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This study focuses on the dolphins populating the water between Gibraltar and Algeciras in the south Iberian Peninsula, an area subjected to pressure due to high human activity. The area is considered an important feeding and breeding ground for common dolphins (Delphinus delphis). Due to the degree of residence of some specimens, and the large gap in knowledge about the evolution of wounds inD. delphisspecimens with lacerations, this work sought to perform the following analyses: identify lacerated individuals; characterize sequences of ‘before – during – after’ with respect to the occurrence of lacerations; and associate the type of injury with its severity. This work will inform future studies by expanding a database on injured individuals and contribute to periodical monitoring of specimens that frequent these geographic areas. Between 2013 and 2017, we were able to track the healing process of five injured individuals of common dolphins from a whale-watching platform thanks to photo identification. The animals exhibited fresh external wounds from different sources. In the majority of individuals, the wound-healing processes lasted 3–21 weeks. The frequency with which sightings are made and knowledge about the local population will help track injured animals, follow their wound evolution, and document their survival rates. The documented injuries inflicted by human interactions described in this paper may include fishing interactions and propeller strikes, probably as a consequence of the high intensity of recreational fishing and whale-watching activities in the area.

Background Nanopore technologies allow high-throughput sequencing of long strands of DNA at the cost of a relatively large error rate. This limits its use in the reading of amplicon libraries in which there are only a few mutations per variant and therefore they are easily confused with the sequencing noise. Consensus calling strategies reduce the error but sacrifice part of the throughput on reading typically 30 to 100 times each member of the library. Findings In this work, we introduce SINGLe (SNPs In Nanopore reads of Gene Libraries), an error correction method to reduce the noise in nanopore reads of amplicons containing point variations. SINGLe exploits that in an amplicon library, all reads are very similar to a wild-type sequence from which it is possible to experimentally characterize the position-specific systematic sequencing error pattern. Then, it uses this information to reweight the confidence given to nucleotides that do not match the wild-type in individual variant reads and incorporates it on the consensus calculation. Conclusions We tested SINGLe in a mutagenic library of the KlenTaq polymerase gene, where the true mutation rate was below the sequencing noise. We observed that contrary to other methods, SINGLe compensates for the systematic errors made by the basecallers. Consequently, SINGLe converges to the true sequence using as little as 5 reads per variant, fewer than the other available methods.

Nanopore sequencing is a powerful single molecule DNA sequencing technology which offers high throughput and long sequence reads. Nevertheless, its high native error rate limits the direct detection of point mutations in individual reads of amplicon libraries, as these mutations are difficult to distinguish from the sequencing noise.In this work, we developed SINGLe (SNPs In Nanopore reads of Gene Libraries), a computational method to reduce the noise in nanopore reads of amplicons containing point variations. Our approach uses the fact that all reads are very similar to a wild type sequence, for which we experimentally characterize the position-specific systematic sequencing error pattern. We then use this information to reweight the confidence given to nucleotides that do not match the wild type in individual variant reads. We tested this method in a set of variants of KlenTaq, where the true mutation rate was well below the sequencing noise. SINGLe improves between 4 and 9 fold the signal to noise ratio, in comparison to the data returned by the basecaller guppy. Downstream, this approach improves variants clustering and consensus calling.SINGLe is simple to implement and requires only a few thousands reads of the wild type sequence of interest, which can be easily obtained by multiplexing in a single minION run. It does not require any modification in the experimental protocol, it does not imply a large loss of sequencing throughput, and it can be incorporated downstream of standard basecalling.

E1A is the main transforming protein in mastadenoviruses. This work uses bioinformatics to extrapolate experimental knowledge from Human adenovirus serotype 5 and 12 E1A proteins to all known serotypes. A conserved domain architecture with a high degree of intrinsic disorder acts as a scaffold for multiple linear motifs with variable occurrence mediating the interaction with over fifty host proteins. While linear motifs contribute strongly to sequence conservation within intrinsically disordered E1A regions, motif repertoires can deviate significantly from those found in prototypical serotypes. Close to one hundred predicted residue-residue contacts suggest the presence of stable structure in the CR3 domain and of specific conformational ensembles involving both short- and long-range intramolecular interactions. Our computational results suggest that E1A sequence conservation and co-evolution reflect the evolutionary pressure to maintain a mainly disordered, yet non-random conformation harboring a high number of binding motifs that mediate viral hijacking of the cell machinery. Fil: Glavina, Juliana. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Roman, Ernesto Andres. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Espada, Rocío. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: de Prat Gay, Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Bioquímicas de Buenos Aires. Fundación Instituto Leloir. Instituto de Investigaciones Bioquímicas de Buenos Aires; Argentina Fil: Chemes, Lucia Beatriz. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas; Argentina Fil: Sánchez Miguel, Ignacio Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina

A case of intergeneric hybridization in the wild between a female bottlenose dolphin (Tursiops truncatus) and a short-beaked common dolphin (Delphinus delphis), considered members of 'vulnerable' and 'endangered' subpopulations in the Mediterranean, respectively, by the International Union of Conservation of Nature is described in this paper. The birth of the hybrid was registered in the Bay of Algeciras (southern Spain) in August 2016, and the animal has been tracked on frequent trips aboard dolphin-watching platforms. This unique occurrence is the result of an apparent ongoing interaction (10 years) between a female bottlenose dolphin and common dolphins. The calf has a robust body with length similar to Tursiops, while its lateral striping and coloration are typical of Delphinus. It displays the common dolphin's 'criss-cross' pattern. However, the thoracic patch is lighter than in D. delphis and its dorsal area is light grey, with a 'V' shape under the dorsal fin. This paper also provides a comprehensive mini-review of hybridizations of T. truncatus with other species.

Structural domains are believed to be modules within proteins that can fold and function independently. Some proteins show tandem repetitions of apparent modular structure that do not fold independently, but rather co-operate in stabilizing structural forms that comprise several repeat-units. For many natural repeat-proteins, it has been shown that weak energetic links between repeats lead to the breakdown of co-operativity and the appearance of folding sub-domains within an apparently regular repeat array. The quasi-1D architecture of repeat-proteins is crucial in detailing how the local energetic balances can modulate the folding dynamics of these proteins, which can be related to the physiological behaviour of these ubiquitous biological systems. Fil: Espada, Rocío. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Parra, Rodrigo Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Sippl, Manfred. University of Salzburg; Austria Fil: Mora, Thierry. Centre National de la Recherche Scientifique; Francia Fil: Walczak, Aleksandra. Centre National de la Recherche Scientifique; Francia Fil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina

Repeat proteins are constituted by a variable number of copies of a given structural element that is tandemly repeated along a longitudinal axis. They mainly function as protein-protein interactors with binding interfaces that are not conserved along members of the same family but specific for each interacting pair. These proteins have been extensively used as scaffolds for protein design that are usually centered on the maximization of the stability of the repeat arrays. Although overall stability is important for obtaining molecules with enhanced solubility and expression, natural occurring repeatproteins have unstable characteristics that are relevant for their binding properties. Here we discuss the state of the art for repeat protein designs and the ideas of allowing energetic conflicts for introducing enhanced functionality in the arrays. Fil: Espada, Rocío. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Parra, Rodrigo Gonzalo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina. Max Planck Institute For Biophysical Chemistry; Alemania

Natural protein molecules are remarkablephysical objects. Despite the astronomicalnumber of competing structuralforms, these systems self-organize intobeautiful structural ensembles in biologicallyshort timescales, puzzlingout the feat of specifically bringingtogether thousands of atoms interactingby a myriad of weak forces. Moreover,most protein domains appear to foldwith ease in a deceptively simple twostatemanner, populating either the fullyfolded or fully unfolded ensembles.This is certainly not a property ofrandom amino acid chains.how doproteins do it? Fil: Espada, Rocío. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Sánchez Miguel, Ignacio Enrique. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina Fil: Ferreiro, Diego. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Instituto de Química Biológica de la Facultad de Ciencias Exactas y Naturales; Argentina

Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repetitions within a single repeat protein can be extremely variable at the sequence level. We propose a mathematical definition of a repeat and investigate the occurrences of these in different protein families. We found that long stretches of perfect repetitions are infrequent in individual natural proteins, even for those which are known to fold into structures of recurrent structural motifs. We found that natural repeat proteins are indeed repetitive in their families, exhibiting abundant stretches of 6 amino acids or longer that are perfect repetitions in the reference family. We provide a systematic quantification for this repetitiveness, and show that this form of repetitiveness is not exclusive of repeat proteins, but also occurs in globular domains. A by-product of this work is a fast classifier of proteins into families, which yields likelihood value about a given protein belonging to a given family., 15 pages, 5 figures and supporting information

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy landscape theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal Frustration" when the folded structure is symmetric (Wolynes, P. G. Symmetry and the Energy Landscapes of Biomolecules. Proc. Natl. Acad. Sci. U.S.A. 1996, 93, 14249-14255). Similarly, repeats and structural mosaics may be fundamentally related to landscapes with multiple embedded funnels. Here we present analytical tools to detect and compare structural repetitions in protein molecules. By an exhaustive analysis of the distribution of structural repeats using a robust metric, we define those portions of a protein molecule that best describe the overall structure as a tessellation of basic units. The patterns produced by such tessellations provide intuitive representations of the repeating regions and their association toward higher order arrangements. We find that some protein architectures can be described as nearly periodic, while in others clear separations between repetitions exist. Since the method is independent of amino acid sequence information, we can identify structural units that can be encoded by a variety of distinct amino acid sequences.

The flash photolysis of "caged" compounds is a powerful experimental technique for producing rapid changes in concentrations of bioactive signaling molecules. These caged compounds are inactive and become active when illuminated with ultraviolet light. This paper describes an inexpensive adaptation of an Olympus confocal microscope that uses as source of ultraviolet light the mercury lamp that comes with the microscope for conventional fluorescence microscopy. The ultraviolet illumination from the lamp (350 - 400 nm) enters through an optical fiber that is coupled to a nonconventional port of the microscope. The modification allows to perform the photolysis of caged compounds over wide areas (∼ 200 μm) and obtain confocal fluorescence images simultaneously. By controlling the ultraviolet illumination exposure time and intensity it is possible to regulate the amount of photolyzed compounds. In the paper we characterize the properties of the system and show its capabilities with experiments done in aqueous solution and in Xenopus Laevis oocytes. The latter demonstrate its applicability for the study of Inositol 1,4,5-trisphosphate-mediated intracellular calcium signals.

Ankyrin repeat containing proteins are one of the most abundant solenoid folds. Usually implicated in specific protein-protein interactions, these proteins are readily amenable for design, with promising biotechnological and biomedical applications. Studying repeat protein families presents technical challenges due to the high sequence divergence among the repeating units. We developed and applied a systematic method to consistently identify and annotate the structural repetitions over the members of the complete Ankyrin Repeat Protein Family, with increased sensitivity over previous studies. We statistically characterized the number of repeats, the folding of the repeat-arrays, their structural variations, insertions and deletions. An energetic analysis of the local frustration patterns reveal the basic features underlying fold stability and its relation to the functional binding regions. We found a strong linear correlation between the conservation of the energetic features in the repeat arrays and their sequence variations, and discuss new insights into the organization and function of these ubiquitous proteins., Author Summary Some natural proteins are formed with repetitions of similar amino acid stretches. Ankyrin-repeat proteins constitute one of the most abundant families of this class of proteins that serve as model systems to analyze how variations in sequences exert effects in structures and biological functions. We present an in-depth analysis of the ankyrin repeat protein family, characterizing the variations in the repeating arrays both at the structural and energetic level. We introduce a consistent annotation for the repeat characteristics and describe how the structural differences are related to the sequences by their underlying energetic signatures.