Time series of freshwater macroinvertebrate abundances and site characteristics of European streams and rivers.

Freshwater macroinvertebrates are a diverse group and play key ecological roles, including accelerating nutrient cycling, filtering water, controlling primary producers, and providing food for predators. Their differences in tolerances and short generation times manifest in rapid community responses to change. Macroinvertebrate community composition is an indicator of water quality. In Europe, efforts to improve water quality following environmental legislation, primarily starting in the 1980s, may have driven a recovery of macroinvertebrate communities. Towards understanding temporal and spatial variation of these organisms, we compiled the TREAM dataset (Time seRies of European freshwAter Macroinvertebrates), consisting of macroinvertebrate community time series from 1,816 river and stream sites (mean length of 19.2 years and 14.9 sampling years) of 22 European countries sampled between 1968 and 2020. In total, the data include >93 million sampled individuals of 2,648 taxa from 959 genera and 212 families. These data can be used to test questions ranging from identifying drivers of the population dynamics of specific taxa to assessing the success of legislative and management restoration efforts.

The Lithbea Domain.

The tree of life is the evolutionary metaphor for the past and present connections of all cellular organisms. Today, to speak of biodiversity is not only to speak of archaea, bacteria, and eukaryotes, but they should also consider the "new biodiversity" that includes viruses and synthetic organisms, which represent the new forms of life created in laboratories. There is even a third group of artificial entities that, although not living systems, pretend to imitate the living. To embrace and organize all this new biodiversity, I propose the creation of a new domain, with the name Lithbea (from life-on-the-border entites) The criteria for inclusion as members of Lithbea are: i) the acellular nature of the living system, ii) its origin in laboratory manipulation, iii) showing new biological traits, iv) the presence of exogenous genetic elements, v) artificial or inorganic nature. Within Lithbea there are two subdomains: Virworld (from virus world) which includes all viruses, regarded as lifeless living systems, and classified according to the International Committee on Taxonomy of Viruses (ICTV), and ii) Humade (from human-made) which includes all synthetic organisms and artificial entities. The relationships of Lithbea members to the three classical woesian domains and their implications are briefly discussed.

Reflections upon a new definition of life.

What is life? Multiple definitions have been proposed to answer this question, but unfortunately, none of them has reached the consensus of the scientific community. Here, the strategy used to define what life is was based on first establishing which characteristics are common to all living systems (organic nature, entropy-producing system, self-organizing, reworkable pre-program, capacity to interact and adapt, reproduction and evolution) and from them constructing the definition taking into account that reproduction and evolution are not essential for life. On this basis, life is defined as an interactive process occurring in entropy-producing, adaptive, and informative (organic) systems. An unforeseen consequence of the inseparable duality between the system (living being) and the process (life) is the interchangeability of the elements of the definition to obtain other equally valid alternatives. In addition, in the light of this definition, cases of temporarily lifeless living systems (viruses, dormant seeds, and ultracold cells) are analyzed, as well as the status of artificial life entities and the hypothetical nature of extraterrestrial life. All living systems are perishable because the passage of time leads to increasing entropy. Life must create order by continuously producing disorder and exporting it to the environment and so we move and stay in the phase transition between order and chaos, far from equilibrium, thanks to the input of energy from the outside. However, the passage of time eventually leads us to an end in which life disappears and entropy increases.

The recovery of European freshwater biodiversity has come to a halt.

Owing to a long history of anthropogenic pressures, freshwater ecosystems are among the most vulnerable to biodiversity loss1. Mitigation measures, including wastewater treatment and hydromorphological restoration, have aimed to improve environmental quality and foster the recovery of freshwater biodiversity2. Here, using 1,816 time series of freshwater invertebrate communities collected across 22 European countries between 1968 and 2020, we quantified temporal trends in taxonomic and functional diversity and their responses to environmental pressures and gradients. We observed overall increases in taxon richness (0.73% per year), functional richness (2.4% per year) and abundance (1.17% per year). However, these increases primarily occurred before the 2010s, and have since plateaued. Freshwater communities downstream of dams, urban areas and cropland were less likely to experience recovery. Communities at sites with faster rates of warming had fewer gains in taxon richness, functional richness and abundance. Although biodiversity gains in the 1990s and 2000s probably reflect the effectiveness of water-quality improvements and restoration projects, the decelerating trajectory in the 2010s suggests that the current measures offer diminishing returns. Given new and persistent pressures on freshwater ecosystems, including emerging pollutants, climate change and the spread of invasive species, we call for additional mitigation to revive the recovery of freshwater biodiversity.

Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens.

Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urbanization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sediments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urbanization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts.

Invasion impacts and dynamics of a European-wide introduced species.

Globalization has led to the introduction of thousands of alien species worldwide. With growing impacts by invasive species, understanding the invasion process remains critical for predicting adverse effects and informing efficient management. Theoretically, invasion dynamics have been assumed to follow an "invasion curve" (S-shaped curve of available area invaded over time), but this dynamic has lacked empirical testing using large-scale data and neglects to consider invader abundances. We propose an "impact curve" describing the impacts generated by invasive species over time based on cumulative abundances. To test this curve's large-scale applicability, we used the data-rich New Zealand mud snail Potamopyrgus antipodarum, one of the most damaging freshwater invaders that has invaded almost all of Europe. Using long-term (1979-2020) abundance and environmental data collected across 306 European sites, we observed that P. antipodarum abundance generally increased through time, with slower population growth at higher latitudes and with lower runoff depth. Fifty-nine percent of these populations followed the impact curve, characterized by first occurrence, exponential growth, then long-term saturation. This behaviour is consistent with boom-bust dynamics, as saturation occurs due to a rapid decline in abundance over time. Across sites, we estimated that impact peaked approximately two decades after first detection, but the rate of progression along the invasion process was influenced by local abiotic conditions. The S-shaped impact curve may be common among many invasive species that undergo complex invasion dynamics. This provides a potentially unifying approach to advance understanding of large-scale invasion dynamics and could inform timely management actions to mitigate impacts on ecosystems and economies.

What is life?

BACKGROUND: Many traditional biological concepts continue to be debated by biologists, scientists and philosophers of science. The specific objective of this brief reflection is to offer an alternative vision to the definition of life taking as a starting point the traits common to all living beings. RESULTS AND CONCLUSIONS: Thus, I define life as a process that takes place in highly organized organic structures and is characterized by being preprogrammed, interactive, adaptative and evolutionary. If life is the process, living beings are the system in which this process takes place. I also wonder whether viruses can be considered living things or not. Taking as a starting point my definition of life and, of course, on what others have thought about it, I am in favor of considering viruses as living beings. I base this conclusion on the fact that viruses satisfy all the vital characteristics common to all living things and on the role they have played in the evolution of species. Finally, I argue that if there were life elsewhere in the universe, it would be very similar to what we know on this planet because the laws of physics and the composition of matter are universal and because of the principle of the inexorability of life.

Biodiversity policy beyond economic growth.

Increasing evidence-synthesized in this paper-shows that economic growth contributes to biodiversity loss via greater resource consumption and higher emissions. Nonetheless, a review of international biodiversity and sustainability policies shows that the majority advocate economic growth. Since improvements in resource use efficiency have so far not allowed for absolute global reductions in resource use and pollution, we question the support for economic growth in these policies, where inadequate attention is paid to the question of how growth can be decoupled from biodiversity loss. Drawing on the literature about alternatives to economic growth, we explore this contradiction and suggest ways forward to halt global biodiversity decline. These include policy proposals to move beyond the growth paradigm while enhancing overall prosperity, which can be implemented by combining top-down and bottom-up governance across scales. Finally, we call the attention of researchers and policy makers to two immediate steps: acknowledge the conflict between economic growth and biodiversity conservation in future policies; and explore socioeconomic trajectories beyond economic growth in the next generation of biodiversity scenarios.

What are the principles that govern life?

We know that living matter must behave in accordance with the universal laws of physics and chemistry. However, these laws are insufficient to explain the specific characteristics of the vital phenomenon and, therefore, we need new principles, intrinsic to biology, which are the basis for developing a theoretical framework for understanding life. Here I propose what I call the seven commandments of life (the Vital Order, the Principle of Inexorability, the reformulated Central Dogma, the Tyranny of Time, the Evolutionary Imperative, the Conservative Rule, the Cooperating Thrust) as a set of principles that help us explain the vital phenomenon from an evolutionary perspective. In a metaphorical way, we can consider life like an endless race in which living beings are the runners, who are changing as the race goes on (the evolutionary process), and the commandments the rules.

Preliminary methylation analysis of prothymosin α genomic sequences.

Prothymosin α is a mammalian nuclear protein involved in cell proliferation and differentiation. Here, we carried out the first study of the methylation status of ProTα genomic sequences in cell lines during differentiation as well as in tumoral tissues. We found that there is hypermethylation in all cell lines analyzed with a pattern that is characteristic of each cell type revealing specific genomic reorganizations. The decrease of ProTα mRNA during differentiation was not accompanied by changes in the methylation status. Remarkably, we found that there is hypomethylation in gastrointestinal tumors when compared with the peritumoral tissue. The biological implications of these findings are discussed.

Células T y sus receptores αß y γδ en biopsias de pacientes con enfermedad periodontal / T cells and its receptords and αß and γδ in biopsies from patients with periodontal disease

El propósito de este estudio es determinar la presencia y localización de las células T y de sus receptores αβ y γδ en biopsias de tejido gingival de pacientes con enfermedad periodontal. Se evaluaron 60 biopsias de 12 pacientes, 4 con diagnostico de periodontitis agresiva, 4 con periodontitis crónica y 4 con gingivitis, las cuales fueron procesados para su análisis histológico, inmunohistoquímico e histomorfometrico. Al analizar los resultados por diagnostico los marcadores que mas predominaron fueron, en Gingivitis CD3, CD8 y TCR γδ en tejido conectivo. En Periodontitis crónica CD3, CD8 y TCR γδ en epitelio oral y CD4 el cual presentó una expresión homogénea en los tejidos analizados. En periodontitis agresiva CD3 y CD8 en epitelio crevicular, con una distribución similar entre CD4 y CD8 tanto en epitelio oral como en tejido conectivo y TCR γδ en conectivo. En cuanto a las cadenas variables del TCR Vβ los más expresados en las diferentes patologías estudiadas fueron el 6.7, 8.1 y 12 a nivel del tejido conectivo. Los estudios sobre la expresión de estas familias parecen indicar que es otra vía de activación a tener en cuenta dentro del modelo de la patogenia de la enfermedad y que debe ser estudiado en modelos longitudinales en pacientes con pérdida de inserción progresiva.

T the purpose of this study is identifying the presence and localization of T cells and their receptor αβ and γδ in biopsies of gingival tissue in patients with periodontal disease. 60 biopsies were evaluated in 12 patients, 4 patients with diagnosis of gingivitis, 4 patients with chronic periodontitis and 4 with aggressive periodontitis, which were processed for the histological, immunohistochemical and histomorphometric analysis. The results by diagnosis showed that in gingivitis the more predominant markers were CD3, CD8 and TCR γδ in connective tissue. In chronic periodontitis the markers with bigger expression were CD3, CD8 and TCR γδ in oral epithelium and CD4 that showed a homogeneous behavior in the analized tissues. In aggressive periodontitis CD3 and CD8 in surcular epithelium, TCR γδ in connective tissue and CD4 and CD8 with a similar distribution in oral epithelium and connective tissue. In relation with variable chains of TCR Vβ, the most predominat in the different diagnosis were 6.7,8.1 and 12 in connective tissue. The investigations about the expression of these families indicate that it can be other important via of activation in the pathogenesis of periodontal disease and it should be study in longitudinal models in patients with progressive loss of attachment level.

Adaptive radiation within marine anisakid nematodes: a zoogeographical modeling of cosmopolitan, zoonotic parasites.

Parasites of the nematode genus Anisakis are associated with aquatic organisms. They can be found in a variety of marine hosts including whales, crustaceans, fish and cephalopods and are known to be the cause of the zoonotic disease anisakiasis, a painful inflammation of the gastro-intestinal tract caused by the accidental consumptions of infectious larvae raw or semi-raw fishery products. Since the demand on fish as dietary protein source and the export rates of seafood products in general is rapidly increasing worldwide, the knowledge about the distribution of potential foodborne human pathogens in seafood is of major significance for human health. Studies have provided evidence that a few Anisakis species can cause clinical symptoms in humans. The aim of our study was to interpolate the species range for every described Anisakis species on the basis of the existing occurrence data. We used sequence data of 373 Anisakis larvae from 30 different hosts worldwide and previously published molecular data (n = 584) from 53 field-specific publications to model the species range of Anisakis spp., using a interpolation method that combines aspects of the alpha hull interpolation algorithm as well as the conditional interpolation approach. The results of our approach strongly indicate the existence of species-specific distribution patterns of Anisakis spp. within different climate zones and oceans that are in principle congruent with those of their respective final hosts. Our results support preceding studies that propose anisakid nematodes as useful biological indicators for their final host distribution and abundance as they closely follow the trophic relationships among their successive hosts. The modeling might although be helpful for predicting the likelihood of infection in order to reduce the risk of anisakiasis cases in a given area.

Effect of monovalent cations and G-quadruplex structures on the outcome of intramolecular homologous recombination.

Homologous recombination is a very important cellular process, as it provides a major pathway for the repair of DNA double-strand breaks. This complex process is affected by many factors within cells. Here, we have studied the effect of monovalent cations (K+, Na+, and NH4+) on the outcome of recombination events, as their presence affects the biochemical activities of the proteins involved in recombination as well as the structure of DNA. For this purpose, we used an in vitro recombination system that includes a protein nuclear extract, as a source of recombination machinery, and two plasmids as substrates for intramolecular homologous recombination, each with two copies of different alleles of the human minisatellite MsH43. We found that the presence of monovalent cations induced a decrease in the recombination frequency, accompanied by an increase in the fidelity of the recombination. Moreover, there is an emerging consensus that secondary structures of DNA have the potential to induce genomic instability. Therefore, we analyzed the effect of the sequences capable of forming G-quadruplex on the production of recombinant molecules, taking advantage of the capacity of some MsH43 alleles to generate these kinds of structure in the presence of K+. We observed that the MsH43 recombinants containing duplications, generated in the presence of K+, did not include the repeats located towards the 5'-side of the G-quadruplex motif, suggesting that this structure may be involved in the recombination events leading to duplications. Our results provide new insights into the molecular mechanisms underlying the recombination of repetitive sequences.

Evolution of a complex minisatellite DNA sequence.

Minisatellites are tandem repeats of short DNA units widely distributed in genomes. However, the information on their dynamics in a phylogenetic context is very limited. Here we have studied the organization of the MsH43 locus in several species of primates and from these data we have reconstructed the evolutionary history of this complex minisatellite. Overall, with the exception of gibbon, MsH43 has an organization that is asymmetric, since the distribution of repeats is distinct between the 5' and 3' halves, and heterogeneous since there are many different repeats, some of them characteristic of each species. Inspection of the MsH43 arrays showed the existence of many duplications and deletions, suggesting the implication of slippage processes in the generation of polymorphism. Concerning the evolutionary history of this minisatellite, we propose that the birth of MsH43 may be situated before the divergence of Old World Monkeys since we found the existence of some MsH43 repeat motifs in prosimians and New World Monkeys. The analysis of MsH43 in apes revealed the existence of an evolutionary breakpoint in the pathway that originated African great apes and humans. Remarkably, human MsH43 is more homologous to orang-utan than to the corresponding sequence in gorilla and chimpanzee. This finding does not comply with the evolutionary paradigm that continuous alterations occur during the course of genome evolution. To adjust our results to the standard phylogeny of primates, we propose the existence of a wandering allele that was maintained almost unaltered during the period that extends between orang-utan and humans.

Linfocito T y su papel en la enfermedad periodontal: Revisión de la literatura / T lymphocytes and their role in periodontal disease. Literature Review

En general es aceptado que la  condición  inmune innata y/o adaptativa puede afectar  la respuesta inmune local, incluyendo al periodonto y dentro de la progresión de la enfermedad  es crítico poder determinar la naturaleza de la respuesta inflamatoria generada por el reto microbiano antigénico subgingival. Existen controversias en la literatura a nivel mundial con respecto al papel de los linfocitos T en la enfermedad periodontal, el entendimiento de su naturaleza y la regulación  de estas células puede estar asociado a condiciones protectoras  o destructivas no estando claro aún los eventos inflamatorios o antiinflamatorios en donde la respuesta inmune celular mediada por células T  puede estar ausente o  deficiente  durante el curso de la infección periodontal. De hecho las opiniones son divididas, algunas señalan que la principal función de estas células  es la de proteger al huésped contra los microorganismos periodontopáticos, mientras que otros han demostrado su participación activa en el inicio y progresión de la enfermedad periodontal,  por esta razón la presente revisión pretende discutir  su participación dentro de la patogenia de la periodontitis  para tratar de esclarecer los mecanismos protectores y  aquellos que pueden estar relacionados con la destrucción del tejido de soporte del diente; lo cual es importante ya que nos permitiría comprender nuevos enfoques terapéuticos para esta enfermedad

In general is accepted that the innate or adaptive immunity affect the local immune response including the periodontium and in the progression of the disease is critical determinate the nature of the inflammatory response produced by the subgingival bacterial challenge. There are controversies in the literature about the role of T lymphocytes in the periodontal disease, the nature and regulation of these cells can be associated to protective o destructive conditions, but today is not clear the inflammatory or anti-inflammatory events where the cellular immune response by T cells can be absent o deficient during the course of periodontal infection. In fact the opinions about this subject are divided: some of these indicate that the main function of this cells is to protect the host against the periodontal bacteria while another had demonstrated that them participate in the beginning and progression of periodontal disease, for this reason this reviews pretend to discuss their participation in the pathogenesis of this pathology and to know the protective and destructive mechanisms relate with the destruction of periodontal tissue, this is important because they let us to understand new ways for the treatment of this disease

Components of uncertainty in species distribution analysis: a case study of the Great Grey Shrike.

Sophisticated statistical analyses are common in ecological research, particularly in species distribution modeling. The effects of sometimes arbitrary decisions during the modeling procedure on the final outcome are difficult to assess, and to date are largely unexplored. We conducted an analysis quantifying the contribution of uncertainty in each step during the model-building sequence to variation in model validity and climate change projection uncertainty. Our study system was the distribution of the Great Grey Shrike in the German federal state of Saxony. For each of four steps (data quality, collinearity method, model type, and variable selection), we ran three different options in a factorial experiment, leading to 81 different model approaches. Each was subjected to a fivefold cross-validation, measuring area under curve (AUC) to assess model quality. Next, we used three climate change scenarios times three precipitation realizations to project future distributions from each model, yielding 729 projections. Again, we analyzed which step introduced most variability (the four model-building steps plus the two scenario steps) into predicted species prevalences by the year 2050. Predicted prevalences ranged from a factor of 0.2 to a factor of 10 of present prevalence, with the majority of predictions between 1.1 and 4.2 (inter-quartile range). We found that model type and data quality dominated this analysis. In particular, artificial neural networks yielded low cross-validation robustness and gave very conservative climate change predictions. Generalized linear and additive models were very similar in quality and predictions, and superior to neural networks. Variations in scenarios and realizations had very little effect, due to the small spatial extent of the study region and its relatively small range of climatic conditions. We conclude that, for climate projections, model type and data quality were the most influential factors. Since comparison of model types has received good coverage in the ecological literature, effects of data quality should now come under more scrutiny.