The regulation of the pyrimidine biosynthetic pathway by pyrimidines was investigated in the biological control agent Pseudomonas aureofaciens ATCC 17418. Using succinate as a carbon source, orotic acid or uracil supplementation had a repressive effect in ATCC 17418 cells on dihydroorotate dehydrogenase or orotidine 5'- monophosphate decarboxylase activity but only orotic acid supplementation appeared to repress the level of orotate phosphoribosyltransferase activity. In glucose-grown ATCC 17418 cells, orotic acid supplementation appeared to repress the level of phosphoribosyltransferase or decarboxylase while uracil supplementation depressed the dihydroorotase, dehydrogenase, and decarboxylase activities. The pyrimidine auxotrophic mutant strain GW-2, isolated from ATCC 17418 using chemical mutagenesis and resistance to 5-fluoroorotic acid, was found to be deficient for orotidine 5'-monophosphate decarboxylase activity. Pyrimidine limitation of the succinate-grown mutant strain cells resulted in only a slight derepression of transcarbamoylase activity while pyrimidine limitation of glucose-grown mutant cells caused a derepression of the four active pyrimidine biosynthetic enzyme activities relative to their activities in the mutant cells grown with excess uracil. The control of the known regulatory enzyme aspartate transcarbamoylase was examined in P. aureofaciens ATCC 17418. Transcarbamoylase activity was shown to be inhibited by pyrophosphate, ATP, UTP, and ADP. It was concluded that the pyrimidine biosynthetic pathway in P. aureofaciens ATCC 17418 was subject to regulation at the transcriptional level and at the level of aspartate transcarbamoylase activity, which could be valuable in comprehending its nucleic acid metabolism as well as its taxonomic assignment to the Pseudomonas chlororaphis homology group.
- MeSH
- aspartátkarbamoyltransferasa metabolismus MeSH
- bakteriální proteiny metabolismus genetika MeSH
- biosyntetické dráhy MeSH
- dihydroorotátdehydrogenasa MeSH
- glukosa metabolismus MeSH
- kyselina jantarová metabolismus MeSH
- kyselina orotová metabolismus MeSH
- orotátfosforibosyltransferasa metabolismus MeSH
- orotidin-5'-fosfátdekarboxylasa metabolismus genetika MeSH
- oxidoreduktasy působící na CH-CH vazby metabolismus MeSH
- Pseudomonas * metabolismus genetika enzymologie MeSH
- pyrimidiny * biosyntéza MeSH
- regulace genové exprese u bakterií * MeSH
- uracil metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
RNA secondary (2D) structure visualization is an essential tool for understanding RNA function. R2DT is a software package designed to visualize RNA 2D structures in consistent, recognizable, and reproducible layouts. The latest release, R2DT 2.0, introduces multiple significant features, including the ability to display position-specific information, such as single nucleotide polymorphisms or SHAPE reactivities. It also offers a new template-free mode allowing visualization of RNAs without pre-existing templates, alongside a constrained folding mode and support for animated visualizations. Users can interactively modify R2DT diagrams, either manually or using natural language prompts, to generate new templates or create publication-quality images. Additionally, R2DT features faster performance, an expanded template library, and a growing collection of compatible tools and utilities. Already integrated into multiple biological databases, R2DT has evolved into a comprehensive platform for RNA 2D visualization, accessible at https://r2dt.bio.
Time-resolved X-ray crystallography experiments were first performed in the 1980s, yet they remained a niche technique for decades. With the recent advent of X-ray free electron laser (XFEL) sources and serial crystallographic techniques, time-resolved crystallography has received renewed interest and has become more accessible to a wider user base. Despite this, time-resolved structures represent < 1 % of models deposited in the world-wide Protein Data Bank, indicating that the tools and techniques currently available require further development before such experiments can become truly routine. In this chapter, we demonstrate how applying data multiplexing to time-resolved crystallography can enhance the achievable time resolution at moderately intense monochromatic X-ray sources, ranging from synchrotrons to bench-top sources. We discuss the principles of multiplexing, where this technique may be advantageous, potential pitfalls, and experimental design considerations.
Sex chromosome replacement is frequent in many vertebrate clades, including fish, frogs, and lizards. In order to understand the mechanisms responsible for sex chromosome turnover and the early stages of sex chromosome divergence, it is necessary to study lineages with recently evolved sex chromosomes. Here we examine sex chromosome evolution in a group of African cichlid fishes (tribe Tropheini) which began to diverge from one another less than 4 MYA. We have evidence for a previously unknown sex chromosome system, and preliminary indications of several additional systems not previously reported in this group. We find a high frequency of sex chromosome turnover and estimate a minimum of 14 turnovers in this tribe. We date the origin of the most common sex determining system in this tribe (XY-LG5/19) near the base of one of two major sub-clades of this tribe, about 3.4 MY ago. Finally, we observe variation in the size of one sex-determining region that suggests independent evolution of evolutionary strata in species with a shared sex-determination system. Our results illuminate the rapid rate of sex chromosome turnover in the tribe Tropheini and set the stage for further studies of the dynamics of sex chromosome evolution in this group.
- MeSH
- cichlidy * genetika MeSH
- fylogeneze MeSH
- jezera MeSH
- mitochondriální DNA genetika MeSH
- molekulární evoluce MeSH
- pohlavní chromozomy genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Tanzanie MeSH
BACKGROUND: While research has documented negative social and academic consequences that occur when students experience peer exclusion, few studies have been conducted to investigate teachers' evaluations of peer exclusion. AIMS: This study investigated whether ethnic and gender biases enter teachers' evaluations of classroom peer exclusion that met criteria for bullying. SAMPLE: Teachers (N = 740; 77% female) of early and middle adolescents participated in the study. Participants were recruited from 118 elementary and secondary schools across the Czech Republic. METHODS: Using a between-subjects design, teachers evaluated a scenario of classroom peer exclusion initiated by majority ethnic (Czech) students. The scenarios varied contextual characteristics: target's ethnicity (majority Czech vs. minority Arab), target's gender, and excluders' gender. RESULTS: Analyses revealed several subtle contextual effects. Although teachers viewed exclusion as having a more negative impact for the fair treatment of Arab targets than for Czech targets, their reasoning about the wrongfulness of such exclusion was less focused on the moral concerns about fairness for Arab than for Czech targets. In contrast to girl targets, teachers were less concerned about the harmful impact on exclusion for boy targets when considering intervention. Excluders' gender had significant interactions with the target's gender on reasoning about wrongfulness of exclusion and the target's ethnicity for viewing exclusion as impairing the target's academic engagement. CONCLUSIONS: The findings of subtle ethnic and gender biases underscore the need for research on teacher perspectives on peer exclusion and for training teachers how to address peer exclusion in the classroom across various contexts.
Cationic and amphiphilic polymers are known to exert broad-spectrum antibacterial activity by a putative mechanism of membrane disruption. Typically, nonspecific binding to hydrophobic components of the complex biological milieu, such as globular proteins, is considered a deterrent to the successful application of such polymers. To evaluate the extent to which serum deactivates antibacterial polymethacrylates, we compared their minimum inhibitory concentrations in the presence and absence of fetal bovine serum. Surprisingly, we discovered that the addition of fetal bovine serum (FBS) to the assay media in fact enhances the antimicrobial activity of polymers against Gram-positive bacteria S. aureus, whereas the opposite is the case for Gram-negative E. coli. Here, we present these unexpected trends and develop a hypothesis to potentially explain this unusual phenomenon.
- MeSH
- antibakteriální látky farmakologie MeSH
- bakteriální léková rezistence účinky léků MeSH
- Escherichia coli účinky léků MeSH
- hydrofobní a hydrofilní interakce MeSH
- kyseliny polymethakrylové farmakologie MeSH
- mikrobiální testy citlivosti MeSH
- sérový albumin hovězí farmakologie MeSH
- Staphylococcus aureus účinky léků MeSH
- synergismus léků MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Apicomplexa is a diverse phylum comprising unicellular endobiotic animal parasites and contains some of the most well-studied microbial eukaryotes including the devastating human pathogens Plasmodium falciparum and Cryptosporidium hominis. In contrast, data on the invertebrate-infecting gregarines remains sparse and their evolutionary relationship to other apicomplexans remains obscure. Most apicomplexans retain a highly modified plastid, while their mitochondria remain metabolically conserved. Cryptosporidium spp. inhabit an anaerobic host-gut environment and represent the known exception, having completely lost their plastid while retaining an extremely reduced mitochondrion that has lost its genome. Recent advances in single-cell sequencing have enabled the first broad genome-scale explorations of gregarines, providing evidence of differential plastid retention throughout the group. However, little is known about the retention and metabolic capacity of gregarine mitochondria. RESULTS: Here, we sequenced transcriptomes from five species of gregarines isolated from cockroaches. We combined these data with those from other apicomplexans, performed detailed phylogenomic analyses, and characterized their mitochondrial metabolism. Our results support the placement of Cryptosporidium as the earliest diverging lineage of apicomplexans, which impacts our interpretation of evolutionary events within the phylum. By mapping in silico predictions of core mitochondrial pathways onto our phylogeny, we identified convergently reduced mitochondria. These data show that the electron transport chain has been independently lost three times across the phylum, twice within gregarines. CONCLUSIONS: Apicomplexan lineages show variable functional restructuring of mitochondrial metabolism that appears to have been driven by adaptations to parasitism and anaerobiosis. Our findings indicate that apicomplexans are rife with convergent adaptations, with shared features including morphology, energy metabolism, and intracellularity.
RECQ5 is one of five RecQ helicases found in humans and is thought to participate in homologous DNA recombination by acting as a negative regulator of the recombinase protein RAD51. Here, we use kinetic and single molecule imaging methods to monitor RECQ5 behavior on various nucleoprotein complexes. Our data demonstrate that RECQ5 can act as an ATP-dependent single-stranded DNA (ssDNA) motor protein and can translocate on ssDNA that is bound by replication protein A (RPA). RECQ5 can also translocate on RAD51-coated ssDNA and readily dismantles RAD51-ssDNA filaments. RECQ5 interacts with RAD51 through protein-protein contacts, and disruption of this interface through a RECQ5-F666A mutation reduces translocation velocity by ∼50%. However, RECQ5 readily removes the ATP hydrolysis-deficient mutant RAD51-K133R from ssDNA, suggesting that filament disruption is not coupled to the RAD51 ATP hydrolysis cycle. RECQ5 also readily removes RAD51-I287T, a RAD51 mutant with enhanced ssDNA-binding activity, from ssDNA. Surprisingly, RECQ5 can bind to double-stranded DNA (dsDNA), but it is unable to translocate. Similarly, RECQ5 cannot dismantle RAD51-bound heteroduplex joint molecules. Our results suggest that the roles of RECQ5 in genome maintenance may be regulated in part at the level of substrate specificity.
- MeSH
- adenosintrifosfát metabolismus MeSH
- bodová mutace MeSH
- helikasy RecQ genetika metabolismus ultrastruktura MeSH
- homologní rekombinace * MeSH
- hydrolýza MeSH
- jednovláknová DNA metabolismus ultrastruktura MeSH
- kinetika MeSH
- lidé MeSH
- mikroskopie atomárních sil MeSH
- missense mutace MeSH
- molekulární motory metabolismus ultrastruktura MeSH
- rekombinantní fúzní proteiny metabolismus MeSH
- rekombinantní proteiny metabolismus MeSH
- rekombinasa Rad51 genetika metabolismus MeSH
- replikační protein A metabolismus MeSH
- substrátová specifita MeSH
- zobrazení jednotlivé molekuly * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Hexameric arginine repressor, ArgR, is the feedback regulator of bacterial L-arginine regulons, and sensor of L-arg that controls transcription of genes for its synthesis and catabolism. Although ArgR function, as well as its secondary, tertiary, and quaternary structures, is essentially the same in E. coli and B. subtilis, the two proteins differ significantly in sequence, including residues implicated in the response to L-arg. Molecular dynamics simulations are used here to evaluate the behavior of intact B. subtilis ArgR with and without L-arg, and are compared with prior MD results for a domain fragment of E. coli ArgR. Relative to its crystal structure, B. subtilis ArgR in absence of L-arg undergoes a large-scale rotational shift of its trimeric subassemblies that is very similar to that observed in the E. coli protein, but the residues driving rotation have distinct secondary and tertiary structural locations, and a key residue that drives rotation in E. coli is missing in B. subtilis. The similarity of trimer rotation despite different driving residues suggests that a rotational shift between trimers is integral to ArgR function. This conclusion is supported by phylogenetic analysis of distant ArgR homologs reported here that indicates at least three major groups characterized by distinct sequence motifs but predicted to undergo a common rotational transition. The dynamic consequences of L-arg binding for transcriptional activation of intact ArgR are evaluated here for the first time in two-microsecond simulations of B. subtilis ArgR. L-arg binding to intact B. subtilis ArgR causes a significant further shift in the angle of rotation between trimers that causes the N-terminal DNA-binding domains lose their interactions with the C-terminal domains, and is likely the first step toward adopting DNA-binding-competent conformations. The results aid interpretation of crystal structures of ArgR and ArgR-DNA complexes.
- MeSH
- alosterická regulace MeSH
- arginin chemie metabolismus MeSH
- Bacillus subtilis chemie genetika metabolismus MeSH
- bakteriální proteiny chemie genetika metabolismus MeSH
- entropie MeSH
- Escherichia coli chemie genetika metabolismus MeSH
- fylogeneze MeSH
- konformace proteinů, alfa-helix MeSH
- konformace proteinů, beta-řetězec MeSH
- proteinové domény MeSH
- regulon genetika MeSH
- represorové proteiny chemie genetika metabolismus MeSH
- sekvence aminokyselin MeSH
- sekvenční seřazení MeSH
- simulace molekulární dynamiky MeSH
- vazba proteinů MeSH
- vodíková vazba MeSH
- Publikační typ
- časopisecké články MeSH
Mexico is one of the most biodiverse countries in the world, with an important proportion of endemism mainly because of the convergence of the Nearctic and Neotropical biogeographic regions, which generate great diversity and species turnover at different spatial scales. However, most of our knowledge of the Mexican ant biota is limited to a few well-studied taxa, and we lack a comprehensive synthesis of ant biodiversity information. For instance, most of the knowledge available in the literature on Mexican ant fauna refers only to species lists by states, or is focused on only a few regions of the country, which prevents the study of several basic and applied aspects of ants, from diversity and distribution to conservation. Our aims in this data paper are therefore (1) to compile all the information available regarding ants across the Mexican territory, and (2) to identify major patterns in the gathered data set and geographic gaps in order to direct future sampling efforts. All records were obtained from raw data, including both unpublished and published information. After exhaustive filtering and updating information and synonyms, we compiled a total of 21,731 records for 887 ant species distributed throughout Mexico from 1894 to 2018. These records were concentrated mainly in the states of Chiapas (n = 6,902, 32.76%) and Veracruz de Ignacio de la Llave (n = 4,329, 19.92%), which together comprise half the records. The subfamily with the highest number of records was Myrmicinae (n = 10,458 records, 48.12%), followed by Formicinae (n = 3,284, 15.11%) and Ponerinae (n = 1,914, 8.8%). Most ant records were collected in the Neotropical region of the country (n = 12,646, 58.19%), followed by the Mexican transition zone (n = 5,237, 24.09%) and the Nearctic region (n = 3,848, 17.72%). Native species comprised 95.46% of the records (n = 20,745). To the best of our knowledge, this is the most complete data set available to date in the literature for the country. We hope that this compilation will encourage researchers to explore different aspects of the population and community research of ants at different spatial scales, and to aid in the establishment of conservation policies and actions. There are no copyright restrictions. Please cite this data paper when using its data for publications or teaching events.
- MeSH
- biodiverzita MeSH
- Formicidae * MeSH
- incidence MeSH
- společenstvo MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, U.S. Gov't, Non-P.H.S. MeSH
- Geografické názvy
- Mexiko MeSH
