Chromosome-level reference genomes of two imperiled desert fishes: spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis).

North American minnows (Cypriniformes: Leuciscidae) comprise a diverse taxonomic group, but many members, particularly those inhabiting deserts, face elevated extinction risks. Despite conservation concerns, leuciscids remain under sampled for reference assemblies relative to other groups of freshwater fishes. Here, we present 2 chromosome-scale reference genome assemblies spikedace (Meda fulgida) and loach minnow (Tiaroga cobitis) using PacBio, Illumina and Omni-C technologies. The complete assembly for spikedace was 882.1 Mb in total length comprised of 83 scaffolds with N50 = 34.8 Mb, L50 = 11, N75 = 32.3 Mb, and L75 = 18. The complete assembly for loach minnow was 1.3 Gb in total length comprised of 550 scaffolds with N50 = 48.6 Mb, L50 = 13, N75 = 42.3 Mb, and L75 = 20. Completeness assessed via Benchmarking Universal Single-Copy Orthologues (BUSCO) metrics using the Actinopterygii BUSCO database showed ∼97% for spikedace and ∼98% for loach minnow of complete BUSCO proportions. Annotation revealed approximately 32.58 and 29.04% of spikedace and loach minnow total genome lengths to be comprised of protein-coding genes, respectively. Comparative genomic analyses of these endangered and co-distributed fishes revealed widespread structural variants, gene family expansions, and evidence of positive selection in both genomes.

A third SARS-CoV-2 mRNA vaccine dose in people receiving hemodialysis overcomes B cell defects but elicits a skewed CD4+ T cell profile

Cellular immune defects associated with suboptimal responses to SARS-CoV-2 mRNA vaccination in people receiving hemodialysis (HD) are poorly understood. We longitudinally analyzed antibody, B cell, CD4+ and CD8+ T cell vaccine responses in 27 HD patients and 26 low-risk control individuals (CI). The first two doses elicit weaker B cell and CD8+ T cell responses in HD than in CI, while CD4+ T cell responses are quantitatively similar. In HD, a third dose robustly boosts B cell responses, leads to convergent CD8+ T cell responses and enhances comparatively more Thelper (TH) immunity. Unsupervised clustering of single-cell features reveals phenotypic and functional shifts over time and between cohorts. The third dose attenuates some features of TH cells in HD (TNF/IL-2 skewing), while others (CCR6, CXCR6, PD-1 and HLA-DR overexpression) persist. Therefore, a third vaccine dose is critical to achieve robust multifaceted immunity in hemodialysis patients, although some distinct TH characteristics endure.

SARS-CoV-2 BA.4/5 Spike recognition and neutralization elicited after the third dose of mRNA vaccine

Several SARS-CoV-2 Omicron subvariants have recently emerged, becoming the dominant circulating strains in many countries. These variants contain a large number of mutations in their Spike glycoprotein, raising concerns about vaccine efficacy. In this study, we evaluate the ability of plasma from a cohort of individuals that received three doses of mRNA vaccine to recognize and neutralize these Omicron subvariant Spikes. We observed that BA.4/5 and BQ.1.1 Spikes are markedly less recognized and neutralized compared to the D614G and the other Omicron subvariant Spikes tested. Also, individuals who have been infected before or after vaccination present better humoral responses than SARS-CoV-2 naive vaccinated individuals, thus indicating that hybrid immunity generates better humoral responses against these subvariants.

A long interval between priming and boosting SARS-CoV-2 mRNA vaccine doses enhances B cell responses with limited impact on T cell immunity

Spacing the first two doses of SARS-CoV-2 mRNA vaccines beyond 3-4 weeks raised initial concerns about vaccine efficacy. While studies have since shown that long-interval regimens induce robust antibody responses, their impact on B and T cell immunity is poorly known. Here, we compare in SARS-CoV-2 naive donors B and T cell responses to two mRNA vaccine doses administered 3-4 versus 16 weeks apart. After boost, the longer interval results in higher magnitude and a more mature phenotype of RBD-specific B cells. While the two geographically distinct cohorts present quantitative and qualitative differences in T cell responses at baseline and after priming, the second dose led to convergent features with overall similar magnitude, phenotype and function of CD4+ and CD8+ T cell responses at post-boost memory timepoints. Therefore, compared to standard regimens, a 16-week interval has a favorable impact on the B cell compartment but minimally affects T cell immunity.

A Reference Genome Assembly of Hybrid-Derived California Wild Radish (Raphanus sativus × raphanistrum).

For agriculturally important plants, pollination and herbivory are 2 ecological factors that play into the success of crop yields. Each is also important in natural environments where invasive plants and their effect on species interactions may alter the native ecology. The California Wild Radish (Raphanus sativus × raphanistrum), a hybrid derived from an agriculturally important crop and a nonnative cultivar, is common in California. Remarkably, it has recently replaced wild populations of both progenitor species. Experiments on phenotypic variation for petal color and antiherbivore defenses suggest both pairs of polymorphisms are maintained as a result of pollinator- and herbivore-mediated natural selection. This species provides an opportunity to understand how natural selection shapes the evolution of ecologically important traits when traits are constrained by 2 opposing forces. Here we provide the genome assembly of the California Wild Radish displaying improvement to currently existing genomes for agronomically important crucifers. This genome sequence provides the tools to dissect the genomic architecture of traits related to herbivory and pollination using natural variation in the wild as well as the ability to infer demographic and selective history in the context of hybridization. Study systems like these will improve our understanding and predictions of evolutionary change for correlated traits.

Temporal associations of B and T cell immunity with robust vaccine responsiveness in a 16-week interval BNT162b2 regimen

Spacing of the BNT162b2 mRNA doses beyond 3 weeks raised concerns about vaccine efficacy. We longitudinally analyzed B cell, T cell and humoral responses to two BNT162b2 mRNA doses administered 16 weeks apart in 53 SARS-CoV-2 naive and previously-infected donors. This regimen elicited robust RBD-specific B cell responses whose kinetics differed between cohorts, the second dose leading to increased magnitude in naive participants only. While boosting did not increase magnitude of CD4+ T cell responses further compared to the first dose, unsupervised clustering analyses of single-cell features revealed phenotypic and functional shifts over time and between cohorts. Integrated analysis showed longitudinal immune component-specific associations, with early Thelper responses post-first dose correlating with B cell responses after the second dose, and memory Thelper generated between doses correlating with CD8 T cell responses after boosting. Therefore, boosting elicits a robust cellular recall response after the 16-week interval, indicating functional immune memory.

Strong humoral immune responses against SARS-CoV-2 Spike after BNT162b2 mRNA vaccination with a sixteen-week interval between doses

While the standard regimen of the BNT162b2 mRNA vaccine includes two doses administered three weeks apart, some public health authorities decided to space them, raising concerns about vaccine efficacy. Here, we analyzed longitudinal humoral responses including antibody binding, Fc-mediated effector functions and neutralizing activity against the D614G strain but also variants of concern and SARS-CoV-1 in a cohort of SARS-CoV-2 naive and previously infected individuals, with an interval of sixteen weeks between the two doses. While the administration of a second dose to previously infected individuals did not significantly improve humoral responses, we observed a significant increase of humoral responses in naive individuals after the 16-weeks delayed second shot, achieving similar levels as in previously infected individuals. We compared these responses to those elicited in individuals receiving a short (4-weeks) dose interval. For the naive donors, these responses were superior to those elicited by the short dose interval.

Evaluation of a suspended radiation protection system to reduce operator exposure in cardiology interventional procedures.

OBJECTIVES: To investigate a novel suspended radiation shield (ZG), in reducing operator radiation exposure during cardiology interventions. BACKGROUND: Radiation exposure to the operator remains an occupational health hazard in the cardiac catheterization laboratory. METHODS: An anthropomorphic mannequin simulating an operator was placed near a phantom, simulating a patient. To measure the operator dose reduction, thermoluminescent detectors (TLDs) were inserted into the head and into the eye bulbs of the mannequin, while electronic dosimeters were positioned on the temple and at the level of the thyroid. Measurements were performed without and with the ZG system in place. Physician exposure was subsequently prospectively measured on the torso, on the left eye and on upper arm using the same electronic dosimeters, during clinical procedures (coronary angiography (CA) and percutaneous coronary intervention (PCI)). The physicians dose reduction was assessed by comparing operator dose when using traditional radioprotection garments (Phase 0) versus using the ZG system (Phase 1). RESULTS: Dose reductions as measured on the mannequin ranged from 66% to the head, to 100% to the torso. No dose was detected at the level of the torso and thyroid with ZG. When comparing CA and PCI procedures between Phase 0 and Phase 1, a significant difference (p < 0.001) was found for the left eye and the left wrist. Dose reduction as measured during clinical procedures for left eye/upper arm were on average 78.9%/95.6% for CA and 83.0%/93.0% for PCI, respectively (p < 0.001 for both). CONCLUSIONS: The ZG systems has a great potential to significantly reduce operator dose through the creation of a nearly zero-radiation work environment.

Role of RadA and DNA Polymerases in Recombination-Associated DNA Synthesis in Hyperthermophilic Archaea.

Among the three domains of life, the process of homologous recombination (HR) plays a central role in the repair of double-strand DNA breaks and the restart of stalled replication forks. Curiously, main protein actors involved in the HR process appear to be essential for hyperthermophilic Archaea raising interesting questions about the role of HR in replication and repair strategies of those Archaea living in extreme conditions. One key actor of this process is the recombinase RadA, which allows the homologous strand search and provides a DNA substrate required for following DNA synthesis and restoring genetic information. DNA polymerase operation after the strand exchange step is unclear in Archaea. Working with Pyrococcus abyssi proteins, here we show that both DNA polymerases, family-B polymerase (PolB) and family-D polymerase (PolD), can take charge of processing the RadA-mediated recombination intermediates. Our results also indicate that PolD is far less efficient, as compared with PolB, to extend the invaded DNA at the displacement-loop (D-loop) substrate. These observations coincide with previous genetic analyses obtained on Thermococcus species showing that PolB is mainly involved in DNA repair without being essential probably because PolD could take over combined with additional partners.

Patient exposure data and operator dose in coronary interventional procedures: Impact of body-mass index and procedure complexity.

PURPOSE: The aim of this study was to assess patient exposure data and operator dose in coronary interventional procedures, when considering patient body-mass index and procedure complexity. METHODS: Total air kerma area product (PKA), Air-Kerma (AK), Fluoroscopy time (FT), operator dose and patient body-mass index (BMI) from 97 patients' procedures (62 coronary angiography (CA) and 35 Percutaneous Coronary Intervention (PCI) were collected for one year. For PCI procedures, also the complexity index-CI was collected. Continuous variables for each of the 2 groups procedures (CA and PCI) were compared as medians with interquartile range and using Mann-Whitney U test. Multiple group data were compared using Kruskal-Wallis test (significance: p < 0.05). RESULTS: Median PKA was 63 and 125 Gy cm2 for CA and PCI respectively (p < 0.001); FT was 3 and 14 min, respectively (p < 0.001). PKA and FT significantly increased (p < 0.05) with BMI class for CA procedures. PKA and FT also increased in function of CI class for PCI, thought significantly only for FT (p < 0.001), possibly because of the low number of PCI procedures included; cine mode contributed most to PKA. Significant dose variability was observed among cardiologists for CA procedures (p < 0.001). CONCLUSIONS: Dose references levels for PKA and FT in interventional cardiology should be defined - on a sufficient number of procedures- in function of CI and BMI classes. These could provide an additional tool for refining a facility's quality assurance and optimization processes. Dose variability associated with cardiologists underlines the importance of continuous training.

Genetically Defined Functional Modules for Spatial Orienting in the Mouse Superior Colliculus.

In order to explore and interact with their surroundings, animals need to orient toward specific positions in space. Throughout the animal kingdom, head movements represent a primary form of orienting behavior. The superior colliculus (SC) is a fundamental structure for the generation of orienting responses, but how genetically distinct groups of collicular neurons contribute to these spatially tuned behaviors remains largely to be defined. Here, through the genetic dissection of the murine SC, we identify a functionally and genetically homogeneous subclass of glutamatergic neurons defined by the expression of the paired-like homeodomain transcription factor Pitx2. We show that the optogenetic stimulation of Pitx2ON neurons drives three-dimensional head displacements characterized by stepwise, saccade-like kinematics. Furthermore, during naturalistic foraging behavior, the activity of Pitx2ON neurons precedes and predicts the onset of spatially tuned head movements. Intriguingly, we reveal that Pitx2ON neurons are clustered in an orderly array of anatomical modules that tile the entire intermediate layer of the SC. Such a modular organization gives origin to a discrete and discontinuous representation of the motor space, with each Pitx2ON module subtending a defined portion of the animal's egocentric space. The modularity of Pitx2ON neurons provides an anatomical substrate for the convergence of spatially coherent sensory and motor signals of cortical and subcortical origins, thereby promoting the recruitment of appropriate movement vectors. Overall, these data support the view of the superior colliculus as a selectively addressable and modularly organized spatial-motor register.

Three-Dimensional Representation of Motor Space in the Mouse Superior Colliculus.

From the act of exploring an environment to that of grasping a cup of tea, animals must put in register their motor acts with their surrounding space. In the motor domain, this is likely to be defined by a register of three-dimensional (3D) displacement vectors, whose recruitment allows motion in the direction of a target. One such spatially targeted action is seen in the head reorientation behavior of mice, yet the neural mechanisms underlying these 3D behaviors remain unknown. Here, by developing a head-mounted inertial sensor for studying 3D head rotations and combining it with electrophysiological recordings, we show that neurons in the mouse superior colliculus are either individually or conjunctively tuned to the three Eulerian components of head rotation. The average displacement vectors associated with motor-tuned colliculus neurons remain stable over time and are unaffected by changes in firing rate or the duration of spike trains. Finally, we show that the motor tuning of collicular neurons is largely independent from visual or landmark cues. By describing the 3D nature of motor tuning in the superior colliculus, we contribute to long-standing debate on the dimensionality of collicular motor decoding; furthermore, by providing an experimental paradigm for the study of the metric of motor tuning in mice, this study also paves the way to the genetic dissection of the circuits underlying spatially targeted motion.

Habitat preference of an herbivore shapes the habitat distribution of its host plant.

Plant distributions can be limited by habitat-biased herbivory, but the proximate causes of such biases are rarely known. Distinguishing plant-centric from herbivore-centric mechanisms driving differential herbivory between habitats is difficult without experimental manipulation of both plants and herbivores. Here we tested alternative hypotheses driving habitat-biased herbivory in bittercress (Cardamine cordifolia), which is more abundant under shade of shrubs and trees (shade) than in nearby meadows (sun) where herbivory is intense from the specialist fly Scaptomyza nigrita. This system has served as a textbook example of habitat-biased herbivory driving a plant's distribution across an ecotone, but the proximate mechanisms underlying differential herbivory are still unclear. First, we found that higher S. nigrita herbivory in sun habitats contrasts sharply with their preference to attack plants from shade habitats in laboratory choice experiments. Second, S. nigrita strongly preferred leaves in simulated sun over simulated shade habitats, regardless of plant source habitat. Thus, herbivore preference for brighter, warmer habitats overrides their preference for more palatable shade plants. This promotes the sun-biased herbivore pressure that drives the distribution of bittercress into shade habitats.

Multidrug transporters and organic anion transporting polypeptides protect insects against the toxic effects of cardenolides.

In the struggle against dietary toxins, insects are known to employ target site insensitivity, metabolic detoxification, and transporters that shunt away toxins. Specialized insects across six taxonomic orders feeding on cardenolide-containing plants have convergently evolved target site insensitivity via specific amino acid substitutions in the Na/K-ATPase. Nonetheless, in vitro pharmacological experiments have suggested a role for multidrug transporters (Mdrs) and organic anion transporting polypeptides (Oatps), which may provide a basal level of protection in both specialized and non-adapted insects. Because the genes coding for these proteins are evolutionarily conserved and in vivo genetic evidence in support of this hypothesis is lacking, here we used wildtype and mutant Drosophila melanogaster (Drosophila) in capillary feeder (CAFE) assays to quantify toxicity of three chemically diverse, medically relevant cardenolides. We examined multiple components of fitness, including mortality, longevity, and LD50, and found that, while the three cardenolides each stimulated feeding (i.e., no deterrence to the toxin), all decreased lifespan, with the most apolar cardenolide having the lowest LD50 value. Flies showed a clear non-monotonic dose response and experienced high levels of toxicity at the cardenolide concentration found in plants. At this concentration, both Mdr and Oatp knockout mutant flies died more rapidly than wildtype flies, and the mutants also experienced more adverse neurological effects on high-cardenolide-level diets. Our study further establishes Drosophila as a model for the study of cardenolide pharmacology and solidifies support for the hypothesis that multidrug and organic anion transporters are key players in insect protection against dietary cardenolides.

Population structure of a vector-borne plant parasite.

Parasites are among the most diverse groups of life on Earth, yet complex natural histories often preclude studies of their speciation processes. The biology of parasitic plants facilitates in situ collection of data on both genetic structure and the mechanisms responsible for that structure. Here, we studied the role of mating, dispersal and establishment in host race formation of a parasitic plant. We investigated the population genetics of a vector-borne desert mistletoe (Phoradendron californicum) across two legume host tree species (Senegalia greggii and Prosopis velutina) in the Sonoran desert using microsatellites. Consistent with host race formation, we found strong host-associated genetic structure in sympatry, little genetic variation due to geographic site and weak isolation by distance. We hypothesize that genetic differentiation results from differences in the timing of mistletoe flowering by host species, as we found initial flowering date of individual mistletoes correlated with genetic ancestry. Hybrids with intermediate ancestry were detected genetically. Individuals likely resulting from recent, successful establishment events following dispersal between the host species were detected at frequencies similar to hybrids between host races. Therefore, barriers to gene flow between the host races may have been stronger at mating than at dispersal. We also found higher inbreeding and within-host individual relatedness values for mistletoes on the more rare and isolated host species (S. greggii). Our study spanned spatial scales to address how interactions with both vectors and hosts influence parasitic plant structure with implications for parasite virulence evolution and speciation.

Aversion and attraction to harmful plant secondary compounds jointly shape the foraging ecology of a specialist herbivore.

Most herbivorous insect species are restricted to a narrow taxonomic range of host plant species. Herbivore species that feed on mustard plants and their relatives in the Brassicales have evolved highly efficient detoxification mechanisms that actually prevent toxic mustard oils from forming in the bodies of the animals. However, these mechanisms likely were not present during the initial stages of specialization on mustard plants ~100 million years ago. The herbivorous fly Scaptomyza nigrita (Drosophilidae) is a specialist on a single mustard species, bittercress (Cardamine cordifolia; Brassicaceae) and is in a fly lineage that evolved to feed on mustards only in the past 10-20 million years. In contrast to many mustard specialists, S. nigrita does not prevent formation of toxic breakdown products (mustard oils) arising from glucosinolates (GLS), the primary defensive compounds in mustard plants. Therefore, it is an appealing model for dissecting the early stages of host specialization. Because mustard oils actually form in the bodies of S. nigrita, we hypothesized that in lieu of a specialized detoxification mechanism, S. nigrita may mitigate exposure to high GLS levels within plant tissues using behavioral avoidance. Here, we report that jasmonic acid (JA) treatment increased GLS biosynthesis in bittercress, repelled adult female flies, and reduced larval growth. S. nigrita larval damage also induced foliar GLS, especially in apical leaves, which correspondingly displayed the least S. nigrita damage in controlled feeding trials and field surveys. Paradoxically, flies preferred to feed and oviposit on GLS-producing Arabidopsis thaliana despite larvae performing worse in these plants versus non-GLS-producing mutants. GLS may be feeding cues for S. nigrita despite their deterrent and defensive properties, which underscores the diverse relationship a mustard specialist has with its host when lacking a specialized means of mustard oil detoxification.

RAD51 deficiency disrupts the corticospinal lateralization of motor control.

Mirror movements are involuntary symmetrical movements of one side of the body that mirror voluntary movements of the other side. Congenital mirror movement disorder is a rare condition characterized by mirror movements that persist throughout adulthood in subjects with no other clinical abnormalities. The affected individuals have mirror movements predominating in the muscles that control the fingers and are unable to perform purely unimanual movements. Congenital mirror movement disorder thus provides a unique paradigm for studying the lateralization of motor control. We conducted a multimodal, controlled study of patients with congenital mirror movements associated with RAD51 haploinsufficiency (n = 7, mean age 33.3 ± 16.8 years) by comparison with age- and gender-matched healthy volunteers (n = 14, mean age 33.9 ± 16.1 years). We showed that patients with congenital mirror movements induced by RAD51 deficiency had: (i) an abnormal decussation of the corticospinal tract; (ii) abnormal interhemispheric inhibition and bilateral cortical activation of primary motor areas during intended unimanual movements; and (iii) an abnormal involvement of the supplementary motor area during both unimanual and bimanual movements. The lateralization of motor control thus requires a fine interplay between interhemispheric communication and corticospinal wiring. This fine interplay determines: (i) the delivery of appropriate motor plans from the supplementary motor area to the primary motor cortex; (ii) the lateralized activation of the primary motor cortex; and (iii) the unilateral transmission of the motor command to the limb involved in the intended movement. Our results also unveil an unexpected function of RAD51 in corticospinal development of the motor system.