Deciphering Organoids: High-Dimensional Analysis of Biomimetic Cultures.

Trends Biotechnol. 2020 Dec 02;:

Authors: Qin X, Tape CJ

Abstract
Organoids are self-organising stem cell-derived ex vivo cultures widely adopted as biomimetic models of healthy and diseased tissues. Traditional low-dimensional experimental methods such as microscopy and bulk molecular analysis have generated remarkable biological insights from organoids. However, as complex heterocellular systems, organoids are especially well-positioned to take advantage of emerging high-dimensional technologies. In particular, single-cell methods offer considerable opportunities to analyse organoids at unprecedented scale and depth, enabling comprehensive characterisation of cellular processes and spatial organisation underpinning organoid heterogeneity. This review evaluates state-of-the-art analytical methods applied to organoids, discusses the latest advances in single-cell technologies, and speculates on the integration of these two rapidly developing fields.

PMID: 33279281 [PubMed - as supplied by publisher]

Biogenic fenton-like reaction involvement in aerobic degradation of C60 by Labrys sp. WJW.

Environ Pollut. 2020 Aug 23;:115300

Authors: Wang J, Ma Q, Zhang Z, Diko CS, Qu Y

Abstract
Buckminster fullerene (C60), the most representative type among fullerenes, has attracted widely attentions because of its many potential applications. The increasing application of fullerene and limited knowledge of its environmental fate are required concerns. Herein, the biotransformation of C60 by Labrys sp. WJW was investigated. Cell numbers reached 25.76 ± 1.85 folds within 8 days using 100 mg/L C60 as sole carbon source. The biotransformation of C60 by Labrys sp. WJW was analyzed by various characterization methods. Raman spectra indicated that strain WJW broke the soccer ball like structure of C60. After 12 days, over 60% of C60 was degraded evidenced by UV-vis spectrophotometry and liquid chromatography-mass spectrometry. The underlying biotransformation mechanism of C60 through an extracellular Fenton-like reaction was illustrated. In this reaction, the •OH production was mediated by reduction of H2O2 involving a continuous cycle of Fe(II)/Fe(III). Bacterial transformation of C60 will provide new insights into the understanding of C60 bioremediation process.

PMID: 33279268 [PubMed - as supplied by publisher]

Editorial overview: Microbial systems biology.

Curr Opin Microbiol. 2020 Oct;57:vi-vii

Authors: Typas AN, Li GW

PMID: 33279101 [PubMed - as supplied by publisher]

F1000Res. 2020 May 11;9:344. doi: 10.12688/f1000research.23214.2. eCollection 2020.

ABSTRACT

Cancer genome sequencing studies have revealed a number of variants in coding regions of several genes. Some of these coding variants play an important role in activating specific pathways that drive proliferation. Coding variants present on cancer cell surfaces by the major histocompatibility complex serve as neo-antigens and result in immune activation. The success of immune therapy in patients is attributed to neo-antigen load on cancer cell surfaces. However, which coding variants are expressed at the protein level can't be predicted based on genomic data. Complementing genomic data with proteomic data can potentially reveal coding variants that are expressed at the protein level. However, identification of variant peptides using mass spectrometry data is still a challenging task due to the lack of an appropriate tool that integrates genomic and proteomic data analysis pipelines. To overcome this problem, and for the ease of the biologists, we have developed a graphical user interface (GUI)-based tool called CusVarDB. We integrated variant calling pipeline to generate sample-specific variant protein database from next-generation sequencing datasets. We validated the tool with triple negative breast cancer cell line datasets and identified 423, 408, 386 and 361 variant peptides from BT474, MDMAB157, MFM223 and HCC38 datasets, respectively.

PMID:33274046 | PMC:PMC7684676 | DOI:10.12688/f1000research.23214.2

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Yield and Integrity of RNA from Brain Samples are Largely Unaffected by Pre-analytical Procedures.

Neurochem Res. 2020 Nov 29;:

Authors: Jensen PSH, Johansen M, Bak LK, Jensen LJ, Kjær C

Abstract
Gene expression studies are reported to be influenced by pre-analytical factors that can compromise RNA yield and integrity, which in turn may confound the experimental findings. Here we investigate the impact of four pre-analytical factors on brain-derived RNA: time-before-collection, tissue specimen size, tissue collection method, and RNA isolation method. We report no significant differences in RNA yield or integrity between 20 mg and 60 mg tissue samples collected in either liquid nitrogen or the RNAlater stabilizing solution. Isolation of RNA employing the TRIzol reagent resulted in a higher yield compared to isolation via the QIAcube kit while the latter resulted in RNA of slightly better integrity. Keeping brain tissue samples at room temperature for up to 160 min prior to collection and isolation of RNA resulted in no significant difference in yield or integrity. Our findings have significant practical and financial consequences for clinical genomic departments and other laboratory settings performing large-scale routine RNA expression analysis of brain samples.

PMID: 33249516 [PubMed - as supplied by publisher]

Multi-omics integration in biomedical research - A metabolomics-centric review.

Anal Chim Acta. 2021 Jan 02;1141:144-162

Authors: Wörheide MA, Krumsiek J, Kastenmüller G, Arnold M

Abstract
Recent advances in high-throughput technologies have enabled the profiling of multiple layers of a biological system, including DNA sequence data (genomics), RNA expression levels (transcriptomics), and metabolite levels (metabolomics). This has led to the generation of vast amounts of biological data that can be integrated in so-called multi-omics studies to examine the complex molecular underpinnings of health and disease. Integrative analysis of such datasets is not straightforward and is particularly complicated by the high dimensionality and heterogeneity of the data and by the lack of universal analysis protocols. Previous reviews have discussed various strategies to address the challenges of data integration, elaborating on specific aspects, such as network inference or feature selection techniques. Thereby, the main focus has been on the integration of two omics layers in their relation to a phenotype of interest. In this review we provide an overview over a typical multi-omics workflow, focusing on integration methods that have the potential to combine metabolomics data with two or more omics. We discuss multiple integration concepts including data-driven, knowledge-based, simultaneous and step-wise approaches. We highlight the application of these methods in recent multi-omics studies, including large-scale integration efforts aiming at a global depiction of the complex relationships within and between different biological layers without focusing on a particular phenotype.

PMID: 33248648 [PubMed - as supplied by publisher]

Rapid desalting during electrospray ionization mass spectrometry for investigating protein-ligand interactions in the presence of concentrated salts.

Anal Chim Acta. 2021 Jan 02;1141:120-126

Authors: Chen Y, Yuan S, Liu Y, Huang G

Abstract
Investigation of protein-ligand interactions in physiological conditions is crucial for better understanding of biochemistry because the binding stoichiometry and conformations of complexes in biological processes, such as various types of regulation and transportation, could reveal key pathways in organisms. Nanoelectrospray ionization mass spectrometry is widely used in studies of biological processes and systems biology. However, non-volatile salts in biological fluid may adversely interfere with nanoelectrospray ionization mass spectrometry. In this study, the previously developed method of induced nanoelectrospray ionization was used to facilitate in situ desalting of protein in solutions with high concentrations of non-volatile salts, and direct investigation of protein-ligand interactions for the first time. In situ desalting occurred at the tip of emitters within a short period lasting for a few to tens of milliseconds, enabling the maintenance of nativelike conditions compatible with mass spectrometry measurements. Induced nanoelectrospray ionization was driven by pulsed potential and exhibited microelectrophoresis effect in each spray cycle, which is not observed in conventional nanoelectrospray ionization because the continuous spray procedure is driven by direct current. Microelectrophoresis caused desalting through micron-sized spray emitters (1-20 μm), as confirmed experimentally with proteins in 100 mM NaCl solution. The method developed in this study has been further illustrated as a potential option for fast and direct identification of protein-ligand (small molecules or metal ions) interactions in complex samples. The results of this study demonstrate that the newly developed method may represent a reliable approach for investigations of proteins and protein complexes in biological samples.

PMID: 33248644 [PubMed - as supplied by publisher]

Where Have All the Emergencies Gone? The impact of the COVID-19 pandemic on obstetric and gynecologic procedures and consults at a New York City hospital.

J Minim Invasive Gynecol. 2020 Nov 25;:

Authors: Spurlin EE, Han ES, Silver ER, May BL, Tatonetti NP, Ingram MA, Jin Z, Hur C, Advincula AP, Hur HC

Abstract
STUDY OBJECTIVE: The purpose of this study was to assess the impact of the coronavirus disease 2019 (COVID-19) pandemic on surgical volume and emergency department (ED) consults across obstetric & gynecologic (OB/GYN) services at a New York City hospital.
DESIGN: Retrospective cohort study SETTING: Tertiary-care academic medical center in New York City PATIENTS OR PARTICIPANTS: Women undergoing OB/GYN ED consults or surgeries between February 1st to April 15th.
INTERVENTIONS: March 16th institutional moratorium on elective surgeries MEASUREMENTS AND MAIN RESULTS: The volume and types of surgeries and ED consults were compared before and after the COVID-19 moratorium. During the pandemic, the average weekly volume of ED consults and GYN surgeries decreased, while OB surgeries remained stable. The proportions of OBGYN ED consults, GYN surgeries, and OB surgeries relative to all ED consults, all surgeries, and all labor and delivery patients were 1.87%, 13.8%, 54.6% in the pre-COVID timeframe (February 1st to March 15th) versus 1.53%, 21.3%, 79.7% in the COVID timeframe (March 16th to April 15th), representing no significant difference in proportions of OBGYN ED consults (p=0.464) and GYN surgeries (p=0.310) before and during COVID, with proportionate increase in OB surgeries (p<.002). The distribution of GYN surgical case types changed significantly during the pandemic with higher proportions of emergent surgeries for ectopics, miscarriages, and concern for cancer (p <.001). Alternatively, the OB surgery distribution of case types remained relatively constant.
CONCLUSIONS: This study highlights how the pandemic has impacted the ways OB/GYN patients access and receive care. As expected, institutional policies suspending elective surgeries during the pandemic decreased GYN surgical volume and affected the types of cases performed. This decrease was not appreciated for OB surgical volume reflecting the non-elective and time-sensitive nature of obstetric care. A decrease in ED consults was noted during the pandemic begging the question "Where have all the emergencies gone?". Although the moratorium on elective procedures was necessary, "elective" GYN surgeries remain medically indicated to address symptoms such as pain and bleeding and to prevent serious medical sequelae such as severe anemia requiring transfusion. As we continue to battle COVID-19, we must not lose sight of those patients whose care has been deferred.

PMID: 33248312 [PubMed - as supplied by publisher]

Pod indehiscence in common bean is associated to the fine regulation of PvMYB26.

J Exp Bot. 2020 Nov 28;:

Authors: Vittori VD, Bitocchi E, Rodriguez M, Alseekh S, Bellucci E, Nanni L, Gioia T, Marzario S, Logozzo G, Rossato M, De Quattro C, Murgia ML, Ferreira JJ, Campa A, Xu C, Fiorani F, Sampathkumar A, Fröhlich A, Attene G, Delledonne M, Usadel B, Fernie AR, Rau D, Papa R

Abstract
In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5-kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated to the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci.

PMID: 33247939 [PubMed - as supplied by publisher]

KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling.

Database (Oxford). 2020 Nov 28;2020:

Authors: Mochão H, Barahona P, Costa RS

Abstract
The KiMoSys (https://kimosys.org), launched in 2014, is a public repository of published experimental data, which contains concentration data of metabolites, protein abundances and flux data. It offers a web-based interface and upload facility to share data, making it accessible in structured formats, while also integrating associated kinetic models related to the data. In addition, it also supplies tools to simplify the construction process of ODE (Ordinary Differential Equations)-based models of metabolic networks. In this release, we present an update of KiMoSys with new data and several new features, including (i) an improved web interface, (ii) a new multi-filter mechanism, (iii) introduction of data visualization tools, (iv) the addition of downloadable data in machine-readable formats, (v) an improved data submission tool, (vi) the integration of a kinetic model simulation environment and (vii) the introduction of a unique persistent identifier system. We believe that this new version will improve its role as a valuable resource for the systems biology community. Database URL:  www.kimosys.org.

PMID: 33247931 [PubMed - as supplied by publisher]

An inducible CRISPR interference library for genetic interrogation of Saccharomyces cerevisiae biology.

Commun Biol. 2020 Nov 27;3(1):723

Authors: Momen-Roknabadi A, Oikonomou P, Zegans M, Tavazoie S

Abstract
Genome-scale CRISPR interference (CRISPRi) is widely utilized to study cellular processes in a variety of organisms. Despite the dominance of Saccharomyces cerevisiae as a model eukaryote, an inducible genome-wide CRISPRi library in yeast has not yet been presented. Here, we present a genome-wide, inducible CRISPRi library, based on spacer design rules optimized for S. cerevisiae. We have validated this library for genome-wide interrogation of gene function across a variety of applications, including accurate discovery of haploinsufficient genes and identification of enzymatic and regulatory genes involved in adenine and arginine biosynthesis. The comprehensive nature of the library also revealed refined spacer design parameters for transcriptional repression, including location, nucleosome occupancy and nucleotide features. CRISPRi screens using this library can identify genes and pathways with high precision and a low false discovery rate across a variety of experimental conditions, enabling rapid and reliable assessment of genetic function and interactions in S. cerevisiae.

PMID: 33247197 [PubMed - as supplied by publisher]

A grass-specific cellulose-xylan interaction dominates in sorghum secondary cell walls.

Nat Commun. 2020 Nov 27;11(1):6081

Authors: Gao Y, Lipton AS, Wittmer Y, Murray DT, Mortimer JC

Abstract
Sorghum (Sorghum bicolor L. Moench) is a promising source of lignocellulosic biomass for the production of renewable fuels and chemicals, as well as for forage. Understanding secondary cell wall architecture is key to understanding recalcitrance i.e. identifying features which prevent the efficient conversion of complex biomass to simple carbon units. Here, we use multi-dimensional magic angle spinning solid-state NMR to characterize the sorghum secondary cell wall. We show that xylan is mainly in a three-fold screw conformation due to dense arabinosyl substitutions, with close proximity to cellulose. We also show that sorghum secondary cell walls present a high ratio of amorphous to crystalline cellulose as compared to dicots. We propose a model of sorghum cell wall architecture which is dominated by interactions between three-fold screw xylan and amorphous cellulose. This work will aid the design of low-recalcitrance biomass crops, a requirement for a sustainable bioeconomy.

PMID: 33247125 [PubMed - as supplied by publisher]