Ancestral aneuploidy and stable chromosomal duplication resulting in differential genome structure and gene expression control in trypanosomatid parasites.

Aneuploidy is widely observed in both unicellular and multicellular eukaryotes, usually associated with adaptation to stress conditions. Chromosomal duplication stability is a tradeoff between the fitness cost of having unbalanced gene copies and the potential fitness gained from increased dosage of specific advantageous genes. Trypanosomatids, a family of protozoans that include species that cause neglected tropical diseases, are a relevant group to study aneuploidies. Their life cycle has several stressors that could select for different patterns of chromosomal duplications and/or losses, and their nearly universal use of polycistronic transcription increases their reliance on gene expansion/contraction, as well as post-transcriptional control as mechanisms for gene expression regulation. By evaluating the data from 866 isolates covering seven trypanosomatid genera, we have revealed that aneuploidy tolerance is an ancestral characteristic of trypanosomatids but has a reduced occurrence in a specific monophyletic clade that has undergone large genomic reorganization and chromosomal fusions. We have also identified an ancient chromosomal duplication that was maintained across these parasite's speciation, named collectively as the trypanosomatid ancestral supernumerary chromosome (TASC). TASC has most genes in the same coding strand, is expressed as a disomic chromosome (even having four copies), and has increased potential for functional variation, but it purges highly deleterious mutations more efficiently than other chromosomes. The evidence of stringent control over gene expression in this chromosome suggests that these parasites have adapted to mitigate the fitness cost associated with this ancient chromosomal duplication.

Regulatory mechanisms of stem cell differentiation: Biotechnological applications for neurogenesis.

The world population's life expectancy is growing, and neurodegenerative disorders common in old age require more efficient therapies. In this context, neural stem cells (NSCs) are imperative for the development and maintenance of the functioning of the nervous system and have broad therapeutic applicability for neurodegenerative diseases. Therefore, knowing all the mechanisms that govern the self-renewal, differentiation, and cell signaling of NSC is necessary. This review will address some of these aspects, including the role of growth and transcription factors, epigenetic modulators, microRNAs, and extracellular matrix components. Furthermore, differentiation and transdifferentiation processes will be addressed as therapeutic strategies showing their significance for stem cell-based therapy.

Strategic use of organoids and organs-on-chip as biomimetic tools.

Organoid development and organ-on-a-chip are technologies based on differentiating stem cells, forming 3D multicellular structures resembling organs and tissues in vivo. Hence, both can be strategically used for disease modeling, drug screening, and host-pathogen studies. In this context, this review highlights the significant advancements in the area, providing technical approaches to organoids and organ-on-a-chip that best imitate in vivo physiology.

Unveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties.

BACKGROUND: Kefir is a complex microbial community that plays a critical role in the fermentation and production of bioactive peptides, and has health-improving properties. The composition of kefir can vary by geographic localization and weather, and this paper focuses on a Brazilian sample and continues previous work that has successful anti-Alzheimer properties. In this study, we employed shotgun metagenomics and peptidomics approaches to characterize Brazilian kefir further. RESULTS: We successfully assembled the novel genome of Lactobacillus kefiranofaciens (LkefirU) and conducted a comprehensive pangenome analysis to compare it with other strains. Furthermore, we performed a peptidome analysis, revealing the presence of bioactive peptides encrypted by L. kefiranofaciens in the Brazilian kefir sample, and utilized in silico prospecting and molecular docking techniques to identify potential anti-Alzheimer peptides, targeting ß-amyloid (fibril and plaque), BACE, and acetylcholinesterase. Through this analysis, we identified two peptides that show promise as compounds with anti-Alzheimer properties. CONCLUSIONS: These findings not only provide insights into the genome of L. kefiranofaciens but also serve as a promising prototype for the development of novel anti-Alzheimer compounds derived from Brazilian kefir.

BioAutoML: automated feature engineering and metalearning to predict noncoding RNAs in bacteria.

Recent technological advances have led to an exponential expansion of biological sequence data and extraction of meaningful information through Machine Learning (ML) algorithms. This knowledge has improved the understanding of mechanisms related to several fatal diseases, e.g. Cancer and coronavirus disease 2019, helping to develop innovative solutions, such as CRISPR-based gene editing, coronavirus vaccine and precision medicine. These advances benefit our society and economy, directly impacting people's lives in various areas, such as health care, drug discovery, forensic analysis and food processing. Nevertheless, ML-based approaches to biological data require representative, quantitative and informative features. Many ML algorithms can handle only numerical data, and therefore sequences need to be translated into a numerical feature vector. This process, known as feature extraction, is a fundamental step for developing high-quality ML-based models in bioinformatics, by allowing the feature engineering stage, with design and selection of suitable features. Feature engineering, ML algorithm selection and hyperparameter tuning are often manual and time-consuming processes, requiring extensive domain knowledge. To deal with this problem, we present a new package: BioAutoML. BioAutoML automatically runs an end-to-end ML pipeline, extracting numerical and informative features from biological sequence databases, using the MathFeature package, and automating the feature selection, ML algorithm(s) recommendation and tuning of the selected algorithm(s) hyperparameters, using Automated ML (AutoML). BioAutoML has two components, divided into four modules: (1) automated feature engineering (feature extraction and selection modules) and (2) Metalearning (algorithm recommendation and hyper-parameter tuning modules). We experimentally evaluate BioAutoML in two different scenarios: (i) prediction of the three main classes of noncoding RNAs (ncRNAs) and (ii) prediction of the eight categories of ncRNAs in bacteria, including housekeeping and regulatory types. To assess BioAutoML predictive performance, it is experimentally compared with two other AutoML tools (RECIPE and TPOT). According to the experimental results, BioAutoML can accelerate new studies, reducing the cost of feature engineering processing and either keeping or improving predictive performance. BioAutoML is freely available at https://github.com/Bonidia/BioAutoML.

BioDeepfuse: a hybrid deep learning approach with integrated feature extraction techniques for enhanced non-coding RNA classification.

The accurate classification of non-coding RNA (ncRNA) sequences is pivotal for advanced non-coding genome annotation and analysis, a fundamental aspect of genomics that facilitates understanding of ncRNA functions and regulatory mechanisms in various biological processes. While traditional machine learning approaches have been employed for distinguishing ncRNA, these often necessitate extensive feature engineering. Recently, deep learning algorithms have provided advancements in ncRNA classification. This study presents BioDeepFuse, a hybrid deep learning framework integrating convolutional neural networks (CNN) or bidirectional long short-term memory (BiLSTM) networks with handcrafted features for enhanced accuracy. This framework employs a combination of k-mer one-hot, k-mer dictionary, and feature extraction techniques for input representation. Extracted features, when embedded into the deep network, enable optimal utilization of spatial and sequential nuances of ncRNA sequences. Using benchmark datasets and real-world RNA samples from bacterial organisms, we evaluated the performance of BioDeepFuse. Results exhibited high accuracy in ncRNA classification, underscoring the robustness of our tool in addressing complex ncRNA sequence data challenges. The effective melding of CNN or BiLSTM with external features heralds promising directions for future research, particularly in refining ncRNA classifiers and deepening insights into ncRNAs in cellular processes and disease manifestations. In addition to its original application in the context of bacterial organisms, the methodologies and techniques integrated into our framework can potentially render BioDeepFuse effective in various and broader domains.

Conchocarpus J. C. Mikan (Rutaceae): Chemical Constituents and Biological Activities.

Rutaceae Juss. stands out as a botanical family recognized for its remarkable diversity in taxonomy, worldwide distribution, chemical composition, and biological activity exhibited by its compounds. Conchocarpus J. C. Mikan is one of the main genera of this family, comprising 50 species distributed throughout the Neotropical America. Brazil is the main center of diversity for this genus, hosting 72% of the species as endemic. This is the first review concerning the genus Conchocarpus, emphasizing its chemical composition and biological activities. The selected papers for this review cover studies on 11 species, of which were identified 88 compounds. Among these, quinoline and acridone alkaloids predominate (57%), followed by flavonoids, amides, coumarins and terpenoids. The biological activities of extracts and compounds indicate trypanocidal and leishmanicidal actions, as well as cytotoxic, fungicidal, molluscicidal, insecticidal, anticholinesterase and antioxidant activities.

Complete assembly, annotation of virulence genes and CRISPR editing of the genome of Leishmania amazonensis PH8 strain.

We report the sequencing and assembly of the PH8 strain of Leishmania amazonensis one of the etiological agents of leishmaniasis. After combining data from long Pacbio reads, short Illumina reads and synteny with the Leishmania mexicana genome, the sequence of 34 chromosomes with 8317 annotated genes was generated. Multigene families encoding three virulence factors, A2, amastins and the GP63 metalloproteases, were identified and compared to their annotation in other Leishmania species. As they have been recently recognized as virulence factors essential for disease establishment and progression of the infection, we also identified 14 genes encoding proteins involved in parasite iron and heme metabolism and compared to genes from other Trypanosomatids. To follow these studies with a genetic approach to address the role of virulence factors, we tested two CRISPR-Cas9 protocols to generate L. amazonensis knockout cell lines, using the Miltefosine transporter gene as a proof of concept.

Comparison of Manual (2D) and Digital (3D) Methods in the Assessment of Simulated Facial Edema.

BACKGROUND: An edema assessment following dental surgeries is essential to improving the dental surgeon's technique and, consequentially, patient comfort. PURPOSE: Two-dimensional (2D) methods are limited in analyzing 3-dimensional (3D) surfaces. Currently, 3D methods are used to investigate postoperative swelling. However, there are no studies that directly compare 2D and 3D methods. The goal of this study is to directly compare 2D and 3D methods used in the assessment of postoperative edema. STUDY DESIGN AND SAMPLE: The investigators implemented a prospective, cross-sectional study with each subject serving as its own control. The sample was composed of dental student volunteers without facial deformities. PREDICTOR VARIABLE: The predictor variable is the method used to measure edema. After simulating edema, manual (2D) and digital (3D) techniques were used to measure edema. The manual method used direct facial perimeter measurements. The two digital methods were photogrammetry using a smartphone (iPhone 11, Apple Inc, Cupertino, California), and facial scanning with a smartphone application (Bellus3D FaceApp, Bellus3D Inc, Campbell, California) [3D measurements] MAIN OUTCOME VARIABLE: The coefficient of variation (CV) (CV = standard deviation /mean) was used to assess homogeneity of edema measurements. ANALYSIS: The Shapiro-Wilk and equal variance tests were applied to assess data homogeneity. Next, one-way analysis of variance was performed, followed by a correlation analysis. Finally, the data were submitted to Tukey's test. The statistical significance threshold was set at 5% (P < .05). RESULTS: The sample was composed of 20 subjects aged 18-38 years. The CV showed higher values using the manual (2D) method (47%; 4.88% ± 2.99), compared with the photogrammetry method (18%; 8.55 mm ± 1.52) and the smartphone application (21%; 8.97 mm ± 1.93). A statistically significant difference was observed between the manual method values and those of the other two groups (P < .001). There was no difference between the facial scanning and photogrammetry groups (3D methods) (P = .778) CONCLUSION AND RELEVANCE: Both digital measuring methods (3D) demonstrated greater homogeneity than the manual method in analyzing facial distortions caused by the same swelling simulation. Therefore, it can be affirmed that digital methods may be more reliable that manual methods for assessing facial edema.

Trypanosoma sp. infection in Boa constrictor snakes: morphological, hematological, clinical biochemistry, molecular, and phylogenetic characteristics.

There are few reports of Trypanosoma in snakes, as well as little information about its pathogenicity in these animals. Thus, the present study aimed to characterize Trypanosoma found in Boa constrictor snakes, to verify the influence of the parasitism on hematological and clinical biochemistry parameters, and to perform a phylogenetic study of the isolates. Blood samples from sixty-one boas were analyzed for the presence of trypanosomatids and by hematological and clinical biochemistry assays. The flagellates that were found in this analysis were used for cell culture, morphometry, and molecular analysis. Later, molecular typing phylogenetic studies were performed. Nine positive animals (14.75%) were identified by microscopy analysis. The hematological results showed that parasitized animals presented significantly lower levels of packed cell volume, hemoglobin, mean corpuscular volume, and mean corpuscular hemoglobin. In the leukogram, eosinophils and heterophils counts were higher in parasitized animals. Considering the molecular analyses, the isolates presented a higher identity of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the 18S small subunit ribosomal RNA (SSU rRNA) gene fragments with Trypanosoma serpentis. The phylogenetic tree, using the GAPDH, clustered all isolates with T. serpentis and Trypanosoma cascavelli. This is the first description of T. serpentis parasitizing boas and of the clinical changes caused by trypanosomatid infection in snakes.

Single intraoperative infrared laser optimized bone repair in rat femoral osteotomies with experimentally induced osteoporosis.

This study aimed to evaluate the effect of infrared laser (IRL) on bone repair in ovariectomized rats subjected to femoral osteotomies. Of 32 rats, half underwent bilateral ovariectomy (OVX) and the other half underwent sham ovariectomy (SHAM). A period of 3 months was defined to observe the presence of osteoporosis. The rats were subjected to osteotomies in the femurs and then fixed with a miniplate and 1.5-mm system screws. Thereafter, half of the rats from both SHAM and OVX groups were not irradiated, and the other half were irradiated by IRL using the following parameters: wavelength, 808 nm; power, 100 mW; 60 s for each point; 6 J/point; and a total of 5 points of bone gap. All animals were euthanized 60 days after surgery. The femur gap was scanned using micro-computed tomography (micro-CT). The samples were then examined under a confocal laser microscope to determine the amounts of calcein and alizarin red. The slides were stained with alizarin red and Stevenel's blue for histometric analysis. In the micro-CT analysis, the OVX groups had the lowest bone volume (P < 0.05). When the laser was applied to the OVX groups, bone turnover increased (P < 0.05). New bone formation (NBF) was comparable between SHAM and OVX/IR (P > 0.05) groups; however, it was less in the OVX groups (P < 0.05). In conclusion, the results encourage the use of IRL intraoperatively as it optimizes bone repair, mainly in animals with low bone mineral density.

Predictability of single versus double-barrel vascularized fibula flaps and dental implants in mandibular reconstructions: A systematic review and meta-analysis of prospective studies.

STATEMENT OF PROBLEM: Patients with vascularized bone flaps from the fibula have reduced bone height, in which case a higher prosthetic abutment is needed for their implant-supported prosthesis. Although the double-flap technique seems promising, systematic reviews and meta-analyses of prospective studies are lacking. PURPOSE: The purpose of this systematic review and meta-analysis was to evaluate the grafted areas of single barrel fibular flaps (SBFF) and double-barrel fibular flaps (DBFF) by considering failure rates, dental implant complications, and bone union at the osteotomy sites. MATERIAL AND METHODS: A systematic review and meta-analysis was performed in accordance with the preferred reporting items for systematic reviews and meta-analyses (PRISMA) statement, population, intervention, control, and outcomes (PICO) question, and the National Health and Medical Research Council scales. The event rate of complications and failures was calculated with a confidence interval (CI) of 95%. RESULTS: A total of 13 prospective studies with 441 participants and 330 graft sites were identified. A total of 235 participants had SBFF with 445 implants, and 95 had DBFF with 164 implants. The overall combined graft failure rates were 4.2% for SBFF and 3.2% for DBFF. The complication rate was 10% for SBFF and 1.9% for DBFF. Implant failure was at 4.7% in the SBFF group and 3.4% in the DBFF group. CONCLUSIONS: Complication rates and implant failures were similar for SBFF and DBFF. Therefore, for long-term oral rehabilitation, both SBFF and DBFF are suitable procedures for mandibular reconstruction.

The Interplay of Raloxifene and Sonochemical Bio-Oss in Early Maxillary Sinus Bone Regeneration: A Histological and Immunohistochemical Analysis in Rabbits.

The study aimed to assess the efficacy of using Raloxifene with ultrasonic processing to enhance Bio-Oss®, a bone graft substitute, for maxillary sinus bone height reconstruction. A total of 24 rabbit maxillary sinuses were distributed into three groups, each receiving different treatments: Bio-Oss® only, sonicated Bio-Oss, and sonicated Bio-Oss® with Raloxifene. Surgical procedures and subsequent histomorphometric and immunohistochemistry analyses were conducted to evaluate the bone formation, connective tissue, and remaining biomaterial, as well as the osteoblastic differentiation and maturation of collagen fibers. Results indicated that the sonicated Bio-Oss® and Bio-Oss® groups showed similar histological behavior and bone formation, but the Raloxifene group displayed inflammatory infiltrate, low bone formation, and disorganized connective tissue. The statistical analysis confirmed significant differences between the groups in terms of bone formation, connective tissue, and remaining biomaterial. In conclusion, the study found that while sonicated Bio-Oss® performed comparably to Bio-Oss® alone, the addition of Raloxifene led to an unexpected delay in bone repair. The findings stress the importance of histological evaluation for accurate bone repair assessment and the necessity for further investigation into the local application of Raloxifene. Future research may focus on optimizing bone substitutes with growth factors to improve bone repair.

Multiplex PCR assay for correct identification of the fish pathogenic species of Edwardsiella genus reveals the presence of E. anguillarum in South America in strains previously characterized as E. tarda.

AIMS: Develop a species-specific multiplex PCR to correctly identify Edwardsiella species in routine diagnostic for fish bacterial diseases. METHODS AND RESULTS: The genomes of 62 Edwardsiella spp. isolates available from the National Center for Biotechnology Information (NCBI) database were subjected to taxonomic and pan-genomic analyses to identify unique regions that could be exploited by species-specific PCR. The designed primers were tested against isolated Edwardsiella spp. strains, revealing errors in commercial biochemical tests for bacterial classification regarding Edwardsiella species. CONCLUSION: Some of the genomes of Edwardsiella spp. in the NCBI platform were incorrectly classified, which can lead to errors in some research. A functional mPCR was developed to differentiate between phenotypically and genetically ambiguous Edwardsiella, with which, we detected the presence of Edwardsiella anguillarum affecting fish in Brazil. SIGNIFICANCE AND IMPACT OF THE STUDY: This study shows that the misclassification of Edwardsiella spp in Brazil concealed the presence of E. anguillarum in South America. Also, this review of the taxonomic classification of the Edwardsiella genus is a contribution to the field to help researchers with their sequencing and identification of genomes, showing some misclassifications in online databases that must be corrected, as well as developing an easy assay to characterize Edwardsiella species in an end-point mPCR.

Temperature and pressure dependent rate constants of the reactions of OH• with cyclopentene from variational TST and SS-QRRK methods.

In this work, the pressure- and temperature-dependent reaction rate constants for the hydrogen abstraction and addition of hydroxyl radicals to the unsaturated cyclopentene were studied. Geometries and vibrational frequencies of reactants, products, and transition states were calculated using density functional theory, with single-point energy corrections determined at the domain-based local pair natural orbital-coupled-cluster single double triple/cc-pVTZ-F12 level. The high-pressure limit rate constants were calculated using the canonical variational transition state theory with the small-curvature tunneling approximation. The vibrational partition functions were corrected by the effects of torsional and ring-puckering anharmonicities of the transition states and cyclopentene, respectively. Variational effects are shown to be relevant for all the hydrogen abstraction reactions. The increasing of the rate constants by tunneling is significant at temperatures below 500 K. The pressure dependence on the rate constants of the addition of OH• to cyclopentene was calculated using the system-specific quantum Rice-Ramsperger-Kassel model. The high-pressure limit rate constants decrease with increasing temperature in the range 250-1000 K. The falloff behavior was studied at several temperatures with pressures varying between 10-3 and 103 bar. At temperatures below 500 K, the effect of the pressure on the addition rate constant is very modest. However, at temperatures around and above 1000 K, taking pressure into account is mandatory for an accurate rate constant calculation. Branching ratio analyses reveal that the addition reaction dominates at temperatures below 500 K, decreasing rapidly at higher temperatures. Arrhenius parameters are provided for all reactions and pressure dependent Arrhenius parameters are given for the addition of OH• to cyclopentene.

Growth performance and rumen morphometrics of Nellore and ½ Angus/Nellore feedlot cattle adapted over 9 and 14 days to high-concentrate diets.

The objective of this study was to evaluate the effects of adapting Nellore and ½ Angus/Nellore (AN) feedlot cattle over periods of 9 and 14 days to high-concentrate diets on performance, feeding behaviour, carcass traits and rumen morphometrics. Seventy-two yearling bulls (313.5 kg ± 24.5), 36 Nellore and 36 AN, were randomly allocated in 24 pens (3 animals/pen; 24 m2 and 2.0 m of bunk space/animal) according to a randomized complete block design with a 2 × 2 factorial arrangement of treatments as follows: Nellore adapted for 9 days, Nellore adapted for 14 days, AN adapted for 9 days, and AN adapted for 14 days. Each treatment was composed by 6 pens (considered the experimental unit in this study). The adaptation lasted either 9 or 14 days and consisted of 3 step-up diets. Therefore, yearling bulls received the finishing diet containing 86% concentrate either on day 10 or 15 of the study, which lasted 89 days taking into account adaptation and finishing periods. Cattle were slaughtered in a commercial abattoir, and two 1-cm2 -rumen fragments, one from cranial and another from ventral sac, were collected. The AN cattle outperformed Nellore in terms of average daily gain (1.71 kg/day vs. 1.27 kg/day, p < 0.01), gain:feed ratio (0.137 kg/kg vs. 0.127 kg/kg, p = 0.02) and hot carcass weight (243.64 kg vs. 228.98 kg, p < 0.01). No main effect of the adaptation period was observed for any of the feedlot performance and carcass traits variables evaluated. Compared to feedlot cattle adapted for 9 days, feedlot cattle adapted for 14 days sorted against long (0.68 vs. 0.91, p < 0.01) and for fine particles (1.04 vs. 1.00, p = 0.01). An interaction (p < 0.01) of genotype and adaptation period was observed for rumenitis, where Nellore bulls adapted for 14 days presented the highest scores. In conclusion, there was no evidence that either Nellore or AN cattle benefit from an adaptation period shorter than 14 days.

Investigation of pre and post environmental impact of the lockdown (COVID-19) on the water quality of the Capibaribe and Tejipió rivers, Recife metropolitan region, Brazil.

The coronavirus pandemic has seriously affected human health, although some improvements on environmental indexes have temporarily occurred, due to changes on socio-cultural and economic standards. The objective of this study was to evaluate the impacts of the coronavirus and the influence of the lockdown associated with rainfall on the water quality of the Capibaribe and Tejipió rivers, Recife, Northeast Brazil, using cloud remote sensing on the Google Earth Engine (GEE) platform. The study was carried out based on eight representative images from Sentinel-2. Among the selected images, two refer to the year 2019 (before the pandemic), three refer to 2020 (during a pandemic), two from the lockdown period (2020), and one for the year 2021. The land use and land cover (LULC) and slope of the study region were determined and classified. Water turbidity data were subjected to descriptive and multivariate statistics. When analyzing the data on LULC for the riparian margin of the Capibaribe and Tejipió rivers, a low permanent preservation area was found, with a predominance of almost 100% of the urban area to which the deposition of soil particles in rivers are minimal. The results indicated that turbidity values in the water bodies varied from 6 mg. L-1 up to 40 mg. L-1. Overall, the reduction in human-based activities generated by the lockdown enabled improvements in water quality of these urban rivers.

Information Theory for Biological Sequence Classification: A Novel Feature Extraction Technique Based on Tsallis Entropy.

In recent years, there has been an exponential growth in sequencing projects due to accelerated technological advances, leading to a significant increase in the amount of data and resulting in new challenges for biological sequence analysis. Consequently, the use of techniques capable of analyzing large amounts of data has been explored, such as machine learning (ML) algorithms. ML algorithms are being used to analyze and classify biological sequences, despite the intrinsic difficulty in extracting and finding representative biological sequence methods suitable for them. Thereby, extracting numerical features to represent sequences makes it statistically feasible to use universal concepts from Information Theory, such as Tsallis and Shannon entropy. In this study, we propose a novel Tsallis entropy-based feature extractor to provide useful information to classify biological sequences. To assess its relevance, we prepared five case studies: (1) an analysis of the entropic index q; (2) performance testing of the best entropic indices on new datasets; (3) a comparison made with Shannon entropy and (4) generalized entropies; (5) an investigation of the Tsallis entropy in the context of dimensionality reduction. As a result, our proposal proved to be effective, being superior to Shannon entropy and robust in terms of generalization, and also potentially representative for collecting information in fewer dimensions compared with methods such as Singular Value Decomposition and Uniform Manifold Approximation and Projection.

GENPPI: standalone software for creating protein interaction networks from genomes.

BACKGROUND: Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results. RESULTS: We developed GENPPI software for the ab initio prediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genus Corynebacterium. Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the species Corynebacterium pseudotuberculosis and created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 min on a conventional computer. Moreover, the interaction networks that our software creates reflect correct evolutionary relationships between species, which we confirmed with average nucleotide identity analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user's choice regarding which set of genomes they are going to study. CONCLUSIONS: GENPPI can help fill the gap concerning the considerable number of novel genomes assembled monthly and our ability to process interaction networks considering the noncore genes for all completed genome versions. With GENPPI, a user dictates how many and how evolutionarily correlated the genomes answer a scientific query.

Increased cholinergic activity under conditions of low estrogen leads to adverse cardiac remodeling.

Cholinesterase inhibitors are used in postmenopausal women for the treatment of neurodegenerative diseases. Despite their widespread use in the clinical practice, little is known about the impact of augmented cholinergic signaling on cardiac function under reduced estrogen conditions. To address this gap, we subjected a genetically engineered murine model of systemic vesicular acetylcholine transporter overexpression (Chat-ChR2) to ovariectomy and evaluated cardiac parameters. Left-ventricular function was similar between Chat-ChR2 and wild-type (WT) mice. Following ovariectomy, WT mice showed signs of cardiac hypertrophy. Conversely, ovariectomized (OVX) Chat-ChR2 mice evolved to cardiac dilation and failure. Transcript levels for cardiac stress markers atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP) were similarly upregulated in WT/OVX and Chat-ChR2/OVX mice. 17ß-Estradiol (E2) treatment normalized cardiac parameters in Chat-ChR2/OVX to the Chat-ChR2/SHAM levels, providing a link between E2 status and the aggravated cardiac response in this model. To investigate the cellular basis underlying the cardiac alterations, ventricular myocytes were isolated and their cellular area and contractility were assessed. Myocytes from WT/OVX mice were wider than WT/SHAM, an indicative of concentric hypertrophy, but their fractional shortening was similar. Conversely, Chat-ChR2/OVX myocytes were elongated and presented contractile dysfunction. E2 treatment again prevented the structural and functional changes in Chat-ChR2/OVX myocytes. We conclude that hypercholinergic mice under reduced estrogen conditions do not develop concentric hypertrophy, a critical compensatory adaptation, evolving toward cardiac dilation and failure. This study emphasizes the importance of understanding the consequences of cholinesterase inhibition, used clinically to treat dementia, for cardiac function in postmenopausal women.