The quantum Cramér-Rao bound is a cornerstone of modern quantum metrology, as it provides the ultimate precision in parameter estimation. In the multiparameter scenario, this bound becomes a matrix ...inequality, which can be cast to a scalar form with a properly chosen weight matrix. Multiparameter estimation thus elicits trade-offs in the precision with which each parameter can be estimated. We show that, if the information is encoded in a unitary transformation, we can naturally choose the weight matrix as the metric tensor linked to the geometry of the underlying algebra su(n), with applications in numerous fields. This ensures an intrinsic bound that is independent of the choice of parametrization.
Multiple immunoinformatic tools have been developed to predict T-cell epitopes from protein amino acid sequences for different major histocompatibility complex (MHC) alleles. These prediction tools ...output hundreds of potential peptide candidates which require further processing; however, these tools are either not graphical or not friendly for non-programming users. We present Epitope-Evaluator, a web tool developed in the Shiny/R framework to interactively analyze predicted T-cell epitopes. Epitope-Evaluator contains six tools providing the distribution of epitopes across a selected set of MHC alleles, the promiscuity and conservation of epitopes, and their density and location within antigens. Epitope-Evaluator requires as input the fasta file of protein sequences and the output prediction file coming out from any predictor. By choosing different cutoffs and parameters, users can produce several interactive plots and tables that can be downloaded as JPG and text files, respectively. Using Epitope-Evaluator, we found the HLA-B*40, HLA-B*27:05 and HLA-B*07:02 recognized fewer epitopes from the SARS-CoV-2 proteome than other MHC Class I alleles. We also identified shared epitopes between Delta, Omicron, and Wuhan Spike variants as well as variant-specific epitopes. In summary, Epitope-Evaluator removes the programming barrier and provides intuitive tools, allowing a straightforward interpretation and graphical representations that facilitate the selection of candidate epitopes for experimental evaluation. The web server Epitope-Evaluator is available at https://fuxmanlab.shinyapps.io/Epitope-Evaluator/.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Summary
Obligate acidophilic members of the thaumarchaeotal genus Candidatus Nitrosotalea play an important role in nitrification in acidic soils, but their evolutionary and physiological adaptations ...to acidic environments are still poorly understood, with only a single member of this genus (Ca. N. devanaterra) having its genome sequenced. In this study, we sequenced the genomes of two additional cultured Ca. Nitrosotalea strains, extracted an almost complete Ca. Nitrosotalea metagenome‐assembled genome from an acidic fen, and performed comparative genomics of the four Ca. Nitrosotalea genomes with 19 other archaeal ammonia oxidiser genomes. Average nucleotide and amino acid identities revealed that the four Ca. Nitrosotalea strains represent separate species within the genus. The four Ca. Nitrosotalea genomes contained a core set of 103 orthologous gene families absent from all other ammonia‐oxidizing archaea and, for most of these gene families, expression could be demonstrated in laboratory culture or the environment via proteomic or metatranscriptomic analyses respectively. Phylogenetic analyses indicated that four of these core gene families were acquired by the Ca. Nitrosotalea common ancestor via horizontal gene transfer from acidophilic representatives of Euryarchaeota. We hypothesize that gene exchange with these acidophiles contributed to the competitive success of the Ca. Nitrosotalea lineage in acidic environments.
Transcription factors (TFs) regulate gene expression by binding to DNA sequences and modulating transcriptional activity through their effector domains. Despite the central role of effector domains ...in TF function, there is a current lack of a comprehensive resource and characterization of effector domains. Here, we provide a catalog of 924 effector domains across 594 human TFs. Using this catalog, we characterized the amino acid composition of effector domains, their conservation across species and across the human population, and their roles in human diseases. Furthermore, we provide a classification system for effector domains that constitutes a valuable resource and a blueprint for future experimental studies of TF effector domain function.
Soto et al. present a catalog of 924 literature-curated human transcription factor effector domains. This catalog is used to describe the biophysical properties of effector domains, their evolutionary conservation, disruption in proteoforms, and relevance in human disease. Finally, a novel effector domain classification is provided.
Little is known about how Drosophila adults behave in the wild, including mating, allocation of food and space, and escape from predators. This lack of information has negative implications for our ...ability to understand the capabilities of the nervous system to integrate sensory cues necessary for the adaptation of organisms in natural conditions. We characterized a set of behavioral routines of D. melanogaster and D. simulans adults in three ecologically different orchards: grape, apple and prickly pear. We also investigated how the flies identify conspecifics and aliens in the wild to better understand relationships between group formation and adaptation of Drosophila to breeding sites. We characterized the locations by recording in each orchard humidity, temperature, illumination conditions, pH of fruits, the presence/absence of other Drosophila species and the predator ant Linepithema humile. Our findings suggest that the home range of these species of Drosophila includes decaying fruits and, principally, a variety of microhabitats that surround the fruits. The ecological heterogeneity of the orchards and odors emitted by adult D. melanogaster and D. simulans influence perch preferences, cluster formation, court and mating, egg-laying site selection, and use of space. This is one of the first large examinations of the association between changing, complex environments and a set of adult behaviors of Drosophila. Therefore, our results have implications for understanding the genetic differentiation and evolution of populations of species in the genus Drosophila.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
The genomes of many bacteria that participate in nitrogen cycling through the process of nitrification contain putative genes associated with acyl-homoserine lactone (AHL) quorum sensing (QS). AHL QS ...or bacterial cell-cell signaling is a method of bacterial communication and gene regulation and may be involved in nitrogen oxide fluxes or other important phenotypes in nitrifying bacteria. Here, we carried out a broad survey of AHL production in nitrifying bacteria in three steps. First, we analyzed the evolutionary history of AHL synthase and AHL receptor homologs in sequenced genomes and metagenomes of nitrifying bacteria to identify AHL synthase homologs in ammonia-oxidizing bacteria (AOB) of the genus
and nitrite-oxidizing bacteria (NOB) of the genera
,
, and
Next, we screened cultures of both AOB and NOB with uncharacterized AHL synthase genes and AHL synthase-negative nitrifiers by a bioassay. Our results suggest that an AHL synthase gene is required for, but does not guarantee, cell density-dependent AHL production under the conditions tested. Finally, we utilized mass spectrometry to identify the AHLs produced by the AOB
and
and the NOB
and
as
-decanoyl-l-homoserine lactone (C
-HSL),
-3-hydroxy-tetradecanoyl-l-homoserine lactone (3-OH-C
-HSL), a monounsaturated AHL (C
-HSL), and
-octanoyl-l-homoserine lactone (C
-HSL), respectively. Our survey expands the list of AHL-producing nitrifiers to include a representative of
lineage II and suggests that AHL production is widespread in nitrifying bacteria.
Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite by nitrifying microorganisms, plays an important role in environmental nitrogen cycling from agricultural fertilization to wastewater treatment. The genomes of many nitrifying bacteria contain genes associated with bacterial cell-cell signaling or quorum sensing (QS). QS is a method of bacterial communication and gene regulation that is well studied in bacterial pathogens, but less is known about QS in environmental systems. Our previous work suggested that QS might be involved in the regulation of nitrogen oxide gas production during nitrite metabolism. This study characterized putative QS signals produced by different genera and species of nitrifiers. Our work lays the foundation for future experiments investigating communication between nitrifying bacteria, the purpose of QS in these microorganisms, and the manipulation of QS during nitrification.
The Schrödinger equation admits smooth and finite solutions that spontaneously evolve into a singularity, even for a free particle. This blowup is generally ascribed to the intrinsic dispersive ...character of the associated time evolution. We resort to the notion of quantum Bohmian trajectories to relate this singular behavior to local phase variations, which generate an underlying velocity field responsible for driving the quantum flux toward the singular region.
•The dispersive blowup of the Schrödinger equation is investigated.•Local phase variations undergone by the wave function generate an underlying velocity field responsible for driving the quantum flux toward singular regions.•Bohmian trajectories are used to relate the wave function singular behavior to local phase variations.
This article is an exercise in intellectual history whose objec-tive is mainly to reveal the almost simultaneous origin be-tween dependency theory in Latin America and world-systems analysis in the ...United States since the second half of the 1960s. Here we offer in great detail and textual evidence the reasons why the world-system perspective (before having been baptized as such) is not a mere US-American (or “grin-go”) copy of dependency theory. This will be addressed, first of all, with an analysis of the “formal” aspects in the main dependency works—Dependencia y desarrollo en América Latina (1969), by Fernando Henrique Cardoso and Enzo Fa-letto; Dialéctica de la dependencia (1973), by Ruy Mauro Ma-rini; and El capitalismo dependiente latinoamericano (1974), by Vania Bambirra—through the theoretical, methodological and epistemological lenses of the essay “The Comparative Study of National Societies” published by Terence K. Hop-kins and Immanuel Wallerstein in 1967 regarding the VI World Congress of Sociology in 1966 in Evian (France). Sec-ondly, we will delve into the “substantive” aspects—that is, the methodological as well as epistemological discrepancies—between both approaches. Although they are not completely antagonistic, we want to make it clear, on the basis of their methodological and epistemological foundations, not fully discussed until now, that the lines of research in dependency theory and in world-systems analysis have divergent implications.
We present a comprehensive and self-contained discussion of the use of the transfer matrix to study propagation in one-dimensional lossless systems, including a variety of examples, such as ...superlattices, photonic crystals, and optical resonators. In all these cases, the transfer matrix has the same algebraic properties as the Lorentz group in a (2+1)-dimensional spacetime, as well as the group of unimodular real matrices underlying the structure of the abcd law, which explains many subtle details. We elaborate on the geometrical interpretation of the transfer-matrix action as a mapping on the unit disk and apply a simple trace criterion to classify the systems into three types with very different geometrical and physical properties. This approach is applied to some practical examples and, in particular, an alternative framework to deal with periodic (and quasiperiodic) systems is proposed.
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