A pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici

OBJECTIVES

High-quality species-specific transposable element (TE) libraries are required for studies to elucidate the evolutionary dynamics of TEs and gain an understanding of their impacts on host genomes. Such high-quality TE resources are severely lacking for species in the fungal kingdom. To facilitate future studies on the putative role of TEs in rapid adaptation observed in the fungal wheat pathogen Zymoseptoria tritici, we produced a manually curated TE library. This was generated by detecting TEs in 19 reference genome assemblies representing the global diversity of the species supplemented by multiple sister species genomes. Improvements over previous TE libraries have been made on TE boundary resolution, detection of ORFs, TE domains, terminal inverted repeats, and class-specific motifs.

DATA DESCRIPTION

A TE consensus library for Z. tritici formatted for use with RepeatMasker. This data is relevant to other researchers investigating TE-host evolutionary dynamics in Z. tritici or who are interested in comparative studies of the fungal kingdom. Further, this TE library can be used to improve gene annotation. Finally, this TE library increases the number of manually curated TE datasets, providing resources to further our understanding of TE diversity.

Anomalous Dissipation and Lack of Selection in the Obukhov-Corrsin Theory of Scalar Turbulence

The Obukhov-Corrsin theory of scalar turbulence [21, 54] advances quantitative predictions on passive-scalar advection in a turbulent regime and can be regarded as the analogue for passive scalars of Kolmogorov's K41 theory of fully developed turbulence [47]. The scaling analysis of Obukhov and Corrsin from 1949 to 1951 identifies a critical regularity threshold for the advection-diffusion equation and predicts anomalous dissipation in the limit of vanishing diffusivity in the supercritical regime. In this paper we provide a fully rigorous mathematical validation of this prediction by constructing a velocity field and an initial datum such that the unique bounded solution of the advection-diffusion equation is bounded uniformly-in-diffusivity within any fixed supercritical Obukhov-Corrsin regularity regime while also exhibiting anomalous dissipation. Our approach relies on a fine quantitative analysis of the interaction between the spatial scale of the solution and the scale of the Brownian motion which represents diffusion in a stochastic Lagrangian setting. This provides a direct Lagrangian approach to anomalous dissipation which is fundamental in order to get detailed insight on the behavior of the solution. Exploiting further this approach, we also show that for a velocity field in C α of space and time (for an arbitrary 0 ≤ α < 1 ) neither vanishing diffusivity nor regularization by convolution provide a selection criterion for bounded solutions of the advection equation. This is motivated by the fundamental open problem of the selection of solutions of the Euler equations as vanishing-viscosity limit of solutions of the Navier-Stokes equations and provides a complete negative answer in the case of passive advection.

Young people's mental and social distress in times of international crisis: evidence from helpline calls, 2019-2022

We document mental and social distress of children, adolescents and adults, using data on 3 million calls to German helplines between January 2019 and May 2022. High-frequency data from crisis helpline logs offer rich information on the evolution of "revealed distress" among the most vulnerable, unaffected by researchers' study design and framing. Distress of adults, measured by the volume of calls, rose significantly after both the outbreak of the pandemic and the Russian invasion of Ukraine. In contrast, the overall revealed distress of children and adolescents did not increase during those crises. The nature of young people's concerns, however, changed more strongly than for adults after the COVID-19 outbreak. Consistent with the effects of social distancing, call topics of young people shifted from problems with school and peers to problems with family and mental health. We find the share of severe mental health problems among young people to have increased with a delay, in the second and third year of the pandemic.

The choroid plexus acts as an immune cell reservoir and brain entry site in experimental autoimmune encephalomyelitis

The choroid plexus (ChP) has been suggested as an alternative central nervous system (CNS) entry site for CCR6⁺ Th17 cells during the initiation of experimental autoimmune encephalomyelitis (EAE), an animal model for multiple sclerosis (MS). To advance our understanding of the importance of the ChP in orchestrating CNS immune cell entry during neuroinflammation, we here directly compared the accumulation of CD45⁺ immune cell subsets in the ChP, the brain and spinal cord at different stages of EAE by flow cytometry. We found that the ChP harbors high numbers of CD45^int resident innate but also of CD45^hi adaptive immune cell subsets including CCR6⁺ Th17 cells. With the exception to tissue-resident myeloid cells and B cells, numbers of CD45⁺ immune cells and specifically of CD4⁺ T cells increased in the ChP prior to EAE onset and remained elevated while declining in brain and spinal cord during chronic disease. Increased numbers of ChP immune cells preceded their increase in the cerebrospinal fluid (CSF). Th17 but also other CD4⁺ effector T-cell subsets could migrate from the basolateral to the apical side of the blood-cerebrospinal fluid barrier (BCSFB) in vitro, however, diapedesis of effector Th cells including that of Th17 cells did not require interaction of CCR6 with BCSFB derived CCL20. Our data underscore the important role of the ChP as CNS immune cell entry site in the context of autoimmune neuroinflammation.

Multi-sample/multi-nucleus parallel polarization and monitoring enabled by a fluid path technology compatible cryogenic probe for dissolution dynamic nuclear polarization

Low throughput is one of dissolution Dynamic Nuclear Polarization (dDNP) main shortcomings. Especially for clinical and preclinical applications, where direct ¹³C nuclei polarization is usually pursued, it takes hours to generate one single hyperpolarized (HP) sample. Being able to hyperpolarize more samples at once represents a clear advantage and can expand the range and complexity of the applications. In this work, we present the design and performance of a highly versatile and customizable dDNP cryogenic probe, herein adapted to a 5 T "wet" preclinical polarizer, that can accommodate up to three samples at once and, most importantly, it is capable of monitoring the solid-state spin dynamics of each sample separately, regardless of the kind of radical used and the nuclear species of interest. Within 30 min, the system was able to dispense three HP solutions with high repeatability across the channels (30.0 ± 1.2% carbon polarization for [1-¹³C]pyruvic acid doped with trityl radical). Moreover, we tested multi-nucleus NMR capability by polarizing and monitoring simultaneously ¹³C, ¹H and ¹²⁹Xe. Finally, we implemented [1-¹³C]lactate/[1-¹³C]pyruvate polarization and back-to-back dissolution and injection in a healthy mouse model to perform multiple-substrate HP Magnetic Resonance Spectroscopy (MRS) at 14.1 T.