Parallel processing of quickly and slowly mobilized reserve vesicles in hippocampal synapses

Vesicles within presynaptic terminals are thought to be segregated into a variety of readily releasable and reserve pools. The nature of the pools and trafficking between them is not well understood, but pools that are slow to mobilize when synapses are active are often assumed to feed pools that are mobilized more quickly, in a series. However, electrophysiological studies of synaptic transmission have suggested instead a parallel organization where vesicles within slowly and quickly mobilized reserve pools would separately feed independent reluctant- and fast-releasing subdivisions of the readily releasable pool. Here, we use FM-dyes to confirm the existence of multiple reserve pools at hippocampal synapses and a parallel organization that prevents intermixing between the pools, even when stimulation is intense enough to drive exocytosis at the maximum rate. The experiments additionally demonstrate extensive heterogeneity among synapses in the relative sizes of the slowly and quickly mobilized reserve pools, which suggests equivalent heterogeneity in the numbers of reluctant and fast-releasing readily releasable vesicles that may be relevant for understanding information processing and storage.

Pooling Saliva Sample as an Effective Strategy for the Systematic CMV Screening of Newborns-A Multicentric Prospective Study

BACKGROUND

Cytomegalovirus is the most common cause of congenital infections worldwide. Screening all newborns in the first 2 weeks of life is the only way to detect all cases of congenital infection, allowing the monitoring of children with asymptomatic infection at birth and early intervention.

AIM

In this multicenter study, we aimed to evaluate the feasibility of using a saliva pool strategy for mass screening in 7 Portuguese hospitals, and to estimate the current prevalence of this congenital infection in these hospitals.

METHODS

A total of 7033 newborns were screened between June 2020 and June 2022, and 704 pools of 10 saliva samples were analyzed by polymerase chain reaction (PCR).

RESULTS

Of the 704 pools analyzed, 685 were negative and 19 had positive PCR results for cytomegalovirus. After individual PCR testing, 26 newborns had positive saliva results, of which 15 were confirmed by urine testing. Thus, this study's prevalence of congenital infection was 0.21% (95% confidence interval: 0.12%-0.35%).

CONCLUSIONS

In this study, the pooling strategy proved to be effective for the systematic screening of newborns, although this low prevalence raises questions regarding the cost-effectiveness of implementing universal screening. However, this prevalence is probably the result of the control measures taken during the pandemic; therefore, the rates are expected to return to prepandemic values, but only a new study after the pandemic will be able to confirm this.

A cross-sectional assessment of PRRSV nucleic acid detection by RT-qPCR in serum, ear-vein blood swabs, nasal swabs, and oral swabs from weaning-age pigs under field conditions

Introduction

The porcine reproductive and respiratory syndrome virus (PRRSV) continues to challenge swine production in the US and most parts of the world. Effective PRRSV surveillance in swine herds can be challenging, especially because the virus can persist and sustain a very low prevalence. Although weaning-age pigs are a strategic subpopulation in the surveillance of PRRSV in breeding herds, very few sample types have been validated and characterized for surveillance of this subpopulation. The objectives of this study, therefore, were to compare PRRSV RNA detection rates in serum, oral swabs (OS), nasal swabs (NS), ear-vein blood swabs (ES), and family oral fluids (FOF) obtained from weaning-age pigs and to assess the effect of litter-level pooling on the reverse transcription-quantitative polymerase chain reaction (RT-qPCR) detection of PRRSV RNA.

Methods

Three eligible PRRSV-positive herds in the Midwestern USA were selected for this study. 666 pigs across 55 litters were sampled for serum, NS, ES, OS, and FOF. RT-qPCR tests were done on these samples individually and on the litter-level pools of the swabs. Litter-level pools of each swab sample type were made by combining equal volumes of each swab taken from the pigs within a litter.

Results

Ninety-six piglets distributed across 22 litters were positive by PRRSV RT-qPCR on serum, 80 piglets distributed across 15 litters were positive on ES, 80 piglets distributed across 17 litters were positive on OS, and 72 piglets distributed across 14 litters were positive on NS. Cohen's kappa analyses showed near-perfect agreement between all paired ES, OS, NS, and serum comparisons (). The serum RT-qPCR cycle threshold values (Ct) strongly predicted PRRSV detection in swab samples. There was a ≥ 95% probability of PRRSV detection in ES-, OS-, and NS pools when the proportion of positive swab samples was ≥ 23%, ≥ 27%, and ≥ 26%, respectively.

Discussion

ES, NS, and OS can be used as surveillance samples for detecting PRRSV RNA by RT-qPCR in weaning-age pigs. The minimum number of piglets to be sampled by serum, ES, OS, and NS to be 95% confident of detecting ≥ 1 infected piglet when PRRSV prevalence is ≥ 10% is 30, 36, 36, and 40, respectively.

SARS-CoV-2 Infection in Captive Hippos (Hippopotamus amphibius), Belgium

Two adult female hippos in Zoo Antwerp who were naturally infected with SARS-CoV-2 showed nasal discharge for a few days. Virus was detected by immunocytochemistry and PCR in nasal swab samples and by PCR in faeces and pool water. Serology was also positive. No treatment was necessary.

Incidence of SARS-COV-2 infection among swimming athletes: data from real life in Apulia (Italy), July 2020/August 2021

BACKGROUND

As other indoor sports facilities, swimming pools were closed in Italy from March to May 2020 and from October 2020 to July 2021 due to the outbreak of the COVID-19 pandemic; access to these facilities was restricted to athletes of national relevance. This decision was based on "precautionary principles" and without evidence of a high risk of SARS-COV-2 circulation among swimming pools' attendants. The aim of this paper is to describe the pattern of SARS-COV-2 circulation among swimming athletes in Apulia (Southern Italy).

STUDY DESIGN

The study aims to investigate the hypothesis that attending a pool increases the risk of SARS-COV-2 infection. The outcome measure is the incidence of SARS-COV-2 infection among swimming athletes compared with the general population.

METHODS

This is a retrospective cross-sectional study carried out in Apulia, Southern Italy. The study was performed through the analysis of both the database of the Italian Swimming Federation and the SARS-COV-2 infections in Apulia Region, from July 2020 to August 2021.

RESULTS

Among 2,939 federally licensed athletes, 221 had an history of SARS-COV-2 infection from July 2020 to August 2021, with an incidence of 75.2 /1,000. In the general Apulian population, during the same time span, the incidence of SARS-COV-2 infection was 67.3/1,000 and - considering the incidence rate ratio - there is no difference between the two populations (IRR=1.1; 95% CI=0.9-1.3; p>0.05).

CONCLUSIONS

The incidence of SARS-COV-2 infection in Apulian swimmers showed no significant differences with the general population.

Recovery of Salmonella bacterial isolates from pooled fecal samples from horses

BACKGROUND

It is important to determine if a horse is shedding Salmonella spp., but a complete culture series can be cost prohibitive.

OBJECTIVES

Determine the optimal pooling technique to maintain high sensitivity of Salmonella spp. culture using spiked samples, and then demonstrate the efficacy of this protocol on clinical submissions.

HYPOTHESIS

Pooled fecal samples are as sensitive as 5 individual cultures for the detection of Salmonella shedding.

ANIMALS

A single Salmonella-negative horse from the university herd, and 19 hospitalized horses.

METHODS

Salmonella-free fecal samples were spiked with different amounts of Salmonella spp. (10² , 10³ , 10⁴ , and 10⁵ colony forming units [cfu]) and homogenized to evaluate pooled samples. Five individual fecal samples were collected from 19 hospitalized horses. Ten-gram aliquots of each individual sample were combined to make a pooled sample. Both individual and pooled samples were cultured for Salmonella spp. The identity of bacterial isolates was confirmed by matrix-assisted laser desorption-ionization time of flight mass spectrometry.

RESULTS

A 10²  cfu concentration of Salmonella spp. could be recovered from a spiked Salmonella-free fecal sample. Homogenization protocols indicated that the addition of 20 mL of broth to the pooled sample improved recovery, whereas homogenization time did not. Of the 19 horses tested, 5 were positive for Salmonella. In all instances, Salmonella spp. were recovered from the fecal pool as well as individual samples.

CONCLUSIONS AND CLINICAL IMPORTANCE

Pooling of 5 fecal samples for Salmonella culture is a sensitive and cost-effective diagnostic approach to detect horses that are shedding the organism.

Influence of expertise level on techniques of applying top and back spins in cue sports

This study compared the kinematics of upper body and cue stick among players of various skill levels when performing back spin and top spin shots. Twenty-eight male cue sports players were assigned to the novice (n = 10), intermediate (n = 9), or skilled groups (n = 9). The back spin and top spin tests were administrated while kinematic data were recorded using a 3D motion capture system. The results revealed greater upper limb joint ranges of motions (all p < 0.05), maximum angular velocities (all p < 0.05), and cue tip speed in the back spin than top spin shots (p < 0.001). None of joint kinematic or shot performance variables investigated was significantly different among the three skill levels (all p > 0.05). For the head movement, the novice group exhibited greater anteroposterior displacement than the skilled group (p = 0.020). In conclusion, except for the head movement, the upper body and cue stick kinematics did not significantly differ among players with varied skill levels. Greater joint ranges of motions and angular velocities were required to generate a faster cue tip speed for the back spin shots when compared with the top spin shots.

Genome-Scale Reconstruction of Microbial Dynamic Phenotype: Successes and Challenges

This review is a part of the SI 'Genome-Scale Modeling of Microorganisms in the Real World'. The goal of GEM is the accurate prediction of the phenotype from its respective genotype under specified environmental conditions. This review focuses on the dynamic phenotype; prediction of the real-life behaviors of microorganisms, such as cell proliferation, dormancy, and mortality; balanced and unbalanced growth; steady-state and transient processes; primary and secondary metabolism; stress responses; etc. Constraint-based metabolic reconstructions were successfully started two decades ago as FBA, followed by more advanced models, but this review starts from the earlier nongenomic predecessors to show that some GEMs inherited the outdated biokinetic frameworks compromising their performances. The most essential deficiencies are: (i) an inadequate account of environmental conditions, such as various degrees of nutrients limitation and other factors shaping phenotypes; (ii) a failure to simulate the adaptive changes of MMCC (MacroMolecular Cell Composition) in response to the fluctuating environment; (iii) the misinterpretation of the SGR (Specific Growth Rate) as either a fixed constant parameter of the model or independent factor affecting the conditional expression of macromolecules; (iv) neglecting stress resistance as an important objective function; and (v) inefficient experimental verification of GEM against simple growth (constant MMCC and SGR) data. Finally, we propose several ways to improve GEMs, such as replacing the outdated Monod equation with the SCM (Synthetic Chemostat Model) that establishes the quantitative relationships between primary and secondary metabolism, growth rate and stress resistance, process kinetics, and cell composition.

Foraminifera-derived carbon contribution to sedimentary inorganic carbon pool: A case study from three Norwegian fjords

Norwegian fjords have been recently recognized as hot spots for carbon burial due to the large amounts of terrestrial organic matter delivered to fjord sediments, as well as the high sediment accumulation rates. Here, we present the first data on the contribution of benthic foraminiferal inorganic carbon to the sediments of three Norwegian fjords. Our study shows that calcareous foraminifera, which are among the most abundant calcifying organisms in the modern global oceans, can constitute between 15% and 33% of inorganic carbon accumulated in the sediments of the two studied southern Norwegian fjords (Raunefjorden and Hjeltefjorden). In a northern Norwegian fjord (Balsfjorden), the contribution of calcareous foraminifera to the inorganic carbon pool is smaller (<1%) than the one observed in southern fjords. We also found that the amount of foraminifera-derived carbon is primarily dependent on the species composition of the foraminifera community. Large calcareous foraminifera species, despite a lower number of individuals, constitute, on average, 13%-29% of the inorganic carbon in the two southern Norwegian fjords, while the contribution of small, highly abundant species does not exceed 4% of the inorganic carbon pools in the sediments. Calcareous foraminifera species that are indicative of dysoxic conditions have been found to have low inorganic carbon contents per specimen compared to other analysed similar-sized calcareous foraminifera species. This relationship most likely exists due to the thin test walls of these foraminifera species, which may facilitate gas exchange. The results of our case study suggest that the climate-driven formation of near-bottom low-oxygen zones may lead to the dominance of foraminifera associated with dysoxic conditions and, in consequence, to the decrease of foraminifera-derived inorganic carbon. However, to properly analyse the contribution of carbon from thin-walled foraminifera to the sedimentary carbon pool, further studies analysing a broader range of these species is needed.

First Aid for Pool Chemical Exposure: A Narrative Review

Over 4500 visits to emergency departments related to pool chemical exposures occur annually in the United States, and it is likely that many more go unreported. Injury can occur due to sensitivity to standard chemical concentrations in pools (such as with opening one’s eyes underwater), accidental exposure to super-concentrated chemicals (such as malfunction of a pool chlorinator), or accidental inhalation of fumes while opening the storage container for chlorination tablets. Therefore, first aid care has the potential to significantly limit morbidity. 

A literature review was undertaken to determine the appropriate first aid for pool chemical exposures. This literature search revealed 25 pertinent articles, of which none were systematic reviews or studies directly related to the first aid treatment of pool chemical exposures. However, five articles were included as indirect evidence, and a hand search of references revealed five additional articles for inclusion. Treatment recommendations were extrapolated from the treatment of chemical exposures from other incidents.

Symptoms of pool chemical exposure reflect irritation secondary to the caustic chemicals involved. Patients may report irritation of the skin, eyes, nose, or throat; cough; chest tightness; and difficulty breathing. Following any exposure to pool chemicals, the victim should be removed from the source, taken to an area with fresh air, and contaminated materials (e.g. clothing, contact lenses) should be removed. Irrigation of the exposed area should take place immediately with uncontaminated fresh water for at least 15 minutes. It is anticipated that an exposed person will be symptomatically improved by leaving the area of exposure, removing their contaminated clothing items, and irrigating the contaminated body parts. However, if symptoms do not resolve during that time or if symptoms are worsening, the victim should be evaluated by trained medical personnel.

[Application of Array-Based Oligonucleotides for Synthesis of Genetic Designs]

The application of array-based oligonucleotides in biological studies is described. These oligonucleotides are mainly used to design large libraries of various nucleotide sequences, which are applied to study protein-nucleic acid interactions, splicing, transcription, translation, and other regulatory processes in mammalian, yeast, and bacterial systems. The application of gene libraries generated by array-based nucleotides along with advanced methods of the combination of DNA duplexes will make it possible to obtain complex genetic designs for synthetic biology.

Can a Good Break Shot Determine the Game Outcome in 9-Ball?

This study aimed to quantify the break shot characteristics and identify their significance in predicting the game outcomes in 9-ball tournaments. The break shots of 275 frames (241 men's, 34 women's) of professional tournaments were analyzed from two aspects: (1) cue ball position, represented by the distance between the cue ball and the table center, and (2) ball distribution, indicated by the standard deviation of Voronoi cell areas determined from all remaining balls on the table. Spearman correlation and binary logistic regression were utilized to identify associations and to predict the frame outcomes, respectively. Results showed that the more balls falling into the pockets during the break, the more clustered the remaining balls (r _s = 0.232, p < 0.001). The closer the cue ball ending toward the table center, the more balls potted in the visit immediately after the break (r _s = -0.144, p = 0.027). Neither cue ball position nor ball distribution could predict table clearance or winning of a frame. In conclusion, pocketing more balls during the break is associated with more clustered balls remaining on the table. Parking the cue ball near the table center after the break can facilitate potting more balls immediately after.

Considerations for Measuring Activity-Dependence of Recruitment of Synaptic Vesicles to the Readily Releasable Pool

The connection strength of most chemical synapses changes dynamically during normal use as a function of the recent history of activity. The phenomenon is known as short-term synaptic plasticity or synaptic dynamics, and is thought to be involved in processing and filtering information as it is transmitted across the synaptic cleft. Multiple presynaptic mechanisms have been implicated, but large gaps remain in our understanding of how the mechanisms are modulated and how they interact. One important factor is the timing of recruitment of synaptic vesicles to a readily-releasable pool. A number of studies have concluded that activity and/or residual Ca²⁺ can accelerate the mechanism, but alternative explanations for some of the evidence have emerged. Here I review the methodology that we have developed for isolating the recruitment and the dependence on activity from other kinds of mechanisms that are activated concurrently.

mSphere of Influence: Hiring of Underrepresented Minority Assistant Professors in Medical School Basic Science Departments Has a Long Way To Go

Michael D. L. Johnson is a molecular microbiologist observing the role of metals in bacterial biology. In this mSphere of Influence article, he discusses the impact that the paper "Decoupling of the minority PhD talent pool and assistant professor hiring in medical school basic science departments in the US" by Kenneth D. Gibbs, Jr., Jacob Basson, Imam M. Xierali, and David A. Broniatowski (eLife 5:e21393, 2016, https://doi.org/10.7554/eLife.21393) had on him regarding hiring underrepresented minorities at research-intensive institutions and what he considers to be the next steps.

Allele Frequency Changes Provide Evidence for Selection and Identification of Candidate Loci for Survival in Red Clover (Trifolium pratense L.)

Survivor populations of red clover (Trifolium pratense L.) from plots in a field experiment in southern Norway were genetically characterized using genotyping by sequencing, and compared with the original population and each other. Genetic differentiation between populations was characterized on the basis of allele frequencies of single nucleotide polymorphisms (SNPs), using principal component analysis. SNPs that had been under selection, i.e., SNPs with significantly different allele frequencies in survivor populations relative to the original population, or between survivor populations that had received different treatments, were identified by analysis of F _ST values, using BayeScan and a simple and stringent F _ST-based test utilizing replicate populations from the field experiment. In addition, we tested the possibility of pooling DNA samples prior to sequencing, and pooling leaf samples prior to DNA extraction and sequencing, followed by allele frequency estimation on the basis of number of variant reads. Overall, survivor populations were more different from each other than from the original population, indicating random changes in allele frequency, selection in response to local variation in conditions between plots in the field experiment, or sampling error. However, some differentiation was observed between plots sown as pure stands or species mixtures, plots sown at different densities, and plots subjected to different harvesting regimes. Allele frequencies could be accurately estimated from pooled DNA, and SNPs under selection could be identified when leaf samples were pooled prior to DNA extraction. However, substantial sampling error required replicate populations and/or a high number of sampled individuals. We identified a number of chromosomal loci that had been under selection in pure stand plots relative to the original sown population, and loci that had been under differential selection in pure stands of red clover vs. red clover grown in species mixtures. These are all candidate loci for establishment success or persistence in red clover.

Occurrence of Antibiotic-Resistant Bacteria in Therapy Pools and Surrounding Surfaces

The number of patients colonized with antibiotic-resistant bacteria is increasing in health care facilities. Because transmission of antibiotic-resistant bacteria is feared, there exist reports that the affected patients are frequently excluded from hydrotherapy, which is a non-invasive and beneficial treatment used for patients with different diseases. Data from the literature suggest that deficient water disinfection measures exist, which are not always sufficient to kill all released bacteria. If the pool water is not disinfected properly, it may also infect the bathers. Immunocompromised patients are particularly susceptible to be infected with (antibiotic-resistant) bacteria. In order to determine the distribution of antibiotic-resistant bacteria in the pool water treatment system and the pool environment and to estimate the associated transmission risk we analyzed samples from eleven health care facilities. Antibiotic-resistant bacteria were found in the water and surface samples collected. One hundred and two antibiotic-resistant isolates from water samples and 307 isolates from surrounding surfaces were obtained, respectively. The majority of the isolates belonged to non-fermenting Gram-negative rods, like Pseudomonas spp. Some isolates were resistant to a wide range of the tested antibiotics. The results indicate a relation between the number of isolates in water samples and the number of patients using the pools in combination with deficiencies in water treatment. In the pool environment the highest number of isolates was obtained from barefoot areas and floor cleaning equipment.

Emergency department visits coded for swimming pool diving injuries

Despite legislative efforts to enhance safety in public swimming pools, diving injuries are still common. This study investigated the characteristics of emergency departments (EDs) visits for diving accidents. This study utilized 2006-2014 data from the Nationwide Emergency Department Sample and examined visits for accidents due to diving or jumping into water (swimming pool). Data were stratified by age categories. Over 83,000 ED visits were found and the majority of visits were by males. Significantly more patients were in the 15-24 age category. The majority of patients were discharged and were covered by private insurance. Total charges for the six-year period approached $620 million. Spinal cord injuries were more common in those over age 25, whereas intracranial injuries occurred more frequently in younger patients. This study provides a profile of patients presenting to US EDs for diving-related injuries.

Newt life after fish introduction: extirpation of paedomorphosis in a mountain fish lake and newt use of satellite pools

Fish introduction is one of the main causes of amphibian decline worldwide. It affects particularly rare aquatic phenotypes such as paedomorphs, which retain gills during the adult stage. In this context, we determined whether small wetlands, such as pools surrounding fished and fishless lakes, could sustain paedomorphic and metamorphic newts. To this end, we surveyed lakes known historically to sustain Alpine newts Ichthyosaura alpestris as well as 35 nearby pools. On the basis of the published records, the only known population exhibiting paedomorphosis in the Swiss Alps was found to be extirpated by salmonid introductions. However, the metamorphs persisted in peripheral pools, paedomorphosis was discovered at a new locality, and overwintering larvae were still present in one of the lakes. These results show the importance of conserving varied aquatic habitats such as pools in mountainous environments where the main resources can become unsuitable for amphibians because of fish introductions. Pools may also function as reservoirs in maintaining newt populations until programs to remove fish from lakes can be carried out. It is not known if paedomorphs could reappear after fish removal. However, the combined resilience of amphibians after fish removal and the genetic basis for paedomorphosis highlighted in other taxa by previous studies suggest that there is the potential to maintain this intraspecific case of diversity even after its disappearance.

Accuracy of allele frequency estimation using pooled RNA-Seq

For nonmodel organisms, genome-wide information that describes functionally relevant variation may be obtained by RNA-Seq following de novo transcriptome assembly. While sequencing has become relatively inexpensive, the preparation of a large number of sequencing libraries remains prohibitively expensive for population genetic analyses of nonmodel species. Pooling samples may be then an attractive alternative. To test whether pooled RNA-Seq accurately predicts true allele frequencies, we analysed the liver transcriptomes of 10 bank voles. Each sample was sequenced both as an individually barcoded library and as a part of a pool. Equal amounts of total RNA from each vole were pooled prior to mRNA selection and library construction. Reads were mapped onto the de novo assembled reference transcriptome. High-quality genotypes for individual voles, determined for 23,682 SNPs, provided information on 'true' allele frequencies; allele frequencies estimated from the pool were then compared with these values. 'True' frequencies and those estimated from the pool were highly correlated. Mean relative estimation error was 21% and did not depend on expression level. However, we also observed a minor effect of interindividual variation in gene expression and allele-specific gene expression influencing allele frequency estimation accuracy. Moreover, we observed strong negative relationship between minor allele frequency and relative estimation error. Our results indicate that pooled RNA-Seq exhibits accuracy comparable with pooled genome resequencing, but variation in expression level between individuals should be assessed and accounted for. This should help in taking account the difference in accuracy between conservatively expressed transcripts and these which are variable in expression level.

The quest for rare variants: pooled multiplexed next generation sequencing in plants

Next generation sequencing (NGS) instruments produce an unprecedented amount of sequence data at contained costs. This gives researchers the possibility of designing studies with adequate power to identify rare variants at a fraction of the economic and labor resources required by individual Sanger sequencing. As of today, few research groups working in plant sciences have exploited this potentiality, showing that pooled NGS provides results in excellent agreement with those obtained by individual Sanger sequencing. The aim of this review is to convey to the reader the general ideas underlying the use of pooled NGS for the identification of rare variants. To facilitate a thorough understanding of the possibilities of the method, we will explain in detail the possible experimental and analytical approaches and discuss their advantages and disadvantages. We will show that information on allele frequency obtained by pooled NGS can be used to accurately compute basic population genetics indexes such as allele frequency, nucleotide diversity, and Tajima's D. Finally, we will discuss applications and future perspectives of the multiplexed NGS approach.