Global indicators of the environmental impacts of invasive alien species and their information adequacy

Monitoring the extent to which invasive alien species (IAS) negatively impact the environment is crucial for understanding and mitigating biological invasions. Indeed, such information is vital for achieving Target 6 of the Kunming-Montreal Global Biodiversity Framework. However, to-date indicators for tracking the environmental impacts of IAS have been either lacking or insufficient. Capitalizing on advances in data availability and impact assessment protocols, we developed environmental impact indicators to track realized and potential impacts of IAS. We also developed an information status indicator to assess the adequacy of the data underlying the impact indicators. We used data on 75 naturalized amphibians from 82 countries to demonstrate the indicators at a global scale. The information status indicator shows variation in the reliability of the data and highlights areas where absence of impact should be interpreted with caution. Impact indicators show that growth in potential impacts are dominated by predatory species, while potential impacts from both predation and disease transmission are distributed worldwide. Using open access data, the indicators are reproducible and adaptable across scales and taxa and can be used to assess global trends and distributions of IAS, assisting authorities in prioritizing control efforts and identifying areas at risk of future invasions. This article is part of the theme issue 'Ecological novelty and planetary stewardship: biodiversity dynamics in a transforming biosphere'.

The mutation R107Q alters mtSSB ssDNA compaction ability and binding dynamics

Mitochondrial single-stranded DNA-binding protein (mtSSB) is essential for mitochondrial DNA (mtDNA) replication. Recently, several mtSSB variants have been associated with autosomal dominant mitochondrial optic atrophy and retinal dystrophy. Here, we have studied at the molecular level the functional consequences of one of the most severe mtSSB variants, R107Q. We first studied the oligomeric state of this variant and observed that the mtSSBR107Q mutant forms stable tetramers in vitro. On the other hand, we showed, using complementary single-molecule approaches, that mtSSBR107Q displays a lower intramolecular ssDNA compaction ability and a higher ssDNA dissociation rate than the WT protein. Real-time competition experiments for ssDNA-binding showed a marked advantage of mtSSBWT over mtSSBR107Q. Combined, these results show that the R107Q mutation significantly impaired the ssDNA-binding and compacting ability of mtSSB, likely by weakening mtSSB ssDNA wrapping efficiency. These features are in line with our molecular modeling of ssDNA on mtSSB showing that the R107Q mutation may destabilize local interactions and results in an electronegative spot that interrupts an ssDNA-interacting-electropositive patch, thus reducing the potential mtSSB-ssDNA interaction sites.

Innovative flow-through reaction system for the sustainable production of phenolic monomers from lignocellulose catalyzed by supported Mo2C

Molybdenum carbide supported on activated carbon (β-Mo2C/AC) has been tested as catalyst in the reductive catalytic fractionation (RCF) of lignocellulosic biomass both in batch and in Flow-Through (FT) reaction systems. High phenolic monomer yields (34 wt.%) and selectivity to monomers with reduced side alkyl chains (up to 80 wt.%) could be achieved in batch in the presence of hydrogen. FT-RCF were made with no hydrogen feed, thus via transfer hydrogenation from ethanol. Similar selectivity could be attained in FT-RCF using high catalyst/biomass ratios (0.6) and high molybdenum loading (35 wt.%) in the catalyst, although selectivity decreased with lower catalyst/biomass ratios or molybdenum contents. Regardless of these parameters, high delignification of the lignocellulosic biomass and similar monomer yields were observed in the FT mode (13-15 wt.%) while preserving the holocellulose fractions in the delignified pulp. FT-RCF system outperforms the batch reaction mode in the absence of hydrogen, both in terms of activity and selectivity to reduced monomers that is attributed to the two-step non-equilibrium processes and the removal of diffusional limitations that occur in the FT mode. Even though some molybdenum leaching was detected, the catalytic performance could be maintained with negligible loss of activity or selectivity for 15 consecutive runs.

Ribonucleotide reductase inhibition improves the symptoms of a Caenorhabditis elegans model of Alzheimer's disease

Alzheimer's disease is the main cause of aging-associated dementia, for which there is no effective treatment. In this work, we reanalyze the information of a previous genome wide association study, using a new pipeline design to identify novel potential drugs. With this approach, ribonucleoside-diphosphate reductase gene (RRM2B) emerged as a candidate target and its inhibitor, 2', 2'-difluoro 2'deoxycytidine (gemcitabine), as a potential pharmaceutical drug against Alzheimer's disease. We functionally verified the effect of inhibiting the RRM2B homolog, rnr-2, in an Alzheimer's model of Caenorhabditis elegans, which accumulates human Aβ1-42 peptide to an irreversible paralysis. RNA interference against rnr-2 and also treatment with 200 ng/ml of gemcitabine, showed an improvement of the phenotype. Gemcitabine treatment increased the intracellular ATP level 3.03 times, which may point to its mechanism of action. Gemcitabine has been extensively used in humans for cancer treatment but at higher concentrations. The 200 ng/ml concentration did not exert a significant effect over cell cycle, or affected cell viability when assayed in the microglia N13 cell line. Thus, the inhibitory drug of the RRM2B activity could be of potential use to treat Alzheimer's disease and particularly gemcitabine might be considered as a promising candidate to be repurposed for its treatment.

Mechanical advantage makes stomatal opening speed a function of evaporative demand

Stomatal opening in the light, observed in nearly all vascular land plants, is essential for providing access to atmospheric CO2 for photosynthesis. The speed of stomatal opening in the light is critical for maximizing carbon gain in environments in which light intensity changes, yet we have little understanding of how other environmental signals, particularly evaporative demand driven by vapor pressure deficit (VPD) influences the kinetics of this response. In angiosperms, and some fern species from the family Marsileaceae, a mechanical interaction between the guard cells and the epidermal cells determines the aperture of the pore. Here, we examine whether this mechanical interaction influences the speed of stomatal opening in the light. To test this, we investigated the speed of stomatal opening in response to light across a range of VPDs in seven plant species spanning the evolutionary diversity of guard cell and epidermal cell mechanical interactions. We found that stomatal opening speed is a function of evaporative demand in angiosperm species and Marsilea, which have guard cell and epidermal cell mechanical interactions. Stomatal opening speeds did not change across a range of VPD in species of gymnosperm and fern, which do not have guard cell mechanical interactions with the epidermis. We find that guard cell and epidermal cell mechanical interactions may play a key role in regulating stomatal responsiveness to light. These results provide valuable insight into the adaptive relevance of mechanical advantage.

The rise of single-cell transcriptomics in yeast

The field of single-cell omics has transformed our understanding of biological processes and is constantly advancing both experimentally and computationally. One of the most significant developments is the ability to measure the transcriptome of individual cells by single-cell RNA-seq (scRNA-seq), which was pioneered in higher eukaryotes. While yeast has served as a powerful model organism in which to test and develop transcriptomic technologies, the implementation of scRNA-seq has been significantly delayed in this organism, mainly because of technical constraints associated with its intrinsic characteristics, namely the presence of a cell wall, a small cell size and little amounts of RNA. In this review, we examine the current technologies for scRNA-seq in yeast and highlight their strengths and weaknesses. Additionally, we explore opportunities for developing novel technologies and the potential outcomes of implementing single-cell transcriptomics and extension to other modalities. Undoubtedly, scRNA-seq will be invaluable for both basic and applied yeast research, providing unique insights into fundamental biological processes.

Density-dependent species interactions modulate alpine treeline shifts

Species interactions such as facilitation and competition play a crucial role in driving species range shifts. However, density dependence as a key feature of these processes has received little attention in both empirical and modelling studies. Herein, we used a novel, individual-based treeline model informed by rich in situ observations to quantify the contribution of density-dependent species interactions to alpine treeline dynamics, an iconic biome boundary recognized as an indicator of global warming. We found that competition and facilitation dominate in dense versus sparse vegetation scenarios respectively. The optimal balance between these two effects was identified at an intermediate vegetation thickness where the treeline elevation was the highest. Furthermore, treeline shift rates decreased sharply with vegetation thickness and the associated transition from positive to negative species interactions. We thus postulate that vegetation density must be considered when modelling species range dynamics to avoid inadequate predictions of its responses to climate warming.

3Dmapper: a command line tool for BioBank-scale mapping of variants to protein structures

MOTIVATION

The interpretation of genomic data is crucial to understand the molecular mechanisms of biological processes. Protein structures play a vital role in facilitating this interpretation by providing functional context to genetic coding variants. However, mapping genes to proteins is a tedious and error-prone task due to inconsistencies in data formats. Over the past two decades, numerous tools and databases have been developed to automatically map annotated positions and variants to protein structures. However, most of these tools are web-based and not well-suited for large-scale genomic data analysis.

RESULTS

To address this issue, we introduce 3Dmapper, a stand-alone command-line tool developed in Python and R. It systematically maps annotated protein positions and variants to protein structures, providing a solution that is both efficient and reliable.

AVAILABILITY AND IMPLEMENTATION

https://github.com/vicruiser/3Dmapper.

Swarms of Enzyme-Powered Nanomotors Enhance the Diffusion of Macromolecules in Viscous Media

Over the past decades, the development of nanoparticles (NPs) to increase the efficiency of clinical treatments has been subject of intense research. Yet, most NPs have been reported to possess low efficacy as their actuation is hindered by biological barriers. For instance, synovial fluid (SF) present in the joints is mainly composed of hyaluronic acid (HA). These viscous media pose a challenge for many applications in nanomedicine, as passive NPs tend to become trapped in complex networks, which reduces their ability to reach the target location. This problem can be addressed by using active NPs (nanomotors, NMs) that are self-propelled by enzymatic reactions, although the development of enzyme-powered NMs, capable of navigating these viscous environments, remains a considerable challenge. Here, the synergistic effects of two NMs troops, namely hyaluronidase NMs (HyaNMs, Troop 1) and urease NMs (UrNMs, Troop 2) are demonstrated. Troop 1 interacts with the SF by reducing its viscosity, thus allowing Troop 2 to swim more easily through the SF. Through their collective motion, Troop 2 increases the diffusion of macromolecules. These results pave the way for more widespread use of enzyme-powered NMs, e.g., for treating joint injuries and improving therapeutic effectiveness compared with traditional methods.

Assessment of hydrological, geological, and biological parameters of a river basin impacted by old Hg mining in NW Spain

Mercury (Hg) is a toxic metal that can cause adverse effects for the health of ecosystems. The Caudal River is one of the main rivers in the Asturias region (NW Spain), whose basin is highly anthropized, hosting several Hg mines, closed in the last century. Arsenic (As) is also found in the mineral paragenesis of the Hg deposits, posing a greater environmental risk. In the mining sites, remaining old facilities and tailings continue to release these elements into the environment. In this work, samples of fluvial sediments and water were taken, both in areas affected by anthropic activity and in pristine areas, in order to establish the background levels for the critical elements. The mineralogical study of the sediments, combined with EDS microanalysis, is useful to identify mineralogical traps such as Fe oxides or clays to retain the As. The As content in all sampled sediments is above the threshold effect levels (TEL), the possible effect range within which adverse effects occasionally occur, according to the Canadian Sediment Quality Guidelines for the Protection of Aquatic Life. This fact is related to a naturally high geochemical background in the basin, due to the existing mineral deposits. The PEL threshold (the probable effect range within which adverse effects frequently occur) is exceeded by more than an order of magnitude in the sediments downstream of the Hg mines. In these points, the As content in the water, exceeding 700 μg L-1 As, is also above the quality standard established in Spanish legislation. As a result, the Caudal River tributaries in the lower part of the basin do not reach a good ecological state, according to the Hydrological Planning Office, and in some cases their state is deficient, showing low richness and high dominance of macroinvertebrates. Although the concentrations decrease with distance from the source, these findings justify the low ecological quality of the affected watercourses.

The evolutionary ecology of bird-ant interactions: a pervasive but under-studied connection

Birds and ants are among the most ubiquitous taxa co-occurring in terrestrial ecosystems, but how they mutually interact is almost unknown. Here, the main features of this neglected interaction are synthetized in a systematic literature review. Interaction with ants has been recorded in 1122 bird species (11.2% of extant species) belonging to 131 families widely distributed across the globe and the avian phylogeny. On the other hand, 47 genus of ants (14.4% of extant genus) belonging to eight subfamilies interact with birds. Interactions include competition, antagonism (either ant-bird mutual predation or parasitism) and living together commensally or mutualistically. Competition (48.9%) and antagonism (36.1%) were the most common reported interactions. The potential for engaging in commensalism and competition with ants has a phylogenetic structure in birds and was present in the birds' ancestor. Interaction is better studied in the tropics, in where the network is less dense and more nested than in temperate or arid biomes. This review demonstrates that ant-bird interactions are a pervasive phenomenon across ecological domains, playing a key role in ecosystem function. Future studies need to combine sensible experimentation within anthropogenic disturbance gradients in order to achieve a better understanding of this interaction.

Hotspot propensity across mutational processes

The sparsity of mutations observed across tumours hinders our ability to study mutation rate variability at nucleotide resolution. To circumvent this, here we investigated the propensity of mutational processes to form mutational hotspots as a readout of their mutation rate variability at single base resolution. Mutational signatures 1 and 17 have the highest hotspot propensity (5-78 times higher than other processes). After accounting for trinucleotide mutational probabilities, sequence composition and mutational heterogeneity at 10 Kbp, most (94-95%) signature 17 hotspots remain unexplained, suggesting a significant role of local genomic features. For signature 1, the inclusion of genome-wide distribution of methylated CpG sites into models can explain most (80-100%) of the hotspot propensity. There is an increased hotspot propensity of signature 1 in normal tissues and de novo germline mutations. We demonstrate that hotspot propensity is a useful readout to assess the accuracy of mutation rate models at nucleotide resolution. This new approach and the findings derived from it open up new avenues for a range of somatic and germline studies investigating and modelling mutagenesis.

A spatio-temporal Dirichlet process mixture model for coronavirus disease-19

Understanding the spatio-temporal patterns of the coronavirus disease 2019 (COVID-19) is essential to construct public health interventions. Spatially referenced data can provide richer opportunities to understand the mechanism of the disease spread compared to the more often encountered aggregated count data. We propose a spatio-temporal Dirichlet process mixture model to analyze confirmed cases of COVID-19 in an urban environment. Our method can detect unobserved cluster centers of the epidemics, and estimate the space-time range of the clusters that are useful to construct a warning system. Furthermore, our model can measure the impact of different types of landmarks in the city, which provides an intuitive explanation of disease spreading sources from different time points. To efficiently capture the temporal dynamics of the disease patterns, we employ a sequential approach that uses the posterior distribution of the parameters for the previous time step as the prior information for the current time step. This approach enables us to incorporate time dependence into our model in a computationally efficient manner without complicating the model structure. We also develop a model assessment by comparing the data with theoretical densities, and outline the goodness-of-fit of our fitted model.

Floristic Similarities between the Lichen Flora of Both Sides of the Drake Passage: A Biogeographical Approach

This paper analyses the lichen flora of Navarino Island (Tierra del Fuego, Cape Horn Region, Chile), identifying species shared with the South Shetland Islands (Antarctic Peninsula). In this common flora, species are grouped by their biogeographic origin (Antarctic-subantarctic endemic, austral, bipolar, and cosmopolitan), their habitat on Navarino Island (coastal, forest, and alpine), their morphotype (crustaceous, foliaceous, fruticulose, and cladonioid), and the substrate from which they were collected (epiphytic, terricolous and humicolous, and saxicolous). A total of 124 species have been recognised as common on both sides of the Drake Passage, predominantly bipolar, crustaceous, and saxicolous species, and with an alpine distribution on Navarino Island. The most interesting fact is that more than 30% of the flora is shared between the southern tip of South America and the western Antarctic Peninsula, which is an indication of the existence of a meridian flow of propagules capable of crossing the Antarctic polar front.

Childhood emotional dysregulation paths for suicide-related behaviour engagement in adolescence

This study aimed at identifying the heterogeneous trajectories of emotional dysregulation across childhood and to study the relationship between specific trajectories and adolescent suicide-related behaviour (SRB). Data from the Millennium Cohort Study (N = 13,853 children; 49.07% female, M = 3.13 years at baseline, SD = 0.2) were used to identify the emotional dysregulation trajectories from 3 to 8 years old, using growth mixture modelling. Moreover, 1992 participants (52.86% female) from the initial sample were used to study the relationship between childhood emotional dysregulation trajectory and engagement in both self-harm and suicide attempt at age 17, using logistic regression. Some other time-invariant and proximal (adolescent) risk factors were incorporated into this analysis. Six emotional dysregulation trajectories were identified. Self-harm at age 17 was significantly associated with the history of self-harm and other proximal factors, but not with emotional dysregulation trajectory membership. Childhood trajectories featured by earlier emotional dysregulation were associated with higher risk of lifetime suicide attempt, as well as other proximal factors (concurrent self-harm). This study found differential risk profiles involved in both SRB forms. A relationship between early emotional dysregulation and suicide attempt engagement in adolescence was identified. Early interventions should be developed to deal with SRB risk factors from childhood.

Soft robotics informs how an early echinoderm moved

The transition from sessile suspension to active mobile detritus feeding in early echinoderms (c.a. 500 Mya) required sophisticated locomotion strategies. However, understanding locomotion adopted by extinct animals in the absence of trace fossils and modern analogues is extremely challenging. Here, we develop a biomimetic soft robot testbed with accompanying computational simulation to understand fundamental principles of locomotion in one of the most enigmatic mobile groups of early stalked echinoderms-pleurocystitids. We show that these Paleozoic echinoderms were likely able to move over the sea bottom by means of a muscular stem that pushed the animal forward (anteriorly). We also demonstrate that wide, sweeping gaits could have been the most effective for these echinoderms and that increasing stem length might have significantly increased velocity with minimal additional energy cost. The overall approach followed here, which we call "Paleobionics," is a nascent but rapidly developing research agenda in which robots are designed based on extinct organisms to generate insights in engineering and evolution.

Predictors of fall risk in older adults using the G-STRIDE inertial sensor: an observational multicenter case-control study

BACKGROUND

There are a lot of tools to use for fall assessment, but there is not yet one that predicts the risk of falls in the elderly. This study aims to evaluate the use of the G-STRIDE prototype in the analysis of fall risk, defining the cut-off points to predict the risk of falling and developing a predictive model that allows discriminating between subjects with and without fall risks and those at risk of future falls.

METHODS

An observational, multicenter case-control study was conducted with older people coming from two different public hospitals and three different nursing homes. We gathered clinical variables ( Short Physical Performance Battery (SPPB), Standardized Frailty Criteria, Speed 4 m walk, Falls Efficacy Scale-International (FES-I), Time-Up Go Test, and Global Deterioration Scale (GDS)) and measured gait kinematics using an inertial measure unit (IMU). We performed a logistic regression model using a training set of observations (70% of the participants) to predict the probability of falls.

RESULTS

A total of 163 participants were included, 86 people with gait and balance disorders or falls and 77 without falls; 67,8% were females, with a mean age of 82,63 ± 6,01 years. G-STRIDE made it possible to measure gait parameters under normal living conditions. There are 46 cut-off values of conventional clinical parameters and those estimated with the G-STRIDE solution. A logistic regression mixed model, with four conventional and 2 kinematic variables allows us to identify people at risk of falls showing good predictive value with AUC of 77,6% (sensitivity 0,773 y specificity 0,780). In addition, we could predict the fallers in the test group (30% observations not in the model) with similar performance to conventional methods.

CONCLUSIONS

The G-STRIDE IMU device allows to predict the risk of falls using a mixed model with an accuracy of 0,776 with similar performance to conventional model. This approach allows better precision, low cost and less infrastructures for an early intervention and prevention of future falls.

CRISPR/Cas9-mediated deletion of adipocyte genes associated with NAFLD alters adipocyte lipid handling and reduces steatosis in hepatocytes in vitro

Obesity is a major risk factor for the development of nonalcoholic fatty liver disease (NAFLD), and the subcutaneous white adipose tissue (scWAT) is the primary lipid storage depot and regulates lipid fluxes to other organs. Our previous work identified genes upregulated in scWAT of patients with NAFLD: SOCS3, DUSP1, and SIK1. Herein, we knocked down (KD) their expression in human adipose-derived mesenchymal stem cells (hADMSCs) using clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology and characterized their phenotype. We found that SOCS3, DUSP1, and SIK1 expression in hADMSC-derived adipocytes was not critical for adipogenesis. However, the metabolic characterization of the cells suggested that the genes played important roles in lipid metabolism. Reduction of SIK1 expression significantly increased both de novo lipogenesis (DNL) and palmitate-induced lipogenesis (PIL). Editing out SOCS3 reduced DNL while increasing isoproterenol-induced lipolysis and insulin-induced palmitate accumulation. Conversely, DUSP1 reduced PIL and DNL. Moreover, RNA-sequencing analysis of edited cells showed that these genes not only altered lipid metabolism but also other biological pathways related to inflammatory processes, in the case of DUSP1, extracellular matrix remodeling for SOCS3, or cellular transport for SIK1. Finally, to evaluate a possible adipocyte-hepatocyte axis, human hepatoma HepG2 cells were cocultured with edited hADMSCs-derived adipocytes in the presence of [3H]-palmitate. All HepG2 cells cultured with DUSP1-, SIK1-, or SOCS3-KD adipocytes decreased [3H]-palmitate accumulation compared with control adipocytes. These results support our hypotheses that SOCS3, DUSP1, and SIK1 regulate multiple aspects of adipocyte function, which may play a role in the progression of obesity-associated comorbidities, such as NAFLD.NEW & NOTEWORTHY Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology successfully edited genomic DNA of human adipose-derived mesenchymal stem cells (hADMSC). SOCS3, SIK1, and DUSP1 regulate adipocyte lipid handling. Silencing SOCS3, SIK1, and DUSP1 expression in hADMSC-derived adipocytes reduces hepatocyte lipid storage in vitro.

Sex-biased TGFβ signalling in pulmonary arterial hypertension

Pulmonary arterial hypertension (PAH) is a rare cardiovascular disorder leading to pulmonary hypertension and, often fatal, right heart failure. Sex differences in PAH are evident, which primarily presents with a female predominance and increased male severity. Disturbed signalling of the transforming growth factor-β (TGFβ) family and gene mutations in the bone morphogenetic protein receptor 2 (BMPR2) are risk factors for PAH development, but how sex-specific cues affect the TGFβ family signalling in PAH remains poorly understood. In this review, we aim to explore the sex bias in PAH by examining sex differences in the TGFβ signalling family through mechanistical and translational evidence. Sex hormones including oestrogens, progestogens, and androgens, can determine the expression of receptors (including BMPR2), ligands, and soluble antagonists within the TGFβ family in a tissue-specific manner. Furthermore, sex-related genetic processes, i.e. Y-chromosome expression and X-chromosome inactivation, can influence the TGFβ signalling family at multiple levels. Given the clinical and mechanistical similarities, we expect that the conclusions arising from this review may apply also to hereditary haemorrhagic telangiectasia (HHT), a rare vascular disorder affecting the TGFβ signalling family pathway. In summary, we anticipate that investigating the TGFβ signalling family in a sex-specific manner will contribute to further understand the underlying processes leading to PAH and likely HHT.

Synthesis and Characterization of Environmentally Friendly Chitosan-Arabic Gum Nanoparticles for Encapsulation of Oregano Essential Oil in Pickering Emulsion

The encapsulation of bioactive agents through the utilization of biodegradable nanoparticles is a topic of considerable scientific interest. In this study, microcapsules composed of chitosan (CS) and Arabic gum (GA) nanoparticles were synthesized, encapsulating oregano essential oil (OEO) through Pickering emulsions and subsequent spray drying. The optimization of hybrid chitosan and Arabic gum (CS-GA) nanoparticle formation was carried out via complex coacervation, followed by an assessment of their behavior during the formation of the emulsion. Measurements of the size, contact angle, and interfacial tension of the formed complexes were conducted to facilitate the development of Pickering emulsions for encapsulating the oil under the most favorable conditions. The chitosan-Arabic gum capsules were physically characterized using scanning electron microscopy and fitted to the Beerkan estimation of soil transfer (BEST) model to determine their size distribution. Finally, the OEO encapsulation efficiency was also determined. The optimum scenario was achieved with the CS-GA 1-2 capsules at a concentration of 2% wt, featuring a contact angle of 89.1 degrees, which is ideal for the formation of oil/water (O/W) emulsions. Capsules of approximately 2.5 μm were obtained, accompanied by an encapsulation efficiency of approximately 60%. In addition, the hybrid nanoparticles that were obtained showed high biodegradability. The data within our study will contribute fundamental insights into CS-GA nanoparticles, and the quantitatively analyzed outcomes presented in this study will hold utility for forthcoming applications in environmentally friendly detergent formulations.

Formononetin, a Beer Polyphenol with Catabolic Effects on Chondrocytes

Beer consumption has been identified as a risk factor for osteoarthritis (OA), a rheumatic disease characterised by cartilage degradation, joint inflammation, and eventual joint failure. One of the main isoflavonoids in beer is formononetin (FNT), an estrogenic compound also found in multiple plants and herbs. In this study, we aimed to investigate the effect of FNT on chondrocyte viability, inflammation, and metabolism. Cells were treated with FNT with or without IL-1β for 48 h and during 7 days of differentiation. Cell viability was determined via MTT assay. Nitrite accumulation was determined by Griess reaction. The expression of genes involved in inflammation and metabolism was determined by RT-PCR. The results revealed that a low concentration of FNT had no deleterious effect on cell viability and decreased the expression of inflammation-related genes. However, our results suggest that FNT overexposure negatively impacts on chondrocytes by promoting catabolic responses. Finally, these effects were not mediated by estrogen receptors (ERs) or aryl hydrocarbon receptor (AhR). In conclusion, factors that favour FNT accumulation, such as long exposure times or metabolic disorders, can promote chondrocyte catabolism. These data may partially explain why beer consumption increases the risk of OA.

Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides

Phosphorothioates (PS) have proven their effectiveness in the area of therapeutic oligonucleotides with applications spanning from cancer treatment to neurodegenerative disorders. Initially, PS substitution was introduced for the antisense oligonucleotides (PS ASOs) because it confers an increased nuclease resistance meanwhile ameliorates cellular uptake and in-vivo bioavailability. Thus, PS oligonucleotides have been elevated to a fundamental asset in the realm of gene silencing therapeutic methodologies. But, despite their wide use, little is known on the possibly different structural changes PS-substitutions may provoke in DNA·RNA hybrids. Additionally, scarce information and significant controversy exists on the role of phosphorothioate chirality in modulating PS properties. Here, through comprehensive computational investigations and experimental measurements, we shed light on the impact of PS chirality in DNA-based antisense oligonucleotides; how the different phosphorothioate diastereomers impact DNA topology, stability and flexibility to ultimately disclose pro-Sp S and pro-Rp S roles at the catalytic core of DNA Exonuclease and Human Ribonuclease H; two major obstacles in ASOs-based therapies. Altogether, our results provide full-atom and mechanistic insights on the structural aberrations PS-substitutions provoke and explain the origin of nuclease resistance PS-linkages confer to DNA·RNA hybrids; crucial information to improve current ASOs-based therapies.

3D-Printed Organic Conjugated Trimer for Visible-Light-Driven Photocatalytic Applications

Small molecule organic semiconductors (SMOSs) have emerged as a new class of photocatalysts that exhibit visible light absorption, tunable bandgap, good dispersion, and solubility. However, the recovery and reusability of such SMOSs in consecutive photocatalytic reactions is challenging. This work concerns a 3D-printed hierarchical porous structure based on an organic conjugated trimer, named EBE. Upon manufacturing, the photophysical and chemical properties of the organic semiconductor are maintained. The 3D-printed EBE photocatalyst shows a longer lifetime (11.7 ns) compared to the powder-state EBE (1.4 ns). This result indicates a microenvironment effect of the solvent (acetone), a better dispersion of the catalyst in the sample, and reduced intermolecular π-π stacking, which results in improved separation of the photogenerated charge carriers. As a proof-of-concept, the photocatalytic activity of the 3D-printed EBE catalyst is evaluated for water treatment and hydrogen production under sun-like irradiation. The resulting degradation efficiencies and hydrogen generation rates are higher than those reported for the state-of-the-art 3D-printed photocatalytic structures based on inorganic semiconductors. The photocatalytic mechanism is further investigated, and the results suggest that hydroxyl radicals (HO⋅) are the main reactive radicals responsible for the degradation of organic pollutants. Moreover, the recyclability of the EBE-3D photocatalyst is demonstrated in up to 5 uses. Overall, these results indicate the great potential of this 3D-printed organic conjugated trimer for photocatalytic applications.

Functional membrane microdomains and the hydroxamate siderophore transporter ATPase FhuC govern Isd-dependent heme acquisition in Staphylococcus aureus

Sufficient access to transition metals such as iron is essential for bacterial proliferation and their active limitation within host tissues effectively restricts infection. To overcome iron limitation, the invasive pathogen Staphylococcus aureus uses the iron-regulated surface determinant (Isd) system to acquire hemoglobin-derived heme. While heme transport over the cell wall is well understood, its transport over the membrane is hardly investigated. In this study, we show the heme-specific permease IsdF to be energized by the general ATPase FhuC. Additionally, we show that IsdF needs appropriate location within the membrane for functionality. The membrane of S. aureus possesses special compartments (functional membrane microdomains - FMMs) to organize membrane complexes. We show IsdF to be associated with FMMs, to directly interact with the FMM scaffolding protein flotillin A (FloA) and to co-localize with the latter on intact bacterial cells. Additionally, Isd-dependent bacterial growth required FMMs and FloA. Our study shows that Isd-dependent heme acquisition requires a highly structured cell envelope to allow coordinated transport over the cell wall and membrane and it gives the first example of a bacterial nutrient acquisition system that depends on FMMs.

Forage quality of consecutive years interact to affect body condition, reproductive rate and rut phenology in Iberian red deer

Body condition for reproduction in capital breeders such as the red deer (Cervus elaphus) is mostly determined by their stored energy reserves. Thus, environmental conditions and resource availability may affect reproductive performance and breeding success. In warm Mediterranean regions, current climate change is driving to a hotter and drier scenario that is expected to affect the biology and dynamics of many populations. We examined the impact of these local climate variations on red deer body condition and the relationship with female reproductive phenology and breeding success. We used satellite information of landscape vegetation along with a 22-year data series of direct field behavioural observations during the rutting season in Doñana National Park (SW Spain). We analyzed faecal nitrogen content (FN) from faeces collected during the rut. We found that poor vegetation availability in drier years was related to worse body condition of deer (measured by FN) and a delay in the rutting season, which associated with lower reproductive rates (measured by the proportion of females with calves observed the next year). We also evidenced an interesting interaction between environmental conditions in consecutive years on the timing of breeding season, with timing of breeding being more delayed when previous year resource availability was high and many females bred, and the consecutive one was poor, so females hardly recovered condition and the rut occurred later. These findings highlight the carry-over effect of reproduction in capital breeders and the potential impact of climate-change conditions on red deer breeding.

Remote analysis of sputum smears for mycobacterium tuberculosis quantification using digital crowdsourcing

Worldwide, TB is one of the top 10 causes of death and the leading cause from a single infectious agent. Although the development and roll out of Xpert MTB/RIF has recently become a major breakthrough in the field of TB diagnosis, smear microscopy remains the most widely used method for TB diagnosis, especially in low- and middle-income countries. This research tests the feasibility of a crowdsourced approach to tuberculosis image analysis. In particular, we investigated whether anonymous volunteers with no prior experience would be able to count acid-fast bacilli in digitized images of sputum smears by playing an online game. Following this approach 1790 people identified the acid-fast bacilli present in 60 digitized images, the best overall performance was obtained with a specific number of combined analysis from different players and the performance was evaluated with the F1 score, sensitivity and positive predictive value, reaching values of 0.933, 0.968 and 0.91, respectively.

GCAT|Panel, a comprehensive structural variant haplotype map of the Iberian population from high-coverage whole-genome sequencing

The combined analysis of haplotype panels with phenotype clinical cohorts is a common approach to explore the genetic architecture of human diseases. However, genetic studies are mainly based on single nucleotide variants (SNVs) and small insertions and deletions (indels). Here, we contribute to fill this gap by generating a dense haplotype map focused on the identification, characterization, and phasing of structural variants (SVs). By integrating multiple variant identification methods and Logistic Regression Models (LRMs), we present a catalogue of 35 431 441 variants, including 89 178 SVs (≥50 bp), 30 325 064 SNVs and 5 017 199 indels, across 785 Illumina high coverage (30x) whole-genomes from the Iberian GCAT Cohort, containing a median of 3.52M SNVs, 606 336 indels and 6393 SVs per individual. The haplotype panel is able to impute up to 14 360 728 SNVs/indels and 23 179 SVs, showing a 2.7-fold increase for SVs compared with available genetic variation panels. The value of this panel for SVs analysis is shown through an imputed rare Alu element located in a new locus associated with Mononeuritis of lower limb, a rare neuromuscular disease. This study represents the first deep characterization of genetic variation within the Iberian population and the first operational haplotype panel to systematically include the SVs into genome-wide genetic studies.

The structural coverage of the human proteome before and after AlphaFold

The protein structure field is experiencing a revolution. From the increased throughput of techniques to determine experimental structures, to developments such as cryo-EM that allow us to find the structures of large protein complexes or, more recently, the development of artificial intelligence tools, such as AlphaFold, that can predict with high accuracy the folding of proteins for which the availability of homology templates is limited. Here we quantify the effect of the recently released AlphaFold database of protein structural models in our knowledge on human proteins. Our results indicate that our current baseline for structural coverage of 48%, considering experimentally-derived or template-based homology models, elevates up to 76% when including AlphaFold predictions. At the same time the fraction of dark proteome is reduced from 26% to just 10% when AlphaFold models are considered. Furthermore, although the coverage of disease-associated genes and mutations was near complete before AlphaFold release (69% of Clinvar pathogenic mutations and 88% of oncogenic mutations), AlphaFold models still provide an additional coverage of 3% to 13% of these critically important sets of biomedical genes and mutations. Finally, we show how the contribution of AlphaFold models to the structural coverage of non-human organisms, including important pathogenic bacteria, is significantly larger than that of the human proteome. Overall, our results show that the sequence-structure gap of human proteins has almost disappeared, an outstanding success of direct consequences for the knowledge on the human genome and the derived medical applications.

Protein structures are key to understand many biological phenomena at the molecular scale: from the effects of genetic variation to how different proteins interact with each other to create molecular pathways that, together, have a biological function. Obtaining experimental structures, however, is extremely consuming in terms of both, time and resources.

For this and other reasons, scientists have long worked to develop computational approaches that predict the structure of a protein using only its sequence as input. Recently, a group of scientists at Deepmind have developed AlphaFold2, a computational tool that is extremely accurate at this task. Moreover, they have used this tool to predict the structures of all human proteins.

In this manuscript we provide an overview of the structural coverage of the human proteome before AlphaFold models were released and how much we have gained thanks to these models. We also show how the gain affects our understanding of human pathogenic variants, both germline and somatic. Finally, we provide evidence suggesting that the gain in non-human organisms is larger than for the human proteome, particularly in the case of bacteria.

Cardiac Changes in Parkinson's Disease: Lessons from Clinical and Experimental Evidence

Dysautonomia is a common non-motor symptom in Parkinson's disease (PD). Most dysautonomic symptoms appear due to alterations in the peripheral nerves of the autonomic nervous system, including both the sympathetic and parasympathetic nervous systems. The degeneration of sympathetic nerve fibers and neurons leads to cardiovascular dysfunction, which is highly prevalent in PD patients. Cardiac alterations such as orthostatic hypotension, heart rate variability, modifications in cardiogram parameters and baroreflex dysfunction can appear in both the early and late stages of PD, worsening as the disease progresses. In PD patients it is generally found that parasympathetic activity is decreased, while sympathetic activity is increased. This situation gives rise to an imbalance of both tonicities which might, in turn, promote a higher risk of cardiac damage through tachycardia and vasoconstriction. Cardiovascular abnormalities can also appear as a side effect of PD treatment: L-DOPA can decrease blood pressure and aggravate orthostatic hypotension as a result of a negative inotropic effect on the heart. This unwanted side effect limits the therapeutic use of L-DOPA in geriatric patients with PD and can contribute to the number of hospital admissions. Therefore, it is essential to define the cardiac features related to PD for the monitorization of the heart condition in parkinsonian individuals. This information can allow the application of intervention strategies to improve the course of the disease and the proposition of new alternatives for its treatment to eliminate or reverse the motor and non-motor symptoms, especially in geriatric patients.

BASHY Dye Platform Enables the Fluorescence Bioimaging of Myelin Debris Phagocytosis by Microglia during Demyelination

Multiple sclerosis (MS) is a demyelinating disease of the central nervous system that is characterized by the presence of demyelinated regions with accumulated myelin lipid debris. Importantly, to allow effective remyelination, such debris must be cleared by microglia. Therefore, the study of microglial activity with sensitive tools is of great interest to better monitor the MS clinical course. Using a boronic acid-based (BASHY) fluorophore, specific for nonpolar lipid aggregates, we aimed to address BASHY's ability to label nonpolar myelin debris and image myelin clearance in the context of demyelination. Demyelinated ex vivo organotypic cultures (OCSCs) and primary microglia cells were immunostained to evaluate BASHY's co-localization with myelin debris and also to evaluate BASHY's specificity for phagocytosing cells. Additionally, mice induced with experimental autoimmune encephalomyelitis (EAE) were injected with BASHY and posteriorly analyzed to evaluate BASHY+ microglia within demyelinated lesions. Indeed, in our in vitro and ex vivo studies, we showed a significant increase in BASHY labeling in demyelinated OCSCs, mostly co-localized with Iba1-expressing amoeboid/phagocytic microglia. Most importantly, BASHY's presence was also found within demyelinated areas of EAE mice, essentially co-localizing with lesion-associated Iba1+ cells, evidencing BASHY's potential for the in vivo bioimaging of myelin clearance and myelin-carrying microglia in regions of active demyelination.

Isolation and Structural Elucidation of New Amphidinol Analogues from Amphidinium carterae Cultivated in a Pilot-Scale Photobioreactor

The demand for valuable products from dinoflagellate biotechnology has increased remarkably in recent years due to their many prospective applications. However, there remain many challenges that need to be addressed in order to make dinoflagellate bioactives a commercial reality. In this article, we describe the technical feasibility of producing and recovering amphidinol analogues (AMs) excreted into a culture broth of Amphidinium carterae ACRN03, successfully cultured in an LED-illuminated pilot-scale (80 L) bubble column photobioreactor operated in fed-batch mode with a pulse feeding strategy. We report on the isolation of new structurally related AMs, amphidinol 24 (1, AM24), amphidinol 25 (2, AM25) and amphidinol 26 (3, AM26), from a singular fraction resulting from the downstream processing. Their planar structures were elucidated by extensive NMR and HRMS analysis, whereas the relative configuration of the C-32→C-47 bis-tetrahydropyran core was confirmed to be antipodal in accord with the recently revised configuration of AM3. The hemolytic activities of the new metabolites and other related derivatives were evaluated, and structure-activity conclusions were established. Their isolation was based on a straightforward and high-performance bioprocess that could be suitable for the commercial development of AMs or other high-value compounds from shear sensitive dinoflagellates.

Perturbations in dynamical models of whole-brain activity dissociate between the level and stability of consciousness

Consciousness transiently fades away during deep sleep, more stably under anesthesia, and sometimes permanently due to brain injury. The development of an index to quantify the level of consciousness across these different states is regarded as a key problem both in basic and clinical neuroscience. We argue that this problem is ill-defined since such an index would not exhaust all the relevant information about a given state of consciousness. While the level of consciousness can be taken to describe the actual brain state, a complete characterization should also include its potential behavior against external perturbations. We developed and analyzed whole-brain computational models to show that the stability of conscious states provides information complementary to their similarity to conscious wakefulness. Our work leads to a novel methodological framework to sort out different brain states by their stability and reversibility, and illustrates its usefulness to dissociate between physiological (sleep), pathological (brain-injured patients), and pharmacologically-induced (anesthesia) loss of consciousness.

Relaxation Mechanisms and Strain-Controlled Oxygen Vacancies in Epitaxial SrMnO3 Films

SrMnO₃ has a rich epitaxial strain-dependent ferroic phase diagram, in which a variety of magnetic orderings, even ferroelectricity, and thus multiferroicity, are accessible by gradually modifying the strain. Different relaxation processes, though, including the presence of strain-induced oxygen vacancies, can severely curtail the possibility of stabilizing these ferroic phases. Here, we report on a thorough investigation of the strain relaxation mechanisms in SrMnO₃ films grown on several substrates imposing varying degrees of strain from slightly compressive (-0.39%) to largely tensile ≈+3.8%. First, we determine the strain dependency of the critical thickness (t _c) below which pseudomorphic growth is obtained. Second, the mechanisms of stress relaxation are elucidated, revealing that misfit dislocations and stacking faults accommodate the strain above t _c. Yet, even for films thicker than t _c, the atomic monolayers below t _c are proved to remain fully coherent. Therefore, multiferroicity may also emerge even in films that appear to be partially relaxed. Last, we demonstrate that fully coherent films with the same thickness present a lower oxygen content for increasing tensile mismatch with the substrate. This behavior proves the coupling between the formation of oxygen vacancies and epitaxial strain, in agreement with first-principles calculations, enabling the strain control of the Mn³⁺/Mn⁴⁺ ratio, which strongly affects the magnetic and electrical properties. However, the presence of oxygen vacancies/Mn³⁺ cations reduces the effective epitaxial strain in the SrMnO₃ films and, thus, the accessibility to the strain-induced multiferroic phase.

Apoptosis-like cell death upon kinetoplastid induction by compounds isolated from the brown algae Dictyota spiralis

BACKGROUND

The in vitro activity of the brown seaweed Dictyota spiralis against both Leishmania amazonensis and Trypanosoma cruzi was evaluated in a previous study. Processing by bio-guided fractionation resulted in the isolation of three active compounds, classified as diterpenes. In the present study, we performed several assays to detect clinical features associated to cell death in L. amazonensis and T. cruzi with the aim to elucidate the mechanism of action of these compounds on parasitic cells.

METHODS

The aims of the experiments were to detect and evaluate specific events involved in apoptosis-like cell death in the kinetoplastid, including DNA condensation, accumulation of reactive oxygen species and changes in ATP concentration, cell permeability and mitochondrial membrane potential, respectively, in treated cells.

RESULTS

The results demonstrated that the three isolated diterpenes could inhibit the tested parasites by inducing an apoptosis-like cell death.

CONCLUSIONS

These results encourage further investigation on the isolated compounds as potential drug candidates against both L. amazonensis and T. cruzi.

Development and Angiogenic Potential of Cell-Derived Microtissues Using Microcarrier-Template

Tissue engineering and regenerative medicine approaches use biomaterials in combination with cells to regenerate lost functions of tissues and organs to prevent organ transplantation. However, most of the current strategies fail in mimicking the tissue's extracellular matrix properties. In order to mimic native tissue conditions, we developed cell-derived matrix (CDM) microtissues (MT). Our methodology uses poly-lactic acid (PLA) and Cultispher® S microcarriers' (MCs') as scaffold templates, which are seeded with rat bone marrow mesenchymal stem cells (rBM-MSCs). The scaffold template allows cells to generate an extracellular matrix, which is then extracted for downstream use. The newly formed CDM provides cells with a complex physical (MT architecture) and biochemical (deposited ECM proteins) environment, also showing spontaneous angiogenic potential. Our results suggest that MTs generated from the combination of these two MCs (mixed MTs) are excellent candidates for tissue vascularization. Overall, this study provides a methodology for in-house fabrication of microtissues with angiogenic potential for downstream use in various tissue regenerative strategies.

The hidden waves in the ECG uncovered revealing a sound automated interpretation method

A novel approach for analysing cardiac rhythm data is presented in this paper. Heartbeats are decomposed into the five fundamental P, Q, R, S and T waves plus an error term to account for artifacts in the data which provides a meaningful, physical interpretation of the heart's electric system. The morphology of each wave is concisely described using four parameters that allow all the different patterns in heartbeats to be characterized and thus differentiated This multi-purpose approach solves such questions as the extraction of interpretable features, the detection of the fiducial marks of the fundamental waves, or the generation of synthetic data and the denoising of signals. Yet the greatest benefit from this new discovery will be the automatic diagnosis of heart anomalies as well as other clinical uses with great advantages compared to the rigid, vulnerable and black box machine learning procedures, widely used in medical devices. The paper shows the enormous potential of the method in practice; specifically, the capability to discriminate subjects, characterize morphologies and detect the fiducial marks (reference points) are validated numerically using simulated and real data, thus proving that it outperforms its competitors.

Ephaptic coupling in white matter fibre bundles modulates axonal transmission delays

Axonal connections are widely regarded as faithful transmitters of neuronal signals with fixed delays. The reasoning behind this is that extracellular potentials caused by spikes travelling along axons are too small to have an effect on other axons. Here we devise a computational framework that allows us to study the effect of extracellular potentials generated by spike volleys in axonal fibre bundles on axonal transmission delays. We demonstrate that, although the extracellular potentials generated by single spikes are of the order of microvolts, the collective extracellular potential generated by spike volleys can reach several millivolts. As a consequence, the resulting depolarisation of the axonal membranes increases the velocity of spikes, and therefore reduces axonal delays between brain areas. Driving a neural mass model with such spike volleys, we further demonstrate that only ephaptic coupling can explain the reduction of stimulus latencies with increased stimulus intensities, as observed in many psychological experiments.

Axonal fibre bundles that connect distant cortical areas contain millions of densely packed axons. When synchronous spike volleys travel through such fibre bundles, the extracellular potential within the bundles is perturbed. We use computer simulations to examine the magnitude and shape of this perturbation, and demonstrate that it is sufficiently strong to affect axonal transmission speeds. Since most spikes within a spike volley are positioned in an area where the extracellular potential is negative (relative to a distant reference), the resulting depolarisation of the axonal membranes accelerates the spike volley on average. This finding is in contrast to previous studies of ephaptic coupling effects between axons, where ephaptic coupling was found to slow down spike propagation. Our finding has consequences for information transmission and synchronisation between cortical areas.

Optimisation of Non-Pharmaceutical Measures in COVID-19 Growth via Neural Networks

On [Formula: see text] March, the World Health Organisation declared a pandemic. Through this global spread, many nations have witnessed exponential growth of confirmed cases brought under control by severe mass quarantine or lockdown measures. However, some have, through a different timeline of actions, prevented this exponential growth. Currently as some continue to tackle growth, others attempt to safely lift restrictions whilst avoiding a resurgence. This study seeks to quantify the impact of government actions in mitigating viral transmission of SARS-CoV-2 by a novel soft computing approach that makes concurrent use of a neural network model, to predict the daily slope increase of cumulative infected, and an optimiser, with a parametrisation of the government restriction time series, to understand the best set of mitigating actions. Data for two territories, Italy and Taiwan, have been gathered to model government restrictions in travelling, testing and enforcement of social distance measures as well as people connectivity and adherence to government actions. It is found that a larger and earlier testing campaign with tighter entry restrictions benefit both regions, resulting in significantly less confirmed cases. Interestingly, this scenario couples with an earlier but milder implementation of nationwide restrictions for Italy, thus supporting Taiwan's lack of nationwide lockdown, i.e. earlier government actions could have contained the growth to a degree that a widespread lockdown would have been avoided, or at least delayed. The results, found with a purely data-driven approach, are in line with the main findings of mathematical epidemiological models, proving that the proposed approach has value and that the data alone contains valuable knowledge to inform decision makers.

Antimicrobial effect of insect chitosan on Salmonella Typhimurium, Escherichia coli O157:H7 and Listeria monocytogenes survival

The antimicrobial capability of chitosan from Tenebrio molitor as compared with chitosan from crustacean (Penaeus monodon) on different pathogenic microorganisms of concern in food safety was studied. The antimicrobial effect was tested at pH 5 and pH 6.2 and at two different initial concentrations (10³ or 10⁶ CFU/mL). Results indicated that chitosan from both sources have antimicrobial activity, although the effect depended on the microorganism considered (Salmonella Typhimurium, Listeria monocytogenes and Escherichia coli O157:H7). Our results indicated that Salmonella was the most resistant bacteria, and that chitosan from insect was less active than chitosan from crustacean, especially against Salmonella. Another important factor on antimicrobial activity was the pH of the sample. When chitosan was added to a solution with a pH of 6.2 it was more active against Listeria and Escherichia coli, than at pH 5.00. Besides, the effect of chitosan appears to decrease with the incubation time, since some increases in counts were observed on E. coli and Salmonella after the 24 and 49 hours of incubation.

Site-Specific Iron Substitution in STA-28, a Large Pore Aluminophosphate Zeotype Prepared by Using 1,10-Phenanthrolines as Framework-Bound Templates

An AlPO4 zeotype has been prepared using the aromatic diamine 1,10-phenanthroline and some of its methylated analogues as templates. In each case the two template N atoms bind to a specific framework Al site to expand its coordination to the unusual octahedral AlO4 N2 environment. Furthermore, using this framework-bound template, Fe atoms can be included selectively at this site in the framework by direct synthesis, as confirmed by annular dark field scanning transmission electron microscopy and Rietveld refinement. Calcination removes the organic molecules to give large pore framework solids, with BET surface areas up to 540 m2  g-1 and two perpendicular sets of channels that intersect to give pore space connected by 12-ring openings along all crystallographic directions.

Representation of foreseeable choice outcomes in orbitofrontal cortex triplet-wise interactions

Shared neuronal variability has been shown to modulate cognitive processing. However, the relationship between shared variability and behavioral performance is heterogeneous and complex in frontal areas such as the orbitofrontal cortex (OFC). Mounting evidence shows that single-units in OFC encode a detailed cognitive map of task-space events, but the existence of a robust neuronal ensemble coding for the predictability of choice outcome is less established. Here, we hypothesize that the coding of foreseeable outcomes is potentially unclear from the analysis of units activity and their pairwise correlations. However, this code might be established more conclusively when higher-order neuronal interactions are mapped to the choice outcome. As a case study, we investigated the trial-to-trial shared variability of neuronal ensemble activity during a two-choice interval-discrimination task in rodent OFC, specifically designed such that a lose-switch strategy is optimal by repeating the rewarded stimulus in the upcoming trial. Results show that correlations among triplets are higher during correct choices with respect to incorrect ones, and that this is sustained during the entire trial. This effect is not observed for pairwise nor for higher than third-order correlations. This scenario is compatible with constellations of up to three interacting units assembled during trials in which the task is performed correctly. More interestingly, a state-space spanned by such constellations shows that only correct outcome states that can be successfully predicted are robust over 100 trials of the task, and thus they can be accurately decoded. However, both incorrect and unpredictable outcome representations were unstable and thus non-decodeable, due to spurious negative correlations. Our results suggest that predictability of successful outcomes, and hence the optimal behavioral strategy, can be mapped out in OFC ensemble states reliable over trials of the task, and revealed by sufficiency complex neuronal interactions.

Neuronal responses can differ substantially during repetitions of the same tasks; however, they are often coordinated (shared) across multiple neighboring neurons. Such correlation between neurons has been related to the capacity of the brain to take decisions, but specifically how this relation is established is still under study. In this work, we address this question by focusing on an intriguing case study, the orbitofrontal cortex, since this brain area has been found in various studies to be useful for decision-making. Here, we question whether orchestrated groups of neurons encode sufficient information for optimizing their decision strategy; that is, whether the outcome of a choice can be predicted or not on the basis of previous experience. We thus designed a decision-making task for a rat in which some of the correct choices can be predicted. We found that only successful outcomes that can actually be predicted were robustly encoded over time. This finding was shown by analyzing sufficiently complex interactions between three neurons, whilst more complex orchestrations did not add further insights. Thus, we propose that coordinated responses of up to three neurons in the OFC could contribute to the capacity of the animal to take the optimal decision.

Evidence of Pathogen-Induced Immunogenetic Selection across the Large Geographic Range of a Wild Seabird

Over evolutionary time, pathogen challenge shapes the immune phenotype of the host to better respond to an incipient threat. The extent and direction of this selection pressure depend on the local pathogen composition, which is in turn determined by biotic and abiotic features of the environment. However, little is known about adaptation to local pathogen threats in wild animals. The Gentoo penguin (Pygoscelis papua) is a species complex that lends itself to the study of immune adaptation because of its circumpolar distribution over a large latitudinal range, with little or no admixture between different clades. In this study, we examine the diversity in a key family of innate immune genes-the Toll-like receptors (TLRs)-across the range of the Gentoo penguin. The three TLRs that we investigated present varying levels of diversity, with TLR4 and TLR5 greatly exceeding the diversity of TLR7. We present evidence of positive selection in TLR4 and TLR5, which points to pathogen-driven adaptation to the local pathogen milieu. Finally, we demonstrate that two positively selected cosegregating sites in TLR5 are sufficient to alter the responsiveness of the receptor to its bacterial ligand, flagellin. Taken together, these results suggest that Gentoo penguins have experienced distinct pathogen-driven selection pressures in different environments, which may be important given the role of the Gentoo penguin as a sentinel species in some of the world's most rapidly changing environments.

Crosstalk between bacterial conjugation and motility is mediated by plasmid-borne regulators

Plasmid conjugation is a major horizontal gene transfer mechanism. The acquisition of a plasmid may cause a perturbation of the cell functions in addition to provide advantageous properties for the recipient cell, such as the gaining of antibiotic resistances. The interplay between plasmid and chromosomal functions has been studied using the IncHI1 plasmid R27. Plasmids of the incompatibility group HI1, isolated from several Gram-negative pathogens, are associated with the spread of multidrug resistance. Their conjugation is tightly regulated by temperature, being repressed at temperatures within the host (37°C). In this report, we described that at permissive temperature, when conjugation of plasmid R27 is prompted, a reduction in the motility of the cells is observed. This reduction is mediated by the plasmid-encoded regulators TrhR/TrhY, which together with HtdA form a plasmid-borne regulatory circuit controlling R27 conjugation. TrhR/TrhY, required to induce R27 conjugation, is responsible for the downregulation of the flagella synthesis and the consequent decrease in motility. TrhR/TrhY repress, direct or indirectly, the expression of the specific flagellar sigma subunit FliA and, consequently, the expression of all genes located bellow in the flagellar expression cascade.

Transience effect in capture-recapture studies: The importance of its biological meaning

Capture-recapture (CR) models are an essential tool for estimating demographic parameters in most animal and some plant populations. To avoid drawing incorrect conclusions in any statistical inference, a crucial prerequisite is to assess the goodness of fit of a general model to the data. In CR models, a frequent cause of lack of fit, is the so-called transience effect, which is due to a lower expectation of re-observation of individuals marked for the first time as compared to other individuals. The transience effect may result either from different biological causes or from the sampling procedure. A transience effect is usually treated by distinguishing at least two age-classes in the survival probability, but other approaches may be more suitable. Here we develop a conceptual and analytical framework for including a transience effect in capture-recapture models. We show the implementation of two additional parametrizations that incorporate a transience effect. With these parametrizations, we can directly estimate the "transience probability" defined as the probability that a newly caught individual disappear from the population beyond what is expected based on the behavior of the previously caught individuals in the same sample. Additionally, these parametrizations allow testing biological hypotheses concerning drivers affecting this probability. Results from our case study show differences between parametrizations, with the parametrization most currently used giving different estimates, especially when including covariates. We advocate for a unifying framework for treating a transience effect, that helps clarifying the ideas and terminology, and where the biological reasons should be the rule for choosing the appropriate analytical procedure. This framework will also open new and powerful ways for the detection and exploration of ecological processes such as the costs of the first reproduction or the deleterious effects of some types of marking.

Molecular Recognition via Hydrogen Bonding in Supramolecular Complexes: A Fourier Transform Infrared Spectroscopy Study

We assess the assembly of supramolecular complexes by hydrogen bonding between azocompounds and a diacylaminopyridine monomer by temperature-dependent Fourier transform infrared spectroscopy (FT-IR) and density functional theory (DFT) calculations. The electronic delocalisation in the supramolecular rings formed by multiple hydrogen bonds stabilises the complexes, which coexist with dimeric species in temperature-dependent equilibria. We show how the application of readily available molecular modelling and spectroscopic techniques can predict the stability of new supramolecular entities coexisting in equilibria, ultimately assessing the success of molecular recognition.

Quality of pomegranate pomace as affected by drying method

During the industrial manufacturing of pomegranate juice, large amounts of pomace are produced. The aim of this work was to find the effective method to dry pomegranate pomace to open new commercial applications for this co-product. The effects of three drying methods: (i) convective drying (CD) at 50, 60, and 70 °C; (ii) vacuum microwave drying (VMD) at 240, 360, and 480 W, and (iii) a combined method (CPD-VMFD); convective pre-drying (60 °C) followed by vacuum microwave finish drying (360 W), on drying kinetics and quality of PomP (pomegranate pomace obtained after preparing pomegranate juice by squeezing only arils) were evaluated. The shortest treatments were VMD at 240 and 360 W (52 and 33 min, respectively); besides, these treatments led to interesting values of the green-red coordinate, a*, (12.2 and 4.1, respectively), total phenolic content (4.0 and 4.1 mg eq gallic acid g-1 dry weight, respectively), and antioxidant activity (30.8 and 29.0 µmol g-1 dry weight, respectively). On the other hand, this study demonstrated that this co-product is a rich source of punicic acid (average value = 66.4%), being a good opportunity for the pharmaceutical and nutraceutical industries. Moreover, no significant changes in the fatty acid profile was observed as affected by the drying treatments, and no off-flavors were generated by any of the drying methods.