A dynamic network model predicts the phenotypes of multicellular clusters from cellular properties.

Cell division without cell separation produces multicellular clusters in budding yeast. Two fundamental characteristics of these clusters are their size (the number of cells per cluster) and cellular composition: the fractions of cells with different phenotypes. Using cells as nodes and links between mother and daughter cells as edges, we model cluster growth and breakage by varying three parameters: the cell division rate, the rate at which intercellular connections break, and the kissing number (the maximum number of connections to one cell). We find that the kissing number sets the maximum possible cluster size. Below this limit, the ratio of the cell division rate to the connection breaking rate determines the cluster size. If links have a constant probability of breaking per unit time, the probability that a link survives decreases exponentially with its age. Modeling this behavior recapitulates experimental data. We then use this framework to examine synthetic, differentiating clusters with two cell types, faster-growing germ cells and their somatic derivatives. The fraction of clusters that contain both cell types increases as either of two parameters increase: the kissing number and difference between the growth rate of germ and somatic cells. In a population of clusters, the variation in cellular composition is inversely correlated (r2 = 0.87) with the average fraction of somatic cells in clusters. Our results show how a small number of cellular features can control the phenotypes of multicellular clusters that were potentially the ancestors of more complex forms of multicellular development, organization, and reproduction.

Multicellular growth as a dynamic network of cells.

Cell division without cell separation produces multicellular clusters in budding yeast. Two fundamental characteristics of these clusters are their size (the number of cells per cluster) and cellular composition: the fractions of cells with different phenotypes. However, we do not understand how different cellular features quantitatively influence these two phenotypes. Using cells as nodes and links between mother and daughter cells as edges, we model cluster growth and breakage by varying three parameters: the cell division rate, the rate at which intercellular connections break, and the kissing number (the maximum number of connections to one cell). We find that the kissing number sets the maximum possible cluster size. Below this limit, the ratio of the cell division rate to the connection breaking rate determines the cluster size. If links have a constant probability of breaking per unit time, the probability that a link survives decreases exponentially with its age. Modeling this behavior recapitulates experimental data. We then use this framework to examine synthetic, differentiating clusters with two cell types, faster-growing germ cells and their somatic derivatives. The fraction of clusters that contain both cell types increases as either of two parameters increase: the kissing number and difference between the growth rate of germ and somatic cells. In a population of clusters, the variation in cellular composition is inversely correlated (r2=0.87) with the average fraction of somatic cells in clusters. Our results show how a small number of cellular features can control the phenotypes of multicellular clusters that were potentially the ancestors of more complex forms of multicellular development, organization, and reproduction.

Extending the reach of homology by using successive computational filters to find yeast pheromone genes.

The mating of fungi depends on pheromones that mediate communication between two mating types. Most species use short peptides as pheromones, which are either unmodified (e.g., α-factor in Saccharomyces cerevisiae) or C-terminally farnesylated (e.g., a-factor in S. cerevisiae). Peptide pheromones have been found by genetics or biochemistry in a small number of fungi, but their short sequences and modest conservation make it impossible to detect homologous sequences in most species. To overcome this problem, we used a four-step computational pipeline to identify candidate a-factor genes in sequenced genomes of the Saccharomycotina, the fungal clade that contains most of the yeasts: we require that candidate genes have a C-terminal prenylation motif, are shorter than 100 amino acids long, and contain a proteolytic-processing motif upstream of the potential mature pheromone sequence and that closely related species contain highly conserved homologs of the potential mature pheromone sequence. Additional manual curation exploits the observation that many species carry more than one a-factor gene, encoding identical or nearly identical pheromones. From 332 Saccharomycotina genomes, we identified strong candidate pheromone genes in 241 genomes, covering 13 clades that are each separated from each other by at least 100 million years, the time required for evolution to remove detectable sequence homology among small pheromone genes. For one small clade, the Yarrowia, we demonstrated that our algorithm found the a-factor genes: deleting all four related genes in the a-mating type of Yarrowia lipolytica prevents mating.

Correction: Ploidy and recombination proficiency shape the evolutionary adaptation to constitutive DNA replication stress.

[This corrects the article DOI: 10.1371/journal.pgen.1009875.].

Alternating selection for dispersal and multicellularity favors regulated life cycles.

The evolution of complex multicellularity opened paths to increased morphological diversity and organizational novelty. This transition involved three processes: cells remained attached to one another to form groups, cells within these groups differentiated to perform different tasks, and the groups evolved new reproductive strategies.1,2,3,4,5 Recent experiments identified selective pressures and mutations that can drive the emergence of simple multicellularity and cell differentiation,6,7,8,9,10,11 but the evolution of life cycles, particularly how simple multicellular forms reproduce, has been understudied. The selective pressure and mechanisms that produced a regular alternation between single cells and multicellular collectives are still unclear.12 To probe the factors regulating simple multicellular life cycles, we examined a collection of wild isolates of the budding yeast S. cerevisiae.12,13 We found that all these strains can exist as multicellular clusters, a phenotype that is controlled by the mating-type locus and strongly influenced by the nutritional environment. Inspired by this variation, we engineered inducible dispersal in a multicellular laboratory strain and demonstrated that a regulated life cycle has an advantage over constitutively single-celled or constitutively multicellular life cycles when the environment alternates between favoring intercellular cooperation (a low sucrose concentration) and dispersal (a patchy environment generated by emulsion). Our results suggest that the separation of mother and daughter cells is under selection in wild isolates and is regulated by their genetic composition and the environments they encounter and that alternating patterns of resource availability may have played a role in the evolution of life cycles.

Erector Spinae Plane Block With Liposomal Bupivacaine: Analgesic Adjunct in Adult Pectus Surgery.

INTRODUCTION: Pain management may be challenging in patients undergoing pectus excavatum (PE) bar removal surgery. To enhance recovery, opioid sparing strategies with regional anesthesia including ultrasound-guided erector spinae plane block (ESPB) have been implemented. The purpose of this study was to evaluate the safety and efficacy of bilateral ESPB with a liposomal bupivacaine/traditional bupivacaine mixture as part of an enhanced patient recovery pathway. MATERIALS AND METHODS: A retrospective review of adult patients who underwent PE bar removal from January 2019 to December 2020 was performed. Perioperative data were reviewed and recorded. Patients who received ESPB were compared to historical controls (non-ESPB patients). RESULTS: A total of 202 patients were included (non-ESPB: 124 patients; ESPB: 78 patients). No adverse events were attributed to ESPB. Non-ESPB patients received more intraoperative opioids (milligram morphine equivalents; 41.8 ± 17.0 mg versus 36.7 ± 17.1, P = 0.05) and were more likely to present to the emergency department within 7 d postoperatively (4.8% versus 0%, P = 0.05) when compared to ESPB patients. No significant difference in total perioperative milligram morphine equivalents, severe pain in postanesthesia care unit (PACU), time from PACU arrival to analgesic administration, PACU length of stay, or postprocedure admission rates between groups were observed. CONCLUSIONS: In patients undergoing PE bar removal surgery, bilateral ESPB with liposomal bupivacaine was performed without complications. ESPB with liposomal bupivacaine may be considered as an analgesic adjunct to enhance recovery in patients undergoing cardiothoracic procedures but further prospective randomized clinical trials comparing liposomal bupivacaine to traditional local anesthetics with and without indwelling nerve catheters are necessary.

Perioperative anaphylactic reactions to central venous and pulmonary artery catheters containing chlorhexidine, sulfadiazine, or latex: a historical cohort study.

PURPOSE: Central venous catheters (CVCs) and pulmonary artery catheters (PACs) containing chlorhexidine, silver sulfadiazine, or latex can cause perioperative anaphylaxis. We examined the incidence of and outcomes associated with anaphylaxis caused by CVCs/PACs. METHODS: In a historical cohort study, we retrospectively identified adult patients fitted with CVCs/PACs at the Mayo Clinics in Minnesota, Arizona, and Florida from 1 January 2008 to 1 March 2018. Potential and confirmed cases of perioperative anaphylactic reactions were individually reviewed and classified. RESULTS: During the study period, 39,505 procedures were performed during which CVCs/PACs were inserted. Of these, 2,937 patients with pre-existing chlorhexidine, sulfonamide (sulfa), and/or latex allergies had CVCs/PACs inserted that contained these substances. Perioperative anaphylaxis, in which CVCs/PACs were the confirmed or potential causative agent, occurred during 53 procedures. Seven patients had a preoperatively reported sulfa or latex allergy; no patients had a preoperative chlorhexidine allergy. Six of the seven patients with reported allergies to sulfa or latex had a CVC/PAC inserted that contained these substances. Twenty-four patients with anaphylaxis had postoperative allergic disease consultation; ten of these (42%) underwent skin testing. CONCLUSION: Perioperative anaphylactic reactions related to CVCs/PACs containing chlorhexidine, silver sulfadiazine, or latex were rare in this large historical cohort study. We identified 2,937 patients with pre-existing chlorhexidine, sulfa, and/or latex allergies and had CVCs/PACs inserted that contained these substances. Although few cases of perioperative anaphylaxis attributable to these substances were observed in patients with corresponding allergies, the potential for substantial complication exists. Providers should be aware of the potential for these hidden exposures.

RéSUMé: OBJECTIF: Les cathéters veineux centraux (CVC) et les cathéters artériels pulmonaires (CAP) contenant de la chlorhexidine, de la sulfadiazine argentique ou du latex peuvent provoquer une anaphylaxie périopératoire. Nous avons examiné l'incidence et les devenirs associés à l'anaphylaxie causée par les CVC/CAP. MéTHODE: Dans une étude de cohorte historique, nous avons identifié rétrospectivement des patients adultes chez lesquels un CVC/CAP avait été installé aux cliniques Mayo du Minnesota, de l'Arizona et de la Floride du 1er janvier 2008 au 1er mars 2018. Les cas potentiels et confirmés de réactions anaphylactiques périopératoires ont été examinés et classés individuellement. RéSULTATS: Au cours de la période à l'étude, 39 505 interventions ont été réalisées au cours desquelles des CVC/CAP ont été insérés. Parmi celles-ci, des CVC/CAP contenant de la chlorhexidine, des sulfamides et/ou du latex ont été insérés chez 2937 patients présentant des allergies préexistantes à ces substances. Une anaphylaxie périopératoire, dont l'agent causal confirmé ou potentiel était le CVC/CAP, s'est produite dans 53 interventions. Sept patients présentaient une allergie aux sulfamides ou au latex signalée avant l'opération; aucun patient n'a eu d'allergie préopératoire à la chlorhexidine. Un CVC/CAP contenant des sulfamides ou du latex a été inséré chez six des sept patients ayant signalé des allergies à ces substances. Vingt-quatre patients atteints d'anaphylaxie ont eu une consultation postopératoire pour une maladie allergique; dix d'entre eux (42 %) ont subi des tests cutanés. CONCLUSION: Les réactions anaphylactiques périopératoires liées aux CVC/CAP contenant de la chlorhexidine, de la sulfadiazine argentique ou du latex étaient rares dans cette vaste étude de cohorte historique. Nous avons identifié 2937 patients présentant des allergies préexistantes à la chlorhexidine, aux sulfamides et/ou au latex chez lesquels des CVC/CAP contenant ces substances ont été insérés. Bien que peu de cas d'anaphylaxie périopératoire attribuable à ces substances aient été observés chez des patients présentant des allergies correspondantes, il existe un risque de complication importante. Les fournisseurs doivent être conscients du potentiel de ces expositions cachées.

Zinc-finger protein Zpr1 is a bespoke chaperone essential for eEF1A biogenesis.

The conserved regulon of heat shock factor 1 in budding yeast contains chaperones for general protein folding as well as zinc-finger protein Zpr1, whose essential role in archaea and eukaryotes remains unknown. Here, we show that Zpr1 depletion causes acute proteotoxicity driven by biosynthesis of misfolded eukaryotic translation elongation factor 1A (eEF1A). Prolonged Zpr1 depletion leads to eEF1A insufficiency, thereby inducing the integrated stress response and inhibiting protein synthesis. Strikingly, we show by using two distinct biochemical reconstitution approaches that Zpr1 enables eEF1A to achieve a conformational state resistant to protease digestion. Lastly, we use a ColabFold model of the Zpr1-eEF1A complex to reveal a folding mechanism mediated by the Zpr1's zinc-finger and alpha-helical hairpin structures. Our work uncovers the long-sought-after function of Zpr1 as a bespoke chaperone tailored to the biogenesis of one of the most abundant proteins in the cell.

Surgical site infections during the COVID-19 era: A retrospective, multicenter analysis.

BACKGROUND: Surgical site infections (SSIs) are an undesired perioperative outcome. Recent studies have shown increases in hospital acquired infections during the coronavirus disease 2019 (COVID-19) pandemic. The objective of this study was to evaluate postoperative SSIs in the COVID-19-era compared to a historical cohort at a large, multicenter, academic institution. METHODS: A retrospective review of all patients who underwent National Health and Safety Network (NHSN) inpatient surgical procedures between January 1, 2018 and December 31, 2020. Patients from the COVID-19-era (March-December 2020) were compared and matched 1:1 with historical controls (2018/2019) utilizing the standardized infection ratio (SIR) to detect difference. RESULTS/DISCUSSION: During the study period, 29,904 patients underwent NHSN procedures at our institution. When patients from the matched cohort (2018/2019) were compared to the COVID-19-era cohort (2020), a decreased risk of SSI was observed following colorectal surgery (RR = 0.94, 95% CI [0.65, 1.37], P = .76), hysterectomy (RR = 0.88, 95% CI [0.39, 1.99], P = .75), and knee prothesis surgery (RR = 0.95, 95% CI [0.52, 1.74], P = .88), though not statistically significant. An increased risk of SSI was observed following hip prosthesis surgery (RR 1.09, 95% CI [0.68, 1.75], P = .72), though not statistically significant. CONCLUSIONS: The risk of SSI in patients who underwent NHSN inpatient surgical procedures in 2020 with perioperative COVID-19 precautions was not significantly different when compared to matched controls at our large, multicenter, academic institution.

Context Analysis of Continued Citation of Retracted Manuscripts Published in Anesthesiology Journals.

The continued citation of retracted publications from the medical literature is a well-known and persistent problem. We describe the contexts of ongoing citations to manuscripts that have been retracted from a selection of anesthesiology journals. We also examine how bibliographic databases and publisher websites document the retracted status of these manuscripts. The authors performed an analysis of retracted publications from anesthesiology journals using the Retraction Watch database. We then examined how the retraction information was displayed on bibliographic databases, search engines, and publisher websites. The primary outcome was the context of continued citation after retraction of flawed publications within the specialty of anesthesiology. Secondary outcomes included comparison of the documentation, bibliographic databases, search engines, and publisher websites used in identifying the retracted status of these publications and provision of access to the respective retraction notices. A total of 245 original publications were retracted over a 28-year period from 9 anesthesiology journals. PubMed, compared to the other databases and search engines, was the most consistent (98.8%) in documenting the retracted status of the publications examined, as well as providing a direct link to the retraction notice. From the 211 publications retracted before January 2020, there were 1307 postretraction citations accessed from Scopus. The median number of postretraction citations was 3.5 (range, 0-88, with at least 1 citation in 164 publications) in Scopus. Of the postretraction citations, 80% affirmed the validity of the retracted publications, while only 5.2% of citations acknowledged the retraction or misconduct. In 10.2% of the citations from original research studies, retracted manuscripts appeared to influence the decision to pursue or the methods used in subsequent original research studies. The frequency of citation of the 15 most cited retracted publications declined in a similar pattern during the 10 years after retraction. Citation of manuscripts retracted from anesthesiology journals remains a common occurrence. Technological innovations and application of standards for handling retracted publications, as suggested by coalitions of researchers across the spectrum of scientific investigation, may serve to reduce the persistence of this error.

Mixing genome annotation methods in a comparative analysis inflates the apparent number of lineage-specific genes.

Comparisons of genomes of different species are used to identify lineage-specific genes, those genes that appear unique to one species or clade. Lineage-specific genes are often thought to represent genetic novelty that underlies unique adaptations. Identification of these genes depends not only on genome sequences, but also on inferred gene annotations. Comparative analyses typically use available genomes that have been annotated using different methods, increasing the risk that orthologous DNA sequences may be erroneously annotated as a gene in one species but not another, appearing lineage specific as a result. To evaluate the impact of such "annotation heterogeneity," we identified four clades of species with sequenced genomes with more than one publicly available gene annotation, allowing us to compare the number of lineage-specific genes inferred when differing annotation methods are used to those resulting when annotation method is uniform across the clade. In these case studies, annotation heterogeneity increases the apparent number of lineage-specific genes by up to 15-fold, suggesting that annotation heterogeneity is a substantial source of potential artifact.

Antagonism between killer yeast strains as an experimental model for biological nucleation dynamics.

Antagonistic interactions are widespread in the microbial world and affect microbial evolutionary dynamics. Natural microbial communities often display spatial structure, which affects biological interactions, but much of what we know about microbial antagonism comes from laboratory studies of well-mixed communities. To overcome this limitation, we manipulated two killer strains of the budding yeast Saccharomyces cerevisiae, expressing different toxins, to independently control the rate at which they released their toxins. We developed mathematical models that predict the experimental dynamics of competition between toxin-producing strains in both well-mixed and spatially structured populations. In both situations, we experimentally verified theory's prediction that a stronger antagonist can invade a weaker one only if the initial invading population exceeds a critical frequency or size. Finally, we found that toxin-resistant cells and weaker killers arose in spatially structured competitions between toxin-producing strains, suggesting that adaptive evolution can affect the outcome of microbial antagonism in spatial settings.

Ploidy and recombination proficiency shape the evolutionary adaptation to constitutive DNA replication stress.

In haploid budding yeast, evolutionary adaptation to constitutive DNA replication stress alters three genome maintenance modules: DNA replication, the DNA damage checkpoint, and sister chromatid cohesion. We asked how these trajectories depend on genomic features by comparing the adaptation in three strains: haploids, diploids, and recombination deficient haploids. In all three, adaptation happens within 1000 generations at rates that are correlated with the initial fitness defect of the ancestors. Mutations in individual genes are selected at different frequencies in populations with different genomic features, but the benefits these mutations confer are similar in the three strains, and combinations of these mutations reproduce the fitness gains of evolved populations. Despite the differences in the selected mutations, adaptation targets the same three functional modules in strains with different genomic features, revealing a common evolutionary response to constitutive DNA replication stress.

Modeling the impact of single-cell stochasticity and size control on the population growth rate in asymmetrically dividing cells.

Microbial populations show striking diversity in cell growth morphology and lifecycle; however, our understanding of how these factors influence the growth rate of cell populations remains limited. We use theory and simulations to predict the impact of asymmetric cell division, cell size regulation and single-cell stochasticity on the population growth rate. Our model predicts that coarse-grained noise in the single-cell growth rate λ decreases the population growth rate, as previously seen for symmetrically dividing cells. However, for a given noise in λ we find that dividing asymmetrically can enhance the population growth rate for cells with strong size control (between a "sizer" and an "adder"). To reconcile this finding with the abundance of symmetrically dividing organisms in nature, we propose that additional constraints on cell growth and division must be present which are not included in our model, and we explore the effects of selected extensions thereof. Further, we find that within our model, epigenetically inherited generation times may arise due to size control in asymmetrically dividing cells, providing a possible explanation for recent experimental observations in budding yeast. Taken together, our findings provide insight into the complex effects generated by non-canonical growth morphologies.

Rapid toxin sequestration modifies poison frog physiology.

Poison frogs sequester chemical defenses from their diet of leaf litter arthropods for defense against predation. Little is known about the physiological adaptations that confer this unusual bioaccumulation ability. We conducted an alkaloid-feeding experiment with the Diablito poison frog (Oophaga sylvatica) to determine how quickly alkaloids are accumulated and how toxins modify frog physiology using quantitative proteomics. Diablito frogs rapidly accumulated the alkaloid decahydroquinoline within 4 days, and dietary alkaloid exposure altered protein abundance in the intestines, liver and skin. Many proteins that increased in abundance with decahydroquinoline accumulation are plasma glycoproteins, including the complement system and the toxin-binding protein saxiphilin. Other protein classes that change in abundance with decahydroquinoline accumulation are membrane proteins involved in small molecule transport and metabolism. Overall, this work shows that poison frogs can rapidly accumulate alkaloids, which alter carrier protein abundance, initiate an immune response, and alter small molecule transport and metabolism dynamics across tissues.

Anesthetic considerations in lung transplantation: past, present and future.

Lung transplantation is a very complex surgical procedure with many implications for the anesthetic care of these patients. Comprehensive preoperative evaluation is an important component of the transplant evaluation as it informs many of the decisions made perioperatively to manage these complex patients effectively and appropriately. These decisions may involve pre-emptive actions like pre-habilitation and nutrition optimization of these patients before they arrive for their transplant procedure. Appropriate airway and ventilation management of these patients needs to be performed in a manner that provides an optimal operating conditions and protection from ventilatory injury of these fragile post-transplant lungs. Pain management can be challenging and should be managed in a multi-modal fashion with or without the use of an epidural catheter while recognizing the risk of neuraxial technique in patients who will possibly be systemically anticoagulated. Complex monitoring is required for these patients involving both invasive and non-invasive including the use of transesophageal echocardiography (TEE) and continuous cardiac output monitoring. Management of the patient's hemodynamics can be challenging and involves managing the systemic and pulmonary vascular systems. Some patients may require extra-corporeal lung support as a planned part of the procedure or as a rescue technique and centers need to be proficient in instituting and managing this sophisticated method of hemodynamic support.

Many, but not all, lineage-specific genes can be explained by homology detection failure.

Genes for which homologs can be detected only in a limited group of evolutionarily related species, called "lineage-specific genes," are pervasive: Essentially every lineage has them, and they often comprise a sizable fraction of the group's total genes. Lineage-specific genes are often interpreted as "novel" genes, representing genetic novelty born anew within that lineage. Here, we develop a simple method to test an alternative null hypothesis: that lineage-specific genes do have homologs outside of the lineage that, even while evolving at a constant rate in a novelty-free manner, have merely become undetectable by search algorithms used to infer homology. We show that this null hypothesis is sufficient to explain the lack of detected homologs of a large number of lineage-specific genes in fungi and insects. However, we also find that a minority of lineage-specific genes in both clades are not well explained by this novelty-free model. The method provides a simple way of identifying which lineage-specific genes call for special explanations beyond homology detection failure, highlighting them as interesting candidates for further study.

A Putative Bet-Hedging Strategy Buffers Budding Yeast against Environmental Instability.

To grow and divide, cells must extract resources from dynamic and unpredictable environments. Many organisms use different metabolic strategies for distinct contexts. Budding yeast can produce ATP from carbon sources by mechanisms that prioritize either speed (fermentation) or yield (respiration). Withdrawing glucose from exponentially growing cells reveals variability in their ability to switch from fermentation to respiration. We observe two subpopulations of glucose-starved cells: recoverers, which rapidly adapt and resume growth, and arresters, which enter a shock state characterized by deformation of many cellular structures, including mitochondria. These states are heritable, and on high glucose, arresters grow and divide faster than recoverers. Recoverers have a fitness advantage during a carbon source shift but are less fit in a constant, high-glucose environment, and we observe natural variation in the frequency of the two states across wild yeast strains. These experiments suggest that bet hedging has evolved in budding yeast.

Cell-size regulation in budding yeast does not depend on linear accumulation of Whi5.

Cells must couple cell-cycle progress to their growth rate to restrict the spread of cell sizes present throughout a population. Linear, rather than exponential, accumulation of Whi5, was proposed to provide this coordination by causing a higher Whi5 concentration in cells born at a smaller size. We tested this model using the inducible GAL1 promoter to make the Whi5 concentration independent of cell size. At an expression level that equalizes the mean cell size with that of wild-type cells, the size distributions of cells with galactose-induced Whi5 expression and wild-type cells are indistinguishable. Fluorescence microscopy confirms that the endogenous and GAL1 promoters produce different relationships between Whi5 concentration and cell volume without diminishing size control in the G1 phase. We also expressed Cln3 from the GAL1 promoter, finding that the spread in cell sizes for an asynchronous population is unaffected by this perturbation. Our findings indicate that size control in budding yeast does not fundamentally originate from the linear accumulation of Whi5, contradicting a previous claim and demonstrating the need for further models of cell-cycle regulation to explain how cell size controls passage through Start.