scholarly journals A New Integrated Tool to Calculate and Map Bilateral Asymmetry on Three-Dimensional Digital Models

Symmetry ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1644
Author(s):  
Marina Melchionna ◽  
Antonio Profico ◽  
Costantino Buzi ◽  
Silvia Castiglione ◽  
Alessandro Mondanaro ◽  
...  
Keyword(s):  
Homo Sapiens ◽  
Three Dimensional ◽  
Directional Asymmetry ◽  
Evolutionary Significance ◽  
Fossil Species ◽  
R Language ◽  
Genus Homo ◽  
Digital Restoration ◽  
Low Levels ◽  
Living Organisms

The observation and the quantification of asymmetry in biological structures are deeply investigated in geometric morphometrics. Patterns of asymmetry were explored in both living and fossil species. In living organisms, levels of directional and fluctuating asymmetry are informative about developmental processes and health status of the individuals. Paleontologists are primarily interested in asymmetric features introduced by the taphonomic process, as they may significantly alter the original shape of the biological remains, hampering the interpretation of morphological features which may have profound evolutionary significance. Here, we provide a new R tool that produces the numerical quantification of fluctuating and directional asymmetry and charts asymmetry directly on the specimens under study, allowing the visual inspection of the asymmetry pattern. We tested this show.asymmetry algorithm, written in the R language, on fossil and living cranial remains of the genus Homo. show.asymmetry proved successful in discriminating levels of asymmetry among sexes in Homo sapiens, to tell apart fossil from living Homo skulls, to map effectively taphonomic distortion directly on the fossil skulls, and to provide evidence that digital restoration obliterates natural asymmetry to unnaturally low levels.

Hominin transition to Upper Pliocene

2017 ◽  
Author(s):  
Francisco J. Ayala ◽  
Camilo J. Cela-Conde
Keyword(s):  
Brain Development ◽  
Late Pleistocene ◽  
Technological Progress ◽  
Homo Sapiens ◽  
Middle Pleistocene ◽  
Evolutionary Significance ◽  
Australopithecus Afarensis ◽  
Phylogenetic Significance ◽  
Homo Neanderthalensis ◽  
Surprising Discovery

This chapter analyzes the transition of the hominins from the Middle Pleistocene to the Late Pleistocene. Two alternative models are explored, the “Multiregional Hypothesis” (MH) and the “Replacement Hypothesis,” and how each model evaluates the existing relationships between the taxa Homo neanderthalensis and Homo sapiens. Next is the investigation of the transitional (or “archaic,” if this grade is taken into account) exemplars found in Europe, Africa, and Asia and their evolutionary significance. In particular, the comparison between H. erectus and H. sapiens in China and Java is investigated, as the main foundation of the MH. The chapter ends with the surprising discovery of Homo floresiensis and its description and interpretations concerning its taxonomic and phylogenetic significance. The correlation between brain development and technological progress is at odds with the attribution of perforators, microblades, and fishing hooks to a hominin with a small cranial volume, similar to that of Australopithecus afarensis.

scholarly journals Towards More Realistic Leaf Shapes in Functional-Structural Plant Models

Symmetry ◽  
2018 ◽  
Vol 10 (7) ◽  
pp. 278 ◽  
Author(s):  
Dominik Schmidt ◽  
Katrin Kahlen
Keyword(s):  
Fluctuating Asymmetry ◽  
Leaf Shape ◽  
Three Dimensional ◽  
Directional Asymmetry ◽  
The Novel ◽  
Shape Model ◽  
Plant Model ◽  
Virtual Plant ◽  
Perfect Symmetry

Fluctuating asymmetry in plant leaves is a widely used measure in geometric morphometrics for assessing random deviations from perfect symmetry. In this study, we considered the concept of fluctuating asymmetry to improve the prototype leaf shape of the functional-structural plant model L-Cucumber. The overall objective was to provide a realistic geometric representation of the leaves for the light sensitive plant reactions in the virtual plant model. Based on three-dimensional data from several hundred in situ digitized cucumber leaves comparisons of model leaves and measurements were conducted. Robust Bayesian comparison of groups was used to assess statistical differences between leaf halves while respecting fluctuating asymmetries. Results indicated almost no directional asymmetry in leaves comparing different distances from the prototype while detecting systematic deviations shared by both halves. This information was successfully included in an improved leaf prototype and implemented in the virtual plant model L-Cucumber. Comparative virtual plant simulations revealed a slight improvement in plant internode development against experimental data using the novel leaf shape. Further studies can now focus on analyses of stress on the 3D-deformation of the leaf and the development of a dynamic leaf shape model.

Molecular Cloning and Structure Analysis of MpARF, an ADP-Ribosylation Factor in Monascus purpureus

2014 ◽  
Vol 884-885 ◽  
pp. 574-577
Author(s):  
Lan Gao ◽  
Bi Yun Zhu
Keyword(s):  
Homo Sapiens ◽  
Three Dimensional ◽  
Monascus Purpureus ◽  
Protein Fold ◽  
Dimensional Model ◽  
Three Dimensional Model ◽  
Gtp Hydrolysis ◽  
Adp Ribosylation ◽  
Vesicular Membrane ◽  
Adp Ribosylation Factor

ADP-ribosylation factors (ARF) are ubiquitous regulators of vesicular membrane traffic in all eukaryotic cells. A full-length cDNA encoding an ARF was cloned from the cDNA library ofMonascus purpureus. The cDNA was 1275 bp in length, contains a predicted 555 bp ORF that encodes 184 amino acids, the gene was designated MpARF. The deduced amino acid sequence showed high homology to ARF6 ofHomo sapiens, ARFB ofAspergillus nidulansand ARF3p ofSaccharomyces cerevisiae, including conserved N-terminal myristoylation site, GTP binding and GTP hydrolysis site, suggesting that the MpARF is a member of the ARF6 protein family. A typical G protein fold three-dimensional model of MpARF was built; the structure is similar to the structure of human ARF6. According to the functions of ARFB and ARF3p in fungi, we implicated that the MpARF would involved in hyphal polarized growth.

Natural history of ABC systems: not only transporters

2011 ◽  
Vol 50 ◽  
pp. 19-42 ◽  
Author(s):  
Elie Dassa
Keyword(s):  
Common Ancestor ◽  
Three Dimensional ◽  
Last Common Ancestor ◽  
Abc Proteins ◽  
Hypothetical Scenario ◽  
History Of ◽  
Phylogenetic Perspective ◽  
Living Organisms

In recent years, our understanding of the functioning of ABC (ATP-binding cassette) systems has been boosted by the combination of biochemical and structural approaches. However, the origin and the distribution of ABC proteins among living organisms are difficult to understand in a phylogenetic perspective, because it is hard to discriminate orthology and paralogy, due to the existence of horizontal gene transfer. In this chapter, I present an update of the classification of ABC systems and discuss a hypothetical scenario of their evolution. The hypothetical presence of ABC ATPases in the last common ancestor of modern organisms is discussed, as well as the additional possibility that ABC systems might have been transmitted to eukaryotes, after the two endosymbiosis events that led to the constitution of eukaryotic organelles. I update the functional information of selected ABC systems and introduce new families of ABC proteins that have been included recently into this vast superfamily, thanks to the availability of high-resolution three-dimensional structures.

scholarly journals 3D laser scanning and digital restoration of an archaeological find

2018 ◽  
Vol 178 ◽  
pp. 03013 ◽  
Author(s):  
Stergios Fragkos ◽  
Emanuel Tzimtzimis ◽  
Dimitrios Tzetzis ◽  
Oana Dodun ◽  
Panagiotis Kyratsis
Keyword(s):  
3D Printing ◽  
Laser Scanning ◽  
Three Dimensional ◽  
3D Laser Scanning ◽  
Analytical Methodology ◽  
3D Cad ◽  
Digital Restoration ◽  
Computer Based ◽  
Ancient Ceramic ◽  
Digital Archaeology

The current paper demonstrates the digital recreation and 3D printing of a missing fragment of an ancient ceramic pottery following digitization using a three dimensional laser scanning. The resulting pointcloud of the laser scans was treated with a series of advanced software for the creation of surfaces and ultimately for a digital model. An analytical methodology is presented revealing the step by step approach, which is an innovative way of recreating a missing fragment. Such approach aims to demonstrate the level of contribution that the ever evolving computer based technologies and 3D printing could bring to cultural heritage. The reverse engineering method presented for the reconstruction of a ceramic pottery, which is a part of the larger field of digital archaeology, is believed to benefit a variety of interested parties including 3D CAD users and designers, archaeologists and museum curators.

scholarly journals Modified HuffBit Compress Algorithm – An Application of R

2018 ◽  
Vol 15 (3) ◽  
Author(s):  
Nahida Habib ◽  
Kawsar Ahmed ◽  
Iffat Jabin ◽  
Mohammad Motiur Rahman
Keyword(s):  
Dna Sequences ◽  
Binary Tree ◽  
Deoxyribonucleic Acid ◽  
Repetitive Sequences ◽  
Huffman Codes ◽  
R Language ◽  
Living Organisms ◽  
Encoding Method ◽  
Dna Sequence Compression ◽  
Sequence Compression

Abstract The databases of genomic sequences are growing at an explicative rate because of the increasing growth of living organisms. Compressing deoxyribonucleic acid (DNA) sequences is a momentous task as the databases are getting closest to its threshold. Various compression algorithms are developed for DNA sequence compression. An efficient DNA compression algorithm that works on both repetitive and non-repetitive sequences known as “HuffBit Compress” is based on the concept of Extended Binary Tree. In this paper, here is proposed and developed a modified version of “HuffBit Compress” algorithm to compress and decompress DNA sequences using the R language which will always give the Best Case of the compression ratio but it uses extra 6 bits to compress than best case of “HuffBit Compress” algorithm and can be named as the “Modified HuffBit Compress Algorithm”. The algorithm makes an extended binary tree based on the Huffman Codes and the maximum occurring bases (A, C, G, T). Experimenting with 6 sequences the proposed algorithm gives approximately 16.18 % improvement in compression ration over the “HuffBit Compress” algorithm and 11.12 % improvement in compression ration over the “2-Bits Encoding Method”.

the cerebral torque and directional asymmetry for hand use are correlates of the capacity for language in homo sapiens

2005 ◽  
Vol 28 (4) ◽  
pp. 595-596 ◽  
Author(s):  
timothy j. crow
Keyword(s):  
Null Hypothesis ◽  
Homo Sapiens ◽  
Population Based ◽  
Directional Asymmetry ◽  
Neural Basis ◽  
Nonhuman Species

the claim of consistent hemispheric specialisations across classes of chordates is undermined by the absence of population-based directional asymmetry of paw/hand use in rodents and primates. no homologue of the cerebral torque from right frontal to left occipital has been established in a nonhuman species. the null hypothesis that the torque is the sapiens-specific neural basis of language has not been disproved.

Recognizing species of Late Cenozoic Scleractinia and their evolutionary patterns

1996 ◽  
Vol 1 ◽  
pp. 59-79 ◽  
Author(s):  
Ann F. Budd ◽  
Kenneth G. Johnson
Keyword(s):  
Three Dimensional ◽  
Cladistic Analysis ◽  
Biological Species ◽  
Similar Species ◽  
Two Dimensional ◽  
Multivariate Statistical ◽  
Fossil Species ◽  
Thin Sections ◽  
Landmark Data ◽  
Stratigraphic Ranges

New morphometric methods for distinguishing morphologically similar species of Recent colonial scleractinian corals involve the analysis of three dimensional landmarks digitized on calical surfaces. Variables suitable for multivariate statistical analysis are derived from the landmark data by applying various geometrical techniques, including Bookstein size and shape coordinates and generalized resistant fitting. Cluster analyses of these variables and study of the relative positions of replicates from the same colony on the resulting dendrograms are used to recognize clusters of colonies representing morphospecies. Comparisons with the results of genetic analyses on the same specimens suggest that these morphospecies correspond closely with biological species.Although slightly less effective, similar analyses of two dimensional landmark data collected on thin sections of the same specimens also distinguish species, and suggest that biological species can be approximated in the fossil record. Multivariate statistical analyses show that variables derived from two dimensional landmarks can be used to trace the stratigraphic ranges of these fossil species. The appropriate method for tracing ranges depends of the evenness of sampling in different geologic horizons. Preliminary comparisons of observed stratigraphic ranges determined by this approach with those determined by cladistic analysis suggest that overall patterns in evolutionary rates through geologic time are the same for both approaches. Thus, nontraditional morphologic characters determined by subsequent examination of morphometrically-defined species have potential for providing sufficient resolution for phylogenetic analysis.

scholarly journals Properties of Carotenoids in Fish Fitness: A Review

Marine Drugs ◽  
2020 ◽  
Vol 18 (11) ◽  
pp. 568
Author(s):  
Toshiki Nakano ◽  
Geert Wiegertjes
Keyword(s):  
Egg Quality ◽  
Fish Tissue ◽  
Feed Additives ◽  
Ros Production ◽  
Oxygen Species ◽  
Farmed Fish ◽  
Natural Pigments ◽  
Aquaculture Industry ◽  
Low Levels ◽  
Living Organisms

Carotenoids, one of the most common types of natural pigments, can influence the colors of living organisms. More than 750 kinds of carotenoids have been identified. Generally, carotenoids occur in organisms at low levels. However, the total amount of carotenoids in nature has been estimated to be more than 100 million tons. There are two major types of carotenoids: carotene (solely hydrocarbons that contain no oxygen) and xanthophyll (contains oxygen). Carotenoids are lipid-soluble pigments with conjugated double bonds that exhibit robust antioxidant activity. Many carotenoids, particularly astaxanthin (ASX), are known to improve the antioxidative state and immune system, resulting in providing disease resistance, growth performance, survival, and improved egg quality in farmed fish without exhibiting any cytotoxicity or side effects. ASX cooperatively and synergistically interacts with other antioxidants such as α-tocopherol, ascorbic acid, and glutathione located in the lipophilic hydrophobic compartments of fish tissue. Moreover, ASX can modulate gene expression accompanying alterations in signal transduction by regulating reactive oxygen species (ROS) production. Hence, carotenoids could be used as chemotherapeutic supplements for farmed fish. Carotenoids are regarded as ecologically friendly functional feed additives in the aquaculture industry.

Sign in / Sign up

Export Citation Format

Share Document