The tRNA methyltransferase TrmB is critical for Acinetobacter baumannii stress responses and pulmonary infection.

IMPORTANCE: As deficiencies in tRNA modifications have been linked to human diseases such as cancer and diabetes, much research has focused on the modifications' impacts on translational regulation in eukaryotes. However, the significance of tRNA modifications in bacterial physiology remains largely unexplored. In this paper, we demonstrate that the m7G tRNA methyltransferase TrmB is crucial for a top-priority pathogen, Acinetobacter baumannii, to respond to stressors encountered during infection, including oxidative stress, low pH, and iron deprivation. We show that loss of TrmB dramatically attenuates a murine pulmonary infection. Given the current efforts to use another tRNA methyltransferase, TrmD, as an antimicrobial therapeutic target, we propose that TrmB, and other tRNA methyltransferases, may also be viable options for drug development to combat multidrug-resistant A. baumannii.

ACP-ADA: A Boosting Method with Data Augmentation for Improved Prediction of Anticancer Peptides.

Cancer is the second-leading cause of death worldwide, and therapeutic peptides that target and destroy cancer cells have received a great deal of interest in recent years. Traditional wet experiments are expensive and inefficient for identifying novel anticancer peptides; therefore, the development of an effective computational approach is essential to recognize ACP candidates before experimental methods are used. In this study, we proposed an Ada-boosting algorithm with the base learner random forest called ACP-ADA, which integrates binary profile feature, amino acid index, and amino acid composition with a 210-dimensional feature space vector to represent the peptides. Training samples in the feature space were augmented to increase the sample size and further improve the performance of the model in the case of insufficient samples. Furthermore, we used five-fold cross-validation to find model parameters, and the cross-validation results showed that ACP-ADA outperforms existing methods for this feature combination with data augmentation in terms of performance metrics. Specifically, ACP-ADA recorded an average accuracy of 86.4% and a Mathew's correlation coefficient of 74.01% for dataset ACP740 and 90.83% and 81.65% for dataset ACP240; consequently, it can be a very useful tool in drug development and biomedical research.

Translating while under attack: Plant defense mRNAs find a way.

In plants, pattern-triggered immunity shuts down global translation while allowing the translation of defense mRNAs. Wang et al. (2022) describe a previously unknown mechanism for how elements in the 5' UTR of these mRNAs can recruit the translation machinery to initiate protein synthesis.

N1-methylpseudouridine found within COVID-19 mRNA vaccines produces faithful protein products.

Synthetic mRNA technology is a promising avenue for treating and preventing disease. Key to the technology is the incorporation of modified nucleotides such as N1-methylpseudouridine (m1Ψ) to decrease immunogenicity of the RNA. However, relatively few studies have addressed the effects of modified nucleotides on the decoding process. Here, we investigate the effect of m1Ψ and the related modification pseudouridine (Ψ) on translation. In a reconstituted system, we find that m1Ψ does not significantly alter decoding accuracy. More importantly, we do not detect an increase in miscoded peptides when mRNA containing m1Ψ is translated in cell culture, compared with unmodified mRNA. We also find that m1Ψ does not stabilize mismatched RNA-duplex formation and only marginally promotes errors during reverse transcription. Overall, our results suggest that m1Ψ does not significantly impact translational fidelity, a welcome sign for future RNA therapeutics.

Canary in a coal mine: collided ribosomes as sensors of cellular conditions.

The recent discovery that collision of ribosomes triggers quality control and stress responses in eukaryotes has shifted the perspective of the field. Collided eukaryotic ribosomes adopt a unique structure, acting as a ubiquitin signaling platform for various response factors. While several of the signals that determine which downstream pathways are activated have been uncovered, we are only beginning to learn how the specificity for the activation of each process is achieved during collisions. This review will summarize those findings and how ribosome-associated factors act as molecular sentinels, linking aberrations in translation to the overall cellular state. Insights into how cells respond to ribosome collision events will provide greater understanding of the role of the ribosome in the maintenance of cellular homeostasis.

Identifying areas of potential critical healthcare shortages: A case study of spatial accessibility to ICU beds during the COVID-19 pandemic in Florida.

Healthcare resource availability is potentially associated with COVID-19 mortality, and the potentially uneven geographical distribution of resources is a looming concern in the global pandemic. Given that access to healthcare resources is important to overall population health, assessing COVID-19 patients' access to healthcare resources is needed. This paper aims to examine the temporal variations in the spatial accessibility of the U.S. COVID-19 patients to medical facilities, identify areas that are likely to be overwhelmed by the COVID-19 pandemic, and explore associations of low access areas with their socioeconomic and demographic characteristics. We use a three-step floating catchment area method, spatial statistics, and logistic regression to achieve the goals. Findings of this research in the State of Florida revealed that North Florida, rural areas, and zip codes with more Latino or Hispanic populations are more likely to have lower access than other regions during the COVID-19 pandemic. Our approach can help policymakers identify potentially possible low access areas and establish appropriate policy intervention paying attention to those areas during a pandemic.

A Comparative Assessment of Cooling Center Preparedness across Twenty-Five U.S. Cities.

Cooling centers have played a significant role in reducing the risks of adverse health impacts of extreme heat exposure. However, there have been no comparative studies investigating cooling center preparedness in terms of population coverage, location efficiency, and population coverage disparities among different subpopulation groups. Using a catchment area method with a 0.8 km walking distance, we compared three aspects of cooling center preparedness across twenty-five cities in the U.S. We first calculated the percentage of the population covered by a single cooling center for each city. Then, the extracted values were separately compared to the city's heat indexes, latitudes, and spatial patterns of cooling centers. Finally, we investigated population coverage disparities among multiple demographics (age, race/ethnicity) and socioeconomic (insurance, poverty) subpopulation groups by comparing the percentage of population coverage between selected subpopulation groups and reference subpopulation groups. Our results showed that cooler cities, higher latitude cities, and cities with dispersed cooling centers tend to be more prepared than warmer cities, lower latitude cities, and cities with clustered cooling centers across the U.S. Moreover, older people (≥65) had 9% lower population coverage than younger people (≤64). Our results suggest that the placement of future cooling centers should consider both the location of other nearby cooling centers and the spatial distribution of subpopulations to maximize population coverage and reduce access disparities among several subpopulations.

Spatial accessibility assessment of COVID-19 patients to healthcare facilities: A case study of Florida.

During the COVID-19 pandemic, healthcare facilities worldwide have been overwhelmed by the amount of coronavirus patients needed to be served. Similarly, the U.S. also experienced a shortage of healthcare resources, which led to a reduction in the efficiency of the whole healthcare system. In order to evaluate this from a transportation perspective, it is critical to understand the extent to which healthcare facilities with intensive care unit (ICU) beds are available in both urban and rural areas. As such, this study aims to assess the spatial accessibility of COVID-19 patients to healthcare facilities in the State of Florida. For this purpose, two methods were used: the two-step floating catchment area (2SFCA) and the enhanced two-step floating catchment area (E2SFCA). These methods were applied to identify the high and low access areas in the entire state. Furthermore, a metric, namely the Accessibility Ratio Difference (ARD), was developed to evaluate the spatial access difference between the models. Results revealed that many areas in the northwest and southern Florida have lower access compared to other locations. The residents in central Florida (e.g., Tampa and Orlando cities) had the highest level of accessibility given their higher access ratios. We also observed that the 2SFCA method overestimates the accessibility in the areas with a lower number of ICU beds due to the "equal access" assumption of the population within the catchment area. The findings of this study can provide valuable insights and information for state officials and decision makers in the field of public health.

Highly Osmotic Oxidized Sucrose-Crosslinked Polyethylenimine for Gene Delivery Systems.

In this work, highly osmotic oxidized sucrose-crosslinked polyethylenimine (SP2K) polymers were developed for gene delivery systems, and the transfection mechanism is examined. First, periodate-oxidized sucrose and polyethylenimine 2K (PEI2K) were crosslinked with various feed ratios via reductive amination. The synthesis was confirmed by 1H NMR and FTIR. The synthesized SP2K polymers could form positively charged (~40 mV zeta-potential) and nano-sized (150-200 nm) spherical polyplexes with plasmid DNA (pDNA). They showed lower cytotoxicity than PEI25K but concentration-dependent cytotoxicity. Among them, SP2K7 and SP2K10 showed higher transfection efficiency than PEI25K in both serum and serum-free conditions, revealing the good serum stability. It was found that SP2K polymers possessed high osmolality and endosome buffering capacity. The transfection experiments with cellular uptake inhibitors suggest that the transfection of SP2K polymers would progress by multiple pathways, including caveolae-mediated endocytosis. It was also thought that caveolae-mediated endocytosis of SP2K polyplexes would be facilitated through cyclooxygenase-2 (COX-2) expression induced by high osmotic pressure of SP2K polymers. Confocal microscopy results also supported that SP2K polyplexes would be internalized into cells via multiple pathways and escape endosomes efficiently via high osmolality and endosome buffering capacity. These results demonstrate the potential of SP2K polymers for gene delivery systems.

Alkylative damage of mRNA leads to ribosome stalling and rescue by trans translation in bacteria.

Similar to DNA replication, translation of the genetic code by the ribosome is hypothesized to be exceptionally sensitive to small chemical changes to its template mRNA. Here we show that the addition of common alkylating agents to growing cultures of Escherichia coli leads to the accumulation of several adducts within RNA, including N(1)-methyladenosine (m1A). As expected, the introduction of m1A to model mRNAs was found to reduce the rate of peptide bond formation by three orders of magnitude in a well-defined in vitro system. These observations suggest that alkylative stress is likely to stall translation in vivo and necessitates the activation of ribosome-rescue pathways. Indeed, the addition of alkylation agents was found to robustly activate the transfer-messenger RNA system, even when transcription was inhibited. Our findings suggest that bacteria carefully monitor the chemical integrity of their mRNA and they evolved rescue pathways to cope with its effect on translation.

TRIM34 restricts HIV-1 and SIV capsids in a TRIM5α-dependent manner.

The HIV-1 capsid protein makes up the core of the virion and plays a critical role in early steps of HIV replication. Due to its exposure in the cytoplasm after entry, HIV capsid is a target for host cell factors that act directly to block infection such as TRIM5α and MxB. Several host proteins also play a role in facilitating infection, including in the protection of HIV-1 capsid from recognition by host cell restriction factors. Through an unbiased screening approach, called HIV-CRISPR, we show that the CPSF6-binding deficient, N74D HIV-1 capsid mutant is sensitive to restriction mediated by human TRIM34, a close paralog of the well-characterized HIV restriction factor TRIM5α. This restriction occurs at the step of reverse transcription, is independent of interferon stimulation, and limits HIV-1 infection in key target cells of HIV infection including CD4+ T cells and monocyte-derived dendritic cells. TRIM34 can also restrict some SIV capsids. TRIM34 restriction requires TRIM5α as knockout or knockdown of TRIM5α results in a loss of antiviral activity. Through immunofluorescence studies, we show that TRIM34 and TRIM5α colocalize to cytoplasmic bodies and are more frequently observed to be associated with infecting N74D capsids than with WT HIV-1 capsids. Our results identify TRIM34 as an HIV-1 CA-targeting restriction factor and highlight the potential role for heteromultimeric TRIM interactions in contributing to restriction of HIV-1 infection in human cells.

HMB in DRAM-less NVMe SSDs: Their usage and effects on performance.

Solid-state drives (SSDs) that do not have internal dynamic random-access memory (DRAM) are being widely spread for client SSD and embedded SSD markets in recent years because they are cheap and consume less power. Obviously, their performance is lower than conventional SSDs because they cannot exploit advantages of DRAM in the controller. However, this problem can be alleviated by using host memory buffer (HMB) feature of Non-Volatile Memory Express (NVMe), which allows SSDs to utilize the DRAM of host. In this paper, we show that commercial DRAM-less SSDs clearly exhibit worse I/O performance than SSDs with internal DRAM, but this can be improved by using the HMB feature. We also present methods that reveal how the host memory buffer is used in commercial DRAM-less SSDs to improve I/O performance. Through extensive experiments, we conclude that DRAM-less SSDs evaluated in this study mainly exploit the host memory buffer as an address mapping table cache rather than a read cache or write buffer to improve I/O performance.

HIV-1-induced cytokines deplete homeostatic innate lymphoid cells and expand TCF7-dependent memory NK cells.

Human immunodeficiency virus 1 (HIV-1) infection is associated with heightened inflammation and excess risk of cardiovascular disease, cancer and other complications. These pathologies persist despite antiretroviral therapy. In two independent cohorts, we found that innate lymphoid cells (ILCs) were depleted in the blood and gut of people with HIV-1, even with effective antiretroviral therapy. ILC depletion was associated with neutrophil infiltration of the gut lamina propria, type 1 interferon activation, increased microbial translocation and natural killer (NK) cell skewing towards an inflammatory state, with chromatin structure and phenotype typical of WNT transcription factor TCF7-dependent memory T cells. Cytokines that are elevated during acute HIV-1 infection reproduced the ILC and NK cell abnormalities ex vivo. These results show that inflammatory cytokines associated with HIV-1 infection irreversibly disrupt ILCs. This results in loss of gut epithelial integrity, microbial translocation and memory NK cells with heightened inflammatory potential, and explains the chronic inflammation in people with HIV-1.

Cyclophilin A protects HIV-1 from restriction by human TRIM5α.

The HIV-1 capsid (CA) protein lattice encases viral genomic RNA and regulates steps essential to target-cell invasion1. Cyclophilin A (CypA) has interacted with the CA of lentiviruses related to HIV-1 for millions of years2-7. Disruption of the CA-CypA interaction decreases HIV-1 infectivity in human cells8-12 but stimulates infectivity in non-human primate cells13-15. Genetic and biochemical data suggest that CypA protects HIV-1 from a CA-specific restriction factor in human cells16-20. Discovery of the CA-specific restriction factor tripartite-containing motif 5α (TRIM5α)21 and multiple, independently derived, TRIM5-CypA fusion genes4,5,15,22-26 pointed to human TRIM5α being the CypA-sensitive restriction factor. However, HIV-1 restriction by human TRIM5α in tumour cell lines is minimal21 and inhibition of such activity by CypA has not been detected27. Here, by exploiting reverse genetic tools optimized for primary human blood cells, we demonstrate that disruption of the CA-CypA interaction renders HIV-1 susceptible to potent restriction by human TRIM5α, with the block occurring before reverse transcription. Endogenous TRIM5α associated with virion cores as they entered the cytoplasm, but only when the CA-CypA interaction was disrupted. These experiments resolve the long-standing mystery of the role of CypA in HIV-1 replication by demonstrating that this ubiquitous cellular protein shields HIV-1 from previously inapparent restriction by human TRIM5α.

TRIM5α Restricts Flavivirus Replication by Targeting the Viral Protease for Proteasomal Degradation.

Tripartite motif-containing protein 5α (TRIM5α) is a cellular antiviral restriction factor that prevents early events in retrovirus replication. The activity of TRIM5α is thought to be limited to retroviruses as a result of highly specific interactions with capsid lattices. In contrast to this current understanding, we show that both human and rhesus macaque TRIM5α suppress replication of specific flaviviruses. Multiple viruses in the tick-borne encephalitis complex are sensitive to TRIM5α-dependent restriction, but mosquito-borne flaviviruses, including yellow fever, dengue, and Zika viruses, are resistant. TRIM5α suppresses replication by binding to the viral protease NS2B/3 to promote its K48-linked ubiquitination and proteasomal degradation. Importantly, TRIM5α contributes to the antiviral function of IFN-I against sensitive flaviviruses in human cells. Thus, TRIM5α possesses remarkable plasticity in the recognition of diverse virus families, with the potential to influence human susceptibility to emerging flaviviruses of global concern.

The snoRNA target of t(4;14) in multiple myeloma regulates ribosome biogenesis.

The orphan small nucleolar RNA (snoRNA) ACA11 is overexpressed as a result of the t(4;14) chromosomal translocation in multiple myeloma (MM), increases reactive oxygen species, and drives cell proliferation. Like other snoRNAs, ACA11 is predominantly localized to a sub-nuclear organelle, the nucleolus. We hypothesized that increased ACA11 expression would increase ribosome biogenesis and protein synthesis. We found that ACA11 overexpression in MM cells increased nucleolar area and number as well as silver-binding nucleolar organizing regions (AgNORs). Supporting these data, samples from t(4;14)-positive patients had higher AgNORs scores than t(4;14)-negative samples. ACA11 also upregulated ribosome production, pre-47S rRNA synthesis, and protein synthesis in a ROS-dependent manner. Lastly, ACA11 overexpression enhanced the response to proteasome inhibitor in MM cells, while no effect was found in response to high doses of melphalan. Together, these data demonstrate that ACA11 stimulates ribosome biogenesis and influences responses to chemotherapy. ACA11 may be a useful target to individualize the treatment for t(4;14)-positive myeloma patients.

Altered Hypothalamus-Pituitary-Adrenal Axis Function: A Potential Underlying Biological Pathway for Multiple Concurrent Symptoms in Patients With Advanced Lung Cancer.

OBJECTIVE: Patients with advanced cancer commonly experience multiple symptoms that present as groups or clusters. The present study aimed to examine whether hypothalamus-pituitary-adrenal (HPA) axis dysfunction underlies the concurrent multiple symptoms in patients with advanced cancer. METHODS: Patients' cortisol levels were determined in saliva samples collected after awakening (0, 30, and 60 minutes after awakening) and at nighttime (21:00-22:00 PM) from 46 patients with lung cancer (15.2% women), with a mean (standard deviation) age of 64.3 (9.2) years and 47 healthy participants (53.2% women; age = 62.0 [4.6] years). Cancer-related symptoms were measured using the M.D. Anderson Symptom Inventory (MDASI). RESULTS: Compared with healthy participants, patients showed a significantly reduced cortisol awakening response (F(1,364) = 46.2, p < .001) and had flatter diurnal slope of cortisol (larger ß values) (mean [standard error of the mean] = -0.64 [0.06] versus -0.18 [0.05], p < .001). Altered HPA axis function was significantly and adversely associated with performance status and burden of symptoms (all p values < .01). However, each MDASI item varied widely in the degree of association with the HPA axis function. Hierarchical clustering analysis based on Spearman's rank correlation with complete linkage identified that nausea was clustered with vomiting, numbness, and dry mouth, whereas the other nine MDASI core symptoms associated with altered HPA axis function were clustered together. CONCLUSIONS: Altered HPA axis function may be a possible biological pathway that can explain the concurrence of core symptoms in patients with advanced lung cancer.

Intron-containing RNA from the HIV-1 provirus activates type I interferon and inflammatory cytokines.

HIV-1-infected people who take drugs that suppress viremia to undetectable levels are protected from developing AIDS. Nonetheless, HIV-1 establishes proviruses in long-lived CD4+ memory T cells, and perhaps other cell types, that preclude elimination of the virus even after years of continuous antiviral therapy. Here we show that the HIV-1 provirus activates innate immune signaling in isolated dendritic cells, macrophages, and CD4+ T cells. Immune activation requires transcription from the HIV-1 provirus and expression of CRM1-dependent, Rev-dependent, RRE-containing, unspliced HIV-1 RNA. If rev is provided in trans, all HIV-1 coding sequences are dispensable for activation except those cis-acting sequences required for replication or splicing. Our results indicate that the complex, post-transcriptional regulation intrinsic to HIV-1 RNA is detected by the innate immune system as a danger signal, and that drugs which disrupt HIV-1 transcription or HIV-1 RNA metabolism would add qualitative benefit to current antiviral drug regimens.

Interactions between the mRNA and Rps3/uS3 at the entry tunnel of the ribosomal small subunit are important for no-go decay.

No-go Decay (NGD) is a process that has evolved to deal with stalled ribosomes resulting from structural blocks or aberrant mRNAs. The process is distinguished by an endonucleolytic cleavage prior to degradation of the transcript. While many of the details of the pathway have been described, the identity of the endonuclease remains unknown. Here we identify residues of the small subunit ribosomal protein Rps3 that are important for NGD by affecting the cleavage reaction. Mutation of residues within the ribosomal entry tunnel that contact the incoming mRNA leads to significantly reduced accumulation of cleavage products, independent of the type of stall sequence, and renders cells sensitive to damaging agents thought to trigger NGD. These phenotypes are distinct from those seen in combination with other NGD factors, suggesting a separate role for Rps3 in NGD. Conversely, ribosomal proteins ubiquitination is not affected by rps3 mutations, indicating that upstream ribosome quality control (RQC) events are not dependent on these residues. Together, these results suggest that Rps3 is important for quality control on the ribosome and strongly supports the notion that the ribosome itself plays a central role in the endonucleolytic cleavage reaction during NGD.