The Plant Pathogen Phytophthora andina Emerged via Hybridization of an Unknown Phytophthora Species and the Irish Potato Famine Pathogen, P. infestans

Emerging plant pathogens have largely been a consequence of the movement of pathogens to new geographic regions. Another documented mechanism for the emergence of plant pathogens is hybridization between individuals of different species or subspecies, which may allow rapid evolution and adaptation to new hosts or environments. Hybrid plant pathogens have traditionally been difficult to detect or confirm, but the increasing ease of cloning and sequencing PCR products now makes the identification of species that consistently have genes or alleles with phylogenetically divergent origins relatively straightforward. We investigated the genetic origin of Phytophthora andina, an increasingly common pathogen of Andean crops Solanum betaceum, S. muricatum, S. quitoense, and several wild Solanum spp. It has been hypothesized that P. andina is a hybrid between the potato late blight pathogen P. infestans and another Phytophthora species. We tested this hypothesis by cloning four nuclear loci to obtain haplotypes and using these loci to infer the phylogenetic relationships of P. andina to P. infestans and other related species. Sequencing of cloned PCR products in every case revealed two distinct haplotypes for each locus in P. andina, such that each isolate had one allele derived from a P. infestans parent and a second divergent allele derived from an unknown species that is closely related but distinct from P. infestans, P. mirabilis, and P. ipomoeae. To the best of our knowledge, the unknown parent has not yet been collected. We also observed sequence polymorphism among P. andina isolates at three of the four loci, many of which segregate between previously described P. andina clonal lineages. These results provide strong support that P. andina emerged via hybridization between P. infestans and another unknown Phytophthora species also belonging to Phytophthora clade 1c

Scintillation light detection in the 6-m drift-length ProtoDUNE Dual Phase liquid argon TPC

DUNE is a dual-site experiment for long-baseline neutrino oscillation studies, neutrino astrophysics and nucleon decay searches. ProtoDUNE Dual Phase (DP) is a 6  ×  6  ×  6 m 3 liquid argon time-projection-chamber (LArTPC) that recorded cosmic-muon data at the CERN Neutrino Platform in 2019-2020 as a prototype of the DUNE Far Detector. Charged particles propagating through the LArTPC produce ionization and scintillation light. The scintillation light signal in these detectors can provide the trigger for non-beam events. In addition, it adds precise timing capabilities and improves the calorimetry measurements. In ProtoDUNE-DP, scintillation and electroluminescence light produced by cosmic muons in the LArTPC is collected by photomultiplier tubes placed up to 7 m away from the ionizing track. In this paper, the ProtoDUNE-DP photon detection system performance is evaluated with a particular focus on the different wavelength shifters, such as PEN and TPB, and the use of Xe-doped LAr, considering its future use in giant LArTPCs. The scintillation light production and propagation processes are analyzed and a comparison of simulation to data is performed, improving understanding of the liquid argon properties

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)1.

In 2008, we published the first set of guidelines for standardizing research in autophagy. Since then, this topic has received increasing attention, and many scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Thus, it is important to formulate on a regular basis updated guidelines for monitoring autophagy in different organisms. Despite numerous reviews, there continues to be confusion regarding acceptable methods to evaluate autophagy, especially in multicellular eukaryotes. Here, we present a set of guidelines for investigators to select and interpret methods to examine autophagy and related processes, and for reviewers to provide realistic and reasonable critiques of reports that are focused on these processes. These guidelines are not meant to be a dogmatic set of rules, because the appropriateness of any assay largely depends on the question being asked and the system being used. Moreover, no individual assay is perfect for every situation, calling for the use of multiple techniques to properly monitor autophagy in each experimental setting. Finally, several core components of the autophagy machinery have been implicated in distinct autophagic processes (canonical and noncanonical autophagy), implying that genetic approaches to block autophagy should rely on targeting two or more autophagy-related genes that ideally participate in distinct steps of the pathway. Along similar lines, because multiple proteins involved in autophagy also regulate other cellular pathways including apoptosis, not all of them can be used as a specific marker for bona fide autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field

A multiproxy analysis of extreme wave deposits in a tropical coastal lagoon in Jamaica, West Indies

The Small Island Developing States (SIDS) of the Caribbean Region are vulnerable to natural hazards including earthquakes, tsunamis and tropical cyclones that can cause widespread devastation. Sedimentary archives of these hazards are often well-preserved in coastal lagoons; however, few studies in the Caribbean have adopted a multiproxy approach to their reconstruction. Here, we present a 1200-year multiproxy record of extreme washover events deposited within a coastal mangrove lagoon on the south coast of Jamaica. Manatee Bay lagoon is a permanent fresh-brackish-water mangrove lagoon separated from the Caribbean Sea by a low-elevation carbonate beach. Fifteen sediment cores recovered along five shore-normal transects contain ostracod-rich authigenic carbonate lake muds interspersed with beds of organic lake mud and mangrove peat. The cores contain evidence of multiple palaeo-washover deposits that are readily distinguished by their sedimentology, geochemistry and microfossil assemblages. Hypersaline conditions dominated the early part of the record (~ 800 to 900 CE), and we infer a freshening of lagoonal waters and the subsequent expansion of the mangrove community following an extreme wave event that occurred some time before ~ 1290 to 1400 CE. We constrain the primary historical-washover deposit to 1810–1924 CE (2σ; 71% probability), a period characterised by extreme tectonic and meteorological events, which include the Great Kingston Earthquake of 1907 and a local episode of enhanced hurricane activity. Whilst the balance of circumstantial evidence indicates that the deposit was probably emplaced during the tsunami generated by the 1907 earthquake, we are currently unable to differentiate between tectonically and meteorologically driven washover events based on their sedimentological characteristics

Genitourinary Pathology (Including Adrenal Gland)

Our aims in constructing the Genitourinary Pathology chapter are to describe neoplasms of the adrenal gland, urothelial tract, kidney, penis, prostate, and testis in a manner that is both useful for the practicing surgical pathologist and that may be used as a reference for all students of urologic pathology. Whereas the text and figures describe the salient morphologic, immunohistochemical, and molecular attributes for each tumor type and encompass the latest classification schemes, the narrative integrates the clinical and pathological findings that are commonly encountered during surgical pathology sign-out of these cases. Accordingly, it is our hope that this chapter will serve as a guide for both general and subspecialized pathologists in contemporary practice