Theoretical study of ArcB and its dimerization, interaction with anaerobic metabolites, and activation of ArcA.

The complex metabolism of has been extensively studied, including its response to oxygen availability. The ArcA/B two-component system (TCS) is the key regulator for the transition between these two environmental conditions and has been thoroughly characterized using genetic and biochemical approaches. Still, to date, limited structural data is available.

Two-Component System Sensor Kinases from Asgardian Archaea May Be Witnesses to Eukaryotic Cell Evolution.

The signal transduction paradigm in bacteria involves two-component systems (TCSs). are archaea that may have originated the current eukaryotic lifeforms. Most research on these archaea has focused on eukaryotic-like features, such as genes involved in phagocytosis, cytoskeleton structure, and vesicle trafficking.

Re-establishment of the genus (Leguminosae, Caesalpinioideae, mimosoid clade): the New World species formerly placed in .

Following recent mimosoid phylogenetic and phylogenomic studies demonstrating the non-monophyly of the genus , we present a new molecular phylogeny focused on the neotropical species in the genus, with much denser taxon sampling than previous studies. Our aims were to test the monophyly of the neotropical section Arthrosamanea, resolve species relationships, and gain insights into the evolution of fruit morphology. We perform a Bayesian phylogenetic analysis of sequences of nuclear internal and external transcribed spacer regions and trace the evolution of fruit dehiscence and lomentiform pods.

Catalases in the pathogenesis of research.

Pathogenic fungal infection success depends on the ability to escape the immune response. Most strategies for fungal infection control are focused on the inhibition of virulence factors and increasing the effectiveness of antifungal drugs. Nevertheless, little attention has been focused on their physiological resistance to the host immune system.

transcription factors of unknown function: sequence features and possible evolutionary relationships.

Organisms need mechanisms to perceive the environment and respond accordingly to environmental changes or the presence of hazards. Transcription factors (TFs) are required for cells to respond to the environment by controlling the expression of genes needed. has been the model bacterium for many decades, and still, there are features embedded in its genome that remain unstudied.

Gene Regulatory Network Inference and Gene Module Regulating Virulence in .

In this work, we inferred the gene regulatory network (GRN) of the fungus by using the regulatory networks of FGSC A4, OR74A, S288c, and PH-1 as templates for sequence comparisons. Topological properties to infer the role of transcription factors (TFs) and to identify functional modules were calculated in the GRN. From these analyzes, five TFs were identified as hubs, including FOXG_04688 and FOXG_05432, which regulate 2,404 and 1,864 target genes, respectively.

The Search for Cryptic L-Rhamnosyltransferases on the Genome.

The fungal cell wall is an attractive structure to look for new antifungal drug targets and for understanding the host-fungus interaction. is one of the main causative agents of both human and animal sporotrichosis and currently is the species most studied of the genus. The cell wall of this organism has been previously analyzed, and rhamnoconjugates are signature molecules found on the surface of both mycelia and yeast-like cells.

Universal Primers for Detection of Novel Plant Capsid-Less Viruses: Papaya Umbra-like Viruses as Example.

For diagnosis of positive-sense single-stranded RNA viruses, primers are usually raised against the sequence encoding capsid proteins, since structural proteins are more conserved. This chapter focuses on the design of primers for a group of novel viruses lacking a capsid, known as papaya Umbra-like viruses (unassigned genus) associated with Papaya Sticky Disease, which represent a threat to papaya production. Based on sequence alignments of a region encoding the RNA-dependent RNA Polymerase, universal primers to detect all the known viruses from four countries are proposed.

Auxin perception in Agave is dependent on the species' Auxin Response Factors.

Auxins are one of the most important and studied phytohormones in nature. Auxin signaling and perception take place in the cytosol, where the auxin is sensed. Then, in the nucleus, the auxin response factors (ARF) promote the expression of early-response genes.

Data mining of metagenomes to find novel enzymes: a non-computationally intensive method.

Currently, there is a need of non-computationally-intensive bioinformatics tools to cope with the increase of large datasets produced by Next Generation Sequencing technologies. We present a simple and robust bioinformatics pipeline to search for novel enzymes in metagenomic sequences. The strategy is based on pattern searching using as reference conserved motifs coded as regular expressions.

A Lineage of Begomoviruses Encode Rep and AC4 Proteins of Enigmatic Ancestry: Hints on the Evolution of Geminiviruses in the New World.

The begomoviruses (BGVs) are plant pathogens that evolved in the Old World during the Cretaceous and arrived to the New World (NW) in the Cenozoic era. A subgroup of NW BGVs, the " (SLCV) lineage" (S-Lin), includes viruses with unique characteristics. To get clues on the evolutionary origin of this lineage, a search for divergent members was undertaken.

Molecular characterization of laccase genes from the basidiomycete Bm-2 and analysis of the 5' untranslated region (5'UTR).

The aim of this study was to identify and characterize laccase genes produced by Bm-2 in a liquid medium, both with and without induction. The amplification of 5'and 3'regions of laccase sequences was obtained by the RACE-PCR method, and these were assembled to obtain a cDNA of total length. Two new laccase genes were isolated from basal medium (-) and lignocellulosic grapefruit substrate (-), both encoding open reading frames of 2566 bp.

Ploidy Determination in the Pathogenic Fungus spp.

The pathogenic clade of the genus comprises the etiological agents of sporotrichosis, a worldwide emergent disease. Despite the growing understanding of their successful pathogen traits, there is little information on genome sizes and ploidy within the genus. Therefore, in this work, we evaluated the ploidy of four species of the genus, specifically , , , and .

Genetic Variability in E6 and E7 Oncogenes from Human Papillomavirus Type 58 in Mexican Women.

Background/aims: The study aimed to describe human papillomavirus (HPV) 58 genetic variability in E6 and E7 oncogenes from women in southeast Mexico and their phylogenetic relationships with the sequences from other geographical regions.

Methods: The E6-E7 region was amplified by nested PCR, and sequenced for identification of polymorphisms, phylogenetic trees construction, and haplotype and fixation tests.

Results: HPV58 positive samples were obtained from a repository, 54 were amplified, 47 sequences for the E6 gene, and 51 sequences for the E7 gene were obtained.

A computationally simplistic poly-phasic approach to explore microbial communities from the Yucatan aquifer as a potential sources of novel natural products.

The need for new antibiotics has sparked a search for the microbes that might potentially produce them. Current sequencing technologies allow us to explore the biotechnological potential of microbial communities in diverse environments without the need for cultivation, benefitting natural product discovery in diverse ways. A relatively recent method to search for the possible production of novel compounds includes studying the diverse genes belonging to polyketide synthase pathways (PKS), as these complex enzymes are an important source of novel therapeutics.

Characterization of N-Acetylglucosamine Biosynthesis in Pneumocystis species. A New Potential Target for Therapy.

N-acetylglucosamine (GlcNAc) serves as an essential structural sugar on the cell surface of organisms. For example, GlcNAc is a major component of bacterial peptidoglycan, it is an important building block of fungal cell walls, including a major constituent of chitin and mannoproteins, and it is also required for extracellular matrix generation by animal cells. Herein, we provide evidence for a uridine diphospho (UDP)-GlcNAc pathway in Pneumocystis species.

Large-scale phylogenetic classification of fungal chitin synthases and identification of a putative cell-wall metabolism gene cluster in Aspergillus genomes.

The cell wall is a protective and versatile structure distributed in all fungi. The component responsible for its rigidity is chitin, a product of chitin synthase (Chsp) enzymes. There are seven classes of chitin synthase genes (CHS) and the amount and type encoded in fungal genomes varies considerably from one species to another.

prfectBLAST: a platform-independent portable front end for the command terminal BLAST+ stand-alone suite.

prfectBLAST is a multiplatform graphical user interface (GUI) for the stand-alone BLAST+ suite of applications. It allows researchers to do nucleotide or amino acid sequence similarity searches against public (or user-customized) databases that are locally stored. It does not require any dependencies or installation and can be used from a portable flash drive.

The sexual state of Aspergillus parasiticus.

The sexual state of Aspergillus parasiticus, a potent aflatoxin-producing fungus within section Flavi, is described. The production of nonostiolate ascocarps surrounded by a separate peridium within the stroma places the teleomorph in genus Petromyces. Petromyces parasiticus differs from P.

Sexual reproduction and recombination in the aflatoxin-producing fungus Aspergillus parasiticus.

The fungal phylum Ascomycota comprises a large proportion of species with no known sexual stage, despite high genetic variability in field populations. One such asexual species, Aspergillus parasiticus, is a potent producer of carcinogenic and hepatotoxic aflatoxins, polyketide-derived secondary metabolites that contaminate a wide variety of agricultural crops. In this study, individuals of A.

Characterization and population analysis of the mating-type genes in Aspergillus flavus and Aspergillus parasiticus.

We characterize the mating-type genes in Aspergillus flavus,Aspergillus parasiticus and Petromyces alliaceus. A single MAT1-1 or MAT1-2 gene was detected in the genomes of A. flavus and A.

Recombination, balancing selection and adaptive evolution in the aflatoxin gene cluster of Aspergillus parasiticus.

Aflatoxins are toxic and carcinogenic polyketides produced by several Aspergillus species that are known to contaminate agricultural commodities, posing a serious threat to animal and human health. Aflatoxin (AF) biosynthesis is almost fully characterized and involves the coordinated expression of approximately 25 genes clustered in a 70-kb DNA region. Aspergillus parasiticus is an economically important and common agent of AF contamination.

Gene duplication, modularity and adaptation in the evolution of the aflatoxin gene cluster.

Background: The biosynthesis of aflatoxin (AF) involves over 20 enzymatic reactions in a complex polyketide pathway that converts acetate and malonate to the intermediates sterigmatocystin (ST) and O-methylsterigmatocystin (OMST), the respective penultimate and ultimate precursors of AF. Although these precursors are chemically and structurally very similar, their accumulation differs at the species level for Aspergilli. Notable examples are A.

cry1Aa lacks stability elements at its 5'-UTR but integrity of its transcription terminator is critical to prevent decay of its transcript.

We analyzed the influence of the 5' and 3' untranslated regions of the Bacillus thuringiensis cry1Aa on its mRNA stability. Although the cry1Aa gene has a stable transcript (8 min), its 5' UTR did not provide stability to the reporter gene uidA. Stability of cry1Aa could be increased to 40 min by addition of an SP82 stability element at the 5' UTR, suggesting that once the 5' and 3' ends were protected initiation of decay could be effectively blocked.