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Rossi, C.

Publications and source records attributed to Rossi, C..

At least 19 recordsLinked to original sources

Assessing the impact of data uncertainty on remote sensing estimation of plant functional diversity

Remote sensing mapping of plant functional diversity (PFD) is increasingly used at the science-policy interface. Yet assessments of uncertainty and quality standards for these products are seldom provided, as the impact of measurement uncertainty on PFD estimates, i.e., the variability across pixels, is still poorly understood. We use trait maps and hyperspectral imagery simulations from the Biodiversity Observing System Simulation Experiment (BOSSE) to assess the impact of different types of uncertainty on the estimation PFD. Results show that uncertainties stemming from random errors affect the estimation of PFD (up to three times) more than those arising from systematic errors, with spectral and spatial error correlation reducing their impact. Standardization computing PFD metrics reduces systematic errors, making in-situ-measured plant traits and remote sensing reflectance factors more robust estimators of PFD than other remote sensing proxies derived from reflectance (e.g., spectral indices or optical traits). The impact of uncertainty propagation from reflectance factors to these often-preferred secondary proxies increases with their complexity. Nonetheless, trait uncertainty can spuriously diminish differences between PFD derived from the ground (plant traits) and satellite imagery, as it can reduce uncertainty-induced or inherent biases between the PFD metrics computed from each trait (plant or spectral). This study provides new understanding of how uncertainty propagates into PFD estimates; this knowledge is relevant for optimizing the selection and defining quality requirements for PFD estimation. It also suggests that random and systematic uncertainties should be quantified separately at the reflectance factor level to guide their use and interpretation in PFD analysis.

ecology↗

Mediterranean dispersal imposed bottlenecks in Neolithic sheep and goats

The Neolithic period in western Eurasia involved major dispersal events, including the translocation of livestock into Europe. These domestic animal translocations likely featured founder effects, fundamentally reshaping their genetic landscape. One well-known example is the Mediterranean dispersal, hypothesised to involve rapid maritime translocation with small founding herds, yet the genetic consequences for the livestock themselves remain poorly understood. To investigate this, we generated 12 palaeogenomes of sheep and goat from La Draga and Cova de lAvellaner, and coanalyzed these with other Neolithic Mediterranean assemblages, including 4 additional novel genomes. We observe a significantly lower genetic diversity and higher runs of homozygosity (ROH) in Iberian sheep and goat populations compared to other ancient European and southwest Asian populations. We quantify the magnitude of the bottleneck in goats at [~]205 Ne, highlighting the severity of the founder event. We further identify species-specific demographic trajectories: goats experienced a severe and prolonged bottleneck, likely driven by regional isolation within the western Mediterranean, intensive exploitation strategies, and small initial founding herds, while sheep were likely more frequently exchanged across the region. Lastly, identity-by-descent (IBD) indicates connectivity along the Mediterranean coast compatible with a cabotage model. This suggests that seaways facilitated rapid initial dispersal but not sustained livestock transfer from southwest Asia, shaping the genetic foundation of Iberian livestock herds. SignificanceThe Neolithic transition in western Eurasia fundamentally restructured human societies, yet the genetic consequences for translocated livestock remain poorly characterized. Analyzing 16 novel palaeogenomes from Mediterranean Neolithic sheep and goats, we demonstrate that maritime dispersal imposed severe founder effects on early Iberian livestock, reducing effective population sizes to as low as [~]205 in goats. Species-specific demographic trajectories reveal that goats experienced prolonged genetic isolation within the western Mediterranean, while sheep maintained broader regional connectivity. Identity-by-descent analyses support a cabotage model of coastal dispersal, indicating that Mediterranean seaways facilitated rapid initial colonization but not sustained genetic exchange with southwest Asian source populations. These findings reveal that the earliest livestock introductions into Europe were demographically constrained events whose genetic signatures persist in the foundations of Iberian pastoral heritage.

genomics↗

First Comprehensive Examination of the Molecular Phylogenetics of Saki Monkeys, Genus Pithecia Desmarest, 1804, Reveals an Unexpectedly Low Taxonomic Diversity

Saki monkeys (Pithecia) are found exclusively in the Amazon, ranging from the Guiana Shield in the east to the Andean foothills in the west. The taxonomy of this genus is complex due to indeterminate type localities, numerous synonyms, sexual dichromatism and considerable geographical diversity in coat colour patterns. Previous assessments have indicated two to four species and a variable few subspecies based on morphological analyses of museum specimens. Just two species have been consistently recognised--Pithecia pithecia and Pithecia monachus. This study presents the first comprehensive molecular phylogeny of the genus, using mitochondrial cytochrome b sequences from 137 individuals across their range and a ddRADseq genomic analysis on 34 individuals. The phylogenetic results revealed three main clades: (1) Guiana Shield sakis, (2) Sedimentary Basin and Brazilian Shield sakis, and (3) a basal P. albicans south of the Rio Solimoes. The ddRADseq data further clarified species boundaries and relationships, identifying six distinct species: P. chrysocephala and P. pithecia sensu Hershkovitz (1987) on the Guiana Shield; P. albicans in central Amazonia south of the Rio Solimoes; P. monachus in western Amazonia; P. irrorata between the rios Purus, Tapajos, and Juruena; and P. vanzolinii in a limited area east of the Rio Jurua.

zoology↗

Metabolic resilience rules sex-specific pain recovery during hormonal aging: a multi-omics analysis of neuropathy in mice.

Biological aging and sex interact to shape systemic metabolism, yet their role in chronic pain resolution remains unexplored. We hypothesized that metabolic resilience -- the ability to flexibly switch fuel sources and maintain energy homeostasis -- rules successful recovery from nerve injury in a sex-dependent manner during aging. In 12-month-old male and female mice -- corresponding to the perimenopausal phase in females and the onset of hormonal decline in both sexes -- we induced sciatic nerve chronic constriction injury and performed multi-omics profiling during Wallerian degeneration, a phase known to trigger long-term neurobiological remodeling. Aging females exhibited early activation of fatty acid oxidation, increased resting energy expenditure, upregulation of mitochondrial redox enzymes and circulating progesterone and corticosterone. Proteomic and metabolomic analysis revealed pentose phosphate pathway enrichment and gluconeogenesis, supporting redox balance and metabolic flexibility. Conversely, males displayed persistent glycolytic reliance, long-chain acylcarnitine accumulation, suppression of adiponectin and PPAR{gamma}, indicating metabolic inflexibility. Longitudinal behavioral analysis revealed that aging females recovered earlier and more fully than aging males, reversing the pattern previously shown in our adult mouse study, where females developed persistent pain and males recovered rapidly. These patterns highlight a non-linear, sex-specific interaction between biological aging and injury response, where hormonal decline reprograms the metabolic trajectory and reshapes pain outcomes. Metabolic resilience governs sex-specific recovery following nerve injury by directing early systemic adaptations that precede and predict long-term pain trajectories. These results define mechanistically anchored, sex- and age-specific biomarkers, and propose preclinical targets for timely, personalized interventions in age-associated neuropathic pain.

neuroscience↗

Adaptive learning of a naturalistic bimanual task in virtual reality

Most purposeful movements require the coordinated control of both hands, yet motor adaptation studies rely on highly constrained tasks that bear little resemblance to everyday bimanual actions. Here, we investigated how task demands shape control strategies during adaptation in a naturalistic bimanual object manipulation task. We tested 73 participants who lifted a virtual plate while we systematically distorted visual feedback of their right hands movement, creating a sensory conflict between arms. Compared to unimanual, bimanual lifting shifted learning away from feedforward adaptation toward use of feedback control--participants moved more slowly with gradual speed scaling, developed compensatory hand adjustments, and showed smaller aftereffects. Relaxing precision demands improved success and reduced feedback reliance, while minimizing interlimb sensory conflict diminished compensatory adjustments and restored plate aftereffects to unimanual levels. Bimanual contexts create distinct learning environments where precision demands and interlimb sensory conflict independently shape control strategy; this may inform bimanual training protocols.

neuroscience↗

Weakened prefrontal activation dynamics associated with slowed information processing speed in multiple sclerosis

Information processing speed (IPS) is a core cognitive deficit in people with multiple sclerosis (PwMS). Previous efforts have associated IPS performance to frontal regions, but were constrained by limited temporal resolution. In this work, we employed a data-driven method, the time delay embedded-hidden Markov model (TDE-HMM), to identify task-specific states that are spectrally defined with distinct temporal and spatial profiles. We used magnetoencephalographic (MEG) data recorded while healthy controls and PwMS performed a cognitive task designed to capture IPS, the Symbol Digit Modalities Test (SDMT). The TDE-HMM identified five task-relevant states, supporting a tri-factor contribution to IPS: sensory speed (occipital visual detection and processing), cognitive speed (prefrontal executive and frontoparietal attention shift), and motor speed (sensorimotor). We observed reduced prefrontal and increased frontoparietal activation in PwMS, which correlated with offline SDMT performance. This work can drive future research for MS treatments targeting IPS improvements.

neuroscience↗

Population structure and domestication history of the Javan banteng (Bos javanicus javanicus)

The domestication of the banteng in Southeast Asia is one of the Worlds least known livestock domestications, yet a vital component of the agricultural system in Indonesia and surrounding countries. Here we generated the first reference genome of the banteng and used it to analyze a set of 78 resequenced wild and domesticated bantengs, including 19 newly generated whole-genome sequenced samples of which three are historical samples. We found low heterozygosity and significant differentiation, the latter primarily driven by recent genetic drift and inbreeding in two populations, and clearly attributable to anthropogenically driven founder events or ex-situ breeding. Population structure when excluding these two populations was limited, and we found that the evolutionary divergence between wild and domestic banteng is moderate (FST = 0.14), relatively young (10,356 years), and with post-divergence gene flow. We found only weak signals of a domestication bottleneck between [~]6100-2900 years ago, and genetic diversity is on average higher in domestic than in wild banteng. Despite the soft domestication history, we found 56 candidate genes under selection during domestication, with the leptin receptor gene (LEPR) of particular interest due to the robust selection signal across methods, and its known association to metabolism, obesity and energy homeostasis. Finally, genetic load estimation revealed that Bali cattle in Australia have high realized load, while Bali cattle from Bali have high masked load. These findings provide the first genomic insights into an understudied bovine that is Critically Endangered in its wild form, and agriculturally important in its domesticated form.

evolutionary biology↗

EasyGrid: A versatile platform for automated cryo-EM sample preparation and quality control

Imaging biological macromolecules in their native state with single-particle cryo-electron microscopy (cryo-EM) or in situ cryo-electron tomography (cryo-ET) requires optimized approaches for the preparation and vitrification of biological samples. Here, we describe EasyGrid, a versatile technology enabling systematic, tailored and advanced sample preparation for cellular and structural biology. This automated, standalone platform combines in-line plasma treatment, microfluidic dispensing, blot-less sample spreading, jet-based vitrification and on-the-fly grid quality control using light interferometry to streamline cryo-EM sample optimization. With EasyGrid, we optimized grid preparation for different purified macromolecular complexes and subsequently determined their structure with cryo-EM. We also demonstrated how the platform allows better vitrification of large, mammalian cells compared to standard plunge-freezing. Automated sample preparation with EasyGrid establishes an advanced, high-throughput platform for both single-particle cryo-EM and cellular cryo-ET sample preparation.

molecular biology↗

Stimulus-related modulation in the 1/f spectral slope suggests an impaired inhibition of irrelevant information in people with multiple sclerosis

BackgroundMultiple sclerosis (MS) is an inflammatory and neurodegenerative disease characterized by neuronal and synaptic loss, resulting in an imbalance of excitatory and inhibitory synaptic transmission. MS leads to cognitive impairment such as reduced information processing speed and impaired working memory (WM). Recent studies have suggested that the 1/f slope of EEG/MEG power spectra can be associated with the excitation/inhibition (E/I) balance. A normal E/I balance is crucial for normal information processing and working memory. MethodsWe analyzed magnetoencephalographic (MEG) recordings of 38 healthy control subjects and 79 people with multiple sclerosis (pwMS) while performing an n-back working task. We computed and compared the steepness of the 1/f spectral slope through the FOOOF algorithm in the time windows [-1 0] and [0 1] s peristimulus time for both target and distractor stimulus for each brain parcel and for different working memory loads (0-back, 1-back, 2-back). ResultsThe spectral slope was significantly steeper after the stimulus onset and was correlated with reaction time. We also observed a steeper 1/f slope after distractor stimuli in healthy subjects compared to pwMS. Finally, we observed significant correlations between the 1/f spectral slope modulation and visuospatial working memory functioning in both healthy subjects and pwMS. ConclusionOur findings are consistent with an increased inhibition following stimulus onset. In pwMS, this increase is reduced, suggesting dysfunctional inhibition of irrelevant information. Finally, this impaired modulation is significantly associated with a pencil-paper test of visuospatial working memory. HighlightsO_LIThe flatter 1/f slope after distractor stimuli in people with multiple sclerosis (pwMS) compared to healthy subjects suggests a less pronounced inhibition of irrelevant information in pwMS. C_LIO_LIThe significantly flatter 1/f slope was observed in the left inferior dorsal prefrontal cortex of pwMS in both 1-back and 2-back conditions. This particular brain parcel is known for its key role in motor planning, and the maintenance of sustained attention and working memory and executive functions. C_LIO_LIA steeper 1/f slope after target and distractor stimuli suggests an increase in inhibition following stimulus onset in both healthy controls (HCs) and people with MS (pwMS). C_LIO_LIThe 1/f slope modulation correlates with visuospatial working memory performance. C_LI

neuroscience↗

Impaired activation of the prefrontal executive network during working memory processing in multiple sclerosis

AbstractIn multiple sclerosis (MS), working memory (WM) impairment occurs soon after disease onset and significantly affects the patients quality of life. Functional imaging research in MS aims to investigate the neurophysiological underpinnings of WM impairment. In this context, we utilized a data-driven technique, the time delay embedded- hidden Markov model (TDE-HMM), to extract spectrally defined functional networks in magnetoencephalographic (MEG) data acquired during a WM visual-verbal n-back task. We observed that two networks show an altered activation in RR-MS patients. First, the activation of an early theta prefrontal network linked to stimulus encoding and attentional control significantly decreased in RR-MS compared to HC. This diminished activation correlated with reduced accuracy in task performance in the MS group, suggesting an impaired encoding and learning process. Secondly, a frontoparietal network characterized by beta coupling is activated between 300 and 600 ms after stimulus onset; this resembles the characteristic event-related P300, a cognitive marker extensively explored in EEG studies. The activation of this network is amplified in patients treated with benzodiazepine, in line with the well-known benzodiazepine-induced beta enhancement. Altogether, the TDE-HMM technique extracted task-relevant functional networks showing disease-specific and treatment- related alterations, revealing potential new markers to assess and track WM impairment in MS. HighlightsO_LIWe decomposed the brain dynamics underlying a WM n-back task in data-driven, spectrally defined whole-brain networks in both healthy controls and people with relapsing-remitting-MS (pwMS). C_LIO_LIPwMS showed a significantly decreased activation of an early theta prefrontal network linked to stimulus encoding and attentional control. C_LIO_LIThe weaker activation of this prefrontal theta network is correlated with worse task performance. C_LIO_LIA beta frontoparietal network with a P300-like temporal evolution was significantly modulated by the use of benzodiazepines. C_LIO_LIThe model distinguished disease-induced and treatment-induced dynamic network alterations. C_LI

neuroscience↗

"Flower power": how flowering affects spectral diversity metrics and their relationship with plant diversity

Biodiversity monitoring is constrained by cost- and labour-intensive field sampling methods. Increasing evidence suggests that remotely sensed spectral diversity (SD) is linked to plant diversity, holding promise for monitoring applications. However, studies testing such a relationship reported conflicting findings, especially in challenging ecosystems such as grasslands, due to their high temporal dynamism and variety. It follows that a thorough investigation of the key factors, such as the metrics applied (i.e., continuous, categorical) and phenology (e.g., flowering), influencing such a relationship is necessary. Thus, this study aims to assess the applicability of SD for plant diversity monitoring at the local scale by testing six different SD metrics while considering the effect of the presence of flowering on the relationship and resampling the original data to assess how spatial resolution affects the results. Taxonomic diversity was calculated based on data collected in 159 plots with 1.5 m x1.5 m experimental mesic grassland communities. Spectral information was collected using a UAV-borne sensor measuring reflectance across six bands in the visible and near-infrared range at [~]2 cm spatial resolution. Our results show that, in the presence of flowering, the relationship is significant and positive only when SD is calculated using categorical metrics. Despite the observed significance, the variance explained by the models had very low values, with no evident differences when resampling spectral data to coarser pixel sizes. Such findings suggest that new insights into the possible confounding effects on the SD[~]plant diversity in grassland communities are needed to use SD for monitoring purposes.

ecology↗

Automatic learning mechanisms for flexible human locomotion.

Movement flexibility and automaticity are necessary to successfully navigate different environments. When encountering difficult terrains such as a muddy trail, we can change how we step almost immediately so that we can continue walking. This flexibility comes at a cost since we initially must pay deliberate attention to how we are moving. Gradually, after a few minutes on the trail, stepping becomes automatic so that we do not need to think about our movements. Canonical theory indicates that different adaptive motor learning mechanisms confer these essential properties to movement: explicit control confers rapid flexibility, while forward model recalibration confers automaticity. Here we uncover a distinct mechanism of treadmill walking adaptation - an automatic stimulus-response mapping - that confers both properties to movement. The mechanism is flexible as it learns stepping patterns that can be rapidly changed to suit a range of treadmill configurations. It is also automatic as it can operate without deliberate control or explicit awareness by the participants. Our findings reveal a tandem architecture of forward model recalibration and automatic stimulus-response mapping mechanisms for walking, reconciling different findings of motor adaptation and perceptual realignment.

neuroscience↗

Lost in HELLS: disentangling the mystery of SALNR existence in senescence cellular models

Long non-coding RNAs (lncRNAs) have emerged as key regulators of cellular senescence by transcriptionally and post-transcriptionally modulating the expression of many important genes involved in senescence-associated pathways and processes. Among the different lncRNAs associated to senescence, Senescence Associated Long Non-coding RNA (SALNR) was found to be down-regulated in different cellular models of senescence. Since its release in 2015, SALNR has not been annotated in any database or public repository, and no other experimental data have been published. The SALNR sequence is located on the long arm of chromosome 10, at band 10q23.33, and it overlaps the 3 end of the HELLS gene. This investigation helped to unravel the mystery of the existence of SALNR by analyzing publicly available short- and long-read RNA sequencing data sets and RT-PCR analysis in human tissues and cell lines. Additionally, the expression of HELLS has been studied in cellular models of replicative senescence, both in silico and in vitro. Our findings, while strongly questioning the actual existence of SALNR as an independent transcript, support the expression of a predicted HELLS isoform entirely covering the SALNR genomic region. Furthermore, we observed a strong down-regulation of HELLS in senescent cells versus proliferating cells, supporting its role in the senescence and aging process. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=106 SRC="FIGDIR/small/526712v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1178eb8org.highwire.dtl.DTLVardef@19ae822org.highwire.dtl.DTLVardef@fe1c49org.highwire.dtl.DTLVardef@f31ae1_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

The spectral slope as a marker of excitation/inhibition ratio and cognitive functioning in multiple sclerosis

BackgroundMultiple sclerosis (MS) is a neurodegenerative disease characterized by neuronal and synaptic loss, resulting in an imbalance of excitatory and inhibitory synaptic transmission and potentially cognitive impairment. Current methods for measuring the excitation/inhibition (E/I) ratio are mostly invasive, but recent research combining neurocomputational modeling with measurements of local field potentials has indicated that the slope with which the power spectrum of neuronal activity captured by electro- and/or magnetoencephalography rolls off, is a non-invasive biomarker of the E/I ratio. A steeper roll- off is associated with a stronger inhibition. This novel method can be applied to assess the E/I ratio in people with multiple sclerosis (pwMS), detect the effect of medication such as benzodiazepines, and explore its utility as a biomarker for cognition. MethodsWe recruited 44 healthy control subjects and 95 people with multiple sclerosis (pwMS) who underwent resting-state magnetoencephalographic recordings. The 1/f spectral slope of the neural power spectra was calculated for each subject and for each brain region. ResultsAs expected, the spectral slope was significantly steeper in pwMS treated with benzodiazepines (BZDs) compared to pwMS not receiving BZDs (p = 0.01). In the sub-cohort of pwMS not treated with BZDs, we observed a steeper slope in cognitively impaired pwMS compared to cognitively preserved pwMS (p = 0.01) and healthy subjects (p = 0.02). Furthermore, we observed a significant correlation between 1/f spectral slope and verbal and spatial working memory functioning in the brain regions located in the prefrontal and parietal cortex. ConclusionsIn this study, we highlighted the value of the spectral slope in MS by quantifying the effect of benzodiazepines and by putting it forward as a potential biomarker of cognitive deficits in pwMS.

neuroscience↗

A novel description of the network dynamics underpinning working memory

Working memory (WM) plays a central role in cognition, prompting neuroscientists to investigate its functional and structural substrates. The WM dynamic recruits large-scale frequency-specific brain networks that unfold over a few milliseconds - this complexity challenges traditional neuroimaging analyses. In this study, we unravel the WM network dynamics in an unsupervised, data-driven way, applying the time delay embedded-hidden Markov model (TDE-HMM). We acquired MEG data from 38 healthy subjects performing an n-back working memory task. The TDE-HMM model inferred four task-specific states with each unique temporal (activation), spectral (phase-coherence connections), and spatial (power spectral density distribution) profiles. A theta frontoparietal state performs executive functions, an alpha temporo-occipital state maintains the information, and a broad-band and spatially complex state with an M300 temporal profile leads the retrieval process and motor response. The HMM states can be straightforwardly interpreted within the neuropsychological multi-component model of WM, significantly improving the comprehensive description of WM. HighlightsO_LIWorking memory recruits different frequency-specific brain networks that wax and wane at a millisecond scale. C_LIO_LIThrough the time-delay embedded hidden (TDE-HMM) we are able to extract data-driven functional networks with unique spatial, spectral, and temporal profiles. C_LIO_LIWe demonstrate the existence of four task-specific brain networks that can be interpreted within the well-known Baddeleys multicomponent model of working memory. C_LIO_LIThis novel WM description unveils new features that will lead to a more in-depth characterization of cognitive processes in MEG data. C_LI

neuroscience↗

A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics.

AO_SCPLOWBSTRACTC_SCPLOWDirekli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a [~]14,000 year old 2.59X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten "Taurasian tur" likely survived Late Pleistocene climatic change in a Taurus Mountain refugia and its genomic fate is unknown.

genomics↗

A highly endemic area of Echinococcus multilocula is identified through a comparative re-assessment of prevalence in red fox (Vulpes vulpes), Alto Adige (Italy: 2019-2020)

BackgroundSurveillance of E. multilocularis at the edge of its range is hindered by fragmented distributional patterns and low prevalence and burden in definitive hosts. Thus, tests with adequate levels of sensitivity are especially important for discriminating between infected and non-infected areas. AimWe reassessed the prevalence of E. multilocularis at the southern border of its distribution in Alto Adige (Italy), to improve surveillance in wildlife and provide more accurate estimates of exposure risk. MethodsWe compared results from the diagnostic test currently implemented for surveillance (based on Coproscopy+Multiplex PCR - CMPCR), against a real-time quantitative PCR (qPCR) for 235 fox faeces collected in 2019-2020. The performances of the two tests were estimated using a scraping technique (SFCT) as the gold standard applied to the small intestines of a subsample (n=123) of the same hosts. True prevalence was calculated and sample size required by each faecal test for the detection of the parasite was then estimated. ResultsTrue prevalence of E. multilocularis in foxes (14.3%) was definitely higher than reported in the last decade (never >5% from 2012 to 2018). The qPCR also had a higher sensitivity (83%) compared to CMPCR (21%). Agreement with the gold standard was far higher for qPCR (0.816) than CMPCR (0.298) as well, determining a smaller sample size required to detect the disease. ConclusionsAlto Adige should be considered a highly endemic area. Surveillance at the edges of E. multilocularis distribution should adopt qPCR diagnostics on definitive hosts on a small geographic scale. AUTHOR SUMMARYEchinococcus multilocularis is an intestinal flatworm, whose adult stage in Europe is harboured mainly by the red fox (Vulpes vulpes), which spreads parasites eggs by faeces. This parasite is the agent of a severe and potentially lethal zoonosis, the alveolar echinococcosis, affecting humans after accidental ingestion of parasites eggs. In the Italian Alpine area, which represents the southernmost border of E. multilocularis European range, surveillance is hindered by a fragmented distributional pattern, where presence in foxes has been consistently reported only in few isolated foci in Alto Adige (Bolzano province - Italy) of low prevalence. In order to improve the efficiency of monitoring efforts, we tested the performances of two diagnostic protocols on fox faeces (sedimentation, filtration, counting technique followed by standard PCR, and whole stool real-time PCR) against a benchmark technique on fox intestines (scraping, filtration, counting technique - considered as the gold standard). This allowed not only to determine qPCR as a far more sensitive and sample-efficient diagnostic tool for E. multilocularis detection in marginally affected areas, but also to re-assess its prevalence in Alto Adige, which should be considered a highly endemic area. Consequent actions in the field and modifications in the surveillance strategy should be therefore considered.

molecular biology↗

Exceptional ancient DNA preservation and fibre remains of a Sasanian saltmine sheep mummy in Chehrabad, Iran

Mummified remains have long attracted interest as a potential source of ancient DNA. However, mummification is a rare process that requires an anhydrous environment to rapidly dehydrate and preserve tissue before complete decomposition occurs. We present the whole genome sequences of a [~]1600 year old naturally mummified sheep recovered from Chehr[a]b[a]d, a salt mine in northwestern Iran. Comparative analyses of published ancient sequences revealed remarkable DNA integrity of this mummy. Hallmarks of postmortem damage, fragmentation and hydrolytic deamination, are substantially reduced, likely due to the high-salinity of this taphonomic environment. Metagenomic analyses reflect the profound influence of high salt content on decomposition; its microbial profile is predominated by halophilic archaea and bacteria, possibly contributing to the preservation of this sample. Applying population genomic analyses we find consistent clustering of this sheep with Southwest Asian modern breeds, suggesting ancestry continuity. Genotyping of a locus influencing the woolly phenotype showed the existence of an ancestral "hairy" allele in this sheep, consistent with hair fibre imaging, further elucidating Sasanian-period animal husbandry.

genomics↗