scholarly journals The frugivorous insectivores? Functional morphological analysis of molar topography for inferring diet in extant treeshrews (Scandentia)

2019 ◽  
Author(s):  
Keegan R Selig ◽  
Eric J Sargis ◽  
Mary T Silcox
Keyword(s):  
Fast Food ◽  
Three Dimensional ◽  
Dental Morphology ◽  
Transit Times ◽  
Primate Origins ◽  
Modern Analogue ◽  
In The Wild ◽  
Alternative Means ◽  
Close Relatives ◽  
Dirichlet Normal Energy

Abstract The ecology, and particularly the diet, of treeshrews (order Scandentia) is poorly understood compared to that of their close relatives, the primates. This stems partially from treeshrews having fast food transit times through the gut, meaning fecal and stomach samples only represent a small portion of the foodstuffs consumed in a given day. Moreover, treeshrews are difficult to observe in the wild, leading to a lack of observational data in the literature. Although treeshrews are mixed feeders, consuming both insects and fruit, it is currently unknown how the relative importance of these food types varies across Scandentia. Previous study of functional dental morphology has provided an alternative means for understanding the diet of living euarchontans. We used dental topographic metrics to quantify aspects of functional dental morphology in a large sample of treeshrews (n = 58). We measured relief index, Dirichlet normal energy, and three-dimensional orientation patch count rotated, which quantify crown relief, occlusal curvature, and complexity, respectively. Our results suggest that treeshrews exhibit dental morphology consistent with high levels of insectivory relative to other euarchontans. They also suggest that taxa such as Dendrogale melanura and Tupaia belangeri appear to be best suited to insectivory, whereas taxa such as T. palawanensis and T. gracilis appear to be best adapted to frugivory. Our results suggest that Ptilocercus lowii is characterized by a dentition better adapted to insectivory than the early primate Purgatorius. If P. lowii represents a good modern analogue for primitive euarchontans, this contrast would support models of primate origins that include a shift to greater frugivory.

scholarly journals Deciphering the Role of Residues Involved in Disorder-To-Order Transition Regions in Archaeal tRNA Methyltransferase 5

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 399
Author(s):  
Ambuj Srivastava ◽  
Dhanusha Yesudhas ◽  
Shandar Ahmad ◽  
M. Michael Gromiha
Keyword(s):  
Three Dimensional ◽  
Md Simulations ◽  
Order Transition ◽  
Free Form ◽  
Wild Type ◽  
Intrinsically Disordered ◽  
Intrinsically Disordered Regions ◽  
Type Complex ◽  
In The Wild ◽  
Trna Methyltransferase

tRNA methyltransferase 5 (Trm5) enzyme is an S-adenosyl methionine (AdoMet)-dependent methyltransferase which methylates the G37 nucleotide at the N1 atom of the tRNA. The free form of Trm5 enzyme has three intrinsically disordered regions, which are highly flexible and lack stable three-dimensional structures. These regions gain ordered structures upon the complex formation with tRNA, also called disorder-to-order transition (DOT) regions. In this study, we performed molecular dynamics (MD) simulations of archaeal Trm5 in free and complex forms and observed that the DOT residues are highly flexible in free proteins and become stable in complex structures. The energetic contributions show that DOT residues are important for stabilising the complex. The DOT1 and DOT2 are mainly observed to be important for stabilising the complex, while DOT3 is present near the active site to coordinate the interactions between methyl-donating ligands and G37 nucleotides. In addition, mutational studies on the Trm5 complex showed that the wild type is more stable than the G37A tRNA mutant complex. The loss of productive interactions upon G37A mutation drives the AdoMet ligand away from the 37th nucleotide, and Arg145 in DOT3 plays a crucial role in stabilising the ligand, as well as the G37 nucleotide, in the wild-type complex. Further, the overall energetic contribution calculated using MMPBSA corroborates that the wild-type complex has a better affinity between Trm5 and tRNA. Overall, our study reveals that targeting DOT regions for binding could improve the inhibition of Trm5.

scholarly journals Isolation and Characterization of Mutations in theEscherichia coli Regulatory Protein XapR

1999 ◽  
Vol 181 (14) ◽  
pp. 4397-4403 ◽  
Author(s):  
Casper Jørgensen ◽  
Gert Dandanell
Keyword(s):  
Amino Acids ◽  
Purine Nucleoside Phosphorylase ◽  
Mutational Analysis ◽  
Regulatory Protein ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Wild Type ◽  
Isolation And Characterization ◽  
In The Wild

ABSTRACT In this work, the LysR-type protein XapR has been subjected to a mutational analysis. XapR regulates the expression of xanthosine phosphorylase (XapA), a purine nucleoside phosphorylase inEscherichia coli. In the wild type, full expression of XapA requires both a functional XapR protein and the inducer xanthosine. Here we show that deoxyinosine can also function as an inducer in the wild type, although not to the same extent as xanthosine. We have isolated and characterized in detail the mutants that can be induced by other nucleosides as well as xanthosine. Sequencing of the mutants has revealed that two regions in XapR are important for correct interactions between the inducer and XapR. One region is defined by amino acids 104 and 132, and the other region, containing most of the isolated mutations, is found between amino acids 203 and 210. These regions, when modelled into the three-dimensional structure of CysB from Klebsiella aerogenes, are placed close together and are most probably directly involved in binding the inducer xanthosine.

Internal reconstruction of elephantid molars: applications for functional anatomy and systematics

Paleobiology ◽  
1995 ◽  
Vol 21 (3) ◽  
pp. 379-392 ◽  
Author(s):  
David J. Froehlich ◽  
Jon E. Kalb
Keyword(s):  
Functional Anatomy ◽  
Three Dimensional ◽  
Dental Morphology ◽  
Systematic Analysis ◽  
Functional Studies ◽  
Three Dimensional Modeling ◽  
Dimensional Modeling ◽  
The Family ◽  
Replacement Pattern ◽  
Unique Manner

The unique manner in which molars from members of the family Elephantidae erupt in the jaw and wear obliquely and sequentially has profound effects upon dental function and phylogenetic change within the group. Three-dimensional modeling using a “molar matrix” of elephantid dentition, and application of such models to systematic and functional studies, allows a more refined description of dental morphology. A method of examining variation within elephantid teeth is presented based on successive staging of worn molars. Results indicate that individual plates exhibit increasingly derived features with wear (relative to the systematic analysis used here), while successively worn plates exhibit successively more plesiomorphic features apically and posteriorly. Further, results indicate that the patterns developed by wear on the surface of elephantid molars are conserved throughout life despite their unique successive replacement pattern. The cheek teeth in a molar series act as a single, continuous masticating unit, here termed a “cheek tooth battery.” Overall, the tools developed here, wear staging and molar matrices, allow for a more refined understanding of morphological variation within and between elephantids, with application to more conservative elephantoid taxa.

scholarly journals Virome of Bat Guano from Nine Northern California Roosts

2020 ◽  
Author(s):  
Yanpeng Li ◽  
Eda Altan ◽  
Gabriel Reyes ◽  
Brian Halstead ◽  
Xutao Deng ◽  
...  
Keyword(s):  
Animal Species ◽  
Amino Acid Identity ◽  
Wide Distribution ◽  
Mouse Kidney ◽  
Northern California ◽  
Dna Viruses ◽  
Viral Genomes ◽  
In The Wild ◽  
Close Relatives ◽  
Viral Sequences

Bats are hosts to a large variety of viruses, including many capable of cross species transmissions to other mammals or humans. We characterized the virome in guano from five common bat species in 9 Northern California roosts and a pool of 5 individual bats. Genomes belonging to 14 viral families known to infect mammals and 17 viral families infecting insects or of unknown tropism were detected. Near or complete genomes of a novel parvovirus, astrovirus, nodavirus, CRESS-DNA viruses and densoviruses and more partial genomes of a novel alphacoronavirus, and bunyavirus were characterized. Lower numbers of reads with >90% amino acid identity to previously described calicivirus, circovirus, adenoviruses, hepatovirus, bocaparvoviruses, and polyomavirus in other bat species were also found likely reflecting their wide distribution among different bats. Unexpectedly a few sequence reads of canine parvovirus 2 and the recently described mouse kidney parvovirus were also detected and their presence confirmed by PCR possibly originating from guano contamination by carnivores and rodents. The majority of eukaryotic viral reads were highly divergent indicating that numerous viruses still remain to be characterized even from such a heavily investigated order as Chiroptera. IMPORTANCE Characterizing the bat virome is important for understanding viral diversity and detecting viral spillover between animal species. Using unbiased metagenomics method, we characterize the virome in guano collected from multiple roosts of common Northern California bat species. We describe several novel viral genomes and report the detection of viruses with close relatives reported in other bat species likely reflecting cross-species transmissions. Viral sequences from well-known carnivore and rodent parvoviruses were also detected whose presence are likely the result of contamination from defecation and urination atop guano and reflect the close interaction of these mammals in the wild.

Effect of ingestion by two frugivorous bat species on the seed germination of Ficus racemosa and F. hispida (Moraceae)

2007 ◽  
Vol 23 (1) ◽  
pp. 125-127 ◽  
Author(s):  
Zhan-Hui Tang ◽  
Aeshita Mukherjee ◽  
Lian-Xi Sheng ◽  
Min Cao ◽  
Bing Liang ◽  
...  
Keyword(s):  
Seed Germination ◽  
Digestive Tract ◽  
Plant Species ◽  
Transit Times ◽  
In The Wild ◽  
Ficus Racemosa ◽  
Seed Dispersers

Frugivorous bats are important seed dispersers for many plant species (Cox et al. 1991, Fleming & Heithaus 1981, Hodgkison et al. 2003a, McConkey & Drake 2006, Nyhagen et al. 2005, Utzurrum 1995). They regularly consume figs in the wild (Fujita & Tuttle 1991, Kalko et al. 1996, Shilton et al. 1999). Various species of pteropodid bats have been reported foraging on the fruits of more than 30 fig species in tropical and subtropical Asia, Africa and Australia (Bhat 1994, Fujita & Tuttle 1991, Marshall & McWilliam 1982, Thomas 1984). Food transit times in frugivorous bats are relatively rapid; generally less than 30 min (Laska 1990, Tedman & Hall 1985). Several studies have demonstrated that seed germination was either enhanced or unaffected after passage through the digestive tract of bats (Figueiredo & Perin 1995, Fleming & Heithaus 1981, Lieberman & Lieberman 1986).

Turbulent relaxation of a confined magnetofluid to a force-free state

1987 ◽  
Vol 37 (2) ◽  
pp. 299-321 ◽  
Author(s):  
Jill P. Dahlburg ◽  
David Montgomery ◽  
Gary D. Doolen ◽  
Leaf Turner
Keyword(s):  
Magnetic Field ◽  
Energy State ◽  
Minimum Energy ◽  
Three Dimensional ◽  
Small Scale ◽  
Current Profile ◽  
Transit Times ◽  
Uniform Current ◽  
Scale Turbulence ◽  
Pseudo Spectral

Three-dimensional, pseudo-spectral computation is used to follow the evolution of a resistive, incompressible magnetofluid. The magnetofluid is confined by rigid, free-slip, perfectly-conducting square boundaries in the x, y directions (‘poloidal’ boundaries), and periodic boundary conditions are assumed in the z direction (‘toroidal’ direction). A constant, uniform d.c. magnetic field B0 is assumed in the z direction and a non-uniform current density j flows along it initially. Starting from a non-equilibrium hollow current profile, the evolution is followed for several tens of Alfvén transit times. Considerable small-scale turbulence develops, which causes energy to decay more rapidly than magnetic helicity. The average toroidal magnetic field at the (x, y) boundary reverses sign spontaneously. The near spatial constancy of the ratio jB/(jB) ≡ cos θ, in the relaxed state at late times, suggests that the state is nearly force-free. However, the ratio j. B/B2 ≡ α is considerably less uniform than is cos θ suggesting more residual disorder than a pure minimum-energy state would display.

scholarly journals A three-dimensional habitat for C. elegans environmental enrichment

PLoS ONE ◽  
2021 ◽  
Vol 16 (1) ◽  
pp. e0245139
Author(s):  
Aurélie Guisnet ◽  
Malosree Maitra ◽  
Sreeparna Pradhan ◽  
Michael Hendricks
Keyword(s):  
Environmental Enrichment ◽  
Expression Patterns ◽  
Three Dimensional ◽  
Model Organisms ◽  
Initial Assessment ◽  
C Elegans ◽  
Laboratory Conditions ◽  
In The Wild ◽  
And Behaviors ◽  
Microbial Environment

As we learn more about the importance of gene-environment interactions and the effects of environmental enrichment, it becomes evident that minimalistic laboratory conditions can affect gene expression patterns and behaviors of model organisms. In the laboratory, Caenorhabditis elegans is generally cultured on two-dimensional, homogeneous agar plates abundantly covered with axenic bacteria culture as a food source. However, in the wild, this nematode thrives in rotting fruits and plant stems feeding on bacteria and small eukaryotes. This contrast in habitat complexity suggests that studying C. elegans in enriched laboratory conditions can deepen our understanding of its fundamental traits and behaviors. Here, we developed a protocol to create three-dimensional habitable scaffolds for trans-generational culture of C. elegans in the laboratory. Using decellularization and sterilization of fruit tissue, we created an axenic environment that can be navigated throughout and where the microbial environment can be strictly controlled. C. elegans were maintained over generations on this habitat, and showed a clear behavioral bias for the enriched environment. As an initial assessment of behavioral variations, we found that dauer populations in scaffolds exhibit high-frequency, complex nictation behavior including group towering and jumping behavior.

scholarly journals A System for the Acquisition and Analysis of Three-Dimensional Data Describing Dental Morphology

2018 ◽  
Vol 17 (3) ◽  
pp. 70-74 ◽  
Author(s):  
Pingzhou Liu ◽  
Sarbin Ranjitkar ◽  
John A. Kaidonis ◽  
Grant C. Townsend ◽  
Lindsay C. Richards
Keyword(s):  
Three Dimensional ◽  
Tooth Wear ◽  
Technical Note ◽  
Personal Computers ◽  
Dental Morphology ◽  
3D Data ◽  
Coefficients Of Variation ◽  
Potential Applications ◽  
Derived Data ◽  
3D Profilometer

Accurate, reproducible three-dimensional (3D) data provide an important contribution to our ability to describe, compare and understand dental morphology but the existing technology is often expensive or has technical limitations. Recently available, inexpensive 3D profilometers interfaced with standard personal computers offer the potential to overcome some of these problems. This technical note describes a system that uses a 3D profilometer and purpose written software to analyse changes in dental morphology resulting from tooth wear. The validity of the derived data was determined by comparing data derived from scans of objects of known dimensions with calculated volumes. These differences were less than 10% from objects that were difficult to scan because of their geometry and were commonly less than 5%. The reproductibility, expressed as intra- and inter-observer coefficients of variation, was less than 1%. The potential applications of systems of this type are outlined.

scholarly journals Dissolved Radiotracers and Numerical Modeling in North European Continental Shelf Dispersion Studies (1982–2016): Databases, Methods and Applications

Water ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 1667 ◽  
Author(s):  
Pascal Bailly du Bois ◽  
Franck Dumas ◽  
Claire Voiseux ◽  
Mehdi Morillon ◽  
Pierre-Emmanuel Oms ◽  
...  
Keyword(s):  
Continental Shelf ◽  
Three Dimensional ◽  
Nuclear Industry ◽  
Hydrodynamic Models ◽  
Anthropogenic Radionuclides ◽  
The North ◽  
Transit Times ◽  
Quantitative Results ◽  
Types Of Information ◽  
Model Measurement

Significant amounts of anthropogenic radionuclides were introduced in ocean waters following nuclear atmospheric tests and development of the nuclear industry. Dispersion of artificial dissolved radionuclides has been extensively measured for decades over the North-European continental shelf. In this area, the radionuclide measurement and release fluxes databases provided here between 1982 and 2016 represent an exceptional opportunity to validate dispersion hydrodynamic models. This work gives accessibility to these data in a comprehensive database. The MARS hydrodynamic model has been applied at different scales to reproduce the measured dispersion in realistic conditions. Specific methods have been developed to obtain qualitative and quantitative results and perform model/measurement comparisons. Model validation concerns short to large scales with dedicated surveys following the dispersion: it was performed within a two- and three-dimensional framework and from minutes and hours following a release up to several years. Results are presented concerning the dispersion of radionuclides in marine systems deduced from standalone measurements, or according to model comparisons. It allows characterizing dispersion over the continental shelf, pathways, transit times, budgets and source terms. This review presents the main approaches developed and types of information derived from studies of artificial radiotracers using observations, hydrodynamic models or a combination of the two, based primarily on the new featured datasets.

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