Evolutionary Boundaries Research Articles

Exploring the Evolutionary Boundaries of Community Business

Community businesses contribute to the economic and social well-being of the communities in which they operate. As a subset of hybrid organizations, community businesses have unique challenges and opportunities related to their community embeddedness. Our study adopts an institutional logic perspective to understand the evolutionary boundaries of community business, which we argue, are shaped by the interplay of tensions between the social, market, and community logics. While existing literature discusses institutional logics from a dichotomous angle, focusing mainly on the social and market logics, we argue that the introduction of a third logic (i.e., community logics) has ramifications for the evolution of hybrid organizations. The different trajectories may have implications for the social, community, and economic impact that organizations can have. We draw on 39 qualitative interviews to provide useful insights for policy and practice on supporting community businesses.

Protective Roles of Hydrogen Sulfide in Alzheimer's Disease and Traumatic Brain Injury.

The gaseous signaling molecule hydrogen sulfide (H2S) critically modulates a plethora of physiological processes across evolutionary boundaries. These include responses to stress and other neuromodulatory effects that are typically dysregulated in aging, disease, and injury. H2S has a particularly prominent role in modulating neuronal health and survival under both normal and pathologic conditions. Although toxic and even fatal at very high concentrations, emerging evidence has also revealed a pronounced neuroprotective role for lower doses of endogenously generated or exogenously administered H2S. Unlike traditional neurotransmitters, H2S is a gas and, therefore, is unable to be stored in vesicles for targeted delivery. Instead, it exerts its physiologic effects through the persulfidation/sulfhydration of target proteins on reactive cysteine residues. Here, we review the latest discoveries on the neuroprotective roles of H2S in Alzheimer's disease (AD) and traumatic brain injury, which is one the greatest risk factors for AD.

Cold temperature extends longevity and prevents disease-related protein aggregation through PA28γ-induced proteasomes

Aging is a primary risk factor for neurodegenerative disorders that involve protein aggregation. Because lowering body temperature is one of the most effective mechanisms to extend longevity in both poikilotherms and homeotherms, a better understanding of cold-induced changes can lead to converging modifiers of pathological protein aggregation. Here, we find that cold temperature (15 °C) selectively induces the trypsin-like activity of the proteasome in Caenorhabditis elegans through PSME-3, the worm orthologue of human PA28γ/PSME3. This proteasome activator is required for cold-induced longevity and ameliorates age-related deficits in protein degradation. Moreover, cold-induced PA28γ/PSME-3 diminishes protein aggregation in C. elegans models of age-related diseases such as Huntington’s and amyotrophic lateral sclerosis. Notably, exposure of human cells to moderate cold temperature (36 °C) also activates trypsin-like activity through PA28γ/PSME3, reducing disease-related protein aggregation and neurodegeneration. Together, our findings reveal a beneficial role of cold temperature that crosses evolutionary boundaries with potential implications for multi-disease prevention.

Beyond S&OP Implementation: A maturity model and meta-framework for assessing and managing evolution paths

Goal: The purpose of this paper is to present an S&OP meta-framework that combines specific S&OP tools and an original S&OP maturity model as an approach to reduce uncertainty and increase commitment in the S&OP implementation process. Design/ Methodology/ Approach: A systematic review led to the development of a six-pillar S&OP tool framework. Then, a maturity model and an S&OP implementation meta-framework, were defined for managing the introduction and evolution of S&OP dimensions. Results: The S&OP maturity model provides a structured model for identifing critical gaps in the S&OP process. Furthermore, the S&OP meta-framework - combining Action Research (AR), Kotter’s 8 steps, and agile project management approaches - provides an holistic implementation guide for promoting large-scale transformation in S&OP implementation efforts. Limitations of the investigation: The S&OP maturity model and implementation system are new empirical contributions to the literature and have not been validated in this article. Practical implications: This work provides a set of tools to address specific S&OP environments; a maturity model to diagnose the S&OP process; and an S&OP implementation framework to reduce uncertainty and increase commitment in the change process. Originality / Value: This article fills a literature gap of necessary S&OP implementation practices, contributing to: (1) an S&OP tools framework, (2) an S&OP maturity model based on evolutionary boundaries correlated to the presence of specific tools, processes and metrics, and (3) an S&OP implementation meta-framework, raising awareness in under researched S&OP dimensions for more oriented research and practices needed to promote sustainable change.

Genomic and phenotypic divergence informs translocation strategies for an endangered freshwater fish.

Translocation, the movement of organisms for conservation purposes, can result in unintended introgression if genetic material flows between populations in new ways. The Bluemask Darter Etheostoma akatulo is a federally endangered species of freshwater fish inhabiting the Caney Fork River system and three of its tributaries (Collins River, Rocky River, and Cane Creek) in Tennessee. The current conservation strategy for Bluemask Darters involves translocating the progeny of broodstock from the Collins River (in the west) to the Calfkiller River (in the east) where the species had been extirpated. In this study, we use ddRAD sequence data from across the extant range to assess this translocation strategy in light of population structure, phylogeny, and demography. We also include museum specimen data to assess morphological variation among extant and extirpated populations. Our analyses reveal substantial genetic and phenotypic disparities between a western population in the Collins River and an eastern population encompassing the Rocky River, Cane Creek, and upper Caney Fork, the two of which shared common ancestry more than 100,000years ago. Furthermore, morphological analyses classify 12 of 13 Calfkiller River specimens with phenotypes consistent with the eastern population. These results suggest that current translocations perturb the evolutionary boundaries between two delimited populations. Instead, we suggest that repopulating the Calfkiller River using juveniles from the Rocky River could balance conflicting signatures of demography, diversity, and divergence. Beyond conservation, the microgeographic structure of Bluemask Darter populations adds another puzzle to the phylogeography of the hyperdiverse freshwater fishes in eastern North America.

Flash forward genetics: new twists in transcription across evolutionary boundaries

"Flash forward genetics" refers to a genetic approach based on the functional interaction of a given factor with unknown partner(s) converging on shared targets across evolutionary boundaries. A study by Li et al (2021), published in this issue of EMBO Reports, illustrates the innovative potential of the approach. The authors applied it to identify interacting factors for FOXN1, a mammalian transcription factor with a highly specialized function in hair follicle morphogenesis and thymus. The authors express FOXN1 in the Drosophila eye to perform an unbiased genetic screen in a totally heterologous system. In a remarkable tour de force, the authors identify and characterize a factor so far known for its ubiquitous function in transcription elongation, AFF4. Li et al show that AFF4 plays also a specific role in hair follicle and thymus development in the mouse overlapping with that of FOXN1.

The ubiquitin-conjugating enzyme UBE2K determines neurogenic potential through histone H3 in human embryonic stem cells

Histones modulate gene expression by chromatin compaction, regulating numerous processes such as differentiation. However, the mechanisms underlying histone degradation remain elusive. Human embryonic stem cells (hESCs) have a unique chromatin architecture characterized by low levels of trimethylated histone H3 at lysine 9 (H3K9me3), a heterochromatin-associated modification. Here we assess the link between the intrinsic epigenetic landscape and ubiquitin-proteasome system of hESCs. We find that hESCs exhibit high expression of the ubiquitin-conjugating enzyme UBE2K. Loss of UBE2K upregulates the trimethyltransferase SETDB1, resulting in H3K9 trimethylation and repression of neurogenic genes during differentiation. Besides H3K9 trimethylation, UBE2K binds histone H3 to induce its polyubiquitination and degradation by the proteasome. Notably, ubc-20, the worm orthologue of UBE2K, also regulates histone H3 levels and H3K9 trimethylation in Caenorhabditis elegans germ cells. Thus, our results indicate that UBE2K crosses evolutionary boundaries to promote histone H3 degradation and reduce H3K9me3 repressive marks in immortal cells.

Selective Persulfide Detection Reveals Evolutionarily Conserved Antiaging Effects of S-Sulfhydration

Life on Earth emerged in a hydrogen sulfide (H2S)-rich environment eons ago and with it protein persulfidation mediated by H2S evolved as a signaling mechanism. Protein persulfidation (S-sulfhydration) is a post-translational modification of reactive cysteine residues, which modulate protein structure and/or function. Persulfides are difficult to label and study due to their reactivity and similarity with cysteine. Here, we report a facile strategy forchemoselective persulfide bioconjugation usingdimedone-based probes, to achieve highly selective, rapid, and robust persulfide labeling in biological samples with broad utility. Using this method, we show persulfidation is an evolutionarily conserved modification and waves of persulfidation are employed by cells to resolve sulfenylation and prevent irreversible cysteine overoxidation preserving protein function. We report an age-associated decline in persulfidation that is conserved across evolutionary boundaries. Accordingly, dietary or pharmacological interventions to increase persulfidation associate with increased longevityand improved capacity to cope with stress stimuli.

The TAM: A Translocation and Assembly Module of the β-Barrel Assembly Machinery in Bacterial Outer Membranes.

Assembly of proteins into the outer membrane is an essential process in the cell biology of bacteria. The integration of β-barrel proteins into the outer membrane is mediated by a system referred to as the β-barrel assembly machinery (BAM) that includes two related proteins: BamA in the BAM complex and TamA in the TAM (translocation and assembly module). Here we review what is known about the TAM in terms of its function and the structural architecture of its two subunits, TamA and TamB. By linking the energy transduction possibilities in the inner membrane to TamA in the outer membrane, the TAM provides additional capability to the β-barrel assembly machinery. Conservation of the TAM across evolutionary boundaries, and the presence of hybrid BAM/TAM complexes in some bacterial lineages, adds insight to our growing understanding of how bacterial outer membranes are built.

Dietary and Endocrine Regulation of Endogenous Hydrogen Sulfide Production: Implications for Longevity.

Hydrogen sulfide (H2S) at the right concentration is associated with numerous health benefits in experimental organisms, ranging from protection from ischemia/reperfusion injury to life span extension. Given the considerable translation potential, two major strategies have emerged: supplementation of exogenous H2S and modulation of endogenous H2S metabolism. Recent Advances: Recently, it was reported that hepatic H2S production capacity is increased in two of the best-characterized mammalian models of life span extension, dietary restriction, and hypopituitary dwarfism, leading to new insights into dietary and hormonal regulation of endogenous H2S production together with broader changes in sulfur amino acid (SAA) metabolism with implications for DNA methylation and redox status. Here, we discuss the role of dietary SAAs and growth hormone (GH)/thyroid hormone (TH) signaling in regulation of endogenous H2S production largely via repression of H2S generating enzymes cystathionine γ-lyase (CGL) and cystathionine β-synthase (CBS) on the level of gene transcription, as well as reciprocal regulation of GH and TH signaling by H2S itself. We also discuss plasticity of CGL and CBS gene expression in response to environmental stimuli and the potential of the microbiome to impact overall H2S levels. The relative contribution of increased H2S to health span or lifespan benefits in models of extended longevity remains to be determined, as does the mechanism by which such benefits occur. Nonetheless, our ability to control H2S levels using exogenous H2S donors or by modifying the endogenous H2S production/consumption equilibrium has the potential to improve health and increase "shelf-life" across evolutionary boundaries, including our own. Antioxid. Redox Signal. 28, 1483-1502.

Detailed biostratigraphic scales as based on the palaeobiogenetical approach (an example of the Upper Bajocian – Lower Bathonian ostracod scale of the Russian Platform)

Two new species of ostracods of the family Progonocytheridae Sylvester-Bradley Camptocythere (C.) lateres Tesakova et Shurupova, sp. nov. and C. (C.) angustius Tesakova et Shurupova, sp. nov. from the Michalskii and Besnosovi ammonite zones (Upper Bajocian – Lower Bathonian, Middle Jurassic) of the Sokur section (Saratov) are described. The changes in ontogenesis in the phylogeny of Camptocythere (C.) lateres Tesakova et Shurupova in the stratigraphical interval corresponding to the Palaeocytheridea kalandadzei ostracod Zone, and especially to the beds with C. (C.) lateres, have been studied. The levels of the change in the predominant type of sculpture (corresponding to evolutionary boundaries) are recognized in the sculpture development among the adult representatives of the species in its phylogeny. This palaeobiogenetic (heterochrony) approach allows subdivision of the beds with C. (C.) lateres into three stratigrapical intervals characterized by changes in the type of sculpture.

Cortinarius section Bicolores and section Saturnini (Basidiomycota, Agaricales), a morphogenetic overview of European and North American species.

Cortinarius is the largest genus of ectomycorrhizal fungi worldwide. Recent molecular studies have shown high levels of morphological homoplasy within the genus. Importantly, DNA phylogenies can reveal characteristics that have been either over- or underemphasized in taxonomic studies. Here we sequenced and phylogenetically analysed a large set of pan-European and North American collections taxonomically studied and placed in Cortinarius sect. Bicolores and sect. Saturnini, according to traditional morpho-anatomical criteria. Our goal was to circumscribe the evolutionary boundaries of the two sections, to stabilize both the limits and nomenclature of relevant species, and to identify described taxa which, according to our current understanding, belong to other lineages. Our analysis resolves two clades: /Bicolores, including 12 species, one of which is new to science, and /Saturnini, including 6 species. Fifteen binomials, traditionally treated in these two sections based on morphology, do not belong to the above two phylogenetic clades. Instead, six of these latter are clearly placed in other clades that represent sect. Bovini, sect. Sciophylli, sect. Duracini and sect. Brunneotincti. The presence or absence of blue pigments and the detection of specific odours emerge as clearly misleading taxonomic features, but more surprisingly, spore size and ecology can be misleading as well. A total of 63 type specimens were sequenced, 4 neotypes and 2 epitypes are proposed here, and 1 new combination is made.

Hypothalamic-Pituitary Axis Regulates Hydrogen Sulfide Production

SummaryDecreased growth hormone (GH) and thyroid hormone (TH) signaling are associated with longevity and metabolic fitness. The mechanisms underlying these benefits are poorly understood, but may overlap with those of dietary restriction (DR), which imparts similar benefits. Recently we discovered that hydrogen sulfide (H2S) is increased upon DR and plays an essential role in mediating DR benefits across evolutionary boundaries. Here we found increased hepatic H2S production in long-lived mouse strains of reduced GH and/or TH action, and in a cell-autonomous manner upon serum withdrawal in vitro. Negative regulation of hepatic H2S production by GH and TH was additive and occurred via distinct mechanisms, namely direct transcriptional repression of the H2S-producing enzyme cystathionine γ-lyase (CGL) by TH, and substrate-level control of H2S production by GH. Mice lacking CGL failed to downregulate systemic T4 metabolism and circulating IGF-1, revealing an essential role for H2S in the regulation of key longevity-associated hormones.

Repurposing proteins for new bioinorganic functions.

Inspired by the remarkable sophistication and complexity of natural metalloproteins, the field of protein design and engineering has traditionally sought to understand and recapitulate the design principles that underlie the interplay between metals and protein scaffolds. Yet, some recent efforts in the field demonstrate that it is possible to create new metalloproteins with structural, functional and physico-chemical properties that transcend evolutionary boundaries. This essay aims to highlight some of these efforts and draw attention to the ever-expanding scope of bioinorganic chemistry and its new connections to synthetic biology, biotechnology, supramolecular chemistry and materials engineering.

Free surface flows over partially erodible beds by a continuous finite element method

This paper presents a continuous finite element model for shallow water equations coupled with a bedload sediment conservation law. The model incorporates a sign-preserving conservative correction based on the flux correction transport methodology. Complete algorithm permits simulation of flows with evolutionary boundaries and erodible–non erodible interfaces under severe conditions without spurious mass exchanges and oscillations. Numerical experiments explore the efficacy of the procedure for dam-break problems on channels with dry beds, for partially and totally erodible beds, and for migration of small bedforms. Computation of real river morphodynamics under intense flooding illustrates practical application of the model.

What Is Peromyscus? Evidence from nuclear and mitochondrial DNA sequences suggests the need for a new classification.

The evolutionary relationships between Peromyscus, Habromys, Isthmomys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are poorly understood. In order to further explore the evolutionary boundaries of Peromyscus and compare potential taxonomic solutions for this diverse group and its relatives, we conducted phylogenetic analyses of DNA sequence data from alcohol dehydrogenase (Adh1-I2), beta fibrinogen (Fgb-I7), interphotoreceptor retinoid-binding protein (Rbp3), and cytochrome-b (Cytb). Phylogenetic analyses of mitochondrial and nuclear genes produced similar topologies although levels of nodal support varied. The best-supported topology was obtained by combining nuclear and mitochondrial sequences. No monophyletic Peromyscus clade was supported. Instead, support was found for a clade containing Habromys, Megadontomys, Neotomodon, Osgoodomys, Podomys, and Peromyscus suggesting paraphyly of Peromyscus and confirming previous observations. Our analyses indicated an early divergence of Isthmomys from Peromyscus (approximately 8 million years ago), whereas most other peromyscine taxa emerged within the last 6 million years. To recover a monophyletic taxonomy from Peromyscus and affiliated lineages, we detail 3 taxonomic options in which Habromys, Megadontomys, Neotomodon, Osgoodomys, and Podomys are retained as genera, subsumed as subgenera, or subsumed as species groups within Peromyscus. Each option presents distinct taxonomic challenges, and the appropriate taxonomy must reflect the substantial levels of morphological divergence that characterize this group while maintaining the monophyletic relationships obtained from genetic data.

Community genomic analyses constrain the distribution of metabolic traits across the Chloroflexi phylum and indicate roles in sediment carbon cycling.

BackgroundSediments are massive reservoirs of carbon compounds and host a large fraction of microbial life. Microorganisms within terrestrial aquifer sediments control buried organic carbon turnover, degrade organic contaminants, and impact drinking water quality. Recent 16S rRNA gene profiling indicates that members of the bacterial phylum Chloroflexi are common in sediment. Only the role of the class Dehalococcoidia, which degrade halogenated solvents, is well understood. Genomic sampling is available for only six of the approximate 30 Chloroflexi classes, so little is known about the phylogenetic distribution of reductive dehalogenation or about the broader metabolic characteristics of Chloroflexi in sediment.ResultsWe used metagenomics to directly evaluate the metabolic potential and diversity of Chloroflexi in aquifer sediments. We sampled genomic sequence from 86 Chloroflexi representing 15 distinct lineages, including members of eight classes previously characterized only by 16S rRNA sequences. Unlike in the Dehalococcoidia, genes for organohalide respiration are rare within the Chloroflexi genomes sampled here. Near-complete genomes were reconstructed for three Chloroflexi. One, a member of an unsequenced lineage in the Anaerolinea, is an aerobe with the potential for respiring diverse carbon compounds. The others represent two genomically unsampled classes sibling to the Dehalococcoidia, and are anaerobes likely involved in sugar and plant-derived-compound degradation to acetate. Both fix CO2 via the Wood-Ljungdahl pathway, a pathway not previously documented in Chloroflexi. The genomes each encode unique traits apparently acquired from Archaea, including mechanisms of motility and ATP synthesis.ConclusionsChloroflexi in the aquifer sediments are abundant and highly diverse. Genomic analyses provide new evolutionary boundaries for obligate organohalide respiration. We expand the potential roles of Chloroflexi in sediment carbon cycling beyond organohalide respiration to include respiration of sugars, fermentation, CO2 fixation, and acetogenesis with ATP formation by substrate-level phosphorylation.

FOXO4 is necessary for neural differentiation of human embryonic stem cells

Proteostasis is critical for maintaining cell function and proteome stability may play an important role in human embryonic stem cell (hESC) immortality. Notably, hESC populations exhibit a high assembly of active proteasomes, a key node of the proteostasis network. FOXO4, an insulin/IGF-1 responsive transcription factor, regulates proteasome activity in hESCs. We find that loss of FOXO4 reduces the potential of hESCs to differentiate into neural lineages. Therefore, FOXO4 crosses evolutionary boundaries and links hESC function to invertebrate longevity modulation.

Defining evolutionary boundaries across parapatric ecomorphs of Black Salamanders (Aneides flavipunctatus) with conservation implications

The accurate delimitation of evolutionary population units represents an important component in phylogeographic and conservation genetic studies. Here, we used a combined population assignment and historical demographic approach to study a complex of ecomorphologically distinctive populations of Black Salamanders (Aneides flavipunctatus) that are parapatrically distributed and meet at a three-way contact zone in north-western California. We used mitochondrial tree-based and multilocus clustering methods to evaluate a priori two- (Northern and Southern) and three (Northern, Coast and Inland) population hypotheses derived from previous studies. Mitochondrial results were consistent with the two- and three-population hypotheses, while the nDNA clustering results supported only the two-population hypothesis. Historical demographic analyses and mtDNA gene divergence estimates revealed that the Northern and Southern populations split during the Pliocene (2-5 Ma). Subdivision of the Southern population into Coast and Inland populations was estimated to be late Pleistocene (0.24 Ma), although our mtDNA results suggested a Pliocene divergence. Effective gene flow estimates (2N(e)m) suggest that either the two- or three-population hypotheses remain valid. However, our results unexpectedly revealed that the Northern population might instead represent two parapatric populations that separated nearly 4 Ma. These results are surprising because the Pliocene divergence between these ecomorphologically conservative forms is similar or older than for the ecomorphologically divergent Coast and Inland sister populations. We conclude that Black Salamanders in north-western California belong to at least three or four populations or species, and these all meet criteria for being Evolutionary Significant Units or 'ESUs' and therefore warrant conservation consideration.

Non-oscillatory continuous FEM for transport and shallow water flows

The paper presents a sign-preserving continuous finite element model (FEM) for coupled transport equations, and in particular for the depth-integrated shallow water equations. The model incorporates an enhanced flux corrected transport method (FCT) with a high order solution given by a generalization of the characteristic based split finite element method (CBS), and a predictor positive algorithm founded in a finite element upwind methodology. Numerical experiments explore the efficacy of the procedure, with emphasis in the simulation of flows with evolutionary boundaries determined by null values of any flow property, and in severe conditions of propagation such as dam-breaking waves.