An evolutionarily conserved prion-like element converts wild fungi from metabolic specialists to generalists.

[GAR(+)] is a protein-based element of inheritance that allows yeast (Saccharomyces cerevisiae) to circumvent a hallmark of their biology: extreme metabolic specialization for glucose fermentation. When glucose is present, yeast will not use other carbon sources. [GAR(+)] allows cells to circumvent this "glucose repression." [GAR(+)] is induced in yeast by a factor secreted by bacteria inhabiting their environment. We report that de novo rates of [GAR(+)] appearance correlate with the yeast's ecological niche. Evolutionarily distant fungi possess similar epigenetic elements that are also induced by bacteria. As expected for a mechanism whose adaptive value originates from the selective pressures of life in biological communities, the ability of bacteria to induce [GAR(+)] and the ability of yeast to respond to bacterial signals have been extinguished repeatedly during the extended monoculture of domestication. Thus, [GAR(+)] is a broadly conserved adaptive strategy that links environmental and social cues to heritable changes in metabolism.

Cross-kingdom chemical communication drives a heritable, mutually beneficial prion-based transformation of metabolism.

In experimental science, organisms are usually studied in isolation, but in the wild, they compete and cooperate in complex communities. We report a system for cross-kingdom communication by which bacteria heritably transform yeast metabolism. An ancient biological circuit blocks yeast from using other carbon sources in the presence of glucose. [GAR(+)], a protein-based epigenetic element, allows yeast to circumvent this "glucose repression" and use multiple carbon sources in the presence of glucose. Some bacteria secrete a chemical factor that induces [GAR(+)]. [GAR(+)] is advantageous to bacteria because yeast cells make less ethanol and is advantageous to yeast because their growth and long-term viability is improved in complex carbon sources. This cross-kingdom communication is broadly conserved, providing a compelling argument for its adaptive value. By heritably transforming growth and survival strategies in response to the selective pressures of life in a biological community, [GAR(+)] presents a unique example of Lamarckian inheritance.

Heritable remodeling of yeast multicellularity by an environmentally responsive prion.

Prion proteins undergo self-sustaining conformational conversions that heritably alter their activities. Many of these proteins operate at pivotal positions in determining how genotype is translated into phenotype. But the breadth of prion influences on biology and their evolutionary significance are just beginning to be explored. We report that a prion formed by the Mot3 transcription factor, [MOT3(+)], governs the acquisition of facultative multicellularity in the budding yeast Saccharomyces cerevisiae. The traits governed by [MOT3(+)] involved both gains and losses of Mot3 regulatory activity. [MOT3(+)]-dependent expression of FLO11, a major determinant of cell-cell adhesion, produced diverse lineage-specific multicellular phenotypes in response to nutrient deprivation. The prions themselves were induced by ethanol and eliminated by hypoxia-conditions that occur sequentially in the natural respiro-fermentative cycles of yeast populations. These data demonstrate that prions can act as environmentally responsive molecular determinants of multicellularity and contribute to the natural morphological diversity of budding yeast.

Motivations and Barriers for Women Orthopaedic Surgeons Considering Arthroplasty Fellowship.

BACKGROUND: Arthroplasty is one of the least gender-diverse orthopaedic subspecialties. While previous studies have looked at factors influencing fellowship choices for women, few studies have attempted to understand the decision for or against arthroplasty specifically. Working to better understand fellowship choice is a critical step in the process of increasing women recruitment. METHODS: An anonymous survey was distributed using REDCap to women orthopaedic surgeons and trainees through listservs, social media groups, and residency programs. Surgeons who had decided on a specific subspecialty or already completed fellowship were included. Responses were obtained from 164 surgeons (72 arthroplasty surgeons, 92 other subspecialties). Chi-squared and Fisher's Exact tests were then performed. RESULTS: The most important factor for those who chose arthroplasty was enjoyment of the surgeries. The biggest concerns from those in the arthroplasty group about the field were work-life balance, ability to become pregnant and/or have a healthy pregnancy, and sex bias from referring physicians. Of those who ultimately chose another subspecialty, 30.4% considered arthroplasty "a little" and 8.7% considered it "strongly." The most important dissuaders for the group that considered arthroplasty were concerns about "boy's club" culture, concerns about the physicality of the surgeries, and a lack of mentors. CONCLUSION: While the decision to choose a career path is multifactorial, our hope is that through the identification of modifiable factors we can increase women representation in arthroplasty. Increasing mentorship, implementing practical solutions to improve work-life balance, supporting healthy pregnancies, and mitigating the physical demands of surgery could help address current disparities.

Occupational Hazards to the Joint Replacement Surgeon: Radiation Exposure.

BACKGROUND: Intraoperative fluoroscopy is an essential tool to assist orthopedic surgeons in accurately and safely implanting hardware. In arthroplasty cases, its use is on the rise with the increasing popularity of the direct anterior (DA) approach for THA. However, exposure of ionizing radiation poses a potential health risk to surgeons. While the benefits of intraoperative fluoroscopy in DA THA is becoming clearer, and are well-described in the literature, the potential health dangers associated with career-long cumulative radiation exposure are rarely discussed. METHODS: In this article, we review the available literature to discuss radiation safety in orthopedics with a focus on total joint arthroplasty. We present the basic science of radiation, discuss the amount of radiation exposure in orthopedic surgery, and review the potential health risks associated with long-term exposure. CONCLUSION: Overall, the radiation dose exposure to arthroplasty surgeons is low and within recommendations for occupation exposure limits. However, due to the stochastic health impacts of ionizing radiation, there is no threshold dose below which radiation exposure is truly safe. Therefore, it is imperative that surgeons practice proper fluoroscopy safety habits, such as wearing proper protective equipment, minimizing fluoroscopy time and magnification, and maximizing distance from the radiation source to minimize the life-long cumulative radiation exposure and associated health risks.

Can I Ski Doc?: Return to Skiing Following Total Joint Arthroplasty.

BACKGROUND: Currently, there are little data on performance, safety, or return to downhill skiing after total joint arthroplasty (TJA). This leaves surgeons with little information for patient counseling regarding skiing. METHODS: An online survey was sent to 4360 patients who had undergone at least 1 primary TJA at a single academic center over the past 10 years (4 surgeons). The survey asked patients about their prior and current skiing activity including ability level, limitations, and reoperations. Demographics, patient-reported outcomes, and reoperations were also captured through chart review. Chi-squared, analysis of variance, and t-tests were used to compare demographics and outcomes. Paired t-tests were used to compare preoperative and postoperative skiing levels. RESULTS: Of the 763 survey respondents, the average follow-up was 4.4 years (range 0.5-10.3). In total, 35.6% had never skied, 26.5% had not skied in the 5 years prior to surgery (remote), and 37.9% had skied in the 5 years prior to surgery (recent). Seventy percent of recent skiers returned to skiing after surgery, compared to 11.9% of remote skiers. The majority of skiers, mostly advanced, returned to their prior level. There was no difference in return rates in those with a single total hip arthroplasty vs total knee arthroplasty vs multiple TJAs. Rates of reoperation were not significantly different between patients who did and did not return to skiing. CONCLUSION: The majority of recent skiers were able to return to skiing after TJA at their same level without an increase in reoperation rate. Further studies are needed to determine long-term consequences of skiing after TJA.

High Rates of Spacer Fracture in the Setting of Extended Trochanteric Osteotomy With a Specific Thin-Core Articulating Antibiotic Hip Spacer.

BACKGROUND: Two-stage revision remains the standard of care for prosthetic joint infection after total hip arthroplasty. However, there are substantial complications associated with articulating antibiotic hip spacers. Handmade and molded spacers have been shown to have higher rates of spacer fracture than antibiotic-coated prostheses (ACPs). The aim of this study is to review outcomes with an implant that is often categorized as an ACP spacer, the Zimmer-Biomet StageOne Select Femoral Spacer (ZBSO). METHODS: A retrospective review was performed of 63 patients who underwent placement of a ZBSO. Patients were compared based on whether or not an extended trochanteric osteotomy (ETO) was performed using Fisher's exact and t-tests. RESULTS: Five patients were excluded due to lack of follow-up or death shortly after stage 1 surgery, leaving 58 patients. Spacer fracture was noted in 5 of 58 patients (8.6%). Sixteen patients underwent ETO and 25.0% suffered a spacer fracture compared to 2.3% without ETO (odds ratio 13.7, P = .0248). There was no association between patient demographics or ETO length and spacer fracture. Two patients had periprosthetic fractures (3.4%) and 4 had dislocations (6.9%). Forty-nine patients (84.4%) went on to second-stage revision; of those 26.5% failed to clear the infection and required an average of 2.2 additional surgeries. CONCLUSION: The ZBSO spacer has overall complication rates similar to previously reported spacer series. Although the ZBSO looks like an ACP spacer, in the setting of ETO, it behaves like a molded or handmade spacer with a high rate of spacer fracture (25%) due to the small diameter of the core. This implant should be used with caution in combination with an ETO.

Inhibiting mitochondrial phosphate transport as an unexploited antifungal strategy.

The development of effective antifungal therapeutics remains a formidable challenge because of the close evolutionary relationship between humans and fungi. Mitochondrial function may present an exploitable vulnerability because of its differential utilization in fungi and its pivotal roles in fungal morphogenesis, virulence, and drug resistance already demonstrated by others. We now report mechanistic characterization of ML316, a thiohydantoin that kills drug-resistant Candida species at nanomolar concentrations through fungal-selective inhibition of the mitochondrial phosphate carrier Mir1. Using genetic, biochemical, and metabolomic approaches, we established ML316 as the first Mir1 inhibitor. Inhibition of Mir1 by ML316 in respiring yeast diminished mitochondrial oxygen consumption, resulting in an unusual metabolic catastrophe marked by citrate accumulation and death. In a mouse model of azole-resistant oropharyngeal candidiasis, ML316 reduced fungal burden and enhanced azole activity. Targeting Mir1 could provide a new, much-needed therapeutic strategy to address the rapidly rising burden of drug-resistant fungal infection.

Luminidependens (LD) is an Arabidopsis protein with prion behavior.

Prion proteins provide a unique mode of biochemical memory through self-perpetuating changes in protein conformation and function. They have been studied in fungi and mammals, but not yet identified in plants. Using a computational model, we identified candidate prion domains (PrDs) in nearly 500 plant proteins. Plant flowering is of particular interest with respect to biological memory, because its regulation involves remembering and integrating previously experienced environmental conditions. We investigated the prion-forming capacity of three prion candidates involved in flowering using a yeast model, where prion attributes are well defined and readily tested. In yeast, prions heritably change protein functions by templating monomers into higher-order assemblies. For most yeast prions, the capacity to convert into a prion resides in a distinct prion domain. Thus, new prion-forming domains can be identified by functional complementation of a known prion domain. The prion-like domains (PrDs) of all three of the tested proteins formed higher-order oligomers. Uniquely, the Luminidependens PrD (LDPrD) fully replaced the prion-domain functions of a well-characterized yeast prion, Sup35. Our results suggest that prion-like conformational switches are evolutionarily conserved and might function in a wide variety of normal biological processes.

Prions are a common mechanism for phenotypic inheritance in wild yeasts.

The self-templating conformations of yeast prion proteins act as epigenetic elements of inheritance. Yeast prions might provide a mechanism for generating heritable phenotypic diversity that promotes survival in fluctuating environments and the evolution of new traits. However, this hypothesis is highly controversial. Prions that create new traits have not been found in wild strains, leading to the perception that they are rare 'diseases' of laboratory cultivation. Here we biochemically test approximately 700 wild strains of Saccharomyces for [PSI(+)] or [MOT3(+)], and find these prions in many. They conferred diverse phenotypes that were frequently beneficial under selective conditions. Simple meiotic re-assortment of the variation harboured within a strain readily fixed one such trait, making it robust and prion-independent. Finally, we genetically screened for unknown prion elements. Fully one-third of wild strains harboured them. These, too, created diverse, often beneficial phenotypes. Thus, prions broadly govern heritable traits in nature, in a manner that could profoundly expand adaptive opportunities.

Fitness trade-offs restrict the evolution of resistance to amphotericin B.

The evolution of drug resistance in microbial pathogens provides a paradigm for investigating evolutionary dynamics with important consequences for human health. Candida albicans, the leading fungal pathogen of humans, rapidly evolves resistance to two major antifungal classes, the triazoles and echinocandins. In contrast, resistance to the third major antifungal used in the clinic, amphotericin B (AmB), remains extremely rare despite 50 years of use as monotherapy. We sought to understand this long-standing evolutionary puzzle. We used whole genome sequencing of rare AmB-resistant clinical isolates as well as laboratory-evolved strains to identify and investigate mutations that confer AmB resistance in vitro. Resistance to AmB came at a great cost. Mutations that conferred resistance simultaneously created diverse stresses that required high levels of the molecular chaperone Hsp90 for survival, even in the absence of AmB. This requirement stemmed from severe internal stresses caused by the mutations, which drastically diminished tolerance to external stresses from the host. AmB-resistant mutants were hypersensitive to oxidative stress, febrile temperatures, and killing by neutrophils and also had defects in filamentation and tissue invasion. These strains were avirulent in a mouse infection model. Thus, the costs of evolving resistance to AmB limit the emergence of this phenotype in the clinic. Our work provides a vivid example of the ways in which conflicting selective pressures shape evolutionary trajectories and illustrates another mechanism by which the Hsp90 buffer potentiates the emergence of new phenotypes. Developing antibiotics that deliberately create such evolutionary constraints might offer a strategy for limiting the rapid emergence of drug resistance.

PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition.

UNLABELLED: Prions are self-templating protein aggregates that stably perpetuate distinct biological states and are of keen interest to researchers in both evolutionary and biomedical science. The best understood prions are from yeast and have a prion-forming domain with strongly biased amino acid composition, most notably enriched for Q or N. PLAAC is a web application that scans protein sequences for domains with P: rion- L: ike A: mino A: cid C: omposition. Users can upload sequence files, or paste sequences directly into a textbox. PLAAC ranks the input sequences by several summary scores and allows scores along sequences to be visualized. Text output files can be downloaded for further analyses, and visualizations saved in PDF and PNG formats. AVAILABILITY AND IMPLEMENTATION: http://plaac.wi.mit.edu/. The Ruby-based web framework and the command-line software (implemented in Java, with visualization routines in R) are available at http://github.com/whitehead/plaac under the MIT license. All software can be run under OS X, Windows and Unix.

COSMOS: Python library for massively parallel workflows.

SUMMARY: Efficient workflows to shepherd clinically generated genomic data through the multiple stages of a next-generation sequencing pipeline are of critical importance in translational biomedical science. Here we present COSMOS, a Python library for workflow management that allows formal description of pipelines and partitioning of jobs. In addition, it includes a user interface for tracking the progress of jobs, abstraction of the queuing system and fine-grained control over the workflow. Workflows can be created on traditional computing clusters as well as cloud-based services. AVAILABILITY AND IMPLEMENTATION: Source code is available for academic non-commercial research purposes. Links to code and documentation are provided at http://lpm.hms.harvard.edu and http://wall-lab.stanford.edu. CONTACT: dpwall@stanford.edu or peter_tonellato@hms.harvard.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Early Radiographic and Clinical Outcomes of an Additive-Manufactured Acetabular Component.

Background: Additive manufacturing has recently gained popularity and is widely adopted in the orthopaedic industry. However, there is a paucity of literature on the radiographic and clinical outcomes of these relatively novel components. The aim of this study was to assess the 2-year clinical and radiographic outcomes of a specific additive-manufactured acetabular component in primary total hip arthroplasty. Methods: We performed a retrospective review of 60 patients who underwent primary total hip arthroplasty with the use of the Stryker's TRIDENT II acetabular component. Evaluation of radiographs was performed at 6 weeks, 1 year, and 2 years postoperatively. Radiographs were evaluated for radiolucencies in Charnley and DeLee zones, signs of biologic fixation, and acetabular inclination and anteversion measurements. Patient-reported outcomes and complications were also obtained. Results: There were no cases of component loosening or changes in component position during follow-up, with an average follow-up time of 1.7 years. A radiolucent line was identified in one patient in zone 1 at 6 weeks; this was absent at 1 year. Radiographic signs of cup biologic fixation were present in 85% of cases by final follow-up. The average inclination was 45.1 (SD = 4.0), and the average anteversion was 26.9 (SD = 5.2). Patient-Reported Outcomes Measurement Information System scores significantly increased at the final follow-up, and there were no complications in this cohort. Conclusions: This study demonstrated excellent radiographic and clinical outcomes with this novel additive-manufactured acetabular component at early follow-up. Although longer-term follow-up is warranted, this additively manufactured highly porous titanium acetabular component demonstrated excellent biologic fixation and reliable fixation at mid-term follow-up.

Direct Anterior Cup-Half Cage for Revision and Complex Primary Total Hip Arthroplasty: Surgical Technique.

As surgeons' comfort with the direct anterior approach (DAA) for total hip arthroplasty continues to increase, there is a growing interest in performing complex surgeries through this approach. Acetabular bone loss and/or pelvic discontinuity in the primary or revision setting often requires specialized implants such as a cup-cage construct. We describe our surgical technique for implanting modified cup-half cages through the DAA and show 2 case examples of how this technique was utilized in the setting of complex acetabular bone loss. In our experience, this is an effective method for complex total hip arthroplasty, with the potential added benefits of the DAA of reduced soft-tissue dissection, direct measurement of leg length, and ease of fluoroscopic navigation for implant positioning.

Talar-tarsal Stabilisation: Goals and Initial Outcomes.

BACKGROUND: While surgical stabilisation of the subtalar joint (arthroeresis) in children remains controversial in the USA, it is widely practised worldwide, with reportedly good outcomes. We are presenting a series of patients who met our criteria for calcaneal lengthening, but whose parents chose the less invasive option of talo-tarsal stabilisation (TTS). The goal of this surgery was to forestall or prevent hindfoot osteotomy. MATERIALS AND METHODS: With IRB approval, we conducted this retrospective review of 32 patients (60 ft), who underwent TTS for flexible planovalgus deformity and had a minimum of 1-year follow-up. The aetiology was idiopathic for the majority, with a few being neurogenic or syndromic. The age range was 6-15 years; the younger patients had neuromuscular aetiology or underlying syndromes. Concomitant procedures included percutaneous Achilles lengthening (33 ft), Kidner (9 ft) and guided growth for ankle valgus (2). RESULTS: In the early post-immobilisation phase, peroneal spasm occurred in four patients (6 ft). This resolved with Botox injection in the peroneus brevis in three patients and required transfer of the peroneus brevis to the peroneus longus in one patient. At follow-up, ranging from 1 to 4.5 years, 50 implants (83.4%) were retained and the patients reported satisfactory outcomes. Henceforth, those patients will be monitored on a p.r.n. basis. Due to lingering discomfort, implants were repositioned in one and removed in five patients (10 ft = 16.6%). Upon further follow-up, these patients have not manifested recurrent deformity. Therefore, subsequent salvage by osteotomy and/or lengthening of the calcaneus has not been necessary. CONCLUSION: TTS for the symptomatic flatfoot, combined with other procedures as indicated, offers advantages over the currently more accepted methods of medial shift osteotomy or calcaneal lengthening. The outcome at 1 year is a good forecast of whether or not further treatment will be required. This is a simpler and preferred option as compared to other methods of surgical management and, in our experience, has obviated the need for osteotomy or lengthening of the calcaneus. LEVEL OF EVIDENCE: IV retrospective case series. HOW TO CITE THIS ARTICLE: Stevens P, Lancaster A, Khwaja A. Talar-tarsal Stabilisation: Goals and Initial Outcomes. Strategies Trauma Limb Reconstr 2021;16(3):168-171.

Behavioural Indicators of Intra- and Inter-Specific Competition: Sheep Co-Grazing with Guanaco in the Patagonian Steppe.

In extensive livestock production, high densities may inhibit regulation processes, maintaining high levels of intraspecific competition over time. During competition, individuals typically modify their behaviours, particularly feeding and bite rates, which can therefore be used as indicators of competition. Over eight consecutive seasons, we investigated if variation in herd density, food availability, and the presence of a potential competitor, the guanaco (Lama guanicoe), was related with behavioural changes in domestic sheep in Chilean Patagonia. Focal sampling, instantaneous scan sampling, measures of bite and movement rates were used to quantify behavioural changes in domestic sheep. We found that food availability increased time spent feeding, while herd density was associated with an increase in vigilant behaviour and a decrease in bite rate, but only when food availability was low. Guanaco presence appeared to have no impact on sheep behaviour. Our results suggest that the observed behavioural changes in domestic sheep are more likely due to intraspecific competition rather than interspecific competition. Consideration of intraspecific competition where guanaco and sheep co-graze on pastures could allow management strategies to focus on herd density, according to rangeland carrying capacity.

Feed-forward regulation adaptively evolves via dynamics rather than topology when there is intrinsic noise.

In transcriptional regulatory networks (TRNs), a canonical 3-node feed-forward loop (FFL) is hypothesized to evolve to filter out short spurious signals. We test this adaptive hypothesis against a novel null evolutionary model. Our mutational model captures the intrinsically high prevalence of weak affinity transcription factor binding sites. We also capture stochasticity and delays in gene expression that distort external signals and intrinsically generate noise. Functional FFLs evolve readily under selection for the hypothesized function but not in negative controls. Interestingly, a 4-node "diamond" motif also emerges as a short spurious signal filter. The diamond uses expression dynamics rather than path length to provide fast and slow pathways. When there is no idealized external spurious signal to filter out, but only internally generated noise, only the diamond and not the FFL evolves. While our results support the adaptive hypothesis, we also show that non-adaptive factors, including the intrinsic expression dynamics, matter.

Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies.

This paper presents a meta-analysis of high-resolution human leukocyte antigen (HLA) allele frequency data describing 497 population samples. Most of the datasets were compiled from studies published in eight journals from 1990 to 2007; additional datasets came from the International Histocompatibility Workshops and from the AlleleFrequencies.net database. In all, these data represent approximately 66,800 individuals from throughout the world, providing an opportunity to observe trends that may not have been evident at the time the data were originally analyzed, especially with regard to the relative importance of balancing selection among the HLA loci. Population genetic measures of allele frequency distributions were summarized across populations by locus and geographic region. A role for balancing selection maintaining much of HLA variation was confirmed. Further, the breadth of this meta-analysis allowed the ranking of the HLA loci, with DQA1 and HLA-C showing the strongest balancing selection and DPB1 being compatible with neutrality. Comparisons of the allelic spectra reported by studies since 1990 indicate that most of the HLA alleles identified since 2000 are very-low-frequency alleles. The literature-based allele-count data, as well as maps summarizing the geographic distributions for each allele, are available online.