Translated small open reading frames (smORFs) can have important regulatory roles and encode microproteins, yet their genome-wide identification has been challenging. We determined the ribosome ...locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. Integration with 456 mass-spectrometry datasets confirms the presence of 603 small peptides at the protein level in humans and provides insights into the subcellular localization of these small proteins. This study provides a comprehensive atlas of high-confidence translated smORFs derived from primary human cells and tissues in order to provide a more complete understanding of the translated human genome.
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•Ribosome profiling (Ribo-seq) of 11 human primary cells and tissues reveals 7,767 high-confidence smORFs•smORFs exhibit cell-type/tissue specificity, and 603 SEPs were detected in MS data•Dynamic changes in the TE of uORF and main ORF pairs are mostly homodirectional•An interactive browser for this study can be found at https://smorfs.ddnetbio.com
Chothani et al. evaluate ribosome-mRNA interactions across six cell types and five tissues and reveal 7,767 small regions outside of the protein-coding genome that are actively translated in humans. These include specifically expressed and highly conserved small open reading frames. The integration of proteomics reveals more than 600 small proteins.
The imaging features of dilated cardiomyopathy (DCM) overlap with physiological exercise-induced cardiac remodeling in active and otherwise healthy individuals. Distinguishing the two conditions is ...challenging. This study examined the diagnostic and prognostic roles of exercise stress imaging in asymptomatic patients with suspected DCM.
Exercise stress cardiovascular magnetic resonance (CMR) was performed in 60 asymptomatic patients with suspected DCM (dilated left ventricle and/or impaired systolic function on CMR), who also underwent DNA sequencing for DCM-causing genetic variants. Confirmed DCM was defined as genotype- and phenotype-positive (G+P+). Another 100 healthy subjects were recruited to establish normal exercise capacities (peak exercise cardiac index; Peak
). The primary outcome was a composite of all-cause mortality, cardiac decompensation and ventricular arrhythmic events.
No patients with confirmed G+P+ DCM had Peak
exceeding the 35th percentile specific for age and sex. Applying this threshold in G-P+ patients, those with Peak
below 35th percentile had characteristics similar to confirmed DCM while patients with higher Peak
were younger, more active and higher longitudinal strain. Adverse cardiovascular events occurred only in patients with low exercise capacity (P = 0.004).
In individuals with suspected DCM, exercise stress CMR demonstrates diagnostic and prognostic potential in distinguishing between pathological DCM and physiological exercise-induced cardiac remodeling.
This study considers the problem of periodic event-triggered (PET) cooperative output regulation for a class of linear multi-agent systems. The advantage of the PET output regulation is that the data ...transmission and triggered condition are only needed to be monitored at discrete sampling instants. It is assumed that only a small number of agents can have access to the system matrix and states of the leader. Meanwhile, the PET mechanism is considered not only in the communication between various agents, but also in the sensor-to-controller and controller-to-actuator transmission channels for each agent. The above problem set-up will bring some challenges to the controller design and stability analysis. Based on a novel PET distributed observer, a PET dynamic output feedback control method is developed for each follower. Compared with the existing works, our method can naturally exclude the Zeno behavior, and the inter-event time becomes multiples of the sampling period. Furthermore, for every follower, the minimum inter-event time can be determined a prior, and computed directly without the knowledge of the leader information. An example is given to verify and illustrate the effectiveness of the new design scheme.
Vehicular incidents, especially those involving tractor trailers, are increasing in number every year. These events are extremely costly for fleets, in terms of damage or loss of property, loss of ...efficiency, and certainly in terms of loss of life. Although the U.S. Department of Transportation (DOT) is responsible for performing inspections, and fleet managers are encouraged to maintain their fleet and participate in regular inspections, it is uncertain whether these inspections are occurring at a frequency that is necessary to prevent incidents. The Federal Motor Carrier Safety Administration (FMCSA) of the DOT manages and maintains the Motor Carrier Management Information System (MCMIS) dataset, which contains all incident and inspection data regarding commercial vehicles in the U.S. The purpose of this preliminary analysis was to explore the MCMIS dataset through spatiotemporal analyses, to uncover findings that may hint at potential improvements in the DOT inspection process and highlight location-specific trends in the dataset. These analyses are novel, as previous research using the MCMIS dataset only examined the data at the state or county level, not at a national scale. The results from the analyses pinpointed specific major metropolitan areas, namely Harris County (Houston), Texas, and three of the New York boroughs (Kings, Queens, and the Bronx), which were found to have increasing incident rates during the study period (2016–2020). An overview of potential causal factors contributing to this increase are provided as well as an overview of the inspection process, and suggestions for improvement relative to the highlighted locations in Texas and New York are also provided. Ultimately, it is suggested that the incorporation of advanced technology and automation may prove beneficial in reducing the occurrence of events that lead to incidents and may also help in the inspection process.
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•The complete genome sequence of W. coagulans HOM5301 was assembled and analyzed.•W. coagulans HOM5301 showed goodinvitroprobioticcharacteristics.•Daily treatment with W. coagulans ...HOM5301 spores boosted immunity in mice.•W. coagulans HOM5301 positively modulated the gut microbiota in mice.
Weizmannia coagulans is considered an ideal probiotic owing to its function and stability during production and storage. This study aims to evaluate the efficacy and safety of W. coagulans HOM5301 as an immunoregulatory probiotic. Whole genome analysis demonstrated that W. coagulans HOM5301 had no antibiotic resistance or virulence genes, but contained four gene clusters of secondary metabolites related to antimicrobial activities. W. coagulans HOM5301 spores tolerated gastrointestinal tract conditions with a survival rate of 86.33%. The spent culture broth of W. coagulans HOM5301 showed strong antimicrobial activity against foodborne pathogens. W. coagulans HOM5301 stimulated macrophages to produce more TNF-α but less IL-10 than that of the controls. Daily treatment with W. coagulans HOM5301 spores for 31 days positively modulated the gut microbiota and boosted both innate and adaptive immunity in a dose-dependent manner in mice. In conclusion, W. coagulans HOM5301 can be safely consumed by humans to induce robust immunity.
Like several Southeast Asian countries, Singapore has a complex eating-out environment and a rising eating-out prevalence. However the determinants and drivers of eating-out in urban Asian ...environments are poorly understood.
We examined the socio-demographic characteristics of persons who frequently ate away from home in local eateries called hawker centres and Western fast-food restaurants, using data from 1647 Singaporean adults participating in the National Nutrition Survey (NNS) 2010. We also assessed the underlying drivers of eating out and evaluated if these were different for eating at local eateries compared to Western fast-food restaurants using 18 focus group discussions of women (130 women).
Participants reported a high eating-out frequency with 77.3% usually eating either breakfast, lunch or dinner at eateries. Main venues for eating-out included hawker centres (61.1% usually ate at least 1 of 3 daily meals at this venue) and school/workplace canteens (20.4%). A minority of participants (1.9%) reported usually eating at Western fast-food restaurants. Younger participants and those of Chinese and Malay ethnicity compared to Indians were more likely to eat at Western fast-food restaurants. Chinese and employed persons were more likely to eat at hawker centres. The ready availability of a large variety of affordable and appealing foods appeared to be a primary driver of eating out, particularly at hawker centres.
Our findings highlight the growing importance of eating-out in an urban Asian population where local eating venues play a more dominant role compared with Western fast-food chains. Interventions focusing on improving the food quality at venues for eating out are important to improve the diet of urban Asian populations.
Assessing habitual food consumption is challenging in multi-ethnic cosmopolitan settings. We systematically developed a semi-quantitative food frequency questionnaire (FFQ) in a multi-ethnic ...population in Singapore, using data from two 24-h dietary recalls from a nationally representative sample of 805 Singapore residents of Chinese, Malay and Indian ethnicity aged 18-79 years. Key steps included combining reported items on 24-h recalls into standardized food groups, developing a food list for the FFQ, pilot testing of different question formats, and cognitive interviews. Percentage contribution analysis and stepwise regression analysis were used to identify foods contributing cumulatively ≥90% to intakes and individually ≥1% to intake variance of key nutrients, for the total study population and for each ethnic group separately. Differences between ethnic groups were observed in proportions of consumers of certain foods (e.g., lentil stews, 1%-47%; and pork dishes, 0%-50%). The number of foods needed to explain variability in nutrient intakes differed substantially by ethnic groups and was substantially larger for the total population than for separate ethnic groups. A 163-item FFQ covered >95% of total population intake for all key nutrients. The methodological insights provided in this paper may be useful in developing similar FFQs in other multi-ethnic settings.
Lactiplantibacillus plantarum
, previously named
Lactobacillus plantarum
, is a facultative, homofermentative lactic acid bacterium widely distributed in nature. Several
Lpb. plantarum
strains have ...been demonstrated to possess good probiotic properties, and
Lpb. plantarum
HOM3204 is a potential probiotic strain isolated from homemade pickled cabbage plants. In this study, whole-genome sequencing was performed to acquire genetic information and predict the function of HOM3204, which has a circular chromosome of 3,232,697 bp and two plasmids of 48,573 and 17,060 bp, respectively. Moreover, various oxidative stress-related genes were identified in the strain, and its antioxidant activity was evaluated in vitro and in vivo. Compared to reference strains, the intracellular cell-free extracts of
Lpb. plantarum
HOM3204 at a dose of 10
10
colony-forming units (CFU)/ml in vitro exhibited stronger antioxidant properties, such as total antioxidant activity, 2,2-diphenyl-1-picrylhydrazyl radical scavenging rate, superoxide dismutase activity, and glutathione (GSH) content. Daily administration of 10
9
CFU
Lpb. plantarum
HOM3204 for 45 days significantly improved the antioxidant function by increasing the glutathione peroxidase activity in the whole blood and GSH concentration in the livers of D-galactose-induced aging mice. These results suggest that
Lpb. plantarum
HOM3204 can potentially be used as a food ingredient with good antioxidant properties.
Infections caused by multidrug-resistant (MDR) bacteria are becoming a serious threat to public health worldwide. With an ever-reducing pipeline of last-resort drugs further complicating the current ...dire situation arising due to antibiotic resistance, there has never been a greater urgency to attempt to discover potential new antibiotics. The use of nanotechnology, encompassing a broad range of organic and inorganic nanomaterials, offers promising solutions. Organic nanomaterials, including lipid-, polymer-, and carbon-based nanomaterials, have inherent antibacterial activity or can act as nanocarriers in delivering antibacterial agents. Nanocarriers, owing to the protection and enhanced bioavailability of the encapsulated drugs, have the ability to enable an increased concentration of a drug to be delivered to an infected site and reduce the associated toxicity elsewhere. On the other hand, inorganic metal-based nanomaterials exhibit multivalent antibacterial mechanisms that combat MDR bacteria effectively and reduce the occurrence of bacterial resistance. These nanomaterials have great potential for the prevention and treatment of MDR bacterial infection. Recent advances in the field of nanotechnology are enabling researchers to utilize nanomaterial building blocks in intriguing ways to create multi-functional nanocomposite materials. These nanocomposite materials, formed by lipid-, polymer-, carbon-, and metal-based nanomaterial building blocks, have opened a new avenue for researchers due to the unprecedented physiochemical properties and enhanced antibacterial activities being observed when compared to their mono-constituent parts. This review covers the latest advances of nanotechnologies used in the design and development of nano- and nanocomposite materials to fight MDR bacteria with different purposes. Our aim is to discuss and summarize these recently established nanomaterials and the respective nanocomposites, their current application, and challenges for use in applications treating MDR bacteria. In addition, we discuss the prospects for antimicrobial nanomaterials and look forward to further develop these materials, emphasizing their potential for clinical translation.
The global prevalence of obesity is rising year by year, which has become a public health problem worldwide. Many animal and clinical studies have shown that Lactiplantibacillus plantarum is ...considered an ideal probiotic and potential supplement for the treatment of obesity. In this study, we aimed to complete the genome sequence of L. plantarum HOM2217, which was isolated from human milk, and study its physiological characteristics and anti-obesity effects in 3T3-L1 cells and rats fed a high-fat diet (HFD) to determine its potential as a starter for functional food products. Whole-genome analysis demonstrated that HOM2217 contained a single circular chromosome of 3,267,529 bp with a GC content of 44.5% and one plasmid (62,350 bp) with a GC content of 38.5%. Compared to the reference strains, HOM2217 demonstrated superior tolerance to gastrointestinal conditions, higher adhesion to intestinal epithelial cell lines, potent antimicrobial activity against Enterobacter cloacae ATCC 13047, and effective cholesterol removal ability in vitro . Treatment with heat-killed HOM2217 significantly reduced lipid accumulation and intracellular triglyceride production in 3T3-L1 adipocytes. Daily treatment of HFD-fed rats with HOM2217 for 7 weeks decreased body weight, body weight gain, and body fat without changes in food intake. HOM2217 also significantly increased the serum high-density lipoprotein cholesterol (HDL-C) level, decreased the serum tumor necrosis factor (TNF-α) and increased short-chain fatty acid (SCFA) (formic acid, acetic acid, and butyric acid) levels in the cecum. Thus, HOM2217 could potentially prevent obesity in rats by inhibiting inflammatory responses and regulating lipid metabolism and SCFAs expression. Therefore, HOM2217 has potential as an alternative treatment for obesity.
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