for PCARE and WASF3 regulate ciliary F-actin assembly that is required for the initiation of photoreceptor outer segment disk formation [Genetics] By www.pnas.org Published On :: 2020-05-05T10:31:24-07:00 The outer segments (OS) of rod and cone photoreceptor cells are specialized sensory cilia that contain hundreds of opsin-loaded stacked membrane disks that enable phototransduction. The biogenesis of these disks is initiated at the OS base, but the driving force has been debated. Here, we studied the function of the... Full Article
for Claims of categorical primacy for musical affect are confounded by using language as a measure [Social Sciences] By www.pnas.org Published On :: 2020-05-05T10:31:24-07:00 Cowen et al. (1) leverage modern gains in data science to describe impressive cross-cultural similarities in the perception of musical affect and do so in unprecedented detail. Their approach is innovative and fundamentally empirical. As such, it should have important applications for prediction in the field of affective computing, which... Full Article
for Requirement of the Cep57-Cep63 Interaction for Proper Cep152 Recruitment and Centriole Duplication [Research Article] By mcb.asm.org Published On :: 2020-04-28T08:00:17-07:00 Cep57 has been characterized as a component of a pericentriolar complex containing Cep63 and Cep152. Interestingly, Cep63 and Cep152 self-assemble into a pericentriolar cylindrical architecture, and this event is critical for the orderly recruitment of Plk4, a key regulator of centriole duplication. However, the way in which Cep57 interacts with the Cep63-Cep152 complex and contributes to the structure and function of Cep63-Cep152 self-assembly remains unknown. We demonstrate that Cep57 interacts with Cep63 through N-terminal motifs and associates with Cep152 via Cep63. Three-dimensional structured illumination microscopy (3D-SIM) analyses suggested that the Cep57-Cep63-Cep152 complex is concentrically arranged around a centriole in a Cep57-in and Cep152-out manner. Cep57 mutant cells defective in Cep63 binding exhibited improper Cep63 and Cep152 localization and impaired Sas6 recruitment for procentriole assembly, proving the significance of the Cep57-Cep63 interaction. Intriguingly, Cep63 fused to a microtubule (MT)-binding domain of Cep57 functioned in concert with Cep152 to assemble around stabilized MTs in vitro. Thus, Cep57 plays a key role in architecting the Cep63-Cep152 assembly around centriolar MTs and promoting centriole biogenesis. This study may offer a platform to investigate how the organization and function of the pericentriolar architecture are altered by disease-associated mutations found in the Cep57-Cep63-Cep152 complex. Full Article
for Determining the Bioenergetic Capacity for Fatty Acid Oxidation in the Mammalian Nervous System [Research Article] By mcb.asm.org Published On :: 2020-04-28T08:00:17-07:00 The metabolic state of the brain can greatly impact neurologic function. Evidence of this includes the therapeutic benefit of a ketogenic diet in neurologic diseases, including epilepsy. However, brain lipid bioenergetics remain largely uncharacterized. The existence, capacity, and relevance of mitochondrial fatty acid β-oxidation (FAO) in the brain are highly controversial, with few genetic tools available to evaluate the question. We have provided evidence for the capacity of brain FAO using a pan-brain-specific conditional knockout (KO) mouse incapable of FAO due to the loss of carnitine palmitoyltransferase 2, the product of an obligate gene for FAO (CPT2B–/–). Loss of central nervous system (CNS) FAO did not result in gross neuroanatomical changes or systemic differences in metabolism. Loss of CPT2 in the brain did not result in robustly impaired behavior. We demonstrate by unbiased and targeted metabolomics that the mammalian brain oxidizes a substantial quantity of long-chain fatty acids in vitro and in vivo. Loss of CNS FAO results in robust accumulation of long-chain acylcarnitines in the brain, suggesting that the mammalian brain mobilizes fatty acids for their oxidation, irrespective of diet or metabolic state. Together, these data demonstrate that the mammalian brain oxidizes fatty acids under normal circumstances with little influence from or on peripheral tissues. Full Article
for Correction for Dietz et al., "2019 Novel Coronavirus (COVID-19) Pandemic: Built Environment Considerations To Reduce Transmission" By msystems.asm.org Published On :: 2020-05-05T07:30:12-07:00 Full Article
for Prognostic Indices for Advance Care Planning in Primary Care: A Scoping Review By www.jabfm.org Published On :: 2020-03-16T09:31:37-07:00 Background: Patient identification is an important step for advance care planning (ACP) discussions. Objectives: We conducted a scoping review to identify prognostic indices potentially useful for initiating ACP. Methods: We included studies that developed and/or validated a multivariable prognostic index for all-cause mortality between 6 months and 5 years in community-dwelling adults. PubMed was searched in October 2018 for articles meeting our search criteria. If a systematic review was identified from the search, we checked for additional eligible articles in its references. We abstracted data on population studied, discrimination, calibration, where to find the index, and variables included. Each index was further assessed for clinical usability. Results: We identified 18 articles with a total of 17 unique prognostic indices after screening 9154 titles. The majority of indices (88%) had c-statistics greater than or equal to 0.70. Only 1 index was externally validated. Ten indices, 8 developed in the United States and 2 in the United Kingdom, were considered clinically usable. Conclusion: Of the 17 unique prognostic indices, 10 may be useful for implementation in the primary care setting to identify patients who may benefit from ACP discussions. An index classified as "clinically usable" may not be easy to use because of a large number of variables that are not routinely collected and the need to program the index into the electronic medical record. Full Article
for Dedicated Workforce Required to Support Large-Scale Practice Improvement By www.jabfm.org Published On :: 2020-03-16T09:31:37-07:00 Background: Facilitation is an effective approach for helping practices implement sustainable evidence-based practice improvements. Few studies examine the facilitation infrastructure and support needed for large-scale dissemination and implementation initiatives. Methods: The Agency for Health care Research and Quality funded 7 Cooperatives, each of which worked with over 200 primary care practices to rapidly disseminate and implement improvements in cardiovascular preventive care. The intervention target was to improve primary care practice capacity for quality initiative and the ABCS of cardiovascular disease prevention: aspirin in high-risk individuals, blood pressure control, cholesterol management, and smoking cessation. We identified the organizational elements and infrastructures Cooperatives used to support facilitators by reviewing facilitator logs, online diary data, semistructured interviews with facilitators, and fieldnotes from facilitator observations. We analyzed these data using a coding and sorting process. Results: Each Cooperative partnered with 2 to 16 organizations, piecing together 16 to 35 facilitators, often from other quality improvement projects. Quality assurance strategies included establishing initial and ongoing training, processes to support facilitators, and monitoring to assure consistency and quality. Cooperatives developed facilitator toolkits, implemented initiative-specific training, and developed processes for peer-to-peer learning and support. Conclusions: Supporting a large-scale facilitation workforce requires creating an infrastructure, including initial training, and ongoing support and monitoring, often borrowing from other ongoing initiatives. Facilitation that recognizes the need to support the vital integrating functions of primary care might be more efficient and effective than this fragmented approach to quality improvement. Full Article
for Peer Reviewers for the Journal of the American Board of Family Medicine in 2019 By www.jabfm.org Published On :: 2020-03-16T09:31:37-07:00 Full Article
for Many Family Medicine Successful Interventions and Clinical Reviews for Common Illnesses By www.jabfm.org Published On :: 2020-03-16T09:31:37-07:00 Family physician researchers continue to provide assistance to improve family medicine care. Commentaries on social determinants of health lead off this issue. Next, we have several papers on successful interventions by clinicians and/or patients to improve diabetes control, and then other provide information on other practice interventions that make a difference in overall care. Drug advertising continues to mislead. There is costly and nonproductive overuse of specific types of care. Herein is also a Scoping Review of possible indices for determining timely initiation of advance care planning. The issue’s clinical reviews on use of transgender care, cervical myelopathy, and inhaled steroids for chronic obstructive pulmonary disease are pertinent, thorough, and timely. Full Article
for Forest protects Heliconius butterflies from climate extremes [INSIDE JEB] By jeb.biologists.org Published On :: 2020-04-16T05:35:47-07:00 Kathryn Knight Full Article
for The glue produced by Drosophila melanogaster for pupa adhesion is universal [RESEARCH ARTICLE] By jeb.biologists.org Published On :: 2020-04-23T02:38:05-07:00 Flora Borne, Alexander Kovalev, Stanislav Gorb, and Virginie Courtier-Orgogozo Insects produce a variety of adhesives for diverse functions such as locomotion, mating, and egg or pupal anchorage to substrates. Although they are important for the biology of organisms and potentially represent a great resource for developing new materials, insect adhesives have been little studied so far. Here, we examined the adhesive properties of the larval glue of Drosophila melanogaster. This glue is made of glycosylated proteins and allows the animal to adhere to a substrate during metamorphosis. We designed an adhesion test to measure the pull-off force required to detach a pupa from a substrate and to evaluate the contact area covered by the glue. We found that the pupa adheres with similar forces to a variety of substrates (with distinct roughness, hydrophilic and charge properties). We obtained an average pull-off force of 217 mN, corresponding to 15,500 times the weight of a pupa and an adhesion strength of 137–244 kPa. Surprisingly, the pull-off forces did not depend on the contact area. Our study paves the way for a genetic dissection of the components of D. melanogaster glue that confer its particular adhesive properties. Full Article
for A fast and effective method for dissecting parasitic spores: myxozoans as an example [METHODS [amp ] TECHNIQUES] By jeb.biologists.org Published On :: 2020-04-06T07:24:08-07:00 Qingxiang Guo, Yang Liu, Yanhua Zhai, and Zemao GuDisassembling the parasitic spores and acquiring the main subunits is a prerequisite for deep understanding of the basic biology of parasites. Herein we present a fast and efficient method to dissect the myxospores in a few steps, which mainly involved sonication, sucrose density gradient and Percoll density gradient. We tested our method on three myxozoans species and demonstrated this method allows the dismembering of myxospores, isolation of intact and clean nematocysts and shell valves within 2h by low-cost. This new tool will facilitate subsequent analyses and enable a better understanding of the ecological and evolutionary significance of parasitic spores. Full Article
for The aerodynamic force platform as an ergometer [METHODS [amp ] TECHNIQUES] By jeb.biologists.org Published On :: 2020-04-06T07:24:08-07:00 Marc E. Deetjen, Diana D. Chin, and David LentinkAnimal flight requires aerodynamic power, which is challenging to determine accurately in vivo. Existing methods rely on approximate calculations based on wake flow field measurements, inverse dynamics approaches, or invasive muscle physiological recordings. In contrast, the external mechanical work required for terrestrial locomotion can be determined more directly by using a force platform as an ergometer. Based on an extension of the recent invention of the aerodynamic force platform, we now present a more direct method to determine the in vivo aerodynamic power by taking the dot product of the aerodynamic force vector on the wing with the representative wing velocity vector based on kinematics and morphology. We demonstrate this new method by studying a slowly flying dove, but it can be applied more generally across flying and swimming animals as well as animals that locomote over water surfaces. Finally, our mathematical framework also works for power analyses based on flow field measurements. Full Article
for Limits to Sustained Energy Intake XXXI: Effect of Graded Levels of Dietary Fat on Lactation Performance in Swiss Mice [RESEARCH ARTICLE] By jeb.biologists.org Published On :: 2020-04-14T06:41:13-07:00 Yi Huang, Jazmin Osorio Mendoza, Catherine Hambly, Baoguo Li, Zengguang Jin, Li Li, Moshen Madizi, Sumei Hu, and John R. SpeakmanThe heat dissipation limit theory predicts lactating female mice consuming diets with lower specific dynamic action (SDA) should have enhanced lactation performance. Dietary fat has lower SDA than other macronutrients. Here we tested the effects of graded dietary fat levels on lactating Swiss mice. We fed females five diets varying in fat content from 8.3 to 66.6%. Offspring of mothers fed diets of 41.7% fat and above were heavier and fatter at weaning compared to those of 8.3% and 25% fat diets. Mice on dietary fat contents of 41.7% and above had greater metabolizable energy intake at peak lactation (8.3%: 229.4±39.6, 25%: 278.8±25.8, 41.7%: 359.6±51.5, 58.3%: 353.7±43.6, 66.6%: 346±44.7 kJ day–1), lower daily energy expenditure (8.3%: 128.5±16, 25%: 131.6±8.4, 41.7%: 124.4±10.8, 58.3%: 115.1±10.5, 66.6%: 111.2±11.5 kJ day–1) and thus delivered more milk energy to their offspring (8.3%: 100.8±27.3, 25%: 147.2±25.1, 41.7%: 225.1±49.6, 58.3%: 238.6±40.1, 66.6%: 234.8±41.1 kJ day–1). Milk fat content (%) was unrelated to dietary fat content, indicating females on higher fat diets (> 41.7%) produced more rather than richer milk. Mothers consuming diets with 41.7% fat or above enhanced their lactation performance compared to those on 25% or less, probably by diverting dietary fat directly into the milk, thereby avoiding the costs of lipogenesis. At dietary fat contents above 41.7% they were either unable to transfer more dietary fat to the milk, or they chose not to do so, potentially because of a lack of benefit to the offspring that were increasingly fatter as maternal dietary fat increased. Full Article
for Responses of activity rhythms to temperature cues evolve in Drosophila populations selected for divergent timing of eclosion [RESEARCH ARTICLE] By jeb.biologists.org Published On :: 2020-04-14T06:41:13-07:00 Lakshman Abhilash, Arshad Kalliyil, and Vasu SheebaEven though the rhythm in adult emergence and rhythm in locomotor activity are two different rhythmic phenomena that occur at distinct life-stages of the fly life cycle, previous studies have hinted at similarities in certain aspects of the organisation of the circadian clock driving these two rhythms. For instance, the period gene plays an important regulatory role in both rhythms. In an earlier study, we have shown that selection on timing of adult emergence behaviour in populations of Drosophila melanogaster leads to the co-evolution of temperature sensitivity of circadian clocks driving eclosion. In this study, we were interested in asking if temperature sensitivity of the locomotor activity rhythm has evolved in our populations with divergent timing of adult emergence rhythm, with the goal of understanding the extent of similarity (or lack of it) in circadian organisation between the two rhythms. We found that in response to simulated jetlag with temperature cycles, late chronotypes (populations selected for predominant emergence during dusk) indeed re-entrain faster than early chronotypes (populations selected for predominant emergence during dawn) to 6-h phase-delays, thereby indicating enhanced sensitivity of the activity/rest clock to temperature cues in these stocks (entrainment is the synchronisation of internal rhythms to cyclic environmental time-cues). Additionally, we found that late chronotypes show higher plasticity of phases across regimes, day-to-day stability in phases and amplitude of entrainment, all indicative of enhanced temperature sensitive activity/rest rhythms. Our results highlight remarkably similar organisation principles between emergence and activity/rest rhythms. Full Article
for Androgenic modulation of extraordinary muscle speed creates a performance trade-off with endurance [RESEARCH ARTICLE] By jeb.biologists.org Published On :: 2020-04-14T06:41:13-07:00 Daniel J. Tobiansky, Meredith C. Miles, Franz Goller, and Matthew J. FuxjagerPerformance trade-offs can dramatically alter an organism's evolutionary trajectory by making certain phenotypic outcomes unattainable. Understanding how these trade-offs arise from an animal's design is therefore an important goal of biology. To explore this topic, we study how androgenic hormones, which regulate skeletal muscle function, influence performance trade-offs relevant to different components of complex reproductive behaviour. We conduct this work in golden-collared manakins (Manacus vitellinus), a Neotropical bird in which males court females by rapidly snapping their wings together above their back. Androgens help mediate the snap displays by radically increasing the twitch speed of a dorsal wing muscle [scapulohumeralis caudalis (SH)], which actuates the bird's wing-snap. Through hormone manipulations and in situ muscle recordings, we test how these positive effects on SH speed influence trade-offs with endurance. Indeed, this trait impacts the display by shaping signal length. We find that androgen-dependent increases in SH speed incur a cost to endurance, particularly when this muscle performs at its functional limits. Moreover, when behavioural data are overlaid on our muscle recordings, displaying animals appear to balance display speed with fatigue-induced muscle fusion (physiological tetanus) to generate the fastest possible signal while maintaining an appropriate signal duration. Our results point to androgenic hormone action as a functional trigger of trade-offs in sexual performance—they enhance one element of a courtship display, but in doing so, impede another. Full Article
for Heat dissipation capacity influences reproductive performance in an aerial insectivore [RESEARCH ARTICLE] By jeb.biologists.org Published On :: 2020-04-22T03:44:39-07:00 Simon Tapper, Joseph J. Nocera, and Gary BurnessClimatic warming is predicted to increase the frequency of extreme weather events, which may reduce an individual's capacity for sustained activity due to thermal limits. We tested whether the risk of overheating may limit parental provisioning of an aerial insectivorous bird in population decline. For many seasonally breeding birds, parents are thought to operate close to an energetic ceiling during the 2-3 week chick-rearing period. The factors determining the ceiling remain unknown, although it may be set by an individual's capacity to dissipate body heat (the heat dissipation limitation hypothesis). Over two breeding seasons we experimentally trimmed the ventral feathers of female tree swallows (Tachycineta bicolor, Vieillot, 1808) to provide a thermal window. We then monitored maternal and paternal provisioning rates, nestling growth rates, and fledging success. We found the effect of our experimental treatment was context-dependent. Females with an enhanced capacity to dissipate heat fed their nestlings at higher rates than controls when conditions were hot, but the reverse was true under cool conditions. Control females and their mates both reduced foraging under hot conditions. In contrast, male partners of trimmed females maintained a constant feeding rate across temperatures, suggesting attempts to match the feeding rate of their partners. On average, nestlings of trimmed females were heavier than controls, but did not have a higher probability of fledging. We suggest that removal of a thermal constraint allowed females to increase provisioning rates, but additionally provided nestlings with a thermal advantage via increased heat transfer during maternal brooding. Our data provide support for the heat dissipation limitation hypothesis and suggest that depending on temperature, heat dissipation capacity can influence reproductive success in aerial insectivores. Full Article
for The effect of ambient oxygen on the thermal performance of a cockroach, Nauphoeta cinerea [RESEARCH ARTICLE] By jeb.biologists.org Published On :: 2020-05-04T02:24:22-07:00 Emily J. Lombardi, Candice L. Bywater, and Craig R. WhiteThe Oxygen and Capacity-Limited Thermal Tolerance (OCLTT) hypothesis proposes that the thermal tolerance of an animal is shaped by its capacity to deliver oxygen in relation to oxygen demand. Studies testing this hypothesis have largely focused on measuring short-term performance responses in animals under acute exposure to critical thermal maximums. The OCLTT hypothesis, however, emphasises the importance of sustained animal performance over acute tolerance. The present study tested the effect of chronic hypoxia and hyperoxia during development on medium to long-term performance indicators at temperatures spanning the optimal temperature for growth in the speckled cockroach, Nauphoeta cinerea. In contrast to the predictions of the OCLTT hypothesis, development under hypoxia did not significantly reduce growth rate or running performance, and development under hyperoxia did not significantly increase growth rate or running performance. The effect of developmental temperature and oxygen on tracheal morphology and metabolic rate were also not consistent with OCLTT predictions, suggesting that oxygen delivery capacity is not the primary driver shaping thermal tolerance in this species. Collectively, these findings suggest that the OCLTT hypothesis does not explain moderate-to-long-term thermal performance in Nauphoeta cinerea, which raises further questions about the generality of the hypothesis. Full Article
for Impact of temperature on bite force and bite endurance in the Leopard Iguana (Diplolaemus leopardinus) in the Andes Mountains [RESEARCH ARTICLE] By jeb.biologists.org Published On :: 2020-05-04T02:24:22-07:00 Nadia Vicenzi, Alejandro Laspiur, Paola L. Sassi, Ruben Massarelli, John Krenz, and Nora R. IbargüengoytiaIn ectotherms, temperature exerts a strong influence on the performance of physiological and ecological traits. One approach to understand the impact of rising temperatures on animals and their ability to cope with climate change is to quantify variation in thermal-sensitive traits. Here, we examined the thermal biology, the temperature dependence and the thermal plasticity of bite force (endurance and magnitude) in Diplolaemus leopardinus, an aggressive and territorial lizard, endemic to Mendoza province, Argentina. Our results indicated that this lizard behaves like a moderate thermoregulator which uses the rocks of its environment as the main heat source. Bite endurance was not influenced by head morphometry and body temperature, whereas bite force was influenced by head length and jaw length, and exhibited thermal dependence. Before thermal acclimation treatments, the maximum bite force for D. leopardinus occured at the lowest body temperature and fell sharply with increasing body temperature. After acclimation treatments, lizards acclimated at higher temperatures exhibited greater bite force. Bite force showed phenotypic plasticity, which reveals that leopard iguanas are able to maintain (and even improve) their bite force under a rising-temperature scenario. Full Article
for Whale sharks increase swimming effort while filter feeding, but appear to maintain high foraging efficiencies [RESEARCH ARTICLE] By jeb.biologists.org Published On :: 2020-05-04T02:24:22-07:00 David E. Cade, J. Jacob Levenson, Robert Cooper, Rafael de la Parra, D. Harry Webb, and Alistair D. M. DoveWhale sharks (Rhincodon typus Smith 1828) – the largest extant fish species – reside in tropical environments, making them an exception to the general rule that animal size increases with latitude. How this largest fish thrives in tropical environments that promote high metabolism but support less robust zooplankton communities has not been sufficiently explained. We used open-source inertial measurement units (IMU) to log 397 hours of whale shark behavior in Yucatan, Mexico, at a site of both active feeding and intense wildlife tourism. Here we show that the strategies employed by whale sharks to compensate for the increased drag of an open mouth are similar to ram-feeders five orders of magnitude smaller and one order of magnitude larger. Presumed feeding constituted 20% of the total time budget of four sharks, with individual feeding bouts lasting up to 11 consecutive hrs. Compared to normal, sub-surface swimming, three sharks increased their stroke rate and amplitude while surface feeding, while one shark that fed at depth did not demonstrate a greatly increased energetic cost. Additionally, based on time-depth budgets, we estimate that aerial surveys of shark populations should consider including a correction factor of 3 to account for the proportion of daylight hours that sharks are not visible at the surface. With foraging bouts generally lasting several hours, interruptions to foraging during critical feeding periods may represent substantial energetic costs to these endangered species, and this study presents baseline data from which management decisions affecting tourist interactions with whale sharks may be made. Full Article
for Fish embryo vulnerability to combined acidification and warming coincides with low capacity for homeostatic regulation [RESEARCH ARTICLE] By jeb.biologists.org Published On :: 2020-05-05T05:22:41-07:00 Flemming Dahlke, Magnus Lucassen, Ulf Bickmeyer, Sylke Wohlrab, Velmurugu Puvanendran, Atle Mortensen, Melissa Chierici, Hans-Otto Pörtner, and Daniela StorchThe vulnerability of fish embryos and larvae to environmental factors is often attributed to a lack of adult-like organ systems (gills) and thus insufficient homeostatic capacity. However, experimental data supporting this hypothesis are scarce. Here, by using Atlantic cod (Gadus morhua) as a model, the relationship between embryo vulnerability (to projected ocean acidification and warming) and homeostatic capacity was explored through parallel analyses of stage-specific mortality and in vitro activity and expression of major ion pumps (ATP-Synthase, Na+/K+-ATPase, H+-ATPase) and co-transporters (NBC1, NKCC1). Immunolocalization of these transporters was used to study ionocyte morphology in newly-hatched larvae. Treatment-related embryo mortality until hatch (+20% due to acidification and warming) occurred primarily during an early period (gastrulation) characterized by extremely low ion transport capacities. Thereafter, embryo mortality decreased in parallel with an exponential increase in activity and expression of all investigated ion transporters. Significant changes in transporter activity and expression in response to acidification (+15% activity) and warming (-30% expression) indicate some potential for short-term acclimatization, although likely associated with energetic trade-offs. Interestingly, whole-larvae enzyme capacities (supported by abundant epidermal ionocytes) reached levels similar to those previously measured in gill tissue of adult cod, suggesting that early-life stages without functional gills are better equipped in terms of ion homeostasis than previously thought. This study implies that the gastrulation period represents a critical transition from inherited (maternal) defenses to active homeostatic regulation, which facilitates enhanced resilience of later stages to environmental factors. Full Article
for A Simple Clinical Tool for Stratifying Risk of Clinically Significant CKD after Nephrectomy: Development and Multinational Validation By jasn.asnjournals.org Published On :: 2020-04-30T10:00:30-07:00 Background Clinically significant CKD following surgery for kidney cancer is associated with increased morbidity and mortality, but identifying patients at increased CKD risk remains difficult. Simple methods to stratify risk of clinically significant CKD after nephrectomy are needed. Methods To develop a tool for stratifying patients’ risk of CKD arising after surgery for kidney cancer, we tested models in a population-based cohort of 699 patients with kidney cancer in Queensland, Australia (2012–2013). We validated these models in a population-based cohort of 423 patients from Victoria, Australia, and in patient cohorts from single centers in Queensland, Scotland, and England. Eligible patients had two functioning kidneys and a preoperative eGFR ≥60 ml/min per 1.73 m2. The main outcome was incident eGFR <45 ml/min per 1.73 m2 at 12 months postnephrectomy. We used prespecified predictors—age ≥65 years old, diabetes mellitus, preoperative eGFR, and nephrectomy type (partial/radical)—to fit logistic regression models and grouped patients according to degree of risk of clinically significant CKD (negligible, low, moderate, or high risk). Results Absolute risks of stage 3b or higher CKD were <2%, 3% to 14%, 21% to 26%, and 46% to 69% across the four strata of negligible, low, moderate, and high risk, respectively. The negative predictive value of the negligible risk category was 98.9% for clinically significant CKD. The c statistic for this score ranged from 0.84 to 0.88 across derivation and validation cohorts. Conclusions Our simple scoring system can reproducibly stratify postnephrectomy CKD risk on the basis of readily available parameters. This clinical tool’s quantitative assessment of CKD risk may be weighed against other considerations when planning management of kidney tumors and help inform shared decision making between clinicians and patients. Full Article
for Chitotriosidase as a Novel Biomarker for Therapeutic Monitoring of Nephropathic Cystinosis By jasn.asnjournals.org Published On :: 2020-04-30T10:00:30-07:00 Background Nephropathic cystinosis, a hereditary lysosomal storage disorder caused by dysfunction of the lysosomal cotransporter cystinosin, leads to cystine accumulation and cellular damage in various organs, particularly in the kidney. Close therapeutic monitoring of cysteamine, the only available disease-modifying treatment, is recommended. White blood cell cystine concentration is the current gold standard for therapeutic monitoring, but the assay is technically demanding and is available only on a limited basis. Because macrophage-mediated inflammation plays an important role in the pathogenesis of cystinosis, biomarkers of macrophage activation could have potential for the therapeutic monitoring of cystinosis. Methods We conducted a 2-year prospective, longitudinal study in which 61 patients with cystinosis who were receiving cysteamine therapy were recruited from three European reference centers. Each regular care visit included measuring four biomarkers of macrophage activation: IL-1β, IL-6, IL-18, and chitotriosidase enzyme activity. Results A multivariate linear regression analysis of the longitudinal data for 57 analyzable patients found chitotriosidase enzyme activity and IL-6 to be significant independent predictors for white blood cell cystine levels in patients of all ages with cystinosis; a receiver operating characteristic analysis ranked chitotriosidase as superior to IL-6 in distinguishing good from poor therapeutic control (on the basis of white blood cell cystine levels of <2 nmol 1/2 cystine/mg protein or ≥2 nmol 1/2 cystine/mg protein, respectively). Moreover, in patients with at least one extrarenal complication, chitotriosidase significantly correlated with the number of extrarenal complications and was superior to white blood cell cystine levels in predicting the presence of multiple extrarenal complications. Conclusions Chitotriosidase enzyme activity holds promise as a biomarker for use in therapeutic monitoring of nephropathic cystinosis. Full Article
for Exocyst Genes Are Essential for Recycling Membrane Proteins and Maintaining Slit Diaphragm in Drosophila Nephrocytes By jasn.asnjournals.org Published On :: 2020-04-30T10:00:30-07:00 Background Studies have linked mutations in genes encoding the eight-protein exocyst protein complex to kidney disease, but the underlying mechanism is unclear. Because Drosophila nephrocytes share molecular and structural features with mammalian podocytes, they provide an efficient model for studying this issue. Methods We silenced genes encoding exocyst complex proteins specifically in Drosophila nephrocytes and studied the effects on protein reabsorption by lacuna channels and filtration by the slit diaphragm. We performed nephrocyte functional assays, carried out super-resolution confocal microscopy of slit diaphragm proteins, and used transmission electron microscopy to analyze ultrastructural changes. We also examined the colocalization of slit diaphragm proteins with exocyst protein Sec15 and with endocytosis and recycling regulators Rab5, Rab7, and Rab11. Results Silencing exocyst genes in nephrocytes led to profound changes in structure and function. Abolition of cellular accumulation of hemolymph proteins with dramatically reduced lacuna channel membrane invaginations offered a strong indication of reabsorption defects. Moreover, the slit diaphragm’s highly organized surface structure—essential for filtration—was disrupted, and key proteins were mislocalized. Ultrastructural analysis revealed that exocyst gene silencing led to the striking appearance of novel electron-dense structures that we named "exocyst rods," which likely represent accumulated membrane proteins following defective exocytosis or recycling. The slit diaphragm proteins partially colocalized with Sec15, Rab5, and Rab11. Conclusions Our findings suggest that the slit diaphragm of Drosophila nephrocytes requires balanced endocytosis and recycling to maintain its structural integrity and that impairment of the exocyst complex leads to disruption of the slit diaphragm and nephrocyte malfunction. This model may help identify therapeutic targets for treating kidney diseases featuring molecular defects in vesicle endocytosis, exocytosis, and recycling. Full Article
for ARHGEF7 ({beta}-PIX) Is Required for the Maintenance of Podocyte Architecture and Glomerular Function By jasn.asnjournals.org Published On :: 2020-04-30T10:00:29-07:00 Background Previous studies showed that Cdc42, a member of the prototypical Rho family of small GTPases and a regulator of the actin cytoskeleton, is critical for the normal development and health of podocytes. However, upstream regulatory mechanisms for Cdc42 activity in podocytes are largely unknown. Methods We used a proximity-based ligation assay, BioID, to identify guanine nucleotide exchange factors that activate Cdc42 in immortalized human podocytes. We generated podocyte-specific ARHGEF7 (commonly known as β-PIX) knockout mice by crossing β-PIX floxed mice with Podocin-Cre mice. Using shRNA, we established cultured mouse podocytes with β-PIX knockdown and their controls. Results We identified β-PIX as a predominant guanine nucleotide exchange factor that interacts with Cdc42 in human podocytes. Podocyte-specific β-PIX knockout mice developed progressive proteinuria and kidney failure with global or segmental glomerulosclerosis in adulthood. Glomerular podocyte density gradually decreased in podocyte-specific β-PIX knockout mice, indicating podocyte loss. Compared with controls, glomeruli from podocyte-specific β-PIX knockout mice and cultured mouse podocytes with β-PIX knockdown exhibited significant reduction in Cdc42 activity. Loss of β-PIX promoted podocyte apoptosis, which was mediated by the reduced activity of the prosurvival transcriptional regulator Yes-associated protein. Conclusions These findings indicate that β-PIX is required for the maintenance of podocyte architecture and glomerular function via Cdc42 and its downstream Yes-associated protein activities. This appears to be the first evidence that a Rho–guanine nucleotide exchange factor plays a critical role in podocytes. Full Article
for Use of Human Induced Pluripotent Stem Cells and Kidney Organoids To Develop a Cysteamine/mTOR Inhibition Combination Therapy for Cystinosis By jasn.asnjournals.org Published On :: 2020-04-30T10:00:29-07:00 Background Mutations in CTNS—a gene encoding the cystine transporter cystinosin—cause the rare, autosomal, recessive, lysosomal-storage disease cystinosis. Research has also implicated cystinosin in modulating the mTORC1 pathway, which serves as a core regulator of cellular metabolism, proliferation, survival, and autophagy. In its severest form, cystinosis is characterized by cystine accumulation, renal proximal tubule dysfunction, and kidney failure. Because treatment with the cystine-depleting drug cysteamine only slows disease progression, there is an urgent need for better treatments. Methods To address a lack of good human-based cell culture models for studying cystinosis, we generated the first human induced pluripotent stem cell (iPSC) and kidney organoid models of the disorder. We used a variety of techniques to examine hallmarks of cystinosis—including cystine accumulation, lysosome size, the autophagy pathway, and apoptosis—and performed RNA sequencing on isogenic lines to identify differentially expressed genes in the cystinosis models compared with controls. Results Compared with controls, these cystinosis models exhibit elevated cystine levels, increased apoptosis, and defective basal autophagy. Cysteamine treatment ameliorates this phenotype, except for abnormalities in apoptosis and basal autophagy. We found that treatment with everolimus, an inhibitor of the mTOR pathway, reduces the number of large lysosomes, decreases apoptosis, and activates autophagy, but it does not rescue the defect in cystine loading. However, dual treatment of cystinotic iPSCs or kidney organoids with cysteamine and everolimus corrects all of the observed phenotypic abnormalities. Conclusions These observations suggest that combination therapy with a cystine-depleting drug such as cysteamine and an mTOR pathway inhibitor such as everolimus has potential to improve treatment of cystinosis. Full Article
for Role of Impaired Nutrient and Oxygen Deprivation Signaling and Deficient Autophagic Flux in Diabetic CKD Development: Implications for Understanding the Effects of Sodium-Glucose Cotransporter 2-Inhibitors By jasn.asnjournals.org Published On :: 2020-04-30T10:00:29-07:00 Growing evidence indicates that oxidative and endoplasmic reticular stress, which trigger changes in ion channels and inflammatory pathways that may undermine cellular homeostasis and survival, are critical determinants of injury in the diabetic kidney. Cells are normally able to mitigate these cellular stresses by maintaining high levels of autophagy, an intracellular lysosome-dependent degradative pathway that clears the cytoplasm of dysfunctional organelles. However, the capacity for autophagy in both podocytes and renal tubular cells is markedly impaired in type 2 diabetes, and this deficiency contributes importantly to the intensity of renal injury. The primary drivers of autophagy in states of nutrient and oxygen deprivation—sirtuin-1 (SIRT1), AMP-activated protein kinase (AMPK), and hypoxia-inducible factors (HIF-1α and HIF-2α)—can exert renoprotective effects by promoting autophagic flux and by exerting direct effects on sodium transport and inflammasome activation. Type 2 diabetes is characterized by marked suppression of SIRT1 and AMPK, leading to a diminution in autophagic flux in glomerular podocytes and renal tubules and markedly increasing their susceptibility to renal injury. Importantly, because insulin acts to depress autophagic flux, these derangements in nutrient deprivation signaling are not ameliorated by antihyperglycemic drugs that enhance insulin secretion or signaling. Metformin is an established AMPK agonist that can promote autophagy, but its effects on the course of CKD have been demonstrated only in the experimental setting. In contrast, the effects of sodium-glucose cotransporter–2 (SGLT2) inhibitors may be related primarily to enhanced SIRT1 and HIF-2α signaling; this can explain the effects of SGLT2 inhibitors to promote ketonemia and erythrocytosis and potentially underlies their actions to increase autophagy and mute inflammation in the diabetic kidney. These distinctions may contribute importantly to the consistent benefit of SGLT2 inhibitors to slow the deterioration in glomerular function and reduce the risk of ESKD in large-scale randomized clinical trials of patients with type 2 diabetes. Full Article
for Transitions between the steps of forward and reverse splicing of group IIC introns [ARTICLE] By rnajournal.cshlp.org Published On :: 2020-04-16T06:30:22-07:00 Group II introns are mobile genetic elements that perform both self-splicing and intron mobility reactions. These ribozymes are comprised of a catalytic RNA core that binds to an intron-encoded protein (IEP) to form a ribonucleoprotein (RNP) complex. Splicing proceeds through two competing reactions: hydrolysis or branching. Group IIC intron ribozymes have a minimal RNA architecture, and splice almost exclusively through hydrolysis in ribozyme reactions. Addition of the IEP allows the splicing reaction to form branched lariat RNPs capable of intron mobility. Here we examine ribozyme splicing, IEP-dependent splicing, and mobility reactions of a group IIC intron from the thermophilic bacterium Thermoanerobacter italicus (Ta.it.I1). We show that Ta.it.I1 is highly active for ribozyme activity, forming linear hydrolytic intron products. Addition of purified IEP switches activity to the canonical lariat forming splicing reaction. We demonstrate that the Ta.it.I1 group IIC intron coordinates the progression of the forward splicing reaction through a –' interaction between intron domains II and VI. We further show that branched splicing is supported in the absence of the IEP when the –' interaction is mutated. We also investigated the regulation of the two steps of reverse splicing during intron mobility into DNA substrates. Using a fluorescent mobility assay that simultaneously visualizes all steps of intron integration into DNA, we show that completion of reverse splicing is tightly coupled to cDNA synthesis regardless of mutation of the –' interaction. Full Article
for Assessing the accuracy of direct-coupling analysis for RNA contact prediction [ARTICLE] By rnajournal.cshlp.org Published On :: 2020-04-16T06:30:22-07:00 Many noncoding RNAs are known to play a role in the cell directly linked to their structure. Structure prediction based on the sole sequence is, however, a challenging task. On the other hand, thanks to the low cost of sequencing technologies, a very large number of homologous sequences are becoming available for many RNA families. In the protein community, the idea of exploiting the covariance of mutations within a family to predict the protein structure using the direct-coupling-analysis (DCA) method has emerged in the last decade. The application of DCA to RNA systems has been limited so far. We here perform an assessment of the DCA method on 17 riboswitch families, comparing it with the commonly used mutual information analysis and with state-of-the-art R-scape covariance method. We also compare different flavors of DCA, including mean-field, pseudolikelihood, and a proposed stochastic procedure (Boltzmann learning) for solving exactly the DCA inverse problem. Boltzmann learning outperforms the other methods in predicting contacts observed in high-resolution crystal structures. Full Article
for RNAconTest: comparing tools for noncoding RNA multiple sequence alignment based on structural consistency [BIOINFORMATICS] By rnajournal.cshlp.org Published On :: 2020-04-16T06:30:22-07:00 The importance of noncoding RNA sequences has become increasingly clear over the past decade. New RNA families are often detected and analyzed using comparative methods based on multiple sequence alignments. Accordingly, a number of programs have been developed for aligning and deriving secondary structures from sets of RNA sequences. Yet, the best tools for these tasks remain unclear because existing benchmarks contain too few sequences belonging to only a small number of RNA families. RNAconTest (RNA consistency test) is a new benchmarking approach relying on the observation that secondary structure is often conserved across highly divergent RNA sequences from the same family. RNAconTest scores multiple sequence alignments based on the level of consistency among known secondary structures belonging to reference sequences in their output alignment. Similarly, consensus secondary structure predictions are scored according to their agreement with one or more known structures in a family. Comparing the performance of 10 popular alignment programs using RNAconTest revealed that DAFS, DECIPHER, LocARNA, and MAFFT created the most structurally consistent alignments. The best consensus secondary structure predictions were generated by DAFS and LocARNA (via RNAalifold). Many of the methods specific to noncoding RNAs exhibited poor scalability as the number or length of input sequences increased, and several programs displayed substantial declines in score as more sequences were aligned. Overall, RNAconTest provides a means of testing and improving tools for comparative RNA analysis, as well as highlighting the best available approaches. RNAconTest is available from the DECIPHER website (http://DECIPHER.codes/Downloads.html). Full Article
for Probiotics for the Prevention of Ventilator-Associated Pneumonia: A Meta-Analysis of Randomized Controlled Trials By rc.rcjournal.com Published On :: 2020-04-28T00:42:49-07:00 BACKGROUND:Ventilator-associated pneumonia (VAP) is a common and serious complication of mechanical ventilation. We conducted a meta-analysis of published randomized controlled trials to evaluate the efficacy and safety of probiotics for VAP prevention in patients who received mechanical ventilation.METHODS:We searched a number of medical literature databases to identify randomized controlled trials that compared probiotics with controls for VAP prevention. The results were expressed as odds ratios (OR) or mean differences with accompanying 95% CIs. Study-level data were pooled by using a random-effects model. Data syntheses were accomplished by using statistical software.RESULTS:Fourteen studies that involved 1,975 subjects met our inclusion criteria. Probiotic administration was associated with a reduction in VAP incidence among all 13 studies included in the meta-analysis (OR 0.62, 95% CI 0.45–0.85; P = .003; I2 = 43%) but not among the 6 double-blinded studies (OR 0.72, 95% CI 0.44–1.19; P = .20; I2 = 55%). We found a shorter duration of antibiotic use for VAP (mean difference −1.44, 95% CI −2.88 to −0.01; P = .048, I2 = 30%) in the probiotics group than in the control group, and the finding comes from just 2 studies. No statistically significant differences were found between the groups in terms of ICU mortality (OR 0.95, 95% CI 0.67–1.34; P = .77; I2 = 0%), ICU stay (mean difference –0.77, 95% CI –2.58 to 1.04; P = .40; I2 = 43%), duration of mechanical ventilation (mean difference –0.91, 95% CI –2.20 to 0.38; P = .17; I2 = 25%), or occurrence of diarrhea (OR 0.72, 95% CI 0.45–1.15; P = .17; I2 = 41%).CONCLUSIONS:The meta-analysis results indicated that the administration of probiotics significantly reduced the incidence of VAP. Furthermore, our findings need to be verified in large-scale, well-designed, randomized, multi-center trials. Full Article
for The Timed Inspiratory Effort Index as a Weaning Predictor: Analysis of Intra- and Interobserver Reproducibility By rc.rcjournal.com Published On :: 2020-04-28T00:42:49-07:00 BACKGROUND:Prolonged ventilatory weaning may expose patients to unnecessary discomfort, increase the risk of complications, and raise the costs of hospital treatment. In this scenario, indexes that reliably predict successful liberation can be helpful.OBJECTIVE:To evaluate the intra- and interobserver reproducibility of the timed inspiratory effort index as a weaning predictor.METHODS:This prospective observational study included subjects judged as able to start liberation from mechanical ventilation. For the intra-observer analysis, the same investigator performed 2 measurements in each selected patient with an interval of 30 min a rest. For interobserver analysis, 2 measurements were obtained in another sample of subjects, also with an interval of 30 min rest, but each of one performed by a different investigator. The Bland-Altman diagram, the coefficient concordance of kappa, and the Pearson correlation coefficient were used to compare the measurements. The performance of the timed inspiratory effort index was assessed by receiver operating characteristic curves. Values of P < .05 were considered significant.RESULTS:We selected 113 subjects (43 males; mean ± SD age, 77 ± 14 y). Fifty-six (49.6%) achieved successful liberation, and 33 (29%) died in the ICU. The mean ± SD duration of mechanical ventilation was 14.4 ± 6.7 d. The Bland-Altman diagrams that addressed intra- and interobservers agreement showed low variability between measurements. Values of the concordance coefficients of kappa were 0.82 (0.68–0.95) and 0.80 (0.65–0.94), and of the linear correlation coefficients, 0.86 (0.77–0.91) and 0.89 (0.82–0.93) for the intra- and interobservers measurements, respectively. The mean ± SD values for the area under the curve for each pair of the intra- and interobserver measurements were 0.96 ± 0.07 versus 0.94 ± 0.07 (P = .41) and 0.94 ± 0.05 versus 0.90 ± 0.07 (P = .14), respectively.CONCLUSIONS:The variability of the measurement of the timed inspiratory effort index by intra- and interobservers showed very high reproducibility, which reinforced the index as a sensible, accurate, and reliable outcome predictor of liberation from mechanical ventilation. Full Article
for Fixed Ratio Versus Lower Limit of Normal: Health Status and Risk Factors for COPD Overdiagnosis By rc.rcjournal.com Published On :: 2020-04-28T00:42:49-07:00 BACKGROUND:The threshold of the lower limit of the normal range of lung function has been suggested to be more accurate than the 0.7 fixed ratio (FEV1/FVC < 0.7) for a diagnosis of COPD. We aimed to explore the health status and risk factors of patients overdiagnosed with COPD when using the lower limit of the normal range as a diagnostic reference.METHODS:Subjects with COPD diagnosed by a pulmonologist according to guidelines of the Global Initiative for Chronic Obstructive Lung Disease were recruited from October 2016 to April 2018. Overdiagnosed COPD was defined as FEV1/FVC that meets the criterion of the 0.7 fixed ratio but not the the lower limit of the normal range criterion. Spirometry and questionnaires were performed by eligible subjects.RESULTS:Of the 513 subjects included in the final analysis, 20 (3.9%) were overdiagnosed when using the lower limit of the normal range as the diagnostic reference. The subjects who were overdiagnosed were older, weighed more, had better lung function, lower modified Medical British Research Council scores, and higher St. George's Respiratory Questionnaire and 36-item Short Form Survey scores than the subjects who were correctly diagnosed. Older age, heavier weight, exposure to cooking oil fumes, or a new-built or newly renovated home were associated with an increased risk of overdiagnosis of COPD (age adjusted odds ratio (OR) 1.17, 95% CI 1.09–1.26; weight adjusted OR 1.08, 95% CI 1.03–1.13; exposure to cooking oil fumes adjusted OR 3.00, 95% CI, 1.04–8.68; exposure to new-built or newly renovated home adjusted OR 10.88, 95% CI 1.46–80.87.CONCLUSIONS:The subjects with overdiagnosed COPD had a better health status and lung function than the subjects who were correctly diagnosed. Older age, heavier weight, and exposure to cooking oil fumes or a new-built or newly renovated home were factors associated with the overdiagnosis of COPD. These findings may help reduce overdiagnosis of COPD. Full Article
for Circadian Clock-Controlled Drug Metabolism: Implications for Chronotherapeutics [Minireview] By dmd.aspetjournals.org Published On :: 2020-04-17T07:49:35-07:00 Dependence of drug metabolism on dosing time has long been recognized. However, only recently are the underlying mechanisms for circadian drug metabolism being clarified. Diurnal rhythmicity in expression of drug-metabolizing enzymes is believed to be a key factor determining circadian metabolism. Supporting the notion that biological rhythms are generated and maintained by the circadian clock, a number of diurnal enzymes are under the control of the circadian clock. In general, circadian clock genes generate and regulate diurnal rhythmicity in drug-metabolizing enzymes via transcriptional actions on one or two of three cis-elements (i.e., E-box, D-box, and Rev-erb response element or RAR-related orphan receptor response element). Additionally, cycling or clock-controlled nuclear receptors such as hepatocyte nuclear factor 4α and peroxisome proliferator–activated receptor are contributors to diurnal enzyme expression. These newly discovered mechanisms for each of the rhythmic enzymes are reviewed in this article. We also discuss how the rhythms of enzymes are translated to circadian pharmacokinetics and drug chronotoxicity, which has direct implications for chronotherapeutics. Our discussion is also extended to two diurnal transporters (P-glycoprotein and multidrug resistance-associated protein 2) that have an important role in drug absorption. Although the experimental evidence is lacking in metabolism-based chronoefficacy, circadian genes (e.g., Rev-erbα) as drug targets are shown to account for diurnal variability in drug efficacy. SIGNIFICANCE STATEMENT Significant progress has been made in understanding the molecular mechanisms for generation of diurnal rhythmicity in drug-metabolizing enzymes. In this article, we review the newly discovered mechanisms for each of the rhythmic enzymes and discuss how the rhythms of enzymes are translated to circadian pharmacokinetics and drug chronotoxicity, which has direct implications for chronotherapeutics. Full Article
for Crystallographic and kinetic analyses of the FdsBG subcomplex of the cytosolic formate dehydrogenase FdsABG from Cupriavidus necator [Molecular Biophysics] By www.jbc.org Published On :: 2020-05-08T03:41:14-07:00 Formate oxidation to carbon dioxide is a key reaction in one-carbon compound metabolism, and its reverse reaction represents the first step in carbon assimilation in the acetogenic and methanogenic branches of many anaerobic organisms. The molybdenum-containing dehydrogenase FdsABG is a soluble NAD+-dependent formate dehydrogenase and a member of the NADH dehydrogenase superfamily. Here, we present the first structure of the FdsBG subcomplex of the cytosolic FdsABG formate dehydrogenase from the hydrogen-oxidizing bacterium Cupriavidus necator H16 both with and without bound NADH. The structures revealed that the two iron-sulfur clusters, Fe4S4 in FdsB and Fe2S2 in FdsG, are closer to the FMN than they are in other NADH dehydrogenases. Rapid kinetic studies and EPR measurements of rapid freeze-quenched samples of the NADH reduction of FdsBG identified a neutral flavin semiquinone, FMNH•, not previously observed to participate in NADH-mediated reduction of the FdsABG holoenzyme. We found that this semiquinone forms through the transfer of one electron from the fully reduced FMNH−, initially formed via NADH-mediated reduction, to the Fe2S2 cluster. This Fe2S2 cluster is not part of the on-path chain of iron-sulfur clusters connecting the FMN of FdsB with the active-site molybdenum center of FdsA. According to the NADH-bound structure, the nicotinamide ring stacks onto the re-face of the FMN. However, NADH binding significantly reduced the electron density for the isoalloxazine ring of FMN and induced a conformational change in residues of the FMN-binding pocket that display peptide-bond flipping upon NAD+ binding in proper NADH dehydrogenases. Full Article
for Quantification of the affinities of CRISPR-Cas9 nucleases for cognate protospacer adȷacent motif (PAM) sequences [Molecular Biophysics] By www.jbc.org Published On :: 2020-05-08T03:41:14-07:00 The CRISPR/Cas9 nucleases have been widely applied for genome editing in various organisms. Cas9 nucleases complexed with a guide RNA (Cas9–gRNA) find their targets by scanning and interrogating the genomic DNA for sequences complementary to the gRNA. Recognition of the DNA target sequence requires a short protospacer adjacent motif (PAM) located outside this sequence. Given that the efficiency of target location may depend on the strength of interactions that promote target recognition, here we sought to compare affinities of different Cas9 nucleases for their cognate PAM sequences. To this end, we measured affinities of Cas9 nucleases from Streptococcus pyogenes, Staphylococcus aureus, and Francisella novicida complexed with guide RNAs (gRNAs) (SpCas9–gRNA, SaCas9–gRNA, and FnCas9–gRNA, respectively) and of three engineered SpCas9–gRNA variants with altered PAM specificities for short, PAM-containing DNA probes. We used a “beacon” assay that measures the relative affinities of DNA probes by determining their ability to competitively affect the rate of Cas9–gRNA binding to fluorescently labeled target DNA derivatives called “Cas9 beacons.” We observed significant differences in the affinities for cognate PAM sequences among the studied Cas9 enzymes. The relative affinities of SpCas9–gRNA and its engineered variants for canonical and suboptimal PAMs correlated with previous findings on the efficiency of these PAM sequences in genome editing. These findings suggest that high affinity of a Cas9 nuclease for its cognate PAM promotes higher genome-editing efficiency. Full Article
for Genetic lineage tracing with multiple DNA recombinases: A user's guide for conducting more precise cell fate mapping studies [Methods and Resources] By www.jbc.org Published On :: 2020-05-08T03:41:14-07:00 Site-specific recombinases, such as Cre, are a widely used tool for genetic lineage tracing in the fields of developmental biology, neural science, stem cell biology, and regenerative medicine. However, nonspecific cell labeling by some genetic Cre tools remains a technical limitation of this recombination system, which has resulted in data misinterpretation and led to many controversies in the scientific community. In the past decade, to enhance the specificity and precision of genetic targeting, researchers have used two or more orthogonal recombinases simultaneously for labeling cell lineages. Here, we review the history of cell-tracing strategies and then elaborate on the working principle and application of a recently developed dual genetic lineage-tracing approach for cell fate studies. We place an emphasis on discussing the technical strengths and caveats of different methods, with the goal to develop more specific and efficient tracing technologies for cell fate mapping. Our review also provides several examples for how to use different types of DNA recombinase–mediated lineage-tracing strategies to improve the resolution of the cell fate mapping in order to probe and explore cell fate–related biological phenomena in the life sciences. Full Article
for Chemical roadblocking of DNA transcription for nascent RNA display [RNA] By www.jbc.org Published On :: 2020-05-08T03:41:14-07:00 Site-specific arrest of RNA polymerases (RNAPs) is fundamental to several technologies that assess RNA structure and function. Current in vitro transcription “roadblocking” approaches inhibit transcription elongation by blocking RNAP with a protein bound to the DNA template. One limitation of protein-mediated transcription roadblocking is that it requires inclusion of a protein factor extrinsic to the minimal in vitro transcription reaction. In this work, we developed a chemical approach for halting transcription by Escherichia coli RNAP. We first established a sequence-independent method for site-specific incorporation of chemical lesions into dsDNA templates by sequential PCR and translesion synthesis. We then show that interrupting the transcribed DNA strand with an internal desthiobiotin-triethylene glycol modification or 1,N6-etheno-2'-deoxyadenosine base efficiently and stably halts Escherichia coli RNAP transcription. By encoding an intrinsic stall site within the template DNA, our chemical transcription roadblocking approach enables display of nascent RNA molecules from RNAP in a minimal in vitro transcription reaction. Full Article
for The testis-specific LINC component SUN3 is essential for sperm head shaping during mouse spermiogenesis [Cell Biology] By www.jbc.org Published On :: 2020-05-08T03:41:14-07:00 Sperm head shaping is a key event in spermiogenesis and is tightly controlled via the acrosome–manchette network. Linker of nucleoskeleton and cytoskeleton (LINC) complexes consist of Sad1 and UNC84 domain–containing (SUN) and Klarsicht/ANC-1/Syne-1 homology (KASH) domain proteins and form conserved nuclear envelope bridges implicated in transducing mechanical forces from the manchette to sculpt sperm nuclei into a hook-like shape. However, the role of LINC complexes in sperm head shaping is still poorly understood. Here we assessed the role of SUN3, a testis-specific LINC component harboring a conserved SUN domain, in spermiogenesis. We show that CRISPR/Cas9-generated Sun3 knockout male mice are infertile, displaying drastically reduced sperm counts and a globozoospermia-like phenotype, including a missing, mislocalized, or fragmented acrosome, as well as multiple defects in sperm flagella. Further examination revealed that the sperm head abnormalities are apparent at step 9 and that the sperm nuclei fail to elongate because of the absence of manchette microtubules and perinuclear rings. These observations indicate that Sun3 deletion likely impairs the ability of the LINC complex to transduce the cytoskeletal force to the nuclear envelope, required for sperm head elongation. We also found that SUN3 interacts with SUN4 in mouse testes and that the level of SUN4 proteins is drastically reduced in Sun3-null mice. Altogether, our results indicate that SUN3 is essential for sperm head shaping and male fertility, providing molecular clues regarding the underlying pathology of the globozoospermia-like phenotype. Full Article
for Geology of the Chang 7 Member oil shale of the Yanchang Formation of the Ordos Basin in central north China By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 We present a review of the Chang 7 Member oil shale, which occurs in the middle–late Triassic Yanchang Formation of the Ordos Basin in central north China. The oil shale has a thickness of 28 m (average), an area of around 30 000 km2 and a Ladinian age. It is mainly brown-black to black in colour with a laminar structure. It is characterized by average values of 18 wt% TOC (total organic carbon), 8 wt% oil yield, a 8.35 MJ kg–1 calorific value, 400 kg t–1 hydrocarbon productivity and kerogen of type I–II1, showing a medium quality. On average, it comprises 49% clay minerals, 29% quartz, 16% feldspar and some iron oxides, which is close to the average mineral composition of global shale. The total SiO2 and Al2O3 comprise 63.69 wt% of the whole rock, indicating a medium ash type. The Sr/Ba is 0.33, the V/Ni is 7.8, the U/Th is 4.8 and the FeO/Fe2O3 is 0.5, indicating formation in a strongly reducing, freshwater or low-salinity sedimentary environment. Multilayered intermediate-acid tuff is developed in the basin, which may have promoted the formation of the oil shale. The Ordos Basin was formed during the northwards subduction of the Qinling oceanic plate during the Ladinian–Norian in a back-arc basin context. The oil shale of the Ordos Basin has a large potential for hydrocarbon generation. Supplementary material: Tables of oil-shale geochemical composition, proximate and organic matter analyses from the Chang 7 Member oil shale, the Ordos Basin, Central north China are available at https://doi.org/10.6084/m9.figshare.c.4411703 Full Article
for Lithological and chemostratigraphic discrimination of facies within the Bowland Shale Formation within the Craven and Edale basins, UK By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 The Carboniferous Bowland Shale Formation of the UK is a proven hydrocarbon source rock and currently a target for shale gas exploration. Most existing analysis details lithofacies and geochemical assessment of a small number of boreholes. Given a paucity of relevant borehole cores, surface samples provide a valuable contribution to the assessment of this unconventional gas source. This study reviews existing literature on the formation's hydrocarbon geochemistry and provides new lithological descriptions of seven lithofacies, XRD mineralogy and hydrocarbon-specific geochemical data for 32 outcrop localities within the Craven and Edale basins, respectively in the northern and southern parts of the resource area. Low oxygen indices suggest that the majority of samples are relatively unaltered (in terms of hydrocarbon geochemistry), and therefore suitable for the characterization of the shale organic character. Total organic carbon (TOC) ranges from 0.7 to 6.5 wt%, with highest values associated with maximum flooding surfaces. Mean Tmax values of 447 and 441°C for the Edale and Craven basins, respectively, suggest that nearly all the samples were too immature to have generated appreciable amounts of dry gas. The oil saturation index is consistently below the >100 mg g–1 TOC benchmark, suggesting that they are not prospective for shale oil. Supplementary material: A table summarizing the location, geological description and age of all of the samples in this paper is available at https://doi.org/10.6084/m9.figshare.c.4444589 Full Article
for Sedimentary and tectonic controls on Lower Carboniferous (Visean) mixed carbonate-siliciclastic deposition in NE England and the Southern North Sea: implications for reservoir architecture By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 Discovery of the Breagh gas field in the Southern North Sea (SNS) has demonstrated the potential that the Lower Carboniferous (Visean, 346.7–330.9 Ma) Farne Group reservoirs have to contribute to the UK's future energy mix. New biostratigraphic correlations provide a basis to compare Asbian and Brigantian sedimentary cores from the Breagh Field and age-equivalent sediments exposed on the Northumberland Coast, which has proved critical in gaining an understanding of exploration and development opportunities. Thirteen facies associations characterize the mixed carbonate–siliciclastic system, grouped into: marine, delta front, delta shoreface, lower delta plain and upper delta plain gross depositional environments. The facies associations are interpreted as depositing in a mixed carbonate and siliciclastic fluvio-deltaic environment, and are arranged into coarsening- and cleaning-upward cycles (parasequences) bounded by flooding surfaces. Most cycles are characterized by mouth bars, distributary channels, interdistributary bays and common braided rivers, interpreted as river-dominated deltaic deposits. Some cycles include rare shoreface and tidally-influenced deposits, interpreted as river-dominated and wave- or tide-influenced deltaic deposits. The depositional processes that formed each cycle have important implications for the reservoir net/gross ratio (where this ratio indicates the proportion of sandstone beds in a cycle), thickness and lateral extent. The deltaic deposits were controlled by a combination of tectonic and eustatic (allocyclic) events and delta avulsion (autocyclic) processes, and are likely to reflect a changing tectonic regime, from extension within elongate fault-bounded basins (synrift) to passive regional thermal subsidence (post-rift). Deep incision by the Base Permian Unconformity across the Breagh Field has removed the Westphalian, Namurian and upper Visean, to leave the more prospective thicker clastic reservoirs within closure. Thematic collection: This article is part of the Under-explored plays and frontier basins of the UK continental shelf collection available at: https://www.lyellcollection.org/cc/under-explored-plays-and-frontier-basins-of-the-uk-continental-shelf Full Article
for Structural evolution of the Breagh area: implications for carboniferous prospectivity of the Mid North Sea High, Southern North Sea By pg.lyellcollection.org Published On :: 2020-05-01T00:30:41-07:00 Exploration success at Breagh demonstrates that western parts of the Mid North Sea High area are prospective despite the absence of an Upper Permian (Rotliegend Group) Leman Sandstone Formation reservoir and source rocks belonging to the Upper Carboniferous Westphalian Coal Measures Group. Detailed seismic and well interpretation shows that the Breagh trap was a long-lived footwall high, the prospectivity of which was enhanced by Variscan folding and uplift, leading to the truncation (subcrop) of Lower Carboniferous reservoirs beneath the Base Permian Unconformity. Its drape (supra-crop) by Upper Permian (Zechstein Super Group) evaporites creates the seal. The complexity of its overburden means that an accurate picture of the Breagh structure only emerges after accurate depth-conversion that takes the effects of the Mesozoic graben into account. Pronounced easterly tilting during the Cenozoic affected the area and controlled gas migration into the structure from palaeostructures lying to the east. However, evidence that Breagh is not filled to spill point (underfill) suggests that charge limitation remained an issue. The study demonstrates that a poorly-documented and under-explored Lower Carboniferous play exists in Southern North Sea, which relies upon careful structural mapping and basin modelling to be undertaken for the play to be understood and its further potential to be realized. Thematic collection: This article is part of the Under-explored plays and frontier basins of the UK continental shelf collection available at: https://www.lyellcollection.org/cc/under-explored-plays-and-frontier-basins-of-the-uk-continental-shelf Full Article
for The progressive development of microfabrics from initial deposition to slump deformation: an example from a modern sedimenary melange on the Nankai Prism By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 The progressive development of microfabrics from initial deposition to slump deformation and then a submarine slide was investigated in an active subduction zone using cores recovered during the Integrated Ocean Drilling Program Expedition 333. A Pleistocene–Holocene sequence was recovered at Site C0018A, which was located on a slope basin on the footwall of the megasplay fault in the Nankai Trough, SW Japan. Six mass-transport deposit units intercalated with coherent intervals were recovered from the upper 190 m of the drilled succession. The initial microfabrics in the undeformed hemipelagic sediments were characterized by random and porous fabrics composed predominantly of clay aggregations and connectors. The initial fabrics were cardhouse fabrics, which consist of clay flakes with edge-to-edge (E–E) and/or edge-to-face (E–F) contacts. These initial microfabrics developed into compacted microfabrics, which are random and consolidated fabrics (bookhouse fabrics) that consist of clay flakes with E–F and/or face-to-face (F–F) contacts and develop during burial as a pure shear deformation. During slumping, these fabrics were then deformed under simple shear to become predominantly F–F contacts and form clay chains. Thus, the microfabrics in these submarine slides are a sedimentary mélange that developed locally into a preferred clay orientation with F–F contacts. Supplementary material: A schematic illustration showing sedimentation processes and fabrics is available at https://doi.org/10.6084/m9.figshare.c.4483385 Thematic collection: This article is part of the Polygenetic mélanges collection available at: https://www.lyellcollection.org/cc/polygenetic-melanges Full Article
for Redefinition of the Ligurian Units at the Alps-Apennines junction (NW Italy) and their role in the evolution of the Ligurian accretionary wedge: constraints from melanges and broken formations By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 We document that the undifferentiated chaotic Ligurian Units of the Monferrato–Torino Hill sector (MO-TH) at the Alps–Apennines junction consist of three different units that are comparable with the Cassio, Caio and Sporno Units of the External Ligurian Units of the Northern Apennines. Their internal stratigraphy reflects the character of units deposited in an ocean–continent transition (OCT) zone between the northwestern termination of the Ligurian–Piedmont oceanic basin and the thinned passive margin of Adria microcontinent. The inherited wedge-shaped architecture of this OCT, which gradually closed toward the north in the present-day Canavese Zone, controlled the Late Cretaceous–early Eocene flysch deposition at the trench of the External Ligurian accretionary wedge during the oblique subduction. This favoured the formation of an accretionary wedge increasing in thickness and elevation toward the SE, from the MO-TH to the Emilia Northern Apennines. Our results therefore provide significant information on both the palaeogeographical reconstruction of the northwestern termination of the Ligurian–Piedmont oceanic basin and the role played by inherited along-strike variations (stratigraphy, structural architecture and morphology) of OCT zones in controlling subduction–accretionary processes. Supplementary material: A spreadsheet with X-ray fluorescence spectrometry and inductively coupled plasma mass spectrometry whole-rock major and trace element composition of mantle peridotites, and photomicrographs of mantle peridotites are available at https://doi.org/10.6084/m9.figshare.c.4519643 Full Article
for High-resolution carbon isotope stratigraphy of the Lower and Middle Ordovician succession of the Yangtze Platform, China: implications for global correlation By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 The Lower and Middle Ordovician of the Yangtze Platform, China, is characterized by a sedimentary succession dominated by carbonate rocks. Three sections spanning the Nantsinkuan/Lunshan, Fenhsiang, Hunghuayuan, and Dawan/Zitai formations, corresponding to the Tremadocian–Dapingian in age, have been sampled for high-resolution 13C chemostratigraphy (542 samples in total). Our new 13C data reveal five tie-points with the potential for global correlation: (1) a positive 13C excursion in the lower Nantsinkuan Formation within the Tremadocian Rossodus manitouensis Zone; (2) an excursion with two peaks roughly within the late Tremadocian Paltodus ‘deltifer’ Zone; (3) a positive 13C shift in the lower Hunghuayuan Formation, within the early Floian Serratognathus diversus Zone; (4) a gradual positive 13C shift in the late Floian, ranging from the uppermost S. diversus Zone to the basal Oepikodus evae Zone; (5) a minor negative shift in the lower Dawan/Zitai Formation, within the early Dapingian Baltoniodus triangularis Zone. These excursions are herein used for correlation of the Yangtze Platform strata with successions from South China, North China, the Argentine Precordillera, North America and Baltica. From a palaeogeographical perspective the Gudongkou, Xiangshuidong and Daling sections represent depositional environments along an inner to outer ramp profile. 13C data from these sections show successively heavier (higher) 13C values with increasing depositional depth. This is interpreted as due to remineralization of organic carbon within the carbonate rocks. Supplementary material: Carbon and oxygen isotope data are available at: https://doi.org/10.6084/m9.figshare.c.4767080 Full Article
for Basement-cover relationships and deformation in the Northern Paraguai Belt, central Brazil: implications for the Neoproterozoic-early Paleozoic history of western Gondwana By jgs.lyellcollection.org Published On :: 2020-05-04T02:10:48-07:00 The Northern Paraguai Belt, at the SE border of the Amazonian Craton, central Brazil, has been interpreted as a Brasiliano–Pan-African (c. 650–600 Ma) belt with a foreland basin, recording collisional polyphase tectonism and greenschist-facies metamorphism extending from the late Precambrian to the Cambrian–Ordovician. New structural investigations indicate that the older metasedimentary rocks of the Cuiabá Group represent a Tonian–Cryogenian basement assemblage deformed in two contemporaneous fault-bounded structural sub-domains of wrench-dominated (rake <10°) and contraction-dominated (rake ~30–40°) sinistral transpression, with tectonic vergence towards the SE. The younger late Cryogenian to early Cambrian sedimentary rocks lying to the NW of the Cuiabá Group are non-metamorphic and display only pervasive brittle transtension characterized by normal-oblique faults, fractures and forced drag folds with no consistent vergence pattern. Our analyses suggest that an unconformity separates the metasedimentary Cuiabá Group basement of the Northern Paraguai Belt from the unmetamorphosed sedimentary cover. It is proposed that the latter units were deposited during a post-glacial marine transgression (after c. 635 Ma) in a post-collisional basin. The Paraguai Belt basement and its post-collisional sedimentary cover share a number of significant geological similarities with sequences in the Bassarides Belt and Taoudéni Basin in the SW portion of the West African Craton. Full Article
for Development of an Extended-Specificity Multiplex Immunoassay for Detection of Streptococcus pneumoniae Serotype-Specific Antigen in Urine by Use of Human Monoclonal Antibodies [Diagnostic Laboratory Immunology] By cvi.asm.org Published On :: 2017-12-05T08:00:30-08:00 Current pneumococcal vaccines cover the 10 to 23 most common serotypes of the 92 presently described. However, with the increased usage of pneumococcal-serotype-based vaccines, the risk of serotype replacement and an increase in disease caused by nonvaccine serotypes remains. Serotype surveillance of pneumococcal infections relies heavily on culture techniques, which are known to be insensitive, particularly in cases of noninvasive disease. Pneumococcal-serotype-specific urine assays offer an alternative method of serotyping for both invasive and noninvasive disease. However, the assays described previously cover mainly conjugate vaccine serotypes, give little information about circulating nonvaccine serotypes, and are currently available only in one or two specialist laboratories. Our laboratory has developed a Luminex-based extended-range antigen capture assay to detect pneumococcal-serotype-specific antigens in urine samples. The assay targets 24 distinct serotypes/serogroups plus the cell wall polysaccharide (CWP) and some cross-reactive serotypes. We report that the assay is capable of detecting all the targeted serotypes and the CWP at 0.1 ng/ml, while some serotypes are detected at concentrations as low as 0.3 pg/ml. The analytical serotype specificity was determined to be 98.4% using a panel of polysaccharide-negative urine specimens spiked with nonpneumococcal bacterial antigens. We also report clinical sensitivities of 96.2% and specificities of 89.9% established using a panel of urine specimens from patients diagnosed with community-acquired pneumonia or pneumococcal disease. This assay can be extended for testing other clinical samples and has the potential to greatly improve serotype-specific surveillance in the many cases of pneumococcal disease in which a culture is never obtained. Full Article
for Is APOE {varepsilon}4 associated with cognitive performance in early MS? By nn.neurology.org Published On :: 2020-05-01T12:45:10-07:00 Objective To assess the impact of APOE polymorphisms on cognitive performance in patients newly diagnosed with clinically isolated syndrome (CIS) or relapsing-remitting MS (RRMS). Methods This multicenter cohort study included 552 untreated patients recently diagnosed with CIS or RRMS according to the 2005 revised McDonald criteria. The single nucleotide polymorphisms rs429358 (4) and rs7412 (2) of the APOE haplotype were assessed by allelic discrimination assays. Cognitive performance was evaluated using the 3-second paced auditory serial addition test and the Multiple Sclerosis Inventory Cognition (MUSIC). Sum scores were calculated to approximate the overall cognitive performance and memory-centered cognitive functions. The impact of the APOE carrier status on cognitive performance was assessed using multiple linear regression models, also including demographic, clinical, MRI, and lifestyle factors. Results APOE 4 homozygosity was associated with lower overall cognitive performance, whereas no relevant association was observed for APOE 4 heterozygosity or APOE 2 carrier status. Furthermore, higher disability levels, MRI lesion load, and depressive symptoms were associated with lower cognitive performance. Patients consuming alcohol had higher test scores than patients not consuming alcohol. Female sex, lower disability, and alcohol consumption were associated with better performance in the memory-centered subtests of MUSIC, whereas no relevant association was observed for APOE carrier status. Conclusion Along with parameters of a higher disease burden, APOE 4 homozygosity was identified as a potential predictor of cognitive performance in this large cohort of patients with CIS and early RRMS. Full Article
for Intranasal midazolam for treating acute respiratory crises in a woman with stiff person syndrome By nn.neurology.org Published On :: 2020-04-01T13:35:23-07:00 Stiff person syndrome (SPS) is a rare neurologic disorder characterized by progressively worsening rigidity and spasms of the axial and limb muscles. Dyspnea has been recently recognized as a common symptom in SPS,1 and life-threatening respiratory crises have been occasionally reported and suspected to be responsible for sudden death in these patients.2,3 The pathophysiologic mechanisms of these respiratory manifestations remain unclear. Some authors have hypothesized that rigidity and/or spasm of the muscles of the trunk could prevent normal rib cage movements and excursion of the diaphragm.1 Full Article