bluuebunny/crossref_metadata_2025 huggingface dataset:
Profiling daptomycin resistance among diverse methicillin-resistant
Staphylococcus aureus
lineages in China
Authors: Jiang Shengnan , Chen Mengzhen , Zhang Junxiong , Ba Xiaoliang , Zhang Hao , Hong Yueqin , Sun Lu , Wang Zhengan , Zhuang Hemu , Zhu Feiteng , Chen Yiyi , Wang Haiping , Zhao Feng , Chen Yan , Yu Yunsong , Ji Shujuan
Published: October 2023

Daptomycin (DAP) is effective against methicillin-resistant
Staphylococcus aureus
(MRSA). However, reduced susceptibility to DAP in MRSA may lead to treatment failures. We aim to determine the distribution of DAP minimum inhibitory concentrations (MICs) and DAP heteroresistance (hDAP) among MRSA lineages in China. A total of 472 clinical MRSA isolates collected from 2015 to 2017 in China were examined for DAP susceptibility. All isolates (
n
= 472) were found to be DAP susceptible, but 35.17% (166/472) of them exhibited a high DAP MIC (MIC >0.5 µg/mL). The high DAP MIC group contained a larger proportion of isolates with a higher vancomycin or teicoplanin MIC (>1.5 µg/mL) than the low DAP MIC group (19.3% vs 7.8%,
P
< 0.001; 22.3% vs 8.2%,
P
< 0.001). We compared the clonal complex (CC) distributions and clinical characteristics in MRSA isolates stratified by DAP MIC. CC5 isolates were less susceptible to DAP (MIC
50
= 1 µg/mL) than CC59 isolates (MIC
50
= 0.5 µg/mL,
P
< 0.001). Population analysis profiling revealed that 5 of 10 ST5 and ST59 DAP-susceptible MRSA isolates investigated exhibited hDAP. The results also showed that CC5 MRSA with an
agrA
mutation (I238K) had a higher DAP MIC than those with a wild-type
agrA
(
P
< 0.001). The
agrA
-I238K mutation was found to be associated with
agr
dysfunction as indicated by the loss of δ-hemolysin production. In addition,
agr/psmα
defectiveness was associated with hDAP in MRSA. Whole-genome sequencing analysis revealed mutations in
mprF
and
walR
/
walK
in DAP-resistant subpopulations, and most DAP-resistant subpopulations (6/8, 75%) were stable. Our study suggests that the increased DAP resistance and hDAP in MRSA may threaten the effectiveness against MRSA infections.
Semirational engineering of
Cytophaga hutchinsonii
polyphosphate kinase for developing a cost-effective, robust, and efficient adenosine 5′-triphosphate regeneration system
Authors: Shen Qi , Zhang Shi-Jia , Xu Bin-Hui , Chen Zhi-Yu , Peng Feng , Xiong Neng , Xue Ya-Ping , Zheng Yu-Guo
Published: October 2023

Adenosine 5′-triphosphate (ATP) is a substrate for the biological synthesis of various valuable compounds, such as pharmaceuticals and agrochemicals. To make these biocatalytic processes more economically valuable, several ATP regeneration systems comprising enzymes and phosphate donors were developed. Due to their ability to synthesize ATP from both 5′-diphosphate and adenosine 5′-monophosphate, polyphosphate kinase 2 class III (PPK2-III) enzymes such as
Cytophaga hutchinsonii
PPK (
Ch
PPK) have attracted considerable attention in the construction of ATP regeneration systems. Furthermore, PPK2-III enzymes employ inorganic polyphosphate, which is a low-cost and stable substrate, as the phosphate donor. To facilitate the application of the PPK2-III ATP regeneration system in biocatalytic processes depending on ATP, a semirational strategy coupled with a high-throughput screening assay based on a fluorescent sensor was performed to engineer
Ch
PPK. Saturation mutagenesis was performed on 16 critical residues of
Ch
PPK. After screening approximately 4,800 colonies, nine single amino acid variants exhibited more than threefold increased activities than wild-type
Ch
PPK. Beneficial mutations were subsequently recombined, resulting in a quadruple variant (
Ch
PPK/A79G/S106C/I108F/L285P), compared with wild-type
Ch
PPK, displaying 18.8-fold enhanced activity and better stability at an elevated temperature and under acidic conditions. The introduction of this variant
Ch
PPK/A79G/S106C/I108F/L285P in the biological synthesis of nicotinamide mononucleotide catalyzed by phosphoribosyl pyrophosphate synthetase and nicotinamide phosphoribosyltransferase increased the yield by approximately threefold compared with wild-type
Ch
PPK. Therefore, the ATP regeneration system described may have implications for bioconversions requiring ATP.

IMPORTANCE

The adenosine 5′-triphosphate (ATP) regeneration system can significantly reduce the cost of many biocatalytic processes. Numerous studies have endeavored to utilize the ATP regeneration system based on
Cytophaga hutchinsonii
PPK (
Ch
PPK). However, the wild-type
Ch
PPK enzyme possesses limitations such as low enzymatic activity, poor stability, and limited substrate tolerance, impeding its application in catalytic reactions. To enhance the performance of
Ch
PPK, we employed a semi-rational design approach to obtain the variant
Ch
PPK/A79G/S106C/I108F/L285P. The enzymatic kinetic parameters and the catalytic performance in the synthesis of nicotinamide mononucleotide demonstrated that the variant
Ch
PPK/A79G/S106C/I108F/L285P exhibited superior enzymatic properties than the wild-type enzyme. All data indicated that our engineered ATP regeneration system holds inherent potential for implementation in biocatalytic processes.
Persistence of SARS-CoV-2 and its surrogate, bacteriophage Phi6, on surfaces and in water
Authors: Pitol Ana K. , Venkatesan Samiksha , Hoptroff Michael , Hughes Grant L.
Published: October 2023

The COVID-19 pandemic spurred research on the persistence of infectious SARS-CoV-2 and its surrogates, including bacteriophage Phi6, in environmental reservoirs. Despite the wide use of Phi6, side-by-side comparisons between Phi6 and SARS-CoV-2 are limited. Here, we quantified the persistence of SARS-CoV-2 and Phi6 on surfaces (PVC plastic and stainless steel), using an initial inoculum of 10
3
plaque forming unit per surface, and evaluated the influence of four commonly used deposition solutions on viral persistence. In addition, we quantified the persistence of SARS-CoV-2 and Phi6 in water. Our findings revealed that Phi6 had a significantly longer half-life than SARS-CoV-2 in water and on surfaces. Phi6 persisted 34 hours in water compared with 13 hours for SARS-CoV-2. Viral persistence on surfaces was significantly influenced by the virus used and the deposition solution but not by the surface material. Phi6 remained infectious significantly longer than SARS-CoV-2 when the inoculation solution was culture media and saliva, leading to half-lives between 9 hours and 2 weeks for Phi6, compared to 0.5–2 hours for SARS-CoV-2. Using phosphate-buffered saline as a deposition solution led to half-lives shorter than 4 hours for both viruses on all surfaces. Our results indicate that bacteriophage Phi6 may lead to an overestimate of infectiousness for studies quantifying SARS-CoV-2 persistence on surfaces and water and highlight the importance of using appropriate deposition solutions when evaluating viral persistence on surfaces.

IMPORTANCE

The COVID-19 pandemic spurred research on the persistence of SARS-CoV-2 and its surrogates. Here we highlight the importance of evaluating viral surrogates and experimental methodologies when studying pathogen survival in the environment.
Evaluation of the Cepheid 3-gene host response blood test for tuberculosis diagnosis and treatment response monitoring in a primary-level clinic in rural China
Authors: Li Meng , Qiu Yong , Guo Mingcheng , Qu Rong , Tian Fajun , Wang Gengsheng , Wang Ya , Ma Jian , Liu Siyuan , Takiff Howard , Tang Yi-Wei , Gao Qian
Published: October 2023

A rapid, accurate, non-sputum-based triage test for diagnosing tuberculosis (TB) is a high-priority need. Cepheid developed a novel prototype blood test, Xpert
Mycobacterium tuberculosis
Host Response (Xpert-MTB-HR), which generates a TB score based on the mRNA expression of three genes. We conducted a case-control study with prospective recruitment to evaluate its accuracy in the clinic of the Wusheng County Centers for Disease Prevention and Control in China. We enrolled 149 TB patients, 248 other respiratory diseases (ORD) patients, and 193 healthy controls. In addition, whole-blood samples taken from TB patients after 2, 5, and 6 months of treatment were tested with Xpert-MTB-HR to evaluate its ability to monitor treatment response. Xpert-MTB-HR discriminated between TB and healthy controls with an area under the curve (AUC) of 0.912 (95% CI, 0.878–0.945). With the specificity of 70% envisioned for a triage test, its sensitivity was 90.1% (84.9%–94.6%). Xpert-MTB-HR discriminated between TB and ORD with an AUC of 0.798 (0.750–0.847), and at specificity of 70%, the sensitivity was only 75.8% (68.5%–82.8%). In patients determined by Ultra to have medium or high sputum bacillary loads, with specificity of 70%, the sensitivity for discriminating patients with TB from healthy controls was 100.0% (100.0–100.0) and from patients with ORD, 95.1% (89.8–100.0). The TB scores generally increased by 2 months of treatment and then remained stable. Xpert-MTB-HR met the criteria for a triage test to discriminate between TB and healthy controls, but not between TB and ORD, except when limited to patients with high sputum bacillary loads. Xpert-MTB-HR showed promise for monitoring response to treatment but needs to be further evaluated in larger prospective studies.
Protein kinase Cdc7 supports viral replication by phosphorylating
Avibirnavirus
VP3 protein
Authors: Deng Tingjuan , Du Liuyang , Ding Shuxiang , Peng Xiran , Chen Wenjing , Yan Yan , Hu Boli , Zhou Jiyong
Published: October 2023

Phosphorylation is an important post-translational modification that has crucial roles in diverse cellular biological pathways and in various viral life cycles. Here, we report that the VP3 protein, the major inner capsid protein of
Avibirnavirus
infectious bursal disease virus (IBDV), regulates viral replication by phosphorylation during infection. Our data showed that IBDV infection induced the upregulation of Cdc7 expression, followed by phosphorylation of residue serine 13 (S13) on VP3 by interaction. Virus rescue showed that phosphorylation of VP3 at site S13 enhanced the replication ability of IBDV. Moreover, further study demonstrated that the increase of IBDV replication was relevant to the addition of negative charge of phosphoserine on VP3. Meanwhile, the knockdown of Cdc7 severely blocked the phosphorylation level of VP3 S13 and impaired the replication of wild-type but not S13A mutant recombinant IBDV. Thus, we demonstrated that Cdc7 was a crucial enzyme that phosphorylated IBDV VP3 at site serine 13 for viral proliferation.

IMPORTANCE

The
Avibirnavirus
infectious bursal disease virus is still an important agent which largely threatens global poultry farming industry economics. VP3 is a multifunctional scaffold structural protein that is involved in virus morphogenesis and the regulation of diverse cellular signaling pathways. However, little is known about the roles of VP3 phosphorylation during the IBDV life cycle. In this study, we determined that IBDV infection induced the upregulation of Cdc7 expression and phosphorylated the VP3 Ser13 site to promote viral replication. Moreover, we confirmed that the negative charge addition of phosphoserine on VP3 at the S13 site was essential for IBDV proliferation. This study provides novel insight into the molecular mechanisms of VP3 phosphorylation-mediated regulation of IBDV replication.
Tectonics of the Paleoproterozoic Rinkian orogen, central West Greenland
Authors: Guarnieri Pierpaolo , Rosa Diogo , Thrane Kristine , Kokfelt Thomas F. , Sørensen Erik V. , DeWolfe Michelle Y. , Baker Nigel
Published: October 2023

A new tectonic model is presented to explain the tectono-stratigraphic evolution of the Paleoproterozoic Karrat Group in central West Greenland and the polyphase deformation, magmatism, and metamorphism of the Rinkian orogen. Sedimentation of the Karrat Group initiated after ca. 2000 Ma in an intracratonic rift basin with basal quartzites overlying Archean gneisses of the Rae craton. Rift-related alkaline volcanic rocks and synrift siliciclastic sediments were deposited in the north while an evaporite-carbonate platform developed in the south. The rift basin evolved to a back-arc basin, with associated subalkaline volcanic rocks, concomitant with the intrusion of arc-related granitoids of the Prøven igneous complex along the basal contact of the Karrat Group between 1900 Ma and 1850 Ma. The Karrat Group and magmatic arc rocks underwent metamorphism ca. 1830−1800 Ma during the collisional phase of the Rinkian orogeny. The metamorphic grade of the Karrat Group increases from greenschist facies in the south to granulite facies in the north, where it is marked by migmatization and emplacement of S-type leucogranites. Extensive east-southeastward thrust emplacement and fold vergence characterize the Rinkian orogen south of the Prøven igneous complex magmatic arc, where the arc-continent collision is established along a top-to-the-ESE shear zone postdating the Rinkian metamorphism. In summary, the Karrat Basin developed on the upper plate above eastward-dipping subduction and, together with the Rinkian orogen, represents the result of arc-continent collision that initiated the structuring of a back-arc fold-and-thrust system antithetic to the subduction system.
Modern Approaches to the Extraction and Preconcentration of Biologically Active Compounds from Plant Samples by Microextraction Methods for Their Determination by Chromatography–Mass Spectrometry
Authors: Bessonova E. A. , Karpitskii D. A. , Kartsova L. A.
Published: October 2023

The review considers the main trends in actively developing methods of solid-phase and liquid–liquid microextraction for the extraction, purification, and preconcentration of analytes from medicinal plants and plant materials, the use of new extractants and approaches to the preparation of samples of plant origin, and their compatibility with mass-spectrometric detection. Particular attention is paid to the analytical capabilities, advantages, and limitations of each of the approaches to extracting analytes from plant materials for the subsequent analysis of the obtained extracts by chromatography–mass spectrometry.
Evaluation of a self-imaging OCT for remote diagnosis and monitoring of retinal diseases
Authors: Liu Zitian , Huang Wenyong , Wang Zhenyu , Jin Ling , Congdon Nathan , Zheng Yingfeng , Chen Shida , Liu Yizhi
Published: October 2023

Objectives

To evaluate the feasibility and accuracy of a portable, self-imaging optical coherence tomography (OCT) for measuring central subfield thickness (CST) and achieving diagnostic concordance for retinal lesions compared with clinic-based spectral-domain OCT (SD-OCT).

Methods

This comparative, cross-sectional study was conducted between August 2020 and February 2021. Two groups of adult participants were recruited: (1) a selected cohort of 160 participants with confirmed diagnosis and (2) a consecutive cohort of 315 participants recruited randomly. All participants underwent self-imaging OCT examination, as well as standard OCT examination. CST was automatically calculated for comparisons between the two OCT devices. Diagnostic concordance for retinal lesions and the success rate of self-imaging were assessed within the consecutive cohort.

Results

In the selected cohort, self-imaging OCT images yielded consistent CST with SD-OCT, with a mean difference of 0.1±7.7 µm for normal eyes, 4.9±10.6 µm for macular oedema, −1.3±9.5 µm for choroidal neovascularisation, 5.0±7.8 µm for epiretinal membrane. The self-imaging OCT also demonstrated good repeatability, with a mean test–retest difference in CST of 0.7±3.9 µm and limits of agreement ranging from −6.9 to 8.3 µm. Additionally, within the consecutive cohort, interdevice κ values ranged for detecting various retinal lesions ranged from 0.8 to 1.0, except in the cases of retinal detachment (κ=0.5). All eyes (100%) in the selected cohort and 242 eyes (76.8%) in the consecutive cohort successfully completed self-imaging. Participants spent less time on self-imaging compared with SD-OCT operated by a technician (66.7±20.1 vs 73.3±32.5, p<0.01). A majority of participants (90%) found the self-imaging process ‘easy’ and ‘comfortable’.

Conclusions and relevance

This study demonstrates that our self-imaging OCT and clinical-used SD-OCT are highly consistent not only in measuring the CST but also in identifying most retinal lesions.
Stent retriever for Tandem Acute Revascularization Technique (START): a novel technique for the endovascular management of tandem occlusions
Authors: Fageeh Areej , Zur Gil , Diouf Ange , La Russa Daniel , Drake Brian , P dos Santos Marlise , Caron Katie , Birch Nicole , Karwaski Stephen , Trussler Laurie , Miller Elizabeth , Fantaneanu Tadeu , Varghaei Parizad , Walker Gregory , Lesiuk Howard , Fahed Robert
Published: October 2023

Tandem occlusions, characterized by the simultaneous presence of an intracranial large vessel occlusion and extracranial carotid artery stenosis or occlusion,1 pose a unique endovascular challenge.2 3 Typically, the extracranial occlusion is a result of atherosclerotic plaque; however, dissections are also a possible cause. It is currently uncertain whether an intracranial first approach or an extracranial first approach should be employed.4 5 A new technique has been developed which allows for the simultaneous treatment of both the intracranial and the extracranial lesion.6 We describe a variation of this technique: the stent retriever for tandem acute revascularization technique (START), which consists of simultaneously treating the intracranial lesion with stent retriever and contact aspiration, and the extracranial lesion with balloon angioplasty. We present a technical video explaining all the steps of START.(video 1)

Video 1

Description and example of the START.
Estimating own-price and cross-price elasticity of cigarette consumption by price tiers in Bangladesh
Authors: Shimul Shafiun N , Hussain A K M Ghulam , Nargis Nigar
Published: October 2023

Objectives

The overall price elasticity of cigarette consumption in Bangladesh has been studied extensively. The estimates of price elasticity by price tiers are not available in the existing literature.

Methods

Using cohort data of nearly 6000 individuals from the International Tobacco Control Bangladesh survey, this study estimated the own-price and cross-price elasticity and income elasticity of cigarette demand by price tiers in Bangladesh. The elasticity was estimated in three stages of consumer decisions: whether to smoke, which brand to smoke and finally, how many cigarettes to smoke per day. The decision to smoke cigarettes and the choice of cigarette brands were modelled using instrumental variable probability regression. The cigarette consumption per day was modelled using seemingly unrelated regression.

Results

The price elasticity of cigarette smoking prevalence with respect to the price of low-price cigarettes is −0.0487. The total elasticity for low-price cigarette consumption with respect to its own price is −0.1678. The own-price elasticity of smoking intensity of high-priced brands is −0.2512. The cross-price elasticity of low-price cigarette consumption with respect to high-price brand prices is 0.2643. The income elasticity of smoking prevalence overall is 0.0564. The income elasticity of daily consumption of low-price cigarettes is −0.1934 and for high-price cigarettes, it is 1.4044. The total income elasticity is 1.4608 for high-price cigarettes.

Conclusion

A cigarette tax policy that raises the prices of both low-price and high-price brands—but increases prices in the low-price tier at a faster rate than in the high-price tier and increases prices of all brands at a pace faster than income growth—can effectively reduce cigarette consumption in Bangladesh.

JEL codes

H29, L66, I18.
Security of Electrical, Optical, and Wireless On-chip Interconnects: A Survey
Authors: Weerasena Hansika , Mishra Prabhat
Published: October 2023

The advancement of manufacturing technologies has enabled the integration of more intellectual property (IP) cores on the same system-on-chip (SoC). Scalable and high throughput on-chip communication architecture has become a vital component in today’s SoCs. Diverse technologies such as electrical, wireless, optical, and hybrid are available for on-chip communication with different architectures supporting them. On-chip communication sub-system is shared across all the IPs and continuously used throughout the lifetime of the SoC. Therefore, the security of the on-chip communication is crucial, because exploiting any vulnerability would be a goldmine for an attacker. In this survey, we provide a comprehensive review of threat models, attacks, and countermeasures over diverse on-chip communication technologies as well as sophisticated architectures.
Real-time Multi-CNN-based Emotion Recognition System for Evaluating Museum Visitors’ Satisfaction
Authors: Kwon Do Hyung , Yu Jeong Min
Published: October 2023

Conventional studies on the satisfaction of museum visitors focus on collecting information through surveys to provide a one-way service to visitors, and thus it is impossible to obtain feedback on the real-time satisfaction of visitors who are experiencing the museum exhibition program. In addition, museum practitioners lack research on automated ways to evaluate a produced content program's lifecycle and its appropriateness. To overcome these problems, we propose a novel multi-convolutional neural network, called VimoNet, which is able to recognize visitors emotions automatically in real-time based on their facial expressions and body gestures. Furthermore, we design a user preference model of content and a framework to obtain feedback on content improvement for providing personalized digital cultural heritage content to visitors. Specifically, we define seven emotions of visitors and build a dataset of visitor facial expressions and gestures with respect to the emotions. Using the dataset, we proceed with feature fusion of face and gesture images trained on the DenseNet-201 and VGG-16 models for generating a combined emotion recognition model. From the results of the experiment, VimoNet achieved a classification accuracy of 84.10%, providing 7.60% and 14.31% improvement, respectively, over a single face and body gesture-based method of emotion classification performance. It is thus possible to automatically capture the emotions of museum visitors via VimoNet, and we confirm its feasibility through a case study with respect to digital content of cultural heritage.
Are IT Workers from Mars? An Examination of Their National Culture Dimensions
Authors: Palvia Prashant , Ghosh Jaideep , Jacks Tim , Serenko Alexander , Turan Aykut H.
Published: October 2023

The information technology (IT) workforce is characterized by several unique and contextual factors, such as the technology, the occupation itself, and the human factors. Among the human factors, global information systems (IS) studies have examined the role of national culture to explain many workforce differences and nuances across nations. In such cross-cultural research, IS researchers have primarily utilized the published scores of national culture dimensions as provided by the preeminent social psychologist and culture scholar Geert Hofstede and have applied them to various IT populations within a country. Given that the IT profession is unique in many respects, and there is cultural heterogeneity within a country, our study embarked on independently measuring and verifying the national culture values of IT employees in 37 countries. By using the original Hofstede scales, scores were obtained on five national culture dimensions: power distance, uncertainty avoidance, individualism, masculinity, and long-term orientation. We found significant differences between the national culture scores of IT employees and those available in the literature for the general population. Our results are novel and have profound significance. There are major implications for both past and future studies in cross-cultural research as well as for practitioners who interpret and utilize the findings of such research.
Freelisting: A Research Guide for Information Systems Researchers
Authors: Califf Christopher B. , Stumpf T. S.
Published: October 2023

Freelisting is a widely used ethnographic data elicitation and analysis technique that can help researchers quickly and systematically collect and quantify qualitative cultural data. The paper discusses the value of freelisting for IS researchers who conduct qualitative and/or quantitative research. Specifically, the paper provides an overview of freelisting; examines how prior research has used freelisting; gives step-by-step instructions about how to collect, analyze, and present freelist data; and describes the benefits of freelisting in the context of IS research. The following items are explained in detail: (1) how to understand when freelisting can be an appropriate choice; (2) the different types of freelists; (3) how to focus freelists on a specific phenomenon; (4) how to analyze freelists; and (5) how to triangulate freelist data. Additionally, the paper details seven ways IS researchers can benefit from using freelisting: (1) creating culturally salient surveys; (2) revisiting or generating new field-specific theories; (3) enhancing a mixed-method research design; (4) uncovering information about cultural similarities and differences in intracultural and cross-cultural research designs; (5) consciously considering the importance of context; (6) developing more robust quantitative analysis techniques; and (7) eliciting culturally relevant data about development or refinement of technology in applied settings.
Differential Evolution with a Level‐Based Learning Strategy for Multimodal Optimization
Authors: Zhang Yuhui , Wei Wenhong , Zhao Tiezhu , Wang Zijia
Published: October 2023

Multimodal optimization aims at efficiently finding multiple optimal solutions of a problem. Owing to the population‐based search mechanism, evolutionary algorithms (EAs) are becoming increasingly popular in solving multimodal optimization problems (MOPs). Most existing work focuses on designing and incorporating niching techniques into EAs so that multiple subpopulations can be formed and assigned to locate different optima. To further enhance the exploration and exploitation abilities of existing EAs, this paper developed a multimodal level‐based learning strategy. The basic idea is that individuals should be treated differently according to their positions in the subpopulation. In the evolutionary process, a subpopulation is formed for each candidate solution by grouping its neighboring solutions. Then, individuals in the subpopulation are sorted according to their fitness. Subsequently, the multimodal level‐based learning strategy applies different mutation operators to different individuals according to their rankings. Experiments are conducted on a set of benchmark problems to verify the efficacy of the multimodal level‐based learning strategy. The results show that the proposed learning strategy can significantly enhance the performance of the existing algorithm. In addition, the algorithm integrated with the proposed strategy is applied to the task of finding multiple roots of nonlinear equation systems (NESs). The results indicate that with the support of the proposed learning strategy, the integrated algorithm compares favorably with state‐of‐the‐art root finding algorithms.
Superb Bifunctional Water Electrolysis Activities of Carbon Nanotube-Decorated Lanthanum Hydroxide Nanocomposites
Authors: Sekar Sankar , Park Seoyeon , Jung Jiwoon , Lee Sejoon
Published: October 2023

For highly efficient hydrogen production from electrocatalytic water electrolysis, developing a high-fidelity electrocatalyst is pivotal. Herein, we demonstrated the excellent water-splitting performances of the carbon allotrope-decorated rare earth oxide nanocomposite system, which was composed of lanthanum hydroxide (La(OH)3) and carbon nanotube (CNT). The nanocomposites of CNT-La(OH)3 were fabricated via facile ultrasonication using La(OH)3 nanoparticles and CNT nanofibers, and they exhibited excellent bifunctional water-splitting activities. For the hydrogen evolution reaction, CNT-La(OH)3 showed low values of both overpotential (150 mV) and Tafel slope (113 mV/dec) in 1 M KOH at -10 mA/cm2. Additionally, for the oxygen evolution reaction, CNT-La(OH)3 also displayed small values for their overpotential (310 mV) as well as the Tafel slope (39 mV/dec). Furthermore, both bifunctional hydrogen- and oxygen-evolution reactions were confirmed to be stable in chronopotentiometric tests. From the material characterization and the electrochemical characterization, such excellent bifunctional water electrolysis performances were ascribed to the synergetic effects of hybridization of La(OH)3 (i.e., a large number of electrochemically active sites of 304 cm2) and CNT (i.e., high charge transport conductivity). The results specify that the present CNT-La(OH)3 nanocomposite system possesses ample aptitude as a superior electrocatalyst for next-generation hydrogen production technology.
Supplementary Table S2 from Mitochondrial-Encoded Complex I Impairment Induces a Targetable Dependency on Aerobic Fermentation in Hürthle Cell Carcinoma of the Thyroid
Authors: Frank Anderson R. , Li Vicky , Shelton Spencer D. , Kim Jiwoong , Stott Gordon M. , Neckers Leonard M. , Xie Yang , Williams Noelle S. , Mishra Prashant , McFadden David G.
Published: October 2023

Supplementary Table S2 shows nuclear genome variants identified in NCI-237-R PDX through whole-exome sequencing.
Supplementary Table S1 from Mitochondrial-Encoded Complex I Impairment Induces a Targetable Dependency on Aerobic Fermentation in Hürthle Cell Carcinoma of the Thyroid
Authors: Frank Anderson R. , Li Vicky , Shelton Spencer D. , Kim Jiwoong , Stott Gordon M. , Neckers Leonard M. , Xie Yang , Williams Noelle S. , Mishra Prashant , McFadden David G.
Published: October 2023

Supplementary Table S1 shows key mtDNA mutations identified through whole-exome sequencing and targeted mtDNA sequencing.
Supplementary Figure S1-S6 from Mitochondrial-Encoded Complex I Impairment Induces a Targetable Dependency on Aerobic Fermentation in Hürthle Cell Carcinoma of the Thyroid
Authors: Frank Anderson R. , Li Vicky , Shelton Spencer D. , Kim Jiwoong , Stott Gordon M. , Neckers Leonard M. , Xie Yang , Williams Noelle S. , Mishra Prashant , McFadden David G.
Published: October 2023

Supplementary Figure S1 shows validation of key genetic features in NCI-237 and metabolic characterization of thyroid cancer cell lines. Supplementary Figure S2 shows growth curves and depletion/enrichment plots for pooled CRISPR-Cas9 screens. Supplementary Figure S3 shows validation of complex I impairment conferring sensitivity to LDH inhibition. Supplementary Figure S4 shows metabolic profiling of LDH inhibition in NCI-237 cells. Supplementary Figure S5 shows the validation of NADH-oxidizing enzymes and that NAD+ regeneration rescues LDH inhibition. Supplementary Figure S6 shows that LDH inhibition impairs NCI-237-R PDX proliferation.
Figure S7 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

ATGL PLIN5 induction
Figure S6 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

LNCaP DHT + NAC + Sigma1 shR proliferation
Figure S6 from Sigma1 Regulates Lipid Droplet–mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

LNCaP DHT + NAC + Sigma1 shR proliferation
Figure S5 from Sigma1 Regulates Lipid Droplet–mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

VCaP ROS and autophagy
Figure S5 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

VCaP ROS and autophagy
Figure S3 from Sigma1 Regulates Lipid Droplet–mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

VCaP data
Figure S2 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

ATG5 and 7 shRNA KD
Figure S2 from Sigma1 Regulates Lipid Droplet–mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

ATG5 and 7 shRNA KD
Figure S1 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

Mander Coefficient of LD-auophagosome overlap in Sigma1 shR KD cells.
Figure S1 from Sigma1 Regulates Lipid Droplet–mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

Mander Coefficient of LD-auophagosome overlap in Sigma1 shR KD cells.
FIGURE 8 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

Working Model. Sigma1 targeting disrupts LD-mediated redox homeostasis in prostate cancer cells. LD, lipid droplet; TG, triacylglycerol; DHT, dihydrotestosterone; ROS, reactive oxygen species.
FIGURE 7 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

GSEA and correlation analysis of Sigma1/SIGMAR1 in prostate tumors. GSEA using Adipogenesis and ROS Pathway Hallmark gene sets on localized prostate tumors from TCGA (A; 60) and metastatic prostate tumors from SU2C/PCF Dream Team (B; 61). C, Heat map of normalized enrichment scores from primary, metastatic, or benign prostate tissue utilizing TCGA, MSKCC, SU2C/PCF Dream Team, and FHCRC datasets (60, 61, 63). D, Single gene correlation analysis between SIGMAR1 and PNPLA2, BCSL2, and PLIN5 using Z-scores from published primary prostate tumor datasets (60, 63, 64).
FIGURE 6 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

Sigma1 small-molecule inhibition disrupts GSH ratios and increases ROS levels in LNCaP and C4-2 cells. A, Quantification of CM-H2DCFDA signal per cell in LNCaP cells cultured in CSS medium for 3 days and treated for 3 days with DHT (1 nmol/L) alone or combined with 10 µmol/L IPAG for the last 16 hours. Data are presented as mean ± SEM from three independent experiments, *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001; ns, no significance. B, Representative fluorescent micrographs showing CM-H2DCFDA levels in LNCaP cells in A. C, Total GSH and GSH:GSSG measurements in LNCaP cells treated as in A. Data are presented as mean ± SEM from three independent experiments. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001; ns, no significance.
FIGURE 4 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

LDs as buffers of DHT induced ROS and DHT promotes ROS homeostasis. A, Confocal micrograph showing HCS LipidTox stained LDs in LNCaP cells cultured in CSS containing medium for 3 days and treated with DMSO (vehicle) and 1 nmol/L DHT alone or combined with 2.5 mmol/L NAC for 3 days. B, LD quantification of LNCaP cells from A. Data represent LDs per cell and error bars represent SEM. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. C, Quantification of ROS, detected with CM-H2DCFDA in LNCaP treated as described above in A. Data are presented as mean ± SEM from at least three independent determinations. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. D, Illustration of concept that DHT initially induces ROS to trigger proliferation (1 day of DHT), and subsequently decreases intracellular ROS levels. LD accumulation is observed as DHT decreases ROS levels. E, Quantification of ROS in control (#1) or Sigma1 shRNA (#5) transduced LNCaP cells treated as described above in A. Each datapoint represents mean CM-H2DCFDA signal per cell from three fields in three independent wells. F, Redox balance. Total GSH levels and ratio of GSH-to-GSSG measured in nonspecific control shRNA (ns) and in Sigma1 shRNA (#5) transduced LNCaP cells treated as described above in A.
FIGURE 4 from Sigma1 Regulates Lipid Droplet–mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

LDs as buffers of DHT induced ROS and DHT promotes ROS homeostasis. A, Confocal micrograph showing HCS LipidTox stained LDs in LNCaP cells cultured in CSS containing medium for 3 days and treated with DMSO (vehicle) and 1 nmol/L DHT alone or combined with 2.5 mmol/L NAC for 3 days. B, LD quantification of LNCaP cells from A. Data represent LDs per cell and error bars represent SEM. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. C, Quantification of ROS, detected with CM-H2DCFDA in LNCaP treated as described above in A. Data are presented as mean ± SEM from at least three independent determinations. *, P < 0.05; **, P < 0.01; ***, P < 0.001; ****, P < 0.0001. D, Illustration of concept that DHT initially induces ROS to trigger proliferation (1 day of DHT), and subsequently decreases intracellular ROS levels. LD accumulation is observed as DHT decreases ROS levels. E, Quantification of ROS in control (#1) or Sigma1 shRNA (#5) transduced LNCaP cells treated as described above in A. Each datapoint represents mean CM-H2DCFDA signal per cell from three fields in three independent wells. F, Redox balance. Total GSH levels and ratio of GSH-to-GSSG measured in nonspecific control shRNA (ns) and in Sigma1 shRNA (#5) transduced LNCaP cells treated as described above in A.
FIGURE 3 from Sigma1 Regulates Lipid Droplet–Mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

Sigma1 KD suppresses DHT induced prostate cancer cell proliferation and tumor growth despite (or due to) increased autophagy. A,In vitro cell proliferation assay of Sigma1 shRNA-transduced LNCaP and C4-2 cells precultured in CSS medium for 3 days and then treated for 3 and 6 days with 1 nmol/L DHT. Live cells were counted by Trypan blue exclusion assay at the start of the time course (day 0), and 3 and 6 days of DHT treatment. Data are represented as fold induction over cells treated with control shRNA at day 0. Datapoints represent mean fold increase in cell number from at least three independent determinations, and error bars represent SEM. Two distinct Sigma1 shRNA clones, #4 and #5, were tested and produced similar results. B, Immunoblots of whole-cell protein extracts from parallel C4-2 cell culture performed in parallel and using same experimental treatment conditions as in A. Data shown for Sigma1 shRNA clone #5 KD C4-2 cell cultures. C, Immunoblot of Sigma1 shRNA clone #4 and #5 transduced C4-2 cells immediately prior to subcutaneous flank implantation into SCID mice. D, C4-2 cells infected with Sigma1 shRNA (#4, #5) and control shRNA (#1) were injected into the right and left flanks of SCID mice. Tumor volume was measured by caliper 12 weeks after implantation, prior to sacrificing the mice. Data are represented as mean volume of six tumors for each condition, and error bars represent SEM. E, Tumor weight was measured at 12 weeks postinjection at the time of harvest. Data are represented as mean volume of six tumors for each condition, and error bars represent SEM. *, P < 0.05; **, P < 0.01. F, Oil Red O staining of control (clone #1) and Sigma1 shRNA (clone #4 and #5) xenografted C4-2 tumors.
Data from Sigma1 Regulates Lipid Droplet–mediated Redox Homeostasis Required for Prostate Cancer Proliferation
Authors: Oyer Halley M. , Steck Alexandra R. , Longen Charles G. , Venkat Sanjana , Bayrak Konuralp , Munger Eleanor B. , Fu Dan , Castagnino Paola A. , Sanders Christina M. , Tancler Nathalia A. , Mai My T. , Myers Justin P. , Schiewer Matthew J. , Chen Nan , Mostaghel Elahe A. , Kim Felix J.
Published: October 2023

Abstract
Lipid droplets (LD) are dynamic organelles that serve as hubs of cellular metabolic processes. Emerging evidence shows that LDs also play a critical role in maintaining redox homeostasis and can mitigate lipid oxidative stress. In multiple cancers, including prostate cancer, LD accumulation is associated with cancer aggressiveness, therapy resistance, and poor clinical outcome. Prostate cancer arises as an androgen receptor (AR)-driven disease. Among its myriad roles, AR mediates the biosynthesis of LDs, induces autophagy, and modulates cellular oxidative stress in a tightly regulated cycle that promotes cell proliferation. The factors regulating the interplay of these metabolic processes downstream of AR remain unclear. Here, we show that Sigma1/SIGMAR1, a unique ligand-operated scaffolding protein, regulates LD metabolism in prostate cancer cells. Sigma1 inhibition triggers lipophagy, an LD selective form of autophagy, to prevent accumulation of LDs which normally act to sequester toxic levels of reactive oxygen species (ROS). This disrupts the interplay between LDs, autophagy, buffering of oxidative stress and redox homeostasis, and results in the suppression of cell proliferation in vitro and tumor growth in vivo. Consistent with these experimental results, SIGMAR1 transcripts are strongly associated with lipid metabolism and ROS pathways in prostate tumors. Altogether, these data reveal a novel, pharmacologically responsive role for Sigma1 in regulating the redox homeostasis required by oncogenic metabolic programs that drive prostate cancer proliferation.
Significance:
To proliferate, cancer cells must maintain productive metabolic and oxidative stress (eustress) while mitigating destructive, uncontrolled oxidative stress (distress). LDs are metabolic hubs that enable adaptive responses to promote eustress. Targeting the unique Sigma1 protein can trigger distress by disrupting the LD-mediated homeostasis required for proliferation.