Anthropogenic mortality threatens the survival of Canarian houbara bustards.

Anthropogenic mortality is a major cause of global mortality in terrestrial vertebrates. Quantifying its impact on the dynamics of threatened species is essential to improve their conservation. We investigated cause-specific mortality in Canarian houbara bustards (Chlamydotis undulata fuertaventurae), an endangered subspecies endemic to the Canary Islands. We monitored 51 individuals tagged with solar-powered GSM/GPRS loggers for an average of 3.15 years, and recorded 7 casualties at aerial lines (13.73% of the sample; 5 at power lines, 2 at telephone lines), 1 (1.96%) at a wire fence, 4 road kills (7.84%) and 1 case of predation by cat (1.96%). Cox proportional hazards models showed that anthropogenic and natural annual mortality rates were similar (respectively, 6.20% and 6.36% of the individuals). We estimate that 33-35 houbaras die each year in the Canary Islands due to anthropogenic causes. Population viability models using these data and juvenile productivity values obtained over seven years predicted the extinction of the species in 50 years. Eliminating anthropogenic mortality, the population could be recovered, but would still require management actions to improve habitat quality. Conservation measures to reduce anthropogenic mortality due to power line fatalities, roadkills and predation by cats, as well as to increase productivity, are urgently needed, particularly on Fuerteventura, where houbaras are on the brink of extinction.

Processing of stalled replication forks in Bacillus subtilis.

Accurate DNA replication and transcription elongation are crucial for preventing the accumulation of unreplicated DNA and genomic instability. Cells have evolved multiple mechanisms to deal with impaired replication fork progression, challenged by both intrinsic and extrinsic impediments. The bacterium Bacillus subtilis, which adopts multiple forms of differentiation and development, serves as an excellent model system for studying the pathways required to cope with replication stress to preserve genomic stability. This review focuses on the genetics, single molecule choreography, and biochemical properties of the proteins that act to circumvent the replicative arrest allowing the resumption of DNA synthesis. The RecA recombinase, its mediators (RecO, RecR, and RadA/Sms) and modulators (RecF, RecX, RarA, RecU, RecD2, and PcrA), repair licensing (DisA), fork remodelers (RuvAB, RecG, RecD2, RadA/Sms, and PriA), Holliday junction resolvase (RecU), nucleases (RnhC and DinG), and translesion synthesis DNA polymerases (PolY1 and PolY2) are key functions required to overcome a replication stress, provided that the fork does not collapse.

Congenital Zika syndrome.

In February 2016, the World Health Organization declared Zika virus (ZIKV) infection a public health emergency of international concern because it caused congenital Zika syndrome (CZS). The CZS is considered a specific pattern of birth defects caused by ZIKV infection, which is transmitted by the bite of the Aedes aegypti mosquito. The CZS clinical manifestations are broad and nonspecific, including microcephaly, subcortical calcifications, ocular alterations, congenital contractures, early hypertonia, and pyramidal as well as extrapyramidal symptoms. The ZIKV has gained great importance because it has affected a large percentage of the population worldwide during the last few years, despite the measures implemented by international organizations. The pathophysiology and non-vectorial transmission routes of the virus are still under study. The diagnosis is made upon suspicion of ZIKV infection, the patient's clinical manifestations, and it is confirmed by molecular laboratory tests demonstrating the presence of viral particles. Unfortunately, there is no specific treatment or vaccine for this condition; however, patients receive multidisciplinary care and constant monitoring. Therefore, the strategies that have been implemented are directed toward preventive measures and vector control.

En febrero de 2016, la Organización Mundial de la Salud declaró a la infección por virus Zika una emergencia de salud pública de importancia internacional por ser la causa del síndrome congénito por virus Zika. Este síndrome es considerado un patrón específico de defectos al nacimiento causados por la infección por virus Zika, que se transmite por la picadura del mosquito vector Aedes aegypti y cuyas manifestaciones clínicas son amplias e inespecíficas, entre las que destacan microcefalia, calcificaciones subcorticales, alteraciones oculares, contracturas congénitas, hipertonía temprana y síntomas de afectación piramidal y extrapiramidal. Este virus ha tomado gran importancia debido a que durante los últimos años ha afectado a un gran porcentaje de la población en todo el mundo, a pesar de las medidas implementadas por organizaciones internacionales. La fisiopatología y las vías de transmisión no vectorial de la infección aún siguen en estudio. El diagnóstico se realiza ante la sospecha por las manifestaciones clínicas del paciente, y se confirma mediante pruebas moleculares de laboratorio en las que se demuestre la presencia de partículas virales. Desafortunadamente, no existe aún un tratamiento ni una vacuna específica para este padecimiento; sin embargo, los pacientes reciben cuidados multidisciplinarios y monitorización constante. Las estrategias que se han implementado se dirigen hacia medidas preventivas de la infección y el control de los vectores.

Display site selection in a ground dwelling bird: the importance of viewshed.

We studied the effects of visibility, female and male distribution, microhabitat and distance to human infrastructure on display site selection in a ground-dwelling bird, the Canarian houbara bustard. Using a very high-resolution digital elevation model based on LIDAR technology, and a complete census of the breeding population, we compared 98 display sites with randomly generated sites through generalized linear models. Univariate analyses showed that males displayed at locations that increased their visibility, both at short and long distances. Interestingly, although numbers of females and males around sites did not differ between display and random locations, from display locations males could see more females and males at both distance ranges. The absence of vegetation and stones was also critical as it allowed males to perform display runs on a ground free of obstacles. The amount of trophic resources did not correlate with the selection of the display site itself, though an appropriate vegetation cover seemed to be important at a wider habitat scale. Finally, display sites were farther away than random sites from sources of human disturbance, such as urban nuclei, buildings and tracks. Logistic regression analyses confirmed the importance of viewshed, low stone and vegetation cover, and distance to urban centres and tracks, and model averaging identified short-range visibility and females visible in the long range as the most important visibility variables. These results are compatible with the sexual advertisement and predator avoidance hypotheses. We provide recommendations to ensure an appropriate management of the breeding habitat of this endangered subspecies.

Bacillus subtilis RadA/Sms-Mediated Nascent Lagging-Strand Unwinding at Stalled or Reversed Forks Is a Two-Step Process: RadA/Sms Assists RecA Nucleation, and RecA Loads RadA/Sms.

Replication fork rescue requires Bacillus subtilis RecA, its negative (SsbA) and positive (RecO) mediators, and fork-processing (RadA/Sms). To understand how they work to promote fork remodeling, reconstituted branched replication intermediates were used. We show that RadA/Sms (or its variant, RadA/Sms C13A) binds to the 5'-tail of a reversed fork with longer nascent lagging-strand and unwinds it in the 5'→3' direction, but RecA and its mediators limit unwinding. RadA/Sms cannot unwind a reversed fork with a longer nascent leading-strand, or a gapped stalled fork, but RecA interacts with and activates unwinding. Here, the molecular mechanism by which RadA/Sms, in concert with RecA, in a two-step reaction, unwinds the nascent lagging-strand of reversed or stalled forks is unveiled. First, RadA/Sms, as a mediator, contributes to SsbA displacement from the forks and nucleates RecA onto single-stranded DNA. Then, RecA, as a loader, interacts with and recruits RadA/Sms onto the nascent lagging strand of these DNA substrates to unwind them. Within this process, RecA limits RadA/Sms self-assembly to control fork processing, and RadA/Sms prevents RecA from provoking unnecessary recombination.

Congenital Zika syndrome / Síndrome congénito por virus Zika

Abstract In February 2016, the World Health Organization declared Zika virus (ZIKV) infection a public health emergency of international concern because it caused congenital Zika syndrome (CZS). The CZS is considered a specific pattern of birth defects caused by ZIKV infection, which is transmitted by the bite of the Aedes aegypti mosquito. The CZS clinical manifestations are broad and nonspecific, including microcephaly, subcortical calcifications, ocular alterations, congenital contractures, early hypertonia, and pyramidal as well as extrapyramidal symptoms. The ZIKV has gained great importance because it has affected a large percentage of the population worldwide during the last few years, despite the measures implemented by international organizations. The pathophysiology and non-vectorial transmission routes of the virus are still under study. The diagnosis is made upon suspicion of ZIKV infection, the patient's clinical manifestations, and it is confirmed by molecular laboratory tests demonstrating the presence of viral particles. Unfortunately, there is no specific treatment or vaccine for this condition; however, patients receive multidisciplinary care and constant monitoring. Therefore, the strategies that have been implemented are directed toward preventive measures and vector control.

Resumen En febrero de 2016, la Organización Mundial de la Salud declaró a la infección por virus Zika una emergencia de salud pública de importancia internacional por ser la causa del síndrome congénito por virus Zika. Este síndrome es considerado un patrón específico de defectos al nacimiento causados por la infección por virus Zika, que se transmite por la picadura del mosquito vector Aedes aegypti y cuyas manifestaciones clínicas son amplias e inespecíficas, entre las que destacan microcefalia, calcificaciones subcorticales, alteraciones oculares, contracturas congénitas, hipertonía temprana y síntomas de afectación piramidal y extrapiramidal. Este virus ha tomado gran importancia debido a que durante los últimos años ha afectado a un gran porcentaje de la población en todo el mundo, a pesar de las medidas implementadas por organizaciones internacionales. La fisiopatología y las vías de transmisión no vectorial de la infección aún siguen en estudio. El diagnóstico se realiza ante la sospecha por las manifestaciones clínicas del paciente, y se confirma mediante pruebas moleculares de laboratorio en las que se demuestre la presencia de partículas virales. Desafortunadamente, no existe aún un tratamiento ni una vacuna específica para este padecimiento; sin embargo, los pacientes reciben cuidados multidisciplinarios y monitorización constante. Las estrategias que se han implementado se dirigen hacia medidas preventivas de la infección y el control de los vectores.

Biological evolution and human cognition are analogous information processing systems.

The mechanisms that govern biological evolution and human cognition are analogous, as both follow the same principles of natural information processing systems. In this article, we describe the following five principles that provide an analogy between biological evolution and human cognition: (a) Randomness as Genesis Principle and (b) Borrowing and Reorganizing Principle, which indicate how natural information processing systems obtain information; (c) Narrow Limits of Change Principle and (d) Information Store Principle, which indicate how information is processed and stored; and (e) Environmental Organizing and Linking Principle, which indicate how stored information is used to generate actions appropriate to an environment. In human cognition, these analogs only apply to cognitive processes associated with biologically secondary knowledge, the knowledge typically taught in educational institutions. Based on these five principles, cognitive load theory researchers have provided diverse prescriptions to optimize instructional activities and materials. We conclude by discussing general instructional implications and future research directions based on this analogy.

The RecD2 helicase balances RecA activities.

DNA helicases of the RecD2 family are ubiquitous. Bacillus subtilis RecD2 in association with the single-stranded binding protein SsbA may contribute to replication fork progression, but its detailed action remains unknown. In this work, we explore the role of RecD2 during DNA replication and its interaction with the RecA recombinase. RecD2 inhibits replication restart, but this effect is not observed in the absence of SsbA. RecD2 slightly affects replication elongation. RecA inhibits leading and lagging strand synthesis, and RecD2, which physically interacts with RecA, counteracts this negative effect. In vivo results show that recD2 inactivation promotes RecA-ssDNA accumulation at low mitomycin C levels, and that RecA threads persist for a longer time after induction of DNA damage. In vitro, RecD2 modulates RecA-mediated DNA strand-exchange and catalyzes branch migration. These findings contribute to our understanding of how RecD2 may contribute to overcome a replicative stress, removing RecA from the ssDNA and, thus, it may act as a negative modulator of RecA filament growth.

Bacillus subtilis RecA, DisA, and RadA/Sms Interplay Prevents Replication Stress by Regulating Fork Remodeling.

Reviving Bacillus subtilis spores require the recombinase RecA, the DNA damage checkpoint sensor DisA, and the DNA helicase RadA/Sms to prevent a DNA replication stress. When a replication fork stalls at a template lesion, RecA filaments onto the lesion-containing gap and the fork is remodeled (fork reversal). RecA bound to single-strand DNA (ssDNA) interacts with and recruits DisA and RadA/Sms on the branched DNA intermediates (stalled or reversed forks), but DisA and RadA/Sms limit RecA activities and DisA suppresses its c-di-AMP synthesis. We show that RecA, acting as an accessory protein, activates RadA/Sms to unwind the nascent lagging-strand of the branched intermediates rather than to branch migrate them. DisA limits the ssDNA-dependent ATPase activity of RadA/Sms C13A, and inhibits the helicase activity of RadA/Sms by a protein-protein interaction. Finally, RadA/Sms inhibits DisA-mediated c-di-AMP synthesis and indirectly inhibits cell proliferation, but RecA counters this negative effect. We propose that the interactions among DisA, RecA and RadA/Sms, which are mutually exclusive, contribute to generate the substrate for replication restart, regulate the c-di-AMP pool and limit fork restoration in order to maintain cell survival.

DisA Restrains the Processing and Cleavage of Reversed Replication Forks by the RuvAB-RecU Resolvasome.

DNA lesions that impede fork progression cause replisome stalling and threaten genome stability. Bacillus subtilis RecA, at a lesion-containing gap, interacts with and facilitates DisA pausing at these branched intermediates. Paused DisA suppresses its synthesis of the essential c-di-AMP messenger. The RuvAB-RecU resolvasome branch migrates and resolves formed Holliday junctions (HJ). We show that DisA prevents DNA degradation. DisA, which interacts with RuvB, binds branched structures, and reduces the RuvAB DNA-dependent ATPase activity. DisA pre-bound to HJ DNA limits RuvAB and RecU activities, but such inhibition does not occur if the RuvAB- or RecU-HJ DNA complexes are pre-formed. RuvAB or RecU pre-bound to HJ DNA strongly inhibits DisA-mediated synthesis of c-di-AMP, and indirectly blocks cell proliferation. We propose that DisA limits RuvAB-mediated fork remodeling and RecU-mediated HJ cleavage to provide time for damage removal and replication restart in order to preserve genome integrity.

Nutritional Status of Non-Institutionalized Adults Aged over 65. Study of Weight and Health in Older Adults (PYSMA).

BACKGROUND: A significant increase in the prevalence of malnourishment, obesity, and sarcopenic obesity has been observed in developed countries over the last few decades. In Spain, this especially happens in populations over 65 who are not institutionalized. Differences in lifestyle, medication, and economic capacity partially explain this increase. OBJECTIVE: To study the nutritional status of a population of 65 year-olds and subjects who are not institutionalized, in the Cádiz region (Spain). METHODS: Observational, transversal study carried out on 2621 subjects who are 65 years old and over, with a direct weight and height measurement, in 150 pharmacy offices from 44 locations. A mobile application was designed for homogeneous data collection in all the pharmacy offices. The data required from all subjects was gender, age, postal code, social security contribution regime, if the patient lives alone, type of food consumed as the main meals, level of physical activity, polypharmacy, weight, and height. RESULTS: The prevalence of overweight and obesity amounts to 82.2% of the population (43.2% overweight and 39% obese). We found an inverse relationship between the prevalence of overweight and obesity with carrying out physical activity and having full dinners. CONCLUSION: We identify the need to reinforce the messages to the elderly aimed at maintaining adequate physical activity and assessing the quality and quantity of dinners, as well as reducing, as much as possible, the treatments that may lead to weight gain.

DisA Limits RecG Activities at Stalled or Reversed Replication Forks.

The DNA damage checkpoint protein DisA and the branch migration translocase RecG are implicated in the preservation of genome integrity in reviving haploid Bacillus subtilis spores. DisA synthesizes the essential cyclic 3', 5'-diadenosine monophosphate (c­di-AMP) second messenger and such synthesis is suppressed upon replication perturbation. In vitro, c-di-AMP synthesis is suppressed when DisA binds DNA structures that mimic stalled or reversed forks (gapped forks or Holliday junctions [HJ]). RecG, which does not form a stable complex with DisA, unwinds branched intermediates, and in the presence of a limiting ATP concentration and HJ DNA, it blocks DisA-mediated c-di-AMP synthesis. DisA pre-bound to a stalled or reversed fork limits RecG-mediated ATP hydrolysis and DNA unwinding, but not if RecG is pre-bound to stalled or reversed forks. We propose that RecG-mediated fork remodeling is a genuine in vivo activity, and that DisA, as a molecular switch, limits RecG-mediated fork reversal and fork restoration. DisA and RecG might provide more time to process perturbed forks, avoiding genome breakage.

Nucleoid-associated Rok differentially affects chromosomal transformation on Bacillus subtilis recombination-deficient cells.

Rok, a Bacillus subtilis nucleoid-associated protein (NAP), negatively regulates competence development and silences xenogeneic genes. We show that rok inactivation increases rpoB482 natural intraspecies chromosomal transformation (CT) and plasmid transformation to a different extent. In ΔaddAB, ΔrecO, recF15, ΔrecU, ΔruvAB or rec+ cells intraspecies CT significantly increases, but the ΔrecD2 mutation reduces, and the ΔrecX, ΔradA or ΔdprA mutation further decreases CT in the Δrok context when compared to rok+ cells. These observations support the idea that rok inactivation, by altering the topology of the recipient DNA, differentially affects the integration of homologous DNA in rec-deficient strains, and in minor extent the competent subpopulation size. The impairment of other NAP (Hbsu or LrpC) also increased intra- and interspecies CT (nonself-DNA, ~8% nucleotide sequence divergence) in rec+ cells, but differentially reduced both types of CTs in certain rec-deficient strains. We describe that rok inactivation significantly stimulates intra and interspecies CT but differentially reduces them in transformation-deficient cells, perhaps by altering the nucleoid architecture. We extend the observation to other NAPs (Hbsu, LrpC).

Low cost and sustainable hyaluronic acid production in a manufacturing platform based on Bacillus subtilis 3NA strain.

Hyaluronic acid (HA) is a high value glycosaminoglycan mostly used in health and cosmetic applications. Commercial HA is produced from animal tissues or in toxigenic bacteria of the genus Streptococcus grown in complex media, which are expensive and raise environmental concerns due to the disposal of large amounts of broth with high organic loads. Other microorganisms were proposed as hosts for the heterologous production of HA, but the methods are still costly. The extraordinary capacity of this biopolymer to bind and retain water attracts interest for large-scale applications where biodegradable materials are needed, but its high cost and safety concerns are barriers for its adoption. Bacillus subtilis 3NA strain is prototrophic, amenable for genetic manipulation, GRAS, and can rapidly reach high cell densities in salt-based media. These phenotypic traits were exploited to create a platform for biomolecule production using HA as a proof of concept. First, the 3NA strain was engineered to produce HA; second, a chemically defined medium was formulated using commodity-priced inorganic salts combined at the stoichiometric ratios needed to build the necessary quantities of biomass and HA; and third, a scalable fermentation process, where HA can be produced at the maximum volumetric productivity (VP), was designed. A comparative economic analysis against other methods indicates that the new process may increase the operating profit of a manufacturing plant by more than 100%. The host, the culture medium, and the rationale employed to develop the fermentation process described here, introduce an IP-free platform that could be adaptable for production of other biomolecules. KEY POINTS: • A biomolecule production platform based on B. subtilis 3NA strain and a synthetic medium was tested for hyaluronic acid biosynthesis • A fermentation process with the maximum volumetric productivity was designed • A techno-economic analysis forecasts a significant reduction in the manufacturing cost compared to the current methods.

Five Strategies for Optimizing Instructional Materials: Instructor- and Learner-Managed Cognitive Load.

Researchers of cognitive load theory and the cognitive theory of multimedia learning have identified several strategies to optimize instructional materials. In this review article we focus on five of these strategies or solutions to problematic instructional designs in multimedia learning: (a) the multimedia principle (use visualizations and drawings to complement texts); (b) the split-attention effect or spatial contiguity principle (show texts contiguously or integrated with visualizations); (c) the redundancy effect, alike the coherence principle (remove nonessential learning information); (d) the signaling principle (cue or signal essential learning information); and (e) the transient information effect or segmenting principle (segment or control the pace of animations and videos). Usually, both cognitive theories have investigated solutions that instructors, teachers, and designers should pursue to optimize students' learning. Here, in a novel approach, we show that these strategies can also be used by learners who want to self-manage their cognitive load and learning process. We provide several examples of both instructor- and learner-managed solutions aligned with these strategies. When assessing which agent, either the instructor or the learner, was most effective, we observed mixed results in the literature. However, the expertise reversal effect may help predict the direction of these effects: novice students may learn better under instructor-managed conditions, whereas more expert students may learn more under learner-managed conditions.

Toxin-Antitoxin Systems in Pathogenic Bacteria.

Toxin-antitoxin (TA) systems, which are ubiquitously present in plasmids, bacterial and archaeal genomes, are classified as types I to VI, according to the nature of the antitoxin and to the mode of toxin inhibition [...].

Recombination proteins differently control the acquisition of homeologous DNA during Bacillus subtilis natural chromosomal transformation.

Natural chromosomal transformation (CT) plays a major role in prokaryote evolution, yet factors that govern the integration of DNA from related species remain poorly understood. We show that in naturally competent Bacillus subtilis cells the acquisition of homeologous sequences is governed by sequence divergence (SD). Integration initiates in a minimal efficient processing segment via homology-directed CT, and its frequency decreases log-linearly with increased SD up to 15%. Beyond this and up to 23% SD the interspecies boundaries prevail, the CT frequency marginally decreases, and short (<10-nucleotides) segments are integrated via homology-facilitated micro-homologous integration. Both mechanisms are RecA dependent. We identify the other recombination proteins required for the acquisition of homeologous DNA. The absence of AddAB, RecF, RecO, RuvAB or RecU, crucial for repair-by-recombination, did not affect CT. However, dprA, radA, recJ, recX or recD2 inactivation strongly decreased intraspecies and interspecies CT. Interspecies CT was not detected beyond ~8% SD in ΔdprA, ~10% in ΔrecJ, ΔradA, ΔrecX and ~14% in ΔrecD2 cells. We propose that DprA, RecX, RadA/Sms, RecJ and RecD2 accessory proteins are important for the generation of genetic diversity. Together with RecA, they facilitate gene acquisition from bacteria of related species.

Quantifying and addressing the prevalence and bias of study designs in the environmental and social sciences.

Building trust in science and evidence-based decision-making depends heavily on the credibility of studies and their findings. Researchers employ many different study designs that vary in their risk of bias to evaluate the true effect of interventions or impacts. Here, we empirically quantify, on a large scale, the prevalence of different study designs and the magnitude of bias in their estimates. Randomised designs and controlled observational designs with pre-intervention sampling were used by just 23% of intervention studies in biodiversity conservation, and 36% of intervention studies in social science. We demonstrate, through pairwise within-study comparisons across 49 environmental datasets, that these types of designs usually give less biased estimates than simpler observational designs. We propose a model-based approach to combine study estimates that may suffer from different levels of study design bias, discuss the implications for evidence synthesis, and how to facilitate the use of more credible study designs.

Antitoxin ε Reverses Toxin ζ-Facilitated Ampicillin Dormants.

Toxin-antitoxin (TA) modules are ubiquitous in bacteria, but their biological importance in stress adaptation remains a matter of debate. The inactive ζ-ε2-ζ TA complex is composed of one labile ε2 antitoxin dimer flanked by two stable ζ toxin monomers. Free toxin ζ reduces the ATP and GTP levels, increases the (p)ppGpp and c-di-AMP pool, inactivates a fraction of uridine diphosphate-N-acetylglucosamine, and induces reversible dormancy. A small subpopulation, however, survives toxin action. Here, employing a genetic orthogonal control of ζ and ε levels, the fate of bacteriophage SPP1 infection was analyzed. Toxin ζ induces an active slow-growth state that halts SPP1 amplification, but it re-starts after antitoxin expression rather than promoting abortive infection. Toxin ζ-induced and toxin-facilitated ampicillin (Amp) dormants have been revisited. Transient toxin ζ expression causes a metabolic heterogeneity that induces toxin and Amp dormancy over a long window of time rather than cell persistence. Antitoxin ε expression, by reversing ζ activities, facilitates the exit of Amp-induced dormancy both in rec+ and recA cells. Our findings argue that an unexploited target to fight against antibiotic persistence is to disrupt toxin-antitoxin interactions.