Latest Articles

• 

  Section: Animal Science ; Topics: Agricultural sciences, Physiology

  Is homeostatic efficiency a positive aspect of health and well-being?

  Colditz, Ian  

  10.24072/pcjournal.808 - Peer Community Journal, Volume 6 (2026), article no. e102

  Get full text PDF

  It has been recognized for more than a century that health entails strength and vitality and is more than the absence of disease. In the 1930s, the capacity of regulatory processes to maintain homeostasis in the face of environmental challenges was proposed as a measure of vitality. More recently, this same capacity has been described as resilience. With growing interest in breeding and managing animals for a better (positive) quality of life it is timely to re-examine vitality and resilience through the lens of homeostatic efficiency. The starting point for considering the impact of environmental perturbations is the nature of the animal – environment relationship. This discussion paper examines the relationship from an ecological perspective that emphasizes the subjective character of environmental perception. The ecological viewpoint recognizes that environmental perturbations provide opportunities as well as challenges to the animal. Processes facilitating acquisition of competence to master environmental perturbations – the attribute described as agency - are described. The characteristic that Walter Cannon and colleagues called homeostatic efficiency is compared with present day concepts of resilience and vitality. The relevance of the term homeostatic efficiency is appraised from the contemporary perspectives of homeorhesis and allostasis. It is suggested that homeostatic efficiency retains utility to describe proficiency of the animal in capturing opportunities and minimizing challenges in everyday life, as well as resilience in adversity. In accord with the biopsychosocial model of health, homeostatic efficiency is a system property of organismal regulation that integrates physiological, immune, cognitive, affective, behavioural, microbiome and social processes. Analyses of deviations from trajectories in outcomes of organismal regulation including milk yield, body weight, egg weight, fibre diameter, and feed intake have attracted attention recently as indicators of resilience. It is suggested that both resilience and vitality influence these outcomes. Better characterization of vitality could help clarify concepts and management of positive health and well-being in animals. A multidisciplinary collaboration to develop complementary definitions of the closely related concepts of vitality, resilience, thriving, flourishing, vigour, physiological reserve, and functional capacity would assist this endeavour.

• 

  Section: Genomics ; Topics: Genetics/genomics, Biophysics and computational biology, Systems biology

  NetSyn: prokaryotic genomic context exploration of protein families

  Stam, Mark;   Langlois, Jordan; Chevalier, Céline; Mainguy, Jean; Reboul, Guillaume;   Bastard, Karine;   Médigue, Claudine;   Vallenet, David  

  10.24072/pcjournal.805 - Peer Community Journal, Volume 6 (2026), article no. e101

  Get full text PDF

  Background. The growing availability of large prokaryotic genomic datasets presents an opportunity to discover new metabolic pathways and enzymatic reactions useful for industrial or synthetic biological applications. Efforts to identify new enzyme functions in this vast number of sequences cannot be achieved without bioinformatics tools and the development of new strategies. Standard methods for assigning a biological function to a gene are based on sequence similarity. However, complementary approaches rely on mining databases to identify conserved gene clusters (e.g., syntenies). In prokaryotic genomes, genes involved in the same pathway are frequently encoded in a single locus with an operonic organisation. This genomic context conservation is considered as a reliable indicator of functional relationships, and is therefore a promising approach for improving gene function prediction. Methods. Here we present NetSyn (Network Synteny), a tool to group protein sequences based on the conservation of their genomic context rather than solely on sequence similarity. From a list of protein sequence identifiers, NetSyn searches for the corresponding genome entries to  retrieve neighbouring genes. Corresponding protein sequences are grouped into families to define homology relationships and compute a synteny conservation score between the different extracted genomic contexts. A network is then created in which the nodes represent the input proteins and the edges indicate that two proteins share a conserved synteny. Finally, the network is partitioned into clusters grouping proteins with similar genomic contexts, using a community detection algorithm. Results. As a proof of concept, we used NetSyn on two different datasets. The first one is the BKACE protein family (formerly named DUF849) which has previously been divided into isofunctional sub-families. NetSyn was able to go a step further by providing additional sub-families beyond those already described. The second dataset corresponds to a set of non-homologous proteins belonging to three different glycoside hydrolase (GH) families. These GHs are known to work cooperatively in Polysaccharide-Utilization Loci (PUL) and are therefore grouped together in the same genomic contexts. NetSyn was able to identify a locus grouping 3 GHs, involved in the degradation of xyloglucan, in 162 prokaryotic genomes. Discussion. By highlighting conserved synteny in distantly related prokaryotic species, NetSyn enables functional links between proteins to be established beyond sequence similarity alone. We showed that NetSyn is efficient for exploring large prokaryotic protein families, enabling the definition of isofunctional groups and the identification of functional interactions between non-homologous enzymes. These features enable the prediction of new genomic structures that have not yet been experimentally characterised. Finally, NetSyn is also useful for pinpointing annotation errors that have been propagated across databases, and for suggesting annotations for proteins lacking functional prediction. NetSyn is freely available at https://github.com/labgem/netsyn. 

   

• 

  Section: Plants ; Topics: Plant biology

  Allometric scaling relationships of biomass for six common understory species in French temperate forests

  Populus, Claire;   Mårell, Anders;   Korboulewsky, Nathalie  

  10.24072/pcjournal.806 - Peer Community Journal, Volume 6 (2026), article no. e100

  Get full text PDF

  Forest ecologists often focus on trees and tend to overlook understory plants. However, understory species, despite representing less aboveground biomass than trees, are essential for forest dynamics and ecosystem functioning. The understory contributes to forest biodiversity, influences the forest microclimate and the availability of water and nutrients, and how disturbances, such as fires and large herbivores, impact the ecosystem. Estimating plant biomass can be difficult and time-consuming, but it is crucial to understanding and managing forest ecosystem services and risks. In this study, we improved biomass measurement methods for six common understory species in European temperate forests and with diverse ecologies and life forms: wood anemone (Anemone nemorosa), common heather (Calluna vulgaris), common honeysuckle (Lonicera periclymenum), purple moor-grass (Molinia caerulea), common bracken (Pteridium aquilinum) and brambles (Rubus fruticosus agg.). Based on vegetation samples and measurements from temperate forests in France, mostly on acidic soils, we developed aboveground biomass models. Our findings demonstrate that simple, rapid, non-destructive measurements – like cover and height – enabled us to accurately and precisely estimate the total aboveground (M_T), leaf (M_L), and stem (M_S) biomass. M_L and M_S scaled isometrically for heather and honeysuckle, and nearly isometrically for bracken, while bramble M_L and M_S scaled to 0.8 (i.e., varying leaf-to-stem ratio). These allometric scaling relationships are applicable at the scale of temperate acidic French forests and may also be applicable to European forests for the six species studied, thus promising a more complete estimation of forest biomass dynamics.

• 

  Section: Paleontology ; Topics: Paleontology, Evolution

  Garamaudo bauciensis, a new freshwater mosasaurid (Reptilia, Squamata) from the Santonian (Late Cretaceous) of Provence, southeastern France

  Bardet, Nathalie; Houssaye, Alexandra; Pelissier, François-Louis; Dutour, Yves; Turini, Eric; Tortosa, Thierry

  10.24072/pcjournal.804 - Peer Community Journal, Volume 6 (2026), article no. e99

  Get full text PDF

  Mosasauroids are primarily known as aquatic squamates that diversified in the marine realm during the Late Cretaceous. While most species had paddles, an elongated skull and body, and a laterally compressed tail, and lived in the open sea, some early species, with limbs similar to those of terrestrial animals and a varanoid-like body, lived in marine coastal shallow waters. Recently, mosasauroid remains have been discovered in freshwater environments in several continental deposits of the Santonian-Campanian of Europe. This study describes new cranial and postcranial mosasauroid remains from Santonian continental deposits in Provence, southeastern France, and attributes them to a new tethysaurine: Garamaudo bauciensis gen. et sp. nov. This mosasauroid, approximately 2.5 m long, with limbs looking adapted for a terrestrial locomotion and a sacrum, and with osteosclerosis in its vertebrae and humerus (at least), probably hovered at shallow depth in freshwater ecosystems. This new discovery reveals that it is only within the Tethysaurinae that multiple freshwater forms evolved, pointing to possible niche partitioning, associated with the retention of the plesiopedal / plesiopelvic condition, in parallel with the invasion of open waters by most other hydropedal and hydropelvic mosasauroids. These considerations suggest a richer evolutionary history of mosasauroids than is currently assumed.