Sperm quality parameters of Iberian toothcarp (Aphanius iberus) and Valencia toothcarp (Valencia hispanica): new conservation tools from a gamete perspective

[EN] The sensitive state of conservation of several endemic fish species such as Iberian toothcarp (Aphanius iberus) and Valencia toothcarp (Valencia hispanica) has led governments to consider the implementation of conservation measures to preserve their populations. However, limited knowledge about the reproductive biology of these species makes it necessary to investigate different aspects of their reproductive cycle. In this sense, the main objectives of this work were i) to advance knowledge of the breeding biology of both species, and ii) to develop protocols for the conservation of gametes for the future management and conservation. During the spring of 2019 a temporal series of samplings were carried out in different places in the Comunitat Valenciana. Sperm samples were collected and sperm motion parameters were assessed for the first time in both species. Kinetic patterns were similar showing high motility and velocity values during the first 30 s, and a rapid decrease from that point. At the same time, an in-depth morphometric analysis was carried out using computer-assisted sperm analysis software. Spermatozoa from A. iberus and V. hispanica showed similar sizes and shapes to other external fertilizers belonging to Cyprinodontiformes, with small spherical heads, uniflagellated and without acrosomes. In addition, a new cryopreservation protocol was designed for cryobanking the sperm of these threatened species. Cryopreserved samples showed lower motility than fresh samples but reaching acceptable percentages of motile cells after thawing of around 20 and 25% (A. iberus and V. hispanica, respectively). This study is the first of its kind to successfully achieve gamete cryopreservation of these two endemic and endangered species from the Iberian Peninsula, providing new and useful tools to complement the management and conservation programs that are being developed for both species.This project has received funding from the Generalitat Valenciana (GV; Valencia, Spain) under the "Subvenciones para la realizacion de proyectos de I+D+I desarrollados por grupos de investigacion emergentes (GV/2019/130)". VG has a postdoc grant from the Ministerio de Economia, Industria y Competitividad (MINECO; Madrid, Spain) under the project IJCI-2017-34200. We would like to thank all the technicians of the CCEDCV for their work and effort during the samplings, specially to J. Velazquez, J. Hernandez and A. Pradillo.Blanes-García, M.; Risueño, P.; Pérez Igualada, LM.; Asturiano, JF.; Gallego Albiach, V. (2021). Sperm quality parameters of Iberian toothcarp (Aphanius iberus) and Valencia toothcarp (Valencia hispanica): new conservation tools from a gamete perspective. Aquaculture. 530:1-9. https://doi.org/10.1016/j.aquaculture.2020.735819S1953

Accurate and efficient constrained molecular dynamics of polymers using Newton's method and special purpose code

In molecular dynamics simulations we can often increase the time step by imposing constraints on bond lengths and bond angles. This allows us to extend the length of the time interval and therefore the range of physical phenomena that we can afford to simulate. We examine the existing algorithms and software for solving nonlinear constraint equations in parallel and we explain why it is necessary to advance the state-of-the-art. We present ILVES-PC, a new algorithm for imposing bond constraints on proteins accurately and efficiently. It solves the same system of differential algebraic equations as the celebrated SHAKE algorithm, but ILVES-PC solves the nonlinear constraint equations using Newton’s method rather than the nonlinear Gauss-Seidel method. Moreover, ILVES-PC solves the necessary linear systems using a specialized linear solver that exploits the structure of the protein. ILVES-PC can rapidly solve constraint equations as accurately as the hardware will allow. The run-time of ILVES-PC is proportional to the number of constraints. We have integrated ILVES-PC into GROMACS and simulated proteins of different sizes. Compared with SHAKE, we have achieved speedups of up to 4.9× in single-threaded executions and up to 76× in shared-memory multi-threaded executions. Moreover, ILVES-PC is more accurate than P-LINCS algorithm. Our work is a proof-of-concept of the utility of software designed specifically for the simulation of polymers

Detection of cytomegalovirus in bronchoalveolar lavage fluid from immunocompromised patients with pneumonitis by viral culture and DNA quantification

Altres ajuts: acords transformatius de la UABTo compare the detection of human cytomegalovirus (HCMV) in bronchoalveolar lavage (BAL) fluid by viral culture and quantitative polymerase chain reaction (qPCR), and to establish a viral load threshold that can identify cases of HCMV replication indicative of pneumonitis. There is currently no universal viral load cut-off to differentiate between patients with and without pneumonitis, and the interpretation of qPCR results is challenging. 176 consecutive BAL samples from immunosuppressed hosts with signs and/or symptoms of respiratory infection were prospectively studied by viral culture and qPCR. Concordant results were obtained in 81.25% of the BAL samples. The rest were discordant, as only 34% of the qPCR-positive BAL samples were positive by culture. The median HCMV load was significantly higher in culture-positive than in culture-negative BAL samples (5038 vs 178 IU/mL). Using a cut-off value of 1258 IU/mL of HCMV in BAL, pneumonia was diagnosed with a sensitivity of 76%, a specificity of 100%, a VPP of 100% and VPN of 98%, and HCMV was isolated in 100% of the BAL cultures. We found that a qPCR-negative was a quick and reliable way of ruling out HCMV pneumonitis, but a positive result did not always indicate clinically significant replication in the lung. However, an HCMV load in BAL fluid of ≥ 1258 IU/mL was always associated with disease, whereas < 200 IU/mL rarely so

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

First embryogenic stages of Citrus microspore-derived embryos

6 p.-2 fig.This work is the first characterization at cellular and subcellular level of the main cellular events occurring in the first stages of microspore embryogenesis. Microspore embryogenesis was induced in two varieties of Citrus clementina (Nules and Monreal). The results showed that one of the most responsive stages for embryogenesis was the vacuolate microspore. Microscopic analysis revealed specific features of the young proembryos still surrounded by the exine:large nuclei, clear areas in the cytoplasm, starch accumulation, and an increase in the thickness of the wall under the exine. Immunogold labelling with JIM 5 antibody showed a high amount of non-esterified pectins in the surrounding cell wall. After exine rupture, different cell types were detected in late proembryos. As embryogenesis proceeded, the normal pattern of development was observed, including heart-shape, torpedo and cotyledonar embryos.The work was supported by the Spanish project DGESIC PB98-0678,CAM 07G/0054/2000 and the Spanish-Italian joint project CSIC/CNR 2001IT0017.Peer reviewe

Recent Memory and Performance Improvements in Octopus Code

In this work we present the improvements made to the Octopus code in order to reduce the memory requirements and to optimise parallel data distribution. Both topics are central for efficiency and feasibility of calculations when the system must be run in a large HPC environment. These modifications were mainly made in the real-space mesh partitioning and mapping algorithms, and are thus transferable to other codes using this type of real-space representation of data. The code became much more efficient, and we present several scalability results showing that it is now possible to address ab-initio quantum-mechanical simulations of the interaction of light with big biomolecules, paving the way for a better understanding of phenomena such as energy conversion in plants

Comparative value of microscopy, serology and real time pcr in the diagnosis of asymptomatic canine Leishmania infantum infection

The sensitivity (SE) of cytological examination of spleen and lymphnode smears by optical microscopy (OM), antibody-ELISA (enzyme-linked immunosorbent assays) and real-time (rt) PCR (polymerase chain reaction), for diagnosing asymptomatic canine Leishmania infantum infection was investigated in 110 apparently healthy dogs from southeast Spain. The percentage of OM, ELISA and rtPCR positive dogs were 2% (2/110), 27% (26/97) y 67% (39/58), respectively, although the percentage of rtPCR-positive dogs were 35-41% in individual tissues and 9% in blood. The estimated SE (95% confidence interval) of OM relative to the rtPCR and ELISA tests was 5% (0-12) and 8% (0-18), respectively. Results confirm that most apparently healthy dogs from L. infantum endemic areas are infected, that approximately only one third of these infected dogs develop antibodies and that very few have parasite loads that are high enough to allow detection by OM. As a result, the degree of agreement between rtPCR, ELISA and OM for L. infantum diagnosis in subclinnically infected dogs is low.Se investigó la sensibilidad (SE) del examen citológico mediante microscopia óptica (MO) de improntas de bazo y linfonodo, de la prueba de anticuerpos ELISA (inmuno-ensayo ligado a enzima) y de la PCR (reacción en cadena de la polimerasa) a tiempo real (tr), para diagnosticar la infección asintomática por Leishmania infantum en 110 perros aparentemente sanos, del sureste de España. El porcentaje de perros positivos a MO, ELISA y PCRtr fue 2% (2/110), 27% (26/97) y 67% (39/58), respectivamente, aunque el porcentaje de PCR-positivos osciló entre 35-41% para cada tejido individualmente y 9% en sangre. La SE estimada (intervalos de confianza del 95%) de la MO en relación a la PCRtr y al ELISA fue 5% (0-12) y 8% (0-18), respectivamente. Estos resultados confirman que la mayoría de perros aparentemente sanos de una población endémica de L. infantum están infectados, que aproximadamente solo la tercera parte de éstos desarrolla anticuerpos frente al parásito y solo unos pocos tienen suficiente carga parasitaria en tejido linfoide como para ser detectada mediante MO. Consecuentemente, el grado de concordancia de la PCRtr, el ELISA y la MO en el diagnóstico de leishmaniosis canina asintomática es escaso

Accelerating Sparse Arithmetic in the Context of Newton's Method for Small Molecules with Bond Constraints

Molecular dynamics is used to study the time evolution of systems of atoms. It is common to constrain bond lengths in order to increase the time step of the simulation. Here we accelerate Newton's method for solving the constraint equations for a system consisting of many identical small molecules. Starting with a modular and generic base code using a sequential data layout, we apply three different optimization techniques. The compiled code approach is used to generate subroutines equivalent to a single step of Newton's method for a user specified molecule. Differing from the generic subroutines, these specific routines contain no loops and no indirect addressing. Interleaving the data describing different molecules generates vectorizable loops. Finally, we apply task fusion. The simultaneous application of all three techniques increases the speed of the base code by a factor of 15 for single precision calculations