bHLH121 and clade IVc bHLH transcription factors synergistically function to regulate iron homeostasis in Arabidopsis thaliana

Iron is an essential micronutrient for plant growth and development. In Arabidopsis thaliana, an intricate regulatory network involving several basic helix-loop-helix (bHLH) transcription factors controls the homeostasis of iron. Among these transcription factors, bHLH121 plays a crucial role. bHLH121 interacts in vivo with clade IVc bHLH transcription factors and activates the expression of FIT and clade Ib bHLH transcription factors to stimulate the uptake of iron. How bHLH121 and clade IVc bHLH transcription factors function collectively and efficiently to maintain iron homeostasis is still unclear. Herein, we found that double loss-of-function mutants involving bhlh121 and one of the clade IVc bHLH transcription factors displayed more severe iron deficiency-associated growth defects than each of the single mutants. We also found that among the four clade IVc bHLH transcription factors, only bHLH34 and bHLH105 could partially complement the iron-associated growth defects of bhlh121 when overexpressed. These data, together with protein localization analysis, support that bHLH121 and clade IVc bHLH transcription factors act synergistically to regulate iron homeostasis and that different bHLH121/clade IVc and clade IVc/clade IVc protein complexes are involved in this process.

Virological profile of upper respiratory tract infections in children under 5 years of age- a cross sectional study in a tertiary care hospital in North India

OBJECTIVE

To study the virological profile of URI among children under 5 years of age. Since, it is very difficult to distinguish between various viral etiologies solely on the basis of symptoms, this study was attempted to generate evidence that majority of URI are caused due to viral illness and no antibiotics should be prescribed in the management of the same.

METHODS

This observational study was conducted over a period of one year (June 2021-May 2022) in a tertiary care teaching hospital in New Delhi. A total of 180 children between the age of 0-5 years with symptoms of URI were included. Nasopharyngeal swabs were taken and processed for detection of viruses using multiplex RT PCR.

RESULTS

Presence of viruses were detected in 136 (75.6%) samples. A single virus was identified in 113 samples, whereas 21 were found to harbour two viruses and 2 were carrying three viruses. The most common virus isolated was Human Rhinovirus (HRV- 55.8%) followed by Respiratory Syncytial Virus (RSV- 23.5%). In samples showing coinfection with two viruses, most common was Human Corona Virus (HCoV)- NL63, 229E, OC43, HKU1. None of the patients were given antibiotics. None of the patients required any hospital admission for severe respiratory illness.

CONCLUSIONS

Viruses are a major cause of URI in children under five years of age, with the most prevalent organisms being HRV and RSV. Antibiotic prescriptions in URI are not warranted.

Automated approach for quality assessment of RDF resources

INTRODUCTION

The Semantic Web community provides a common Resource Description Framework (RDF) that allows representation of resources such that they can be linked. To maximize the potential of linked data - machine-actionable interlinked resources on the Web - a certain level of quality of RDF resources should be established, particularly in the biomedical domain in which concepts are complex and high-quality biomedical ontologies are in high demand. However, it is unclear which quality metrics for RDF resources exist that can be automated, which is required given the multitude of RDF resources. Therefore, we aim to determine these metrics and demonstrate an automated approach to assess such metrics of RDF resources.

METHODS

An initial set of metrics are identified through literature, standards, and existing tooling. Of these, metrics are selected that fulfil these criteria: (1) objective; (2) automatable; and (3) foundational. Selected metrics are represented in RDF and semantically aligned to existing standards. These metrics are then implemented in an open-source tool. To demonstrate the tool, eight commonly used RDF resources were assessed, including data models in the healthcare domain (HL7 RIM, HL7 FHIR, CDISC CDASH), ontologies (DCT, SIO, FOAF, ORDO), and a metadata profile (GRDDL).

RESULTS

Six objective metrics are identified in 3 categories: Resolvability (1), Parsability (1), and Consistency (4), and represented in RDF. The tool demonstrates that these metrics can be automated, and application in the healthcare domain shows non-resolvable URIs (ranging from 0.3% to 97%) among all eight resources and undefined URIs in HL7 RIM, and FHIR. In the tested resources no errors were found for parsability and the other three consistency metrics for correct usage of classes and properties.

CONCLUSION

We extracted six objective and automatable metrics from literature, as the foundational quality requirements of RDF resources to maximize the potential of linked data. Automated tooling to assess resources has shown to be effective to identify quality issues that must be avoided. This approach can be expanded to incorporate more automatable metrics so as to reflect additional quality dimensions with the assessment tool implementing more metrics.

Silence of URI in gastric cancer cells promotes cisplatin-induced DNA damage and apoptosis

URI, a prefoldin family member, has been implicated roles in cancer development. We have previously shown that URI can attenuate DNA damage in gastric cancer cells treated with potassium dichromate. The aim of this study was to investigate how URI involves cisplatin-induced DNA damage response (DDR) in gastric cancer cells and its possible mechanism relating to the ATM/CHK2 pathway. Here, MGC-803 and SGC-7901 gastric cancer cells were treated with different concentrations of cisplatin. Comet assay was used to detect DNA damage and the results confirmed the dose-effect of cisplatin-induced DNA damage in gastric cancer cells. URI knockdown cell lines were established with siRNA transfection. Cell viability and proliferation were detected by counting kit 8 (CCK-8) and 5-ethynyl-2'-deoxyuridine (EdU) assays respectively. Apoptosis and cell cycle were analyzed by flow cytometry. The results indicated that URI knockdown increased the sensitivity of cells to cisplatin by inhibiting proliferation and promoting apoptosis. The levels of P-ATM, P-CHK2 and γH2AX were detected by Western blot. Increased levels of P-ATM, P-CHK2, and γH2AX were observed in cisplatin treated cells, indicating that cisplatin induced a DNA damage response (DDR). URI knockdown in cisplatin-treated cells significantly decreased the levels of P-ATM and P-CHK2 at 12 hours, but not at 0 and 6 hours after drug withdrawal, while significantly increased γH2AX levels were detected at 6 hours, but not at 0 and 12 hours after drug withdrawal compared with the control cells. However, the levels of γH2AX were significantly increased in URI knockdown cells after cisplatin treatment for 12 hours. The cell cycle analysis showed that the number of cells entering S phase was significantly reduced and the cells were arrested in the G1 phase in URI-silenced cisplatin-exposed cells, indicating that cell cycle progression was inhibited. In conclusion, our results suggest that URI is involved in the cisplatin-induced DNA damage response via the ATM/CHK2 pathway, and silencing URI can increase cisplatin-induced DNA damage and enhance drug sensitivity in gastric cancer cells.

A short review on important drugs under clinical trial against Covid-19

Corona virus spreads from one to other person, either by touching the hands or by touching the surface contaminated with this virus, and then touching the nose or mouth. Covid-19 infected human symptoms are like any pneumonia symptoms, dry cough and high fever. Upper respiratory tract infections symptoms and sore throat are rare. First notified in china dated 12th December 2019 as a respiratory illness. In addition to travel restrictions and quarantine measures everyone should follow the World Health Organization advice guidelines on the management of humans infected with known or suspected infection with SARS-CoV-2 virus at the personal level. The development of vaccine or medicines for the same are under progress and this short review will summarize the most potential candidates such as Remdesivir, Lopinavir and Ritonavir, Chloroquine, Hydroxychloroquine, Hydroxychloroquine with Azithromycin, Favipiravir, Umifenovir, and Ribavirin for its medicinal treatment.

Long-term symptom control following resection of cervical lymphatic malformations: a case series

Background

Previous literature has reported on the incidence of short-term complications following resection of cervical lymphatic malformations (LMs) in children, however no research has yet investigated the long-term symptomatic course in these patients. This study aims to provide families and providers with an understanding of expectations for long-term symptom control, specifically in association with subsequent upper respiratory infections (URIs).

Methods

A retrospective chart review produced a case series of patients who underwent resection of cervical LM at a pediatric tertiary care center between 2007 and 2016. Demographic data, disease characteristics, operative details, and postoperative care were evaluated. Telephone surveys were conducted to ascertain the course of postoperative symptoms at the surgical site.

Results

Forty-three patients responded to the telephone survey. Thirty-seven (86.0%) had at least one postoperative surgical site symptom during subsequent URIs, with 28 (65.1%) reporting redness, 34 (79.1%) reporting swelling, and 18 (41.9%) reporting pain. Patients who experienced any of these symptoms universally indicated that they developed soon after the surgical resection, and over half reported that they improved over time. Postoperative seroma was associated with swelling during subsequent URIs (p = 0.04). Patients age 7 or were greater were more likely than those under 7 to report pain with URIs (p = 0.006). All 8 patients with drain placement for at least 2 days reported swelling during subsequent URIs. The incidence of the queried symptoms did not vary significantly based on sex, stage, histology, surgical subsite, or presence of residual disease.

Conclusion

While preoperative symptoms associated with cervical LMs are also frequently encountered postoperatively, particularly in some patient subgroups, improvement over time should be expected.

Level of evidence

4

Vitamin C supplementation reduces the odds of developing a common cold in Republic of Korea Army recruits: randomised controlled trial

INTRODUCTION

The Republic of Korea (ROK) military has a high incidence of respiratory diseases at training centres. Vitamin C has been reported to reduce the incidence of colds. For the purpose of preventing soldiers' respiratory diseases, this study aimed to investigate whether vitamin C intake can prevent common colds in the ROK Army soldiers.

METHODS

This was a randomised, placebo-controlled, and double-blind trial of soldiers who enlisted in the Korea Army Training Centre for 30 days from 12 February to 13 March 2018. The study participants were divided into groups (vitamin C vs placebo). The military medical records were searched to determine whether the participants had a common cold. Multiple logistic regression analysis was performed to identify the association between vitamin C intake and diagnosis of common colds. In addition, subgroup analysis on the relationship between vitamin C intake and common cold according to smoking status, training camp and physical rank was conducted.

RESULTS

A total of 1444 participants were included in our study. Of these participants, 695 received vitamin C (6000 mg/day, vitamin C group), while 749 participants received placebo (0 mg/day, placebo group). The vitamin C group had a 0.80-fold lower risk of getting a common cold than did the placebo group. Subgroup analyses showed that this effect was stronger among subjects in camp A, among never smokers and among those in physical rank 3.

CONCLUSION

Vitamin C intake provides evidence to suggest that reducing the common colds in Korean Army soldiers. Our results may serve as a basis for introducing military healthcare policies that can provide vitamin C supplementation for military personnel in basic military training.

Cost of inappropriate antimicrobial use for upper respiratory infection in Japan

BACKGROUND

Antibiotics are often prescribed inappropriately to patients with upper respiratory infection (URI) in ambulatory care settings; however, the economic burden of such prescription has not been quantitatively assessed. Here, we aimed to evaluate the additional cost of antimicrobial prescription for URI at the population level in Japan.

METHODS

We conducted a retrospective observational survey using longitudinal claims data between 2013 and 2016 obtained from JMDC Claims Database, which contains data from 5·1 million corporate employees and family members under the age of 65 years. Appropriateness of antibiotic prescription was assessed by a panel of six infectious disease physicians according to ICD-10 code in JMDC Claims Database. Total additional cost of antibiotic prescription for URI at the national level was estimated by weighting of age-structured population data.

RESULTS

The annual additional cost of inappropriate antibiotic prescription for URI was estimated at 423·6 (95% CI: 416·8-430·5) million USD in 2013, 340·9 (95% CI: 335·7-346·2) million USD in 2014, 349·9 (95% CI: 344·5-355·3) million USD in 2015, and 297·1 (95% CI: 292·4-301·9) million USD in 2016. Three classes of broad-spectrum oral antibiotics (third-generation cephalosporins, macrolides, and fluoroquinolones) accounted for > 90% of the total additional cost.

CONCLUSIONS

Although a decreasing trend was observed, annual additional costs of inappropriate antibiotic prescriptions for URI could be a substantial economic burden in Japan. Appropriately prescribing broad-spectrum oral antibiotics might be an important issue to reduce unnecessary medical costs in Japanese ambulatory care.

The Expression of MicroRNA-598 Inhibits Ovarian Cancer Cell Proliferation and Metastasis by Targeting URI

Unconventional prefoldin RPB5 interactor (URI, or RMP, a member of the prefoldin family of molecular chaperones) exhibits oncogenic activity in several types of cancer, including ovarian cancer. However, the underlying regulatory mechanism in ovarian cancer remains unclear. MicroRNAs (miRNAs) negatively regulate gene expression, and their dysregulation has been implicated in tumorigenesis. To elucidate the role of miRNAs in URI-induced ovarian cancer, miR-598 and URI were overexpressed in the SKOV3 ovarian cancer cell line. The CCK8 kit was used to determine cell proliferation, and the Transwell assay was used to measure cell invasion and migration. RT-PCR and western blotting were used to analyze the expression of miR-598 and URI, and the luciferase reporter assay was used to examine the interaction between miR-598 and URI. Nude mice were used to characterize the regulation of tumor growth in vivo. The results showed that the expression of miR-598 inhibited the proliferation, invasion, and migration of ovarian cancer cells by targeting URI. The inhibitory effect of miR-598 was reversed by overexpression of URI. The luciferase reporter assay showed that miR-598 downregulated URI by directly targeting the 3′ UTR of URI. In vivo studies showed that the expression of miR-598 significantly inhibited the growth of tumors. Taken together, the results suggested that miR-598 inhibited tumor growth and metastasis by targeting URI.

URI knockdown induces autophagic flux in gastric cancer cells

URI, a member of the prefoldin family of molecular chaperones, functions in the regulation of nutrient-sensitive, mTOR-dependent transcription signaling pathways. Previous studies of several tumor types demonstrated that URI exhibits characteristics similar to those of an oncoprotein. URI has been shown as a mitochondrial substrate of S6 kinase 1 (S6K1), which acts to integrate nutrient and growth factor signals to promote cell growth and survival. Notably, the Akt/mTOR/p70S6K signaling pathway constitutes major negative regulatory mechanism of autophagy. However, the role of URI in autophagy has not been explored. Here, we investigated the involvement of URI in autophagy by manipulating its expression in MGC-803 and HGC-27 cells using siRNA and transfection approaches. GFP-LC3 punctum aggregation was assessed by confocal microscopy, whereas formation of autophagic vesicles was assessed using transmission electron microscopy. NH₄Cl was used to inhibit autophagosome-lysosome fusion and to monitor autophagic flux. Expression of LC3-I, LC3-II, beclin1, total and phosphorylated mTOR, and p70S6k was assessed by Western blotting. The results showed that knockdown of URI induced significant autophagic flux in gastric cancer cells. URI regulates the expression of beclin1, which is essential for initiation of conventional autophagy. Levels of p-mTOR (Ser2448) and p-p70S6K (Thr389) increased in URI-overexpressing cells treated with the mTOR inhibitor rapamycin but decreased in URI-silenced cells. The inhibitory effect of URI silencing on mTOR and p70S6K phosphorylation was antagonized by the autophagy inhibitor 3-methyladenine. These results suggest that URI knockdown-induced autophagy is associated with the mTOR/p70S6K signaling pathway, indicating the potential existence of a novel autophagy regulatory mechanism mediated by URI.

Vitamin D receptor genotype influences risk of upper respiratory infection

SNP in the vitamin D receptor (VDR) gene is associated with risk of lower respiratory infections. The influence of genetic variation in the vitamin D pathway resulting in susceptibility to upper respiratory infections (URI) has not been investigated. We evaluated the influence of thirty-three SNP in eleven vitamin D pathway genes (DBP, DHCR7, RXRA, CYP2R1, CYP27B1, CYP24A1, CYP3A4, CYP27A1, LRP2, CUBN and VDR) resulting in URI risk in 725 adults in London, UK, using an additive model with adjustment for potential confounders and correction for multiple comparisons. Significant associations in this cohort were investigated in a validation cohort of 737 children in Manchester, UK. In all, three SNP in VDR (rs4334089, rs11568820 and rs7970314) and one SNP in CYP3A4 (rs2740574) were associated with risk of URI in the discovery cohort after adjusting for potential confounders and correcting for multiple comparisons (adjusted incidence rate ratio per additional minor allele ≥1·15, P for trend ≤0·030). This association was replicated for rs4334089 in the validation cohort (P for trend=0·048) but not for rs11568820, rs7970314 or rs2740574. Carriage of the minor allele of the rs4334089 SNP in VDR was associated with increased susceptibility to URI in children and adult cohorts in the United Kingdom.

A prospective, multi-centre US clinical trial to determine accuracy of FebriDx point-of-care testing for acute upper respiratory infections with and without a confirmed fever

BACKGROUND

FebriDx is a 10-minute disposable point-of-care test designed to identify clinically significant systemic host immune responses and aid in the differentiation of bacterial and viral respiratory infection by simultaneously detecting C-reactive protein (CRP) and myxovirus resistance protein A (MxA) from a fingerstick blood sample. FebriDx diagnostic accuracy was evaluated in the emergency room and urgent care setting.

METHODS

A prospective, multicentre, observational cohort study of acute upper respiratory tract infections (URIs), with and without a confirmed fever at the time of enrolment, was performed to evaluate the diagnostic accuracy of FebriDx to identify clinically significant bacterial infection with host response and acute pathogenic viral infection. The reference method consisted of an algorithm with physician override that included bacterial cell culture, respiratory PCR panels for viral and atypical pathogens, procalcitonin, and white blood cell count.

RESULTS

Among 220 patients enrolled, 100% reported fever 100.5°F within the last 72 hours while 55% had a measured hyperthermia (T > 100.4) at the time of enrolment. FebriDx demonstrated a sensitivity of 95% (95% CI: 77-100%), specificity of 94% (88-98%), PPV of 76% (59-87%), and a NPV of 99% (93-100%).

CONCLUSION

FebriDx may identify clinically significant bacterial URI's and supports outpatient antibiotic decisions. Key messages FebriDx is an outpatient POC test designed to identify a clinically significant systemic host immune response and aid in the differentiation of viral and bacterial infection through rapid measurement of MxA and CRP from a fingerstick blood sample. FebriDx test was determined to be an accurate test, with a 85% sensitivity, 93% specificity and 97% NPV to rule out bacterial infection for any patient presenting with symptoms and reported fever within the prior 3 days, and when confirming fever (hyperthermia) at the time of testing, the test was even more sensitive (95%) and specific (94%) with a 99% NPV. FebriDx may support antibiotic stewardship by rapidly identifying clinically significant bacterial URIs.

The impact of nasal aspiration with an automatic device on upper and lower respiratory symptoms in wheezing children: a pilot case-control study

Background

The impact of proper aspiration of nasal secretions during upper respiratory infection on the frequency and severity of symptoms of lower airways has never been investigated. The study was aimed at testing if cleaning the nasal cavities of children with recurrent wheezing using an automatic nasal aspirator improves the upper and lower respiratory symptoms during the cold season.

Methods

Parents of wheezing children (age 3-72 mo.) answered questionnaires and learned using a nebulizer equipped (cases) or not equipped (controls) with an automatic nasal aspirator (DuoBaby, OMRON, Japan). During a 90-days monitoring period parents filled an electronic diary (BreathMonitor, TPS, Rome, Italy) on their child’s symptoms of the upper and lower airways.

Results

Eighty-nine/91 patients (43 cases, 46 controls) completed the study. Less days with upper (25.0% vs 46.4%, p = 0.004) or lower (21.8% vs 32.8%, p = 0.022) airways symptoms and less days with salbutamol inhalation (12.2% vs 16.9%, p < 0.001) were reported by cases than by controls. The episodes of upper respiratory symptoms were shorter [4.3 days (95%CI:3.8–4.9) vs 5.7 days (95%CI:5.0–6.4), p = 0.007] but not less frequent [2.3 (95%CI: 1.8–2.8) vs 2.6 (95%CI:2.2–3.0), p = 0.122] among cases than among controls. Similarly, the episodes of lower respiratory symptoms tended to be shorter [3.8 days, (95%CI: 3.4–4.2) vs 4.4 days, (95%CI: 4.4–6.0), p = 0.067] but not less frequent [1.9 (95%CI:1.5–2.3) vs 2.1 (95%CI:1.7–2.4), p = 0.240] among the group using the nasal aspirator.

Conclusions

In our pilot study, the use of an automatic nasal aspirator in children with a history of recurrent wheezing was associated with an improved respiratory health during the cold season.

Electronic supplementary material

The online version of this article (10.1186/s13052-018-0489-6) contains supplementary material, which is available to authorized users.

Functional Contributions of Prefoldin to Gene Expression

Prefoldin is a co-chaperone that evolutionarily originates in archaea, is universally present in all eukaryotes and acts as a co-chaperone by facilitating the supply of unfolded or partially folded substrates to class II chaperonins. Eukaryotic prefoldin is known mainly for its functional relevance in the cytoplasmic folding of actin and tubulin monomers during cytoskeleton assembly. However, the role of prefoldin in chaperonin-mediated folding is not restricted to cytoskeleton components, but extends to both the assembly of other cytoplasmic complexes and the maintenance of functional proteins by avoiding protein aggregation and facilitating proteolytic degradation. Evolution has favoured the diversification of prefoldin subunits, and has allowed the so-called prefoldin-like complex, with specialised functions, to appear. Subunits of both canonical and prefoldin-like complexes have also been found in the nucleus of yeast and metazoan cells, where they have been functionally connected with different gene expression steps. Plant prefoldin has also been detected in the nucleus and is physically associated with a gene regulator. Here we summarise information available on the functional involvement of prefoldin in gene expression, and discuss the implications of these results for the relationship between prefoldin structure and function.

Roles and Functions of the Unconventional Prefoldin URI

Almost 15 years ago, the URI prefoldin-like complex was discovered by Krek and colleagues in immunoprecipitation experiments conducted in mammalian cells with the aim of identifying new binding partners of the E3 ubiquitin-protein ligase S-phase kinase-associated protein 2 (SKP2) (Gstaiger et al. Science 302(5648):1208-1212, 2003). The URI prefoldin-like complex is a heterohexameric chaperone complex comprising two α and four β subunits (α2β4). The α subunits are URI and STAP1, while the β subunits are PFDN2, PFDN6, and PFDN4r, one of which is probably present in duplicate. Elucidating the roles and functions of these components in vitro and in vivo will help to clarify the mechanistic behavior of what appears to be a remarkably important cellular machine.

Surveillance of upper respiratory infections using a new multiplex PCR assay compared to conventional methods during the influenza season in Taiwan

•

This is the first study to evaluate the suitability of the FilmArray Respiratory Panel among influenza-like illness (ILI) patients during influenza season in Taiwan.

•

Around 60% of ILI cases seen at the sentinel sites were not caused by influenza virus.

•

Using this highly sensitive assay with clinical samples is feasible and has led to an increased rate of diagnosis.

•

Modern diagnostic systems along with clinician prescription can help to avoid the misuse or overuse of medical resources and improve patient outcomes.

Objectives

To improve diagnosis as part of laboratory surveillance in Taiwan, influenza-like illness (ILI) surveillance was conducted using a new multiplex PCR assay (FilmArray) and the results compared to those of conventional methods The study was performed during the winter months.

Methods

Throat swabs from patients with an ILI presenting to physicians in sentinel practices were collected during the 2016–2017 influenza season.

Results

A total of 52 samples tested positive by FilmArray Respiratory Panel. Forty percent were influenza A virus, and subtype H3N2 virus was the major epidemic strain. However, nearly 60% of ILI cases seen at sentinel sites were caused by non-influenza pathogens. The results of the FilmArray assay and cell culture were identical, and this assay was more sensitive than a rapid influenza diagnostic test. Genetic analyses revealed new influenza A H3N2 variants belonging to a novel subclade 3C.2a2.

Conclusions

The FilmArray assay facilitates urgent testing and laboratory surveillance for common viral and bacterial respiratory pathogens. This study demonstrated the use of a highly sensitive assay using clinical samples that is feasible for application worldwide. This may lead to an increased rate of diagnosis of viral infections and to improved patient outcomes, and in particular to a reduction in the overuse of antibiotics and antivirals.

URI promotes the migration and invasion of human cervical cancer cells potentially via upregulation of vimentin expression

URI is known to act as an oncoprotein in several tumors. Our previous studies have shown that URI is associated with the migration process in cervical and gastric cancer cells, but the mechanisms remain to be determined. Given the fact that URI positively regulates vimentin expression, we therefore investigated how URI regulated vimentin expression affects the migration and invasion of cells from two human cervical cancer cell lines HeLa and C33A, which differentially express URI. We have shown that knock-down of URI in HeLa cells using URI siRNA caused decreased vimentin mRNA and protein levels along with attenuated cell motility. Meanwhile, overexpression of URI by transfection of PCMV6-URI in C33A cells resulted in increased vimentin expression and enhanced cell migration and invasion. We have also used TGF-β to induce vimentin expression, which enhanced the cell migration and invasion abilities affected by URI, while inhibition of vimentin by siRNA attenuated URI's effect on cell migration and invasion. In addition, we have performed luciferase reporter and ChIP assays, and the results support that URI indirectly enhances the activity of vimentin promoter. Taken together, our results suggest that URI plays essential roles in the migration and invasion of human cervical cancer cells, possibly via targeting vimentin expression.

URI prevents potassium dichromate-induced oxidative stress and cell death in gastric cancer cells

Chromium VI can provoke oxidative stress, DNA damage, cytotoxicity, mutagenesis and carcinogenesis. Aberrantly high level of reactive oxygen species (ROS) has been associated with oxidative stress and subsequent DNA damage. Notably, multiple previous studies have shown the increased level of ROS in chromium (VI) induced oxidative stress, but its effect on cell death and the underlying mechanism remain to be determined. In this study, we aimed to investigate the role of URI, an unconventional prefoldin RBP5 interactor, in potassium dichromate induced oxidative stress and cell death through in vitro loss-of-function studies. We have shown that knockdown of URI in human gastric cancer SGC-7901 cells by URI siRNA enhanced potassium dichromate-induced production of ROS. The level of rH2AX, a marker of DNA damage, was significantly increased, along with a reduced cell viability in URI siRNA treated cells that were also exposed to potassium dichromate. Comet assay showed that URI knockdown increased the tail moment in potassium dichromate-treated SGC-7901 cells. Accordingly, the cell rates of apoptosis and necrosis were also increased in URI knockdown cells treated with potassium dichromate at different concentrations. Together, these results suggest that URI is preventive for the oxidative stress and cell death induced by potassium dichromate, which potentially leads to cancer cell survival and therapeutic resistance.

Nasopharyngeal microbiota composition of children is related to the frequency of upper respiratory infection and acute sinusitis

BACKGROUND

Upper respiratory infections (URI) and their complications are a major healthcare burden for pediatric populations. Although the microbiology of the nasopharynx is an important determinant of the complications of URI, little is known of the nasopharyngeal (NP) microbiota of children, the factors that affect its composition, and its precise relationship with URI.

RESULTS

Healthy children (n = 47) aged 49-84 months from a prospective cohort study based in Wisconsin, USA, were examined. Demographic and clinical data and NP swab samples were obtained from participants upon entry to the study. All NP samples were profiled for bacterial microbiota using a phylogenetic microarray, and these data were related to demographic characteristics and upper respiratory health outcomes. The composition of the NP bacterial community of children was significantly related prior to the history of acute sinusitis (R (2) = 0.070, P < 0.009). History of acute sinusitis was associated with significant depletion in relative abundance of taxa including Faecalibacterium prausnitzii and Akkermansia spp. and enrichment of Moraxella nonliquefaciens. Enrichment of M. nonliquefaciens was also a characteristic of baseline NP samples of children who subsequently developed acute sinusitis over the 1-year study period. Time to develop URI was significantly positively correlated with NP diversity, and children who experienced more frequent URIs exhibited significantly diminished NP microbiota diversity (P ≤ 0.05).

CONCLUSIONS

These preliminary data suggest that previous history of acute sinusitis influences the composition of the NP microbiota, characterized by a depletion in relative abundance of specific taxa. Diminished diversity was associated with more frequent URIs.

URI promotes gastric cancer cell motility, survival, and resistance to adriamycin in vitro

Unconventional prefoldin RPB5 interactor (URI), a RNA polymerase II Subunit 5-Interacting protein, is known to participate in the regulation of nutrient-sensitive mTOR-dependent transcription programs. Multiple studies have recently demonstrated that URI functions as an oncoprotein, possibly through the mTOR pathway, and regulates tumor cell motility, invasion, and metastasis. However, whether and how URI plays a role in gastric oncogenesis has not been elucidated. Due to drug resistance, recurrence and metastasis, the prognosis of gastric cancer remains poor. This study aims to explore the effects of URI on gastric cancer cells by focusing on their migratory ability and resistance to adriamycin. URI was over-expressed or knocked-down in MGC-803 and HGC-27 gastric cancer cells using URI plasmid or siRNA transfection approach. The cell viability, apoptosis, and migration ability were then examined by the CCK-8 assay, flow cytometer Annexin V/PI staining, and the Transwell cell migration assay respectively. The protein levels of apoptosis and EMT related genes were detected by western blot. The results showed that overexpression of URI promoted while knock-down of URI inhibited gastric cancer cell proliferation. URI overexpression resulted in increased Bcl-2 expression but decreased levels of Bax, cleaved PARP-1 and cleaved caspase-3. Conversely, cells treated with URI siRNA showed increased adriamycin induced apoptosis, along with reduced Bcl-2, but increased Bax, cleaved PARP-1 and cleaved caspase-3 expression. We have also shown that overexpression of URI enhanced cancer cell proliferation and migration with higher levels of Snail and Vimentin, whereas knockdown of URI in MGC-803 and HGC-27 cells inhibited proliferation and migration with decreased Snail and Vimentin expression. Together, our results support that URI promotes cell survival and mobility and acts as a chemotherapeutics resistant protein in MGC-803 and HGC-27 cells. URI might be a potential biomarker for gastric cancer diagnostics and prognostics.

Rasch Analysis of The WURSS-21 Dimensional Validation and Assessment of Invariance

BACKGROUND

The purpose of this study is to use Rasch analysis to explore the validity of considering self-report scores from Wisconsin Upper Respiratory Symptom Survey (WURSS-21) as a single global illness severity domain. The WURSS-21 is a widely used questionnaire instrument that assesses symptom severity and functional impact of common cold and flu-like illness.

METHODS

This study applies item response theory, specifically Rasch modeling, to investigate dimensional and measurement properties of the WURSS-21, and looks at invariance over time. The data assessed represents 1167 people, each scoring the WURSS-21 once daily for up to seven consecutive days of acute upper respiratory infection (URI) illness.

RESULTS

Rasch analysis supports a single domain WURSS-21 global symptom score. Assessment of differential item functioning across seven days of illness provides evidence for measurement invariance. While individual items rating physical symptoms were somewhat variable, items rating functional impairment and quality of life impact appeared quite consistent across a single domain over seven days of illness.

CONCLUSION

Rasch analysis of WURSS-21 items provides evidential support for a single invariant domain. These findings support the practice of using a simply summed daily global illness severity score to represent the overall symptomatic and functional impairments arising from URI.

URI expression in cervical cancer cells is associated with higher invasion capacity and resistance to cisplatin

Cervical cancer is a common and devastating female cancer worldwide. The etiology of cervical cancer has been largely attributed to human papillomavirus (HPV) infection and activation of the P13K/AKT/mTOR (mammalian target of rapamycin) pathway. However, the limited HPV-directed therapy, as well as therapeutic approach targeting P13K/AKT/mTOR pathway, has not yet been established or effective. A deeper understanding of cervical carcinogenesis and finding of novel candidate molecules for cervical cancer therapeutics is largely warranted. The unconventional prefoldin RPB5 interactor (URI or URI1), a known transcription factor involving the TOR signaling pathway, has recently been implicated a role in multiple tumorigenesis. We recently reported significant upregulation of URI in precancerous cervical intra-epithelial neoplasia (CIN) and invasive cervical cancer, suggesting its role in cervical carcinogenesis. However, the effect and underlying mechanism of URI in cervical cancer development have never been elucidated. Here, we aimed to investigate the in vitro effect of URI on cervical cancer using two cervical cancer cell lines CaSki and C33A, which are HPV-positive and HPV-negative respectively. We have shown that forced over-expression of URI in C33A and CaSki cells markedly promoted cell growth, while down-regulation of URI mediated by siRNA inhibited cell proliferation. We have found that URI over-expression enhanced resistance of cervical cancer cells to cisplatin. In contrast, knockdown of URI promoted apoptosis by influencing cell response to cisplatin, supporting URI as an oncogenic protein for cervical cancer cells. We have also shown that URI promoted the migration and invasive capacity of cervical cancer cells by up-regulation of Vimentin, a mesenchymal cell migration marker relating to the epithelial-mesenchymal transition (EMT) program. Our data support an important function of URI in the biological behavior of cervical cancer cells and provide novel mechanistic insights into the role of URI in cervical cancer progression and possibly, metastasis.

Boosting NAD(+) for the prevention and treatment of liver cancer

Hepatocellular carcinoma (HCC) is the third leading cause of cancer death worldwide yet has limited therapeutic options. We recently demonstrated that inhibition of de novo nicotinamide adenine dinucleotide (NAD⁺) synthesis is responsible for DNA damage, thereby initiating hepatocarcinogenesis. We propose that boosting NAD⁺ levels might be used as a prophylactic or therapeutic approach in HCC.

Characterization of the 19q12 amplification including CCNE1 and URI in different epithelial ovarian cancer subtypes

BACKGROUND

CCNE1 is frequently amplified in high grade serous ovarian cancer and may serve as a target for ovarian cancer treatment. URI is closely related to CCNE1 at the 19q12 amplicon and may also contribute to the oncogenic effect. Our objective was to investigate the relevance of CCNE1 and URI gene amplification and protein expression in different histological subtypes of epithelial ovarian cancer (EOC).

METHODS

A novel dual-color 19q12 in situ hybridization (ISH), covering CCNE1 and URI, and chromosome 19 as a surrogate using Ventana BenchMark XT platform was developed and applied to 148 EOCs. URI and CCNE1 amplifications were separately assessed by fluorescence in situ hybridization (FISH). Immunohistochemistry using a Cyclin E1 and a novel URI monoclonal antibody was performed.

RESULTS

Amplification of 19q12 was found in 36.6%, CCNE1 in 21.7%, URI in 9.9%, and both genes simultaneously in 9% of EOC cases. High Cyclin E1 and URI protein expression were observed in 52.2% and 26.1%, respectively. Amplification of 19q12 occurred in all EOC subtypes and was associated with amplification and expression of CCNE1/Cyclin E1, URI, TP53 mutation, and advanced stage.

CONCLUSION

The novel 19q12 ISH probe reliably detects both CCNE1 and URI amplifications as confirmed by FISH. The combination of 19q12 amplification with Cyclin E1 and URI protein expression may help to select patients more likely to benefit from CDK2 targeted therapies.

Controlled vocabularies and ontologies in proteomics: overview, principles and practice

This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mapping files" used to ensure correct controlled vocabulary terms that are placed within PSI standards and the fulfillment of the MIAPE (Minimum Information about a Proteomics Experiment) requirements. This article is part of a Special Issue entitled: Computational Proteomics in the Post-Identification Era. Guest Editors: Martin Eisenacher and Christian Stephan.

Association of CYP2C19 polymorphisms and lansoprazole-associated respiratory adverse effects in children

OBJECTIVE

To determine whether cytochrome P450 (CYP)2C19 haplotype associates with lansoprazole-associated adverse event frequency.

STUDY DESIGN

Respiratory adverse events from a clinical trial of lansoprazole in children with asthma were analyzed for associations with extensive or poor metabolizer (PM) phenotype based on CYP2C19 haplotypes. Carriers of CYP2C19*2, *3, *8, or *9 alleles were PMs; carriers of 2 wild-type alleles were extensive metabolizers (EMs). Plasma concentrations of lansoprazole were determined in PM and EM phenotypes.

RESULTS

The frequency of upper respiratory infection among PMs (n = 45) was higher than that among EMs (n = 91), which in turn was higher than that in placebo subjects (n = 135; P = .0039). The frequency of sore throat (ST) was similarly distributed among EMs and PMs (P = .0015). The OR (95% CI) for upper respiratory infections in PMs was 2.46 (1.02-5.96) (P = .046); for EMs, the OR (95% CI) was 1.55 (0.86-2.79). The OR (95% CI) for ST in EMs and PMs was 2.94 (1.23-7.05, P = .016) vs 1.97 (1.09-3.55, P = .024), respectively. Mean ± SD plasma concentrations of lansoprazole were higher in PMs than in EMs: 207 ± 179 ng/mL vs 132 ± 141 ng/mL (P = .04).

CONCLUSIONS

Lansoprazole-associated upper respiratory infections and ST in children are related in part to CYP2C19 haplotype. Our data suggest that lansoprazole-associated adverse events in children may be mitigated by adjusting the conventional dose in PMs. Additional studies are required to replicate our findings.