Within-host genetic diversity of SARS-CoV-2 in the context of large-scale hospital-associated genomic surveillance.

The COVID-19 pandemic has resulted in extensive surveillance of the genomic diversity of SARS-CoV-2. Sequencing data generated as part of these efforts can also capture the diversity of the SARS-CoV-2 virus populations replicating within infected individuals. To assess this within-host diversity of SARS-CoV-2 we quantified low frequency (minor) variants from deep sequence data of thousands of clinical samples collected by a large urban hospital system over the course of a year.

Ecological mechanism of climate-mediated selection in a rapidly evolving invasive species.

Recurring seasonal changes can lead to the evolution of phenological cues. For example, many arthropods undergo photoperiodic diapause, a programmed developmental arrest induced by short autumnal day length. The selective mechanisms that determine the timing of autumnal diapause initiation have not been empirically identified.

Animal-Microbe Interactions in the Context of Diapause.

Dormancy and diapause are key adaptations in many organisms, enabling survival of temporarily or seasonally unsuitable environmental conditions. In this review, we examine how our understanding of programmed developmental and metabolic arrest during diapause intersects with the increasing body of knowledge about animal co-development and co-evolution with microorganisms. Host-microbe interactions are increasingly understood to affect a number of metabolic, physiological, developmental, and behavioral traits and to mediate adaptations to various environments.

Environmental Sources of Bacteria and Genetic Variation in Behavior Influence Host-Associated Microbiota.

In many organisms, host-associated microbial communities are acquired horizontally after birth. This process is believed to be shaped by a combination of environmental and host genetic factors. We examined whether genetic variation in animal behavior could affect the composition of the animal's microbiota in different environments.

Presence of microbiota reverses the relative performance of Daphnia on two experimental diets.

The outcomes of host-symbiont interactions may differ according to environmental context, and symbioses may enable host adaptation to diverse environments. We find that the effects of two different experimental diets, algae and yeast, on the water flea Daphnia magna depend on whether the animals possess microbiota, suggesting that the presence of microbiota determines which diet is superior. Our study hints at both diet-dependent and diet-independent effects of microbiota on Daphnia fitness.

The microbiota of diapause: How host-microbe associations are formed after dormancy in an aquatic crustacean.

A critical question in symbiosis research is where and how organisms obtain beneficial microbial symbionts in different ecological contexts. Microbiota of juveniles are often derived directly from their mother or from the immediate environment. The origin of beneficial symbionts, however, is less obvious in organisms with diapause and dispersal stages, such as plants with dormant seeds and animals in ephemeral or strongly seasonal habitats.

Blocking a signal to host cell histones.

A plant pathogen suppresses the host immune response by preventing histone acetylation.

Stress signals in plants.

Selective autophagy mediates the cross-talk between plant growth and stress signaling pathways.

NLS protects DNA damage protein.

A single motif targets a protein to the nucleus and directs its deubiquitylation, promoting high-fidelity DNA damage repair.

Impaired phagocytosis in fragile X.

Defects in phagocytosis underlie both neurological and immunological symptoms in a fly model of fragile X syndrome.

Polyglutamine makes the switch.

In worms, a regulator of noncoding RNA directly catalyzes formation of toxic protein aggregates in the presence of polyglutamine.

Autophagy and vitamin D.

Vitamin D receptor represses basal autophagy in breast tissue, which is derepressed by vitamin D, slowing cancer progression.

An insulin-like message from mother.

Nematodes experiencing osmotic stress signal to the germ-line to prepare their offspring.

UV radiation induces a gene's dual functionality.

A protein and noncoding RNA encoded by the same gene have opposing roles in the response to UV radiation-induced damage.

Ferroptosis-like cell death in plants.

Heat stress induces a form of cell death in plants that is morphologically and biochemically similar to ferroptosis in animal cells.

Sources of variation: Animal microbiota.

The diverse effects of microbiota on animal physiology contribute to experimental variability.

Microbiome-dependent recombination shapes the host antibody repertoire.

Secreted IgD concentration depends on the presence of microbiota.

When silencing mRNA, position matters.

The mechanism of posttranscriptional silencing by an RNA-binding protein depends on the position of the protein-binding sequence in the mRNA.

Recovering rRNA processing after heat shock.

NF-κB repressing factor controls localization and activation of an rRNA processing protein in heat stress response.

Guanidine throws the riboswitch.

A bacterial riboswitch responds to endogenously produced guanidine.

Harnessing innate immunity to fight neurodegeneration.

TRIM21 prevents antibody-bound tau proteins from aggregating in cells.

Temperature-dependent benefits of bacterial exposure in embryonic development of Daphnia magna resting eggs.

The environments in which animals develop and evolve are profoundly shaped by bacteria, which affect animals both indirectly through their role in biogeochemical processes and directly through antagonistic or beneficial interactions. The outcomes of these activities can differ according to environmental context. In a series of laboratory experiments with diapausing eggs of the water flea Daphnia magna, we manipulated two environmental parameters, temperature and presence of bacteria, and examined their effect on development.

Rethinking "mutualism" in diverse host-symbiont communities.

While examples of bacteria benefiting eukaryotes are increasingly documented, studies examining effects of eukaryote hosts on microbial fitness are rare. Beneficial bacteria are often called "mutualistic" even if mutual reciprocity of benefits has not been demonstrated and despite the plausibility of other explanations for these microbes' beneficial effects on host fitness. Furthermore, beneficial bacteria often occur in diverse communities, making mutualism both empirically and conceptually difficult to demonstrate.

Water fleas require microbiota for survival, growth and reproduction.

Microbiota have diverse roles in the functioning of their hosts; experiments using model organisms have enabled investigations into these functions. In the model crustacean Daphnia, little knowledge exists about the effect of microbiota on host well being. We assessed the effect of microbiota on Daphnia magna by experimentally depriving animals of their microbiota and comparing their growth, survival and fecundity to that of their bacteria-bearing counterparts.