France

Elucidating transcriptional regulatory networks requires knowledge of transcription factor (TF) binding sites and their occupancy, ideally in a native chromatin context. Towards this goal, we have adapted the use of micrococcal nuclease (MNase) as a biochemical probe of fixed chromatin structure with emphasis on small DNA fragments from sub-nucleosome-sized particles. Specifically, we developed MNase-defined cistrome-Occupancy Analysis (MOA-seq) to achieve high-resolution genome-wide detection of TF-bound sites within accessible chromatin regions, illustrated with a proof of concept study on field-grown maize ear shoots (Savadel, Hartwig, et al., 2021; PLOS Genetics). Fragment center plotting focused the footprint detection down to small particles with an average peak size of ~30bp. These MOA footprints (MFs) exhibited (1) expression-correlated associations with gene promoters, (2) enrichment at known TF-binding sites, (3) enrichment at known long-range chromatin interaction sites, and (4) enrichment at known open chromatin regions defined by other non-MNase assays such as ATAC-seq. Motif analysis of 145,000 maize earshoot MFs led to the detection of 215 sequence motif families, which were merged into non-overlapping regions numbering just above 100,000 loci and covering just below 0.1% of the maize genome. We also used MOA-seq to examine genomic response to hypoxia in human cells. From these initial studies, we conclude that MOA-seq is ideal for genome-wide identification of cistrome occupancy at high resolution using a single antibody-free assay. The technology adds a valuable method to the genomic toolkit for pinpointing cis-regulatory candidates in agriculture and medicine.

SEB Annual Conference 2022

MNase-based MOA-Seq Pinpoints Native Cistrome Occupancy at 30-bp Resolution Amid Accessible Chromatin

Discover the art of creating extraordinary science at SEB’s Annual Conference at Le Corum Conference Center     in Montpellier, France from 5 to  8 July 2022.

SEB’s Annual Conference is celebrated for creating the perfect composition of research, new discoveries and collaborative connections. Be creative and innovative by exchanging ideas and knowledge with masters of biology from all over the world.

2022 will find over 1500 experimental biologists from across the globe converging on the third-largest French city near the Mediterranean coast and the fastest-growing city in the country over the past 25 years.
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Please register for the conference by clicking on this link:

https://www.sebiology.org/events/seb-annual-conference-2022/registration.html

The site will be open for registered participants closer to the event.

2022 will find over 1500 experimental biologists from across the globe converging on the third-largest French city near the Mediterranean coast and the fastest-growing city in the country over the past 25 years - Montpellier, France

technical paper

Many small vertebrates and arthropods are able to run with sticky feet, and must hence be able to rapidly switch between strong attachment and effortless detachment. The timescale over which contacts are formed and broken precludes chemical control. Instead, terrestrial climbing animals appear to rely on mechanical `switches’. Recently, strong evidence has emerged that at least some of these switches are universal: Whether adhesive pads are `hairy’, `smooth’, `wet’ or `dry’ pads, there appears to exist a linear relationship between the shear force, applied in parallel to the surface, and the adhesive force, normal to the surface, required to detach them. This ‘shear-sensitivity’ provides a rapid mechanical switch, enables larger animals to maintain approximately constant safety factors despite smaller surface-to-volume ratios, and has implications for optimal step coordination patterns during climbing on vertical and inverted substrates. The control of adhesion via shear forces is deeply integrated with the anatomy and locomotion of climbing animals, and involves both active neuro-muscular control, and rapid passive responses. The resulting dynamic adhesive systems are robust, reliable, versatile and nevertheless remarkably simple. They may thus serve as suitable inspiration for the design of climbing robots.

Biomechanics of controllable attachment in climbing animals

Plastic particles smaller than 5 mm, so-called microplastics, are constantly released into the environment through everyday behaviours. Besides emissions from tyre wear, cosmetics, or artificial turfs, microplastic fibres from washing machines have a high share of microplastic emissions in Europe, with around 20 to 220 g per person and year. To identify innovative filtration mechanisms that lay beyond conventional engineered solutions, 35 particle separation mechanisms of suspension feeders were reviewed for their potential to develop a bio-inspired filter module for washing machines. Ram-feeding fishes were selected for detailed analysis based on their ability to use cross-flow filtration, process large volumes of water, retain particles in a similar size range, and have an inherent cleaning mechanism. The gill arch system of five species (Clupeiformes, Scombriformes), in which elongated gill rakers with denticles retain particles, was studied using optical microscopy, µCT, and videography to determine relevant filtration parameters. The results show differences in gill raker morphology, filtration area, and mesh size, indicating two cross-flow filtration variations: Scomber scombrus and Rastrelliger kanagurta (Scombriformes) use surface structures and mucus as adhesive material to increase particle retention, whereas Clupea harengus, Sardina pilchardus, and Engraulis encrasicolus (Clupeiformes) use a purely mechanical separation mechanism. The morphological traits of the clupeid filters were abstracted into parametric models to study fluid dynamics and determine the filtration efficiency in numerical and experimental experiments. Through an iterative process, the models are currently optimised to fit the requirements of washing machines and retain microplastic fibres.

From fish to filter: development of a bio-inspired filter module to reduce microplastic emissions from washing machines

For small, winter active endotherms living in cold ecosystems, thermal performance is critical for survival. Its unsurprising that populations of deer mice (Peromyscus maniculatus) adapted to high altitude, where ambient temperature is consistently lower than at sea level, have evolved an enhanced thermoregulatory capacity. As adults, these animals rely on an evolved, oxidative skeletal muscle phenotype to perform high rates of shivering thermogenesis. However, like most altricial mammals, the muscles of newborn deer mice are immature and unable to shiver. What happens when young animals face the same environmental challenges without the physiological tools as adults? In this talk I will discuss my recent work on the evolution of brown adipose tissue (BAT) and whole animal thermal performance in young Peromyscus mice. I have shown that during postnatal development, high altitude deer mice have evolved to suppress thermogenesis by impeding BAT function. I will discuss both the proximate and ultimate mechanisms we hypothesize are driving this phenomenon, including how BAT acts as an endocrine organ and may help program adult metabolic phenotype. These data will highlight how selection can act differently on the same physiological system depending on life stage.

Baby animals are not small adults! Proximate and ultimate mechanisms of brown adipose tissue evolution in the North American deer mouse

Diving as a lifestyle has evolved on multiple occasions when air-breathing terrestrial animals invaded the aquatic realm, and diving performance shapes the ecology and behaviour of all air-breathing aquatic taxa, from small insects to great whales. Using the largest dataset yet assembled, we show that maximum dive duration increases predictably with body mass in both ectotherms and endotherms. Compared to endotherms, ectotherms can remain submerged for longer, but the mass scaling relationship for dive duration is much steeper in endotherms than in ectotherms. These differences in diving allometry can be fully explained by inherent differences between the two groups in their metabolic rate and how metabolism scales with body mass and temperature. We therefore suggest that similar constraints on oxygen storage and usage have shaped the evolutionary ecology of diving in all air-breathing animals, irrespective of their evolutionary history and metabolic mode.

Universal metabolic constraints shape the evolutionary ecology of diving in animals

In birds, embryos use acoustic signals to synchronize hatching, learn calls or even solicit parental care. In zebra finches (Taeniopygia guttata), parents produce a peculiar “heat-call” during incubation at high ambient temperatures, which results in reduced nestling growth, in a temperature-dependent manner. Whilst being smaller may facilitate heat dissipation, we do not know whether being exposed to heat-calls prenatally affects thermoregulatory capacities and heat tolerance, and whether these effects persist into adulthood. Here, we tested the effects of experimentally delivered prenatal playback of heat-calls on thermoregulation at high temperatures at adulthood. We used a respirometry system to measure individuals’ metabolic rate and evaporative water loss at air temperatures (Ta) gradually increasing from 25°C to 44°C, while simultaneously monitoring their body temperature. Remarkably, prenatal exposure to heat-calls affected heat tolerance at adulthood, with individuals exposed to heat-calls as embryos more likely to reach the highest Ta in morning trials. This was despite higher metabolic rate and evaporative water loss in heat-call individuals, partly driven by a stronger metabolic effect of moderate activity. At low Ta, however, heat-call exposed individuals had greater relative water economy, as predicted if heat-calls improve offspring thermoregulatory capacities. These results provide the first evidence that prenatal sound can have long-term effect on thermoregulation. Moreover, our findings point to a novel mechanism underlying developmental plasticity of thermal tolerance. 

Prenatal acoustic communication affects thermoregulation capacities in an arid-adapted bird.

Social behavior is an important part of the life of many animals with consequences for foraging and predator avoidance. In many species, individuals consistently vary in how social they are, which has consequences for group level dynamics. Recent work has found that individuals with a higher metabolic rate are less social, likely because they prioritize finding food over avoiding predators. In ectothermic animals like fish, temperature influences metabolic activity with higher temperatures leading to an increase in metabolic rate. As an individual fish moves through its environment, it is exposed to temporally and spatially different temperatures which could alter the individual motivation to engage in social behavior. Warming temperatures caused by climate change could also lead to reductions in social behavior and changes in overall group cohesion via effects on metabolic rate. However, the speed by which changes in metabolic rate affect expressed social behavior is not well understood. To test this, we acclimated common minnows (Phoxinus phoxinus) to three different temperatures (14, 17 and 20˚C) over 4 weeks.  We then measured maximum metabolic rate, standard metabolic rate and aerobic scope at acclimation temperature. In addition, we measured the routine metabolic rate, individual social behavior and group cohesiveness over a gradient of ramping temperatures (up to 23˚C). The results of this study will shed light into the effects of environmental change not only on an individual’s physiology and behavior but also on group behavior, which is essential to better predict the capacity of species to cope with climate change.

Effects of changing temperatures on social behavior via effects to metabolism in the common minnow (Phoxinus phoxinus)

The evolution of endothermy was instrumental to the diversification of birds and mammals, and enabled colonization of previously uninhabitable niches around the globe. However, in extreme environments such as high altitude, with extremely cold temperatures and limited O2 and food availability, the significant energetic demands of maintaining high body temperature (Tb) could offset the advantages of endothermy. We hypothesised that evolved reductions in Tb help overcome the metabolic challenges of cold hypoxia (CH) in deer mice native to high altitude. Deer mice with lowland or highland ancestry were held in warm normoxia (WN) or CH for 6 weeks, and then surgically instrumented with physiological telemeters. Mice in CH had significantly higher fH than mice in WN, underlain by reduced vagal tone and increased beta1-adrenergic tone on the heart, reflecting the metabolic challenges of CH. CH exposure led to marked reductions in Tb (~2˚C) in both lowlanders and highlanders. However, overlaid upon this plastic response to CH, highlanders had consistently lower Tb (~1˚C) than lowlanders. The combined effects of these plastic and evolved reductions in Tb were estimated to reduce metabolic demands by ~20%, based on theoretical expectations of Q10 effects and empirical measurements of the relationship between Tb and O2 consumption rate in these mice. Our results suggest that plastic and evolved reductions in Tb are important for overcoming the challenges at high altitudes, and provide a relatively rare example of evolved changes in Tb setpoint in a non-hibernating endotherm to cope with extreme environmental conditions.

Cool running: evolved reductions in body temperature and the metabolic costs of thermoregulation in deer mice native to high altitude

The interaction between chromatin and the nuclear lamina (NL) is intrinsically important to the establishment of three-dimensional chromatin architecture and spatiotemporal regulation of gene expression. However, critical regulators involved in this process are poorly understood in plants. Here, we report that Arabidopsis PNET2 and its two homologs are bona fide inner nuclear membrane proteins and integral components of the NL. PNET2s physically interact with the plant nucleoskeleton and engage nucleosome-enriched chromatin at the nuclear periphery. Loss of all three PNET2s leads to severely disrupted growth and development, concomitant activation of abiotic and biotic stress responses, and ultimate lethality in Arabidopsis. The pnet2 triple mutant also displays drastic transcriptome changes accompanied by a globally altered chromatin architecture revealed by HiC analysis. Our study identified PNET2 as an inner nuclear membrane (INM) component of the NL, which associates with chromatin and plays a critical role in orchestrating gene expression and chromatin organization in plants.











PNET2 is a component of the plant nuclear lamina and is required for proper genome organization and activity

Higher animals and plants are two evolutionary outcomes of complex multicellularity. An important driver
of cellular specialization and body plan expansion in both phyla was the evolution of vascular distribution
networks. Most prominently, the cardiovascular network of mammals distributes oxygen and nutrients
throughout the body, driven by the pumping action of the heart. By comparison, the vascular transport
systems of the dominant group of higher plants, the angiosperms, are fundamentally different. For instance,
transport of photosynthates in the phloem network is governed by dynamic source-sink relations and driven
by a pressure differential that builds up through locally controlled cellular osmolarity. The conducting
phloem channels are the so-called sieve tubes, which not only transport nutrients but also developmental
signals such as the phytohormone auxin. Sieve tubes are formed from interconnected individual sieve
elements that are meticulously aligned in cell files as they develop. Sieve elements represent a cellular
between-life-and-death state, because they lack numerous organelles, including the nucleus, and are
nurtured by their neighboring, so-called companion cells. The peculiar sieve element differentiation process
can be observed in growth apices. For example, in the root meristem of Arabidopsis thaliana seedlings their
development from stem cell into mature sieve element is laid out in a spatiotemporal gradient. My lab has
characterized a molecular network that guides this differentiation process through the interplay between
controlled transcellular auxin transport across developing sieve element cell files and autocrine receptor
kinase signaling pathways that respond to small peptide ligands. Key players in this network constitute a
molecular rheostat that finetunes transcellular auxin flux and maintains its pronounced cellular polarity
through a self-reinforcing mechanism. Our research suggests that this module is intimately connected to
the evolution of phloem, which enabled plants to effectively colonize land and thereby had a major impact
on the extant biosphere.

MNase-based MOA-Seq Pinpoints Native Cistrome Occupancy at 30-bp Resolution Amid Accessible Chromatin

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Biomechanics of controllable attachment in climbing animals

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