Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation

Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. Mass spectrometry-based strategies for glycomic quantitation have grown to include metabolic incorporation of stable isotopes, deposition of mass difference and mass defect isotopic labels, and isobaric chemical labeling, providing researchers with ample tools for accurate and robust quantitation. Beyond this, workflows have been designed to harness instrument capability for label-free quantification and numerous software packages have been developed to facilitate reliable spectrum scoring. In this review, we present and highlight the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification.

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Fast Proteome Identification and Quantification from Data-Dependent Acquisition–Tandem Mass Spectrometry (DDA MS/MS) Using Free Software Tools

Methods and Protocols ◽

10.3390/mps2010008 ◽

2019 ◽

Vol 2 (1) ◽

pp. 8 ◽

Cited By ~ 4

Author(s):

Jesse Meyer

Keyword(s):

Mass Spectrometry ◽

Tandem Mass Spectrometry ◽

Gene Knockout ◽

Tandem Mass ◽

Label Free ◽

Software Packages ◽

Complex Process ◽

Data Files ◽

Using Data ◽

Free Quantification

The identification of nearly all proteins in a biological system using data-dependent acquisition (DDA) tandem mass spectrometry has become routine for organisms with relatively small genomes such as bacteria and yeast. Still, the quantification of the identified proteins may be a complex process and often requires multiple different software packages. In this protocol, I describe a flexible strategy for the identification and label-free quantification of proteins from bottom-up proteomics experiments. This method can be used to quantify all the detectable proteins in any DDA dataset collected with high-resolution precursor scans and may be used to quantify proteome remodeling in response to drug treatment or a gene knockout. Notably, the method is statistically rigorous, uses the latest and fastest freely-available software, and the entire protocol can be completed in a few hours with a small number of data files from the analysis of yeast.

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Recent Advances in Continuous-Flow Particle Manipulations Using Magnetic Fluids

Micromachines ◽

10.3390/mi10110744 ◽

2019 ◽

Vol 10 (11) ◽

pp. 744 ◽

Cited By ~ 7

Author(s):

Xiangchun Xuan

Keyword(s):

Continuous Flow ◽

Lab On A Chip ◽

Microfluidic Devices ◽

Magnetic Fluids ◽

Label Free ◽

Particle Manipulation ◽

The Past ◽

Recent Advances ◽

Medium Exchange ◽

Flow Particle

Magnetic field-induced particle manipulation is simple and economic as compared to other techniques (e.g., electric, acoustic, and optical) for lab-on-a-chip applications. However, traditional magnetic controls require the particles to be manipulated being magnetizable, which renders it necessary to magnetically label particles that are almost exclusively diamagnetic in nature. In the past decade, magnetic fluids including paramagnetic solutions and ferrofluids have been increasingly used in microfluidic devices to implement label-free manipulations of various types of particles (both synthetic and biological). We review herein the recent advances in this field with focus upon the continuous-flow particle manipulations. Specifically, we review the reported studies on the negative magnetophoresis-induced deflection, focusing, enrichment, separation, and medium exchange of diamagnetic particles in the continuous flow of magnetic fluids through microchannels.

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Calcium imaging analysis – how far have we come?

F1000Research ◽

10.12688/f1000research.51755.1 ◽

2021 ◽

Vol 10 ◽

pp. 258

Author(s):

Miranda Robbins ◽

Charles N. Christensen ◽

Clemens F. Kaminski ◽

Marta Zlatic

Keyword(s):

Machine Learning ◽

Image Analysis ◽

Future Development ◽

Calcium Imaging ◽

Cellular Activity ◽

Imaging Analysis ◽

Signal To Noise ◽

The Past ◽

Software Packages ◽

Recent Advances

Techniques for calcium imaging were first achieved in the mid-1970s, whilst tools to analyse these markers of cellular activity are still being developed and improved. For image analysis, custom tools were developed within labs and until relatively recently, software packages were not widely available between researchers. We will discuss some of the most popular, alongside our preferred, methods for calcium imaging analysis that are now widely available and describe why these protocols are so effective. We will also describe some of the newest innovations in the field that are likely to benefit researchers, particularly as calcium imaging is often an inherently low signal-to-noise method. Although calcium imaging analysis has seen recent advances, particularly following the rise of machine learning, we will end by highlighting the outstanding requirements and questions that hinder further progress, and pose the question of how far we have come in the past sixty years and what can be expected for future development in the field.

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Calcium imaging analysis – how far have we come?

F1000Research ◽

10.12688/f1000research.51755.2 ◽

2021 ◽

Vol 10 ◽

pp. 258

Author(s):

Miranda Robbins ◽

Charles N. Christensen ◽

Clemens F. Kaminski ◽

Marta Zlatic

Keyword(s):

Machine Learning ◽

Image Analysis ◽

Future Development ◽

Calcium Imaging ◽

Cellular Activity ◽

Imaging Analysis ◽

Signal To Noise ◽

The Past ◽

Software Packages ◽

Recent Advances

Techniques for calcium imaging were first demonstrated in the mid-1970s, whilst tools to analyse these markers of cellular activity are still being developed and improved today. For image analysis, custom tools were developed within labs and until relatively recently, software packages were not widely available between researchers. We will discuss some of the most popular methods for calcium imaging analysis that are now widely available and describe why these protocols are so effective. We will also describe some of the newest innovations in the field that are likely to benefit researchers, particularly as calcium imaging is often an inherently low signal-to-noise method. Although calcium imaging analysis has seen recent advances, particularly following the rise of machine learning, we will end by highlighting the outstanding requirements and questions that hinder further progress and pose the question of how far we have come in the past sixty years and what can be expected for future development in the field.

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RESEARCH COLLABORATION AMONG LIBRARY AND INFORMATION SCIENCE SCHOOLS IN SOUTH AFRICA (1991â€“2012): AN INFORMETRICS STUDY

Mousaion ◽

10.25159/0027-2639/1082 ◽

2017 ◽

Vol 34 (3) ◽

pp. 36-59 ◽

Cited By ~ 2

Author(s):

Jan R. Maluleka ◽

Omwoyo B. Onyancha

Keyword(s):

South Africa ◽

Information Science ◽

Research Collaboration ◽

Science And Technology ◽

Library And Information Science ◽

Limited Extent ◽

Microsoft Excel ◽

The Past ◽

Software Packages ◽

Collaborative Activities

This study sought to assess the extent of research collaboration in Library and Information Science (LIS) schools in South Africa between 1991 and 2012. Informetric research techniques were used to obtain relevant data for the study. The data was extracted from two EBSCO-hosted databases, namely, Library and Information Science Source (LISS) and Library, Information Science and Technology Abstracts (LISTA). The search was limited to scholarly peer reviewed articles published between 1991 and 2012. The data was analysed using Microsoft Excel Â©2010 and UCINET for Windows Â©2002 software packages. The findings revealed that research collaboration in LIS schools in South Africa has increased over the past two decades and mainly occurred between colleagues from the same department and institution; there were also collaborative activities at other levels, such as inter-institutional and inter-country, although to a limited extent; differences were noticeable when ranking authors according to different computations of their collaborative contributions; and educator-practitioner collaboration was rare. Several conclusions and recommendations based on the findings are offered in the article.

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Recent Advances in Therapeutic Applications of Bisbenzimidazoles

Medicinal Chemistry ◽

10.2174/1573406415666190416120801 ◽

2020 ◽

Vol 16 (4) ◽

pp. 454-486 ◽

Cited By ~ 2

Author(s):

Smita Verma ◽

Vishnuvardh Ravichandiran ◽

Nihar Ranjan ◽

Swaran J.S. Flora

Keyword(s):

Heterocyclic Compounds ◽

Wide Spectrum ◽

Dna Recognition ◽

Present Review ◽

Pharmacological Activities ◽

Structural Motifs ◽

Therapeutic Applications ◽

The Past ◽

Recent Advances

Nitrogen-containing heterocycles are one of the most common structural motifs in approximately 80% of the marketed drugs. Of these, benzimidazoles analogues are known to elicit a wide spectrum of pharmaceutical activities such as anticancer, antibacterial, antiparasitic, antiviral, antifungal as well as chemosensor effect. Based on the benzimidazole core fused heterocyclic compounds, crescent-shaped bisbenzimidazoles were developed which provided an early breakthrough in the sequence-specific DNA recognition. Over the years, a number of functional variations in the bisbenzimidazole core have led to the emergence of their unique properties and established them as versatile ligands against several classes of pathogens. The present review provides an overview of diverse pharmacological activities of the bisbenzimidazole analogues in the past decade with a brief account of its development through the years.

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Characterizing Bilingual Effects on Cognition: The Search for Meaningful Individual Differences

Brain Sciences ◽

10.3390/brainsci11010081 ◽

2021 ◽

Vol 11 (1) ◽

pp. 81

Author(s):

Kristina C. Backer ◽

Heather Bortfeld

Keyword(s):

Individual Differences ◽

Cognitive Processes ◽

Language Background ◽

Bilingual Advantage ◽

The Past ◽

General Movement ◽

And Performance ◽

Task Irrelevant ◽

Analytical Approaches ◽

The Relationship

A debate over the past decade has focused on the so-called bilingual advantage—the idea that bilingual and multilingual individuals have enhanced domain-general executive functions, relative to monolinguals, due to competition-induced monitoring of both processing and representation from the task-irrelevant language(s). In this commentary, we consider a recent study by Pot, Keijzer, and de Bot (2018), which focused on the relationship between individual differences in language usage and performance on an executive function task among multilingual older adults. We discuss their approach and findings in light of a more general movement towards embracing complexity in this domain of research, including individuals’ sociocultural context and position in the lifespan. The field increasingly considers interactions between bilingualism/multilingualism and cognition, employing measures of language use well beyond the early dichotomous perspectives on language background. Moreover, new measures of bilingualism and analytical approaches are helping researchers interrogate the complexities of specific processing issues. Indeed, our review of the bilingualism/multilingualism literature confirms the increased appreciation researchers have for the range of factors—beyond whether someone speaks one, two, or more languages—that impact specific cognitive processes. Here, we highlight some of the most salient of these, and incorporate suggestions for a way forward that likewise encompasses neural perspectives on the topic.

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Recent advances in plasmonic nanostructures applied for label‐free single‐cell analysis

Electroanalysis ◽

10.1002/elan.202100330 ◽

2021 ◽

Author(s):

Xue-Wei Liao ◽

Qiu-Yang Xu ◽

Zheng Tan ◽

Yang Liu ◽

Chen Wang

Keyword(s):

Single Cell ◽

Single Cell Analysis ◽

Plasmonic Nanostructures ◽

Cell Analysis ◽

Label Free ◽

Recent Advances

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Label-Free Mass Spectrometry-Based Quantification of Linker Histone H1 Variants in Clinical Samples

International Journal of Molecular Sciences ◽

10.3390/ijms21197330 ◽

2020 ◽

Vol 21 (19) ◽

pp. 7330

Author(s):

Roberta Noberini ◽

Cristina Morales Torres ◽

Evelyn Oliva Savoia ◽

Stefania Brandini ◽

Maria Giovanna Jodice ◽

...

Keyword(s):

Mass Spectrometry ◽

Histone H1 ◽

Histone Variants ◽

Linker Histone ◽

Clinical Samples ◽

Label Free ◽

Complex Samples ◽

Linker Histone H1 ◽

Ideal Tool ◽

Free Quantification

Epigenetic aberrations have been recognized as important contributors to cancer onset and development, and increasing evidence suggests that linker histone H1 variants may serve as biomarkers useful for patient stratification, as well as play an important role as drivers in cancer. Although traditionally histone H1 levels have been studied using antibody-based methods and RNA expression, these approaches suffer from limitations. Mass spectrometry (MS)-based proteomics represents the ideal tool to accurately quantify relative changes in protein abundance within complex samples. In this study, we used a label-free quantification approach to simultaneously analyze all somatic histone H1 variants in clinical samples and verified its applicability to laser micro-dissected tissue areas containing as low as 1000 cells. We then applied it to breast cancer patient samples, identifying differences in linker histone variants patters in primary triple-negative breast tumors with and without relapse after chemotherapy. This study highlights how label-free quantitation by MS is a valuable option to accurately quantitate histone H1 levels in different types of clinical samples, including very low-abundance patient tissues.

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