bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing dry mass and volume changes in human multiple myeloma cells upon treatment with proteotoxic and genotoxic drugs
Authors: Liu Xili , Moscvin Maria , Oh Seungeun , Chen Tianzeng , Choi Wonshik , Evans Benjamin , Rowell Sean M. , Nadeem Omar , Mo Clifton C. , Sperling Adam S. , Anderson Kenneth C. , Yaqoob Zahid , Bianchi Giada , Sung Yongjin 
Published: March 2022

AbstractMultiple myeloma (MM) is a cancer of terminally differentiated plasma cells. MM remains incurable, but overall survival of patients has progressively increased over the past two decades largely due to novel agents such as proteasome inhibitors (PI) and the immunomodulatory agents. While these therapies are highly effective, MM patients can be de novo resistant and acquired resistance with prolonged treatment is inevitable. There is growing interest in early, accurate identification of responsive versus non-responsive patients, however limited sample availability and need for rapid assays are limiting factors. Here, we test dry mass and volume as label-free biomarkers to monitor early response of MM cells to treatment with bortezomib, doxorubicin, and ultraviolet light. For the dry mass measurement, we use two types of phase-sensitive optical microscopy techniques: digital holographic tomography and computationally-enhanced quantitative phase microscopy. We show that human MM cell lines (RPMI8226, MM.1S, KMS20, and AMO1) increase dry mass upon bortezomib treatment. This dry mass increase after bortezomib treatment occurs as early as 1 hour for sensitive cells and 4 hours for all tested cells. We further confirm this observation using primary multiple myeloma cells derived from patients and show that a correlation exists between increase in dry mass and sensitivity to bortezomib, supporting the use of dry mass as a biomarker. The volume measurement using Coulter counter shows a more complex behavior; RPMI8226 cells increase the volume at an early stage of apoptosis, but MM.1S cells show the volume decrease typically observed with apoptotic cells. Altogether, this cell study presents complex kinetics of dry mass and volume at an early stage of apoptosis, which may serve as a basis for the detection and treatment of MM cells.
One-Pot Exosome Proteomics Enabled by a Photocleavable Surfactant
Authors: Buck Kevin M. , Roberts David S. , Aballo Timothy J. , Inman David R. , Jin Song , Ponik Suzanne , Brown Kyle A. , Ge Ying 
Published: March 2022

AbstractExosomes are small extracellular vesicles (EVs) secreted by all cells and found in biological fluids, which can serve as minimally invasive liquid biopsies with high therapeutic and diagnostic potential. Mass spectrometry (MS)-based proteomics is a powerful technique to profile and quantify the protein content of exosomes but the current methods require laborious and time-consuming multi-step sample preparation that significantly limit throughput. Herein, we report a one-pot exosome proteomics method enabled by a photocleavable surfactant, Azo, for rapid and effective exosomal lysis, protein extraction, and digestion. We have applied this method to exosomes derived from isolated mammary fibroblasts and confidently identified 3,466 proteins and quantified 2,288 proteins using reversed-phase liquid chromatography coupled to trapped ion mobility spectrometry (TIMS) quadrupole time-of-flight mass spectrometer. 3,166 (91%) of the identified proteins are annotated in the exosome/EVs databases, ExoCarta and Vesiclepedia, including important exosomal markers, CD63, PDCD6IP, and SDCBP. This method is fast, simple, and highly effective at extracting exosomal proteins with high reproducibility for deep exosomal proteome coverage. We envision this method could be generally applicable for exosome proteomics applications in biomedical research, therapeutic interventions, and clinical diagnostics.
SPDEF promotes the classical subtype of pancreatic ductal adenocarcinoma
Authors: Tonelli Claudia , Yordanov Georgi N. , Hao Yuan , Deschênes Astrid , Klingbeil Olaf , Ting Hsiu-Chi , Brosnan Erin , Doshi Abishek , Park Youngkyu , Vakoc Christopher R. , Preall Jonathan , Tuveson David A. 
Published: March 2022

ABSTRACTPancreatic ductal adenocarcinoma (PDA) samples reveal extensive cellular heterogeneity. Using single-cell RNA sequencing, we uncover multiple tumor cell populations distinguished by their differentiation state and associated with different stages of tumor progression in a mouse model of PDA. We identify Spdef as a factor required for tumorigenesis in pancreatic cancer cells of epithelial and mucinous nature. By comparative analysis of cell differentiation states in mice and humans, we find that the Spdef program is highly expressed by human PDAs of the classical subtype. Mouse and human PDA cells expressing elevated levels of Spdef are dependent upon this transcription factor for tumor progression in vivo. The tumor-promoting function of Spdef is recapitulated by two Spdef target genes that regulate protein folding and endoplasmic reticulum activity, Agr2 and Ern2/Ire1β. These findings offer insights into the factors controlling differentiation states in PDA and identify new vulnerabilities in the most common subtype of pancreatic cancer.
Activation of the chemokine receptor CCR1 and preferential recruitment of Gαi suppress RSV replication: implications for developing novel RSV treatment strategies
Authors: Li Jiao , Xue Ling , Wang Jiachao , Meng Aihong , Qiao Jiajun , Li Miao , Wang Xiuli , Meng Lingtong , Ning Jingyuan , Gao Xue , Li Wenjian , Ma Cuiqing , Wei Lin 
Published: March 2022

ABSTRACTRespiratory syncytial virus (RSV) is a major pathogen that can cause acute respiratory infectious diseases of the upper and lower respiratory tract, especially in children, elderly individuals and immunocompromised people. Generally, following viral infection, respiratory epithelial cells secrete cytokines and chemokines to recruit immune cells and initiate innate and/or adaptive immune responses. However, whether chemokines affect viral replication in non-immune cells is rarely clear. In this study, we detect that chemokine CCL5 was highly expressed, while expression of its receptor, CCR1, was downregulated in respiratory epithelial cells after RSV infection. When we overexpressed CCR1 on respiratory epithelial cells in vivo/in vitro, viral load was significantly suppressed, which can be restored by the neutralizing antibody for CCR1. Interestingly, the antiviral effect of CCR1 was not related to type I interferon (IFN-I), apoptosis induction or viral adhesion or entry inhibition; in contrast, it was related to the preferential recruitment and activation of adaptor Gαi, which promoted inositol 1,4,5-triphosphate receptor type 3 (ITPR3) expression, leading to inhibited STAT3 phosphorylation, explicitly, phosphorylated (p)-STAT3 was verified to be among the important factors regulating the activity of HSP90, which has been previously reported to be a chaperone of RSV RNA polymerase. In summary, we are the first to reveal that CCR1 on the surface of non-immune cells regulates RSV replication through a previously unknown mechanism that does not involve IFN-I induction.
Chloroplast protein import determines plant proteostasis and retrograde signaling
Authors: Llamas Ernesto , Koyuncu Seda , Lee Hyun Ju , Gutierrez-Garcia Ricardo , Dunken Nick , Charura Nyasha , Torres-Montilla Salvador , Schlimgen Elena , Pulido Pablo , Rodriguez-Concepcion Manuel , Zuccaro Alga , Vilchez David 
Published: March 2022

AbstractProteins containing polyglutamine (polyQ) repeats are prone to aggregation and can lead to distinct human pathologies. For instance, Huntington’s disease is caused by an abnormal expansion of the polyQ stretch (> Q35) of Huntingtin (HTT) protein. However, plants express hundreds of proteins containing polyQ regions, but no pathologies arising from these factors have been reported to date. Here, we ask how plants maintain the proteostasis of polyQ-containing proteins, which are intrinsically enriched in the plant proteomes. To this end, we overexpressed an aggregation-prone fragment of human HTT (Q69) in plant cells. In contrast to invertebrate and mammalian transgenic models, we find that Arabidopsis thaliana plants suppress Q69 aggregation. This elevated proteostasis ability is mediated through the import and degradation of Q69 in chloroplasts. Conversely, inhibition of chloroplast protein import either genetically or pharmacologically reduces the capacity of plant cells to prevent Q69 aggregation. We find that Q69 interacts with the chloroplast stromal processing peptidase (SPP). Notably, expression of synthetic Arabidopsis SPP is sufficient to suppress aggregation of polyQ-expanded HTT in human cells. Beyond ectopically expressed Q69-HTT, endogenous polyQ-containing proteins also aggregate in Arabidopsis upon inhibition of chloroplast import. Among them, the plastid casein kinase 2 (pCK2), which contains a polyQ region next to the chloroplast targeting sequence motif, can also be localized into the nucleus. Upon inhibition of chloroplast import, pCK2 accumulates at higher levels in the nucleus and forms diamond-shaped amyloid-like fibrils surrounding the chloroplasts. These results indicate that the differential conformation and redistribution of pCK2 to the nucleus depends on chloroplast import efficiency, providing a role of polyQ repeats in chloroplast to nucleus communication (i.e. retrograde signaling). Together, our findings establish chloroplast protein import and proteases as determinants of polyQ proteostasis, with important implications for plant biology that can also lead to therapeutic approaches for human diseases that involve protein aggregation.
Configurable Compartmentation Enables In Vitro Reconstitution of Sustained Synthetic Biology Systems
Authors: Li Luyao , Zhang Rong , Tian Xintong , Li Ting , Pu Bingchun , Ma Conghui , Ba Fang , Xiong Chenwei , Shi Yunfeng , Li Jian , Keasling Jay , Zhang Jingwei , Liu Yifan 
Published: March 2022

AbstractThe compartmentalized and communicative nature of biological cells contributes to the complexity and endurance of living organisms. Current in vitro compartmentalization systems such as droplet emulsions reproduce the compartmentalization property of cells yet fail to recapture the configurability of cellular communication with the environment. To mimic biological cells a step further and expand the capabilities of in vitro compartmentalization, we present here a general strategy that inherits the passive transport phenomenon of biology. The strategy incorporates layered, micrometer-sized, hydrogel-based compartments featuring configurability in composition, functionality, and selective permeability of biomolecules. We demonstrated the unique advantage of our strategy in two scenarios of synthetic biology. First, a compartmentalized cell-free protein synthesis system was reconstituted that could support multiple rounds of reactions. Second, we constructed living bacteria-based biosensors in the hydrogel compartments, which could achieve long-lasting functioning with markedly enhanced fitness in complex environments. Looking forward, our strategy should be widely applicable for constructing complex, robust, and sustained in vitro synthetic molecular and cellular systems, paving the way for their practical applications.
Programmed-DNA Elimination in the free-living nematodes Mesorhabditis
Authors: Rey Carine , Launay Caroline , Wenger Eva , Delattre Marie 
Published: March 2022

AbstractIn most species, elaborate programs exist to protect chromatin and maintain its integrity over cell cycles and generations. However some species systematically undergo excision and elimination of portions of their genome in somatic cells in a process called programmed-DNA elimination (PDE). PDE involves the elimination of mainly repeated elements but also protein-coding genes. PDE has been described in approximately 100 species from very distinct phyla, and more extensively in the parasitic nematodes Ascaris and in the unicellular Ciliates. In Ciliates, where PDE is pervasive, the underlying mechanisms have been studied and involve small RNA-guided heterochromatinization. In striking contrast, chromatin recognition and excision mechanisms remain mysterious in Metazoans, because the study species are not amenable to functional approaches. Above all, the function of such a mechanism, which has emerged repeatedly throughout evolution, is unknown. Answering these questions will provide significant insights into our understanding of chromatin regulation and genome stability.We fortuitously discovered the phenomenon of PDE in all species of the free-living nematode genus Mesorhabditis. Mesorhabditis, which belong to the same family as C. elegans, have a small ∼150 Mb genome and offer many experimental advantages to start elucidating the elimination mechanisms in Metazoans. In this first study, we have used a combination of cytological observation and genomic approaches to describe PDE in Mesorhabditis. We found that the dynamics of chromosome fragmentation and loss are very similar to those described in Ascaris. Elimination occurs once in development, at the third embryonic cell division in all 5 presomatic blastomeres. Similar to other species, Mesorhabditis eliminate repeated elements but also about a hundred unique sequences. Most of the eliminated unique sequences are either pseudogenes or poorly conserved protein-coding genes. Our results raise the possibility that PDE has not been selected for a gene regulatory function in Mesorhabditis but rather mainly is a mechanism to irreversibly silence repeated elements in the soma.
Thermodynamic coupling between neighboring binding sites in homo-oligomeric ligand sensing proteins from mass resolved ligand dependent population distributions
Authors: Li Weicheng , Norris Andrew S. , Lichtenthal Katie , Kelly Skyler , Ihms Elihu C. , Gollnick Paul , Wysocki Vicki H. , Foster Mark P. 
Published: March 2022

AbstractHomo-oligomeric ligand-activated proteins are ubiquitous in biology. The functions of such molecules are commonly regulated by allosteric coupling between ligand binding sites. Understanding the basis for this regulation requires both quantifying the free energy ΔG transduced between sites, and the structural basis by which it is transduced. We consider allostery in three variants of the model ring-shaped homo-oligomeric trpRNA binding attenuation protein, TRAP. First, we developed nearest-neighbor statistical thermodynamic binding models comprising microscopic free energies for ligand binding to isolated sites ΔGN0, and for coupling between one or both adjacent sites, ΔGN1 and ΔGN2. Using the resulting partition function (PF) we explored the effects of these parameters on simulated population distributions for the 2N possible liganded states. We then experimentally monitored liganddependent population shifts using conventional spectroscopic and calorimetric methods, and using native mass spectrometry (MS). By resolving species with differing numbers of bound ligands by their mass, native MS revealed striking differences in their ligand-dependent population shifts. Fitting the populations to a binding polynomial derived from the PF yielded coupling free energy terms corresponding to orders of magnitude differences in cooperativity. Uniquely, this approach predicts which of the possible 2N liganded states are populated at different ligand concentrations, providing necessary insights into regulation. The combination of statistical thermodynamic modeling with native MS may provide the thermodynamic foundation for a meaningful understanding of the structure-thermodynamic linkage that drives cooperativity.TOC Figure (draft)TOC Figure.Ligand (Trp) binding to multiple sites on homo-oligomeric ring-shaped proteins like TRAP alters their functional states. Homotropic cooperativity is expected to alter the activation pathway in response to cellular ligand concentration. In the presence of positive nearest-neighbor cooperativity, ligand binding is favored at adjacent sites, whereas in the absence of cooperativity, a random “Normal” distribution is expected.
Survey of young consumer’s attitudes using food sharing attitudes and behaviors model
Authors: Wiśniewska Małgorzata , Czernyszewicz Eugenia 
Published: March 2022

PurposeGiven the importance of food wastes in households, the purpose was to identify the attitudes of young consumers towards the food sharing (FS) phenomenon in its cognitive, emotional and behavioral dimensions and to verify the reliability of the FAB (food sharing attitudes and behaviors) model, used as a research tool.Design/methodology/approachThe study was conducted in 2021 using the computer assisted web interview (CAWI) method. The FAB model was based on the ABC (affect, behavior and cognition) model of attitudes, which includes three components: affect, behavior and cognition. Questions on the phenomenon of FS were scaled on a 5-point Likert scale. A total of 469 correctly completed forms were obtained. To assess the reliability of the FAB model the Cronbach’s alpha was used. In the statistical analysis SPSS Statistics 27 was used.FindingsYoung consumers have a positive attitude towards the idea of FS and the initiative of FS points. Gender is a significant factor in FS attitudes. The FAB model has proven to be a reliable tool for exploring consumer attitudes towards FS. A set of activities was proposed to promote the idea of FS on university campuses and among other potential stakeholders.Originality/valueTo contribute to the body of knowledge on FS, the authors proposed the FAB model. The results of this study are relevant for reducing food wastes; they promote sustainable food consumption and the European Green Deal (EGD).
Conjoint assessment of rural water security and system sustainability in Nagpur, India
Authors: Sukhwani Vibhas , Shaw Rajib 
Published: March 2022

Purpose
In spite of the growing usage of “water security” as a policy template, the sustainable delivery of adequate quantity/quality of water remains a major challenge, specifically in the rural areas of developing countries. Focusing on the specific case of Nagpur (India), this study aims to establish a broader understanding of rural water security and (water supply) system sustainability issues at grassroots-level.

Design/methodology/approach
Taking due account of the existing assessment methods and the study context of Nagpur, contextualized indicator-based frameworks have been developed for conjointly assessing both the research subjects. Within the identified eight rural clusters (comprising 72 settlements), focus group discussions (with the residents) and semi-structured interviews [with the members of village water and sanitation committees) (VWSCs)] are then conducted to methodically investigate the local stakeholder perception.

Findings
Through the rural water security (state change) assessment in selected settlements, the water accessibility indicators are consistently reported to have witnessed mostly positive changes, whereas contrasting changes have been reported for various indicators of availability, quality and risks. Superimposing these findings with those of system sustainability assessment (e.g. only 56% VWSCs are reported to be actively functioning), it has been realized that the sustainability of water supply systems is imperative to attain water security goals in the long term.

Originality/value
Through the conjoint assessment of water security and system sustainability issues, this research responds to the growing call for a broader consideration of these concepts. Moreover, it reports practical ground-level challenges based on primary surveys.
Divergence of beliefs and IPO initial return: the quasi-moderating role of investor demand
Authors: Albada Ali , Low Soo-Wah , Toh Moau Yong 
Published: March 2022

PurposeThis study aims to investigate the moderating role of investor demand on the relationship between the investors' divergence of beliefs and the first-day initial public offering (IPO) return.Design/methodology/approachThe study sample covers the period from 2010 to 2019 and consists of 117 IPOs that are priced using the fixed price and listed on the Malaysian stock exchange (Bursa Malaysia). This study employed both the ordinary least square (OLS) and the quantile regression (QR) methods.FindingsInvestor demand, proxied by the over-subscription ratio (OSR), plays a moderating role in increasing the effect of investors' divergence of beliefs on initial return, and the moderation effects vary across the quantile of initial return. Pure moderation effects are observed at the bottom and top quantiles, suggesting that investor demand is necessary for divergence of beliefs to influence IPO initial return. However, at the middle quantile of initial return, investor demand is a quasi-moderator. That is, the OSR not only moderates the relationship between the divergence of beliefs and initial return but also has a positive effect on the initial return.Practical implicationsInvestors' excessive demand for an IPO issue exacerbates the IPO under-pricing issue induced by a divergence of beliefs amongst investors, thus rendering greater equity market inefficiency.Originality/valueTo the authors' knowledge, this study is amongst the first to empirically investigate the moderating role of investor demand on the investors' divergence of beliefs and IPO initial return relationship.
Host genotype interacts with aerial spore communities and influences the needle mycobiome of Norway spruce
Authors: Redondo Miguel A. , Oliva Jonàs , Elfstrand Malin , Boberg Johanna , Capador‐Barreto Hernán D. , Karlsson Bo , Berlin Anna 
Published: March 2022

SummaryThe factors shaping the composition of the tree mycobiome are still under investigation. We tested the effects of host genotype, site, host phenotypic traits, and air fungal spore communities on the assembly of the fungi inhabiting Norway spruce needles. We used Norway spruce clones and spore traps within the collection sites and characterized both needle and air mycobiome communities by high‐throughput sequencing of the ITS2 region. The composition of the needle mycobiome differed between Norway spruce clones, and clones with high genetic similarity had a more similar mycobiome. The needle mycobiome also varied across sites and was associated with the composition of the local air mycobiome and climate. Phenotypic traits such as diameter at breast height or crown health influenced the needle mycobiome to a lesser extent than host genotype and air mycobiome. Altogether, our results suggest that the needle mycobiome is mainly driven by the host genotype in combination with the composition of the local air spore communities. Our work highlights the role of host intraspecific variation in shaping the mycobiome of trees and provides new insights on the ecological processes structuring fungal communities inhabiting woody plants.
The Logic of Policies to Address Income‐Related Health Inequity: A Problem‐Oriented Approach
Authors: BERKOWITZ SETH A. 
Published: March 2022

Policy Points
Income is a fundamental cause of health across the life course. To address income‐related health inequities, we need a set of overlapping and complementary policy approaches rather than focusing on a single policy.
During their lives, individuals inhabit different roles with regard to their ability to earn wages, and at any given time, only about 50% of the US population are expected to earn wages, while the rest (e.g., children, older adults, those who are disabled, unemployed, students, and/or caregivers) are not.
Three key “branch points” for designing policy approaches to address income‐related health inequity are (1) should the needed good or service be obtained on the market? (2) do policy beneficiaries currently earn income? and (3) have policy beneficiaries earned income previously? The responses to these questions suggest one of four policy approaches: social services, social enfranchisement, social insurance, or social assistance.