A validated protocol for eDNA-based monitoring of within-species genetic diversity in a pond-breeding amphibian

In light of the dramatic decline in amphibian biodiversity, new cost-efficient tools to rapidly monitor species abundance and population genetic diversity in space and time are urgently needed. It has been amply demonstrated that the use of environmental DNA (eDNA) for single-species detection and characterization of community composition can increase the precision of amphibian monitoring compared to traditional (observational) approaches. However, it has been suggested that the efficiency and accuracy of the eDNA approach could be further improved by more timely sampling; in addition, the quality of genetic diversity data derived from the same DNA has been confirmed in other vertebrate taxa, but not amphibians. Given the availability of previous tissue-based genetic data, here we use the common frog Rana temporaria Linnaeus, 1758 as our target species and an improved eDNA protocol to: (i) investigate differences in species detection between three developmental stages in various freshwater environments; and (ii) study the diversity of mitochondrial DNA (mtDNA) haplotypes detected in eDNA (water) samples, by amplifying a specific fragment of the COI gene (331 base pairs, bp) commonly used as a barcode. Our protocol proved to be a reliable tool for monitoring population genetic diversity of this species, and could be a valuable addition to amphibian conservation and wetland management

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The management plan of Austropotamobius pallipes in Trentino

The management plan for conservation of the crayfish Austropotamobius pallipes complex in Trentino, in the Eastern Italian Alps, is one of the outcomes of the European Project Life+T.E.N. The monitoring of the species and its habitats represent the first result of the management plan application. Two-hundred-twenty-four water bodies were surveyed in 2019-2021, and 79 of these resulted unsuitable for A. pallipes due to their environmental characteristics. In each remaining site, which were confirmed to be suitable, we georeferenced a 100 m transect, representative of the water body, where we recorded the main physical characteristics of the habitats, the physical-chemical parameters of water and, in streams, macrobenthos to calculate the Extended Biotic Index. The presence/absence of the species was evaluated along each transect and was detected/confirmed in 42 of them. Counts method was applied to 35 populations to measure the abundance calculated as CPUE. In 28 populations, all animals were collected and biometric data, sex, presence of visible infestations by parasites and pathogens were recorded, to assess the populations’ structure and their conservation status. The main threats for the populations of A. pallipes we detected are represented by habitat alteration and the presence of the two invasive alien species Procambarus clarkii and Faxonius limosus in one and six water bodies, respectively. The populations status and the detected threats suggest a management strategy that increases the ecological conditions and connectivity of the aquatic habitats and ensures the control of the spread of alien species and their pathogens

How much do crayfish plague and microsporidiosis affect the conservation status of the white-clawed crayfish Austropotamobius pallipes complex in Trentino (NE Italy)?

The white-clawed crayfish Austropotamobius pallipes complex is an endangered species, with decreasing trend in distribution and abundance throughout Europe. One of the causes of decline is the widespread invasion of alien crayfish and the associated spread of infectious diseases, primarily of the crayfish plague caused by Aphanomyces astaci. Although this disease usually causes mass mortality in A. pallipes, some wild populations appear to be resistant or/and tolerant towards A. astaci. A further disease, poorly investigated and understood, is microsporidiosis, i.e., the porcelain disease, caused by the microsporidian parasites Astathelohania contejeani and Nosema austropotamobii. We present the results of a 2021-2022 monitoring survey, aimed at mapping the distribution of A. astaci, A. contejeani and N. austropotamobii in the wild populations of A. pallipes in Trentino. We applied non-invasive sampling methods to collect cuticular swabs from 17 of 44 known populations, concurrently collecting eDNA at one of the sampling sites, to investigate the presence of A. astaci and if possible, identify its genotype through molecular analyses. Sixteen 16 specimens from 5 populations showed abdominal muscles with macroscopic signs of porcelain disease, tissue from these specimens were collected and subjected to molecular evaluation to confirm the presence of microsporidia and identify the species. Aphanomyces astaci was detected in 5 populations and the presence of a low pathogenic genotype (genotype A) was confirmed in one of them. The presence of A. contejeani was identified in 5 populations. In 2 of them, N. austropotamobii was detected in co-infection with A. contejeani in the same individual

Compensatory recruitment allows amphibian population persistence in anthropogenic habitats

International audienceHabitat anthropization is a major driver of global biodiversity decline. Although most species are negatively affected, some benefit from anthropogenic habitat modifications by showing intriguing life-history responses. For instance, increased recruitment through higher allocation to reproduction or improved performance during early-life stages could compensate for reduced adult survival, corresponding to “compensatory recruitment”. To date, evidence of compensatory recruitment in response to habitat modification is restricted to plants, limiting understanding of its importance as a response to global change. We used the yellow-bellied toad ( Bombina variegata ), an amphibian occupying a broad range of natural and anthropogenic habitats, as a model species to test for and to quantify compensatory recruitment. Using an exceptional capture–recapture dataset composed of 21,714 individuals from 67 populations across Europe, we showed that adult survival was lower, lifespan was shorter, and actuarial senescence was higher in anthropogenic habitats, especially those affected by intense human activities. Increased recruitment in anthropogenic habitats fully offset reductions in adult survival, with the consequence that population growth rate in both habitat types was similar. Our findings indicate that compensatory recruitment allows toad populations to remain viable in human-dominated habitats and might facilitate the persistence of other animal populations in such environments

Understanding Factors Associated With Psychomotor Subtypes of Delirium in Older Inpatients With Dementia

Objectives: Few studies have analyzed factors associated with delirium subtypes. In this study, we investigate factors associated with subtypes of delirium only in patients with dementia to provide insights on the possible prevention and treatments. Design: This is a cross-sectional study nested in the \u201cDelirium Day\u201d study, a nationwide Italian point-prevalence study. Setting and Participants: Older patients admitted to 205 acute and 92 rehabilitation hospital wards. Measures: Delirium was evaluated with the 4-AT and the motor subtypes with the Delirium Motor Subtype Scale. Dementia was defined by the presence of a documented diagnosis in the medical records and/or prescription of acetylcholinesterase inhibitors or memantine prior to admission. Results: Of the 1057 patients with dementia, 35% had delirium, with 25.6% hyperactive, 33.1% hypoactive, 34.5% mixed, and 6.7% nonmotor subtype. There were higher odds of having venous catheters in the hypoactive (OR 1.82, 95% CI 1.18-2.81) and mixed type of delirium (OR 2.23, CI 1.43-3.46), whereas higher odds of urinary catheters in the hypoactive (OR 2.91, CI 1.92-4.39), hyperactive (OR 1.99, CI 1.23-3.21), and mixed types of delirium (OR 2.05, CI 1.36-3.07). We found higher odds of antipsychotics both in the hyperactive (OR 2.87, CI 1.81-4.54) and mixed subtype (OR 1.84, CI 1.24-2.75), whereas higher odds of antibiotics was present only in the mixed subtype (OR 1.91, CI 1.26-2.87). Conclusions and Implications: In patients with dementia, the mixed delirium subtype is the most prevalent followed by the hypoactive, hyperactive, and nonmotor subtype. Motor subtypes of delirium may be triggered by clinical factors, including the use of venous and urinary catheters, and the use of antipsychotics. Future studies are necessary to provide further insights on the possible pathophysiology of delirium in patients with dementia and to address the optimization of the management of potential risk factors

Drug Prescription and Delirium in Older Inpatients: Results From the Nationwide Multicenter Italian Delirium Day 2015-2016

Objective: This study aimed to evaluate the association between polypharmacy and delirium, the association of specific drug categories with delirium, and the differences in drug-delirium association between medical and surgical units and according to dementia diagnosis. Methods: Data were collected during 2 waves of Delirium Day, a multicenter delirium prevalence study including patients (aged 65 years or older) admitted to acute and long-term care wards in Italy (2015-2016); in this study, only patients enrolled in acute hospital wards were selected (n = 4,133). Delirium was assessed according to score on the 4 "A's" Test. Prescriptions were classified by main drug categories; polypharmacy was defined as a prescription of drugs from 5 or more classes. Results: Of 4,133 participants, 969 (23.4%) had delirium. The general prevalence of polypharmacy was higher in patients with delirium (67.6% vs 63.0%, P =.009) but varied according to clinical settings. After adjustment for confounders, polypharmacy was associated with delirium only in patients admitted to surgical units (OR = 2.9; 95% CI, 1.4-6.1). Insulin, antibiotics, antiepileptics, antipsychotics, and atypical antidepressants were associated with delirium, whereas statins and angiotensin receptor blockers exhibited an inverse association. A stronger association was seen between typical and atypical antipsychotics and delirium in subjects free from dementia compared to individuals with dementia (typical: OR = 4.31; 95% CI, 2.94-6.31 without dementia vs OR = 1.64; 95% CI, 1.19-2.26 with dementia; atypical: OR = 5.32; 95% CI, 3.44-8.22 without dementia vs OR = 1.74; 95% CI, 1.26-2.40 with dementia). The absence of antipsychotics among the prescribed drugs was inversely associated with delirium in the whole sample and in both of the hospital settings, but only in patients without dementia. Conclusions: Polypharmacy is significantly associated with delirium only in surgical units, raising the issue of the relevance of medication review in different clinical settings. Specific drug classes are associated with delirium depending on the clinical setting and dementia diagnosis, suggesting the need to further explore this relationship