Proteome allocation and the evolution of metabolic cross-feeding

Metabolic cross-feeding (MCF) is a widespread type of ecological interaction where organisms share nutrients. In a common instance of MCF, an organism incompletely metabolizes sugars and releases metabolites that are used by another as a carbon source to produce energy. Why would the former waste edible food, and why does this preferentially occur at specific locations in the sugar metabolic pathway (acetate and glycerol are preferentially exchanged) have challenged evolutionary theory for decades. After showing that cells should in principle prioritise upstream reactions, we investigate how a special feature of these metabolites - their high diffusivity across the cell membrane - may trigger the emergence of cross feeding in a population. We explicitly model metabolic reactions, their enzyme-driven catalysis, and the cellular constraints on the proteome that may incur a cost to expressing all enzymes along the metabolic pathway. We find that up to high permeability coefficients of an intermediate metabolite, the expected evolutionary outcome is not a diversification that resembles cross-feeding but a single genotype that instead overexpresses the enzymes downstream the metabolite to limit its diffusion. Only at very high permeabilities and under restricted sets of parameters should the population diversify and MCF evolve.

Micro- and macroevolutionary change of colony-level traits in bryozoans

The evolution of trait variation among populations of animals is difficult to study due to the many overlapping genetic and environmental influences that control phenotypic expression. In a group of animals, bryozoans, it is possible to isolate genetic contributions to phenotypic variation, due to the modular nature of bryozoan colonies. Each bryozoan colony represents a snapshot of the phenotypes that correspond to a single genotype, which can be summarized as a phenotypic distribution. We test whether these phenotypic distributions are heritable across generations of colonies in two sister species of the bryozoan Stylopoma, grown and bred in a common garden breeding experiment. We find that components of phenotypic distributions, specifically median trait values of colony members, are heritable between generations of colonies. Furthermore, this heredity has macroevolutionary importance because it correlates with the morphological distance between these two species. Because parts of phenotypic distributions are heritable, and this heritability corresponds to evolutionary divergence between species, we infer that these distributions have the potential to evolve. The evolutionary potential of these phenotypic distributions may underpin the emergence of colony-level traits, like division of labor in colonies.

Genotypic correlation between Salmonella Enteritidis isolates from broiler breeders and hatchery flocks

In this study, Salmonella Enteritidis strains isolated from dust and environmental materials from different flocks located in Turkey’s Western Black Sea region were examined by pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). A total of 59 S. Enteritidis strains isolated from broiler breeder and hatchery flocks, and one S. Enteritidis strain isolated from a stool sample of a farm worker were examined. PFGE analysis revealed two major PFGE groups and nine different macro restriction profiles. It was determined that 85% (51/60) of the strains were close to each other and comprised Group I. All S. Enteritidis strains had the same sequence type (ST): ST11. Isolation of strains with a single genotype suggests that there may be a cross transmission between the flocks.

New Clade 2.3.4.4b H5N1 Highly Pathogenic Avian Influenza Genotype Detected in Europe in 2021

Despite their widespread distribution, the clade 2.3.4.4b H5N1 viruses have so far only been known in a single genotype variant in Europe. In the study presented, we report the first detection of a new highly pathogenic avian influenza H5N1 genotype in geese and ducks from a backyard farm in the Czech Republic. Phylogenetic analysis has revealed that the Czech H5N1 virus retained the A/Eurasian_Wigeon/Netherlands/1/2020-like backbone with an altered PB2 segment from co-circulating low pathogenic avian influenza viruses.

Norovirus Structure and Classification

Norovirus are a major cause of acute gastroenteritis worldwide. Diarrheal disease is now the fourth common cause of mortality children under the age of 5 years but remain the 2nd most cause of morbidity. NoV are associated with 18% diarrheal diseases worldwide where rotavirus vaccinations has been successfully introduced. NoV has become major cause of gastroenteritis in children. NoV belong to family caliciviridae. They are non-enveloped, single stranded positive sense RNA Viruses. The genome consists of 3 Open reading frames, ORF-1 codes for non-structural protein, ORF-2 codes for major capsid protein VP1 and ORF-3 for minor capsid protein VP2. Based on sequence difference of the capsid gene (VP1), NoV have been classified in to seven genogroup GI-GVII with over 30 genotypes. Genogroups I, II, IV are associated with human infection. Despite this extensive diversity a single genotype GII.4 has been alone to be the more prevalent. Basic epidemiological disease burden data are generated from developing countries. NoV are considered fast evolving viruses and present an extensive diversity that is driven by acquisition of point mutations and recombinations. Immunity is strain or genotype specific with little or no protection conferred across genogroups. Majority of outbreaks and sporadic norovirus cases worldwide are associated with a single genotype, GII.4 which was responsible for 62% of reported NoV outbreaks in 5 continents from 2001 to 2007. GII.4 variants have been reported as major cause of global gastroenteritis pandemics starting in 1995 frequent emergence of novel GII.4 variants is known to be due to rapid evolution and antigenic variation in response to herd immunity. Novel GII.4 variants appear almost every 2 years. Recent GII.4 variant reported include Lordsdale 1996, Farmington Hills 2002, Hunter 2004, Yerseke 2006a, Den Haag 2006b, Apeldoon 2007, New Orleans 2009,most recently Sydney 2012. Detailed molecular epidemiologic investigation of NoV is associated for understanding the genetic diversity of NoV strain and emergence of novel NoV variants. However, reports have revealed that not all individuals develop symptoms and a significant proportion remains asymptomatic after NoV infections.

Stochastic fluctuations drive non-genetic evolution of proliferation in clonal cancer cell populations

Evolutionary dynamics allows to understand many changes happening in a broad variety of biological systems, ranging from individuals to complete ecosystems. It is also behind a number of remarkable organizational changes that happen during the natural history of cancers. These reflect tumour heterogeneity, which is present at all cellular levels, including the genome, proteome and phenome, shaping its development and interrelation with its environment. An intriguing observation in different cohorts of oncological patients is that tumours exhibit an increased proliferation as the disease progresses, while the timescales involved are apparently too short for the fixation of sufficient driver mutations to promote an explosive growth. In this paper we discuss how phenotypic plasticity, emerging from a single genotype, may play a key role and provide a ground for a continuous acceleration of the proliferation rate of clonal populations with time. Here we address this question by means of stochastic and deterministic mathematical models that capture proliferation trait heterogeneity in clonal populations and elucidate the contribution of phenotypic transitions on tumour growth dynamics.

Genetic diversity analysis through cluster constellation in Brinjal (Solanum melongena L.)

In present investigation, 110 locally developed genotypes from different breeding programmes in brinjal were classified into eleven clusters on the basis of their D2 values computed from Mahalanobis D2 statistics of twelve morphological traits, wherein inter-and intra-cluster distances highlighted the genetic divergence of the genotypes grouped among and within different clusters. Among all, fourth cluster was the largest with 33 genotypes; however, each of second, fifth, ninth, tenth and eleventh clusters contained only single genotype. The genotypes of eighth and tenth clusters were highly diverse (1584.40) followed by third and eighth (1431.31), eighth and ninth (1302.69), sixth and eighth (1126.33) and first and eighth (1042.91) clusters. Intra-cluster (within cluster) variation was the highest in seventh cluster (74.43) followed by eighth (61.20) and sixth (54.36) that described the diverse nature of eighteen, five and nineteen genotypes in these groups, respectively. However, PBL-268, PBGL-401, PBL-243, PSR 308 and PBOB-518 were grouped individually in IInd, Vth, IXth, Xth and XIth clusters, respectively. Overall, fifth cluster had most vigorous and high yielding ((2.82 kg/plant) genotype (PBGL-405); eighth cluster included genotypes with big round fruits and maximum fruit weight (317.43g); and tenth cluster had the earliest genotype (PSR-308) with the maximum number of fruits per plant (43.17). Out of twelve morphological traits, 94.19% diversity was brought by average fruit weight (67.86%), number of fruits per plant (17.26%), fruit yield per plant (5.37%) and fruit breadth (3.70%), however, other traits had negligible share towards the variation. This study created the foundation for future hybridization programmes in brinjal, where the parents can be selected on the basis of highly diverse groups as well as traits.

Birth order as a source of within-genotype diversification in the clonal duckweed, Spirodela polyrhiza (Araceae: Lemnoideae)

Organismal persistence attests to adaptive responses to environmental variation. Diversification bet hedging, in which risk is reduced at the cost of expected fitness, is increasingly recognized as an adaptive response, yet mechanisms by which a single genotype generates diversification remain obscure. The clonal greater duckweed, Spirodela polyrhiza (L.), facultatively expresses a seed-like but vegetative form, the ‘turion’, that allows survival through otherwise lethal conditions. Turion reactivation phenology is a key fitness component, yet little is known about turion reactivation phenology in the field, or sources of variation. Here, using floating traps deployed in the field, we found a remarkable extent of variation in natural reactivation phenology that could not be explained solely by spring cues, occurring over a period of ≥ 200 days. In controlled laboratory conditions, we found support for the hypothesis that turion phenology is influenced jointly by phenotypic plasticity to temperature and diversification within clones. Turion ‘birth order’ consistently accounted for a difference in reactivation time of 46 days at temperatures between 10 and 18 °C, with turions early in birth order reactivating more rapidly than turions late in birth order. These results should motivate future work to evaluate the variance in turion phenology formally as a bet-hedging trait.

Woltereck's Genotype

The reaction norm, originally introduced by Richard Woltereck in 1909, describes the range of phenotypes available to a single genotype under different environments. It is a foundational concept in genetics and evolutionary thought. At its inception, it represented a counterpoint to a hereditarian Mendelism championed by Wilhelm Johannsen, though both authors ultimately agreed that the reaction norm was essentially identical to the “genotype” term introduced by Johannsen. Woltereck literally and figuratively wrote “Genotypus = Reaktionsnorm”. However, some have argued that Woltereck’s interpretation of the reaction norm was incomplete up to the point of Johannsen’s commentary on it. Here, I demonstrate that the reaction norm constituted a direct and intentional challenge to Johannsen’s original notion of fixed differences between types, and present new translations of relevant texts from both Johannsen and Woltereck. I conclude that both authors’ acceptance of the equivalence between genotypes and reaction norms constituted a redefinition of the genotype by Woltereck that was ultimately accepted (with apparent poor grace) by Johannsen.