Using morphology to infer physiology: case studies on rorqual whales (Balaenopteridae)

2015 ◽  
Vol 93 (9) ◽  
pp. 687-700 ◽  
Author(s):  
Jeremy A. Goldbogen ◽  
Robert E. Shadwick ◽  
Margo A. Lillie ◽  
Marina A. Piscitelli ◽  
Jean Potvin ◽  
...  
Keyword(s):  
Experimental Studies ◽  
Model Systems ◽  
Morphological Data ◽  
Sensory Physiology ◽  
Aquatic Life ◽  
Baleen Whales ◽  
Physiological Processes ◽  
Morphological Studies ◽  
Large Size ◽  
Wide Range

Whales are important model systems for understanding the physiological and ecological consequences of extreme body size. However, whales are also some of the most difficult animals to study because their large size precludes experimental studies under controlled conditions. Here we review a wide range of morphological studies that enable greater inference of physiological processes. In particular, we focus on baleen whales that exhibit extensive diving and foraging adaptations. Using morphological data, we (i) explore the biomechanics and sensory physiology of lunge-feeding rorqual whales (Balaenopteridae), (ii) determine the effects of scale and diving pressures on the circulatory physiology of fin whales (Balaenoptera physalus (L., 1758)), and (iii) better understand the adaptations of the cetacean respiratory system that facilitate a fully aquatic life history. These studies underscore the value of understanding functional morphology in animals that cannot be studied using traditional laboratory techniques.

scholarly journals Morphological and Genomic Features of the New Klosneuvirinae Isolate Fadolivirus IHUMI-VV54

2021 ◽  
Vol 12 ◽  
Author(s):  
Julien Andreani ◽  
Frederik Schulz ◽  
Fabrizio Di Pinto ◽  
Anthony Levasseur ◽  
Tanja Woyke ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
Experimental Studies ◽  
Morphological Data ◽  
Metagenomic Data ◽  
Translation System ◽  
Proton Pumps ◽  
Dna Viruses ◽  
Successful Isolation ◽  
Wide Range ◽  
Nucleocytoplasmic Large Dna Viruses

Since the discovery of Mimivirus, viruses with large genomes encoding components of the translation machinery and other cellular processes have been described as belonging to the nucleocytoplasmic large DNA viruses. Recently, genome-resolved metagenomics led to the discovery of more than 40 viruses that have been grouped together in a proposed viral subfamily named Klosneuvirinae. Members of this group had genomes of up to 2.4Mb in size and featured an expanded array of translation system genes. Yet, despite the large diversity of the Klosneuvirinae in metagenomic data, there are currently only two isolates available. Here, we report the isolation of a novel giant virus known as Fadolivirus from an Algerian sewage site and provide morphological data throughout its replication cycle in amoeba and a detailed genomic characterization. The Fadolivirus genome, which is more than 1.5Mb in size, encodes 1,452 predicted proteins and phylogenetic analyses place this viral isolate as a near relative of the metagenome assembled Klosneuvirus and Indivirus. The genome encodes for 66 tRNAs, 23 aminoacyl-tRNA synthetases and a wide range of transcription factors, surpassing Klosneuvirus and other giant viruses. The Fadolivirus genome also encodes putative vacuolar-type proton pumps with the domains D and A, potentially constituting a virus-derived system for energy generation. The successful isolation of Fadolivirus will enable future hypothesis-driven experimental studies providing deeper insights into the biology of the Klosneuvirinae.

scholarly journals Phylogeny and biogeography of the carnivorous plant family Droseraceae with representative Drosera species from Northeast India

F1000Research ◽  
2017 ◽  
Vol 6 ◽  
pp. 1454
Author(s):  
Devendra Kumar Biswal ◽  
Sureni Yanthan ◽  
Ruchishree Konhar ◽  
Manish Debnath ◽  
Suman Kumaria ◽  
...  
Keyword(s):  
Evolutionary Dynamics ◽  
Experimental Studies ◽  
Northeast India ◽  
Carnivorous Plant ◽  
Model Systems ◽  
Its2 Region ◽  
Plant Family ◽  
Sister Relationship ◽  
Bisphosphate Carboxylase ◽  
Wide Range

Background: Botanical carnivory is spread across four major angiosperm lineages and five orders: Poales, Caryophyllales, Oxalidales, Ericales and Lamiales. The carnivorous plant family Droseraceae is well known for its wide range of representatives in the temperate zone. Taxonomically, it is regarded as one of the most problematic and unresolved carnivorous plant families. In the present study, the phylogenetic position and biogeographic analysis of the genus Drosera is revisited by taking two species from the genus Drosera (D. burmanii and D. Peltata) found in Meghalaya (Northeast India). Methods: The purposes of this study were to investigate the monophyly, reconstruct phylogenetic relationships and ancestral area of the genus Drosera, and to infer its origin and dispersal using molecular markers from the whole ITS (18S, 28S, ITS1, ITS2) region and ribulose bisphosphate carboxylase (rbcL) sequences. Results: The present study recovered most of the findings by previous studies. The basal position of Droseraceae within the non-carnivorous Caryophyllales indicated in the tree topologies and fossil findings strongly support a date of origin for Droseraceae during the Paleocene (55-65 mya). Within the family Droseraceae, the sister relationship between Aldrovanda and Dionaea is supported by our ITS and rbcL dataset. This information can be used for further comparative and experimental studies. Conclusions: Drosera species are best suited as model systems for addressing a wide array of questions concerning evolutionary dynamics and ecological processes governing botanical carnivory.

Melatonin: Implications for Ocular Disease and Therapeutic Potential

2019 ◽  
Vol 25 (39) ◽  
pp. 4185-4191 ◽  
Author(s):  
Luca Scuderi ◽  
Sergio Davinelli ◽  
Clemente Maria Iodice ◽  
Silvia Bartollino ◽  
Giovanni Scapagnini ◽  
...  
Keyword(s):  
Therapeutic Potential ◽  
Single Agent ◽  
Experimental Studies ◽  
Age Related Macular Degeneration ◽  
Ocular Diseases ◽  
Physiological Processes ◽  
Age Related ◽  
Wide Range ◽  
Ocular Disorders ◽  
High Doses

Melatonin, an indoleamine secreted mainly by the pineal gland, is known to modulate a wide range of circadian functions. However, this neurohormone is also synthesized within the eye and acts directly on ocular structures to mediate a variety of physiological processes. This review is focused on the role and therapeutic potential of melatonin in ocular diseases. We summarize data indicating that melatonin may represent a powerful tool to counteract ocular dysfunctions such as uveitis, glaucoma, age-related macular degeneration, and diabetic retinopathy. A search strategy was conducted to identify studies in PubMed (January 1990 to September 2017). In particular, we included experimental studies, clinical trials, and reviews to provide suitable insights and elucidations regarding the action of melatonin on age-related ocular disorders. Literature data suggest that melatonin could potentially protect ocular tissues by decreasing the production of free radicals and pro-inflammatory mediators. Additionally, melatonin appears to be safe and well-tolerated, even at high doses, and no adverse/side effects were reported. Although this topic remains under intense investigation, we can conclude that melatonin, as a single agent or in combination with other drugs, is an attractive pharmacological candidate for age-related ocular diseases.

scholarly journals The pygmy right whale Caperea marginata : the last of the cetotheres

2013 ◽  
Vol 280 (1753) ◽  
pp. 20122645 ◽  
Author(s):  
R. Ewan Fordyce ◽  
Felix G. Marx
Keyword(s):  
Morphological Characters ◽  
Total Evidence ◽  
Baleen Whales ◽  
Virtual Absence ◽  
Right Whale ◽  
Morphological Studies ◽  
Wide Range ◽  
Evolutionary Context ◽  
Living Species ◽  
Cladistic Analyses

The pygmy right whale, Caperea marginata , is the most enigmatic of the living baleen whales (Mysticeti). Its highly disparate morphology and the virtual absence of a described fossil record have made it extremely difficult to place Caperea into a broader evolutionary context, and molecular and morphological studies have frequently contradicted each other as to the origins and phylogenetic relationships of the species. Our study of a wealth of material from New Zealand collections, representing a wide range of ontogenetic stages, has identified several new features previously unreported in Caperea , which suggest that the pygmy right whale may be the last survivor of the supposedly extinct family Cetotheriidae. This hypothesis is corroborated by both morphology-based and total evidence cladistic analyses, including 166 morphological characters and 23 taxa, representing all the living and extinct families of toothless baleen whales. Our results allow us to formally refer Caperea to Cetotheriidae, thus resurrecting the latter from extinction and helping to clarify the origins of a long-problematic living species.

A standardized and statistically defensible framework for quantitative morphological analyses in taxonomic studies

Zootaxa ◽  
2021 ◽  
Vol 5023 (2) ◽  
pp. 293-300
Author(s):  
KIN ONN CHAN ◽  
L. LEE GRISMER
Keyword(s):  
Body Size ◽  
Meta Analysis ◽  
Morphological Data ◽  
Statistical Hypothesis ◽  
Statistical Hypothesis Testing ◽  
Morphological Studies ◽  
Wide Range ◽  
Size Correction ◽  
Taxonomic Groups ◽  
Taxonomic Studies

Although body size correction and inferential statistics have been used in morphological studies for many decades, their applications are far from being ubiquitous. We performed a meta-analysis to quantify the extent of taxonomic papers that performed body size correction and implemented a statistical hypothesis testing framework during the analysis of morphological data. Our results indicate that in most papers, neither of these analyses were performed but instead, cursory comparisons of descriptive statistics were presented. With the development of numerous freely available and powerful statistical programs such as R, we find it prudent to outline a standardized and statistically defensible framework to enhance the workflow of morphological analyses in taxonomic studies. This 5-step approach can be applied to meristic and mensural data across a wide range of taxonomic groups. We include an easy-to-use companion R script to facilitate the implementation of this workflow. Our proposed framework is not rooted in phylogenetic or evolutionary theory and hence, should not be used in place of explicit species delimitation techniques. Nevertheless, it can be incorporated into a more robust integrative taxonomic framework and is particularly useful for identifying diagnostic characters for species diagnoses.  

Mapping of Protein-Protein Interactions: Web-Based Resources for Revealing Interactomes

2019 ◽  
Vol 26 (21) ◽  
pp. 3890-3910 ◽  
Author(s):  
Branislava Gemovic ◽  
Neven Sumonja ◽  
Radoslav Davidovic ◽  
Vladimir Perovic ◽  
Nevena Veljkovic
Keyword(s):  
Drug Discovery ◽  
Protein Interactions ◽  
Protein Complexes ◽  
Experimental Studies ◽  
Protein Protein Interactions ◽  
Web Based ◽  
Prediction Tools ◽  
Physiological Processes ◽  
Modern Drug ◽  
Ppi Prediction

Background: The significant number of protein-protein interactions (PPIs) discovered by harnessing concomitant advances in the fields of sequencing, crystallography, spectrometry and two-hybrid screening suggests astonishing prospects for remodelling drug discovery. The PPI space which includes up to 650 000 entities is a remarkable reservoir of potential therapeutic targets for every human disease. In order to allow modern drug discovery programs to leverage this, we should be able to discern complete PPI maps associated with a specific disorder and corresponding normal physiology. Objective: Here, we will review community available computational programs for predicting PPIs and web-based resources for storing experimentally annotated interactions. Methods: We compared the capacities of prediction tools: iLoops, Struck2Net, HOMCOS, COTH, PrePPI, InterPreTS and PRISM to predict recently discovered protein interactions. Results: We described sequence-based and structure-based PPI prediction tools and addressed their peculiarities. Additionally, since the usefulness of prediction algorithms critically depends on the quality and quantity of the experimental data they are built on; we extensively discussed community resources for protein interactions. We focused on the active and recently updated primary and secondary PPI databases, repositories specialized to the subject or species, as well as databases that include both experimental and predicted PPIs. Conclusion: PPI complexes are the basis of important physiological processes and therefore, possible targets for cell-penetrating ligands. Reliable computational PPI predictions can speed up new target discoveries through prioritization of therapeutically relevant protein–protein complexes for experimental studies.

scholarly journals Understanding sex differences in long-term blood pressure regulation: insights from experimental studies and computational modeling

2019 ◽  
Vol 316 (5) ◽  
pp. H1113-H1123 ◽  
Author(s):  
Sameed Ahmed ◽  
Rui Hu ◽  
Jessica Leete ◽  
Anita T. Layton
Keyword(s):  
Blood Pressure ◽  
Sex Differences ◽  
Computational Models ◽  
Experimental Studies ◽  
Pressure Control ◽  
Blood Pressure Regulation ◽  
Pressure Regulation ◽  
Physiological Processes ◽  
Key Players

Sex differences in blood pressure and the prevalence of hypertension are found in humans and animal models. Moreover, there has been a recent explosion of data concerning sex differences in nitric oxide, the renin-angiotensin-aldosterone system, inflammation, and kidney function. These data have the potential to reveal the mechanisms underlying male-female differences in blood pressure control. To elucidate the interactions among the multitude of physiological processes involved, one may apply computational models. In this review, we describe published computational models that represent key players in blood pressure regulation, and highlight sex-specific models and their findings.

scholarly journals Image Statistics Preserving Encrypt-then-Compress Scheme Dedicated for JPEG Compression Standard

Entropy ◽  
2021 ◽  
Vol 23 (4) ◽  
pp. 421
Author(s):  
Dariusz Puchala ◽  
Kamil Stokfiszewski ◽  
Mykhaylo Yatsymirskyy
Keyword(s):  
Statistical Analysis ◽  
Image Encryption ◽  
Experimental Studies ◽  
Quality Measures ◽  
Input Image ◽  
Jpeg Compression ◽  
Image Statistics ◽  
Compression Stage ◽  
Wide Range ◽  
The Impact

In this paper, the authors analyze in more details an image encryption scheme, proposed by the authors in their earlier work, which preserves input image statistics and can be used in connection with the JPEG compression standard. The image encryption process takes advantage of fast linear transforms parametrized with private keys and is carried out prior to the compression stage in a way that does not alter those statistical characteristics of the input image that are crucial from the point of view of the subsequent compression. This feature makes the encryption process transparent to the compression stage and enables the JPEG algorithm to maintain its full compression capabilities even though it operates on the encrypted image data. The main advantage of the considered approach is the fact that the JPEG algorithm can be used without any modifications as a part of the encrypt-then-compress image processing framework. The paper includes a detailed mathematical model of the examined scheme allowing for theoretical analysis of the impact of the image encryption step on the effectiveness of the compression process. The combinatorial and statistical analysis of the encryption process is also included and it allows to evaluate its cryptographic strength. In addition, the paper considers several practical use-case scenarios with different characteristics of the compression and encryption stages. The final part of the paper contains the additional results of the experimental studies regarding general effectiveness of the presented scheme. The results show that for a wide range of compression ratios the considered scheme performs comparably to the JPEG algorithm alone, that is, without the encryption stage, in terms of the quality measures of reconstructed images. Moreover, the results of statistical analysis as well as those obtained with generally approved quality measures of image cryptographic systems, prove high strength and efficiency of the scheme’s encryption stage.

scholarly journals Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Alexey Bondar ◽  
Olga Rybakova ◽  
Josef Melcr ◽  
Jan Dohnálek ◽  
Petro Khoroshyy ◽  
...  
Keyword(s):  
Biological Systems ◽  
Linear Dichroism ◽  
Quantitative Information ◽  
Living Cells ◽  
Software Tools ◽  
Model Systems ◽  
Membrane Properties ◽  
Polarization Microscopy ◽  
Molecular Processes ◽  
Wide Range

AbstractFluorescence-detected linear dichroism microscopy allows observing various molecular processes in living cells, as well as obtaining quantitative information on orientation of fluorescent molecules associated with cellular features. Such information can provide insights into protein structure, aid in development of genetically encoded probes, and allow determinations of lipid membrane properties. However, quantitating and interpreting linear dichroism in biological systems has been laborious and unreliable. Here we present a set of open source ImageJ-based software tools that allow fast and easy linear dichroism visualization and quantitation, as well as extraction of quantitative information on molecular orientations, even in living systems. The tools were tested on model synthetic lipid vesicles and applied to a variety of biological systems, including observations of conformational changes during G-protein signaling in living cells, using fluorescent proteins. Our results show that our tools and model systems are applicable to a wide range of molecules and polarization-resolved microscopy techniques, and represent a significant step towards making polarization microscopy a mainstream tool of biological imaging.

scholarly journals Regulation of Cytochrome c Oxidase by Natural Compounds Resveratrol, (–)-Epicatechin, and Betaine

Cells ◽  
2021 ◽  
Vol 10 (6) ◽  
pp. 1346
Author(s):  
Icksoo Lee
Keyword(s):  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Model Systems ◽  
Health Improvement ◽  
Published Data ◽  
Mitochondrial Electron Transport Chain ◽  
Naturally Occurring ◽  
Transport Chain ◽  
Wide Range ◽  
Experimental Model Systems

Numerous naturally occurring molecules have been studied for their beneficial health effects. Many compounds have received considerable attention for their potential medical uses. Among them, several substances have been found to improve mitochondrial function. This review focuses on resveratrol, (–)-epicatechin, and betaine and summarizes the published data pertaining to their effects on cytochrome c oxidase (COX) which is the terminal enzyme of the mitochondrial electron transport chain and is considered to play an important role in the regulation of mitochondrial respiration. In a variety of experimental model systems, these compounds have been shown to improve mitochondrial biogenesis in addition to increased COX amount and/or its enzymatic activity. Given that they are inexpensive, safe in a wide range of concentrations, and effectively improve mitochondrial and COX function, these compounds could be attractive enough for possible therapeutic or health improvement strategies.

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