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Topology-function conservation in protein–protein interaction networks

Darren Davis, Ömer Nebil Yaveroğlu, Noël Malod-Dognin, Aleksandar Stojmirovic, Nataša Pržulj
2015 Computer applications in the biosciences : CABIOS  
relationships in a given species, and (ii) uncovers the functions that have conserved topology in PINs of different species, which we term topologically orthologous functions.  ...  Results: To improve our understanding of topology-function relationships and of their conservation among species, we develop a statistical framework that is built upon canonical correlation analysis.  ...  Butts for his comments and suggestions on developing the methodology. Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btv026 pmid:25609797 pmcid:PMC4426845 fatcat:teq5qz2ufzd7vaf3xme4ak342u

A Comparison of the Cortical Structure of the Bowhead Whale ( Balaena mysticetus ), a Basal Mysticete, with Other Cetaceans

Mary Ann Raghanti, Bridget Wicinski, Rachel Meierovich, Tahia Warda, Dara L. Dickstein, Joy S. Reidenberg, Cheuk Y. Tang, John C. George, J.G.M. Hans Thewissen, Camilla Butti, Patrick R. Hof
2018 The Anatomical Record  
Cell density, composition, and width of layers III, V, and VI vary among cortical regions, and cetacean cortex is cell-sparse relative to that of terrestrial mammals.  ...  Here, we present an overview of the structure and cytoarchitecture of the bowhead whale cerebral cortex gleaned from Nissl-stained sections and magnetic resonance imaging (MRI) in comparison with other  ...  Craig George, Barrow captains and crew  ... 
doi:10.1002/ar.23991 pmid:30332717 fatcat:vgqvn527cjhvdihbzvrhzn43sa

Multiview learning for understanding functional multiomics

Nam D Nguyen, Daifeng Wang
2020 PLoS Computational Biology  
In particular, multiview learning is more effective than previous integrative methods for learning data's heterogeneity and revealing cross-talk patterns.  ...  and caveats of using multiview learning to discover the molecular mechanisms and functions of these systems.  ...  and sparse generalized CCA (SGCCA).  ... 
doi:10.1371/journal.pcbi.1007677 pmid:32240163 pmcid:PMC7117667 fatcat:jqpizdutnrgtnlymfmjhh4qo4q

Hydrochemical and microbiological distinction and function of ombrotrophic peatland lagg as ecotone betweenSphagnumpeatland and forest catchment (Poleski National Park, eastern Poland)

Tomasz Mieczan, Monika Tarkowska-Kukuryk, Irena Bielańska-Grajner
2012 Annales de Limnologie  
However, species composition of ciliates and rotifers was explained by nitrate nitrogen and/or phosphates concentrations.  ...  The results suggest that lagg zone of a raised bog can fulfil the function of an ecotone zone, distinguished by a significant increase in biodiversity, abundance and species specificity of micro-organisms  ...  The CCA on individual environmental variables revealed that the proportion of testate amoebae, ciliates and rotifers data explained by each of variable and the significance varied strongly among variables  ... 
doi:10.1051/limn/2012022 fatcat:sd6d4z2a4nf7jdrobnjqsfxmsm

Effects of land-use on Collembola diversity patterns in a Mediterranean landscape

José Paulo Sousa, Maria Manuela da Gama, Cristina Pinto, António Keating, Filipa Calhôa, Marco Lemos, Catarina Castro, Tiago Luz, Pedro Leitão, Susana Dias
2004 Pedobiologia  
Overall analysis revealed that Collembola reacted to changes in the landscape structure, with community composition giving a more robust response than diversity indices.  ...  Species composition in all these units was mainly determined by soil-use types present at each LUU (open cork-oak land and pastures vs. closed cork-oak areas), the proportion of the different soil-use  ...  Acknowledgements This study was sponsored by the EU, integrated in the BIOASSESS project (Contract No.: EVK4 -1999-00280).  ... 
doi:10.1016/j.pedobi.2004.06.004 fatcat:m2ddtogigvgm7irdd7c2tgcptq

Benthic grazing and functional compensation in stressed and recovered lakes

Kristy L Hogsden, Rolf D Vinebrooke
2006 Canadian Journal of Fisheries and Aquatic Sciences  
We tested these hypotheses by conducting a 90-day experiment in which three size categories of benthic consumers were excluded from producers in three chemically stressed and three recovered lakes.  ...  [Traduit par la Rédaction] Hogsden and Vinebrooke 2010 Fig. 4 .  ...  Mark Graham and Lindsay Hogsden provided invaluable assistance in the field. This project was funded by  ... 
doi:10.1139/f06-098 fatcat:kojlh6vewfftzboobaxu6t3xle

Comparative Anatomy of the Carotid-Basilar Arterial Trunk and Hindbrain Penetrating Arteries in Vertebrates

Sulman Rahmat, Edwin Gilland
2014 The Open Anatomy Journal  
The gross anatomy and embryology of cyclostomes, elasmobranchs, actinopterygians and tetrapods reveal a conserved suite of hindbrain vascular features including the: 1) origin and branching of cerebral  ...  carotids; 2) ontogenetic origins of the basilar artery from paired precursors, often followed by midline fusion to form an unpaired basilar; and 3) presence of a quasi-segmental series of transverse basilar  ...  While the ICA is similarly absent as an adult structure in chinchillas [96] and capybaras [93] , the brain is supplied in these species almost solely by the vertebral arteries.  ... 
doi:10.2174/1877609401406010001 fatcat:b2zesv2rc5cjdhrgheqgavcglq

Longitudinal variation in fish prey utilization, trophic guilds, and indicator species along a large subtropical river, China

Sai Wang, Tuan-Tuan Wang, Jin-Peng Tang, Lin Wang, Yang Yang, Hsing-Juh Lin, Hao-Yen Chang, Xing-An Zhou, Xing Li, Ming Wang
2018 Ecology and Evolution  
Site-specific differences in fish diet composition (DC) revealed longitudinal shifts in utilized prey taxa, from upstream lotic to downstream semi-lentic items, and these were characterized by a decrease  ...  and indicator species is important.  ...  reveal the roles that fish play in the structure and functioning of river ecosystems (Elliott et al., 2007; Romanuk et al., 2006) .  ... 
doi:10.1002/ece3.4577 pmid:30598749 pmcid:PMC6303697 fatcat:baqjkpjuzfbzpcqjte53cqnsyq


Vanessa L. Lougheed, Patricia Chow-Fraser
2002 Ecological Applications  
The WZI was found to be more useful than indices of diversity (HЈ, species richness) and measures of community structure (mean cladoceran size, total abundance) for indicating wetland quality.  ...  Furthermore, an independent test of the WZI in a coastal wetland of the Great Lakes, Cootes Paradise Marsh, correctly detected moderate improvements in water quality following carp exclusion.  ...  This research was funded by an Ontario Graduate Scholarship to  ... 
doi:10.1890/1051-0761(2002)012[0474:dauoaz];2 fatcat:svqqwhtuinczdgnippirwqbnry

Development and Use of a Zooplankton Index of Wetland Quality in the Laurentian Great Lakes Basin

Vanessa L. Lougheed, Patricia Chow-Fraser
2002 Ecological Applications  
The WZI was found to be more useful than indices of diversity (HЈ, species richness) and measures of community structure (mean cladoceran size, total abundance) for indicating wetland quality.  ...  Furthermore, an independent test of the WZI in a coastal wetland of the Great Lakes, Cootes Paradise Marsh, correctly detected moderate improvements in water quality following carp exclusion.  ...  This research was funded by an Ontario Graduate Scholarship to  ... 
doi:10.2307/3060956 fatcat:chjr2u5wavfq5jh2x7orbfgs2i

Fish Assemblages in Subarctic Lakes: Does Fire Affect Fish–Environment Relations in Northern Alberta?

William M. Tonn, Shelly M. Boss, Peter K. M. Aku, Garry J. Scrimgeour, Cynthia A. Paszkowski
2004 Transactions of the American Fisheries Society  
Correspondence analysis revealed three simple but distinct small-lake fish assemblages in the Caribou Mountains: those dominated by northern pike Esox lucius, suckers Catostomus spp., or Arctic grayling  ...  Percentage disturbance accounted for less than 10% of the variation in fish assemblage structure among lakes, and reference and burned lakes were represented among all three assemblage types.  ...  Additional financial and logistical support was provided by the Little Red River/Tallcree First Nations. We thank E. Prepas, P. Dinsmore, and L.  ... 
doi:10.1577/t03-030 fatcat:tkqjr7whsvdm5hpsh5yieoz33m

Bioinformatics of prokaryotic RNAs

Rolf Backofen, Fabian Amman, Fabrizio Costa, Sven Findeiß, Andreas S Richter, Peter F Stadler
2014 RNA Biology  
The genome of most prokaryotes gives rise to surprisingly complex transcriptomes comprising not only protein-coding mRNAs, often organized as operons, but also harbors dozens or even hundreds of highly structured  ...  small regulatory RNAs and unexpectedly large levels of anti-sense transcripts.  ...  Acknowledgements This work was supported by the DFG under the auspices of Priority Program SPP 1258: Sensory and regulatory RNAs in Prokaryotes, grant nos. BA 2168/2 and STA 850/7.  ... 
doi:10.4161/rna.28647 pmid:24755880 pmcid:PMC4152356 fatcat:5mwl6uhug5ga3pznryreryz7bu

Relationships between characteristics of macrobenthic assemblages and environmental variables in the Heihe River Basin, China

Yu Wang, Juan-juan Liu, Bao-long Li, Wei Liu, Yi-feng Zuo, De-xing Kong, Jia-le Zhu
2021 Journal of Water Supply: Research and Technology - Aqua  
The results showed that 50 species of macrobenthos were identified, belonging to 3 phyla, 7 classes, 15 orders and 32 families, mainly arthropods (37 species) and mollusks (11 species).  ...  Canonical correspondence analysis showed that the spatial heterogeneity of the macrobenthos was affected by the water temperature and the total nitrogen and total phosphorus in sediments (P < 0.05).  ...  ACKNOWLEDGEMENTS This work was supported by the National Natural Science Foundation of China (Grant Nos. 51669011 and 41771252) and the Major Program of the National Nature Science Foundation of Gansu  ... 
doi:10.2166/aqua.2021.022 fatcat:c6ihgskyxbaaloax6dcmsik4um

Brazilian Semi-Arid Mangroves-Associated Microbiome as Pools of Richness and Complexity in a Changing World

Tallita Cruz Lopes Tavares, Walderly Melgaço Bezerra, Leonardo Ribeiro Oliveira Normando, Alexandre Soares Rosado, Vânia Maria Maciel Melo
2021 Frontiers in Microbiology  
In the face of changes in climate, land cover, biodiversity, and chemical composition, the richness and complexity harbored by semi-arid mangrove microbiomes may hold the key to mangrove adaptability in  ...  We demonstrated that, although the northern and southern sites are over 4,000 km apart, and despite R. mangle genetic divergences between north and south populations, their microbiomes resemble each other  ...  TT, AR, and VM are members of the Mangrove Microbiome Initiative (MMI) international network.  ... 
doi:10.3389/fmicb.2021.715991 pmid:34512595 pmcid:PMC8427804 fatcat:7cwojjp535fldgu7h66a3bikim

Structural Snapshots of Actively Translating Human Ribosomes

Elmar Behrmann, Justus Loerke, Tatyana V. Budkevich, Kaori Yamamoto, Andrea Schmidt, Pawel A. Penczek, Matthijn R. Vos, Jörg Bürger, Thorsten Mielke, Patrick Scheerer, Christian M.T. Spahn
2015 Cell  
chemical and conformational heterogeneity d Human 80S ribosome map at near-atomic resolution reveals native interactions In Brief Multiparticle cryo-EM analysis reveals 11 distinct functional states from  ...  Graphical Abstract Highlights d Structural analysis of actively translating ribosomes d Identification of significantly populated states at close to in vivo conditions d Functional states feature localized  ...  heterogeneity, which in turn may be caused by small differences among different tRNA species and/or flexibility/mobility.  ... 
doi:10.1016/j.cell.2015.03.052 pmid:25957688 pmcid:PMC4432480 fatcat:57nexbhpibgglaehphsqtvbduy
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