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FAMSA: Fast and accurate multiple sequence alignment of huge protein families

Sebastian Deorowicz, Agnieszka Debudaj-Grabysz, Adam Gudyś
2016 Scientific Reports  
For example, a family of 415 519 sequences was analysed in less than two hours and required only 8GB of RAM. FAMSA is freely available at http://sun.aei.polsl.pl/REFRESH/famsa.  ...  In the article we introduce FAMSA, a new progressive algorithm designed for fast and accurate alignment of thousands of protein sequences.  ...  To verify this we compared algorithms on ABC tran, the largest family in extHomFam with 415 519 proteins. FAMSA processed this set in less then 2 hours.  ... 
doi:10.1038/srep33964 pmid:27670777 pmcid:PMC5037421 fatcat:5kwct7i2vrcq5bp4kvcyeafp6m

Rapid and scale-independent microfluidic manufacture of liposomes entrapping protein incorporating in-line purification and at-line size monitoring

Neil Forbes, Maryam T. Hussain, Maria L. Briuglia, Darren P. Edwards, Joop H. ter Horst, Nicolas Szita, Yvonne Perrie
2019 International Journal of Pharmaceutics  
In addition, the CD spectrum, containing information on the 415 OVA structure, with nine alpha helical structures and two beta sheets (Stein et al., 1990) , is in keeping 416 with literature (Paolinelli  ...  Results show 366 13 that after 12 wash cycles solvent levels were below ICH guidelines of less than 3000 parts per million 367 (or less than 0.3% of residual solvent remaining) (International conference  ... 
doi:10.1016/j.ijpharm.2018.11.060 fatcat:3hhqlyv6pjgzvifakny33jku2q

Dose-dependent response to infection with SARS-CoV-2 in the ferret model: evidence of protection to re-challenge [article]

Kathryn A Ryan, Kevin R Bewley, Susan A Fotheringham, Phillip Brown, Yper Hall, Anthony C Marriott, Julia A Tree, Lauren Allen, Marilyn J Aram, Emily Brunt, Karen R Buttigieg, Breeze E Cavell (+37 others)
2020 bioRxiv   pre-print
(5x102 pfu) resulted in only one of six displaying signs of URT viral RNA replication.  ...  In addition, intermittent viral shedding on days 14-21 parallel observations reported in a minority of clinical cases.  ...  neutrophils, but also macrophages and lymphocytes, in approximately 10-15% of the 209 lung section at day 3 pc decreasing to less than 5% at days 5 and 7 pc.  ... 
doi:10.1101/2020.05.29.123810 fatcat:5wscwtuvprftjpqvf6ysm73hwa

Intrinsic control of muscle attachment sites matching

Alexandre Carayon, Laetitia Bataillé, Gaëlle Lebreton, Laurence Dubois, Aurore Pelletier, Yannick Carrier, Antoine Wystrach, Alain Vincent, Jean-Louis Frendo
2020 eLife  
Thus, engineering Drosophila muscle identity mutants allows to investigate, in vivo, physiological and mechanical properties of abnormal muscles.  ...  By deleting transcription cis-regulatory modules of one iTF, Collier, we generated viable muscle identity mutants, allowing live imaging and locomotion assays.  ...  Fillets were then fixed 1 hour in 4% formaldehyde 491 and washed in PBT. 492 493 In situ hybridization 494 5.0 using unpaired t-test. 519 520 Phenotype quantification at embryonic and larval stages521  ... 
doi:10.7554/elife.57547 pmid:32706334 pmcid:PMC7431191 fatcat:pebeadt3cfdhdejapjtoa2od2e

Revisiting the early evolution of Cyanobacteria with a new thylakoid-less and deeply diverged isolate from a hornwort [article]

Nasim Rahmatpour, Duncan A. Hauser, Jessica M. Nelson, Pa Yu Chen, Juan Carlos Villarreal A., Ming-Yang Ho, Fay-Wei Li
2021 bioRxiv   pre-print
Furthermore, Anthocerobacter has one of the most reduced gene sets for photosystems and phycobilisomes among Cyanobacteria.  ...  Despite this, Anthocerobacter is capable of oxygenic photosynthesis under a wide range of light intensities, albeit with much less efficiency.  ...  Nanopore 414 libraries were prepared using the Ligation Sequencing kit (SQK-LSK109) and sequenced on two MinION 415 R9 flowcells (FLO-MIN106D) for 60 hours.  ... 
doi:10.1101/2021.02.18.431691 fatcat:buwf6bejyvgovfsvw4t5mbhh7m

Genome analysis of two Lactobacillus plantarum strains, LLY-606 and pc-26, for evaluating their potential as probiotics [article]

Dun Su, Lifeng Liang, Zhenzhen Li, Qingnan Lin, Can Peng, Xuejing Lei, songling liu
2019 bioRxiv   pre-print
Lactobacillus plantarum was not only one of the most popular probiotics, but also one of the most versatile lactic acid bacteria.  ...  In this study, the genome sequences of LLY-606 and pc-26 were sequenced, and multiple genes related to probiotic properties were analyzed.  ...  to perform multiple sequence alignment of single-copy proteins.  ... 
doi:10.1101/841163 fatcat:zxyssqpjpvdd7brnlh3yqbjdjm

Mitotic R-loops direct Aurora b kinase to maintain centromeric cohesion [article]

Erin Moran, Limin Liu, Ewelina Zasadzinska, Courtney Kestner, Ali Sarkeshik, Henry De Hoyos, John Robert Yates, Daniel Foltz, Todd Stukenberg
2021 bioRxiv   pre-print
CPC purified from mitotic chromosomes interacts with thirty-two proteins involved with R-loop biology. One of these, the RNA regulator RBMX, controls Aurora B localization and activity in vivo.  ...  They accumulate on chromosome arms in prophase, where they are quickly resolved and continue to be produced at repetitive sequences including centromeres during a mitotic stall.  ...  We then treated 345 the cells with Aurora-B inhibitors for an additional two hours and measured PCS by mitotic 346 spreads ( Figure 7A ).  ... 
doi:10.1101/2021.01.14.426738 fatcat:zeumme7zavc5npu3gtadu56mv4

Protein phosphatase 2B dual function facilitates synaptic integrity and motor learning

Zhanmin Lin, Bin Wu, Maarten W Paul, Ka Wan Li, Yao Yao, Ihor Smal, Martina Proietti Onori, Hana Hasanbegovic, Karel Bezstarosti, Jeroen Demmers, Adriaan B Houtsmuller, Erik Meijering (+5 others)
2021 Journal of Neuroscience  
Here we identified different types of proteins that interact with PP2B, among which structural proteins of the postsynaptic densities (PSDs) of Purkinje cells (PCs) in mice of either se.  ...  In contrast, lateral mobility of surface glutamate receptors solely depended on PP2B phosphatase activity.  ...  The 375 cerebellum was removed, kept in fixative for two hours, and cut transversely with a Vibratome 376 into 70 µm sections.  ... 
doi:10.1523/jneurosci.1741-20.2021 pmid:34021041 pmcid:PMC8244972 fatcat:d6pge2e6izefnbqxgech4bmkci

Translational contributions to tissue-specificity in rhythmic and constitutive gene expression [article]

Violeta Castelo-Szekely, A. Bulak Arpat, Peggy Janich, David Gatfield
2016 bioRxiv   pre-print
RESULTS: Rhythmic translation of constantly abundant mRNAs affected largely non-overlapping transcript sets with distinct phase clustering in the two organs.  ...  Between tissues, many transcripts showed differences in translation efficiency, which were, however, of markedly smaller scale than mRNA abundance differences.  ...  two hours (ZT0 --ZT22, with ZT0 corresponding to "lights--on") for two daily cycles.  ... 
doi:10.1101/060368 fatcat:q3s2o4f5vzdvhedjj4miy2r6o4

The Chlamydomonas FLA10 gene encodes a novel kinesin-homologous protein

Z. Walther
1994 Journal of Cell Biology  
The quantity of KHP1 protein in axonemes of the mutant fla/0-1 was markedly reduced, although no reduction was observed in two other uni linkage group mutants, fla9 and tall.  ...  Many genes on the uni linkage group of Chlamydomonas affect the basal body/flagellar apparatus.  ...  Novel hetezotrimeric kinesin-related protein purified from sea urchin eggs. Nature (Lond.). 366:268-270).  ... 
doi:10.1083/jcb.126.1.175 pmid:8027176 pmcid:PMC2120091 fatcat:mumpkiu52bf6tkn5fiwkbpyelq

Analysis of the liver lipidome reveals insights into the protective effect of exercise on high-fat diet-induced hepatosteatosis in mice

Andreas B. Jordy, Michael J. Kraakman, Tim Gardner, Emma Estevez, Helene L. Kammoun, Jacqui M. Weir, Bente Kiens, Peter J. Meikle, Mark A. Febbraio, Darren C. Henstridge
2015 American Journal of Physiology. Endocrinology and Metabolism  
(protein name ChREBP)) 73 NAFLD: non-alcoholic fatty liver disease 74 NASH: non-alcoholic steatohepatitis 75 NC: normal chow diet 76 4 PC: phosphatidylcholine 77 PE: phosphatidylethanolamine 78 PNPLA3  ...  Furthermore, 39 the ratio of phosphatidylcholine (PC) to phosphatidylethanolamine (PE) (the PC/PE ratio), 40 which is associated with membrane integrity and linked to hepatic disease progression was 41  ...  In the current study, the hepatic PC/PE ratio 397 decreased with high fat feeding (Fig 7E) due to a decrease in PC levels ( Fig 7D) rather than 398 an increase in PE levels ( Fig 7C) .  ... 
doi:10.1152/ajpendo.00547.2014 pmid:25714675 fatcat:m2kwsqvrebbglbd36vrs47wl6q

Age-related changes in Polycomb gene regulation disrupt lineage fidelity in intestinal stem cells

Helen M Tauc, Imilce A Rodriguez-Fernandez, Jason A Hackney, Michal Pawlak, Tal Ronnen Oron, Jerome Korzelius, Hagar F Moussa, Subhra Chaudhuri, Zora Modrusan, Bruce A Edgar, Heinrich Jasper
2021 eLife  
Our results identify Pc group proteins as central regulators of lineage identity in the intestinal epithelium and highlight the impact of age-related decline in chromatin regulation on tissue homeostasis  ...  We further confirm that Pc-mediated chromatin regulation is a critical determinant of EE cell specification in the Drosophila intestine.  ...  Nuclei were pelleted and 752 washed with 500 ul hypotonic buffer prior to acid extraction (100 ul volume for two hours at 4 753 °C).  ... 
doi:10.7554/elife.62250 pmid:33724181 pmcid:PMC7984841 fatcat:jm5kbomgl5hojjg3ehth3qziie

The RNA-binding protein RBP10 controls a regulatory cascade that defines bloodstream-form trypanosome identity [article]

Elisha Mugo, Christine Clayton
2016 bioRxiv   pre-print
Gene expression control in the pathogen Trypanosoma brucei relies almost exclusively on post-transcriptional mechanisms, so RNA binding proteins must assume the burden that is usually borne by transcription  ...  in RBP10 trigger a regulatory cascade.  ...  -117 (1:500) for 737 one hour on ice.  ... 
doi:10.1101/076273 fatcat:7jtbuhhmzbcl7fhtgxk52nlq4e

Structural basis of Toxoplasma gondii Perforin-Like Protein 1 membrane interaction and activity during egress [article]

Alfredo J. Guerra, Ou Zhang, Constance M. E. Bahr, My-Hang Huynh, James DelProposto, William C. Brown, Zdzislaw Wawrzak, Nicole M. Koropatkin, Vern B. Carruthers
2018 bioRxiv   pre-print
Additionally, solving the high-resolution crystal structure of the TgPLP1 APCβ domain within the CTD reveals an unusual double-layered βprism fold that resembles only one other protein of known structure  ...  One subdomain features a protruding hydrophobic loop with an exposed tryptophan at its tip.  ...  Subdomain 3 (Figure S2C blue), however, aligns less 134 well with subdomain 1 (RMSD 3.207 Å) and subdomain 2 (RMSD 3.175 Å), with the majority 135 of the alignment differences attributed to two loops  ... 
doi:10.1101/399204 fatcat:mghnauej6ra7fpr4we2dnr3c5q

Interaction of NPC2 protein with Lysobisphosphatidic Acid is required for normal endolysosomal cholesterol trafficking [article]

Leslie A McCauliff, Annette Langan, Ran Li, Olga Ilnytska, Debosreeta Bose, Peter C Kahn, Judith Storch
2019 bioRxiv   pre-print
in normal LE/LY cholesterol egress.  ...  Unesterified cholesterol accumulation in the late endosomal/lysosomal (LE/LY) compartment is the cellular hallmark of Niemann-Pick C (NPC) disease, caused by defects in the genes encoding NPC1 or NPC2.  ...  As two other anionic 190 phospholipids assayed, PG and PA, show even less interaction with NPC2 than does zwitterionic PC, the 191 mechanism by which NPC2 binds to LBPA is likely not solely dependent on  ... 
doi:10.1101/559849 fatcat:5te4e3covbeihow42zoivy7yom
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