Homologous Elements Research Articles

Quantifying the configurational complexity of biological systems in multivariate 'complexity space'.

An increasing number of evolutionary studies seek to quantify the morphological complexity of organisms, particularly those comprising serially homologous elements at different hierarchical levels of organization. Numerous operational frameworks have been proposed for doing this, but most focus on one or multiple conflated aspects of what is really a multidimensional concept. Here, we advocate the use of 'complexity spaces': multidimensional spaces defined by different vectors of complexity. We explore their application to biological systems composed of homologous parts and identify three axes on which those systems differ: part number, part differentiation and the regularity of that differentiation. Such complexity spaces can be constructed for systems at different hierarchical levels of biological organization. To illustrate this, we explore the complexity spaces for trilobite body plans (comprising body segments of varying number and form), and for ant colonies (comprising differentiated worker polymorphisms of varying number and form within a 'superorganism'). Many different complexity spaces are possible, but all seek to distinguish different aspects of complexity within an information-theoretic framework, and thereby to clarify patterns of complexity evolution.

DNA duplication-mediated activation of a two-component regulatory system serves as a bet-hedging strategy for Burkholderia thailandensis.

Transposable elements naturally accumulate within genomes in all kingdoms of life. When present in the same orientation, a pair of homologous elements can act as substrates for DNA recombination reactions that can duplicate and delete intervening sequences - giving rise to genetically heterogenous populations. We showed here that Burkholderia thailandensis strain E264 uses this mechanism to amplify genes encoding a two-component regulatory system and an archaic chaperone usher pilus, priming the cells for rapid biofilm formation. The formation of a small subpopulation of biofilm-ready bacteria serves as a bet- hedging strategy, ensuring overall population survival should conditions change rapidly from those in which planktonic growth is optimal to those in which adherence and biofilm formation is required.

Assessment of bioaccumulation factors of trace metals for Upper Gangetic fish

The River Ganga basin is home to over 520 million people and 2500 species of flora and fauna, including several fish species. This study determines the bioaccumulation factors of fish for five trace metals, namely Cu, Fe, Zn, Mn, and Cr, in a stretch of the River Ganga in the upper Gangetic alluvial plain with limited industrial activities. The abundance of different trace metals in the water follows the order Fe > Zn > Mn > Cu > Cr. The concentrations in fish show a slightly different pattern and follow the relative quantitative order as Zn >≈ Fe >Mn > Cu >Cr. The trace metal levels in fish are well below the permissible limits set by various regulatory agencies. The bioaccumulation factor values are in order Zn>Cr>Mn>Cu>Fe. This stretch of the Ganga has not been extensively investigated for bioaccumulation by aquatic organisms. These values, therefore, represent site-specific baseline data for future anthropogenic activities that may affect the trace metal profile in this part of the Gangetic aquatic system. The study is also significant due to the presence of the Narora nuclear power plants, as the bioaccumulation factors of stable elements help predict the behavior of their radioactive counterparts and homologous elements in the environment.

Comparative microscopic anatomy of Schizomida – 2. The rostrosoma and the pharyngeal suction pump

This paper tests hypotheses of independent parallel evolution of the rostrosoma among euchelicerate taxa by analyzing the microscopic anatomy and histology of the rostrosoma of Uropygi (Schizomida and Thelyphonida) and comparing it with the morphology of the snout region in other euchelicerates. The study employs analysis of multiple histological serial sections, μCT-imaging, and graphical as well as computer-based 3D reconstruction. Results of the study are that Thelyphonida and Schizomida share the same morphology of the rostrosoma. The rostrosoma of both groups contains a unique arrangement of musculature that is functionally interpreted as pre-oral suction pump. This is followed by a pharyngeal suction pump. The muscles of the pharyngeal suction pump attach to the epistome and the epipharyngeal sclerite. Neither Schizomida nor Thelyphonida possess a postcerebral suction pump as reported earlier. The microscopic anatomy of the rostrosoma of both taxa is unique and does not compare with any of the other euchelicerates, thus supporting the idea of independent evolutionary origin of the rostrosoma. Thelyphonida, Amblypygi and Scorpiones share the occurrence of a large epipharyngeal/epistomal sclerite with associated musculature, which is a feature that lines up with the Arachnopulmonata concept. A comparison with all Euchelicerata taxa shows that the snout region is formed by homologous morphological elements but the specific arrangement, additions and reductions shape the formation of the rostrosoma, so that parallel evolution of homologous parts of the arachnid ground pattern can be assumed that has formed those elements into convergent morphologies.

Efficient Spiking Neural Networks with Biologically Similar Lithium-Ion Memristor Neurons.

Benefiting from the brain-inspired event-driven feature and asynchronous sparse coding approach, spiking neural networks (SNNs) are becoming a potentially energy-efficient replacement for conventional artificial neural networks. However, neuromorphic devices used to construct SNNs persistently result in considerable energy consumption owing to the absence of sufficient biological parallels. Drawing inspiration from the transport nature of Na+ and K+ in synapses, here, a Li-based memristor (LixAlOy) was proposed to emulate the biological synapse, leveraging the similarity of Li as a homologous main group element to Na and K. The Li-based memristor exhibits ∼8 ns ultrafast operating speed, 1.91 and 0.72 linearity conductance modulation, and reproducible switching behavior, enabled by lithium vacancies forming a conductive filament mechanism. Moreover, these memristors are capable of simulating fundamental behaviors of a biological synapse, including long-term potentiation and long-term depression behaviors. Most importantly, a threshold-tunable leaky integrate-and-fire (TT-LIF) neuron is built using LixAlOy memristors, successfully integrating synaptic signals from both temporal and spatial levels and achieving an optimal threshold of SNNs. A computationally efficient TT-LIF-based SNN algorithm is also implemented for image recognition schemes, featuring a high recognition rate of 90.1% and an ultralow firing rate of 0.335%, which is 4 times lower than those of other memristor-based SNNs. Our studies reveal the ion dynamics mechanism of the LixAlOy memristor and confirm its potential in rapid switching and the construction of SNNs.

A transposon-based genetic marker for conspecific identity within the Bactrocera dorsalis species complex.

Here we describe a molecular approach to assess conspecific identity that relies on the comparison of an evolved mutated transposable element sequence and its genomic insertion site in individuals from closely related species. This was explored with the IFP2 piggyBac transposon, originally discovered in Trichoplusia ni as a 2472bp functional element, that was subsequently found as mutated elements in seven species within the Bactrocera dorsalis species complex. In a B. dorsalis [Hendel] strain collected in Kahuku, Hawaii, a degenerate 2420bp piggyBac sequence (pBacBd-Kah) having ~ 94.5% sequence identity to IFP2 was isolated, and it was reasoned that common species, or strains within species, should share the same evolved element and its precise genomic insertion site. To test this assumption, PCR using primers to pBacBd-Kah and adjacent genomic sequences was used to isolate and compare homologous sequences in strains of four sibling species within the complex. Three of these taxa, B. papayae, B. philippinensis, and B. invadens, were previously synonymized with B. dorsalis, and found to share nearly identical pBacBd-Kah homologous elements (> 99% nucleotide identity) within the identical insertion site consistent with conspecific species. The fourth species tested, B. carambolae, considered to be a closely related yet independent species sympatric with B. dorsalis, also shared the pBacBd-Kah sequence and insertion site in one strain from Suriname, while another divergent pBacBd-Kah derivative, closer in identity to IFP2, was found in individuals from French Guiana, Bangladesh and Malaysia. This data, along with the absence of pBacBd-Kah in distantly related Bactrocera, indicates that mutated descendants of piggyBac, as well as other invasive mobile elements, could be reliable genomic markers for common species identity.

ON SMALL CONTINENTAL MAMMOTHS AND DWARFISM

In the evolution of proboscideans, the appearance of dwarf and semi-dwarf forms occurred repeatedly, in different territories and at different times, due to a lack of resources caused by geographic isolation on islands and by landscape isolation on the mainland. Despite a significant amount of information on the insular forms of mammoths and elephants, the question of the relationship between a decrease in body size and morphological changes in the dental system remains a matter of debate. Some data show that dwarfism was accompanied by a decreasing number of plates (lophs) and by tooth enamel thickening. Other data show that changes in the dental system on the islands indicate that the number of plates could either decrease or remain unchanged, or even increase. Taking into account the importance of the number of plates as a diagnostic feature in the species identification of proboscidean taxa and the lack of a consensus on the stability of the trend towards a decrease in the number of plates from large continental ancestors to insular dwarf descendants, we (1) summarize the data on the records of small tooth-mammoths of the genus Mammuthus with a reduced number of plates in sites across northern Eurasia, (2) provide new radiocarbon dates, and (3) consider the number of plates as a possible sign of dwarfization in continental mammoths. The small teeth of the last generation of M. primigenius from the coastal part of northeastern Siberia and a comparison with data from other regions show that the posterior sections of mammoth cheek teeth are the most variable and represent a reduction complex. For the woolly mammoth, reduction primarily affects that part of the crown which became more complex by the gradually increasing number of plates during the phyletic evolution in the Middle to Late Pleistocene. The rapid loss of the evolutionary achievements through reduction is not a unique feature of woolly mammoth teeth. This has been observed in other mammals as well. Similar reduction complexes are observed for the cheek teeth of proboscideans and rodents of the subfamily Arvicolinae, as is shown by a decrease in the number of serially homologous crown elements: plates in proboscideans and pairs of prisms in voles. A comparison of the number of plates with the size of the teeth of M. primigenius suggests that a decrease in the number of dental plates, while retaining other specific features of the tooth, can be used as a criterion for separating semi-dwarf and small specimens of the woolly mammoth. The largest decrease in size of mainland mammoths is observed during warming periods, which also showed significant transformations of landscapes in a reduction of available resources.

Tuning Electrical and Mechanical Properties of Metal-Organic Frameworks by Metal Substitution.

Metal-organic frameworks (MOFs), synthesized by the self-assembly of organic ligands and metal centers, are structurally designable materials. In the current study, first-principles calculation based on density functional theory (DFT) was performed to investigate the intrinsic mechanical and electrical properties and mechanical-electrical coupling behavior of MOF-5. To improve the conductivity of MOF-5, homologous elements of Cu, Ag, and Au were adopted to replace the Zn atom in MOF-5, reducing the band gap and improving its electrical performance. Cu-MOF-5 and Au-MOF-5, with stable structures, exhibit better conductivity. The intrinsic mechanical properties such as independent elastic constants of MOF-5 and M-MOF-5 (M = Cu, Ag, Au) were obtained. MOF-5 and Cu-MOF-5 were experimentally synthesized to demonstrate the reduction in the band gap after metal substitution. The study of the strain effect of MOF-5 and Cu-MOF-5 proves that strain engineering is an effective method to regulate the band gap and this modulation is repeatable. This study clarifies the tunability of the band gap of MOF-5 with metal substituents and provides an efficient strategy for the development of new types of MOFs with desired physical properties using the combination of theoretical prediction and experimental synthesis and validation.

Crystal structure of a cap-independent translation enhancer RNA.

In eukaryotic messengerRNAs, the 5' cap structure binds to the translation initiation factor 4E to facilitate early stages of translation. Although many plant viruses lack the 5' cap structure, some contain cap-independent translation elements (CITEs) in their 3' untranslated region. The PTE (Panicum mosaic virus translation element) class of CITEs contains a G-rich asymmetric bulge and a C-rich helical junction that were proposed to interact via formation of a pseudoknot. SHAPE analysis of PTE homologs reveals a highly reactive guanosine residue within the G-rich region proposed to mediate eukaryotic initiation factor 4E (eIF4E) recognition. Here we have obtained the crystal structure of the PTE from Pea enation mosaic virus 2 (PEMV2) RNA in complex with our structural chaperone, Fab BL3-6. The structure reveals that the G-rich and C-rich regions interact through a complex network of interactions distinct from those expected for a pseudoknot. The motif, which contains a short parallel duplex, provides a structural mechanism for how the guanosine is extruded from the core stack to enable eIF4E recognition. Homologous PTE elements harbor a G-rich bulge and a three-way junction and exhibit covariation at crucial positions, suggesting that the PEMV2 tertiary architecture is conserved among these homologs.

An innovative scheme for the separation of potassium from lithium-bearing solution: A jarosite precipitation method

As an indispensable raw material for green energy, securing an adequate supply of lithium has become a worldwide policy. However, the difficult separation of the homologous elements lithium and potassium severely hinders the efficient extraction of lithium from lithium minerals. Current research provides an industrialization promising technology, the highly selective precipitation of potassium through the jarosite process, for the separation of potassium from lithium-bearing solution. The conditions for precipitating potassium in the jarosite process without or with seed were optimized. Results showed the precipitation ratios of potassium and lithium at optimized conditions are 99.17 % and 0.43 %, respectively, corresponding to a selectivity coefficient (SKLi) as high as 28.00×103. The effectiveness of the jarosite process in selective precipitating potassium is barely influenced by the initial concentrations of lithium and potassium. Adding seed enables the separation of lithium and potassium at lower temperatures with a faster speed in a broader pH range. Compared to some other separation technologies, both the jarosite process without or with seed can achieve significantly higher SKLi in a shorter time. Overall, the jarosite process is an effective and commercially promising technology for separating potassium from lithium-bearing solution, favoring the sustainability of the lithium industry.

Multifunctional Proteins and Their Role in the Vital Activity of Cells

The function of a newly discovered protein is often assessed by matching its new sequence to sequences of proteins with known functions. However, protein superfamilies can contain homologous elements that catalyze different reactions. Some homologous proteins differ in that they perform a second or even a third function and are called moonlighting proteins, which can be translated as mate proteins or underwork proteins. Also, such proteins are called multifunctional. In addition to these, the superfamilies of proteins with multiple functions also include pseudoenzymes that have a common catalytically active domain but no catalytic activity, as well as metamorphs and morpheins. This review discusses examples of such proteins, their diversity of functions, and their importance in the life of the cell.

Ternary compound heterojunction from isomerism h-CdS/c-CdSe exhibits boosting photoelectrochemical and hydrogen evolution reaction properties

A novel h-CdS/c-CdSe ternary compound heterojunction catalyst CdSS is constructed from isomerism hexagonal CdS and cubic CdSe. The isomerism hexagonal CdS and cubic CdSe is the key factor to obtain the CdSS heterojunction, as compared, ternary compound CdSSe can only be prepared from isomorphic hexagonal CdS and hexagonal CdSe. Under different S:Se ratio, the main XRD peaks of CdSS displayed continuous shift between related CdS and CdSe peaks that confirms the S and Se atoms embedding CdSe and CdS lattice respectively to form atomic level ternary compound heterojunction. The photoelectrochemical and electrocatalytic results show that the CdSS catalysts have boosting properties. Under an optimal S:Se ratio, the photocurrent density of the CdSS reach 8.23 μA/cm2, which was 4.5 times that of original CdS (1.83 μA/cm2), 4.9 times of CdSe (1.67 μA/cm2) and 5.1 times of CdSSe (1.60 μA/cm2). The hydrogen evolution reaction Tafel slope of CdSS also declined 60% compared with CdS and 64% compared with CdSe. The electrocatalytic impedance and fluorescence spectra fully show that CdSS has lower internal resistance and low electron-hole recombination efficiency due to the atomic level heterojunction. The work develops a new strategy to construct high efficiency atomic level ternary compound heterojunction between isomerism homologous element compounds.

Re‐evaluating the correlated evolution of human hands and feet using viability selection modeling

AbstractObjectivesBipedalism and enhanced manipulative abilities are defining features of the hominin lineage, associated with derived foot and hand skeletal morphology, respectively. These unique morphologies are traditionally thought to have evolved independently, but previous work suggests that some aspects of hand and foot skeletal morphology coevolved, due to strong phenotypic correlations among serially homologous elements.Materials and MethodsHere, I further tested this hypothesis using viability selection modeling, which simulates phenotypic evolution based on the likelihood of individual survival, determined using individuals' distance to a predetermined adaptive peak, in this case modern Homo. Using chimpanzees (Pan) as a proxy for hominin ancestral hand and foot morphology, I quantified morphological changes in the hand when only homologous foot elements were targets of selection, as well as the reverse scenario in which only hand morphology influences viability.ResultsSimulation results show that in both scenarios, one autopod evolves as correlated response to selection acting on the other. Importantly, however, simulation outcomes show that the adaptive evolution of the uniquely derived human foot can indirectly produce Homo‐like manual proportions, but the reverse is not true: adaptive evolution of an African ape‐like hand is not sufficient to produce a Homo‐like human foot.DiscussionThese simulations thus lend further empirical support to the hypothesis that human hands and feet coevolved, and indicate that selection acting on the foot may have produced derived hand morphology that facilitated the evolution of enhanced manipulative behaviors.

Cycloisomerization of enynones by aluminum halides: construction of bicyclo[3.1.0]hexanes by introducing halides

Cycloisomerization of 7-en-2-ynone with an aluminum halide gives different cyclic products from those with BF3 as a homologous element halide.

Neuromodulation and the toolkit for behavioural evolution: can ecdysis shed light on an old problem?

The geneticist Thomas Dobzhansky famously declared: 'Nothing in biology makes sense except in the light of evolution'. A key evolutionary adaptation of Metazoa is directed movement, which has been elaborated into a spectacularly varied number of behaviours in animal clades. The mechanisms by which animal behaviours have evolved, however, remain unresolved. This is due, in part, to the indirect control of behaviour by the genome, which provides the components for both building and operating the brain circuits that generate behaviour. These brain circuits are adapted to respond flexibly to environmental contingencies and physiological needs and can change as a function of experience. The resulting plasticity of behavioural expression makes it difficult to characterize homologous elements of behaviour and to track their evolution. Here, we evaluate progress in identifying the genetic substrates of behavioural evolution and suggest that examining adaptive changes in neuromodulatory signalling may be a particularly productive focus for future studies. We propose that the behavioural sequences used by ecdysozoans to moult are an attractive model for studying the role of neuromodulation in behavioural evolution.

Exploration of homologous substitution element on phase ratio and high temperature properties in high Nb-containing TiAl alloy

To reveal homologous substitution and refined mechanisms, and improve mechanical properties, Ti42Al6Nb 2.5 CxTa alloys were prepared by arc melting. Element distribution, lamellar colony size, length-diameter radio of Ti2AlC phase, tensile properties, and the corresponding influence mechanism were studied. Results show that the relative contents of γ and Ti2AlC phase increase, the content of α2 phase decreases, when Ta content increases from 0 to 2.0 at%. The relative content of B2 phase increases among the lamellar colonies and the length-diameter ratio of Ti2AlC particle decreases. Lamellar colony size decreases from 24.9 to 10.6 µm. With the increase of Ta content, the supercooling at the front of the solid-liquid interface increases and the β phase is refined. The increase of the precipitated phase content leads to the increase of the number of α phase heterogeneous nucleation particles, which will refine the lamellar colony. Tensile results show that the strength increases from 238 to 513 MPa and strain increases from 2.7 % to 11.1 % of Ti42Al6Nb 2.5 C1.6Ta alloy when the tested temperature increases from 750 to 950 ℃. The high temperature tensile properties of the alloy with more Ta content are relatively higher. Ta forms large lattice distortion after solid solution into the matrix due to its large atomic size, and Ta makes more Nb dissolve into the collective to increase the effect of solid solution strengthening. Another reason is the refinement of microstructure.

Morphological integration of the hominoid postcranium

Previous research has suggested that magnitudes of integration may be distinct in the postcranium of hominoids when compared to other primate species. To test this hypothesis, we estimated and compared magnitudes of integration of eight postcranial bones from three-dimensional surface scans for 57 Hylobates lar, 58 Gorilla gorilla, 60 Pan troglodytes, 60 Homo sapiens, 60 Chlorocebus pygerythrus, and 60 Macaca fascicularis. We tested the hypotheses that 1) magnitudes of integration would be distinct in the postcranium of hominoids compared to cercopithecoids, with the explicit prediction that magnitudes of integration would be lower in hominoids than in cercopithecoids, and 2) girdle elements (scapula, os coxa) would have lower magnitudes of integration across all taxa. Integration was quantified using the integration coefficient of variation from interlandmark distances reflecting anatomical and developmental modules defined according to a priori criteria. A resampling protocol was employed to generate distributions of integration values that were then compared statistically using Mann–Whitney U tests with Bonferroni adjustment. Support for hypothesis 1 was mixed: with the exception of Gorilla, hominoid taxa were less integrated than the cercopithecoids for all anatomical modules. However, Homo, Gorilla, and, to a lesser extent, Pan showed higher integration than Hylobates and the cercopithecoids for homologous limb elements, with magnitudes of integration for both modules being lowest for Hylobates. These results generally support the hypothesis of distinct patterns of magnitudes of integration in the hominoid postcranium. The high integration of Gorilla may be explained by the effects of overall body size. The results supported the predictions of the second hypothesis. Regardless of taxon, the os coxa and scapula were generally the least integrated skeletal elements, while the femur and radius were the most integrated. The lower integration of the girdle elements suggests that the geometric complexities of particular elements may significantly influence study outcomes.

Synchronous collision tumor of malignant phyllodes and invasive ductal carcinoma

Phyllodes tumor (PT) constitutes <1% of breast tumors. Malignancy usually arises from the stromal component forming homologous or heterologous elements such as chondrosarcoma, liposarcoma, fibrosarcoma, osteosarcoma, or rhabdomyosarcoma. Rarely, carcinoma can arise from the epithelial cells within the PT. Rarer is the occurrence of collision tumor of malignant phyllodes and carcinoma in the breast which lacks the exact incidence since only few cases are reported in the literature. This is another such rare case of synchronous collision tumor of malignant phyllodes having chondrosarcomatous and osteosarcomatous differentiation associated with invasive and in situ ductal carcinoma having metastatic carcinomatous deposits in axillary lymph nodes in a 43-year-old female. Hence, extensive sampling of the gross specimen is crucial in diagnosing the collision tumors which are not detected either in breast imaging studies or during the surgery. Since malignant PT usually spreads through a hematogenous route, it has to be treated by wide local excision or simple mastectomy without the axillary lymph node dissection. If a PT is associated with carcinoma, the patient management and prognosis depend on the stage of the carcinoma.

Recombination of repeat elements generates somatic complexity in human genomes

Non-allelic recombination between homologous repetitive elements contributes to evolution and human genetic disorders. Here, we combine short- and long-DNA read sequencing of repeat elements with a new bioinformatics pipeline to show that somatic recombination of Alu and L1 elements is widespread in the human genome. Our analysis uncovers tissue-specific non-allelic homologous recombination hallmarks; moreover, we find that centromeres and cancer-associated genes are enriched for retroelements that may act as recombination hotspots. We compare recombination profiles in human-induced pluripotent stem cells and differentiated neurons and find that the neuron-specific recombination of repeat elements accompanies chromatin changes during cell-fate determination. Finally, we report that somatic recombination profiles are altered in Parkinson's and Alzheimer's disease, suggesting a link between retroelement recombination and genomic instability in neurodegeneration. This work highlights a significant contribution of the somatic recombination of repeat elements to genomic diversity in health and disease.

Female terminalia morphology and cladistic relations among Tok-Tok beetles (Tenebrionidae: Sepidiini).

Tok-tokkies are one of the most iconic lineages within Tenebrionidae. In addition to containing some of the largest darkling beetles, this tribe is recognized for its remarkable form of sexual communication known as substrate tapping. Nevertheless, the phylogenetic relationships within the group remain poorly understood. This study investigates the usefulness of female terminalia morphology for delimiting Sepidiini and reconstructing relationships among it. Data on the structure of the ovipositors, genital tubes and spicula ventrali have been generated for >200 species representing 28 Pimeliinae tribes. This dataset was used in a comparative analysis at the subfamilial level, which resulted in recognition of several unique features of tok-tokkie terminalia. Additionally, new features linking phenotypically challenging tribes also were recovered (Cryptochilini + Idisiini + Pimeliini). Secondly, 23 characters linked to the structure of female terminalia were defined for tok-tok beetles. Cladistic analysis demonstrates the nonmonophyletic nature of most of the recognized subtribes. The morphological dataset was analysed separately and in combination with available molecular data (CAD, Wg, cox1, cox2, 28S). All obtained topologies were largely congruent, supporting the following changes: Palpomodina Kamiński & Gearner subtr.n. is erected to accommodate the genera Namibomodes and Palpomodes; Argenticrinis and Bombocnodulus are transferred from Hypomelina to Molurina; 153 species and subspecies previously classified within Psammodes are distributed over three separate genera (Mariazofia Kamiński nom.n., Piesomera stat.r., Psammodes sens.n.). Psammodes sklodowskae Kamiński & Gearner sp.n. is described. Preliminary investigation of the ovipositor of Mariazofia basuto (Koch) comb.n. was carried out with the application of microcomputed tomography, illuminating the muscular system as a reliable reference point for recognizing homologous elements in highly modified ovipositors.