China
Africa
Explore chapters and articles related to this topic
Chloroplast DNA and Phylogenetic Relationships
Published in S. K. Dutta, DNA Systematics, 2019
In spite of the large number of studies that have exploited chloroplast DNA restriction fragment variation for phylogenetic purposes, there has been relatively little effort in developing methods for constructing phylogenetic trees from this variation. Hence, the following discussion will focus on the methodology for phylogenetic reconstruction used by the author and his collaborators,19,20,23,28 The approach taken in these studies is essentially cladistic in nature. Each restriction site mutation, and in one case also length mutation and inversion,23 is treated as a separate character. The principle of parsimony29,30 is used to construct phylogenetic trees in which the total number of independent mutations required to account for the observed distribution of different states of these characters is minimized.31–34
The Role of the Computer in Estimates of DNA Nucleotide Sequence Divergence
Published in S. K. Dutta, DNA Systematics, 2019
In general, the process of constructing a phylogenetic tree consists of taking sequences and considering where they may be added to a proposed tree to result in the maximization or minimization of some criterion. The algorithms move through the tree, rearranging where necessary to generate an improvement. There are three major approaches to the prediction of phylogenetic trees: methods using parsimony, methods based on compatibility, and maximum likelihood approaches. It should be noted that parsimony is strictly an heuristic principle, based on no mathematical or statistical foundation, and that results obtained using this approach do not guarantee the generation of the unique phylogenetic tree. On the other hand, compatibility methods are based on the well-known phenomenon that different data sets, or the order in which the individual sequences in a given data set are used for the analysis, can lead to different phylogenies. Indeed, compatibility, or preferably, incompatibility, has been mathematically proven by Estabrook et al.65 and others. Although proven for cladistic characters, its application to sequences is clear, as long as parallelism is not too great.41
The ecological context
Published in Loretta A. Cormier, Pauline E. Jolly, The Primate Zoonoses, 2017
Loretta A. Cormier, Pauline E. Jolly
Colloquially, primates are divided into four categories: humans, monkeys, apes, and prosimians. Two taxonomic conventions exist for dividing the two suborders of primates, which differ in where the tarsiers are placed. The tarsiers are similar to the prosimians in terms of their behavioral ecology, but are evolutionarily more closely related to monkeys, apes, and humans. In gradistic classification, the tarsiers are grouped with the suborder “Prosimii” with the lemurs and lorises; all other primates are grouped under “Anthropoidea.” In cladistic classification, the tarsiers are grouped in the suborder “Haplorrhini” with monkeys, apes, and humans, while the suborder “Strepsirrhini” only contains the lemurs and lorises. The terms strepsirrhine and haplorrhine refer specifically to nose morphology (wet versus dry rhinarium), which is one of the features that separate the lemurs and lorises from the other primates.
Immunodominant regions prediction of nucleocapsid protein for SARS-CoV-2 early diagnosis: a bioinformatics and immunoinformatics study
Published in Pathogens and Global Health, 2020
Yufeng Dai, Hongzhi Chen, Siqi Zhuang, Xiaojing Feng, Yiyuan Fang, Haoneng Tang, Ruchun Dai, Lingli Tang, Jun Liu, Tianmin Ma, Guangming Zhong
Influenza virus infection causes respiratory symptoms similar to COVID-19, which makes it difficult to distinguish the diseases by symptoms [45]. Hence, we compared the N protein sequences between the influenza virus and SARS-CoV-2 (File S2). The results showed that the sequence similarity is low, which suggested that direct detection of N protein could distinguish COVID-19 from influenza virus infection. Besides, we noticed that the full-length N protein of SARS-CoV-2 may cross-react with the serum of patients infected with SARS-CoV [4], while truncated protein was proved to reduce the cross-reactivity without reducing sensitivity [46,47]. Hence, we chose to use truncated recombinant protein rather than the full-length N protein for developing diagnostic antibodies. Recently, cladistic studies based on N protein sequence of SARS-CoV-2 have been reported [48–51]. None of the reported mutations are located in the selected immunodominant regions of the current study (data not shown). Nevertheless, attention should be paid to the diagnostic efficiency of mAbs derived from the fragments of SARS-CoV-2 N protein, which need to be evaluated by experiments.
Proteomes of the past: the pursuit of proteins in paleontology
Published in Expert Review of Proteomics, 2019
As novel and even unforeseen technologies find application in this field, it is our opinion that an increasing weight of evidence will enable researchers to move beyond questions of the mere existence of biomolecular remnants in fossils to reveal unanticipated and fundamental connections across fields including taphonomy, geochemistry, diagenesis, and cladistics. So far, the protein collagen has received attention partly because of its widespread natural abundance in living things, its resistance to degradation over long periods and the relative ease by which it may be detected. As techniques progress, other less abundant and more ephemeral proteins such as globin may become the focus of greater attention.
On Who Matters—and Why
Published in AJOB Neuroscience, 2023
However, what animals kindle within us rests not just on our improving awareness of their neurology and potential for consciousness. We’re also woven together in cultures often deeply rooted in living alongside one another. Even in city offices, people still quip about being as stubborn as a mule or like a bear with a sore head. These roots are exposed too in cladistic trees that trace the evolution of the tale widely known as “Little Red Riding Hood” (Tehrani 2013). While precise animal and human roles mutate in its passage around the world, the tale still feels recognizable—perhaps because, whether as shared fears or thirst for retribution, the affective persists.