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Topic Review
Bird’s-Eye View of Chromosomic Evolution in Class Aves
Birds (Aves) are the most speciose of terrestrial vertebrates, displaying Class-specific characteristics yet incredible external phenotypic diversity. Critical to agriculture and as model organisms, birds have adapted to many habitats. The only extant examples of dinosaurs, birds emerged ~150 mya and >10% are currently threatened with extinction.
  • 94
  • 28 Feb 2024
Topic Review
Transgenderizations of the Collective Psyche of Humanity
The evolving collective psyche of humanity reveals a shift from predominantly masculine to increasingly feminine characteristics since around 1500 A.D. This transformation, termed 'transgenderization,' is attributed to identified psychological factors. Remarkably, the collective psyche has undergone similar transitions in the past since the emergence of humanity.
  • 102
  • 21 Feb 2024
Topic Review
Insights into AMR Mechanisms from Laboratory Evolution
Laboratory evolution studies provide invaluable insights into the dynamic landscape of resistance, revealing intricate details about the evolutionary trajectories, population dynamics, and metabolic adaptations shaping bacterial responses to drug exposure. The complex interplay of cross-resistance and collateral sensitivity in the evolution of antimicrobial resistance (AMR) has been intensively analyzed using E. coli as a model bacterium.
  • 183
  • 05 Feb 2024
Topic Review
Zinc in Modern and Fossil Hominoid Teeth
Teeth begin to grow in the jaws before birth and continue to appear in an overlapping sequence until each is complete in length. Subsequently, the central pulp (nerve) chamber of each tooth slowly fills in with dentine and the root of the tooth continues to accumulate thin layers of cementum until the individual dies. Each of the tooth tissues, the hard enamel cap, the dentine core of the tooth and the root cementum grow incrementally and incorporate small quantities of blood-born trace elements ingested from our diet into their structure. A chronological record of zinc incorporation exists in each tooth tissue and can be visualised in thin sections, or slices, of teeth using a beam of synchrotron light. Zinc markings in teeth are especially useful and occur at birth in enamel and dentine and annually in the cementum layers. This work shows that zinc is consistently concentrated within surface enamel and in the dentine surrounding the central pulp chamber. Knowing where to sample Zn in modern and fossil teeth enables us to reconstruct a chronology of growth and to determine something about diet in the past from the remnants of different Zn isotopes contained in different foodstuffs.
  • 147
  • 12 Dec 2023
Topic Review
Directed Cycles Evolve with Junk DNA
Cell responses are usually viewed as transitive events with fixed inputs and outputs that are regulated by feedback loops. In contrast, directed cycles (DCs) have all nodes connected, and the flow is in a single direction. Consequently, DCs can regenerate themselves and implement intransitive logic. DCs are able to couple unrelated chemical reactions to each edge. The output depends upon which node is used as input.
  • 145
  • 22 Nov 2023
Topic Review
Retrovirus-Derived RTL/SIRH Genes in Eutherian Developmental System
Eutherians have 11 retrotransposon Gag-like (RTL)/sushi-ichi retrotransposon homolog (SIRH) genes presumably derived from a certain retrovirus. Accumulating evidence indicates that the RTL/SIRH genes play a variety of roles in the mammalian developmental system, such as in the placenta, brain, and innate immune system, in a eutherian-specific manner. It has been shown that the functional role of Paternally Expressed 10 (PEG10) in placental formation is unique to the therian mammals, as are the eutherian-specific roles of PEG10 and PEG11/RTL1 in maintaining the fetal capillary network and the endocrine regulation of RTL7/SIRH7 (aka Leucine Zipper Down-Regulated in Cancer 1 (LDOCK1)) in the placenta. In the brain, PEG11/RTL1 is expressed in the corticospinal tract and hippocampal commissure, mammalian-specific structures, and in the corpus callosum, a eutherian-specific structure. Unexpectedly, at least three RTL/SIRH genes, RTL5/SIRH8, RTL6/SIRH3, and RTL9/SIRH10, play important roles in combating a variety of pathogens, namely viruses, bacteria, and fungi, respectively, suggesting that the innate immunity system of the brain in eutherians has been enhanced by the emergence of these new components. 
  • 156
  • 25 Oct 2023
Topic Review
Genetic Requirement for Minimal Genome
Genome reduction is a top-down approach to achieve the minimal genetic information essential for a living cell. Exploring the minimal genetic requirements for cells to maintain free living is an exciting topic in biology. Multiple approaches are employed to address the question of the minimal genome. In addition to constructing the synthetic genome in the test tube, reducing the size of the wild-type genome is a practical approach for obtaining the essential genomic sequence for living cells. The well-studied Escherichia coli has been used as a model organism for genome reduction owing to its fast growth and easy manipulation.
  • 124
  • 06 Sep 2023
Topic Review
Cenancestor
Cenancestor, the last universal cellular ancestor (LUCA), is assumed to exist on the basis of extensive sharing of inferred homologous characters among representatives of living cellular organisms. These characters include the near universal genetic code, the concordance of phylogenetic trees from different genes, the sharing of fundamental biochemical processes and the existence of numerous transitional fossils. A cenancestor is a logical necessity if the cellular structure originated only once, given the cell theory stating that news cells are created by old cells dividing into two. The recent empirical search for the cenancestor started with the prediction that eukaryotes could not possibly have evolved from the common ancestor of extant bacterial species. This led to the discovery of Archaebacteria and the three domains of life. Archaebacteria was found to be "archae" only to eukaryotes and consequently renamed to Archaea. The molecular substantiation of the endosymbiotic hypothesis of mitochondrial and chloroplast origin led to the hypothesis that the nucleus in eukaryotes is also an organelle originating from endosymbiosis or cell fusion, followed by massive horizontal gene transfer (HGT) between an engulfing host and engulfed guests which serve as mitochondrial and chloroplast progenitors. The cenancestor is expected to coexist with a variety of viruses that may mediate HGT to bring heterogeneous genomes together. This virus-mediated and plasmid-mediated genomic assembly and exchange could abolish one major difficulty in creating endosymbiotic genomes, i.e., the need of primitive cells engulfing each other – a difficult feat if they had cell walls.
  • 214
  • 05 Sep 2023
Topic Review
Sex Determination and Differentiation in Southern Swordtail Fishes
Southern swordtail fishes, which belong to the viviparous teleosts called Xiphophorus, are unique models for studies of evolution of sex chromosomes. Monofactorial sex-determining systems, with either the male or the female being the heterogametic sex, as well as sex determination involving more than two sex chromosomes, are found in swordtails and related species. Some swordtail species seem to have originated by crossing between two closely related species. Although the sword has disappeared in many Xiphophorus species during evolution, females of non-sworded species still prefer sworded males, demonstrating a discrepancy between natural and sexual selection. Natural sex change has not been documented sufficiently convincingly in swordtails, but, at least in some subspecies, two or more male phenotypes exist.
  • 201
  • 14 Aug 2023
Topic Review Video Peer Reviewed
The Domestication of Humans
The domestication of humans is not an issue of domesticity but of the effects of the domestication syndrome on a hominin species and its genome. These effects are well expressed in the ‘anatomically modern humans’, in their physiology, behavior, genetic defects, neuropathology, and distinctive neoteny. The physiological differences between modern (gracile) humans and their ancestors, robust Homo sapiens types, are all accounted for by the domestication syndrome. From deductions we can draw about early human behavior, it appears that modifications are attributable to the same cause. The domestication hypothesis ascribes the initiation of the changes to selective breeding introduced by the consistent selection of neotenous features. That would trigger genetic pleiotropy, causing the changes that are observed.
  • 414
  • 31 Jul 2023
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