Variations in tumor growth, intra-individual biological variability, and the interpretation of changes.

OBJECTIVES: The identification of changes in tumor markers (TMs) in cancer patients that indicate response to treatment, stabilization or disease progression is a challenge for laboratory medicine. Several approaches have been proposed: assessing percentage increases, applying discriminant values, and estimating half-life (t1/2) or doubling time (DT). In all of them it is assumed that the TM is a surrogate of the variation in tumor size. In general this variation is time-dependent, but this is not the case of intraindividual biological variability (CVi), which can range from 6 % in CA15-3 to 22 % in CA125. When decisions are made on the basis of DT or t1/2, these values can be affected by the CVi; if it is very large, the growth rate very slow and the period of time between determinations very short, the result obtained for DT may be due mainly to the CVi. The aim of this study is to establish the relationship between the CVi and temporal variables. METHODS: We related equations for calculating DT and t1/2 to the reference change values in tumor markers. RESULTS: The application of the formula obtained allows the calculation of the optimal time between measurements to ensure that the influence of the CVi is minimal in different types of tumors and different scenarios. CONCLUSIONS: Intraindividual variation affects the calculation of DT and t1/2. It is necessary to establish the minimum time between two measurements to ensure that the CVi does not affect their calculation or lead to misinterpretation.

Lung cancer tumor markers in serous effusions and other body fluids.

From its onset and during its progression, lung cancer may affect various extrapulmonary structures. These include the serous membranes, the pleura and pericardium, and less frequently the central nervous system, with leptomeningeal involvement. In these cases, fluid accumulates in the serous membranes which may contain substances secreted by the tumor. Measuring the concentrations of these substances can provide useful information for elucidating the origin of the fluid accumulation, either in pleural and pericardial effusions or in cerebrospinal fluid. This paper describes the histological types of lung cancer that most frequently affect the serosa and leptomeninges. It also reviews the literature on tumor markers in different fluids and makes recommendations for their interpretation.

The Influence of Nanoparticle Shape on Protein Corona Formation.

Nanoparticles have become an important utility in many areas of medical treatment such as targeted drug and treatment delivery as well as imaging and diagnostics. These advances require a complete understanding of nanoparticles' fate once placed in the body. Upon exposure to blood, proteins adsorb onto the nanoparticles surface and form a protein corona, which determines the particles' biological fate. This study reports on the protein corona formation from blood serum and plasma on spherical and rod-shaped nanoparticles. These two types of mesoporous silica nanoparticles have identical chemistry, porosity, surface potential, and size in the y-dimension, one being a sphere and the other a rod shape. The results show a significantly larger amount of protein attaching from both plasma and serum on the rod-like particles compared to the spheres. Interrogation of the protein corona by liquid chromatography-mass spectrometry reveals shape-dependent differences in the adsorption of immunoglobulins and albumin proteins from both plasma and serum. This study points to the need for taking nanoparticle shape into consideration because it can have a significant impact on the fate and therapeutic potential of nanoparticles when placed in the body.

Gene regulatory networks on transfer entropy (GRNTE): a novel approach to reconstruct gene regulatory interactions applied to a case study for the plant pathogen Phytophthora infestans.

BACKGROUND: The increasing amounts of genomics data have helped in the understanding of the molecular dynamics of complex systems such as plant and animal diseases. However, transcriptional regulation, although playing a central role in the decision-making process of cellular systems, is still poorly understood. In this study, we linked expression data with mathematical models to infer gene regulatory networks (GRN). We present a simple yet effective method to estimate transcription factors' GRNs from transcriptional data. METHOD: We defined interactions between pairs of genes (edges in the GRN) as the partial mutual information between these genes that takes into account time and possible lags in time from one gene in relation to another. We call this method Gene Regulatory Networks on Transfer Entropy (GRNTE) and it corresponds to Granger causality for Gaussian variables in an autoregressive model. To evaluate the reconstruction accuracy of our method, we generated several sub-networks from the GRN of the eukaryotic yeast model, Saccharomyces cerevisae. Then, we applied this method using experimental data of the plant pathogen Phytophthora infestans. We evaluated the transcriptional expression levels of 48 transcription factors of P. infestans during its interaction with one moderately resistant and one susceptible cultivar of yellow potato (Solanum tuberosum group Phureja), using RT-qPCR. With these data, we reconstructed the regulatory network of P. infestans during its interaction with these hosts. RESULTS: We first evaluated the performance of our method, based on the transfer entropy (GRNTE), on eukaryotic datasets from the GRNs of the yeast S. cerevisae. Results suggest that GRNTE is comparable with the state-of-the-art methods when the parameters for edge detection are properly tuned. In the case of P. infestans, most of the genes considered in this study, showed a significant change in expression from the onset of the interaction (0 h post inoculum - hpi) to the later time-points post inoculation. Hierarchical clustering of the expression data discriminated two distinct periods during the infection: from 12 to 36 hpi and from 48 to 72 hpi for both the moderately resistant and susceptible cultivars. These distinct periods could be associated with two phases of the life cycle of the pathogen when infecting the host plant: the biotrophic and necrotrophic phases. CONCLUSIONS: Here we presented an algorithmic solution to the problem of network reconstruction in time series data. This analytical perspective makes use of the dynamic nature of time series data as it relates to intrinsically dynamic processes such as transcription regulation, were multiple elements of the cell (e.g., transcription factors) act simultaneously and change over time. We applied the algorithm to study the regulatory network of P. infestans during its interaction with two hosts which differ in their level of resistance to the pathogen. Although the gene expression analysis did not show differences between the two hosts, the results of the GRN analyses evidenced rewiring of the genes' interactions according to the resistance level of the host. This suggests that different regulatory processes are activated in response to different environmental cues. Applications of our methodology showed that it could reliably predict where to place edges in the transcriptional networks and sub-networks. The experimental approach used here can help provide insights on the biological role of these interactions on complex processes such as pathogenicity. The code used is available at https://github.com/jccastrog/GRNTE under GNU general public license 3.0.

Evolutionary Origins of Rhizarian Parasites.

The SAR group (Stramenopila, Alveolata, Rhizaria) is one of the largest clades in the tree of eukaryotes and includes a great number of parasitic lineages. Rhizarian parasites are obligate and have devastating effects on commercially important plants and animals but despite this fact, our knowledge of their biology and evolution is limited. Here, we present rhizarian transcriptomes from all major parasitic lineages in order to elucidate their evolutionary relationships using a phylogenomic approach. Our results suggest that Ascetosporea, parasites of marine invertebrates, are sister to the novel clade Apofilosa. The phytomyxean plant parasites branch sister to the vampyrellid algal ectoparasites in the novel clade Phytorhiza. They also show that Ascetosporea + Apofilosa + Retaria + Filosa + Phytorhiza form a monophyletic clade, although the branching pattern within this clade is difficult to resolve and appears to be model-dependent. Our study does not support the monophyly of the rhizarian parasitic lineages (Endomyxa), suggesting independent origins for rhizarian animal and plant parasites.

Protein Interactions with Nanoengineered Polyoxazoline Surfaces Generated via Plasma Deposition.

Protein adsorption to biomaterials is critical in determining their suitability for specific applications, such as implants or biosensors. Here, we show that surface nanoroughness can be tailored to control the covalent binding of proteins to plasma-deposited polyoxazoline (PPOx). Nanoengineered surfaces were created by immobilizing gold nanoparticles varying in size and surface density on PPOx films. To keep the surface chemistry consistent while preserving the nanotopography, all substrates were overcoated with a nanothin PPOx film. Bovine serum albumin was chosen to study protein interactions with the nanoengineered surfaces. The results demonstrate that the amount of protein bound to the surface is not directly correlated with the increase in surface area. Instead, it is determined by nanotopography-induced geometric effects and surface wettability. A densely packed array of 16 and 38 nm nanoparticles hinders protein adsorption compared to smooth PPOx substrates, while it increases for 68 nm nanoparticles. These adaptable surfaces could be used for designing biomaterials where proteins adsorption is or is not desirable.

LOVA: the role of endoscopic third ventriculostomy and a new proposal for diagnostic criteria.

The diagnostic criteria and management of this condition continue to be a topic of debate in the literature. The term definitive symptomatic LOVA (longstanding overt ventriculomegaly in adults) is applied to patients that fulfil a series of diagnostic criteria,which are reviewed in our paper. The main subject of our study is to propose a rearrangement of the criteria for the diagnosis of this entity and adjusted treatment strategies. We present our data evaluating the role of endoscopy in this pathology. This descriptive and analytical study comprised 27 adult patients with LOVA who underwent endoscopic third ventriculostomy (ETV). Data regarding age, gender and onset of symptoms, a previously implanted shunt, clinical examination and radiological findings at the time of diagnosis, and the intracranial pressure (ICP) recordings in some cases, were carefully retrospectively reviewed. ETV success was determined based on clinical state and radiological criteria. ETV was performed in all 27 cases. Mean follow up period was 4.2 years (6 months to 8 years). 2/27 patients (7.40%) were lost to follow-up. The overall success rate for ETV was 76% (21/25 patients). ETV resulted in shunt independency in two of the three patients with a previous shunt. Based on our results, we believe that ETV must be considered as the treatment of choice for patients with symptomatic LOVA.

Neuroendoscopic treatment for hydrocephalus associated to midline arachnoid cysts in a series of nine pediatric patients.

BACKGROUND: Arachnoid cysts are extra-axial cerebrospinal fluid (CSF) collections surrounded by a membrane. Occasionally, hydrocephalus is associated due to a change in CSF circulatory dynamics. Neuroendoscopic treatment has been recommended for patients who develop symptoms resulting from the cyst location. METHODS: We retrospectively evaluate the results in our series of 9 patients with hydrocephalus associated to midline arachnoid cysts treated endoscopically. Success was rated on a scale of five degrees of neuroendoscopical success. RESULTS: We performed endoscopic third ventriculostomy (ETV) in three cases; ETV was associated to ventriculocystostomy (VC) in three cases; ETV, VC and septostomy (SPT) were performed in one patient; neuroendoscopic Monro foraminoplasty (NEFPMO) plus SPT were associated in one case; last patient was performed ETV, VC and cystocysternostomy (CC). For first procedures, 6 patients completed permanent Success (grade I). In one case success was transitory (grade II) and required a second procedure (ETV). In one patient VC success and ETV failure implied partial success (grade III). One patient's early failure (grade V) required a second procedure (ETV + NEFPMO). Success in second procedures was grade I in both patients. Follow-up period was over 12 months and altogether success was grade I in 8/9 patients and grade III in 1/9 patients. Shunt independency went over 88%. CONCLUSIONS: Endoscopy allows a solution avoiding the implantation of cerebrospinal fluid shunt devices. When possible, we likely approach both, hydrocephalus and arachnoid cyst, with different endoscopic maneuvers in a single procedure. It is important to expand the usage of success classifications for combined procedures.

Ethmoidal meningoencephalocele and CSF leak after posthaemorrhagic ventricular dilatation in a newborn child.

BACKGROUND: Rhinoliquorrhoea suggests a communication between the subarachnoid space and the sinonasal tract. Clinical presentation includes clear nasal discharge, headache, pneumocephalus, meningitis or brain abscess. Cerebrospinal fluid (CSF) leaks are mostly of traumatic origin (skull base fractures), iatrogenic (secondary to endoscopic endonasal surgery) or associated with tumour aetiology. Occasionally, hydrocephalus has been the cause of rhinoliquorrhoea in adults, presumably secondary to the chronically raised intracranial pressure with skull base erosion and meningocele. To our knowledge, the association of hydrocephalus and ethmoid meningoencephalocele/CSF leak has not been previously reported in a newborn child. CASE PRESENTATION: We present the case of a 9-month-old girl who was referred for rhinorrhoea. She had a history of posthaemorrhagic ventricular dilatation. Brain computed tomography (CT) and magnetic resonance imaging (MRI) showed a left ethmoidal meningoencephalocele and small ventricular size. The meningoencephalocele was surgically repaired using an intradural subfrontal approach. During the postoperative period, after the transient lumbar drain was withdrawn, she developed symptomatic hydrocephalus. Ventriculoperitoneal shunting was required. CONCLUSION: Progressive ventricular dilatation may arise from a meningoencephalocele/CSF leak in paediatric patients. Early identification and repair of the meningoencephalocele are critical to avoid development of complications.

Prognosis of atypical teratoid rhabdoid tumors (AT/RT) treated with multimodal therapy protocols. Report of our series.

OBJECTIVE: Atypical teratoid rhabdoid tumors (AT/RT) of the central nervous system are rare, very aggressive embryological tumors, typically diagnosed in young patients and having a low survival rate after diagnosis. The aim of this study was to emphasize, based on the latest results in the literature, the need for protocols for multidisciplinary treatment in these patients. MATERIAL AND METHODS: We report our series of 3 cases treated, diagnosed and followed up between 2009 and 2014. They were treated with multimodal therapy protocols (Rhabdoid SIOP-2007 and European Rhabdoid Registry EU-RHAB-2010). In addition, we carried out a literature review. RESULTS: Two of our 3 cases (supratentorial and spinal tumors) did not show any progression of the disease after long follow-up, in contrast with most of the cases available in the literature. The second patient had a shorter survival. CONCLUSIONS: Patient age at the time of diagnosis, supratentorial location of the mass and fewer complications with adjuvant treatments seem to be factors yielding good prognosis for AT/RT tumors. In agreement with the latest international protocols, multidisciplinary treatment is the ideal treatment, consisting of radiotherapy and chemotherapy after complete tumor resection.

Endoscopic endonasal resection of clival xanthoma: case report and literature review.

Bone xanthoma is an extremely rare and benign tumor in terms of its nature and growth over time. We describe the first case coexisting with ventriculomegaly secondary to aqueduct stenosis (non-tumoral hydrocephalus), the second xanthoma of the clivus described to date. The patient was a 51-year-old woman with headaches and absence seizures. Axial T1-weighted MRI showed a well-demarcated, hypointense, osteolytic, 25 × 18 × 15 mm lesion with cortical erosion located at the right margin of the clivus. Sagittal T2-weighted MRI demonstrated a hypointense mass without associated edema. Sagittal gadolinium-enhanced T1-weighted MRI showed contrast uptake with a partially hypointense rim. The increased ventricular size without periventricular edema was associated with aqueduct stenosis, and there was no contiguity with the tumor. A neuronavigation image-guided transsphenoidal approach was chosen to perform a macroscopically complete resection. Intraoperative histopathological study showed a chordoma of the clivus. Exhaustive postsurgical study revealed the benign nature of a bone xanthoma. Given the finding of a clival lesion, the differential diagnosis is essentially with other malignant entities with a rapidly fatal outcome, such as metastases, or with a possible invasive evolution, such as clivus chordomas. This report describes the clinical, radiological, and pathological keys for such differentiation in order to avoid unnecessarily aggressive treatment with ablative surgery and radiotherapy.

Predicting the "usefulness" of 5-ALA-derived tumor fluorescence for fluorescence-guided resections in pediatric brain tumors: a European survey.

BACKGROUND: Five-aminolevulinic acid (Gliolan, medac, Wedel, Germany, 5-ALA) is approved for fluorescence-guided resections of adult malignant gliomas. Case reports indicate that 5-ALA can be used for children, yet no prospective study has been conducted as of yet. As a basis for a study, we conducted a survey among certified European Gliolan users to collect data on their experiences with children. METHODS: Information on patient characteristics, MRI characteristics of tumors, histology, fluorescence qualities, and outcomes were requested. Surgeons were further asked to indicate whether fluorescence was "useful", i.e., leading to changes in surgical strategy or identification of residual tumor. Recursive partitioning analysis (RPA) was used for defining cohorts with high or low likelihoods for useful fluorescence. RESULTS: Data on 78 patients <18 years of age were submitted by 20 centers. Fluorescence was found useful in 12 of 14 glioblastomas (85 %), four of five anaplastic astrocytomas (60 %), and eight of ten ependymomas grades II and III (80 %). Fluorescence was found inconsistently useful in PNETs (three of seven; 43 %), gangliogliomas (two of five; 40 %), medulloblastomas (two of eight, 25 %) and pilocytic astrocytomas (two of 13; 15 %). RPA of pre-operative factors showed tumors with supratentorial location, strong contrast enhancement and first operation to have a likelihood of useful fluorescence of 64.3 %, as opposed to infratentorial tumors with first surgery (23.1 %). CONCLUSIONS: Our survey demonstrates 5-ALA as being used in pediatric brain tumors. 5-ALA may be especially useful for contrast-enhancing supratentorial tumors. These data indicate controlled studies to be necessary and also provide a basis for planning such a study.

The evolutionary history of three Baracoffea species from western Madagascar revealed by chloroplast and nuclear genomes.

The wild species of the Coffea genus present a very wide morphological, genetic, and biochemical diversity. Wild species are recognized more resistant to diseases, pests, and environmental variations than the two species currently cultivated worldwide: C. arabica (Arabica) and C. canephora (Robusta). Consequently, wild species are now considered as a crucial resource for adapting cultivated coffee trees to climate change. Within the Coffea genus, 79 wild species are native to the Indian Ocean islands of Comoros, Mayotte, Mauritius, Réunion and Madagascar, out of a total of 141 taxa worldwide. Among them, a group of 9 species called "Baracoffea" are particularly atypical in their morphology and adaptation to the sandy soils of the dry deciduous forests of western Madagascar. Here, we have attempted to shed light on the evolutionary history of three Baracoffea species: C. ambongensis, C. boinensis and C. bissetiae by analyzing their chloroplast and nuclear genomes. We assembled the complete chloroplast genomes de novo and extracted 28,800 SNP (Single Nucleotide Polymorphism) markers from the nuclear genomes. These data were used for phylogenetic analysis of Baracoffea with Coffea species from Madagascar and Africa. Our new data support the monophyletic origin of Baracoffea within the Coffea of Madagascar, but also reveal a divergence with a sister clade of four species: C. augagneurii, C. ratsimamangae, C. pervilleana and C. Mcphersonii (also called C. vohemarensis), belonging to the Subterminal botanical series and living in dry or humid forests of northern Madagascar. Based on a bioclimatic analysis, our work suggests that Baracoffea may have diverged from a group of Malagasy Coffea from northern Madagascar and adapted to the specific dry climate and low rainfall of western Madagascar. The genomic data generated in the course of this work will contribute to the understanding of the adaptation mechanisms of these particularly singular species.

Pituitary-Adrenal Axis and Peripheral Immune Cell Profile in Long COVID.

In Long COVID, dysfunction in the pituitary-adrenal axis and alterations in immune cells and inflammatory status are warned against. We performed a prospective study in a cohort of 42 patients who suffered COVID-19 at least 6 months before attending the Long COVID unit at Althaia Hospital. Based on Post-COVID Functional Status, 29 patients were diagnosed with Long COVID, while 13 were deemed as recovered. The hormones of the pituitary-adrenal axis, adrenocorticotropin stimulation test, and immune cell profiles and inflammatory markers were examined. Patients with Long COVID had significantly lower EuroQol and higher mMRC scores compared to the recovered individuals. Their symptoms included fatigue, myalgia, arthralgia, persistent coughing, a persistent sore throat, dyspnoea, a lack of concentration, and anxiety. We observed the physiological levels of cortisol and adrenocorticotropin in individuals with or without Long COVID. The results of the adrenocorticotropin stimulation test were similar between both groups. The absolute number of neutrophils was lower in the Long COVID patients compared to recovered individuals (p < 0.05). The total count of B lymphocytes remained consistent, but Long COVID patients had a higher percentage of mature B cells compared to recovered participants (p < 0.05) and exhibited a higher percentage of circulating resident memory CD8+ T cells (p < 0.05) and Treg-expressing exonucleases (p < 0.05). Our findings did not identify adrenal dysfunction related to Long COVID, nor an association between adrenal function and clinical symptoms. The data indicated a dysregulation in certain immune cells, pointing to immune activation. No overt hyperinflammation was observed in the Long COVID group.

Unveiling potential virulence determinants in Vibrio isolates from Anadara tuberculosa through whole genome analyses.

The genus Vibrio includes pathogenic bacteria able to cause disease in humans and aquatic organisms, leading to disease outbreaks and significant economic losses in the fishery industry. Despite much work on Vibrio in several marine organisms, no specific studies have been conducted on Anadara tuberculosa. This is a commercially important bivalve species, known as "piangua hembra," along Colombia's Pacific coast. Therefore, this study aimed to identify and characterize the genomes of Vibrio isolates obtained from A. tuberculosa. Bacterial isolates were obtained from 14 A. tuberculosa specimens collected from two locations along the Colombian Pacific coast, of which 17 strains were identified as Vibrio: V. parahaemolyticus (n = 12), V. alginolyticus (n = 3), V. fluvialis (n = 1), and V. natriegens (n = 1). Whole genome sequence of these isolates was done using Oxford Nanopore Technologies (ONT). The analysis revealed the presence of genes conferring resistance to ß-lactams, tetracyclines, chloramphenicol, and macrolides, indicating potential resistance to these antimicrobial agents. Genes associated with virulence were also found, suggesting the potential pathogenicity of these Vibrio isolates, as well as genes for Type III Secretion Systems (T3SS) and Type VI Secretion Systems (T6SS), which play crucial roles in delivering virulence factors and in interbacterial competition. This study represents the first genomic analysis of bacteria within A. tuberculosa, shedding light on Vibrio genetic factors and contributing to a comprehensive understanding of the pathogenic potential of these Vibrio isolates.IMPORTANCEThis study presents the first comprehensive report on the whole genome analysis of Vibrio isolates obtained from Anadara tuberculosa, a bivalve species of great significance for social and economic matters on the Pacific coast of Colombia. Research findings have significant implications for the field, as they provide crucial information on the genetic factors and possible pathogenicity of Vibrio isolates associated with A. tuberculosa. The identification of antimicrobial resistance genes and virulence factors within these isolates emphasizes the potential risks they pose to both human and animal health. Furthermore, the presence of genes associated with Type III and Type VI Secretion Systems suggests their critical role in virulence and interbacterial competition. Understanding the genetic factors that contribute to Vibrio bacterial virulence and survival strategies within their ecological niche is of utmost importance for the effective prevention and management of diseases in aquaculture practices.

[Cranial fasciitis: a case report and review of the literature]. / Fascitis craneal: caso clínico y revisión de la literatura.

Cranial fasciitis is an uncommon, rapidly-growing, benign, non-tumoural, myofibroblastic lesion of the skull, found mainly among young children in their first year of life. It is histologically similar to nodular fasciitis and pseudosarcomatous fasciitis. It may mimic more aggressive pathologies, such as sarcomatosis or histiocytosis, due to its rapid, nodular growth in subcutaneous tissue. Complete resection is considered curative and, therefore, entails a low risk of metastases or malignant recurrences. We present the clinical, radiological and pathological findings in a 4-year-old boy with cranial fasciitis in the deep, subcutaneous, soft tissue, with erosion of the outer table of the cranium, which also produced periosteal reaction, while respecting the inner table and meninges. The objective of this article is to highlight the absence of radiotherapeutic or chemotherapeutic adjuvant treatment. In addition, an exhaustive review of the literature is also presented.

Efficient homology-based annotation of transposable elements using minimizers.

Premise: Transposable elements (TEs) make up more than half of the genomes of complex plant species and can modulate the expression of neighboring genes, producing significant variability of agronomically relevant traits. The availability of long-read sequencing technologies allows the building of genome assemblies for plant species with large and complex genomes. Unfortunately, TE annotation currently represents a bottleneck in the annotation of genome assemblies. Methods and Results: We present a new functionality of the Next-Generation Sequencing Experience Platform (NGSEP) to perform efficient homology-based TE annotation. Sequences in a reference library are treated as long reads and mapped to an input genome assembly. A hierarchical annotation is then assigned by homology using the annotation of the reference library. We tested the performance of our algorithm on genome assemblies of different plant species, including Arabidopsis thaliana, Oryza sativa, Coffea humblotiana, and Triticum aestivum (bread wheat). Our algorithm outperforms traditional homology-based annotation tools in speed by a factor of three to >20, reducing the annotation time of the T. aestivum genome from months to hours, and recovering up to 80% of TEs annotated with RepeatMasker with a precision of up to 0.95. Conclusions: NGSEP allows rapid analysis of TEs, especially in very large and TE-rich plant genomes.

Selection signatures and population dynamics of transposable elements in lima bean.

The domestication process in lima bean (Phaseolus lunatus L.) involves two independent events, within the Mesoamerican and Andean gene pools. This makes lima bean an excellent model to understand convergent evolution. The mechanisms of adaptation followed by Mesoamerican and Andean landraces are largely unknown. Genes related to these adaptations can be selected by identification of selective sweeps within gene pools. Previous genetic analyses in lima bean have relied on Single Nucleotide Polymorphism (SNP) loci, and have ignored transposable elements (TEs). Here we show the analysis of whole-genome sequencing data from 61 lima bean accessions to characterize a genomic variation database including TEs and SNPs, to associate selective sweeps with variable TEs and to predict candidate domestication genes. A small percentage of genes under selection are shared among gene pools, suggesting that domestication followed different genetic avenues in both gene pools. About 75% of TEs are located close to genes, which shows their potential to affect gene functions. The genetic structure inferred from variable TEs is consistent with that obtained from SNP markers, suggesting that TE dynamics can be related to the demographic history of wild and domesticated lima bean and its adaptive processes, in particular selection processes during domestication.

MONICET: The Azores whale watching contribution to cetacean monitoring.

Background: The Azores islands have been historically linked to cetaceans, becoming an example of a successful transition from whaling to whale watching. Twenty-eight cetacean species have been sighted in these waters, making the archipelago one of the most recognised whale and dolphin watching destinations worldwide. The business is well-established in the region, operates in four of the nine islands year-round or seasonally and provides an excellent opportunity to collect long term information on cetacean distribution and abundance in an affordable way. Continuous monitoring is indeed essential to establish baseline knowledge and to evaluate cetacean response to potential natural or anthropogenic impacts. Opportunistic data greatly complement traditional dedicated surveys, providing additional support for appropriate management plans. New information: The MONICET platform has been running continuously since 2009 as a collaborative instrument to collect, store, organise and disseminate cetacean data voluntarily collected by whale watching companies in the Azores. In the period covered by this dataset (2009-2020), 11 whale watching companies have voluntarily provided data from the four islands of the archipelago where whale watching takes place. The dataset contains more than 37,000 sightings of 25 species (22 cetaceans and three turtles). This manuscript presents the first long-term whale watching cetacean occurrence dataset openly available for the Azores. We explain the methodology used for data collection and address the potential biases and limitations inherent to the opportunistic nature of the dataset to maximise its usability by external users.

NGSEP 4: Efficient and accurate identification of orthogroups and whole-genome alignment.

Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.