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Bulletin of Mathematical Biology Jun 2024We introduce a model that can be used for the description of the distribution of species when there is scarcity of data, based on our previous work (Ballesteros et al. J...
We introduce a model that can be used for the description of the distribution of species when there is scarcity of data, based on our previous work (Ballesteros et al. J Math Biol 85(4):31, 2022). We address challenges in modeling species that are seldom observed in nature, for example species included in The International Union for Conservation of Nature's Red List of Threatened Species (IUCN 2023). We introduce a general method and test it using a case study of a near threatened species of amphibians called Plectrohyla Guatemalensis (see IUCN 2023) in a region of the UNESCO natural reserve "Tacaná Volcano", in the border between Mexico and Guatemala. Since threatened species are difficult to find in nature, collected data can be extremely reduced. This produces a mathematical problem in the sense that the usual modeling in terms of Markov random fields representing individuals associated to locations in a grid generates artificial clusters around the observations, which are unreasonable. We propose a different approach in which our random variables describe yearly averages of expectation values of the number of individuals instead of individuals (and they take values on a compact interval). Our approach takes advantage of intuitive insights from environmental properties: in nature individuals are attracted or repulsed by specific features (Ballesteros et al. J Math Biol 85(4):31, 2022). Drawing inspiration from quantum mechanics, we incorporate quantum Hamiltonians into classical statistical mechanics (i.e. Gibbs measures or Markov random fields). The equilibrium between spreading and attractive/repulsive forces governs the behavior of the species, expressed through a global control problem involving an energy operator.
Topics: Animals; Endangered Species; Mathematical Concepts; Models, Biological; Mexico; Conservation of Natural Resources; Guatemala; Markov Chains; Population Density; Anura; Ecosystem; Animal Distribution; Population Dynamics
PubMed: 38935181
DOI: 10.1007/s11538-024-01315-y -
BMC Biotechnology Jun 2024Mammalian display is an appealing technology for therapeutic antibody development. Despite the advantages of mammalian display, such as full-length IgG display with...
BACKGROUND
Mammalian display is an appealing technology for therapeutic antibody development. Despite the advantages of mammalian display, such as full-length IgG display with mammalian glycosylation and its inherent ability to select antibodies with good biophysical properties, the restricted library size and large culture volumes remain challenges. Bxb1 serine integrase is commonly used for the stable genomic integration of antibody genes into mammalian cells, but presently lacks the efficiency required for the display of large mammalian display libraries. To increase the Bxb1 integrase-mediated stable integration efficiency, our study investigates factors that potentially affect the nuclear localization of Bxb1 integrase.
METHODS
In an attempt to enhance Bxb1 serine integrase-mediated integration efficiency, we fused various nuclear localization signals (NLS) to the N- and C-termini of the integrase. Concurrently, we co-expressed multiple proteins associated with nuclear transport to assess their impact on the stable integration efficiency of green fluorescent protein (GFP)-encoding DNA and an antibody display cassette into the genome of Chinese hamster ovary (CHO) cells containing a landing pad for Bxb1 integrase-mediated integration.
RESULTS
The nucleoplasmin NLS from Xenopus laevis, when fused to the C-terminus of Bxb1 integrase, demonstrated the highest enhancement in stable integration efficiency among the tested NLS fusions, exhibiting over a 6-fold improvement compared to Bxb1 integrase lacking an NLS fusion. Subsequent additions of extra NLS fusions to the Bxb1 integrase revealed an additional 131% enhancement in stable integration efficiency with the inclusion of two copies of C-terminal nucleoplasmin NLS fusions. Further improvement was achieved by co-expressing the Ran GTPase-activating protein (RanGAP). Finally, to validate the applicability of these findings to more complex proteins, the DNA encoding the membrane-bound clinical antibody abrilumab was stably integrated into the genome of CHO cells using Bxb1 integrase with two copies of C-terminal nucleoplasmin NLS fusions and co-expression of RanGAP. This approach demonstrated over 14-fold increase in integration efficiency compared to Bxb1 integrase lacking an NLS fusion.
CONCLUSIONS
This study demonstrates that optimizing the NLS sequence fusion for Bxb1 integrase significantly enhances the stable genomic integration efficiency. These findings provide a practical approach for constructing larger libraries in mammalian cells through the stable integration of genes into a genomic landing pad.
Topics: Animals; CHO Cells; Integrases; Cricetulus; Nuclear Localization Signals; Cell Nucleus; Serine; Green Fluorescent Proteins; Cricetinae; Xenopus laevis
PubMed: 38926833
DOI: 10.1186/s12896-024-00871-4 -
Brazilian Journal of Biology = Revista... 2024Many anuran amphibians deposit their eggs in foam nests, biostructures that help protect the eggs and tadpoles from predators. Currently, there are no other...
Many anuran amphibians deposit their eggs in foam nests, biostructures that help protect the eggs and tadpoles from predators. Currently, there are no other identification and description studies of the cultivable microbiota role in the nests of the Leptodactylid frogs such as Physalaemus cuvieri, Leptodactylus vastus and Adenomera hylaedactyla. This study aimed to isolate and identify the culturable bacteria from these three anuran species' nests, as well as to prospect enzymes produced by this microbiota. Foam nests samples and environmental samples were diluted and viable cell count was determined. Bacterial morphotypes from foam nest samples were isolated through spread plate technique. Isolates' DNAs were extracted followed by rRNA 16S gene amplification and Sanger sequencing. To evaluate their enzymatic potential, the isolates were cultured in ATGE medium supplemented with starch (0.1% w/v), gelatin (3% w/v) and skimmed milk (1% w/v), to verify amylase and protease activity. A total of 183 bacterial morphotypes were isolated, comprising 33 bacterial genera. Proteobacteria phylum was the most abundant in all the three nests (79%). The genera Pseudomonas and Aeromonas were the most abundant taxon in P. cuvieri and L. vastus. In A. Hylaedactyla, were Enterobacter and Bacillus. Regarding enzymatic activities, 130 isolates displayed protease activity and 45 isolates were positive for amylase activity. Our results provide unprecedented information concerning culturable bacterial microbiota of the foam nests of the Leptodactylid frogs, as well as their potential for biomolecules of biotechnological interest.
Topics: Animals; Anura; Bacteria; RNA, Ribosomal, 16S; Nesting Behavior; Microbiota; DNA, Bacterial
PubMed: 38922194
DOI: 10.1590/1519-6984.280884 -
Toxins Jun 2024Studies on the interaction sites of peptide toxins and ion channels typically involve site-directed mutations in toxins. However, natural mutant toxins exist among them,... (Comparative Study)
Comparative Study
Studies on the interaction sites of peptide toxins and ion channels typically involve site-directed mutations in toxins. However, natural mutant toxins exist among them, offering insights into how the evolutionary process has conserved crucial sequences for activities and molecular target selection. In this study, we present a comparative investigation using electrophysiological approaches and computational analysis between two alpha toxins from evolutionarily close scorpion species of the genus , namely, Tst3 and Ts3 from and , respectively. These toxins exhibit three natural substitutions near the C-terminal region, which is directly involved in the interaction between alpha toxins and Nav channels. Additionally, we characterized the activity of the Tst3 toxin on Nav1.1-Nav1.7 channels. The three natural changes between the toxins did not alter sensitivity to Nav1.4, maintaining similar intensities regarding their ability to alter opening probabilities, delay fast inactivation, and induce persistent currents. Computational analysis demonstrated a preference for the down conformation of VSD4 and a shift in the conformational equilibrium towards this state. This illustrates that the sequence of these toxins retained the necessary information, even with alterations in the interaction site region. Through electrophysiological and computational analyses, screening of the Tst3 toxin on sodium isoform revealed its classification as a classic α-NaTx with a broad spectrum of activity. It effectively delays fast inactivation across all tested isoforms. Structural analysis of molecular energetics at the interface of the VSD4-Tst3 complex further confirmed this effect.
Topics: Scorpion Venoms; Animals; Scorpions; Brazil; Humans; Xenopus laevis; Ion Channel Gating; Amino Acid Sequence; Animals, Poisonous
PubMed: 38922152
DOI: 10.3390/toxins16060257 -
PeerJ 2024The Jambato Harlequin toad (), a formerly abundant species in the Andes of Ecuador, faced a dramatic population decline in the 1980s, with its last recorded sighting in...
The Jambato Harlequin toad (), a formerly abundant species in the Andes of Ecuador, faced a dramatic population decline in the 1980s, with its last recorded sighting in 1988. The species was considered Extinct by the IUCN until 2016, when a fortuitous discovery of one Jambato by a local boy reignited hope. In this study, we present findings from an investigation conducted in the Angamarca parish, focusing on distribution, abundance, habitat preferences, ecology, disease susceptibility, and dietary habits of the species. In one year we identified 71 individuals at different stages of development in various habitats, with a significant presence in agricultural mosaic areas and locations near water sources used for crop irrigation, demonstrating the persistence of the species in a complex landscape, with considerable human intervention. The dietary analysis based on fecal samples indicated a diverse prey selection, primarily comprising arthropods such as Acari, Coleoptera, and ants. Amphibian declines have been associated with diseases and climate change; notably, our study confirmed the presence of the pathogen (), but, surprisingly, none of the infected Jambatos displayed visible signs of illness. When analyzing climatic patterns, we found that there are climatic differences between historical localities and Angamarca; the temporal analysis also exposes a generalized warming trend. Finally, in collaboration with the local community, we developed a series of management recommendations for terrestrial and aquatic environments occupied by the Jambato.
Topics: Animals; Ecuador; Bufonidae; Ecosystem; Batrachochytrium; Conservation of Natural Resources
PubMed: 38915382
DOI: 10.7717/peerj.17344 -
Scientific Reports Jun 2024Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality...
Reintroduction efforts are increasingly used to mitigate biodiversity losses, but are frequently challenged by inadequate planning and uncertainty. High quality information about population status and threats can be used to prioritize reintroduction and restoration efforts and can transform ad hoc approaches into opportunities for improving conservation outcomes at a landscape scale. We conducted comprehensive environmental DNA (eDNA) and visual encounter surveys to determine the distribution of native and non-native aquatic species in two high-priority watersheds to address key uncertainties-such as the distribution of threats and the status of existing populations-inherent in restoration planning. We then used these occurrence data to develop a menu of potential conservation actions and a decision framework to benefit an endangered vertebrate (foothill yellow-legged frog, Rana boylii) in dynamic stream systems. Our framework combines the strengths of multiple methods, allowing managers and conservation scientists to incorporate conservation science and site-specific knowledge into the planning process to increase the likelihood of achieving conservation goals.
Topics: Animals; Conservation of Natural Resources; Rivers; DNA, Environmental; Biodiversity; Endangered Species; Ecosystem; Ranidae
PubMed: 38906892
DOI: 10.1038/s41598-024-64612-5 -
PloS One 2024[This corrects the article DOI: 10.1371/journal.pone.0258594.].
[This corrects the article DOI: 10.1371/journal.pone.0258594.].
PubMed: 38905207
DOI: 10.1371/journal.pone.0306069 -
Communications Biology Jun 2024DNA methylation maintenance is essential for cell fate inheritance. In differentiated cells, this involves orchestrated actions of DNMT1 and UHRF1. In mice, the...
DNA methylation maintenance is essential for cell fate inheritance. In differentiated cells, this involves orchestrated actions of DNMT1 and UHRF1. In mice, the high-affinity binding of DPPA3 to the UHRF1 PHD finger regulates UHRF1 chromatin dissociation and cytosolic localization, which is required for oocyte maturation and early embryo development. However, the human DPPA3 ortholog functions during these stages remain unclear. Here, we report the structural basis for human DPPA3 binding to the UHRF1 PHD finger. The conserved human DPPA3 VRT motif binds to the acidic surface of UHRF1 PHD finger, whereas mouse DPPA3 binding additionally utilizes two unique α-helices. The binding affinity of human DPPA3 for the UHRF1 PHD finger was weaker than that of mouse DPPA3. Consequently, human DPPA3, unlike mouse DPPA3, failed to inhibit UHRF1 chromatin binding and DNA remethylation in Xenopus egg extracts effectively. Our data provide novel insights into the distinct function and structure of human DPPA3.
Topics: Animals; Ubiquitin-Protein Ligases; Humans; CCAAT-Enhancer-Binding Proteins; Mice; Protein Binding; PHD Zinc Fingers; DNA Methylation; Chromatin; Amino Acid Sequence; Xenopus laevis
PubMed: 38898124
DOI: 10.1038/s42003-024-06434-9 -
Anais Da Academia Brasileira de Ciencias 2024The following work presents the first study applying the passive acoustic monitoring of anurans at lotic environments for a long time. This study aims to test the...
The following work presents the first study applying the passive acoustic monitoring of anurans at lotic environments for a long time. This study aims to test the efficiency of the passive acoustic monitoring method and active monitoring in detecting anurans in lotic environments of Itinguçu State Park. Specifically, we tested whether species richness differs when comparing active and passive monitoring surveys. Therefore, this study aims to test the efficiency of the passive acoustic monitoring method and active monitoring in detecting anurans in lotic environments of the Itinguçu State Park. The passive acoustic monitoring period was 72 uninterrupted hours at each collection point with intervals of 45 days. Finally, species richness was calculated, and the efficiency of the methods was compared in different scenarios. Our results demonstrated that the park has species that vocalize day and night, but most at night, there is overlapping acoustic niche; waterfall environments harm the quality of recordings; and in lotic environments the active monitoring method was more efficient than the passive acoustic monitoring in all sampling scales. Although the passive acoustic monitoring was not as efficient in a low temporal scale, it tends to increase in efficiency with longer sampling duration.
Topics: Animals; Peru; Acoustics; Anura; Parks, Recreational; Environmental Monitoring; Vocalization, Animal; Biodiversity
PubMed: 38896695
DOI: 10.1590/0001-3765202420231057 -
Molecules (Basel, Switzerland) May 2024With the global population on the rise, an escalating interest exists in environmentally sustainable and friendly protein sources. Insects have emerged as multifaceted...
With the global population on the rise, an escalating interest exists in environmentally sustainable and friendly protein sources. Insects have emerged as multifaceted resources, viewed not only as potential food items, but also as sources of traditional medicines and proteins. This study utilized response surface methodology (RSM) to ascertain the optimal extraction conditions for proteins from used in toad feeding, denoted as MDPs-T. The yield of MDPs-T was elevated to 18.3% ± 0.2% under these optimized conditions. Subsequently, the particle size, ζ-potentials, and structures of MDPs-T were analyzed and compared with the proteins derived from fed on a normal diet (MDPs-ND). This comparative analysis utilized a range of advanced techniques, involving UV spectroscopy, Fourier transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD), high-performance gel permeation chromatography (HPGPC), and scanning electron microscopy (SEM). The outcomes have revealed a marginal disparity in the physical and chemical properties between MDPs-T and MDPs-ND. Derosination led to a reduction in the particle size of the MDPs by 10.98% to 62.81%. MDPs-T exhibited a higher proportion of low-molecular-weight components relative to MDPs-ND. Additionally, in a comparative analysis of amino acids, MDPs-T displayed a greater abundance of essential and total amino acids relative to MDPs-ND. Consequently, MDPs-T holds potential as a valuable food supplement for human consumption or as a nutrient-rich feed supplement for animals.
Topics: Animals; Houseflies; Insect Proteins; Larva; Spectroscopy, Fourier Transform Infrared; Bufonidae; X-Ray Diffraction; Particle Size; Animal Feed
PubMed: 38893470
DOI: 10.3390/molecules29112595