Yiyi Liu, Joshua L. Warren, Hongyu Zhao.

Source: The Annals of Applied Statistics, Volume 13, Number 3, 1733--1752.

Abstract:
Understanding the heterogeneity of cells is an important biological question. The development of single-cell RNA-sequencing (scRNA-seq) technology provides high resolution data for such inquiry. A key challenge in scRNA-seq analysis is the high variability of measured RNA expression levels and frequent dropouts (missing values) due to limited input RNA compared to bulk RNA-seq measurement. Existing clustering methods do not perform well for these noisy and zero-inflated scRNA-seq data. In this manuscript we propose a Bayesian hierarchical model, called BasClu, to appropriately characterize important features of scRNA-seq data in order to more accurately cluster cells. We demonstrate the effectiveness of our method with extensive simulation studies and applications to three real scRNA-seq datasets.

Arun K. Kuchibhotla, Rohit K. Patra.

Source: Bernoulli, Volume 26, Number 2, 1587--1618.

Abstract:
We consider estimation and inference in a single index regression model with an unknown but smooth link function. In contrast to the standard approach of using kernels or regression splines, we use smoothing splines to estimate the smooth link function. We develop a method to compute the penalized least squares estimators (PLSEs) of the parametric and the nonparametric components given independent and identically distributed (i.i.d.) data. We prove the consistency and find the rates of convergence of the estimators. We establish asymptotic normality under mild assumption and prove asymptotic efficiency of the parametric component under homoscedastic errors. A finite sample simulation corroborates our asymptotic theory. We also analyze a car mileage data set and a Ozone concentration data set. The identifiability and existence of the PLSEs are also investigated.

Divyansh Agarwal, Jingshu Wang, Nancy R. Zhang.

Source: Statistical Science, Volume 35, Number 1, 112--128.

Abstract:
Single cell sequencing technologies are transforming biomedical research. However, due to the inherent nature of the data, single cell RNA sequencing analysis poses new computational and statistical challenges. We begin with a survey of a selection of topics in this field, with a gentle introduction to the biology and a more detailed exploration of the technical noise. We consider in detail the problem of single cell data denoising, sometimes referred to as “imputation” in the relevant literature. We discuss why this is not a typical statistical imputation problem, and review current approaches to this problem. We then explore why the use of denoised values in downstream analyses invites novel statistical insights, and how denoising uncertainty should be accounted for to yield valid statistical inference. The utilization of denoised or imputed matrices in statistical inference is not unique to single cell genomics, and arises in many other fields. We describe the challenges in this type of analysis, discuss some preliminary solutions, and highlight unresolved issues.

Chao Du, S. C. Kou.

Source: Statistical Science, Volume 35, Number 1, 75--91.

Abstract:
Toward the last quarter of the 20th century, the emergence of single-molecule experiments enabled scientists to track and study individual molecules’ dynamic properties in real time. Unlike macroscopic systems’ dynamics, those of single molecules can only be properly described by stochastic models even in the absence of external noise. Consequently, statistical methods have played a key role in extracting hidden information about molecular dynamics from data obtained through single-molecule experiments. In this article, we survey the major statistical methodologies used to analyze single-molecule experimental data. Our discussion is organized according to the types of stochastic models used to describe single-molecule systems as well as major experimental data collection techniques. We also highlight challenges and future directions in the application of statistical methodologies to single-molecule experiments.

Zhixiang Lin, Mahdi Zamanighomi, Timothy Daley, Shining Ma, Wing Hung Wong.

Source: Statistical Science, Volume 35, Number 1, 2--13.

Abstract:
Unsupervised methods, including clustering methods, are essential to the analysis of single-cell genomic data. Model-based clustering methods are under-explored in the area of single-cell genomics, and have the advantage of quantifying the uncertainty of the clustering result. Here we develop a model-based approach for the integrative analysis of single-cell chromatin accessibility and gene expression data. We show that combining these two types of data, we can achieve a better separation of the underlying cell types. An efficient Markov chain Monte Carlo algorithm is also developed.

Carrie J. McAdams
Jan 1, 1999; 19:431-441
Articles

Jeremy R. Manning
Oct 28, 2009; 29:13613-13620
BehavioralSystemsCognitive

Theoretical models and experimental evidence have suggested that connections from the dentate gyrus (DG) to CA3 play important roles in representing orthogonal information (i.e., pattern separation) in the hippocampus. However, the effects of eliminating the DG on neural firing patterns in the CA3 have rarely been tested in a goal-directed memory task that requires both the DG and CA3. In this study, selective lesions in the DG were made using colchicine in male Long–Evans rats, and single units from the CA3 were recorded as the rats performed visual scene memory tasks. The original scenes used in training were altered during testing by blurring to varying degrees or by using visual masks, resulting in maximal recruitment of the DG–CA3 circuits. Compared with controls, the performance of rats with DG lesions was particularly impaired when blurred scenes were used in the task. In addition, the firing rate modulation associated with visual scenes in these rats was significantly reduced in the single units recorded from the CA3 when ambiguous scenes were presented, largely because DG-deprived CA3 cells did not show stepwise, categorical rate changes across varying degrees of scene ambiguity compared with controls. These findings suggest that the DG plays key roles not only during the acquisition of scene memories but also during retrieval when modified visual scenes are processed in conjunction with the CA3 by making the CA3 network respond orthogonally to ambiguous scenes.

SIGNIFICANCE STATEMENT Despite the behavioral evidence supporting the role of the dentate gyrus in pattern separation in the hippocampus, the underlying neural mechanisms are largely unknown. By recording single units from the CA3 in DG-lesioned rats performing a visual scene memory task, we report that the scene-related modulation of neural firing was significantly reduced in the DG-lesion rats compared with controls, especially when the original scene stimuli were ambiguously altered. Our findings suggest that the dentate gyrus plays an essential role during memory retrieval and performs a critical computation to make categorical rate modulation occur in the CA3 between different scenes, especially when ambiguity is present in the environment.

Watch a recording of the physically distant performance of The Gay Card.

AppleInsider has rounded up the best 16-inch MacBook Pro deals going on right now, with coupon savings knocking up to $450 off every single model. Whether you're in the market for a standard config or looking for a loaded Core i9 model, it pays to check out the cash discounts.

The post Can You Handle a Single Source of Product Truth? appeared first on The SOLIDWORKS Blog.

LOS ANGELES (AP) — It's been over a decade since reggae king Buju Banton and R&B star John Legend collaborated on a song, and the Grammy winners have reunited for a new track.Banton and Legend released the easy-going love song Memories on yesterday. It is the first single from Banton's upcoming album Upside Down, his first studio project since 2010's Before the Dawn.

Candidate genes involved in thrombophilia, inflammation, and preterm birth have previously been associated with cerebral palsy. Most studies to date have included small cohorts, did not allow for multiple testing, and require replication.

This study of children with cerebral palsy and their mothers did not confirm previously reported candidate gene associations. Prothrombin gene mutation was associated with hemiplegia in children born at term to mothers with a reported infection during pregnancy. (Read the full article)

A single inhalation of laninamivir octanoate has previously been shown to be as effective as repeated doses of zanamivir in vitro and in vivo, but it is not known whether this is also the case for children.

Median time to fever resolution was not significantly different between laninamivir octanoate and zanamivir for pediatric patients with influenza. The severity of influenza symptoms and the frequency of complications were similar in the 2 groups. (Read the full article)

Children born small for gestational age (SGA) have increased risk of perinatal morbidity and mortality, neonatal death, and cerebral palsy (CP). Causes of SGA, such as congenital malformations, intrauterine infections, and preeclampsia, are also risk factors for the same outcomes.

In 90% of singletons born SGA, CP is apparently of prenatal origin. Low proportions of intrapartum events leading to CP could not be fully explained by a higher neonatal mortality rate in SGA than in non-SGA children. (Read the full article)

Neonatal respiratory distress syndrome is the most common respiratory cause of mortality and morbidity among US infants aged <1 year. Although neonatal respiratory distress syndrome is a heritable disorder, common genetic variants do not fully explain disease heritability.

Single ABCA3 mutations are overrepresented among term and late preterm (≥34 weeks’ gestation) European-descent infants with RDS. Although ABCA3 mutations are individually rare, they are collectively common in the European- and African-descent general population, present in ~4% of individuals. (Read the full article)

Neonatal mortality rate and causes of death have been relatively stable in recent years. Decision-making practices preceding death of sick neonates affect the circumstances of death. These practices vary worldwide according to the team approach and local population background.

Although our population is mostly religious, we observed a decline in maximal intensive care along with increasing redirection of care over a decade. Changes in the team approach and increasing level of parental involvement influence type and duration of treatment. (Read the full article)

Preterm infants are born with low serum levels and low body stores of tocopherol. Serum levels ≥0.5 mg/dL are required for protection against lipid peroxidation. Previous studies have shown good intestinal absorption of vitamin E given intragastrically to preterm infants.

Serum α-tocopherol increases after a single 50-IU/kg dose of vitamin E as dl-α-tocopheryl acetate given intragastrically to very preterm infants soon after birth; however, 30% of infants still have serum α-tocopherol level <0.5 mg/dL 24 hours after dosing. (Read the full article)

Food insecurity is best measured by comprehensive assessments. However, rapid assessments can be useful in certain circumstances, but their validity is not characterized.

Rapid assessment of food insecurity is feasible among Inuit adults and children. (Read the full article)

The single-family room (SFR) NICU is a major response to improve care and reduce developmental morbidity in preterm infants. However, no studies have examined how and why this model is associated with changes in medical and neurobehavioral outcome.

This study shows improved medical and neurodevelopmental outcome in infants hospitalized in the SFR model of care. More important, improvements occurred specifically in relation to increases in maternal involvement and developmental support afforded by the SFR environment. (Read the full article)

It is unclear whether developmental delays observed among infants with single-suture craniosynostosis (SSC) persist at school age. Few neurodevelopmental studies have examined children with SSC beyond age 3, with most having methodological limitations.

This study is the first to follow and test infants with SSC and a control group at school age. Infancy delays among children with SSC persisted at school age in some areas (IQ, math) but not others (reading, spelling). (Read the full article)

Since 2012, single low dose of primaquine (SLDPQ, 0.25mg/kg) has been recommended with artemisinin-based combination therapies, as first-line treatment of acute uncomplicated Plasmodium falciparum malaria, to interrupt its transmission, especially in low transmission settings of multidrug, including artemisinin, resistance. Policy makers in Cambodia have been reluctant to implement this recommendation due to primaquine safety concerns and lack of data on its efficacy.

In this randomized controlled trial, 109 Cambodians with acute uncomplicated P. falciparum malaria received dihydroartemisinin-piperaquine (DP) alone or combined with SLDPQ on the first treatment day. Transmission-blocking efficacy of SLDPQ was evaluated on Days 0, 1, 2, 3, 7, 14, 21, 28 and recrudescence by reverse transcriptase polymerase chain reaction (RT-PCR) (gametocyte prevalence) and membrane-feeding assays with Anopheles minimus mosquitoes (gametocyte infectivity). Without the influence of recrudescent infections, DP+SLDPQ reduced gametocyte carriage 3 fold compared to DP. Of 48 patients tested on Day 0, only three patients were infectious to mosquitoes (~6%). Post-treatment, three patients were infectious: on D14 (3.5%, 1/29), and on the first and seventh day of recrudescence (8.3%, 1/12 for each); this overall low infectivity precluded our ability to assess its transmission blocking efficacy.

Our study confirms effective gametocyte clearance of SLDPQ when combined with DP in multidrug resistant P. falciparum and the negative impact of recrudescent infections due to poor DP efficacy. Artesunate-mefloquine (ASMQ) has replaced DP and ASMQ-SLDPQ has been deployed to treat all P. falciparum symptomatic patients to further support the elimination of multidrug resistant P. falciparum in Cambodia.

QPX7728 is an ultra-broad-spectrum boronic acid beta-lactamase inhibitor with potent inhibition of key serine and metallo beta-lactamases observed in biochemical assays. Microbiological studies using characterized strains were used to provide a comprehensive characterization of the spectrum of beta-lactamase inhibition by QPX7728. The MIC of multiple IV only (ceftazidime, piperacillin, cefepime, ceftolozane and meropenem) and orally bioavailable (ceftibuten, cefpodoxime, tebipenem) antibiotics alone and in combination with QPX7728 (4 μg/ml), as well as comparator agents, were determined against the panels of laboratory strains of P. aeruginosa and K. pneumoniae expressing over 55 diverse serine and metallo beta-lactamases. QPX7728 significantly enhanced the potency of antibiotics against the strains expressing Class A extended spectrum beta-lactamases (CTX-M, SHV, TEM, VEB, PER) and carbapenemases (KPC, SME, NMC-A, BKC-1), consistent with beta-lactamase inhibition demonstrated in biochemical assays. It also inhibits both plasmidic (CMY, FOX, MIR, DHA) and chromosomally encoded (P99, PDC, ADC) Class C beta-lactamases and Class D enzymes including carbapenemases such as OXA-48 from Enterobacteriaceae and OXA enzymes from Acinetobacter baumannii (OXA-23/24/72/58). QPX7728 is also a potent inhibitor of many class B metallo beta-lactamases (NDM, VIM, CcrA1, IMP, GIM but not SPM or L1). Addition of QPX7728 (4 μg/ml) reduced the MICs in a majority of strains to the level observed for the vector alone control, indicative of complete beta-lactamase inhibition. The ultra-broad-spectrum beta-lactamase inhibition profile makes QPX7728 a viable candidate for further development.

Single women dominated property sales in 2017, 2018 and 2019, compared to single men and even married couples, according to data analytics firm Lightstone.

The Maruti Suzuki S-Presso has finally been launched in India at a very competitive price. We get behind the wheel of the manual and aAMT AGS automatic versions of the mini SUV which rivals the Renault Kwid and see what the entry-level SUV styled hatchback has to offer.

According to dealers, firms like Reliance Industries (RIL), NABARD, and Tata Steel are likely to hit the bond market on Thursday with an intention to raise a cumulative Rs 15,000 crore.

Since the outbreak of the pandemic on March 31 in the state, two persons have died of the infection while one COVID-19 patient died due to underlying health condition after testing negative.

Hi all,

         I want to know how to run a regressive test in cadence and merge all ncsim .trn file of each test case into a single file to view all waveform in simvision. I am using Makefile to invoke the test case.

         eg:-

               test0:

                     irun -uvm -sv -access +rwc $(RTL) $(INTER) $(PKG) $(TOP) $(probe) +UVM_VERBOSITY=UVM_MEDIUM +UVM_TESTNAME=test0

             test1:

                   irun -uvm -sv -access +rwc $(RTL) $(INTER) $(PKG) $(TOP) $(probe) +UVM_VERBOSITY=UVM_MEDIUM +UVM_TESTNAME=test1

          I just to call test0 followed by test1 or parallel both test and view the waveform for both tests case.

        I new to this tool and help me with it

Variants seem to be defined as present or not present.

Is there a variant that can assign different parts to the same reference designator? i.e.  R17 can be either 0 ohm 0805 jumper or 12k ohms 0805 resistor.

The simplest way I can think of is to use two parts with the same footprint and overlay them.

Is there a more functional way of doing this?  So that the variant would put the correct part in the BOM and the parts would of course have the same identical footprint.

In October of this year, the European Parliament voted in favor of a ban of the ten most notorious single-use plastics that harm our planet and marine life, including straws, plastic cutlery and cotton buds. The vote also committed to a move towards a circular economy – recognizing the inherent value of the 2.12 billion tonnes of waste that is dumped globally each year. Yet questions remain about how we deal with the items not on the list, the ones where there are no obvious alternatives; the fruit trays, the ice cream tubs, the burger boxes. With waste generation expected to double by 2025 we must continue to act on this growing crisis and be more innovative with waste.

On 6 January 2016, the European Commission published an implementing regulation establishing a standard form for the European Single Procurement Document (“ESPD”). The ESPD is one of the new features of EU procurement regulation introduc...

Court of Appeal upholds single collective bargaining unit for only 1.2% of employees in an otherwise non-unionised employer In a significant development for employers, particularly those without recognised trade unions and those with dispersed busin...

(MENAFN - Kuwait News Agency (KUNA)) DOHA, May 9 (KUNA) -- Qatari ministry of health declared on Saturday recording a single death due to the novel co... ......

The 2020 DNC in Milwaukee is scheduled for the week of August 17 as planning continues to stage event in the middle of a pandemic. ......

The Donald Trump administration stepped up its criticism of Russia’s role in Libya’s civil war on Thursday.

Alarmed by the amount of rubbish they were generating by just drinking coffee and eating cup noodles, two former garments entrepreneurs decided it was time to find an eco-friendly alternative to all the plastic packaging that ends up in landfills globally.George Chen Dah-ren and Vivian Chang first approached material scientists in Hong Kong and mainland China, and were in 2013 pointed in the direction of Alexander Bismarck, then a Materials Science professor at Imperial College London. The…

"Eight," the new single by singer IU and Suga, a member of boy band Bangtan Boys, also known as BTS, swept many global music charts shortly after its release on Wednesday."Eight" reached No. 1 on major music-streaming sites here including Melon. It also topped iTunes charts in some 59 countries.The ...

radeep Sharma Tribune News Service Chandigarh, January 23 The group-housing societies, residential colonies of employers and commercial-cum-residential complexes of developers will be supplied power on single-point (bulk supply) system by the electricity department from April 1. While the electricity bills for February/March would be issued as per the existing practice, the bills from April onwards would be issued as per the single-point metering system, according to an order issued by the Chief General Manager (Commercial), Uttar Haryana Bijli Vitran Nigam (UHBVN). The new system would be implemented in housing colonies having 20 or more houses. The order said on the basis of the reading of April 1, the bills of […]

ISLAMABAD: The country witnessed a record rise in Covid-19 cases on Friday, a day before lifting of the nationwide lockdown in phases announced by Prime Minister Imran Khan.

Although the decision to lift the lockdown from Saturday was taken in consultation with all the provinces, Punjab and Sindh on Friday expressed their desire to extend the lockdown restrictions for some more time.

With the addition of 2,000 new cases during the last 24 hours, the total number of infections in the country on Friday stood at 26,954.

Prime Minister Khan, after chairing a meeting of the National Coordination Committee (NCC) on Thursday, announced the lifting of the lockdown by opening several industries, businesses and markets from Saturday (today).

Punjab, Sindh express wish to extend lockdown restrictions; Umar dismisses Murad’s claim about unilateral decisions by Centre; PM reviews economic situation

On Friday, Sindh Chief Minister Syed Murad Ali Shah and Punjab Information Minister Fayyazul Hassan Chohan said they wanted to extend the lockdown but agreed to the Centre’s call at the NCC meeting that the restrictions should be lifted from Saturday.

“It was our desire that the lockdown should be extended, but we agreed to whatever decided at the NCC meeting on Thursday,” CM Shah said at a press briefing.

The PTI-led Punjab government took a step forward and recommended that major cities of the province should remain under lockdown as there was an increasing trend of the viral disease there. “We want continuation of lockdown in eight to 10 cities, including Lahore, Rawalpindi, Multan and Gujranwala,” Mr Chohan said at a press conference.

In a related development, the federal government expressed its surprise and dismay over Sindh chief minister’s remarks that Islamabad was imposing its decision regarding ending the lockdown. Federal Minister for Planning and Development Asad Umar, who also heads the National Command and Operation Centre, in a television programme categorically on Friday evening, said that all decisions were made with the approval of the provincial governments. He even said that some of the federal government’s proposals on which there were objections, or difference of opinion, were not included as the government wanted to have complete consensus on the matter.

Prime Minister Khan has urged people to follow the standard operating procedures (SOPs) evolved by the government when the lockdown is lifted, otherwise there will be trajectory of Covid-19 and then the government will have no option but to enforce another lockdown.

The prime minister presided over a meeting on Friday to review the economic situation and its future outlook in the wake of the Covid-19 pandemic. The finance ministry briefed the meeting on the overall situation and the performance of various macroeconomic indicators during the last nine months of the current financial year, as well as the impact of coronavirus on the economy, an official press release said.

The meeting reviewed the progress and impact of the Rs1.25 trillion economic stimulus package announced by the government to provide relief to the poor and vulnerable segments of society and support various sectors of the economy affected by the pandemic.

The prime minister appreciated the efforts made by the finance ministry to ensure financial discipline and provision of relief during the Coved-19 situation. He emphasised that greater attention should be paid to supporting small and medium enterprises and the agriculture sector, enabling them to create greater job opportunities for people. “The process of reforming public sector organisations should be expedited to plug leakages of the economy,” he added.

The prime minister said the process of provision of subsidies should also be reviewed to make these interventions more effective and target-oriented. “Out of the box solutions are needed to meet the present day economic challenges,” he emphasised.

Reviewing the future economic outlook, Mr Khan said all-out efforts should be made to provide maximum possible relief to the people. He emphasised that priorities and targets for the next Public Sector Development Programme (PSDP) should be clearly defined with a focus on completion of projects rather than mere initiation. He stressed the need for maximum utilisation of the public-private partnership model and involving international development partners to enhance and broaden the PSDP scope.

Meanwhile, Special Assistant to the PM on Health Dr Zafar Mirza said the government had signed a memorandum of understanding with the International Organisation of Migration, which helps connect countries with expatriates.

At a press conference, he said the government wanted to develop a networking system with overseas Pakistani doctors in order to learn from their experiences and expertise even after the coronavirus crisis is over.

Published in Dawn, May 9th, 2020

INDORE: To ensure hassle-free establishment of special economic zones (SEZs) in Indore, the state government is all set to go for Development Control Regulation (DCR). On the lines of Gujarat, a single window clearance system is being planned for them. A decision to this effect is likely to be taken during the meeting of the state cabinet in Bhopal on Wednesday. Once cleared, the Act will empower the SEZ development commissioner to sort out the issues and give necessary permission to the SEZs that have already been allotted land by the state government and received notifications for the SEZ status. They include TCS, Infosys and Impetus. While TCS and Impetus […]

Genetic analysis suggests all Arabica coffee plants are descended from a single common ancestor, and this lack of genetic diversity makes them vulnerable to extinction

The discovery of a link between anxiety, depression, OCD and more is set to revolutionise how we think about these conditions – and offer new treatments

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ABSTRACT

Population-level analyses are rapidly becoming inadequate to answer many of biomedical science and microbial ecology’s most pressing questions. The role of microbial populations within ecosystems and the evolutionary selective pressure on individuals depend fundamentally on the metabolic activity of single cells. Yet, many existing single-cell technologies provide only indirect evidence of metabolic specialization because they rely on correlations between transcription and phenotype established at the level of the population to infer activity. In this study, we take a top-down approach using isotope labels and secondary ion mass spectrometry to track the uptake of carbon and nitrogen atoms from different sources into biomass and directly observe dynamic changes in anabolic specialization at the level of single cells. We investigate the classic microbiological phenomenon of diauxic growth at the single-cell level in the model methylotroph Methylobacterium extorquens. In nature, this organism inhabits the phyllosphere, where it experiences diurnal changes in the available carbon substrates, necessitating an overhaul of central carbon metabolism. We show that the population exhibits a unimodal response to the changing availability of viable substrates, a conclusion that supports the canonical model but has thus far been supported by only indirect evidence. We anticipate that the ability to monitor the dynamics of anabolism in individual cells directly will have important applications across the fields of ecology, medicine, and biogeochemistry, especially where regulation downstream of transcription has the potential to manifest as heterogeneity that would be undetectable with other existing single-cell approaches.

IMPORTANCE Understanding how genetic information is realized as the behavior of individual cells is a long-term goal of biology but represents a significant technological challenge. In clonal microbial populations, variation in gene regulation is often interpreted as metabolic heterogeneity. This follows the central dogma of biology, in which information flows from DNA to RNA to protein and ultimately manifests as activity. At present, DNA and RNA can be characterized in single cells, but the abundance and activity of proteins cannot. Inferences about metabolic activity usually therefore rely on the assumption that transcription reflects activity. By tracking the atoms from which they build their biomass, we make direct observations of growth rate and substrate specialization in individual cells throughout a period of growth in a changing environment. This approach allows the flow of information from DNA to be constrained from the distal end of the regulatory cascade and will become an essential tool in the rapidly advancing field of single-cell metabolism.

ABSTRACT

Pseudomonas aeruginosa is an opportunistic human pathogen, particularly noted for causing infections in the lungs of people with cystic fibrosis (CF). Previous studies have shown that the gene expression profile of P. aeruginosa appears to converge toward a common metabolic program as the organism adapts to the CF airway environment. However, we still have only a limited understanding of how these transcriptional changes impact metabolic flux at the systems level. To address this, we analyzed the transcriptome, proteome, and fluxome of P. aeruginosa grown on glycerol or acetate. These carbon sources were chosen because they are the primary breakdown products of an airway surfactant, phosphatidylcholine, which is known to be a major carbon source for P. aeruginosa in CF airways. We show that the fluxes of carbon throughout central metabolism are radically different among carbon sources. For example, the newly recognized "EDEMP cycle" (which incorporates elements of the Entner-Doudoroff [ED] pathway, the Embden-Meyerhof-Parnas [EMP] pathway, and the pentose phosphate [PP] pathway) plays an important role in supplying NADPH during growth on glycerol. In contrast, the EDEMP cycle is attenuated during growth on acetate, and instead, NADPH is primarily supplied by the reaction catalyzed by isocitrate dehydrogenase(s). Perhaps more importantly, our proteomic and transcriptomic analyses revealed a global remodeling of gene expression during growth on the different carbon sources, with unanticipated impacts on aerobic denitrification, electron transport chain architecture, and the redox economy of the cell. Collectively, these data highlight the remarkable metabolic plasticity of P. aeruginosa; that plasticity allows the organism to seamlessly segue between different carbon sources, maximizing the energetic yield from each.

IMPORTANCE Pseudomonas aeruginosa is an opportunistic human pathogen that is well known for causing infections in the airways of people with cystic fibrosis. Although it is clear that P. aeruginosa is metabolically well adapted to life in the CF lung, little is currently known about how the organism metabolizes the nutrients available in the airways. In this work, we used a combination of gene expression and isotope tracer ("fluxomic") analyses to find out exactly where the input carbon goes during growth on two CF-relevant carbon sources, acetate and glycerol (derived from the breakdown of lung surfactant). We found that carbon is routed ("fluxed") through very different pathways during growth on these substrates and that this is accompanied by an unexpected remodeling of the cell’s electron transfer pathways. Having access to this "blueprint" is important because the metabolism of P. aeruginosa is increasingly being recognized as a target for the development of much-needed antimicrobial agents.

ABSTRACT

Middle East respiratory syndrome coronavirus (MERS-CoV) can cause severe and fatal acute respiratory disease in humans and remains endemic in the Middle East since first being identified in 2012. There are currently no approved vaccines or therapies available for MERS-CoV. In this study, we evaluated parainfluenza virus 5 (PIV5)-based vaccine expressing the MERS-CoV envelope spike protein (PIV5/MERS-S) in a human DPP4 knockin C57BL/6 congenic mouse model (hDPP4 KI). Following a single-dose intranasal immunization, PIV5-MERS-S induced neutralizing antibody and robust T cell responses in hDPP4 KI mice. A single intranasal administration of 10⁴ PFU PIV5-MERS-S provided complete protection against a lethal challenge with mouse-adapted MERS-CoV (MERS_MA6.1.2) and improved virus clearance in the lung. In comparison, single-dose intramuscular immunization with 10⁶ PFU UV-inactivated MERS_MA6.1.2 mixed with Imject alum provided protection to only 25% of immunized mice. Intriguingly, an influx of eosinophils was observed only in the lungs of mice immunized with inactivated MERS-CoV, suggestive of a hypersensitivity-type response. Overall, our study indicated that PIV5-MERS-S is a promising effective vaccine candidate against MERS-CoV infection.

IMPORTANCE MERS-CoV causes lethal infection in humans, and there is no vaccine. Our work demonstrates that PIV5 is a promising vector for developing a MERS vaccine. Furthermore, success of PIV5-based MERS vaccine can be employed to develop a vaccine for emerging CoVs such as SARS-CoV-2, which causes COVID-19.

Objective

To investigate the pattern of progression of neurologic impairment in Friedreich ataxia (FRDA) and identify patients with fast disease progression as detected by clinical rating scales.