ALBERT

Description: Deoxyribozymes, DNA enzymes or simply DNAzymes are single-stranded oligo-deoxyribonucleotide molecules that, like proteins and ribozymes, possess the ability to perform catalysis. Although DNAzymes have not yet been found in living organisms, they have been isolated in the laboratory through in vitro selection. The selected DNAzyme sequences have the ability to catalyze a broad range of chemical reactions, utilizing DNA, RNA, peptides or small organic compounds as substrates. DNAmoreDB is a comprehensive database resource for DNAzymes that collects and organizes the following types of information: sequences, conditions of the selection procedure, catalyzed reactions, kinetic parameters, substrates, cofactors, structural information whenever available, and literature references. Currently, DNAmoreDB contains information about DNAzymes that catalyze 20 different reactions. We included a submission form for new data, a REST-based API system that allows users to retrieve the database contents in a machine-readable format, and keyword and BLASTN search features. The database is publicly available at https://www.genesilico.pl/DNAmoreDB/.

Description: DNA cytosine methylation is central to many biological processes, including regulation of gene expression, cellular differentiation and development. This DNA modification is conserved across animals, having been found in representatives of sponges, ctenophores, cnidarians and bilaterians, and with very few known instances of secondary loss in animals. Myxozoans are a group of microscopic, obligate endoparasitic cnidarians that have lost many genes over the course of their evolution from free-living ancestors. Here, we investigated the evolution of the key enzymes involved in DNA cytosine methylation in 29 cnidarians, and found that these enzymes were lost in an ancestor of Myxosporea (the most speciose class of Myxozoa). Additionally, using whole genome bisulfite sequencing (WGBS), we confirmed that the genomes of two distant species of myxosporeans, Ceratonova shasta and Henneguya salminicola, completely lack DNA cytosine methylation. Our results add a notable and novel taxonomic group, the Myxosporea, to the very short list of animal taxa lacking DNA cytosine methylation, further illuminating the complex evolutionary history of this epigenetic regulatory mechanism.

Description: Mitochondrial protein import is one of the key processes during mitochondrial biogenesis that involves a series of events necessary for recognition and delivery of nucleus-encoded/cytosol-synthesized mitochondrial proteins into the organelle. The past research efforts have mainly unraveled how membrane translocases ensure the correct protein sorting within the different mitochondrial subcompartments. However, early steps of recognition and delivery remain relatively uncharacterized. In this review, we discuss our current understanding about the signals on mitochondrial proteins, as well as in the mRNAs encoding them, which with the help of cytosolic chaperones and membrane receptors support protein targeting to the organelle in order to avoid improper localization. In addition, we discuss recent findings that illustrate how mistargeting of mitochondrial proteins triggers stress responses, aiming to restore cellular homeostasis.

Description: We present a new catalogue of H ii regions based on the integral field spectroscopy (IFS) data of the extended CALIFA and PISCO samples. The selection of H ii regions was based on two assumptions: a clumpy structure with high contrast of H α emission and an underlying stellar population comprising young stars. The catalogue provides the spectroscopic information of 26 408 individual regions corresponding to 924 galaxies, including the flux intensities and equivalent widths of 51 emission lines covering the wavelength range between 3745 and 7200 Å. To our knowledge, this is the largest catalogue of spectroscopic properties of H ii regions. We explore a new approach to decontaminate the emission lines from diffuse ionized gas contribution. This diffuse gas correction was estimated to correct every emission line within the considered spectral range. With the catalogue of H ii regions corrected, new demarcation lines are proposed for the classical diagnostic diagrams. Finally, we study the properties of the underlying stellar populations of the H ii regions. It was found that there is a direct relationship between the ionization conditions on the nebulae and the properties of stellar populations besides the physicals condition on the ionized regions.

Description: We study the presence of optically-selected active galactic nuclei (AGNs) within a sample of 867 galaxies extracted from the extended Calar-Alto Legacy Integral Field spectroscopy Area (eCALIFA) spanning all morphological classes. We identify 10 Type-I and 24 Type-II AGNs, amounting to ∼4 per cent of our sample, similar to the fraction reported by previous explorations in the same redshift range. We compare the integrated properties of the ionized and molecular gas, and stellar population of AGN hosts and their non-active counterparts, combining them with morphological information. The AGN hosts are found in transitory parts (i.e. green-valley) in almost all analysed properties which present bimodal distributions (i.e. a region where reside star-forming galaxies and another with quiescent/retired ones). Regarding morphology, we find AGN hosts among the most massive galaxies, with enhanced central stellar-mass surface density in comparison to the average population at each morphological type. Moreover, their distribution peaks at the Sab-Sb classes and none are found among very late-type galaxies (>Scd). Finally, we inspect how the AGN could act in their hosts regarding the quenching of star-formation. The main role of the AGN in the quenching process appears to be the removal (or heating) of molecular gas, rather than an additional suppression of the already observed decrease of the star-formation efficiency from late-to-early type galaxies.

Description: Background In three recent studies, Maul demonstrated that sets of nonsense items can acquire excellent psychometric properties. Our aim was to find out why responses to nonsense items acquire a well-defined structure and high internal consistency. Method We designed two studies. In the first study, 610 participants responded to eight items where the central term (intelligence) was replaced by the term “gavagai”. In the second study, 548 participants responded to seven items whose content was totally invented. We asked the participants if they gave any meaning to “gavagai”, and conducted analyses aimed at uncovering the most suitable structure for modeling responses to meaningless items. Results In the first study, 81.3% of the sample gave “gavagai” meaning, while 18.7% showed they had given it no interpretation. The factorial structures of the two groups were very different from each other. In the second study, the factorial model fitted almost perfectly. However, further analysis revealed that the structure of the data was not continuous but categorical with three unordered classes very similar to midpoint, disacquiescent, and random response styles. Discussion Apparently good psychometric properties on meaningless scales may be due to (a) respondents actually giving an interpretation to the item and responding according to that interpretation, or (b) a false positive because the statistical fit of the factorial model is not sensitive to cases where the actual structure of the data does not come from a common factor. In conclusion, the problem is not in factor analysis, but in the ability of the researcher to elaborate substantive hypotheses about the structure of the data, to employ analytical procedures congruent with those hypotheses, and to understand that a good fit in factor analysis does not have a univocal interpretation and is not sufficient evidence of either validity nor good psychometric properties.

Description: For understanding the water deficit stress mechanism in sorghum, we conducted a physiological and proteomic analysis in the leaves of Sorghum bicolor L. Moench (a drought tolerant crop model) of non-colonized and colonized plants with a consortium of arbuscular mycorrhizal fungi. Physiological results indicate that mycorrhizal fungi association enhances growth and photosynthesis in plants, under normal and water deficit conditions. 2D-electrophoresis profiles revealed 51 differentially accumulated proteins in response to water deficit, of which HPLC/MS successfully identified 49. Bioinformatics analysis of protein–protein interactions revealed the participation of different metabolic pathways in nonmycorrhizal compared to mycorrhizal sorghum plants under water deficit. In noninoculated plants, the altered proteins are related to protein synthesis and folding (50S ribosomal protein L1, 30S ribosomal protein S10, Nascent polypeptide-associated complex subunit alpha), coupled with multiple signal transduction pathways, guanine nucleotide-binding beta subunit (Rack1) and peptidyl-prolyl-cis-trans isomerase (ROC4). In contrast, in mycorrhizal plants, proteins related to energy metabolism (ATP synthase-24kDa, ATP synthase β), carbon metabolism (malate dehydrogenase, triosephosphate isomerase, sucrose-phosphatase), oxidative phosphorylation (mitochondrial-processing peptidase) and sulfur metabolism (thiosulfate/3-mercaptopyruvate sulfurtransferase) were found. Our results provide a set of proteins of different metabolic pathways involved in water deficit produced by sorghum plants alone or associated with a consortium of arbuscular mycorrhizal fungi isolated from the tropical rain forest Los Tuxtlas Veracruz, México.

Description: Environmental DNA (eDNA) detection of aquatic invasive species is currently at the forefront of aquatic conservation efforts because the methodology provides a cost effective and sensitive means to detect animals at low densities. Developments in eDNA technologies have improved detection probabilities for rare, indicator, and invasive species over the past decade. However, standard lab analysis can take days or weeks before results are available and is prohibitive when rapid management decisions are required for mitigation. Here, we investigated the performance of a real-time quantitative PCR system for on-site eDNA detection of New Zealand mud snails (Potamopyrgus antipodarum). Six sites in western Washington, USA were sampled using the rapid eDNA technique and traditional methods, with five samples per site. On-site eDNA detection of mud snails resulted in a 10% increase in positive sites (16/30 = 53% positive) relative to visual surveys (13/30 = 43% positive). In addition, positive associations were observed between mud snail eDNA concentration (eDNA copies per reaction) and the number of mud snail individuals at each site (R2 = 0.78). We show that the rapid on-site eDNA technology can be effective for detection and quantification of New Zealand mud snails in freshwaters. This on-site eDNA detection approach could possibly be used to initiate management protocols that allow for more rapid responses during the onset of biological invasions.

Description: Demographic data of the great sturgeon, Huso huso, from the Iranian coastal waters of the Caspian Sea were derived from measurements of individuals with a fork length ranging from 84 to 255 cm, obtained from commercial fisheries. The maximum age of fish caught in the south Caspian Sea was 30 years. The estimates of the asymptotic length L∞ and the growth coefficient (K) were 265.255 cm and 0.062 per year for males and 275.78 cm and 0.08 per year for females, respectively. Total mortality rates obtained by Gulland's method were larger for males (0.64) than for females (0.46). Annual mortality rates were calculated as 47% for males and 37% for females. Data obtained in this study and their comparison with data from previous studies indicate that the great sturgeon stock is definitely exploited in an unsustainable manner.

Description: This study was carried out during January 2020–December 2020 in a semi-desert ecosystem in southern Sonora, Mexico, to determine the annual and daily variations in water potential and the normalized difference vegetation index (NDVI) of Bursera fagaroides Engl., Monogr. Phan., Parkinsonia aculeata L., Sp. Pl.; Prosopis laevigata (Humb. & Bonpl. ex Willd.), and Atriplex canescens (Pursh) Nutt. Soil electrical conductivity, cation content, and physical characteristics were determined at two depths, and water potential (ψ) was measured in roots, stems, and leaves. The daily leaf ψ was measured every 15 days each month to determine the duration of stress (hours) and the stress intensity (SI). The electrical conductivity determinations classified the soil in the experimental area as strongly saline. A significant difference was noted in electrical conductivity between soil depths. The four studied species showed significant gradients of ψ in their organs. In this soil, all four species remained in a stressed condition for approximately 11 h per day. The mean SI was 27%, and B. fagaroides Engl., Monogr. Phan. showed the lowest value. The four species showed increased NDVI values during the rainy months, with P. laevigata (Humb. & Bonpl. ex Willd.) and Parkinsonia aculeata L., Sp. Pl. showing the highest values. The capacity for ψ decrease under saline conditions identified A. canescens (Pursh) Nutt., B. fagaroides Engl., Monogr. Phan. and P. aculeata L., Sp. Pl. as practical and feasible alternatives for establishment in saline soils in southern Sonora for purposes of soil recovery and reforestation.