This parody of evo devo makes it sound a lot like ID

_{News
December 19, 2017

Cell biology, Evolution, Evolutionary biology

1}_{Categories
Cell biology
Evolution
Evolutionary biology}

Share: Facebook; Twitter/X; LinkedIn; Flipboard; Print; Email

“This is how we go from single cells to people.” Hmmm.

See also: From Biology Direct: Darwinism, now thoroughly detached from its historical roots as a falsifiable theory, “must be abandoned”

Comments

Esophageal cancer (EC) was one of the most lethal malignancies worldwide with intricate mechanisms. Here we reported that Forkhead box C1 (FoxC1), a member of the forkhead family transcription factors, was up-regulated in EC tissues and cell lines in comparison with controls. FoxC1 levels were negatively correlated with tumor stage, lymph node metastasis and survival status of EC patients. Knockdown of FoxC1 inhibited the proliferation, colony formation and epithelial-mesenchymal transition (EMT) of EC cells, while overexpression of FoxC1 promoted these biological behaviors. Mechanically, serial deletion and chromatin immunoprecipitation assays showed that ZEB2, a well-reported transcriptional suppressor of E-cadherin, was a direct transcriptional target of FoxC1. Moreover, FoxC1 was recruited to the ZEB2 promoter by its interaction with the pioneer transcription factor pre-B-cell leukemia homeobox 1 (PBX1). Importantly, significant correlation between levels of FoxC1 and ZEB2 was observed in EC tissues and the two proteins could be used as prognostic biomarkers together. Hence, our results revealed a critical role of FoxC1 in the EMT process of EC and uncovered a novel mechanism for the regulation of ZEB2-E-cadherin axis in EC. Zhu, Xiaoming & Wei, Li & Bai, Yangqiu & Wu, Sen & Han, Shuangyin. (2017). FoxC1 promotes epithelial-mesenchymal transition through PBX1 dependent transactivation of ZEB2 in esophageal cancer. American journal of cancer research. 7. 1642-1653.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
05:09 PM
5
05
09
PM
PDT}

Pioneer factors are proteins that can recognize their target sites in barely accessible chromatin and initiate a cascade of events that allows for later transcriptional activation of the respective genes. Pioneer factors are therefore particularly well-suited to initiate cell fate changes. To date, only a small number of pioneer factors have been identified and studied in depth, such as FOXD3/FOXA1, OCT4, or SOX2. Interestingly, several recent studies reported that the PBC transcription factor PBX1 can access transcriptionally inactive genomic loci. Here, we summarize the evidence linking PBX1 with transcriptional pioneer functions, suggest potential mechanisms involved and discuss open questions to be resolved. Grebbin, Moyo & Schulte, Dorothea. (2017). PBX1 as pioneer factor: A case still open. Frontiers in Cell and Developmental Biology. 5. . 10.3389/fcell.2017.00009.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
05:07 PM
5
05
07
PM
PDT}

Zinc (Zn) is one of the essential mineral elements for both plants and humans. Zn deficiency in human is one of the major causes of hidden hunger, a serious health problem observed in many developing countries. Therefore, increasing Zn concentration in edible part is an important issue for improving human Zn nutrition. Here, we found that an Australian wild rice O. meridionalis showed higher grain Zn concentrations compared with cultivated and other wild rice species. The quantitative trait loci (QTL) analysis was then performed to identify the genomic regions controlling grain Zn levels using backcross recombinant inbred lines derived from O. sativa ‘Nipponbare’ and O. meridionalis W1627. Four QTLs responsible for high grain Zn were detected on chromosomes 2, 9, and 10. The QTL on the chromosome 9 (named qGZn9), which showed the largest effect on grain Zn concentration was confirmed with the introgression line, which had a W1627 chromosomal segment covering the qGZn9 region in the genetic background of O. sativa ‘Nipponbare’. Fine mapping of this QTL resulted in identification of two tightly linked loci, qGZn9a and qGZn9b. The candidate regions of qGZn9a and qGZn9b were estimated to be 190 and 950 kb, respectively. Furthermore, we also found that plants having a wild chromosomal segment covering qGZn9a, but not qGZn9b, is associated with fertility reduction. qGZn9b, therefore, provides a valuable allele for breeding rice with high Zn in the grains. Ishikawa, Ryo & Iwata, Masahide & Taniko, Kenta & Monden, Gotaro & Miyazaki, Naoya & Orn, Chhourn & Tsujimura, Yuki & Yoshida, Shusaku & Feng Ma, Jian & Ishii, Takashige. (2017). Detection of quantitative trait loci controlling grain zinc concentration using Australian wild rice, Oryza meridionalis, a potential genetic resource for biofortification of rice. PLOS ONE. 12. e0187224. 10.1371/journal.pone.0187224.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
05:06 PM
5
05
06
PM
PDT}

Mineral elements taken up by the roots will be delivered to different organs and tissues depending on their requirements. In Poaceae, this selective distribution is mainly mediated in the nodes, which have highly developed and fully organized vascular systems. Inter-vascular transfer of mineral elements from enlarged vascular bundles to diffuse vascular bundles is required for their preferential distribution to developing tissues and reproductive organs. A number of transporters involved in this inter-vascular transfer processes have been identified mainly in rice. They are localized at the different cell layers and form an efficient machinery within the node. Furthermore, some these transporters show rapid response to the environmental changes of mineral elements at the protein level. In addition to the node-based transporters, distinct nodal structures including enlarged xylem area, folded plasma membrane of xylem transfer cells and presence of an apoplastic barrier are also required for the efficient inter-vascular transfer. Manipulation of node-based transporters will provide a novel breeding target to improve nutrient use efficiency, productivity, nutritional value and safety in cereal crops. Yamaji, Naoki & Feng, Jian. (2017). Node-controlled allocation of mineral elements in Poaceae. Current Opinion in Plant Biology. 39. . 10.1016/j.pbi.2017.05.002.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
05:03 PM
5
05
03
PM
PDT}

Monocot stems lack the vascular cambium and instead have characteristic structures in which intercalary meristems generate internodes and veins remain separate and scattered. Developmental processes of these unique structures, however, have been poorly described. BELL1-like Homeobox (BLH) transcription factors (TFs) are known to heterodimerize with KNOTTED1-like Homeobox (KNOX) TFs to play crucial roles in shoot meristem maintenance, but their functions are elusive in monocots. We found that maize BLH12 and BLH14 have redundant but important roles in stem development. BLH12/14 interact with KNOTTED1 (KN1) in vivo, and accumulate in overlapping domains in shoot meristems, young stems and provascular bundles. Similar to kn1 loss-of-function mutants, blh12 blh14 (blh12/14) double mutants fail to maintain axillary meristems. Unique to blh12/14 is an abnormal tassel branching and precocious internode differentiation that results in dwarfism and reduced veins in stems. Micro-computed tomography (CT) observation of vascular networks revealed that blh12/14 double mutants had reduced vein number due to fewer intermediate veins in leaves and precocious anastomosis in young stems. Based on these results, we propose two functions of BLH12/14 during stem development: (1) maintaining intercalary meristems that accumulate KN1 and prevent precocious internode differentiation, (2) preventing precocious anastomosis of provascular bundles in young stems to ensure the production of sufficient independent veins. Tsuda, Katsutoshi & Abraham, Jazmin & Maeno, Akiteru & Dong, Zhaobin & Aromdee, Dale & Meeley, Robert & Shiroishi, Toshihiko & Nonomura, Kenichi & Hake, Sarah. (2017). KNOTTED1 cofactors, BLH12 and BLH14, regulate internode patterning and vein anastomosis in maize. The Plant cell. 29. . 10.1105/tpc.16.00967.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
05:01 PM
5
05
01
PM
PDT}

In addition to protein-coding genes, RNA polymerase II (pol II) transcribes numerous genes for non-coding RNAs, including the small-nuclear (sn)RNA genes. snRNAs are an important class of non-coding RNAs, several of which are involved in pre-mRNA splicing. The molecular mechanisms underlying expression of human pol II-transcribed snRNA genes are less well characterized than for protein-coding genes and there are important differences in expression of these two gene types. Here, we review the DNA features and proteins required for efficient transcription of snRNA genes and co-transcriptional 3? end formation of the transcripts. Guiro, Joana & Murphy, Shona. (2017). Regulation of expression of human RNA polymerase II-Transcribed snRNA genes. Open Biology. 7. 170073. 10.1098/rsob.170073.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
05:00 PM
5
05
00
PM
PDT}

Transcription factors (TFs) are gene expression regulators that bind to DNA in a sequence-specific manner and determine the functional characteristics of the gene. It is worthwhile to study the unique characteristics of such specific TF-binding pattern in DNA. Sox2 recognizes a 6- to 7-base pair consensus DNA sequence; the central four bases of the binding site are highly conserved, whereas the two to three flanking bases are variable. Here, we attempted to analyze the binding affinity and specificity of the Sox2 protein for distinct DNA sequence patterns via steered molecular dynamics, in which a pulling force is employed to dissociate Sox2 from Sox2-DNA during simulation to study the behavior of a complex under nonequilibrium conditions. The simulation results revealed that the first two stacking bases of the binding pattern have an exclusive impact on the binding affinity, with the corresponding mutant complexes showing greater binding and longer dissociation time than the experimental complexes do. In contrast, mutation of the conserved bases tends to reduce the affinity, and mutation of the complete conserved region disrupts the binding. It might pave the way to identify the most likely binding pattern recognized by Sox2 based on the affinity of each configuration. The ?2-helix of Sox2 was found to be the key player in the Sox2-DNA association. The characterization of Sox2's binding patterns for the target genes in the genome helps in understanding of its regulatory functions. Yesudhas, Dhanusha & Anwar, Muhammad Ayaz & Panneerselvam, Suresh & Kim, Han-Kyul & Choi, Sangdun. (2017). Evaluation of Sox2 binding affinities for distinct DNA patterns using steered molecular dynamics simulation. FEBS Open Bio. 7. . 10.1002/2211-5463.12316.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:58 PM
4
04
58
PM
PDT}

Proteins in the form of transcription factors (TFs) bind to specific DNA sites that regulate cell growth, differentiation, and cell development. The interactions between proteins and DNA are important toward maintaining and expressing genetic information. Without knowing TFs structures and DNA-binding properties, it is difficult to completely understand the mechanisms by which genetic information is transferred between DNA and proteins. The increasing availability of structural data on protein-DNA complexes and recognition mechanisms provides deeper insights into the nature of protein-DNA interactions and therefore, allows their manipulation. TFs utilize different mechanisms to recognize their cognate DNA (direct and indirect readouts). In this review, we focus on these recognition mechanisms as well as on the analysis of the DNA-binding domains of stem cell TFs, discussing the relative role of various amino acids toward facilitating such interactions. Unveiling such mechanisms will improve our understanding of the molecular pathways through which TFs are involved in repressing and activating gene expression. Yesudhas, Dhanusha & Batool, Maria & Anwar, Muhammad Ayaz & Panneerselvam, Suresh & Choi, Sangdun. (2017). Proteins Recognizing DNA: Structural Uniqueness and Versatility of DNA-Binding Domains in Stem Cell Transcription Factors. Genes. 8. . 10.3390/genes8080192.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:57 PM
4
04
57
PM
PDT}

Objectives Homeobox genes are a group of conserved class of transcription factors that function as key regulators during the embryonic developmental processes. They act as master regulator for developmental genes, which involves coordinated actions of various auto and cross-regulatory mechanisms. In this review, we summarize the expression pattern of homeobox genes in relation to the tooth development and various signaling pathways or molecules contributing to the specific actions of these genes in the regulation of odontogenesis. Materials and methods An electronic search was undertaken using combination of keywords e.g. Homeobox genes, tooth development, dental diseases, stem cells, induced pluripotent stem cells, gene control region was used as search terms in PubMed and Web of Science and relevant full text articles and abstract were retrieved that were written in English. A manual hand search in text books were also carried out. Articles related to homeobox genes in dentistry and tissue engineering and regenerative medicine of odontogenesis were selected. Results The possible perspective of stem cells technology in odontogenesis and subsequent analysis of gene correction pertaining to dental disorders through the possibility of induced pluripotent stem cells technology is also inferred. Conclusions We demonstrate the promising role of tissue engineering and regenerative medicine on odontogenesis, which can generate a new ray of hope in the field of dental science. Ramanathan, Anand & Srijaya, Thekkeparambil & Sukumaran, Prema & Zain, Rosnah & Noor Hayaty, Abu Kasim. (2017). Homeobox genes and tooth development: Understanding the biological pathways and applications in regenerative dental science. Archives of Oral Biology. 85. . 10.1016/j.archoralbio.2017.09.033.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:53 PM
4
04
53
PM
PDT}

We report and discuss the results of a quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis of the expression patterns of seven three amino acid loop extension (TALE) homeobox genes (four KNOTTED-like homeobox (KNOX) and three BEL1-like homeobox (BELL) genes) identified after next generation sequencing (NGS) and assembly of the sporophyte and gametophyte transcriptomes of the endangered fern species Vandenboschia speciosa. Among the four KNOX genes, two belonged to the KNOX1 class and the other two belonged to the KNOX2 class. Analysis of the deduced amino acid sequences supported the typical domain structure of both types of TALE proteins, and the homology to TALE proteins of mosses, lycophytes, and seed plant species. The expression analyses demonstrate that these homeodomain proteins appear to have a key role in the establishment and development of the gametophyte and sporophyte phases of V. speciosa lifecycle, as well as in the control of the transition between both phases. Vandenboschia speciosa VsKNAT3 (a KNOX2 class protein) as well as VsBELL4 and VsBELL10 proteins have higher expression levels during the sporophyte program. On the contrary, one V. speciosa KNOX1 protein (VsKNAT6) and one KNOX2 protein (VsKNAT4) seem important during the development of the gametophyte phase. TALE homeobox genes might be among the key regulators in the gametophyte-to-sporophyte developmental transition in regular populations that show alternation of generations, since some of the genes analyzed here (VsKNAT3, VsKNAT6, VsBELL4, and VsBELL6) are upregulated in a non-alternating population in which only independent gametophytes are found (they grow by vegetative reproduction outside of the range of sporophyte distribution). Thus, these four genes might trigger the vegetative propagation of the gametophyte and the repression of the sexual development in populations composed of independent gametophytes. This study represents a comprehensive identification and characterization of TALE homeobox genes in V. speciosa, and gives novel insights about the role of these genes in fern development. Ruiz-Estévez, Mercedes & Bakkali, Mohammed & Martín-Blázquez, Rubén & Garrido-Ramos, Manuel. (2017). Identification and Characterization of TALE Homeobox Genes in the Endangered Fern Vandenboschia speciosa. Genes. 8. 275. 10.3390/genes8100275.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:51 PM
4
04
51
PM
PDT}

Background Hox gene clusters with at least 13 paralog group (PG) members are common in vertebrate genomes and in that of amphioxus. Ascidians, which belong to the subphylum Tunicata (Urochordata), are phylogenetically positioned between vertebrates and amphioxus, and traditionally divided into two groups: the Pleurogona and the Enterogona. An enterogonan ascidian, Ciona intestinalis (Ci), possesses nine Hox genes localized on two chromosomes; thus, the Hox gene cluster is disintegrated. We investigated the Hox gene cluster of a pleurogonan ascidian, Halocynthia roretzi (Hr) to investigate whether Hox gene cluster disintegration is common among ascidians, and if so, how such disintegration occurred during ascidian or tunicate evolution. Results Our phylogenetic analysis reveals that the Hr Hox gene complement comprises nine members, including one with a relatively divergent Hox homeodomain sequence. Eight of nine Hr Hox genes were orthologous to Ci-Hox1, 2, 3, 4, 5, 10, 12 and 13. Following the phylogenetic classification into 13 PGs, we designated Hr Hox genes as Hox1, 2, 3, 4, 5, 10, 11/12/13.a, 11/12/13.b and HoxX. To address the chromosomal arrangement of the nine Hox genes, we performed two-color chromosomal fluorescent in situ hybridization, which revealed that the nine Hox genes are localized on a single chromosome in Hr, distinct from their arrangement in Ci. We further examined the order of the nine Hox genes on the chromosome by chromosome/scaffold walking. This analysis suggested a gene order of Hox1, 11/12/13.b, 11/12/13.a, 10, 5, X, followed by either Hox4, 3, 2 or Hox2, 3, 4 on the chromosome. Based on the present results and those previously reported in Ci, we discuss the establishment of the Hox gene complement and disintegration of Hox gene clusters during the course of ascidian or tunicate evolution. Conclusions The Hox gene cluster and the genome must have experienced extensive reorganization during the course of evolution from the ancestral tunicate to Hr and Ci. Nevertheless, some features are shared in Hox gene components and gene arrangement on the chromosomes, suggesting that Hox gene cluster disintegration in ascidians involved early events common to tunicates as well as later ascidian lineage-specific events. Electronic supplementary material The online version of this article (10.1186/s40851-017-0078-3) contains supplementary material, which is available to authorized users. Sekigami, Yuka & Kobayashi, Takuya & Omi, Ai & Nishitsuji, Koki & Ikuta, Tetsuro & Fujiyama, Asao & Satoh, Noriyuki & Saiga, Hidetoshi. (2017). Hox gene cluster of the ascidian, Halocynthia roretzi, reveals multiple ancient steps of cluster disintegration during ascidian evolution. Zoological Letters. 3. . 10.1186/s40851-017-0078-3.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:49 PM
4
04
49
PM
PDT}

Like many transcription factors, the yeast protein MATalpha2 (?2) undergoes rapid proteolysis via the ubiquitin-proteasome system (UPS). At least two ubiquitylation pathways regulate ?2 degradation: one pathway utilizes the ubiquitin ligase (E3) Doa10 and the other the heterodimeric E3 Slx5/Slx8. Doa10 is a transmembrane protein of the endoplasmic reticulum/inner nuclear membrane, whereas Slx5/Slx8 localizes to the nucleus and binds DNA nonspecifically. While a single protein can often be ubiquitylated by multiple pathways, the reasons for this 'division of labor' are not well understood. Here we show that ?2 mutants with impaired DNA binding become inaccessible to the Slx5/Slx8 pathway but are still rapidly degraded through efficient shunting to the Doa10 pathway. These results are consistent with the distinct localization of these E3s. We also characterized a novel class of DNA binding-defective ?2 variants whose degradation is strongly impaired. Our genetic data suggest this is due to a gain-of-function interaction that limits their access to Doa10. Together, these results suggest multiple ubiquitin-ligation mechanisms may have evolved to promote rapid destruction of a transcription factor that resides in distinct cellular subcompartments under different conditions. Moreover, gain-of-function mutations, which also occur with oncogenic forms of human transcription factors such as p53, may derail this fail-safe system. M. Hickey, Christopher & Xie, Yang & Hochstrasser, Mark. (2018). DNA Binding by the MAT?2 Transcription Factor Controls its Access to Alternative Ubiquitin-modification Pathways. Molecular Biology of the Cell. mbc.E17-10. 10.1091/mbc.E17-10-0589.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:47 PM
4
04
47
PM
PDT}

Here, we provide an update of our review on homeobox genes that we wrote together with Walter Gehring in 1994. Since then, comprehensive surveys of homeobox genes have become possible due to genome sequencing projects. Using the 103 Drosophila homeobox genes as example, we present an updated classification. In animals, there are 16 major classes, ANTP, PRD, PRD-LIKE, POU, HNF, CUT (with four subclasses: ONECUT, CUX, SATB, and CMP), LIM, ZF, CERS, PROS, SIX/SO, plus the TALE superclass with the classes IRO, MKX, TGIF, PBC, and MEIS. In plants, there are 11 major classes, i.e., HD-ZIP (with four subclasses: I to IV), WOX, NDX, PHD, PLINC, LD, DDT, SAWADEE, PINTOX, and the two TALE classes KNOX and BEL. Most of these classes encode additional domains apart from the homeodomain. Numerous insights have been obtained in the last two decades into how homeodomain proteins bind to DNA and increase their specificity by interacting with other proteins to regulate cell- and tissue-specific gene expression. Not only protein-DNA base pair contacts are important for proper target selection; recent experiments also reveal that the shape of the DNA plays a role in specificity. Using selected examples, we highlight different mechanisms of homeodomain protein-DNA interaction. The PRD class of homeobox genes was of special interest to Walter Gehring in the last two decades. The PRD class comprises six families in Bilateria, and tinkers with four different motifs, i.e., the PAIRED domain, the Groucho-interacting motif EH1 (aka Octapeptide or TN), the homeodomain, and the OAR motif. Homologs of the co-repressor protein Groucho are also present in plants (TOPLESS), where they have been shown to interact with small amphipathic motives (EAR), and in yeast (TUP1), where we find an EH1-like motif in MAT?2. Electronic supplementary material The online version of this article (doi:10.1007/s00412-015-0543-8) contains supplementary material, which is available to authorized users. R Bürglin, Thomas & Affolter, Markus. (2015). Homeodomain proteins: an update. Chromosoma. 125. . 10.1007/s00412-015-0543-8.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:46 PM
4
04
46
PM
PDT}

This Special Issue of Journal of Developmental Biology (JDB) covers an indeed very “special” (at least to me) family of highly evolutionarily conserved genes, the Hox genes. Despite over three decades having passed since the discovery of the homeobox, the excellent level and the wide range of topics of the articles and reviews published in this Special Issue testify the long-standing and ongoing interest in the functions of this unique gene family. The studies gathered in this issue of JDB cover subjects ranging from the use of Hox genes as a paradigm for the development of computational methods of protein family classification, to the role of Hox genes in the development and evolution of appendices, and the mechanisms underlying the expression of specific Hox proteins. Zappavigna, Vincenzo. (2017). Special Issue on HOX Genes in Development. Journal of Developmental Biology. 5. 5. 10.3390/jdb5020005.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:43 PM
4
04
43
PM
PDT}

Genitalia are among the most studied phenotypes because they exhibit high anatomical diversity, experience fast evolutionary rates and may be shaped by several evolutionary mechanisms. A key element to uncover the mechanisms behind such impressive diversity is their copulatory function. This topic has been overlooked, especially concerning structures not directly involved in sperm transfer and reception. Here, we conduct a hypothesis-driven experimental study to elucidate the operation of various external genital parts in five species of stink bugs with differing levels of phylogenetic relatedness. These insects are unique because their male and female genitalia are externally well developed, rigid and composed of multiple components. In contrast with their anatomical complexity and diversity, we show that genital structures work jointly to perform a single function of mechanical stabilization during copula. However, distinct lineages have evolved alternative strategies to clasp different parts of the opposite sex. In spite of a high functional correspondence between male and female traits, the overall pattern of our data does not clearly support an intersexual coevolutionary scenario. We propose that the extraordinary male genital diversity in the family is probably a result of a process of natural selection enhancing morphological accommodation, but we consider alternative mechanisms. Genevcius, Bruno. (2017). Strong functional integration among multiple parts of the complex male and female genitalia of stink bugs. Biological Journal of the Linnean Society. 1-13. 10.1093/biolinnean/blx095.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:33 PM
4
04
33
PM
PDT}

The copulatory process in animals is preceded by a series of integrated communication processes which are often under selection to guarantee species-specific courtship and copula. However, individuals of species supposedly in reproductive isolation frequently copulate in nature, which has sparked the attention of evolutionary biologists for decades. While studies on this topic have strongly focused on recently diverged species or populations, few instances of heterospecific copula between distantly related species are known. Here we report an intriguing case of interspecific copula between two distantly related species of stink bugs in nature. We replicated this observation in laboratory conditions and revealed an asymmetric relation: males of Chinavia obstinata copulated with females of C. erythrocnemis but the reverse combination did not occur. We propose a series of hypotheses to explain our observations in the light of the current knowledge on mate recognition and reproductive isolation in stink bugs, considering the potential pre- and postcopulatory barriers involved. Once these two species have probably evolved in allopatry and contacted secondarily, the absence of directional selection against mating signals differentiation is a probable process. We argue that similarities in genital shape and size, most likely a result of convergent evolution, may have played a fundamental role in guaranteeing that these species achieved proper coupling. Bianchi, Filipe & Genevcius, Bruno & da S. Vicentini, Barbara. (2017). Heterospecific mating between distantly related species of stink bugs and its evolutionary implications. Journal of Natural History. 51. 1-9. 10.1080/00222933.2017.1395095.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:29 PM
4
04
29
PM
PDT}

Despite claims that genitalia are among the fastest evolving phenotypes, few studies have tested this trend in a quantitative and phylogenetic framework. In systems where male and female genitalia coevolve, there is a growing effort to explore qualitative patterns of evolution and their underlying mechanisms, but the temporal aspect remains overlooked. An intriguing question is how fast male and female genitalia may change in a coevolutionary scenario. Here we apply a series of comparative phylogenetic analyses to reveal a scenario of correlated evolution and to investigate how fast male and female external, non-homologous and functionally integrated genitalia change in a group of stink bugs. We report three findings: the female gonocoxite 8 and the male pygophore showed a clear pattern of correlated evolution, both genitalia were estimated to evolve much faster than non-genital traits, and rates of evolution of the male genitalia were twice as fast as the female genitalia. Our results corroborate the widely held view that male genitalia evolve fast and add to the scarce evidence for rapidly evolving female genitalia. Different rates of evolution exhibited by males and females suggest either distinct forms or strengths of selection, despite their tight functional integration and coevolution. The morphological characteristic of this coevolutionary trend are more consistent with a cooperative adjustment of the genitalia, suggesting a scenario of female choice, morphological accommodation, lock-and-key or some combination of the three This article is protected by copyright. All rights reserved. Genevcius, Bruno & Caetano, Daniel & Schwertner, Cristiano. (2016). Rapid differentiation and asynchronous coevolution of male and female genitalia in stink bugs. Journal of evolutionary biology. 30. . 10.1111/jeb.13026.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:28 PM
4
04
28
PM
PDT}

RNF20/Bre1 mediated H2B ubiquitination (H2Bub) has various physiological functions. Recently, we found that H2Bub participates in meiotic recombination by promoting chromatin relaxation during meiosis. We then analyzed the phylogenetic relationships among the E3 ligase for H2Bub, its E2 Rad6 and their partner WW domain-containing adapter with a coiled-coil (WAC) or Lge1, and found that the molecular mechanism underlying H2Bub is evolutionarily conserved from yeast to mammals. However, RNF20 has diverse physiological functions in different organisms, which might be caused by the evolutionary divergency of their domain/motif architectures. In the current extra view, we not only elucidate the evolutionarily conserved molecular mechanism underlying H2Bub, but also discuss the diverse physiological functions of RNF20 during meiosis. Wang, Liying & Cao, Cunwei & Wang, Fang & Zhao, Jianguo & Li, Wei. (2017). H2B ubiquitination: Conserved molecular mechanism, diverse physiologic functions of the E3 ligase during meiosis. Nucleus. 8. 00-00. 10.1080/19491034.2017.1330237.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:25 PM
4
04
25
PM
PDT}

Gene transcription requires the complex association of several factors, such as histone-modifying complexes, transcription factors, and chromatin remodeling factors. Among them, histone marks coordinate with each other extensively to modulate transcription. These marks can crosstalk with adjacent marks in cis or with marks present on other histones in trans to promote transcriptional activation or repression. In this chapter, we describe various crosstalk mechanisms potentiated by different histone marks, mainly histone lysine methylation, acetylation, monoubiquitination, phosphorylation, and arginine methylation. We also explain the role of chromatin-associated complexes that contain subunits with different functions and their coordination to modulate a single transcriptional response. These crosstalk mechanisms overall function as a cascade of events to help in the activation or repression of gene expression. Deregulation of these mechanisms result in pathological conditions like cancers, and understanding these pathways may greatly help in the development of specific therapeutic targets to cure diseases. Nagarajan, Sankari & Johnsen, Steven. (2016). Crosstalk Between Histone Modifications Integrates Various Signaling Inputs to Fine-Tune Transcriptional Output. Chromatin Signaling and Diseases. 217-239. 10.1016/B978-0-12-802389-1.00012-5.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
04:23 PM
4
04
23
PM
PDT}

Background Monoubiquitination of H2B (H2Bub1) is a largely enigmatic histone modification that has been linked to transcriptional elongation. Because of this association, it has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with increased gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes. Results Using conditional Rnf40 knockout mouse embryo fibroblasts, we show that genes occupied by low to moderate amounts of H2Bub1 are selectively regulated in response to Rnf40 deletion, whereas genes marked by high levels of H2Bub1 are mostly unaffected by Rnf40 loss. Furthermore, we find that decreased expression of RNF40-dependent genes is highly associated with widespread narrowing of H3K4me3 peaks. H2Bub1 promotes the broadening of H3K4me3 to increase transcriptional elongation, which together lead to increased tissue-specific gene transcription. Notably, genes upregulated following Rnf40 deletion, including Foxl2, are enriched for H3K27me3, which is decreased following Rnf40 deletion due to decreased expression of the Ezh2 gene. As a consequence, increased expression of some RNF40-“suppressed” genes is associated with enhancer activation via FOXL2. Conclusion Together these findings reveal the complexity and context-dependency whereby one histone modification can have divergent effects on gene transcription. Furthermore, we show that these effects are dependent upon the activity of other epigenetic regulatory proteins and histone modifications. Xie, Wanhua & Nagarajan, Sankari & J. Baumgart, Simon & Kosinsky, Robyn Laura & Najafova, Zeynab & Kari, Vijayalakshmi & Hennion, Magali & Indenbirken, Daniela & Bonn, Stefan & Grundhoff, Adam & Wegwitz, Florian & Mansouri, Ahmed & Johnsen, Steven. (2017). RNF40 regulates gene expression in an epigenetic context-dependent manner. Genome Biology. 18. . 10.1186/s13059-017-1159-5.Dionisio_{January 24, 2018
January
01
Jan
24
24
2018
12:56 PM
12
12
56
PM
PDT}

Usually I may not pay much attention to details and my reading comprehension is poor, but I 'cheaply' justify myself saying that I'm not a scientist, specially a mathematician. Here I've been disappointed by an alleged mathematician's apparent poor attention to accuracy, coherence, comprehension: 42 DiEb critical comment on Dionisio’s post @22 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648751 43 Dionisio responds to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648760 49 DiEb responds to Dionisio https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648890 50 Dionisio responds to DiEb 51 DiEb responds to Dionisio 52 Dionisio writes a related commentary https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648896 53 Dionisio writes a related commentary 55 DiEb comments on Dionisio @52 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648909 58 Dionisio responds to DiEb @49 in reference to 43 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648958 59 Dionisio responds to DiEb @55 60 DiEb responds 62 Dionisio responds to DiEb @55 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648985 63 DiEb responds 70 gpuccio writes to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649057 87 gpuccio writes to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649126 98 DiEb writes to gpuccio https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649257 103 gpuccio writes to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649277 122 gpuccio writes insightful comment https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649412 123 gpuccio writes insightful comment https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649414 152 Dionisio notes absence of DiEb’s response to gpuccio @103 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649598 186 Dionisio writes about the referenced papers 187 DiEb refers to gpuccio @186 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649680 188 DiEb comments 189 DiEb comments 190 DiEb comments 192 gpuccio writes to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649700 196 DiEb responds to gpuccio https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649714 202 gpuccio responds to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649723Dionisio_{January 23, 2018
January
01
Jan
23
23
2018
06:33 AM
6
06
33
AM
PDT}

@210 addendum (between 60 and 70) 62 Dionisio responds to DiEb @55 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648985 63 DiEb respondsDionisio_{January 23, 2018
January
01
Jan
23
23
2018
05:24 AM
5
05
24
AM
PDT}

@209 addendum (what preceded 70?) 42 DiEb comments on Dionisio's post @22 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648751 43 Dionisio responds to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648760 49 DiEb responds to Dionisio https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648890 50 Dionisio responds to DiEb 51 DiEb responds to Dionisio 52 Dionisio writes a related commentary https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648896 53 Dionisio writes a related commentary 55 DiEb comments on Dionisio @52 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648909 58 Dionisio responds to DiEb @49 in reference to 43 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-648958 59 Dionisio responds to DiEb @55 60 DiEb respondsDionisio_{January 23, 2018
January
01
Jan
23
23
2018
05:00 AM
5
05
00
AM
PDT}

@208 addendum (what preceded 103?) 70 gpuccio writes to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649057 87 gpuccio writes to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649126 98 DiEb writes to gpuccio https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649257Dionisio_{January 23, 2018
January
01
Jan
23
23
2018
03:52 AM
3
03
52
AM
PDT}

Mathematician's attention to details? 103 gpuccio writes to DiEb https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649277 122 gpuccio writes insightful comment https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649412 123 gpuccio writes insightful comment https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649414 152 Dionisio notes absence of DiEb's response to gpuccio @103 https://uncommondescent.com/evolution/this-parody-of-evo-devo-makes-it-sound-a-lot-like-id/#comment-649598 186 Dionisio writes about the referenced papers 187 DiEb refers to gpucchio @186Dionisio_{January 23, 2018
January
01
Jan
23
23
2018
03:30 AM
3
03
30
AM
PDT}

@204 addendum Off topic quote:
Due to the lapse in government funding, the information on this web site may not be up to date, transactions submitted via the web site may not be processed, and the agency may not be able to respond to inquiries until appropriations are enacted. Updates regarding government operating status and resumption of normal operations can be found at opm.gov.
just thought it’s an interesting example of the effects of sociopolitical situations on science.Dionisio_{January 22, 2018
January
01
Jan
22
22
2018
04:59 PM
4
04
59
PM
PDT}

ET @198, Thanks for reminding us not to take some objectors seriously. They lack what is required for engaging in serious discussions. They are usually experts in making noise. No substance. Poor things. BTW, there's hope. I've been there, done that too. For many years. A piece of wood or a rock were more serious discussants than I was. Really shameful. Simply embarrassing.Dionisio_{January 22, 2018
January
01
Jan
22
22
2018
02:21 PM
2
02
21
PM
PDT}

KF @201,
[...] many really important domains defy precising definition. For instance, define biological life.
You've touched a highly sensitive point indeed. Thanks for that important reminder. [emphasis added]Dionisio_{January 22, 2018
January
01
Jan
22
22
2018
02:06 PM
2
02
06
PM
PDT}

KF, Off topic quote:
PubMed is open, however it is being maintained with minimal staffing due to the lapse in government funding. Information will be updated to the extent possible, and the agency will attempt to respond to urgent operational inquiries. Updates regarding government operating status and resumption of normal operations can be found at opm.gov.
just thought it's an interesting example of the effects of sociopolitical events on science.Dionisio_{January 22, 2018
January
01
Jan
22
22
2018
01:57 PM
1
01
57
PM
PDT}

ET, I am positively trembling with fear of how my utter lack of intelligence, knowledge and ability to add up 2 and 3 have been exposed before the watching penumbra of animus sites. KFkairosfocus_{January 22, 2018
January
01
Jan
22
22
2018
01:30 PM
1
01
30
PM
PDT}

Prev 1 … 3 4 5 6 7 … 12 Next