1016/j.jddst.2015.05.012 pmid:26688694 pmcid:PMC4681002 fatcat:ifjm7i2wfnawxghy7jwzpnf4ge

Endogenous archeological sciences: Physiology, Neuroscience, Biochemistry, Immunology, Pharmacology, Oncology and Genetics as instrument for a new field of investigation? Modern global aspects for a new discipline

Luisetto* M
2018 Journal of Neuroscience and Neurological Disorders  
Endogenous archeological sciences: Physiology, Neuroscience, Biochemistry, Immunology, Pharmacology, Oncology and Genetics as instrument for a new fi eld of investigation?  ...  Modern global aspects for a new discipline.  ...  of a number of induced mutations and the introduction of an F1 hybrid system.  ... 
doi:10.29328/journal.jnnd.1001017 fatcat:a6mltukg4vf5dabpwlusv5e5hi

Molecular epigenetics of Angelman syndrome

M. Lalande, M. A. Calciano
2007 Cellular and Molecular Life Sciences (CMLS)  
A. (2000) Genetic studies in autistic disorder and chromosome 15. Neuro- genetics 2, 219 — 26.  ...  E. and Beaudet, A. L. (2004) A mixed epigenetic/genetic model for oligogenic inheritance of autism with a limited role for UBE3A. Am. J. Med. Genet. A 131, 1 - 10.  ... 
doi:10.1007/s00018-007-6460-0 pmid:17347796 fatcat:e5nwnyxqzfazzafcecrs2dskoi

Cloning and Biochemical Characterization of the Hectochlorin Biosynthetic Gene Cluster from the Marine CyanobacteriumLyngbya majuscula

Aishwarya V. Ramaswamy, Carla M. Sorrels, William H. Gerwick
2007 Journal of natural products  
Initial attempts to isolate the hectochlorin biosynthetic gene cluster led to the identification of a mixed PKS/NRPS gene cluster, LMcryl, whose genetic architecture did not substantiate its involvement  ...  This gene cluster was designated as a cryptic gene cluster because a corresponding metabolite  ...  Labeled probes were used at a concentration of 20 ng/mL. Detection was also carried out as described for colony hybridizations.  ... 
doi:10.1021/np0704250 pmid:18001088 fatcat:y72dhwjie5gydhdodyd4a65y3u

Predictive molecular pathology and its role in targeted cancer therapy: a review focussing on clinical relevance

M Dietel, K Jöhrens, Mv Laffert, M Hummel, H Bläker, B M Müller, A Lehmann, C Denkert, F L Heppner, A Koch, C Sers, I Anagnostopoulos
2013 Cancer Gene Therapy  
) sequencing, next-generation sequencing, DNA-arrays, methylation analyses, and so on) to be applicable for formalin-fixed paraffinembedded (FFPE) tissue.  ...  To meet this challenge, surgical pathology has adapted a number of molecular methods (semi-quantitative immunohistochemistry, fluorescence in situ hybridization), PCR and its multiple variants, (pyro/Sanger  ...  This review considers state-of-the-art of molecular pathology for guiding targeted cancer treatment.  ... 
doi:10.1038/cgt.2013.13 pmid:23492822 fatcat:zhkziohh7ffxzfsk4tugvrwfeu

A High-Sensitivity, Medium-Density, and Target Amplification-Free Planar Waveguide Microarray System for Gene Expression Analysis of Formalin-Fixed and Paraffin-Embedded Tissue

S. Schwers, E. Reifenberger, M. Gehrmann, A. Izmailov, K. Bohmann
2009 Clinical Chemistry  
We observed a correlation coefficient of 0.87 to state-of-the-art RT-qPCR technology with RNA isolated from FFPE tissue, despite a compressed dynamic range for the PWG system (a 2.9-log dynamic range for  ...  The ZeptoCARRIER can accommodate 24 arrays in a single run. Also given is the total time for 24 samples, which depends on the hybridization time. b RDAb, RNA/DNA hybrid-specific antibody.  ...  Depending on the chip coating, the hybridization time could be shortened from the generally applied overnight incubation to a 4-h incubation with only a small decrease in performance (data not shown).  ... 
doi:10.1373/clinchem.2009.128215 pmid:19745061 fatcat:25lhwjfihvcxnf44bbxl5sporu

TaqMan (RT-PCR, real time PCR) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
[Lond] 289:271; Bacillus subtilis: Gollnick P et al 2005 Annu Rev Genet 39:47.Tryptophan Repressor: Consists of a repressor protein (using a helix-turn-helix motif ) for binding to the operator site of  ...  ▶mismatch, ▶tran- sition mismatch Transversion Mutation: The substitution of a purine for a pyrimidine, or a pyrimidine for a purine in the genetic material.  ...  The purpose is to generate antitumor immune reaction. Cancer cells may be ex vivo genetically modified and reintroduced into the body.  ... 
doi:10.1007/978-1-4020-6754-9_16672 fatcat:mxuz2ae7pfbs3dzpwonncixegm

Tetrahydrofolate (THF) [chapter]

2008 Encyclopedia of Genetics, Genomics, Proteomics and Informatics  
[Lond] 289:271; Bacillus subtilis: Gollnick P et al 2005 Annu Rev Genet 39:47.Tryptophan Repressor: Consists of a repressor protein (using a helix-turn-helix motif ) for binding to the operator site of  ...  ▶mismatch, ▶tran- sition mismatch Transversion Mutation: The substitution of a purine for a pyrimidine, or a pyrimidine for a purine in the genetic material.  ...  The purpose is to generate antitumor immune reaction. Cancer cells may be ex vivo genetically modified and reintroduced into the body.  ... 
doi:10.1007/978-1-4020-6754-9_16854 fatcat:24e4irafhfh47bwq3q6vlbdwpu
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