New insights into sex chromosome evolution in anole lizards (Reptilia, Dactyloidae).

Anoles are a clade of iguanian lizards that underwent an extensive radiation between 125 and 65 million years ago. Their karyotypes show wide variation in diploid number spanning from 26 (Anolis evermanni) to 44 (A. insolitus). This chromosomal variation involves their sex chromosomes, ranging from simple systems (XX/XY), with heterochromosomes represented by either micro- or macrochromosomes, to multiple systems (X1X1X2X2/X1X2Y). Here, for the first time, the homology relationships of sex chromosomes have been investigated in nine anole lizards at the whole chromosome level. Cross-species chromosome painting using sex chromosome paints from A. carolinensis, Ctenonotus pogus and Norops sagrei and gene mapping of X-linked genes demonstrated that the anole ancestral sex chromosome system constituted by microchromosomes is retained in all the species with the ancestral karyotype (2n = 36, 12 macro- and 24 microchromosomes). On the contrary, species with a derived karyotype, namely those belonging to genera Ctenonotus and Norops, show a series of rearrangements (fusions/fissions) involving autosomes/microchromosomes that led to the formation of their current sex chromosome systems. These results demonstrate that different autosomes were involved in translocations with sex chromosomes in closely related lineages of anole lizards and that several sequential microautosome/sex chromosome fusions lead to a remarkable increase in size of Norops sagrei sex chromosomes.

A ZZ/ZW sex chromosome system in the thick-tailed Gecko ( Underwoodisaurus milii; Squamata: Gekkota: Carphodactylidae), a member of the ancient gecko lineage.

Geckos (Gekkota) are a highly diversified group of lizards with an exceptional diversity in sex-determining systems. Despite this intriguing documented variability, data on sex determination in many lineages is still scarce. Here, we document the previously overlooked heteromorphic ZZ/ZW sex chromosomes in the thick-tailed gecko, Underwoodisaurus milii, a member of the ancient lineage of pygopodoid geckos. The finding of female heterogamety within pygopodoid geckos was unexpected, as until now only male heterogamety and environmental sex determination have been reported in this group, and female heterogamety was known only in distantly related gecko families separated from the pygopodoid geckos around 150 million years ago. The W chromosome in U. milii is highly heterochromatic and contains a large number of telomeric-like repeats comparable to around 50% of all telomeric-like sequences present in male genomes. The accumulation of these repeats might have been responsible for the considerable size expansion of the W chromosome in comparison to the Z chromosome. The heteromorphic ZZ/ZW sex chromosomes with accumulated telomeric-like repeats in the thick-tailed geckos further illustrate the exceptional diversity of sex-determining systems in geckos and add important information to our understanding of the evolution and phylogeny of sex-determining systems in reptiles.

Cytogenetic mapping of H1 histone and ribosomal RNA genes in hybrids between catfish species Pseudoplatystoma corruscans and Pseudoplatystoma reticulatum.

A physical chromosome mapping of the H1 histone and 5S and 18S ribosomal RNA (rRNA) genes was performed in interspecific hybrids of Pseudoplatystoma corruscans and P. reticulatum. The results showed that 5S rRNA clusters were located in the terminal region of 2 chromosomes. H1 histone and 18S ribosomal genes were co-localized in the terminal portion of 2 chromosomes (distinct from the chromosomes bearing 5S clusters). These results represent the first report of association between H1 histone and 18S genes in fish genomes. The chromosome clustering of ribosomal and histone genes was already reported for different organisms and suggests a possible selective pressure for the maintenance of this association.

A multicomponent intervention program to Prevent and Reduce AgItation and phySical rEstraint use in the ICU (PRAISE): study protocol for a multicenter, stepped-wedge, cluster randomized controlled trial.

BACKGROUND: Physical restraints remain to be commonly used in agitated intensive care unit (ICU) patients worldwide, despite a lack of evidence on efficacy and safety and reports of detrimental short and long-term consequences, such as prolonged delirium and a longer ICU length of stay. Physical restraint minimization approaches have focused mainly on educational strategies and other non-pharmacological interventions. Combining these interventions with goal-directed light sedation therapy if needed may play an important contributory role in further reducing the use of physical restraints. The aim of the study is to determine the effectiveness of a multicomponent intervention (MCI) program, combining person-centered non-pharmacological interventions with goal-directed light sedation, compared to physical restraints. METHODS: A multicenter stepped-wedge cluster randomized controlled trial will be conducted in six Dutch ICUs. A power calculation based total of 480 (expected to become) agitated adult patients will be included in 26 months with a subsequent 2-year follow-up. Patients included in the control period will receive standard care with the current agitation management protocol including physical restraints. Patients included in the intervention period will be treated with the MCI program, consisting of four components, without physical restraints: education of ICU professionals, identification of patients at risk for agitation, formulation of a multidisciplinary person-centered care plan including non-pharmacological and medical interventions, and protocolized goal-directed light sedation using dexmedetomidine. Primary outcome is the number of days alive and outside of the ICU within 28 days after ICU admission. Secondary outcomes include length of hospital stay; 3-, 12-, and 24-month post-ICU quality of life; physical (fatigue, frailty, new physical problems), mental (anxiety, depression, and post-traumatic stress disorder), and cognitive health; and 1-year cost-effectiveness. A process evaluation will be conducted. DISCUSSION: This will be the first multicenter randomized controlled trial determining the effect of a combination of non-pharmacological interventions and light sedation using dexmedetomidine compared to physical restraints in agitated ICU patients. The results of this study, including long-term patient-centered outcomes, will provide relevant insights to aid ICU professionals in the management of agitated patients. TRIAL REGISTRATION: NCT05783505, registration date 23 March 2023.

Differences in long-term outcomes between ICU patients with persistent delirium, non-persistent delirium and no delirium: A longitudinal cohort study.

PURPOSE: Determine differences in physical, mental and cognitive outcomes 1-year post-ICU between patients with persistent delirium (PD), non-persistent delirium (NPD) and no delirium (ND). MATERIALS AND METHODS: A longitudinal cohort study was performed in adult ICU patients of two hospitals admitted between July 2016-February 2020. Questionnaires on physical, mental and cognitive health, frailty and QoL were completed regarding patients' pre-ICU health status and 1-year post-ICU. Delirium data were from patients' total hospital stay. Patients were divided in PD (≥14 days delirium), NPD (<14 days delirium) or ND patients. RESULTS: 2400 patients completed both questionnaires, of whom 529 (22.0%) patients developed delirium; 35 (6.6%) patients had PD and 494 (93.4%) had NPD. Patients with delirium (PD or NPD) had worse outcomes in all domains compared to ND patients. Compared to NPD, more PD patients were frail (34.3% vs. 14.6%, p = 0.006) and fatigued (85.7% vs. 61.1%, p = 0.012). After adjustment, PD was significantly associated with long-term cognitive impairment only (aOR 3.90; 95%CI 1.31-11.63). CONCLUSIONS: Patients with PD had a higher likelihood to develop cognitive impairment 1-year post-ICU compared to NPD or ND. Patients with PD and NPD were more likely to experience impairment on all health domains (i.e. physical, mental and cognitive), compared to ND patients.

Fruit and seed traits and vertebrate-fruit interactions of tree species occurring in Guyana, Suriname, and French Guiana.

Seed dispersal is widely considered an important mechanism for the conservation of plant diversity. In tropical regions, over 80% of woody plant species are dispersed by vertebrates, often through the consumption of fruits. Our understanding of what drives interactions between vertebrates and fruits is limited. Through a systematic literature search, we compiled a database of fruit and seed traits and vertebrate-fruit interactions for tree and vertebrate species occurring in the Guianas, with the aim of facilitating research into seed dispersal and seed predation of tree species in the Guianas. The database was compiled by extracting data from 264 published sources. It consists of 21,082 records, of which 19,039 records contain information about 19 different fruit and seed traits belonging to 1622 different tree species. The other 2043 records contain information on vertebrate-fruit interactions between 161 vertebrate species and 464 tree species. Our analyses showed a taxonomic bias, particularly in the interaction data, toward large-bodied vertebrates, with most interactions recorded for the bearded saki (Chiropotes chiropotes), followed by the lowland tapir (Tapirus terrestris). For plants we found an overrepresentation of the Sapotaceae and Moraceae families and an underrepresentation of the Rubiaceae, Myrtaceae, and Lauraceae families in the interactions. There are no copyright restrictions on the data set; please cite this publication when using these data.

Defaunation changes leaf trait composition of recruit communities in tropical forests in French Guiana.

Hunting impacts tropical vertebrate populations, causing declines of species that function as seed dispersers and predators, or that browse seedlings and saplings. Whether and how the resulting reductions in seed dispersal, seed predation, and browsing translate to changes in the tree composition is poorly understood. Here, we assess the effect of defaunation on the functional composition of communities of tree recruits in tropical rainforests in French Guiana. We selected eight sites along a gradient of defaunation, caused by differences in hunting pressure, in otherwise intact old-growth forests in French Guiana. We measured shifts in functional composition by comparing leaf and fruit traits and wood density between tree recruits (up to 5 cm diameter at breast height) and adults, and tested whether and how these compositional shifts related to defaunation. We found a positive relationship with defaunation for shifts in specific leaf area, a negative relationship for shifts of leaf toughness and wood density, and a weak relationship for shifts in fruit traits. Our results suggest that the loss of vertebrates affects ecological processes such as seed dispersal and browsing, of which browsing remains understudied. Even though these changes sometimes seem minor, together they result in major shifts in forest composition. These changes have long-term ramifications that may alter forest dynamics for generations.

The evolution of marsupial and monotreme chromosomes.

Marsupial and monotreme mammals fill an important gap in vertebrate phylogeny between reptile-mammal divergence 310 million years ago (mya) and the eutherian (placental) mammal radiation 105 mya. They possess many unique features including their distinctive chromosomes, which in marsupials are typically very large and well conserved between species. In contrast, monotreme genomes are divided into several large chromosomes and many smaller chromosomes, with a complicated sex chromosome system that forms a translocation chain in male meiosis. The application of molecular cytogenetic techniques has greatly advanced our understanding of the evolution of marsupial chromosomes and allowed the reconstruction of the ancestral marsupial karyotype. Chromosome painting and gene mapping have played a vital role in piecing together the puzzle of monotreme karyotypes, particularly their complicated sex chromosome system. Here, we discuss the significant insight into karyotype evolution afforded by the combination of recently sequenced marsupial and monotreme genomes with cytogenetic analysis, which has provided a greater understanding of the events that have shaped not only marsupial and monotreme genomes, but the genomes of all mammals.

Chromosome mapping of H1 histone and 5S rRNA gene clusters in three species of Astyanax (Teleostei, Characiformes).

We report here on the physical mapping of the H1 histone genes (hisDNA) and the 5S ribosomal DNA (rDNA) in 3 Neotropical fish species of the genus Astyanax(A. altiparanae, A. bockmanni and A. fasciatus) and the comparative analysis of the chromosomes bearing these genes. Nucleotide analyses by sequencing of both genes were also performed. The distribution of the H1 histone genes was more conserved than that of the rRNA genes, since these were always located in the pericentromeric regions of 2 chromosome pairs. 5S rDNA was found on one of the pairs that presented an H1 histone cluster; this seems to be a conserved chromosomal feature of the genus Astyanax. In addition, individuals of A. bockmanni and A. fasciatus showed clusters of 5S rDNA on 1 pair of acrocentric chromosomes, not found in A. altiparanae. The results obtained by chromosome mapping as well as by sequencing of both genes showed that A.bockmanni is more closely related to A. fasciatus than to A. altiparanae. The results allow the characterization of cytogenetic markers for improved elucidation of the processes involved in karyotype differentiation of fish genomes.

Factors associated with a persistent delirium in the intensive care unit: A retrospective cohort study.

PURPOSE: To explore differences between ICU patients with persistent delirium (PD), non-persistent delirium (NPD) and no delirium (ND), and to determine factors associated with PD. MATERIALS AND METHODS: Retrospective cohort study including all ICU adults admitted for ≥12 h (January 2015-February 2020), assessable for delirium and followed during their entire hospitalization. PD was defined as ≥14 days of delirium. Factors associated with PD were determined using multivariable logistic regression analysis. RESULTS: Out of 10,295 patients, 3138 (30.5%) had delirium, and 284 (2.8%) had PD. As compared to NPD (n = 2854, 27.7%) and ND (n = 7157, 69.5%), PD patients were older, sicker, more physically restrained, longer comatose and mechanically ventilated, had a longer ICU and hospital stay, more ICU readmissions and a higher mortality rate. Factors associated with PD were age (adjusted odds ratio [aOR] 1.03; 95% confidence interval [CI] 1.02-1.04); emergency surgical (aOR 1.84; 95%CI 1.26-2.68) and medical (aOR 1.57; 95%CI 1.12-2.21) referral, mean Sequential Organ Failure Assessment (SOFA) score before delirium onset (aOR 1.18; 95%CI 1.13-1.24) and use of physical restraints (aOR 5.02; 95%CI 3.09-8.15). CONCLUSIONS: Patients with persistent delirium differ in several characteristics and had worse short-term outcomes. Physical restraints were the most strongly associated with PD.

The unique sex chromosome system in platypus and echidna.

A striking example of the power of chromosome painting has been the resolution of the male platypus karyotype and the pairing relationships of the chain often sex chromosomes. We have extended our analysis to the nine sex chromosomes of the male echidna. Cross-species painting with platypus shows that the first five chromosomes in the chain are identical in both, but the order of the remainder are different and, in each species, a different autosome replaces one of the five X chromosomes. As the therian X is homologous mainly to platypus autosome 6 and echidna 16, and as SRY is absent in both, the sex determination mechanism in monotremes is currently unknown. Several of the X and Y chromosomes contain genes orthologous to those in the avian Z but the significance of this is also unknown. It seems likely that a novel testis determinant is carried by a Y chromosome common to platypus and echidna. We have searched for candidates for this determinant among the many genes known to be involved in vertebrate sex differentiation. So far fourteen such genes have been mapped, eleven are autosomal in platypus, two map to the differential regions of X chromosomes, and one maps to a pairing segment and is likewise excluded. Search for the platypus testis-determining gene continues, and the extension of comparative mapping between platypus and birds and reptiles may shed light on the ancestral origin of monotreme sex chromosomes.

Unobtrusive monitoring: Statistical dissemination latency estimation in Bitcoin's peer-to-peer network.

The cryptocurrency system Bitcoin uses a peer-to-peer network to distribute new transactions to all participants. For risk estimation and usability aspects of Bitcoin applications, it is necessary to know the time required to disseminate a transaction within the network. Unfortunately, this time is not immediately obvious and hard to acquire. Measuring the dissemination latency requires many connections into the Bitcoin network, wasting network resources. Some third parties operate that way and publish large scale measurements. Relying on these measurements introduces a dependency and requires additional trust. This work describes how to unobtrusively acquire reliable estimates of the dissemination latencies for transactions without involving a third party. The dissemination latency is modelled with a lognormal distribution, and we estimate their parameters using a Bayesian model that can be updated dynamically. Our approach provides reliable estimates even when using only eight connections, the minimum connection number used by the default Bitcoin client. We provide an implementation of our approach as well as datasets for modelling and evaluation. Our approach, while slightly underestimating the latency distribution, is largely congruent with observed dissemination latencies.

Patterns of chromosomal evolution in Sigmodon, evidence from whole chromosome paints.

Of the superfamily Muroidea (31 genera, 1578 species), the Sigmodontinae (74 genera, 377 species) is the second largest subfamily in number of species and represents a significant radiation of rodent biodiversity. Only 2 of the 74 genera are found in both North and South America (Sigmodon and Oryzomys) and the remainder are exclusively from South America. In recent molecular studies, the genus Sigmodon (Cricetidae, Sigmodontinae) has been considered sister to many other South American Sigmodontines [Steppan et al., 2004]. We examine the chromosomal evolution of 9 species of Sigmodon utilizing chromosomal paints isolated from S. hispidus, proposed to be similar to the ancestral karyotype [Elder, 1980]. Utilizing a phylogenetic hypothesis of a molecular phylogeny of Sigmodon [Henson and Bradley, 2009], we mapped shared chromosomal rearrangements of taxa on a molecular tree to estimate the evolutionary position of each rearrangement. For several species (S. hirsutus, S. leucotis, S. ochrognathus, S. peruanus, and S. toltecus), the karyotype accumulated few or no changes, but in three species (S. arizonae, S. fulviventer, and S. mascotensis) numerous karyotype rearrangements were observed. These rearrangements involved heterochromatic additions, centric fusions, tandem fusions, pericentric inversions, as well as the addition of interstitial DNA not identified by chromosome paints or C-banding. The hypothesis that the ancestral karyotype for this complex had a diploid number of 52, a fundamental number of 52, and a G-band pattern of which most, if not all are similar to that present in modern day S. hispidus fails to be rejected. This hypothesis remains viable as an explanation of chromosomal evolution in Sigmodontine rodents.

Macrocephaly in bull spermatozoa is associated with nuclear vacuoles, diploidy and alteration of chromatin condensation.

Spermatozoa from 2 dairy AI (artificial insemination) bulls (A and B), identified by their abnormal spermiogram with cells depicting frequent macrocephaly, double tails and nuclear vacuoles, were case-investigated and compared to normal spermatozoa from a control AI sire (C). Head sizes were measured and morphological abnormalities scored using brightfield and differential interference contrast microscopy. The degree of sperm maturation and of resistance to acid-induced DNA denaturation in situ were determined after uploading of acridine orange using flow cytometry of 5,000 cells/sample. Nuclear fragmentation, i.e. the ratio of red to total (red + green) fluorescence, reached 7.1% and 31% in bulls A and B, compared to 2% in bull C. The proportion of immature spermatozoa, i.e. those with incomplete histone-protamine exchange and depicting higher green fluorescence compared to the main population of the control bull, reached 9.54% in A and 7.75% in B, compared to only 0.47% in the control. In the second part of this study the previously unknown chromosomal constitution of large-headed spermatozoa of bull A was investigated by fluorescence in situ hybridization using an X-Y painting probe set. The 7.5% XY-bearing cells and the presence of diploid spermatozoa detected by flow cytometry indicate a meiotic arrest in the first division in bull A, becoming the first proven case of association of macrocephaly and M1 diploidy. The diverse approaches used for the investigation of spermatozoal DNA provide insights into the etiology of macrocephaly.

Skinks (Reptilia: Scincidae) have highly conserved karyotypes as revealed by chromosome painting.

Skinks represent the most diversified squamate reptiles with a great variation in body size and form, and are found worldwide in a variety of habitats. Their remarkable diversification has been accompanied by only a few chromosome rearrangements, resulting in highly-conservative chromosomal complements of these lizards. In this study cross-species chromosome painting using Scincus scincus (2n = 32) as the source genome, was used to detect the chromosomal rearrangements and homologies between the following skinks: Chalcides chalcides (2n = 28), C. ocellatus (2n = 28), Eumeces schneideri (2n = 32), Lepidothyris fernandi (2n = 30), Mabuya quinquetaeniata (2n = 32). The results of this study confirmed a high degree of chromosome conservation between these species. The main rearrangements in the studied skinks involve chromosomes 3, 5, 6 and 7 of S. scincus. These subtelocentric chromosomes are homologous to the p and q arms of metacentric pair 3 and 4 in C. chalcides, C. ocellatus, L. fernandi, and M. quinquetaeniata, while they are entirely conserved in E. schneideri. Other rearrangements involve S. scincus 11 in L. fernandi and M. quinquetaeniata, supporting the monophyly of Lygosominae, and one of the chromosomes S. scincus 12-16, in M. quinquetaeniata. In conclusion, our data support the monophyly of Scincidae and confirm that Scincus-Eumeces plus Chalcides do not form a monophyletic clade, suggesting that the Scincus-Eumeces clade is basal to other members of this family. This study represents the first time the whole genome of any reptile species has been used for cross-species chromosome painting to assess chromosomal evolution in this group of vertebrates.

Peromyscus maniculatus--Mus musculus chromosome homology map derived from reciprocal cross species chromosome painting.

The Mus musculus and Rattus norvegicus genomes have been extensively studied, yet despite the emergence of Peromyscus maniculatus as an NIH model for genome sequencing and biomedical research much remains unknown about the genome organization of Peromyscines. Contrary to their phylogenetic relationship, the genomes of Rattus and Peromyscus appear more similar at the gross karyotypic level than either does to Mus. We set out to define the chromosome homologies between Peromyscus, Mus and Rattus. Reciprocal cross-species chromosome painting and G-band homology assignments were used to delineate the conserved chromosome homology map between P. maniculatus and M. musculus. These data show that each species has undergone extensive chromosome rearrangements since they last shared a common ancestor 25 million years ago (mya). This analysis coupled with an inferred homology map with Rattus revealed a high level of chromosome conservation between Rattus and Peromyscus and indicated that the chromosomes of Mus are highly derived.

Mapping platypus SOX genes; autosomal location of SOX9 excludes it from sex determining role.

In the absence of an SRY orthologue the platypus sex determining gene is unknown, so genes in the human testis determining pathway are of particular interest as candidates. SOX9 is an attractive choice because SOX9 deletions cause male-to-female sex reversal in humans and mice, and SOX9 duplications cause female-to-male sex reversal. We have localized platypus SOX9, as well as the related SOX10, to platypus chromosomes 15 and 10, respectively, the first assignments to these platypus chromosomes, and the first comparative mapping markers from human chromosomes 17 and 22. The autosomal localization of platypus SOX9 in this study contradicts the hypothesis that SOX9 acts as the sex determining switch in platypus.

The discovery of the Amazonian tree flora with an updated checklist of all known tree taxa.

Amazonia is the most biodiverse rainforest on Earth, and the debate over how many tree species grow there remains contentious. Here we provide a checklist of all tree species collected to date, and describe spatial and temporal trends in data accumulation. We report 530,025 unique collections of trees in Amazonia, dating between 1707 and 2015, for a total of 11,676 species in 1225 genera and 140 families. These figures support recent estimates of 16,000 total Amazonian tree species based on ecological plot data from the Amazonian Tree Diversity Network. Botanical collection in Amazonia is characterized by three major peaks, centred around 1840, 1920, and 1980, which are associated with flora projects and the establishment of inventory plots. Most collections were made in the 20th century. The number of collections has increased exponentially, but shows a slowdown in the last two decades. We find that a species' range size is a better predictor of the number of times it has been collected than the species' estimated basin-wide population size. Finding, describing, and documenting the distribution of the remaining species will require coordinated efforts at under-collected sites.

The impact of chromosome sorting and painting on the comparative analysis of primate genomes.

Chromosome sorting by flow cytometry is the main source of chromosome-specific DNA for the production of painting probes. These probes have been used for cross-species in situ hybridization in the construction of comparative maps, in the study of karyotype evolution and phylogenetics, in delineating territories in interphase nuclei, and in the analysis of chromosome breakpoints. We review here the contributions that this technology has made to the analysis of primate genomes.

[Leptospirosis]. / Leptospirose.

Leptospirosis is a zoonosis caused by pathogenic Leptospira species. Leptospira infection can range from subclinical to life-threatening disease. Renal failure and severe respiratory symptoms may occur and are associated with a high mortality rate. It is important to realise that renal failure and other symptoms can occur in the absence of icterus. Leptospiraemia occurs mostly during the first week of acute illness, so blood cultures should be taken as soon as possible. Most cases of leptospirosis are diagnosed by serology. Antibodies are detectable in the blood approximately 5 to 7 days after onset of symptoms. Early recognition and treatment with either cephalosporins or penicillin may shorten the duration and severity of multi-organ failure and is therefore mandatory.