RegulonDB v12.0: a comprehensive resource of transcriptional regulation in E. coli K-12.

RegulonDB is a database that contains the most comprehensive corpus of knowledge of the regulation of transcription initiation of Escherichia coli K-12, including data from both classical molecular biology and high-throughput methodologies. Here, we describe biological advances since our last NAR paper of 2019. We explain the changes to satisfy FAIR requirements. We also present a full reconstruction of the RegulonDB computational infrastructure, which has significantly improved data storage, retrieval and accessibility and thus supports a more intuitive and user-friendly experience. The integration of graphical tools provides clear visual representations of genetic regulation data, facilitating data interpretation and knowledge integration. RegulonDB version 12.0 can be accessed at https://regulondb.ccg.unam.mx.

Unitarity and Low Energy Expansion of the Coon Amplitude.

The Coon amplitude is a deformation of the Veneziano amplitude with logarithmic Regge trajectories and an accumulation point in the spectrum, which interpolates between string theory and field theory. With string theory, it is the only other solution to duality constraints explicitly known and it constitutes an important data point in the modern S-matrix bootstrap. Yet, its basics properties are essentially unknown. In this Letter, we fill this gap and derive the conditions of positivity and the low energy expansion of the amplitude. On the positivity side, we discover that the amplitude switches from a regime where it is positive in all dimensions to a regime with critical dimensions, which connects to the known d=26, 10 when the deformation is removed. Incidentally, we find that the Veneziano amplitude can be extended to massive scalars of masses up to m^{2}=1/3, where it has critical dimension 6.3. On the low-energy side, we compute the first few couplings of the theory in terms of q-deformed analogs of the standard Riemann zeta values of the string expansion. We locate their location in the EFT-hedron, and find agreement with a recent conjecture that theories with accumulation points populate this space. We also discuss their relation to low spin dominance. Finally, we comment on the length of the Coon parton.

RegulonDB 11.0: Comprehensive high-throughput datasets on transcriptional regulation in Escherichia coli K-12.

Genomics has set the basis for a variety of methodologies that produce high-throughput datasets identifying the different players that define gene regulation, particularly regulation of transcription initiation and operon organization. These datasets are available in public repositories, such as the Gene Expression Omnibus, or ArrayExpress. However, accessing and navigating such a wealth of data is not straightforward. No resource currently exists that offers all available high and low-throughput data on transcriptional regulation in Escherichia coli K-12 to easily use both as whole datasets, or as individual interactions and regulatory elements. RegulonDB (https://regulondb.ccg.unam.mx) began gathering high-throughput dataset collections in 2009, starting with transcription start sites, then adding ChIP-seq and gSELEX in 2012, with up to 99 different experimental high-throughput datasets available in 2019. In this paper we present a radical upgrade to more than 2000 high-throughput datasets, processed to facilitate their comparison, introducing up-to-date collections of transcription termination sites, transcription units, as well as transcription factor binding interactions derived from ChIP-seq, ChIP-exo, gSELEX and DAP-seq experiments, besides expression profiles derived from RNA-seq experiments. For ChIP-seq experiments we offer both the data as presented by the authors, as well as data uniformly processed in-house, enhancing their comparability, as well as the traceability of the methods and reproducibility of the results. Furthermore, we have expanded the tools available for browsing and visualization across and within datasets. We include comparisons against previously existing knowledge in RegulonDB from classic experiments, a nucleotide-resolution genome viewer, and an interface that enables users to browse datasets by querying their metadata. A particular effort was made to automatically extract detailed experimental growth conditions by implementing an assisted curation strategy applying Natural language processing and machine learning. We provide summaries with the total number of interactions found in each experiment, as well as tools to identify common results among different experiments. This is a long-awaited resource to make use of such wealth of knowledge and advance our understanding of the biology of the model bacterium E. coli K-12.

Fisiología del esfínter velofaríngeo durante la deglución. Revisión sistemática de literatura

Resumen El objetivo de este artículo es describir el funcionamiento del esfínter velofaríngeo (EVF) durante la deglución, mediante una revisión de literatura. En febrero de 2020, las bases de datos electrónicas Medline, LILACS, SciELO e IBECS, fueron consultadas retrospectivamente, usando las palabras claves en inglés: "velopharyngeal sphincter" o "pharyngeal muscles". Fueron seleccionados artículos originales que describen la fisiología del EVF en la deglución de adultos sanos. Para este estudio fue creado un protocolo que contempla lo siguiente: autor, año, país, número y características de los participantes, actividades evaluadas, metodologías e instrumentos utilizados y principales resultados. Fueron encontrados 4.124 artículos. 3.863 fueron excluidos luego de la lectura de los títulos, 239 luego de lectura de los resúmenes y 8 luego de la revisión de los textos completos. Finalmente, 14 artículos fueron analizados en esta revisión. Se discuten eventos espaciales y temporales del EVF, la actividad electromiográfica de la musculatura del EVF y la presión velofaríngea durante la deglución en adultos sanos. Se concluye que el esfínter velofaríngeo cumple un rol importante en la fase faríngea de la deglución, que debe ser profundizado en futuras investigaciones.

Abstract The aim of this article is to describe the functioning of the velopharyngeal sphincter (VPS) during swallowing, through a literature review. In February 2020, the electronic databases Medline, LILACS, SciELO and IBECS were retrospectively consulted, using the key words in English: "velopharyngeal sphincter" or "pharyngeal muscles". Original articles were selected that describe the physiology of VPS in healthy adult swallowing. For this study it was created a protocol that includes the following items: author, year, country, number and characteristics of the participants, evaluated activities, methodologies and instruments used, and main results. 4124 articles were found. 3,863 were excluded after reading the titles, 239 after reading the abstracts and 8 after reviewing the full texts. Finally, 14 articles were analyzed in this review. Spatial and temporal events of the VPS, the electromyographic activity of the VPS musculature, and velopharyngeal pressure during swallowing in healthy adults are discussed. We conclude that the velopharyngeal sphincter plays an important role in the pharyngeal phase of swallowing, which should be studied in depth in future research.

An image J plugin for the high throughput image analysis of in vitro scratch wound healing assays.

In vitro scratch wound healing assay, a simple and low-cost technique that works along with other image analysis tools, is one of the most widely used 2D methods to determine the cellular migration and proliferation in processes such as regeneration and disease. There are open-source programs such as imageJ to analyze images of in vitro scratch wound healing assays, but these tools require manual tuning of various parameters, which is time-consuming and limits image throughput. For that reason, we developed an optimized plugin for imageJ to automatically recognize the wound healing size, correct the average wound width by considering its inclination, and quantify other important parameters such as: area, wound area fraction, average wound width, and width deviation of the wound images obtained from a scratch/ wound healing assay. Our plugin is easy to install and can be used with different operating systems. It can be adapted to analyze both individual images and stacks. Additionally, it allows the analysis of images obtained from bright field, phase contrast, and fluorescence microscopes. In conclusion, this new imageJ plugin is a robust tool to automatically standardize and facilitate quantification of different in vitro wound parameters with high accuracy compared with other tools and manual identification.

A key for hypoxia genetic adaptation in alpaca could be a HIF1A truncated bHLH protein domain / Una clave para la adaptacion genética de la hypoxia en las alpacas podria ser un dominio de proteina bHLH truncado con HIF1A

Animals exposed to hypobaric hypoxia triggers a physiological hypoxia response via Hypoxia Inducible Factor (HIF) proteins that functions as transcriptional complexes. As the South American camelids inhabit at high Andean altitudes we have asked if they have developed genetic adaptations to live at high altitudes. In the present study we investigate genetic structures of the HIF1A proteins carried by members of the superorder Cetartiodactyla. During our investigation we discovered the existence of a genetic event that caused the loss of most of the bHLH domain in the proteins borne by the Alpaca and other members of the Cetartiodactyla superorder; we designate them as bHLH short sequences. Further analysis at the nucleotide level revealed in the 12 short sequences included in the study the presence at the 5´end of the bHLH domains stop codons. Seven out of the 12 short HIF1A proteins, have an identical or almost identical nucleotide sequence at their 5´end with a same TAA stop codon and at the same position. As the mutations affects to both the Artiodactyls and Cetaceans, we postulate that the mutation(s) occurred before their divergence about 55 million years ago. The relevance of these findings for genetic adaptation of Alpacas to hypobaric hypoxia of high altitude conditions is discussed.

Los animales expuestos a hypoxia hipobárica generan una respuesta hipóxica fisiológica debido a unas proteinas de Factor-Hipoxia Inducible (HIF) que funcionan como complejos transcripcionales. Debido a que los camelidos Americanos habitan en las grandes alturas andinas, nos hemos preguntado si han desarrollado una adaptación genética para vivir a grandes alturas. Eneste estudio hemos investigado la estructura genética de las proteinas HIF1A que llevan consigo los miembros de la superorden de los cetartiodáctilos. Durante nuestra investigación, descubrimos la existencia de un evento genético que causó la perdida de la mayoría del dominio bHLH en las proteinas transmitidas por la alpaca y otros miembros de la superorden de los cetartiodáctilos; las hemos designado como secuencias cortas de bHLH. Análisis posteriores a nivel nucleótido revelaron que en la doceava secuencia corta incluida en el studio, hubo presencia de codones de terminación en el extreme 5' del dominio de bHLH. Siete de las doce proteinas cortas HIF1A, tiene una secuencia idéntica o casi idéntica de nucleotidos en su extremo 5', con el mismo codón de terminación TAA y en la misma posición. Debido a que la mutación afecta tanto a Artiodáctilos como Cetáceos, proponemos que la mutación(es) ocurrió antes de su divergencia hace unos 55 millones de años. Analizamos la relevancia de estos descubrimientos sobre la adaptación genética de las alpacas a la hipoxia hipobárica en condiciones de grandes alturas.

Role of gap junctions and hemichannels in parasitic infections.

In vertebrates, connexins (Cxs) and pannexins (Panxs) are proteins that form gap junction channels and/or hemichannels located at cell-cell interfaces and cell surface, respectively. Similar channel types are formed by innexins in invertebrate cells. These channels serve as pathways for cellular communication that coordinate diverse physiologic processes. However, it is known that many acquired and inherited diseases deregulate Cx and/or Panx channels, condition that frequently worsens the pathological state of vertebrates. Recent evidences suggest that Cx and/or Panx hemichannels play a relevant role in bacterial and viral infections. Nonetheless, little is known about the role of Cx- and Panx-based channels in parasitic infections of vertebrates. In this review, available data on changes in Cx and gap junction channel changes induced by parasitic infections are summarized. Additionally, we describe recent findings that suggest possible roles of hemichannels in parasitic infections. Finally, the possibility of new therapeutic designs based on hemichannel blokers is presented.

A genome-wide survey of Major Histocompatibility Complex (MHC) genes and their paralogues in zebrafish.

BACKGROUND: The genomic organisation of the Major Histocompatibility Complex (MHC) varies greatly between different vertebrates. In mammals, the classical MHC consists of a large number of linked genes (e.g. greater than 200 in humans) with predominantly immune function. In some birds, it consists of only a small number of linked MHC core genes (e.g. smaller than 20 in chickens) forming a minimal essential MHC and, in fish, the MHC consists of a so far unknown number of genes including non-linked MHC core genes. Here we report a survey of MHC genes and their paralogues in the zebrafish genome. RESULTS: Using sequence similarity searches against the zebrafish draft genome assembly (Zv4, September 2004), 149 putative MHC gene loci and their paralogues have been identified. Of these, 41 map to chromosome 19 while the remaining loci are spread across essentially all chromosomes. Despite the fragmentation, a set of MHC core genes involved in peptide transport, loading and presentation are still found in a single linkage group. CONCLUSION: The results extend the linkage information of MHC core genes on zebrafish chromosome 19 and show the distribution of the remaining MHC genes and their paralogues to be genome-wide. Although based on a draft genome assembly, this survey demonstrates an essentially fragmented MHC in zebrafish.

The phylogenetic relationship of tetrapod, coelacanth, and lungfish revealed by the sequences of forty-four nuclear genes.

The origin of tetrapods is a major outstanding issue in vertebrate phylogeny. Each of the three possible principal hypotheses (coelacanth, lungfish, or neither being the sister group of tetrapods) has found support in different sets of data. In an attempt to resolve the controversy, sequences of 44 nuclear genes encoding amino acid residues at 10,404 positions were obtained and analyzed. However, this large set of sequences did not support conclusively one of the three hypotheses. Apparently, the coelacanth, lungfish, and tetrapod lineages diverged within such a short time interval that at this level of analysis, their relationships appear to be an irresolvable trichotomy.

Origin and speciation of haplochromine fishes in East African crater lakes investigated by the analysis of their mtDNA, Mhc genes, and SINEs.

The Western Branch of the East African Great Rift Valley is pocketed with craters of extinct or dormant volcanoes. Many of the craters are filled with water, and the lakes are inhabited by fishes. The objective of the present study was to determine the amount and nature of genetic variation in haplochromine fishes inhabiting two of these crater lakes, Lake Lutoto and Lake Nshere, and to use this information to infer the origin and history of the two populations. To this end, sequences of mitochondrial (mt) DNA control region, exon 2 of major histocompatibility complex (Mhc) class II B genes, and short interspersed elements (SINEs) were analyzed. The results indicate that the Lake Nshere and Lake Lutoto fishes originated from different but related large founding populations derived from the Kazinga Channel, which connects Lake Edward and Lake George. Some of the genetic polymorphism that existed in the ancestral populations was lost in the populations of the two lakes. The polymorphism that has been retained has persisted for some 50000 generations (years). During this time, new mutations arose and became fixed in each of the two populations in the mtDNA, giving rise to sets of diagnostic substitutions. Each population evolved in isolation after the colonization of the lakes less than 50000 years ago. There appears to be no population structure within the crater lake fishes, and their present effective population sizes are in the order of 104 to 105 individuals. Comparisons with the endemic haplochromine species of Lake Victoria reveal interesting parallels, as well as differences, which may help to understand the nature of the speciation process.

Identification of chemokines and a chemokine receptor in cichlid fish, shark, and lamprey.

Chemokines are small, inducible, structurally related proteins that guide cells expressing the right chemokine receptors to sites of immune response. They have been identified and studied extensively in mammals, but little is known about their presence in other vertebrate groups. Here we describe seven new chemokines in bony fish and one in a cartilaginous fish, as well as one chemokine receptor in a jawless vertebrate. All eight chemokines belong to the SCYA (CC) subfamily characterized by four conserved cysteine residues of which the first two are adjacent. The chemokine receptor is of the CXCR4 type. Phylogenetic analysis does not reveal any clear evidence of orthology of fish and human chemokines. Although the divergence of the subfamilies began before the fish-tetrapod split, much of the divergence within the subfamilies took place separately in the two vertebrate groups. The existence of a chemokine receptor in the lamprey indicates that chemokines are apparently also present in the Agnatha.

Macrophage migration inhibitory factor (MIF) of jawed and jawless fishes: implications for its evolutionary origin.

The macrophage migration inhibitory factor (MIF) is a cytokine produced by T lymphocytes and macrophages in response to inflammatory stimuli. We sequenced MIF cDNA clones of two jawless fishes, the sea lamprey (Petromyzon marinus) and the North Atlantic hagfish (Myxine glutinosa), as well as of the jawed (cichlid) fish Paralabidochromis chilotes. The fish MIF-encoding genes have the same exon-intron organization as the mammalian MIF genes and are present in one copy per haploid genome. Secondary and tertiary structure predictions suggest that the fish MIF proteins have a topology characteristic of the entire MIF-family of proteins. Phylogenetic analysis separates the known nematode members of the family into two groups, one having a sister group relationship with the mammalian D-dopachrome tautomerase (DDT) proteins and the other being related to vertebrate MIFs. It also reveals a high degree of convergent evolution among the members of the family. Finally, it suggests that the divergence of MIF and DDT occurred before the emergence of nematodes in metazoan evolution.

Molecular phylogeny of early vertebrates: monophyly of the agnathans as revealed by sequences of 35 genes.

Extant vertebrates are divided into three major groups: hagfishes (Hyperotreti, myxinoids), lampreys (Hyperoartia, petromyzontids), and jawed vertebrates (Gnathostomata). The phylogenetic relationships among the groups and within the jawed vertebrates are controversial, for both morphological and molecular studies have rendered themselves to conflicting interpretations. Here, we use the sequences of 35 nuclear protein-encoding genes to provide definitive evidence for the monophyly of the Agnatha (jawless vertebrates, a group encompassing the hagfishes and lampreys). Our analyses also give a strong support for the separation of Chondrichthyes (cartilaginous fishes) before the divergence of Osteichthyes (bony fishes) from the other gnathostomes.

Evidence that the separation of Mhc class II from class I loci in the zebrafish, Danio rerio, occurred by translocation.

In the zebrafish, Danio rerio, and other teleosts, the class I and class II loci of the major histocompatibility complex ( Mhc) reside on different chromosomes. To shed light on the events that might have generated this difference from tetrapods, in which these two types of loci are clustered in a single chromosomal region, the organization of the class II loci in linkage group 8 of the zebrafish was determined by the characterization of contigs of PAC clones. Three contigs were defined: DAB, DCB, and DBB. The 350-kb-long DAB contig contained only four genes: DDB, DAB, SLC7A4, and DAA. The 150-kb-long DCB contig contained the DCB, DCA, and fz10 genes at an undetermined distance from the DAB contig. And the 120-kb-long DBB contig comprised the DBB gene presumably in another linkage group. The low gene density of the linkage group 8 contigs, contrasting with the high gene density of the zebrafish class I region, and the close association with genes [ SLC7A4 coding for an amino acid transporter, and fz10 (frizzled 10) coding for a receptor of the WNT glycoprotein] that are not linked with the tetrapod Mhc, is interpreted to mean that the separation of the class II from class I loci in teleosts occurred by translocation rather than by genomic or chromosomal duplication.

Sequencing of amphioxus PSMB5/8 gene and phylogenetic position of agnathan sequences.

Reanalyses of vertebrate PSMB5 and PSMB8 genes were conducted with a newly obtained amphioxus sequence. The phylogenetic analysis indicated that the amphioxus sequence is an outgroup of both vertebrate PSMB5 and PSMB8 genes. The agnathan sequences were previously thought to be closer to PSMB5 than PSMB8 sequences. However, in this study the phylogenetic trees supported the clustering of agnathan sequences with PSMB8 rather than with PSMB5 sequences. In the alignment there are many sites in which the agnathan sequences are more similar to PSMB5 than PSMB8 sequences. Parsimony analysis showed that the amino acid pattern at these sites could be explained by one substitution on the ancestral branch leading to the jawed vertebrate PSMB8 cluster. The number of substitutions required at these sites was the same for different tree topologies with respect to the position of agnathans. The phylogenetic analyses of PSMB6/PSMB9 and PSMB7/PSMB10 genes indicated that all the interferon-gamma-inducible forms have evolved two to three times faster than the housekeeping forms in the jawed vertebrate lineage. Hence although the agnathan sequences cluster with the PSMB8 sequences, they have a slower rate of evolution similar to that of the housekeeping forms, and may be functioning as housekeeping forms.

Persistence of Mhc heterozygosity in homozygous clonal killifish, Rivulus marmoratus: implications for the origin of hermaphroditism.

The mangrove killifish Rivulus marmoratus, a neotropical fish in the order Cyprinodontiformes, is the only known obligatorily selfing, synchronous hermaphroditic vertebrate. To shed light on its population structure and the origin of hermaphroditism, major histocompatibility complex (Mhc) class I genes of the killifish from seven different localities in Florida, Belize, and the Bahamas were cloned and sequenced. Thirteen loci and their alleles were identified and classified into eight groups. The loci apparently arose approximately 20 million years ago (MYA) by gene duplications from a single common progenitor in the ancestors of R. marmoratus and its closest relatives. Distinct loci were found to be restricted to different populations and different individuals in the same population. Up to 44% of the fish were heterozygotes at Mhc loci, as compared to near homozygosity at non-Mhc loci. Large genetic distances between some of the Mhc alleles revealed the presence of ancestral allelic lineages. Computer simulation designed to explain these findings indicated that selfing is incomplete in R. marmoratus populations, that Mhc allelic lineages must have diverged before the onset of selfing, and that the hermaphroditism arose in a population containing multiple ancestral Mhc lineages. A model is proposed in which hermaphroditism arose stage-wise by mutations, each of which spread through the entire population and was fixed independently in the emerging clones.