Ribosomal protein s15 phosphorylation mediates LRRK2 neurodegeneration in Parkinson's disease.

Mutations in leucine-rich repeat kinase 2 (LRRK2) are a common cause of familial and sporadic Parkinson's disease (PD). Elevated LRRK2 kinase activity and neurodegeneration are linked, but the phosphosubstrate that connects LRRK2 kinase activity to neurodegeneration is not known. Here, we show that ribosomal protein s15 is a key pathogenic LRRK2 substrate in Drosophila and human neuron PD models. Phosphodeficient s15 carrying a threonine 136 to alanine substitution rescues dopamine neuron degeneration and age-related locomotor deficits in G2019S LRRK2 transgenic Drosophila and substantially reduces G2019S LRRK2-mediated neurite loss and cell death in human dopamine and cortical neurons. Remarkably, pathogenic LRRK2 stimulates both cap-dependent and cap-independent mRNA translation and induces a bulk increase in protein synthesis in Drosophila, which can be prevented by phosphodeficient T136A s15. These results reveal a novel mechanism of PD pathogenesis linked to elevated LRRK2 kinase activity and aberrant protein synthesis in vivo.

Nanotrap Grafted Anionic MOF for Superior Uranium Extraction from Seawater.

On-demand uranium extraction from seawater (UES) can mitigate growing sustainable energy needs, while high salinity and low concentration hinder its recovery. A novel anionic metal-organic framework (iMOF-1A) is demonstrated adorned with rare Lewis basic pyrazinic sites as uranyl-specific nanotrap serving as robust ion exchange material for selective uranium extraction, rendering its intrinsic ionic characteristics to minimize leaching. Ionic adsorbents sequestrate 99.8% of the uranium in 120 mins (from 20,000 ppb to 24 ppb) and adsorb large amounts of 1336.8 mg g-1 and 625.6 mg g-1 from uranium-spiked deionized water and artificial seawater, respectively, with high distribution coefficient, Kd U ≥ 0.97 × 106  mL g-1 . The material offers a very high enrichment index of ≈5754 and it achieves the UES standard of 6.0 mg g-1 in 16 days, and harvests 9.42 mg g-1 in 30 days from natural seawater. Isothermal titration calorimetry (ITC) studies quantify thermodynamic parameters, previously uncharted in uranium sorption experiments. Infrared nearfield nanospectroscopy (nano-FTIR) and tip-force microscopy (TFM) enable chemical and mechanical elucidation of host-guest interaction at atomic level in sub-micron crystals revealing extant capture events throughout the crystal rather than surface solely. Comprehensive experimentally guided computational studies reveal ultrahigh-selectivity for uranium from seawater, marking mechanistic insight.

Integrating multi-omics summary data using a Mendelian randomization framework.

Mendelian randomization is a versatile tool to identify the possible causal relationship between an omics biomarker and disease outcome using genetic variants as instrumental variables. A key theme is the prioritization of genes whose omics readouts can be used as predictors of the disease outcome through analyzing GWAS and QTL summary data. However, there is a dearth of study of the best practice in probing the effects of multiple -omics biomarkers annotated to the same gene of interest. To bridge this gap, we propose powerful combination tests that integrate multiple correlated $P$-values without assuming the dependence structure between the exposures. Our extensive simulation experiments demonstrate the superiority of our proposed approach compared with existing methods that are adapted to the setting of our interest. The top hits of the analyses of multi-omics Alzheimer's disease datasets include genes ABCA7 and ATP1B1.

Sub-Cluster Identification through Semi-Supervised Optimization of Rare-Cell Silhouettes (SCISSORS) in single-cell RNA-sequencing.

MOTIVATION: Single-cell RNA-sequencing (scRNA-seq) has enabled the molecular profiling of thousands to millions of cells simultaneously in biologically heterogenous samples. Currently, the common practice in scRNA-seq is to determine cell type labels through unsupervised clustering and the examination of cluster-specific genes. However, even small differences in analysis and parameter choosing can greatly alter clustering results and thus impose great influence on which cell types are identified. Existing methods largely focus on determining the optimal number of robust clusters, which can be problematic for identifying cells of extremely low abundance due to their subtle contributions toward overall patterns of gene expression. RESULTS: Here, we present a carefully designed framework, SCISSORS, which accurately profiles subclusters within broad cluster(s) for the identification of rare cell types in scRNA-seq data. SCISSORS employs silhouette scoring for the estimation of heterogeneity of clusters and reveals rare cells in heterogenous clusters by a multi-step semi-supervised reclustering process. Additionally, SCISSORS provides a method for the identification of marker genes of high specificity to the cell type. SCISSORS is wrapped around the popular Seurat R package and can be easily integrated into existing Seurat pipelines. AVAILABILITY AND IMPLEMENTATION: SCISSORS, including source code and vignettes, are freely available at https://github.com/jr-leary7/SCISSORS.

Excessive iron deposition in root apoplast is involved in growth arrest of roots in response to low pH.

The rhizotoxicity of protons (H+) in acidic soils is a fundamental constraint that results in serious yield losses. However, the mechanisms underlying H+-mediated inhibition of root growth are poorly understood. In this study, we revealed that H+-induced root growth inhibition in Arabidopsis depends considerably on excessive iron deposition in the root apoplast. Reducing such aberrant iron deposition by decreasing the iron supply or disrupting the ferroxidases LOW PHOSPHATE ROOT 1 (LPR) and LPR2 attenuates the inhibitory effect of H+ on primary root growth efficiently. Further analysis showed that excessive iron deposition triggers a burst of highly reactive oxygen species, consequently impairing normal root development. Our study uncovered a valuable strategy for improving the ability of plants to tolerate H+ toxicity by manipulating iron availability.

STOP1 activates NRT1.1-mediated nitrate uptake to create a favorable rhizospheric pH for plant adaptation to acidity.

Protons (H+) in acidic soils arrest plant growth. However, the mechanisms by which plants optimize their biological processes to diminish the unfavorable effects of H+ stress remain largely unclear. Here, we showed that in the roots of Arabidopsis thaliana, the C2H2-type transcription factor STOP1 in the nucleus was enriched by low pH in a nitrate-independent manner, with the spatial expression pattern of NITRATE TRANSPORTER 1.1 (NRT1.1) established by low pH required the action of STOP1. Additionally, the nrt1.1 and stop1 mutants, as well as the nrt1.1 stop1 double mutant, had a similar hypersensitive phenotype to low pH, indicating that STOP1 and NRT1.1 function in the same pathway for H+ tolerance. Molecular assays revealed that STOP1 directly bound to the promoter of NRT1.1 to activate its transcription in response to low pH, thus upregulating its nitrate uptake. This action improved the nitrogen use efficiency (NUE) of plants and created a favorable rhizospheric pH for root growth by enhancing H+ depletion in the rhizosphere. Consequently, the constitutive expression of NRT1.1 in stop1 mutants abolished the hypersensitive phenotype to low pH. These results demonstrate that STOP1-NRT1.1 is a key module for plants to optimize NUE and ensure better plant growth in acidic media.

Confinement of Luminescent Guests in Metal-Organic Frameworks: Understanding Pathways from Synthesis and Multimodal Characterization to Potential Applications of LG@MOF Systems.

This review gives an authoritative, critical, and accessible overview of an emergent class of fluorescent materials termed "LG@MOF", engineered from the nanoscale confinement of luminescent guests (LG) in a metal-organic framework (MOF) host, realizing a myriad of unconventional materials with fascinating photophysical and photochemical properties. We begin by summarizing the synthetic methodologies and design guidelines for representative LG@MOF systems, where the major types of fluorescent guest encompass organic dyes, metal ions, metal complexes, metal nanoclusters, quantum dots, and hybrid perovskites. Subsequently, we discuss the methods for characterizing the resultant guest-host structures, guest loading, photophysical properties, and review local-scale techniques recently employed to elucidate guest positions. A special emphasis is paid to the pros and cons of the various methods in the context of LG@MOF. In the following section, we provide a brief tutorial on the basic guest-host phenomena, focusing on the excited state events and nanoscale confinement effects underpinning the exceptional behavior of LG@MOF systems. The review finally culminates in the most striking applications of LG@MOF materials, particularly the "turn-on" type fluorochromic chemo- and mechano-sensors, noninvasive thermometry and optical pH sensors, electroluminescence, and innovative security devices. This review offers a comprehensive coverage of general interest to the multidisciplinary materials community to stimulate frontier research in the vibrant sector of light-emitting MOF composite systems.

Analysis of Factors and T-Lymphocyte Subset Changes in Pediatric Recurrent Respiratory Infections Post-Pidotimod Treatment.

Objective: This study aims to analyze factors contributing to recurrent respiratory tract infections (RRTIs) in pediatric patients and evaluate the efficacy of pidotimod (PI) treatment. Methods: This study utilized a retrospective cohort design, enrolling a total of 85 children diagnosed with RRTIs between September 2020 and September 2022, alongside 54 healthy children. Logistic regression analysis was employed to identify factors contributing to RRTI occurrence. Among the participants, 40 children underwent conventional treatment (control group), while 45 received PI treatment (research group). Comparative analyses were conducted to assess clinical efficacy and adverse effects between the two treatment groups. Results: The history of family members' smoking and parental allergy emerged as independent risk factors for RRTIs (P < .05, OR>1), whereas parental education level, outdoor activity, and micronutrient intake were identified as independent protective factors for RRTIs (P < .05, OR<1). Symptoms such as cough, fever, rhonchi, moist rales, and tonsillar enlargement resolved significantly faster in the research group compared to the control group (P < .05). Additionally, the research group exhibited reduced infection duration and fewer recurrent infections (P < .05). Following treatment, the overall treatment efficacy was superior in the research group compared to the control group (P < .05), with no significant difference in the incidence of adverse effects (P > .05). Post-treatment, levels of CD3+, CD4+, and CD4+/CD8+ were elevated in the research group compared to the control group, while CD8+ levels were lower (P < .05). Conclusions: Daily outdoor activity among children, family members' history of smoking, parental allergy history, education level, and micronutrient intake emerged as independent factors influencing pediatric RRTIs. Furthermore, PI was identified as a significant treatment option for RRTIs.

Inhibition of shoot-expressed NRT1.1 improves reutilization of apoplastic iron under iron-deficient conditions.

Iron deficiency is a major constraint for plant growth in calcareous soils. The interplay between NO3 - and Fe nutrition affects plant performance under Fe-deficient conditions. However, how NO3 - negatively regulates Fe nutrition at the molecular level in plants remains elusive. Here, we showed that the key nitrate transporter NRT1.1 in Arabidopsis plants, especially in the shoots, was markedly downregulated at post-translational levels by Fe deficiency. However, loss of NRT1.1 function alleviated Fe deficiency chlorosis, suggesting that downregulation of NRT1.1 by Fe deficiency favors plant tolerance to Fe deficiency. Further analysis showed that although disruption of NRT1.1 did not alter Fe levels in both the shoots and roots, it improved the reutilization of apoplastic Fe in shoots but not in roots. In addition, disruption of NRT1.1 prevented Fe deficiency-induced apoplastic alkalization in shoots by inhibiting apoplastic H+ depletion via NO3 - uptake. In vitro analysis showed that reduced pH facilitates release of cell wall-bound Fe. Thus, foliar spray with an acidic buffer promoted the reutilization of Fe in the leaf apoplast to enhance plant tolerance to Fe deficiency, while the opposite was true for the foliar spray with a neutral buffer. Thus, downregulation of the shoot-part function of NRT1.1 prevents apoplastic alkalization to ensure the reutilization of apoplastic Fe under Fe-deficient conditions. Our findings may provide a basis for elucidating the link between N and Fe nutrition in plants and insight to scrutinize the relevance of shoot-expressed NRT1.1 to the plant response to stress.

A systematic scoping review of reflective writing in medical education.

BACKGROUND: Reflective writing (RW) allows physicians to step back, review their thoughts, goals and actions and recognise how their perspectives, motives and emotions impact their conduct. RW also helps physicians consolidate their learning and boosts their professional and personal development. In the absence of a consistent approach and amidst growing threats to RW's place in medical training, a review of theories of RW in medical education and a review to map regnant practices, programs and assessment methods are proposed. METHODS: A Systematic Evidence-Based Approach guided Systematic Scoping Review (SSR in SEBA) was adopted to guide and structure the two concurrent reviews. Independent searches were carried out on publications featured between 1st January 2000 and 30th June 2022 in PubMed, Embase, PsychINFO, CINAHL, ERIC, ASSIA, Scopus, Google Scholar, OpenGrey, GreyLit and ProQuest. The Split Approach saw the included articles analysed separately using thematic and content analysis. Like pieces of a jigsaw puzzle, the Jigsaw Perspective combined the themes and categories identified from both reviews. The Funnelling Process saw the themes/categories created compared with the tabulated summaries. The final domains which emerged structured the discussion that followed. RESULTS: A total of 33,076 abstracts were reviewed, 1826 full-text articles were appraised and 199 articles were included and analysed. The domains identified were theories and models, current methods, benefits and shortcomings, and recommendations. CONCLUSIONS: This SSR in SEBA suggests that a structured approach to RW shapes the physician's belief system, guides their practice and nurtures their professional identity formation. In advancing a theoretical concept of RW, this SSR in SEBA proffers new insight into the process of RW, and the need for longitudinal, personalised feedback and support.

High-rate nanofluidic energy absorption in porous zeolitic frameworks.

Optimal mechanical impact absorbers are reusable and exhibit high specific energy absorption. The forced intrusion of liquid water in hydrophobic nanoporous materials, such as zeolitic imidazolate frameworks (ZIFs), presents an attractive pathway to engineer such systems. However, to harness their full potential, it is crucial to understand the underlying water intrusion and extrusion mechanisms under realistic, high-rate deformation conditions. Here, we report a critical increase of the energy absorption capacity of confined water-ZIF systems at elevated strain rates. Starting from ZIF-8 as proof-of-concept, we demonstrate that this attractive rate dependence is generally applicable to cage-type ZIFs but disappears for channel-containing zeolites. Molecular simulations reveal that this phenomenon originates from the intrinsic nanosecond timescale needed for critical-sized water clusters to nucleate inside the nanocages, expediting water transport through the framework. Harnessing this fundamental understanding, design rules are formulated to construct effective, tailorable and reusable impact energy absorbers for challenging new applications.

Apolipoprotein E Genotype Contributes to Motor Progression in Parkinson's Disease.

BACKGROUND: Emerging evidence indicates that the apolipoprotein E (APOE) ε4 exacerbates α-synuclein pathology. OBJECTIVE: To determine whether APOE ε4 contributes to motor progression in early Parkinson's disease (PD). METHODS: Longitudinal data were obtained from 384 patients with PD divided into APOE ε4 carriers (n = 85) and noncarriers (n = 299) in the Parkinson's Progression Marker Initiative. Participants underwent yearly motor assessments over a mean follow-up period of 78.9 months. Repeated measures and linear mixed models were used to test the effects of APOE ε4. RESULTS: The motor progression was significantly more rapid in patients with PD carrying APOE ε4 than in noncarriers (ß = 0.283, P = 0.026, 95% confidence interval: 0.033-0.532). Through subgroup analysis, we found that the effect of APOE ε4 was significant only in patients with high amyloid ß burden (ß = 0.761, P < 0.001, 95% confidence interval: 0.0356-1.167). CONCLUSIONS: APOE ε4 may be associated with rapid motor progression in PD. © 2021 International Parkinson and Movement Disorder Society.

Associations of Body Mass Index-Metabolic Phenotypes with Cognitive Decline in Parkinson's Disease.

BACKGROUND: Growing evidence suggests important effects of body mass index (BMI) and metabolic status on neurodegenerative diseases. However, the roles of BMI and metabolic status on cognitive outcomes in Parkinson's disease (PD) may vary and are yet to be determined. METHODS: In total, 139 PD patients from the whole PD cohort in Parkinson's Progression Markers Initiative database underwent complete laboratory measurements, demographic and anthropometric parameters at baseline, and were enrolled in this study. Further, they were categorized into 4 different BMI-metabolic status phenotypes using Adult Treatment Panel-III criteria. Motor and cognition scales at baseline and longitudinal changes after a 48-month follow-up were compared among the 4 groups. Repeated-measure linear mixed models were performed to compare PD-related biomarkers among BMI-metabolic status phenotypes across time. RESULTS: We found that PD patients in the metabolically unhealthy normal weight group showed more cognitive decline in global cognition and visuospatial perception after a 48-month follow-up than those in the other 3 groups (p < 0.05). No difference was found in motor scales among different BMI-metabolic status phenotypes. Finally, compared to the metabolically healthy normal weight group, the metabolically healthy obesity group had lower CSF Aß42 and serum neurofilament levels in repeated-measure linear mixed models adjusting for age, gender, APOE e4 carrier status, and years of education (p = 0.031 and 0.046, respectively). CONCLUSION: The MUNW phenotype was associated with a rapid cognitive decline in PD.

Reverse "cheese wire" fenestration for abdominal aortic dissection repair: a case report and literature review.

BACKGROUND: Aortic dissection is one of the most common emergency condition leading to internal organs or lower limb ischemia and aortic rupture. Herein, we described a reverse "cheese wire" endovascular fenestration repair (CWFER) in a patient with complicated abdominal aortic dissection which had never been reported. CASE PRESENTATION: A 62-year-old male presented abdominal tear-like pain and acute ischemia of the right lower extremity during the endovascular treatment of celiac trunk aneurysms. Computed tomography angiography (CTA) and digital subtraction angiography (DSA) showed abdominal aortic type B dissection with acute ischemia of the right lower extremity preoperatively. After a detailed preoperative examination, the patient then was performed a reverse CWFER. So far, the patient has been followed-up for 6 months, postoperative CTA demonstrated good stent-graft expansion and perfusion of bilateral common iliac arteries; also, no endoleak was detected. CONCLUSIONS: The right iliac artery in this patient supplied by false lumen, which lead to acute ischemia of the right lower extremity, needed to be treated as an emergency and dealt with promptly. CWFER is a very high-risk treatment that requires the rich experience of vascular surgeon and accurate assessment of aortic dissection. After interventional treatment, the patient recovered uneventfully after 6 months' follow-up.

The K+ and NO3 - Interaction Mediated by NITRATE TRANSPORTER1.1 Ensures Better Plant Growth under K+-Limiting Conditions.

K+ and NO3 - are the major forms of potassium and nitrogen that are absorbed by the roots of most terrestrial plants. In this study, we observed that a close relationship between NO3 - and K+ in Arabidopsis (Arabidopsis thaliana) is mediated by NITRATE TRANSPORTER1.1 (NRT1.1). The nrt1.1 knockout mutants showed disturbed K+ uptake and root-to-shoot allocation, and were characterized by growth arrest under K+-limiting conditions. The K+ uptake and root-to-shoot allocation of these mutants were partially recovered by expressing NRT1.1 in the root epidermis-cortex and central vasculature using SULFATE TRANSPORTER1;2 and PHOSPHATE1 promoters, respectively. Two-way analysis of variance based on the K+ contents in nrt1.1-1/K + transporter1, nrt1.1-1/high-affinity K + transporter5-3, nrt1.1-1/K + uptake permease7, and nrt1.1-1/stelar K + outward rectifier-2 double mutants and the corresponding single mutants and wild-type plants revealed physiological interactions between NRT1.1 and K+ channels/transporters located in the root epidermis-cortex and central vasculature. Further study revealed that these K+ uptake-related interactions are dependent on an H+-consuming mechanism associated with the H+/NO3 - symport mediated by NRT1.1. Collectively, these data indicate that patterns of NRT1.1 expression in the root epidermis-cortex and central vasculature are coordinated with K+ channels/transporters to improve K+ uptake and root-to-shoot allocation, respectively, which in turn ensures better growth under K+-limiting conditions.

Study of the collagen type VI alpha 3 (COL6A3) gene in Parkinson's disease.

BACKGROUND: To date, the genetic contribution to Parkinson's disease (PD) remains unclear. Mutations in the collagen type VI alpha 3 (COL6A3) gene were recently identified as a cause of isolated dystonia. Since PD and dystonia are closely related disorders with shared clinical and genetic characteristics, we explored the association between COL6A3 and PD in a Chinese cohort. METHODS: We performed genetic screening of COL6A3 in a Chinese cohort of 173 patients with sporadic PD and 200 healthy controls. We identified variants that are likely to have pathogenic effects based on: 1) a minor allele frequency of < 0.01; and 2) the variant being recognized as deleterious by at least 15 different in silico predicting tools. Finally, we tested the aggregate burden of COL6A3 on PD via SKAT-O analysis. RESULTS: First, we found compound heterozygous COL6A3 gene mutations in one early-onset PD patients. Then, we explored whether COL6A3 variants contributed to increased risk of developing PD in a Chinese population. We detected 21 rare non-synonymous variants. Pathogenicity predictions identified 7 novel non-synonymous variants as likely to be pathogenic. SKAT-O analysis further revealed that an aggregate burden of variants in COL6A3 contributes to PD (p = 0.038). CONCLUSION: An increased aggregate burden of the COL6A3 gene was detected in patients with PD.

Near-Field Infrared Nanospectroscopy Reveals Guest Confinement in Metal-Organic Framework Single Crystals.

Metal-organic frameworks (MOFs) can provide exceptional porosity for molecular guest encapsulation useful for emergent applications in sensing, gas storage, drug delivery, and optoelectronics. Central to the realization of such applications, however, is the successful incorporation of a functional guest confined within the host framework. Here, we demonstrate, for the first time, the feasibility of scattering-type scanning near-field optical microscopy (s-SNOM) and nano-Fourier transform infrared (nanoFTIR) spectroscopy, in concert with density functional theory (DFT) calculations to reveal the vibrational characteristics of the Guest@MOF systems. Probing individual MOF crystals, we pinpoint the local molecular vibrations and, thus, shed new light on the host-guest interactions at the nanoscale. Our strategy not only confirms the successful encapsulation of luminescent guest molecules in the porous host framework in single crystals but also further provides a new methodology for nanoscale-resolved physical and chemical identification of wide-ranging framework materials and designer porous systems for advanced applications.

A Luminescent Guest@MOF Nanoconfined Composite System for Solid-State Lighting.

A series of rhodamine B (RhB) encapsulated zeolitic imidazolate framework-8 (RhB@ZIF-8) composite nanomaterials with different concentrations of guest loadings have been synthesized and characterized in order to investigate their applicability to solid-state white-light-emitting diodes (WLEDs). The nanoconfinement of the rhodamine B dye (guest) in the sodalite cages of ZIF-8 (host) is supported by fluorescence spectroscopic and photodynamic lifetime data. The quantum yield (QY) of the luminescent RhB@ZIF-8 material approaches unity when the guest loading is controlled at a low level: 1 RhB guest per ~7250 cages. We show that the hybrid (luminescent guest) LG@MOF material, obtained by mechanically mixing a suitably high-QY RhB@ZIF-8 red emitter with a green-emitting fluorescein@ZIF-8 "phosphor" with a comparably high QY, could yield a stable, intensity tunable, near-white light emission under specific test conditions described. Our results demonstrate a novel LG@MOF composite system exhibiting a good combination of photophysical properties and photostability, for potential applications in WLEDs, photoswitches, bioimaging and fluorescent sensors.

Inhibition of DNA demethylation enhances plant tolerance to cadmium toxicity by improving iron nutrition.

Although the alteration of DNA methylation due to abiotic stresses, such as exposure to the toxic metal cadmium (Cd), has been often observed in plants, little is known about whether such epigenetic changes are linked to the ability of plants to adapt to stress. Herein, we report a close linkage between DNA methylation and the adaptational responses in Arabidopsis plants under Cd stress. Exposure to Cd significantly inhibited the expression of three DNA demethylase genes ROS1/DML2/DML3 (RDD) and elevated DNA methylation at the genome-wide level in Col-0 roots. Furthermore, the profile of DNA methylation in Cd-exposed Col-0 roots was similar to that in the roots of rdd triple mutants, which lack RDD, indicating that Cd-induced DNA methylation is associated with the inhibition of RDD. Interestingly, the elevation in DNA methylation in rdd conferred a higher tolerance against Cd stress and improved cellular Fe nutrition in the root tissues. In addition, lowering the Fe supply abolished improved Cd tolerance due to the lack of RDD in rdd. Together, these data suggest that the inhibition of RDD-mediated DNA demethylation in the roots by Cd would in turn enhance plant tolerance to Cd stress by improving Fe nutrition through a feedback mechanism.

Joint analysis of single-cell and bulk tissue sequencing data to infer intratumor heterogeneity.

Many computational methods have been developed to discern intratumor heterogeneity (ITH) using DNA sequence data from bulk tumor samples. These methods share an assumption that two mutations arise from the same subclone if they have similar mutant allele-frequencies (MAFs), and thus it is difficult or impossible to distinguish two subclones with similar MAFs. Single-cell DNA sequencing (scDNA-seq) data can be very informative for ITH inference. However, due to the difficulty of DNA amplification, scDNA-seq data are often very noisy. A promising new study design is to collect both bulk and single-cell DNA-seq data and jointly analyze them to mitigate the limitations of each data type. To address the analytic challenges of this new study design, we propose a computational method named BaSiC (Bulk tumor and Single Cell), to discern ITH by jointly analyzing DNA-seq data from bulk tumor and single cells. We demonstrate that BaSiC has comparable or better performance than the methods using either data type. We further evaluate BaSiC using bulk tumor and single-cell DNA-seq data from a breast cancer patient and several leukemia patients.