The Std1 Activator of the Snf1/AMPK Kinase Controls Glucose Response in Yeast by a Regulated Protein Aggregation.

The ability to respond to available nutrients is critical for all living cells. The AMP-activated protein kinase (SNF1 in yeast) is a central regulator of metabolism that is activated when energy is depleted. We found that SNF1 activity in the nucleus is regulated by controlled relocalization of the SNF1 activator Std1 into puncta. This process is regulated by glucose through the activity of the previously uncharacterized protein kinase Vhs1 and its substrate Sip5, a protein of hitherto unknown function. Phosphorylation of Sip5 prevents its association with Std1 and triggers Std1 accretion. Reversible Std1 puncta formation occurs under non-stressful, ambient conditions, creating non-amyloid inclusion bodies at the nuclear-vacuolar junction, and it utilizes cellular chaperones similarly to the aggregation of toxic or misfolded proteins such as those associated with Parkinson's, Alzheimer's, and CJD diseases. Our results reveal a controlled, non-pathological, physiological role of protein aggregation in the regulation of a major metabolic cellular pathway.

Reporting Guideline for RULER: Rasch Reporting Guideline for Rehabilitation Research: Explanation and Elaboration.

The Rasch Reporting Guideline for Rehabilitation Research (RULER) provides peer-reviewed, evidence-based, transparent, and consistent recommendations for reporting studies that apply Rasch Measurement (RM) Theory in a rehabilitation context. The purpose of the guideline is to ensure that authors, reviewers, and editors have uniform guidance about how to write and evaluate research on rehabilitation outcome assessments. The RULER statement includes an organizing framework and a checklist of 59 recommendations. This companion article supports the RULER statement by providing details about the framework, rationale for the domains and recommendations in the checklist and explaining why these considerations are important for improving consistency and transparency in reporting the results of RM studies. This article is not intended to describe how to conduct RM studies but provides rationale for the essential elements that authors should address in each domain. Consistency and transparency in reporting RM studies will advance rehabilitation research if authors consider these issues when planning their study and include the checklist when they submit their manuscript for peer review. A copy of the checklist can be found at [table 2 in https://doi.org/10.1016/j.apmr.2022.03.013].

Rasch Reporting Guideline for Rehabilitation Research (RULER): the RULER Statement.

The application of Rasch Measurement (RM) Theory to rehabilitation assessments has proliferated in recent years. RM Theory helps design and refine assessments so that items reflect a unidimensional construct in an equal interval metric that distinguishes among persons of different abilities in a manner that is consistent with the underlying trait. Rapid growth of RM in rehabilitation assessment studies has led to inconsistent results reporting. Clear, consistent, transparent reporting of RM Theory results is important for advancing rehabilitation science and practice based on precise measures. Precise measures, in turn, provide researchers, practitioners, patients, and other stakeholders with tools for effective decision making. The goal of this Rasch Reporting Guideline for Rehabilitation Research (RULER: Rasch Reporting Guideline for Rehabilitation Research) is to provide peer-reviewed, evidence-based, transparent, and consistent recommendations for reporting studies that apply RM Theory in a rehabilitation context. The purpose of the guideline is to ensure that authors, reviewers, and editors have uniform expectations about how to write and evaluate research on rehabilitation outcome assessments. A task force of rehabilitation researchers, clinicians, and editors met regularly between November 2018 and August 2020 to identify the need for the guideline, develop an organizing framework, identify content areas, and develop the recommendations. This RULER: Rasch Reporting Guideline for Rehabilitation Research statement includes the organizing framework and a checklist of 59 recommendations. The guideline is supported by an Explanation and Elaboration article that provides more detail about the framework and recommendations in the checklist. A glossary of key terms and a recommended iterations table are provided in supplemental online only materials.

Observations of a species-record deep dive by a central Pacific female scalloped hammerhead shark (Sphyrna lewini).

A female scalloped hammerhead shark (Sphyrna lewini) conducted a species record deep dive to 1240 m in coastal-pelagic waters off Hawaii Island. This extends the deepest known depth range of the species by over 200 m (650 ft) and highlights the question of the extent to which deep-diving activity is mediated by physiological constraints, such as temperature and oxygen availability.

Variable-order fractional master equation and clustering of particles: non-uniform lysosome distribution.

In this paper, we formulate the space-dependent variable-order fractional master equation to model clustering of particles, organelles, inside living cells. We find its solution in the long-time limit describing non-uniform distribution due to a space-dependent fractional exponent. In the continuous space limit, the solution of this fractional master equation is found to be exactly the same as the space-dependent variable-order fractional diffusion equation. In addition, we show that the clustering of lysosomes, an essential organelle for healthy functioning of mammalian cells, exhibit space-dependent fractional exponents. Furthermore, we demonstrate that the non-uniform distribution of lysosomes in living cells is accurately described by the asymptotic solution of the space-dependent variable-order fractional master equation. Finally, Monte Carlo simulations of the fractional master equation validate our analytical solution. This article is part of the theme issue 'Transport phenomena in complex systems (part 1)'.

Meeting report - Dynamic Cell III.

Dynamic Cell III, a meeting jointly organized by the British Society of Cell Biology (BSCB) and the Biochemical Society, took place at the Manchester Conference Centre, Manchester, UK in March 2018. It brought together a diverse group of scientists from around the world, all with a shared interest in understanding how dynamic functions of the cell are fulfilled. A particular focus was the regulation of the cytoskeleton: in cell division, cell migration and cell-cell interactions. Moreover, a key theme that ran through all presented work was the development of new and exciting technologies to study dynamic cell behaviour.

Initial development of a measure of evidence-informed professional thinking.

BACKGROUND AND AIMS: A number of theories have been proposed on clinical expertise and its development in occupational therapy and allied health professions. Clinical reasoning, outcome measurement and evidence-based practice are names for leading conceptualisations. The aim of this research was to develop an operational measure of habits of mind and practice that constitute these desirable professional activities amongst professional therapists. METHODS: Items were developed on the basis of literature review and feedback from an expert panel. An online self-report survey was completed by 107 occupational therapists and other allied health clinicians. Rasch analysis was used to identify and calibrate items that fit the criteria for equal-interval measurement. Residuals from identified equal-interval dimensions were examined using principal components analysis to identify multidimensionality. RESULTS: A two-dimension solution employing 32 items was identified. The first dimension comprised items on Critical Clinical Reasoning and had an item separation of 8.49 (0.99 reliability) and a person separation of 2.93 (0.90 reliability). The second dimension comprised items on Evidence-Informed Practice behaviours and had an item separation of 6.19 (0.97 reliability) and a person separation of 2.97 (0.90 reliability). These dimensions were positively correlated (r = .778, p < .001). We named the overall scale 'Evidence-Informed Professional Thinking', or EIPT. The EIPT measures correlated significantly with 12 of 13 relevant external criterion items. CONCLUSION: Evidence-informed professional thinking can be measured in terms of two correlated probabilistically equal-interval dimensions: Critical Clinical Reasoning and Evidence-Informed Practice behaviours. The EIPT measure should be useful in research on development and application of clinical expertise, quality and outcomes of care and implementation of improved practices among practicing therapists in clinical treatment settings. Further research is recommended to understand the generalisability, strengths, limitations and correlates of EIPT.

Shifts in pollen release envelope differ between genera with non-uniform climate change.

PREMISE OF THE STUDY: Plant phenological responses to climate change now constitute one of the best studied areas of the ecological impacts of climate change. Flowering time responses to climate change of wind-pollinated species have, however, been less well studied. A novel source of flowering time data for wind-pollinated species is allergen monitoring records. METHODS: We studied the male flowering time response to climatic variables of two wind-pollinated genera, Betula (Betulaceae) and Populus (Salicaceae), using pollen count records over a 17-year period. KEY RESULTS: We found that changes in the pollen release envelope differed between the two genera. Over the study period, the only month with a significant rise in temperature was April, resulting in the duration of pollen release of the April-flowering Populus to shorten and the start and peak of the May-flowering Betula to advance. The quantity of pollen released by Betula has increased and was related to increases in the previous year's August precipitation, while the quantity of pollen released by Populus has not changed and was related to the previous year's summer and autumn temperatures. CONCLUSIONS: Our findings suggest that taxa differ in the reproductive consequences of environmental change. Differing shifts in phenology among species may be related to different rates of change in climatic variables in different months of the year. While our study only considers two genera, the results underscore the importance of understanding non-uniform intra-annual variation in climate when studying the ecological implications of climate change.

Global biogeography of mating system variation in seed plants.

Latitudinal gradients in biotic interactions have been suggested as causes of global patterns of biodiversity and phenotypic variation. Plant biologists have long speculated that outcrossing mating systems are more common at low than high latitudes owing to a greater predictability of plant-pollinator interactions in the tropics; however, these ideas have not previously been tested. Here, we present the first global biogeographic analysis of plant mating systems based on 624 published studies from 492 taxa. We found a weak decline in outcrossing rate towards higher latitudes and among some biomes, but no biogeographic patterns in the frequency of self-incompatibility. Incorporating life history and growth form into biogeographic analyses reduced or eliminated the importance of latitude and biome in predicting outcrossing or self-incompatibility. Our results suggest that biogeographic patterns in mating system are more likely a reflection of the frequency of life forms across latitudes rather than the strength of plant-pollinator interactions.

Linking cell cycle to histone modifications: SBF and H2B monoubiquitination machinery and cell-cycle regulation of H3K79 dimethylation.

To identify regulators involved in determining the differential pattern of H3K79 methylation by Dot1, we screened the entire yeast gene deletion collection by GPS for genes required for normal levels of H3K79 di- but not trimethylation. We identified the cell cycle-regulated SBF protein complex required for H3K79 dimethylation. We also found that H3K79 di- and trimethylation are mutually exclusive, with M/G1 cell cycle-regulated genes significantly enriched for H3K79 dimethylation. Since H3K79 trimethylation requires prior monoubiquitination of H2B, we performed genome-wide profiling of H2BK123 monoubiquitination and showed that H2BK123 monoubiquitination is not detected on cell cycle-regulated genes and sites containing H3K79me2, but is found on H3K79me3-containing regions. A screen for genes responsible for the establishment/removal of H3K79 dimethylation resulted in identification of NRM1 and WHI3, both of which impact the transcription by the SBF and MBF protein complexes, further linking the regulation of methylation status of H3K79 to the cell cycle.

Remarkably ancient balanced polymorphisms in a multi-locus gene network.

Local adaptations within species are often governed by several interacting genes scattered throughout the genome. Single-locus models of selection cannot explain the maintenance of such complex variation because recombination separates co-adapted alleles. Here we report a previously unrecognized type of intraspecific multi-locus genetic variation that has been maintained over a vast period. The galactose (GAL) utilization gene network of Saccharomyces kudriavzevii, a relative of brewer's yeast, exists in two distinct states: a functional gene network in Portuguese strains and, in Japanese strains, a non-functional gene network of allelic pseudogenes. Genome sequencing of all available S. kudriavzevii strains revealed that none of the functional GAL genes were acquired from other species. Rather, these polymorphisms have been maintained for nearly the entire history of the species, despite more recent gene flow genome-wide. Experimental evidence suggests that inactivation of the GAL3 and GAL80 regulatory genes facilitated the origin and long-term maintenance of the two gene network states. This striking example of a balanced unlinked gene network polymorphism introduces a remarkable type of intraspecific variation that may be widespread.

SUMOylation regulates the SNF1 protein kinase.

The AMP-activated protein kinase (AMPK) is a major stress sensor of mammalian cells. AMPK's homolog in the yeast Saccharomyces cerevisiae, the SNF1 protein kinase, is a central regulator of carbon metabolism that inhibits the Snf3/Rgt2-Rgt1 glucose sensing pathway and activates genes involved in respiration. We present evidence that glucose induces modification of the Snf1 catalytic subunt of SNF1 with the small ubiquitin-like modifier protein SUMO, catalyzed by the SUMO (E3) ligase Mms21. Our results suggest that SUMOylation of Snf1 inhibits its function in two ways: by interaction of SUMO attached to lysine 549 with a SUMO-interacting sequence motif located near the active site of Snf1, and by targeting Snf1 for destruction via the Slx5-Slx8 (SUMO-directed) ubiquitin ligase. These findings reveal another way SNF1 function is regulated in response to carbon source.

Binary Image Classification: A Genetic Programming Approach to the Problem of Limited Training Instances.

In the computer vision and pattern recognition fields, image classification represents an important yet difficult task. It is a challenge to build effective computer models to replicate the remarkable ability of the human visual system, which relies on only one or a few instances to learn a completely new class or an object of a class. Recently we proposed two genetic programming (GP) methods, one-shot GP and compound-GP, that aim to evolve a program for the task of binary classification in images. The two methods are designed to use only one or a few instances per class to evolve the model. In this study, we investigate these two methods in terms of performance, robustness, and complexity of the evolved programs. We use ten data sets that vary in difficulty to evaluate these two methods. We also compare them with two other GP and six non-GP methods. The results show that one-shot GP and compound-GP outperform or achieve results comparable to competitor methods. Moreover, the features extracted by these two methods improve the performance of other classifiers with handcrafted features and those extracted by a recently developed GP-based method in most cases.

Retrotransposon profiling of RNA polymerase III initiation sites.

Although retroviruses are relatively promiscuous in choice of integration sites, retrotransposons can display marked integration specificity. In yeast and slime mold, some retrotransposons are associated with tRNA genes (tDNAs). In the Saccharomyces cerevisiae genome, the long terminal repeat retrotransposon Ty3 is found at RNA polymerase III (Pol III) transcription start sites of tDNAs. Ty1, 2, and 4 elements also cluster in the upstream regions of these genes. To determine the extent to which other Pol III-transcribed genes serve as genomic targets for Ty3, a set of 10,000 Ty3 genomic retrotranspositions were mapped using high-throughput DNA sequencing. Integrations occurred at all known tDNAs, two tDNA relics (iYGR033c and ZOD1), and six non-tDNA, Pol III-transcribed types of genes (RDN5, SNR6, SNR52, RPR1, RNA170, and SCR1). Previous work in vitro demonstrated that the Pol III transcription factor (TF) IIIB is important for Ty3 targeting. However, seven loci that bind the TFIIIB loader, TFIIIC, were not targeted, underscoring the unexplained absence of TFIIIB at those sites. Ty3 integrations also occurred in two open reading frames not previously associated with Pol III transcription, suggesting the existence of a small number of additional sites in the yeast genome that interact with Pol III transcription complexes.

Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins.

Transcription factors direct gene expression, so there is much interest in mapping their genome-wide binding locations. Current methods do not allow for the multiplexed analysis of TF binding, and this limits their throughput. We describe a novel method for determining the genomic target genes of multiple transcription factors simultaneously. DNA-binding proteins are endowed with the ability to direct transposon insertions into the genome near to where they bind. The transposon becomes a "Calling Card" marking the visit of the DNA-binding protein to that location. A unique sequence "barcode" in the transposon matches it to the DNA-binding protein that directed its insertion. The sequences of the DNA flanking the transposon (which reveal where in the genome the transposon landed) and the barcode within the transposon (which identifies the TF that put it there) are determined by massively parallel DNA sequencing. To demonstrate the method's feasibility, we determined the genomic targets of eight transcription factors in a single experiment. The Calling Card method promises to significantly reduce the cost and labor needed to determine the genomic targets of many transcription factors in different environmental conditions and genetic backgrounds.

The sexual neighborhood through time: competition and facilitation for pollination in Lobelia cardinalis.

Reproductive success in flowering plants is influenced by the morphology and timing of reproductive structures as well as the density of surrounding conspecifics. In species with separate male and female flower phases, successful pollen transfer is also expected to vary with the density and ratio of surrounding male and female flowers. Increased density of surrounding flowers may increase pollinator visitation rates, but the densities of male and female flowers will determine the availability of pollen and the strength of competition for pollen receipt. Here we (1) quantify the influence of surrounding plant density on total seasonal fruit and seed production, (2) quantify the influence of sexual neighborhood (surrounding sex ratio and densities of male- and female-phase flowers) on fruit and seed production for individual flowers presented within the season, and (3) compare the influence of plant density on fitness to that of focal plant phenotype, specifically stigma-nectary distance and plant height, in a natural population of the pollen-limited, hummingbird-pollinated hermaphrodite Lobelia cardinalis. These relationships were examined at four spatial scales (10, 20, 50, and 100 cm). By examining temporal and spatial scales we found that (1) total seed production per plant decreased with increasing plant density at the smallest scale but increased with increasing density at all larger scales; (2) at any given time, a female-phase flower benefited from a higher density of surrounding male-phase flowers and a lower density of surrounding female-phase flowers; (3) when sex ratio was explicitly analyzed, a female-phase flower benefited from a lower proportion of surrounding female flowers as well as a lower total flower density; and (4) at the whole-plant level, taller plants were more likely to produce fruit (even when accounting for total number of flowers produced), consistent with pollinator preference for taller floral displays. Our results suggest that the local density of male and female flowers (and surrounding sex ratio) influences successful pollen transfer, implying that the local floral environment may shape how attraction traits like plant height are related to fitness.

Microbe domestication and the identification of the wild genetic stock of lager-brewing yeast.

Domestication of plants and animals promoted humanity's transition from nomadic to sedentary lifestyles, demographic expansion, and the emergence of civilizations. In contrast to the well-documented successes of crop and livestock breeding, processes of microbe domestication remain obscure, despite the importance of microbes to the production of food, beverages, and biofuels. Lager-beer, first brewed in the 15th century, employs an allotetraploid hybrid yeast, Saccharomyces pastorianus (syn. Saccharomyces carlsbergensis), a domesticated species created by the fusion of a Saccharomyces cerevisiae ale-yeast with an unknown cryotolerant Saccharomyces species. We report the isolation of that species and designate it Saccharomyces eubayanus sp. nov. because of its resemblance to Saccharomyces bayanus (a complex hybrid of S. eubayanus, Saccharomyces uvarum, and S. cerevisiae found only in the brewing environment). Individuals from populations of S. eubayanus and its sister species, S. uvarum, exist in apparent sympatry in Nothofagus (Southern beech) forests in Patagonia, but are isolated genetically through intrinsic postzygotic barriers, and ecologically through host-preference. The draft genome sequence of S. eubayanus is 99.5% identical to the non-S. cerevisiae portion of the S. pastorianus genome sequence and suggests specific changes in sugar and sulfite metabolism that were crucial for domestication in the lager-brewing environment. This study shows that combining microbial ecology with comparative genomics facilitates the discovery and preservation of wild genetic stocks of domesticated microbes to trace their history, identify genetic changes, and suggest paths to further industrial improvement.

Genetic programming for evolving due-date assignment models in job shop environments.

Due-date assignment plays an important role in scheduling systems and strongly influences the delivery performance of job shops. Because of the stochastic and dynamic nature of job shops, the development of general due-date assignment models (DDAMs) is complicated. In this study, two genetic programming (GP) methods are proposed to evolve DDAMs for job shop environments. The experimental results show that the evolved DDAMs can make more accurate estimates than other existing dynamic DDAMs with promising reusability. In addition, the evolved operation-based DDAMs show better performance than the evolved DDAMs employing aggregate information of jobs and machines.

A quantitative model of glucose signaling in yeast reveals an incoherent feed forward loop leading to a specific, transient pulse of transcription.

The ability to design and engineer organisms demands the ability to predict kinetic responses of novel regulatory networks built from well-characterized biological components. Surprisingly, few validated kinetic models of complex regulatory networks have been derived by combining models of the network components. A major bottleneck in producing such models is the difficulty of measuring in vivo rate constants for components of complex networks. We demonstrate that a simple, genetic approach to measuring rate constants in vivo produces an accurate kinetic model of the complex network that Saccharomyces cerevisiae employs to regulate the expression of genes encoding glucose transporters. The model predicts a transient pulse of transcription of HXT4 (but not HXT2 or HXT3) in response to addition of a small amount of glucose to cells, an outcome we observed experimentally. Our model also provides a mechanistic explanation for this result: HXT2-4 are governed by a type 2, incoherent feed forward regulatory loop involving the Rgt1 and Mig2 transcriptional repressors. The efficiency with which Rgt1 and Mig2 repress expression of each HXT gene determines which of them have a pulse of transcription in response to glucose. Finally, the model correctly predicts how lesions in the feed forward loop change the kinetics of induction of HXT4 expression.