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Aging is accompanied by the gradual deregulation of the transcriptome. However, whether age-dependent changes in the transcriptome are evolutionarily conserved or diverged remains largely unexplored. Here, we performed a meta-analysis examining the age-dependent changes in the transcriptome using publicly available datasets of 11 representative metazoans, ranging from Caenorhabditis elegans to humans. To identify the transcriptomic changes associated with aging, we analyzed various aspects of the transcriptome, including genome composition, RNA processing, and functional consequences. The use of introns and novel splice sites tended to increase with age, particularly in the brain. In addition, our analysis suggests that the age-dependent accumulation of premature termination codon-containing transcripts is a common feature of aging across multiple animal species. Using C. elegans as a test model, we showed that several splicing factors that are evolutionarily conserved and age-dependently downregulated were required to maintain a normal lifespan. Thus, aberrant RNA processing appears to be associated with aging and a short lifespan in various species. [ABSTRACT FROM AUTHOR]

Tumor necrosis factor alpha (TNFa) is an inflammatory cytokine that is involved in the pathogenesis of various inflammatory disorders including rheumatoid arthritis. TNF -alpha receptor I (TNFR1a) is one of the receptors TNFa binds with for its activation. Any variation in this receptor might affect the role of TNFa in successive events. Amino acid residue substitutions might happen in TNFR1a through non-synonymous single nucleotide polymorphisms (nsSNPs) which may alter the functioning of TNFa , hence, identifying any such substitutions is of paramount significance. In this study, six nsSNPs at five different evolutionary conserved regions are predicted to be detrimental to the structure and/or function of TNFR1a by using numerous computational tools. Their 3D models are also proposed in this study. Besides, they were found to reduce the stability and affect the molecular mechanisms of this protein. Two contrasting possibilities might happen because of these substitutions. One, they might reduce the production of TNFa which is overexpressed in inflammatory diseases, hence can play therapeutic role in such diseases. Second, they might possibly hinder the apoptosis to occur which can effectuate the uncontrolled division of cells, hence can be pathogenic in diseases like cancer. Further investigations on these nsSNPs using animal models and at cellular level will open doors to understand the underlying mechanisms behind various diseases. [ABSTRACT FROM AUTHOR]

The short-chain dehydrogenase/reductase (SDR) superfamily encompasses enzymes that play essential roles in the metabolism of steroid hormones and lipids. Despite an enigmatic function, recent genetic studies have linked the novel SDR 42 extended-1 (SDR42E1) gene to 25-hydroxyvitamin D levels. This study investigated the potential SDR42E1 functions and interactions with vitamin D using bioinformatics and molecular docking studies. Phylogenetic analysis unveiled that the nucleotide sequences of human SDR42E1 exhibit high evolutionary conservation across nematodes and fruit flies. Molecular docking analysis identified strong binding affinities between SDR42E1 and its orthologs with vitamin D 3 and essential precursors, 8-dehydrocholesterol, followed by 7-dehydrocholesterol and 25-hydroxyvitamin D. The hydrophobic interactions observed between the protein residues and vitamin D compounds supported the predicted transmembrane localization of SDR42E1. Our investigation provides valuable insights into the potential role of SDR42E1 in skin vitamin D biosynthesis throughout species. This provides the foundation for future research and development of targeted therapies for vitamin D deficiency and related health conditions. • SDR42E1 protein demonstrates a strong affinity for key vitamin D intermediates, notably 8-dehydrocholesterol. • The evolutionary conservation of hydrophobic interactions between vitamin D and SDR42E1 emphasizes its crucial role in regulating vitamin D skin synthesis. [ABSTRACT FROM AUTHOR]

• Zebrafish is becoming increasingly popular in behavioral neuroscience. • This review explores theoretical and practical reasons for it. • It emphasizes the need for the comparative approach. • It discusses questions about evolution and translational relevance. • It focusses on relational learning and memory. The zebrafish is becoming increasingly well utilized in several fields of biology, including behavioral neuroscience. This review, based upon an Outstanding Achievement Award lecture presented by the author at an IBNS conference, explores the potential reasons for the popularity of this species. First, some theoretical questions are discussed, including why a comparative approach using more than a single laboratory animal species (the mouse) may be important. Points about evolutionary conservation are considered. Discussion on why complexity may build over time, and what it means when a species is considered "primitive" vs "advanced", are also included. Arguments about how using a "primitive" species may work to the researcher's advantage are made in the context of translational relevance. Most discussions center around a complex functional aspect of the brain, relational learning and memory, and use empirical examples from the author's own laboratory. It is hoped that these examples will show how a simple vertebrate, like the zebrafish, may help the investigator address fundamental mechanistic questions about complex brain function and behavior. [ABSTRACT FROM AUTHOR]

Phosphorylation is one of the most prevalent post-translational modifications and plays a key role in regulating cellular processes. We carried out a bioinformatics analysis of pre-existing phosphoproteomics data, to profile two model species representing the largest subclasses in flowering plants the dicot Arabidopsis thaliana and the monocot Oryza sativa , to understand the extent to which phosphorylation signaling and function is conserved across evolutionary divergent plants. We identified 6537 phosphopeptides from 3189 phosphoproteins in Arabidopsis and 2307 phosphopeptides from 1613 phosphoproteins in rice. We identified phosphorylation motifs, finding nineteen pS motifs and two pT motifs shared in rice and Arabidopsis . The majority of shared motif-containing proteins were mapped to the same biological processes with similar patterns of fold enrichment, indicating high functional conservation. We also identified shared patterns of crosstalk between phosphoserines with enrichment for motifs pSXpS, pSXXpS and pSXXXpS, where X is any amino acid. Lastly, our results identified several pairs of motifs that are significantly enriched to co-occur in Arabidopsis proteins, indicating cross-talk between different sites, but this was not observed in rice. Significance Our results demonstrate that there are evolutionary conserved mechanisms of phosphorylation-mediated signaling in plants, via analysis of high-throughput phosphorylation proteomics data from key monocot and dicot species: rice and Arabidposis thaliana . The results also suggest that there is increased crosstalk between phosphorylation sites in A. thaliana compared with rice. The results are important for our general understanding of cell signaling in plants, and the ability to use A. thaliana as a general model for plant biology. [ABSTRACT FROM AUTHOR]

T-UCRs, a class of long non-coding RNAs that are transcribed from ultra-conserved regions (UCRs), might play an important role in development and diseases. However, the amount of T-UCRs that are conservatively expressed in the developing nervous systems of mice, monkeys and humans is still unknown. In this study, we screened the RNA sequence signals of 481 identified UCRs in an E14.5 mouse brain from the ENCODE database and found 76 UCRs that may be transcribed into T-UCRs. To verify the expression of these potential T-UCRs, we used an RT-PCR experiment and identified that 60 T-UCRs can be expressed in the E14.5 mouse brain. Furthermore, we detected the expression conservation of 76 potential T-UCRs in two comparisons: postnatal day 0 brains of a mouse and a rhesus monkey and neural stem cells of mouse and human by RT-PCR experimentation. It was found that up to 65% of these T-UCRs were expressed in mouse, rhesus monkey and human nervous systems. Next, by testing the spatiotemporal expression pattern of these T-UCRs expressed in mouse, rhesus monkey and human nervous systems, we found that approximately 30% of the T-UCRs showed a relatively high and dynamical expression during mouse brain development. Finally, through biological process and molecular function gene ontology analysis of the host genes of intronic or exonic-antisense T-UCRs, it was discovered that most of the genes were involved in RNA splicing or RNA binding. These results suggest that T-UCRs are likely to participate in nervous system development through RNA processing. [ABSTRACT FROM AUTHOR]

The pregnane X receptor (PXR) is a nuclear receptor belonging to the NR1I sub-family and a known master regulator of xenobiotic metabolism. New roles have been recently proposed in mammals through its activation by vitamin K (VK) such as regulation of glucose metabolism, bone homeostasis, reproduction, neuronal development and cognitive capacities. In marine fish species little is known about PXR and its potential roles. Here, expression patterns of pxr transcripts and conservation of protein domains were determined in the Senegalese sole ( Solea senegalensis ), a marine flatfish model species in aquatic ecotoxicology. In addition to a full coding sequence transcript ( sspxr1 ), two variants lacking DNA and/or ligand binding domains ( sspxr2 and sspxr3 ) were also identified. The expression of sspxr1 during early development and in adult tissues was ubiquitous, but highest levels were observed in liver, intestine and skin. Expression was also detected by in situ hybridization in chondrocytes and cells from the granular and inner nuclear layers in three month old fish. Finally, sspxr1 expression was shown to be differentially regulated under physiological conditions related with fasting, VK and warfarin metabolism. The present work provides new and basic knowledge regarding pxr sequence and expression patterns in a marine flatfish species to unveil the potential impact of xenobiotics on marine fish physiology, and will allow a better and more ecosystemic environmental risk assessment of different pollutants over the marine environments with the development of reporter assays using PXR sequences from evolutionary distantly marine species (such as vertebrate and invertebrate marine species). [ABSTRACT FROM AUTHOR]

Plant transcription factors (TFs) that interact with specific sequences via DNA-binding domains are crucial for regulating transcriptional initiation and are fundamental to plant development and environmental response. In addition, expansion of TF families has allowed functional divergence of duplicate copies, which has contributed to novel, and in some cases adaptive, traits in plants. Thus, TFs are central to the generation of the diverse plant species that we see today. Major plant agronomic traits, including those relevant to domestication, have also frequently arisen through changes in TF coding sequence or expression patterns. Here our goal is to provide an overview of plant TF evolution by first comparing the diversity of DNA-binding domains and the sizes of these domain families in plants and other eukaryotes. Because TFs are among the most highly expanded gene families in plants, the birth and death process of TFs as well as the mechanisms contributing to their retention are discussed. We also provide recent examples of how TFs have contributed to novel traits that are important in plant evolution and in agriculture.This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer. [ABSTRACT FROM AUTHOR]

Joubert syndrome (JS) is a clinically and genetically heterogeneous ciliopathy characterized by episodic hyperpnea and apnea, hypotonia, ataxia, cognitive impairment and ocular motor apraxia. The “molar tooth sign” is pathognomonic of this condition. Mutations in the MKS1 gene are a major cause of Meckel-Gruber syndrome (MKS), the most common form of syndromic neural tube defects, frequently resulting in perinatal lethality. We present the phenotype and genotype of a child with severe JS and agenesis of the corpus callosum (ACC). In our patient, a next generation sequencing (NGS) approach revealed the following two variants of the MKS1 gene: first, a novel missense variant [ c.240G > T (p.Trp80Cys)], which affects a residue that is evolutionarily highly conserved in mammals and ciliates; second, a 29 bp deletion in intron 15 [c.1408-35_1408-7del29], a founder mutation, which in a homozygous state constitutes the major cause of MKS in Finland. We review the MKS1 -variants in all of the eleven JS patients reported to date and compare these patients to our case. To our knowledge, this is the first patient with Joubert syndrome and agenesis of the corpus callosum where a potentially causal genotype is provided. [ABSTRACT FROM AUTHOR]

Human mitochondrial antiviral signaling protein (hMAVS, also known as IPS-1, VISA, or Cardif) is essential for antiviral innate immunity. The Chinese tree shrew ( Tupaia belangeri chinenses ), a close relative of primates, is emerging as a potential animal model for investigating viral infection. However, there is a lack of biological knowledge about the antiviral innate immunity of the tree shrew. In this study, we identified and characterized the function of the Chinese tree shrew MAVS gene ( tMAVS ). The cDNA of tMAVS was 2771 bp in length and encoded a polypeptide of 501 amino acids. Phylogenetic analyses based on the amino acid sequences revealed a closer affinity of tMAVS with those of primates. Quantitative real-time PCR analysis indicated that tMAVS mRNA was constitutively expressed in all seven tissues analyzed in this study. The tMAVS mRNA expression was rapidly and significantly increased after RNA virus infections. Ectopic-expression of tMAVS significantly potentiated the virus-triggered activation of IRF3, NF-κB and interferon-β (IFN-β), whereas knockdown of tMAVS displayed the opposite effect. Furthermore, tMAVS mutants lacking the caspase activation and recruitment (CARD) domains or the transmembrane (TM) domain were unable to induce IFN-β. Similar with hMAVS, mitochondrial localization of tMAVS was dependent on its domain. Collectively, this study revealed evolutionary conservation of the MAVS antiviral signaling pathway in the Chinese tree shrew. [ABSTRACT FROM AUTHOR]

Abstract: Crystal (Cry) toxins are widely used for insect control, but their mechanism of toxicity is still uncertain. These toxins can form lytic pores in vitro, and water soluble tetrameric pre-pore intermediates have been reported. Even the precise oligomeric state of the toxin in membranes, trimeric or tetrameric, is still a debated issue. Based on previous reports, we have assumed that interactions between toxin monomers in solution are at least partly mediated by domain I, and we have analyzed in silico the homo-oligomerization tendencies of the domain I α-helices individually. Using many homologous sequences for each α-helix, our strategy allows selection of evolutionarily conserved interactions. These interactions appeared only in helices α3 and α5, but only α3 produced a suitably oriented or α-helical sample in lipid bilayers, forming homotetramers in C14-betaine, and allowing determination of its rotational orientation in lipid bilayers using site-specific infrared dichroism (SSID). The determined orientation in the tetrameric model is in agreement with only one of the evolutionarily conserved models. In addition mutation R99E, which was found to inhibit oligomerization experimentally, greatly destabilized the tetramer in molecular dynamic simulations. In this model, helix 3 is able to form inter-monomer interactions without significant rearrangements of domain I, which is compatible with the available crystal structure of Cry toxins in solution. The model presented here at least partially explains the reported tetrameric oligomerization of Cry toxins in solution and the inhibition of this oligomerization by a synthetic α3 peptide. [Copyright &y& Elsevier]

Highlights: [•] Our model combines evolutionary conservation and other sequences-derived descriptors. [•] Evolutionary conservation is higher in carboxylation sites than non-ones. [•] Composition of Arg in carboxylation sites is higher than non-carboxylation sites. [Copyright &y& Elsevier]

Abstract: Mitochondrial tRNA point mutations are important causes of human disease, and have been associated with a diverse range of clinical phenotypes. Definitively proving the pathogenicity of any given mt-tRNA mutation requires combined molecular, genetic and functional studies. Subsequent evaluation of the mutation using a pathogenicity scoring system is often very helpful in concluding whether or not the mutation is causing disease. Despite several independent reports linking the m.3291T>C mutation to disease in humans, albeit in association with several different phenotypes, its pathogenicity remains controversial. A lack of conclusive functional evidence and an over-emphasis on the poor evolutionary conservation of the affected nucleotide have contributed to this controversy. Here we describe an adult patient who presented with deafness and lipomas and evidence of mitochondrial abnormalities in his muscle biopsy, who harbours the m.3291T>C mutation, providing conclusive evidence of pathogenicity through analysis of mutation segregation with cytochrome c oxidase (COX) deficiency in single muscle fibres, underlining the importance of performing functional studies when assessing pathogenicity. [Copyright &y& Elsevier]

Abstract: Assigning pathogenicity to mt-tRNA variants requires multiple strands of evidence. Evolutionary conservation is often considered mandatory, but lack of a standard panel of organisms to assess conservation complicates comparison between reports and undermines the value of conservation-based evidence. We demonstrate that intra-species MTT sequence variation is sufficiently low for sequence data from a single organism to adequately represent a species. On this basis, we propose a standardised panel of organisms for conservation assessment and describe integration of this conservation panel into a pathogenicity scoring system designed to assess mt-tRNA variation associated with mitochondrial disease. [Copyright &y& Elsevier]

Abstract: Monoacylglycerol lipases (MGLs) catalyse the hydrolysis of monoacylglycerol into free fatty acid and glycerol. MGLs have been identified throughout all genera of life and have adopted different substrate specificities depending on their physiological role. In humans, MGL plays an integral part in lipid metabolism affecting energy homeostasis, signalling processes and cancer cell progression. In bacteria, MGLs degrade short-chain monoacylglycerols which are otherwise toxic to the organism. We report the crystal structures of MGL from the bacterium Bacillus sp. H257 (bMGL) in its free form at 1.2Å and in complex with phenylmethylsulfonyl fluoride at 1.8Å resolution. In both structures, bMGL adopts an α/β hydrolase fold with a cap in an open conformation. Access to the active site residues, which were unambiguously identified from the protein structure, is facilitated by two different channels. The larger channel constitutes the highly hydrophobic substrate binding pocket with enough room to accommodate monoacylglycerol. The other channel is rather small and resembles the proposed glycerol exit hole in human MGL. Molecular dynamics simulation of bMGL yielded open and closed states of the entrance channel and the glycerol exit hole. Despite differences in the number of residues, secondary structure elements, and low sequence identity in the cap region, this first structure of a bacterial MGL reveals striking structural conservation of the overall cap architecture in comparison with human MGL. Thus it provides insight into the structural conservation of the cap amongst MGLs throughout evolution and provides a framework for rationalising substrate specificities in each organism. [Copyright &y& Elsevier]

Abstract: One major goal of functional genomics has been to identify and analyze molecular interactions in a cellular context to better understand the underlying design principles and mechanisms. To investigate into a PPI network from both topological and functional points of view, this work proposes a methodology that exploits ontology-based biological knowledge for network analysis. To speed up the procedure, an agent-based framework is also presented for supporting distributed computing. The preliminary results show that through the knowledge obtained from gene ontology, our work in analyzing building blocks of PPI networks can give a higher resolution than that of previous ones. Also our agent-based framework can successfully speed up the task of network analysis in an adaptive manner. [Copyright &y& Elsevier]

Abstract: RNA-binding proteins (RBPs) perform fundamental and diverse functions within the cell. Approximately 15% of proteins sequences are annotated as RNA-binding, but with a significant number of proteins without functional annotation, many RBPs are yet to be identified. A percentage of uncharacterised proteins can be annotated by transferring functional information from proteins sharing significant sequence homology. However, genomes contain a significant number of orphan open reading frames (ORFs) that do not share significant sequence similarity to other ORFs, but correspond to functional proteins. Hence methods for protein function annotation that go beyond sequence homology are essential. One method of annotation is the identification of ligands that bind to proteins, through the characterisation of binding site residues. In the current work RNA-binding residues (RBRs) are characterised in terms of their evolutionary conservation and the patterns they form in sequence space. The potential for such characteristics to be used to identify RBPs from sequence is then evaluated. In the current work the conservation of residues in 261 RBPs is compared for (a) RBRs vs. non-RBRs surface residues, and for (b) specific and non-specific RBRs. The analysis shows that RBRs are more conserved than other surface residues, and RBRs hydrogen-bonded to the RNA backbone are more conserved than those making hydrogen bonds to RNA bases. This observed conservation of RBRs was then used to inform the construction of RBR sequence patterns from known protein–RNA structures. A series of RBR patterns were generated for a case study protein aspartyl-tRNA synthetase bound to tRNA; and used to differentiate between RNA-binding and non-RNA-binding protein sequences. Six sequence patterns performed with high precision values of >80% and recall values 7 times that of an homology search. When the method was expanded to the complete dataset of 261 proteins, many patterns were of poor predictive value, as they had not been manipulated on a family-specific basis. However, two patterns with precision values ≥85% were used to make function predictions for a set of hypothetical proteins. This revealed a number of potential RBPs that require experimental verification. [Copyright &y& Elsevier]

Abstract: Lymphotoxin alpha (LTA) is a member of the TNF cytokine superfamily, produced principally by lymphocytes. It plays an important role in immune and inflammatory responses. Many TNF superfamily members have functionally important isoforms generated by alternative splicing but alternative splicing of LTA has never been studied. The known LTA protein is encoded by a transcript containing four exons. Here we report seven new LTA splice variants, three of them evolutionary conserved. We demonstrate their presence in cytoplasmic RNA suggesting that they could be translated into new LTA isoforms. We observed that their expression is differentially regulated upon activation of peripheral blood mononuclear cells and lymphocyte subpopulations (CD4+, CD8+, and CD19+). Our data suggest that the new LTA splice variants might play a role in the regulation of the immune response. [Copyright &y& Elsevier]

Abstract: In recent years, the complexity of the 5′ region of the Vitamin D receptor (VDR) gene has become apparent. Six exons, 1a–1f, lie upstream of the translation start codon in exon 2. Transcription has been reported beginning in exons 1f, 1a, 1d and 1c and alternative splicing can produce a large number of alternative mRNA transcripts. Exon 1d transcripts can code for two alternative proteins. This pattern of transcription produces several potential promoter regions. We have used a number of in silico tools to study the evolutionary conservation of the exon and promoter sequences of the 5′ region. Those exons involved in the alternative VDR proteins, exons 1d and 1c, were well conserved from mouse and rat, unlike exons 1f, 1e and 1b which showed little homology. Exon 1a was also well conserved. Furthermore, 1a was shown to be within a strong CpG island and TraFac revealed a Sp1-MazR-Sp1-MazR cluster of transcription factor binding sites immediately upstream of exon 1a, a common motif in strong promoters. The promoter region upstream of 1f showed a highly conserved pattern of transcription factor binding sites and was also shown to be within a CpG island. No significant clusters of conserved sites were observed in the 1c promoter region, despite reports of 1c promoter activity. [Copyright &y& Elsevier]

Abstract: The clk-1 gene of the nematode Caenorhabditis elegans encodes an evolutionarily conserved enzyme that is necessary for ubiquinone biosynthesis. Loss-of-function mutations in clk-1, as well as in its mouse orthologue mclk1, increase lifespan in both organisms. In nematodes, clk-1 extends lifespan by a mechanism that is distinct from the insulin signaling-like pathway but might have similarities to calorie restriction. The evolutionary conservation of the effect of clk-1/mclk1 on lifespan suggests that the gene affects a fundamental mechanism of aging. The clk-1/mclk1 system could allow for the understanding of this mechanism by combining genetic and molecular investigations in worms with studies in mice, where age-dependent disease processes relevant to human health can be modeled. [Copyright &y& Elsevier]

The zebrafish hoxd4a locus was compared to its murine ortholog, Hoxd4. The sequence of regulatory elements, including a DR5 type retinoic acid response element (RARE) required for Hoxd4 neural enhancer activity, are highly conserved. Additionally, zebrafish and mouse neural enhancers function identically in transgenic mouse embryos. We tested whether sequence conservation reflects functional importance by altering the spacing and sequence of the RARE in the Hoxd4 neural enhancer. Stabilizing receptor-DNA interactions did not anteriorize transgene expression. By contrast, conversion of the RARE from a DR5 to a DR2 type element decreased receptor-DNA stability and posteriorized expression. Hence, the setting of the Hox anterior expression border is not a simple function of the affinity of retinoid receptors for their cognate element. [Copyright &y& Elsevier]

Establishing the embryonic body plan of multicellular organisms relies on precisely orchestrated cell divisions coupled with pattern formation, which, in animals, are regulated by Polycomb group (PcG) proteins. The conserved Polycomb Repressive Complex 2 (PRC2) mediates H3K27 trimethylation and comes in different flavors in Arabidopsis. The PRC2 catalytic subunit MEDEA is required for seed development; however, a role for PRC2 in embryonic patterning has been dismissed. Here, we demonstrate that embryos derived from medea eggs abort because MEDEA is required for patterning and cell lineage determination in the early embryo. Similar to PcG proteins in mammals, MEDEA regulates embryonic patterning and growth by controlling cell-cycle progression through repression of CYCD1;1, which encodes a core cell-cycle component. Thus, Arabidopsis embryogenesis is epigenetically regulated by PcG proteins, revealing that the PRC2-dependent modulation of cell-cycle progression was independently recruited to control embryonic cell proliferation and patterning in animals and plants. [Display omitted] • MEDEA , a Polycomb Repressive Complex 2 (PRC2) subunit, is required in embryo and endosperm • MEDEA links cell proliferation and differentiation during embryonic pattern formation • The PRC2 protein MEDEA directly regulates core cell-cycle components, i.e., cyclin CYCD1;1 • Body plan and cell proliferation are epigenetically regulated in both animals and plants In animals, Polycomb group (PcG) proteins are essential for embryogenesis. Simonini et al. show that growth and patterning of plant embryos are also epigenetically regulated by PcG proteins, with the PRC2 histone methyltransferase MEDEA directly repressing the core cell-cycle component CYCD1;1 in the Arabidopsis embryo. [ABSTRACT FROM AUTHOR]

Spectroscopy can be used to investigate ecosystem functioning and phylogenetic relationships, since it can provide information about the optical properties of a plant – a critical functional trait with regard to light usage. The link between phylogenetic relationships and foliar reflectance spectra of Neotropical species has rarely been considered and no previous studies have explored this in relation to forest regeneration following natural gap formation. We investigated phylogenetic signatures, i.e. evolutionary conservation, of foliar spectra in gap-regenerating woody species in conserved Neotropical forests. We collected foliar spectra of 53 regenerating woody species in the forest gaps at two sites of Atlantic Seasonal Semi-deciduous forest, and quantified the phylogenetic signal for spectral wavelengths using Blomberg's K, Pagel's lambda (λ) and LIPA (Local indicator of phylogenetic association) statistics. Analysis of foliar reflectance spectra showed that the largest portion of phylogenetic signature from both K and λ occurred within the first part of the shortwave infrared region (SWIR-1: 1551–1849 nm), followed by the near infrared (NIR: 701–1349 nm), and the lowest portion within the visible region (VIS: 400–700 nm). Most of the significant phylogenetic signal found for wavelengths of all spectral regions suggested convergent conservation, i.e. homoplasy. The largest portion of positive LIPA (i.e. phylogenetic similarity) was found for wavelengths within the second part of the SWIR (SWIR-2: 2051–2450 nm), while most of the negative LIPA (i.e. phylogenetic distinctiveness) occurred within the VIS. We conclude that there is a tendency towards evolutionary convergence in the phylogenetic signature of foliar spectra in certain parts of the spectrum. The extent of phylogenetic signal found in the SWIR allows us to conclude that this region carries the most potential for future investigations of phylogenetic influence on spectral community dynamics within Neotropical forests. Unlabelled Image • New information on the behavior of foliar spectra of regenerating Neotropical plants. • Evolutionary homoplasy in foliar spectral signatures in distinct spectral regions. • Environmental variables explain a minor portion of the spectral variation. • Phenotypic similarity of the spectral signatures among phylogenetic neighbors. • SWIR carries most of the homoplastic phylogenetic signatures on foliar spectra. [ABSTRACT FROM AUTHOR]

The unprecedented access to annotated genomes now facilitates the investigation of the molecular basis of epigenetic phenomena in phenotypically diverse animals. In this critical review, we describe the roles of molecular epigenetic mechanisms in regulating mitotically and meiotically stable spatiotemporal gene expression, phenomena that provide the molecular foundation for the intra-, inter-, and trans-generational emergence of physiological phenotypes. By focusing principally on emerging comparative epigenetic roles of DNA-level and transcriptome-level epigenetic mark dynamics in the emergence of phenotypes, we highlight the relationship between evolutionary conservation and innovation of specific epigenetic pathways, and their interplay as a priority for future study. This comparative approach is expected to significantly advance our understanding of epigenetic phenomena, as animals show a diverse array of strategies to epigenetically modify physiological responses. Additionally, we review recent technological advances in the field of molecular epigenetics (single-cell epigenomics and transcriptomics and editing of epigenetic marks) in order to (1) investigate environmental and endogenous factor dependent epigenetic mark dynamics in an integrative manner; (2) functionally test the contribution of specific epigenetic marks for animal phenotypes via genome and transcript-editing tools. Finally, we describe advantages and limitations of emerging animal models, which under the Krogh principle, may be particularly useful in the advancement of comparative epigenomics and its potential translational applications in animal science, ecotoxicology, ecophysiology, climate change science and wild-life conservation, as well as organismal health. Unlabelled Image • Epigenetics regulate mitotically and meiotically stable spatiotemporal gene expression. • Comparative approaches are needed for understanding of epigenetics in animals. • Epigenetic mark is dynamic and should be studied in an integrative manner. • Emerging animal models will contribute to the advancement of comparative epigenomics. [ABSTRACT FROM AUTHOR]

• Sub-family conserved residues predict incidence and progression of diseases. • 3D structure of human D2 receptor (DRD2) was modeled. • The E3 domain consisted of both super-family and sub family conserved residues. Dopamine D2-like receptors (D2) mediate various effects of dopamine. Characterizing the structural and functional regions can contribute to understanding the mechanism of biological effects of dopamine. A large scale phylogeny was utilized to construct a comprehensive dataset of D2 receptor, the evolutionary conserved residues were calculated at both super-family and sub-family (included human D2clade) levels, and then 3D structure of human D2 receptor (DRD2) was modeled to evaluate the significance of these conserved residues and motifs linked with structural stability, genetic variants, functional activation, protein interaction and drug binding. All the drug binding sites and important protein-complex binding motifs showed evolutionary super-family conservation. However, genetic variants linked to different diseases all belonged to sub-family conservation. The extra cellular loop (ECL3) domain consisted of both super-family and sub-family conserved residues. Sub-family conserved residues probably play a vital role in the incidence and progression of diseases. [ABSTRACT FROM AUTHOR]