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Some respiratory viruses can cause a viral interference through the activation of the interferon (IFN) pathway that reduces the replication of another virus. Epidemiological studies of coinfections between SARS-CoV-2 and other respiratory viruses have been hampered by non-pharmacological measures applied to mitigate the spread of SARS-CoV-2 during the COVID-19 pandemic. With the ease of these interventions, SARS-CoV-2 and influenza A viruses can now co-circulate. It is thus of prime importance to characterize their interactions. In this work, we investigated viral interference effects between an Omicron variant and a contemporary influenza A/H3N2 strain, in comparison with an ancestral SARS-CoV-2 strain and the 2009 pandemic influenza A/H1N1 virus. We infected nasal human airway epitheliums with SARS-CoV-2 and influenza, either simultaneously or 24 h apart. Viral load was measured by RT-qPCR and IFN-α/β/λ1/λ2 proteins were quantified by immunoassay. Expression of four interferon-stimulated genes (ISGs; OAS1/IFITM3/ISG15/MxA) was also measured by RT-droplet digital PCR. Additionally, susceptibility of each virus to IFN-α/β/λ2 recombinant proteins was determined. Our results showed that influenza A, and especially A/H3N2, interfered with both SARS-CoV-2 viruses, but that SARS-CoV-2 did not significantly interfere with A/H3N2 or A/H1N1. Consistently with these results, influenza, and particularly the A/H3N2 strain, caused a higher production of IFN proteins and expression of ISGs than SARS-CoV-2. SARS-CoV-2 induced a marginal IFN production and reduced the IFN response during coinfections with influenza. All viruses were susceptible to exogenous IFNs, with the ancestral SARS-CoV-2 and Omicron being less susceptible to type I and type III IFNs, respectively. Thus, influenza A causes a viral interference towards SARS-CoV-2 most likely through an IFN response. The opposite is not necessarily true, and a concurrent infection with both viruses leads to a lower IFN response. Taken together, these results help us to understand how SARS-CoV-2 interacts with another major respiratory pathogen.

Introduction: Bone marrow adipose tissue (BMAT) is associated with aging, osteoporosis, and chronic kidney disease (CKD). To date, the association between BMAT and kidney function in postmenopausal women has not been thoroughly investigated. The main purpose of this study was to determine whether a relationship exists between proton density fat fraction (PDFF) and kidney function in postmenopausal women. Methods: We investigated the cross-sectional association between estimated glomerular filtration rate (eGFR) – calculated using the Chronic Kidney Disease Epidemiology Collaboration (CKD-EPI) equation – and PDFF – measured at the lumbar spine and proximal femur using Water Fat Imaging (WFI) MRI – in 199 postmenopausal women from the ADIMOS cohort study. We also performed DXA scans and laboratory measurements of sclerostin and c-terminal Fibroblast Growth Factor 23 (cFGF23). Results: Participants' mean age was 67.5 (standard deviation, SD 10.0) years. Their median eGFR was 85.0 (interquartile range, IQR 72.2–95.0) ml/min/1.73 cm2, and their mean lumbar spine PDFF was 57.9 % (SD 9.6). When classified by eGFR-based CKD stages, 41.7 % of the cohort had an eGFR ≥ 90 (n = 83), 47.2 % had an eGFR of 60–89.9 (n = 94), and 11.1 % had an eGFR of 30–59.9 (n = 22). Participants with eGFR ≥ 90 had a lower lumbar spine PDFF than those with eGFR 60–89.9 (mean 55.8 % (9.8) vs. 58.9 % (9.0), p = 0.031) and those with eGFR 30–59.9 (55.8 % (9.8) vs. 60.8 % (9.8), p = 0.043). However, the differences did not remain significant after adjusting for predetermined confounders, including age, diabetes, Charlson comorbidity index, recent history of fragility fracture, appendicular lean mass, and lumbar spine BMD. The inclusion of sclerostin and/or cFGF23 as suspected mediators did not alter the findings. When proximal hip imaging-based PDFF was considered, no significant differences were found between the eGFR categories in the unadjusted and adjusted analyses. Conclusion: No evidence of an association between kidney function and bone marrow adiposity was found either in the lumbar spine or proximal femur in a cohort of postmenopausal women.

Abstract Background The tetranucleotide GATC is methylated in Escherichia. coli by the DNA methyltransferase (Dam) and is known to be implicated in numerous cellular processes. Mutants lacking Dam are characterized by a pleiotropic phenotype. The existence of a GATC regulated network, thought to be involved in cold and oxygen shift, had been proposed and its existence has recently been confirmed. The aim of this article is to describe the components of the GATC regulated network of E. coli in detail and propose a role of this network in the light of an evolutionary advantage for the organism. Results We have classified the genes of the GATC network according to the EcoCyc functional classes. Comparisons with all of E. coli's genes and the genes involved in the SOS and stress response show that the GATC network forms a group apart. The functional classes that characterize the network are the Energy metabolism (in particular respiration), Fatty acid/ Phospholipid metabolism and Nucleotide metabolism. Conclusions The network is thought to come into play when the cell undergoes coldshock and is likely to enter stationary phase. The respiration is almost completely under GATC control and according to our hypothesis it will be blocked at the moment of coldshock; this might give the cell a selective advantage as it increases its chances for survival when entering stationary phase under coldshock. We predict the accumulation of formate and possibly succinate, which might increase the cell's resistance, in this case to antimicrobial agents, when entering stationary phase.

Abstract Background The processes of gene transcription, translation, as well as the reactions taking place between gene products, are subject to stochastic fluctuations. These stochastic events are being increasingly examined as it emerges that they can be crucial in the cell's survival. In a previous study we had examined the transcription patterns of two bacterial species (Escherichia coli and Bacillus subtilis) to elucidate the nucleoid's organization. The basic idea is that genes that share transcription patterns, must share some sort of spatial relationship, even if they are not close to each other on the chromosome. We had found that picking any gene at random, its transcription will be correlated with genes at well-defined short – as well as long-range distances, leaving the explanation of the latter an open question. In this paper we study the transcription correlations when the only transcription taking place is stochastic, in other words, no active or "deterministic" transcription takes place. To this purpose we use transcription data of Sinorhizobium meliloti. Results Even when only stochastic transcription takes place, the co-expression of genes varies as a function of the distance between genes: we observe again the short-range as well as the regular, long-range correlation patterns. Conclusion We explain these latter with a model based on the physical constraints acting on the DNA, forcing it into a conformation of groups of a few successive large and transcribed loops, which are evenly spaced along the chromosome and separated by small, non-transcribed loops. We discuss the question about the link between shared transcription patterns and physiological relationship and come to the conclusion that when genes are distantly placed along the chromosome, the transcription correlation does not imply a physiological relationship.

Abstract Background Current histo-pathological prognostic factors are not very helpful in predicting the clinical outcome of breast cancer due to the disease's heterogeneity. Molecular profiling using a large panel of genes could help to classify breast tumours and to define signatures which are predictive of their clinical behaviour. Methods To this aim, quantitative RT-PCR amplification was used to study the RNA expression levels of 47 genes in 199 primary breast tumours and 6 normal breast tissues. Genes were selected on the basis of their potential implication in hormonal sensitivity of breast tumours. Normalized RT-PCR data were analysed in an unsupervised manner by pairwise hierarchical clustering, and the statistical relevance of the defined subclasses was assessed by Chi2 analysis. The robustness of the selected subgroups was evaluated by classifying an external and independent set of tumours using these Chi2-defined molecular signatures. Results Hierarchical clustering of gene expression data allowed us to define a series of tumour subgroups that were either reminiscent of previously reported classifications, or represented putative new subtypes. The Chi2 analysis of these subgroups allowed us to define specific molecular signatures for some of them whose reliability was further demonstrated by using the validation data set. A new breast cancer subclass, called subgroup 7, that we defined in that way, was particularly interesting as it gathered tumours with specific bioclinical features including a low rate of recurrence during a 5 year follow-up. Conclusion The analysis of the expression of 47 genes in 199 primary breast tumours allowed classifying them into a series of molecular subgroups. The subgroup 7, which has been highlighted by our study, was remarkable as it gathered tumours with specific bioclinical features including a low rate of recurrence. Although this finding should be confirmed by using a larger tumour cohort, it suggests that gene expression profiling using a minimal set of genes may allow the discovery of new subclasses of breast cancer that are characterized by specific molecular signatures and exhibit specific bioclinical features.

Abstract Background Although the organisation of the bacterial chromosome is an area of active research, little is known yet on that subject. The difficulty lies in the fact that the system is dynamic and difficult to observe directly. The advent of massive hybridisation techniques opens the way to further studies of the chromosomal structure because the genes that are co-expressed, as identified by microarray experiments, probably share some spatial relationship. The use of several independent sets of gene expression data should make it possible to obtain an exhaustive view of the genes co-expression and thus a more accurate image of the structure of the chromosome. Results For both Bacillus subtilis and Escherichia coli the co-expression of genes varies as a function of the distance between the genes along the chromosome. The long-range correlations are surprising: the changes in the level of expression of any gene are correlated (positively or negatively) to the changes in the expression level of other genes located at well-defined long-range distances. This property is true for all the genes, regardless of their localisation on the chromosome. We also found short-range correlations, which suggest that the location of these co-expressed genes corresponds to DNA turns on the nucleoid surface (14–16 genes). Conclusion The long-range correlations do not correspond to the domains so far identified in the nucleoid. We explain our results by a model of the nucleoid solenoid structure based on two types of spirals (short and long). The long spirals are uncoiled expressed DNA while the short ones correspond to coiled unexpressed DNA.

Pea is a major pulse crop in temperate regions and a model plant in genetics. Large genetic marker resources are needed to assess the genetic diversity in the species genepool and to provide selection tools for breeders. In this study, we used second-generation sequencing to perform an exome-capture protocol using a diverse pea germplasm collection, and produced a resource of over 2 million Single Nucleotide Polymorphisms. This dataset was then used to characterize the genetic diversity present in the panel and compute phylogenetic and structure analyses. The development of this resource paves the way for Genome-wide association studies and the development of powerful genotyping tools.

Flaviviruses have emerged as major arthropod-transmitted pathogens and represent an increasing public health problem worldwide. High-throughput screening can be facilitated using viruses that easily express detectable marker proteins. Therefore, developing molecular tools, such as reporter-carrying versions of flaviviruses, for studying viral replication and screening antiviral compounds represents a top priority. However, the engineering of flaviviruses carrying either fluorescent or luminescent reporters remains challenging due to the genetic instability caused by marker insertion; therefore, new approaches to overcome these limitations are needed. Here, we describe reverse genetic methods that include the design and validation of infectious clones of Zika, Kunjin, and Dengue viruses harboring different reporter genes for infection, rescue, imaging, and morphology using super-resolution microscopy. It was observed that different flavivirus constructs with identical designs displayed strikingly different genetic stabilities, and corresponding virions resembled wild-type virus particles in shape and size. A successful strategy was assessed to increase the stability of rescued reporter virus and permit antiviral drug screening based on quantitative automated fluorescence microscopy and replication studies.

Abstract Background A new variant of Creutzfeldt-Jakob disease was described in the United Kingdom. It is often claimed that it is caused by consumption of food infected with the agent of bovine spongiform encephalopathy. However, this remains open to question because the number of cases of the variant is, at the present time, less than would be expected from a major food-borne source. Discussion The EUROCJD cooperative study presents currently available epidemiological data of Creutzfeldt-Jakob disease and its new variant, for nine European countries plus Australia and Canada. Unexpectedly, for the United Kingdom where all but a few cases of the new variant have been reported, these cases have to be included in the incidence curve of the sporadic forms of the disease in order to obtain the best fit with the median curve from all the countries. This variant could be merely a rare clinical phenotype within the sporadic disease. The published clinical and experimental data which suggest that it is linked with bovine spongiform encephalopathy, lead us to propose that this link could be a common etiological origin other than consumption of bovine infected food. In any case, public health recommendations hold and further investigation is required. Summary The lack of a relative increase of the Creutzfeldt-Jakob-disease mortality rate in the United Kingdom, does not fit well with the new variant being the consequence of consumption of food infected with the agent of bovine spongiform encephalopthy.

Frost is a major abiotic stress of winter type faba beans (Vica faba L.) and has adverse effects on crop yield. Climate change, far from reducing the incidence of frost events, is making these phenomena more and more common, severe, and prolonged. Despite the important interaction that the environment has in the tolerance of faba bean to frost, this trait seems to have good levels of heritability. Several QTLs for frost tolerance have already been reported, however, a more robust identification is needed to more precisely identify the genomic regions involved in faba bean tolerance to sub-zero temperatures. Several pea (Pisum sativum L.) and barrel medic (Medicago truncatula L.) frost tolerance QTLs appear to be conserved between these two species, furthering the hypothesis that the genetic control of frost tolerance in legume species might be more generally conserved. In this work, the QTL mapping in two faba bean recombinant inbred line (RIL) populations connected by a common winter-type parent has led to the identification of five genomic regions involved in the control of frost tolerance on linkage groups I, III, IV, and V. Among them, a major and robust QTL of great interest for marker-assisted selection was identified on the lower part of the long-arm of LGI. The synteny between the faba bean frost tolerance QTLs and those previously identified in other legume species such as barrel medic, pea or soybean highlighted at least partial conservation of the genetic control of frost tolerance among different faba bean genetic pools and legume species. Four novel RILs showing high and stable levels of tolerance and the ability to recover from freezing temperatures by accumulating frost tolerance QTLs are now available for breeding programs.

Abstract SARS-CoV-2 is an enveloped virus responsible for the Coronavirus Disease 2019 (COVID-19) pandemic. Here, single viruses were analyzed by atomic force microscopy (AFM) operating directly in a level 3 biosafety (BSL3) facility, which appeared as a fast and powerful method to assess at the nanoscale level and in 3D infectious virus morphology in its native conformation, or upon inactivation treatments. AFM imaging reveals structurally intact infectious and inactivated SARS-CoV-2 upon low concentration of formaldehyde treatment. This protocol combining AFM and plaque assays allows the preparation of intact inactivated SARS-CoV-2 particles for safe use of samples out of level 3 laboratory to accelerate researches against the COVID-19 pandemic. Overall, we illustrate how adapted BSL3-AFM is a remarkable toolbox for rapid and direct virus analysis based on nanoscale morphology.

Abstract Chronic kidney disease (CKD) worsens ischemic stroke severity in both patients and animals. In mice, these poorer functional outcomes are associated with decreased brain activity of AMP-activated protein kinase (AMPK), a molecule that recently emerged as a potential therapeutic target for ischemic stroke. The antidiabetic drug metformin, a well-known activator of AMPK, has improved stroke outcomes in diabetic patients with normal renal function. We investigated whether chronic metformin pre-conditioning can rescue AMPK activity and prevent stroke damage in non-diabetic mice with CKD. Eight-week-old female C57BL/6J mice were assigned to CKD or SHAM groups. CKD was induced through right kidney cortical electrocautery, followed by left total nephrectomy. Mice were then allocated to receive metformin (200 mg/kg/day) or vehicle for 5 weeks until stroke induction by transient middle cerebral artery occlusion (tMCAO). The infarct volumes were lower in CKD mice exposed to metformin than in vehicle-treated CKD mice 24 h after tMCAO. Metformin pre-conditioning of CKD mice improved their neurological score, grip strength, and prehensile abilities. It also enhanced AMPK activation, reduced apoptosis, increased neuron survival and decreased microglia/macrophage M1 signature gene expression as well as CKD-induced activation of the canonical NF-κB pathway in the ischemic lesions of CKD mice.

Some respiratory viruses can cause a viral interference through the activation of the interferon (IFN) pathway that reduces the replication of another virus. Epidemiological studies of coinfections between SARS-CoV-2 and other respiratory viruses have been hampered by non-pharmacological measures applied to mitigate the spread of SARS-CoV-2 during the COVID-19 pandemic. With the ease of these interventions, SARS-CoV-2 and influenza A viruses can now co-circulate. It is thus of prime importance to characterize their interactions. In this work, we investigated viral interference effects between an Omicron variant and a contemporary influenza A/H3N2 strain, in comparison with an ancestral SARS-CoV-2 strain and the 2009 pandemic influenza A/H1N1 virus. We infected nasal human airway epitheliums with SARS-CoV-2 and influenza, either simultaneously or 24 h apart. Viral load was measured by RT-qPCR and IFN-α/β/λ1/λ2 proteins were quantified by immunoassay. Expression of four interferon-stimulated genes (ISGs; OAS1/IFITM3/ISG15/MxA) was also measured by RT-droplet digital PCR. Additionally, susceptibility of each virus to IFN-α/β/λ2 recombinant proteins was determined. Our results showed that influenza A, and especially A/H3N2, interfered with both SARS-CoV-2 viruses, but that SARS-CoV-2 did not significantly interfere with A/H3N2 or A/H1N1. Consistently with these results, influenza, and particularly the A/H3N2 strain, caused a higher production of IFN proteins and expression of ISGs than SARS-CoV-2. SARS-CoV-2 induced a marginal IFN production and reduced the IFN response during coinfections with influenza. All viruses were susceptible to exogenous IFNs, with the ancestral SARS-CoV-2 and Omicron being less susceptible to type I and type III IFNs, respectively. Thus, influenza A causes a viral interference towards SARS-CoV-2 most likely through an IFN response. The opposite is not necessarily true, and a concurrent infection with both viruses leads to a lower IFN response. Taken together, these results help us to understand how SARS-CoV-2 interacts with another major respiratory pathogen. Author summary: During the COVID-19 pandemic, non-pharmacological measures were able to reduce the spread of SARS-CoV-2 and most respiratory viruses. Since the ease of these measures, SARS-CoV-2 variants and other viruses, such as influenza A, have started to co-circulate and can now infect a same host and interact with each other. These interactions can lead to attenuated or aggravated infections and can affect the timing of epidemics. Therefore, it is very important to elucidate how the new SARS-CoV-2 interacts with other viruses to better predict their implications in human health and their epidemic activity. Our work contributes to better understand these interactions using viruses that have likely co-circulated after lifting mitigation interventions, i.e., SARS-CoV-2 Omicron variant and a contemporary influenza A/H3N2 strain. We studied how each virus may affect the other virus' growth and how these interactions were associated with the innate immune response of the host. We found that a prior infection with influenza A can decrease the growth of SARS-CoV-2 while the latter reduces the innate immune response. Our results help to understand the interplay between SARS-CoV-2 and influenza A in the host and may improve mathematical models predicting epidemics. [ABSTRACT FROM AUTHOR]

Mild cognitive impairment (MCI) is common in people with chronic kidney disease (CKD), and its prevalence increases with progressive loss of kidney function. MCI is characterized by a decline in cognitive performance greater than expected for an individual age and education level but with minimal impairment of instrumental activities of daily living. Deterioration can affect one or several cognitive domains (attention, memory, executive functions, language, and perceptual motor or social cognition). Given the increasing prevalence of kidney disease, more and more people with CKD will also develop MCI causing an enormous disease burden for these individuals, their relatives, and society. However, the underlying pathomechanisms are poorly understood, and current therapies mostly aim at supporting patients in their daily lives. This illustrates the urgent need to elucidate the pathogenesis and potential therapeutic targets and test novel therapies in appropriate preclinical models. Here, we will outline the necessary criteria for experimental modeling of cognitive disorders in CKD. We discuss the use of mice, rats, and zebrafish as model systems and present valuable techniques through which kidney function and cognitive impairment can be assessed in this setting. Our objective is to enable researchers to overcome hurdles and accelerate preclinical research aimed at improving the therapy of people with CKD and MCI. [ABSTRACT FROM AUTHOR]

Studies on the cognitive abilities of manatees are limited despite their importance for the environmental enrichment and welfare of individuals in captivity and the understanding of manatee behaviour in the wild. Our study analyses how the presence of new stimuli and their association with food may have changed the behaviour of an Antillean manatee called Daniel. First, Daniel was observed in the absence of stimuli and subsequently, in step two, presented with the presence of four different geometrical shapes. During step three, we trained Daniel to eat from the square, while in step four he was presented with the four shapes without food. The behaviour and interaction of the manatee with the square increased considerably. We observed that three and twelve months after training the manatee still chose the square and displayed behaviours toward this specific shape. This study allowed us to formally demonstrate the ability of manatees to associate visual cues with food and increase activity with environmental and occupational devices. Our results open up new perspectives for behavioural studies on manatees, in particular those associated with cognition, management and welfare in captivity.

Despite the risks associated, some species choose to shield behind a predator to decrease predation risk by another predator. In this study, we demonstrate how Baird’s tapirs (Tapirus bairdii) use humans as a “shield” to reduce the risk of being preyed upon by jaguars (Panthera onca). We collected georeferenced photographic records of 23 tapirs (seven of them injured) sighted near human settlements (0 to 5 km) in the Calakmul region of Mexico from 2008 to 2019. Using multidimensional scale analysis, we determined which possible factors (tapir health status, injuries, distance to the settlement, as well as seasonality) are related to the decision of tapirs to approach human settlements. To support our claims of jaguars’ attacks, we described the pattern of injuries believed to have been inflicted by jaguars on tapirs, and we analysed photographs and videos of species of the genus Panthera attacking larger prey than themselves to establish a pattern of injuries and compare it to the injuries observed on tapirs. Our study shows that tapir sightings near human settlements are related to health deterioration, injuries by jaguars and seasonality. The injuries found on tapirs are similar to those caused by other big cats on large prey, providing strong support for jaguar-inflicted wounds. Further studies should investigate whether the increasing human presence in different habitats in the Neotropical region could be influencing the behaviour and distribution of prey and predators.

Abstract The French government has supported as part of its “Investments for the Future” program a 9‐year research project, PeaMUST, devoted to pea and to a lesser extent, faba bean improvement. Focusing on the main causes of yield irregularity that limit pea and faba bean cultivation, an integrated approach, including molecular exploitation of the pea genome sequence, was applied to identify and incorporate favorable alleles and allele combinations in prebreeding material.

Antiviral therapy based on neuraminidase (oseltamivir) or polymerase (baloxavir marboxil) inhibitors plays an important role in the management of influenza infections. However, the emergence of drug resistance and the uncontrolled inflammatory response are major limitations in the treatment of severe influenza disease. Protectins D1 (PD1) and DX (PDX), part of a family of pro‐resolving mediators, have previously demonstrated anti‐influenza activity as well as anti‐inflammatory properties in various clinical contexts. Herein, we synthetized a series of simplified PDX analogs and assessed their in vitro antiviral activity against influenza A(H1N1) viruses, including oseltamivir‐ and baloxavir‐resistant variants. In ST6GalI‐MDCK cells, the PDX analog AN‐137B reduced viral replication in a dose‐dependent manner with IC50 values of 23.8 for A/Puerto Rico/8/1934 (H1N1) and between 32.6 and 36.7 µM for susceptible and resistant A(H1N1)pdm09 viruses. In MTS‐based cell viability experiments, AN‐137B showed a 50% cellular cytotoxicity (CC50) of 638.7 µM with a resulting selectivity index of 26.8. Of greater importance, the combination of AN‐137B with oseltamivir or baloxavir resulted in synergistic and additive in vitro effects, respectively. Treatment of lipopolysaccharide (LPS)‐stimulated macrophages with AN‐137B resulted in a decrease of iNOS activity as shown by the reduction of nitrite production, suggesting an anti‐inflammatory effect. In conclusion, our results indicate that the protectin analog AN‐137B constitutes an interesting therapeutic modality against influenza A virus, warranting further evaluation in animal models. [ABSTRACT FROM AUTHOR]