Methods Collections

Protein-Protein interaction methods

Guest Editors: Michael Overduin, Alastair Barr
The study of protein-protein interactions is key to understanding the network of molecular interactions underlying biological effects, and defining how individual proteins perform their functional role within a cell.  Detailed understanding of t Show More

Multi-modal methods to study the neural reward system in humans


Guest Editor: Katherine Stavropoulos
The neural reward system plays a key role in human learning, motivation, pleasure, and the ability to change one’s behavior to maximize desired outcomes. Given the wide range of behaviors affected by the reward system, it is unsurprising that a Show More

Complexity reduction methods for molecular biology


Guest Editor: Milo Lin
Complexity is a key obstacle in understanding and engineering biological systems.The details of this complexity rapidly accumulate due to advances in sequencing, imaging, and multiplexing. This leads to larger and more precise datasets. Longstanding Show More

Neuroepigenetics and neurotranscriptomics: from molecules to behaviors

Guest Editor: Pavan Agrawal
Rapid advances in the field of neuroepigenetics and neurotranscriptomics have transformed our understanding of gene regulation in the nervous system. These discoveries have put to rest the mechanistic dichotomy between nature and nurture,  effec Show More

Alternative rodent models of brain injury and post-injury assessment 


Guest Editor: Matthew Boyko
Animal models are an important tool to evaluate the pathophysiology of cerebral injury and to advance the development of novel treatment options for improving neurological outcomes. Appropriate animal models are valued for their reproducibility and s Show More

Molecular imaging from bench to bedside in translational medicine


Guest Editor: Sergio Souza
Molecular imaging has the ability to non-invasively imaging functional aspects of different organs in the body and has been used as a bridge to translate preclinical results to the clinical scenario, playing a critical role in diagnosis and therapeut Show More

Mass spectrometry methodologies for biomolecule analyses

Guest Editor: Azad Eshghi
Knowledge of biochemical pathways is part of the foundation of basic and applied research in the field of biochemistry. Mass spectrometers are indispensable tools for the study of biomolecules due to the afforded specificity, multiplexing and quantit Show More

Methods in neuronal cell culture

Guest Editor: Ramiro Almeida
Neurons are the primary cells of the nervous system and are responsible for the distinctive roles of the brain. Understanding the mechanisms that regulate their differentiation, development, and function is essential to understand the nervous system Show More

Zebrafish models of central nervous system disorders


Guest Editors: Mohd. Farooq Shaikh, Ayanabha Chakraborti
Neurological disorders have a high global prevalence. However, the molecular mechanisms mediating these disorders remain poorly understood. Animal models play a significant role in better understanding the pathophysiology of a variety of diseases aff Show More

Methods to study cancer cell phenotypes and drug efficacy in vitro and in vivo 


Guest Editor: Giridhar Mudduluru
Cancer is a leading cause of death worldwide. Increased lethality of cancer is due to delayed diagnosis and especially due to the metastasis of the disease to different tissues. Secondly, the tumor microenvironment is different between the primary si Show More

Molecular and cellular methods to study neuron development

Guest Editor: Daniel Vogt
The proper development of the brain requires multiple developmental events that eventually establish a balanced network of excitatory and inhibitory neurons that work in tandem with glia. Disruptions in molecular and cellular events during developmen Show More

Preclinical models and imaging modalities of tumor microenvironment in metastasis

Guest Editor: Sofia Sousa
Cancer research has focused on the cancer cell, its proliferation rates, apoptosis resistance, mutation rates, sensitivity to radio and chemotherapy. However, tumor metastatic progression involves many other cellular and molecular players, the tumor Show More

Methods to study converging molecular pathways in ALS

Guest Editor: Karthik Krishnamurthy
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that ultimately leads to fatal paralysis due to impaired neuromuscular function. At the cellular level, ALS is caused by motor neuron degeneration either intrinsically or Show More

Emerging Techniques for 3D Imaging in Neuroscience

Guest Editor: Matheus de Castro Fonseca
Imaging is an increasingly important tool in both basic and applied research in biology. An array of imaging techniques provides the unprecedented capability of visualizing organs and cell architecture and function. These techniques show a great reso Show More

Optical 3D Microscopy

Guest Editor: Herbert Schneckenburger
Optical microscopy plays an increasing role in studies of 3-dimensional cell cultures as well as whole organisms. Since the sample thickness often exceeds the depth of focus considerably, confocal methods have been developed more than 30 years ago in Show More

Multi-parametric flow cytometry applications

Guest Editor: Manoj Muthukuru
Flow cytometry combines the dynamism and the versatility for a wide range of phenotypic and functional characterization of cells and molecules.. Flow cytometry plays vital role in clinical discovery which is exemplified in the areas of immunological Show More

New ways to analyze local clinical data

Guest Editor: Gal Almogy
Mathematical models are widely used in the study of infectious diseases, providing valuable theoretical insights into the logic of pathogen spread, as well as guiding public health strategies. Digital technologies have the potential to transform heal Show More

Study of Ca2+ associated signaling transduction in plant cells

Guest Editor: Yi Ma
Ca2+ is a ubiquitous secondary messenger involved in numerous plant signaling transduction cascades, such as defense responses to environmental cues including abiotic and biotic stresses, gravitropism, pollen tube growth, nodulation, etc. Ligand bind Show More

Minimally invasive pancreatic surgery 

Guest Editors: Sanne Lof, Frederique Vissers, Maarten Korrel, Amer Zureikat, Safi Dokmak, Ugo Boggi, Mohammed Abu Hilal, Marc Besselink
Minimally invasive pancreatic surgery is on the rise worldwide. Minimally invasive distal pancreatectomy (MIDP) has been reported to be superior to open distal pancreatectomy (ODP) in terms of blood loss and hospital stay. The oncological safety of M Show More

Current research methods in sinoatrial and atrioventricular nodes with advancing age

Guest Editor: Mingyi Wang
Aging populations are on the rise worldwide. Aging is the major risk factor for the development of cardiac arrythmia. Age-related alterations throughout the sinoatrial node (SAN), atrioventricular node (AVN), and His Show More

Ex vivo techniques to study molecular/cellular mechanisms of neurodevelopment and neurodegeneration

Guest Editor: Lynette Foo
In vitro techniques have been widely used to study neurodevelopment and neurodegeneration with great success. However, frequently these in vitro cultures contain only one or two cell types.  Naturally, a next step in complexity prior to in vivo Show More

Standard and novel methods in the study of corticogenesis

Guest Editor: Isabel Garay
The cerebral cortex is the seat of higher brain function and plays a key role in memory, attention, thought, perception and language. Development of this cerebral structure is a complex process in which different steps need to be tightly regulated an Show More

Zebrafish models for exploring early stages of neurological diseases 

Guest Editor: Chris Shaw

The proposed edition will focus on the value of zebrafish models for exploring early stages of neurological diseases such as in ALS, Parkinson's disease and Alzheimer's disease. Such stages are largely a mystery in curre Show More

Methods to study the structure and function of olfactory receptors

Guest Editor: Chiquito Crasto
Biomedical research related to olfactory receptors (OR) and their role in olfaction came into prominence after the discovery of these receptors in the early nineteen nineties and the subsequent Nobel Prize award to the discoverers of ORs in 2004. OR Show More

Cardio-oncology assessment methods

Guest Editor: Kyuwan Lee
Cancer survivors remain distinctly at risk for cardiovascular diseases. Cardiovascular toxicity induced by cancer treatment such as radiation or chemotherapy has been strongly suggested to increase cardiovascular diseases in cancer survivors. While a Show More

Pluripotent stem cell differentiation, genome editing and tissue engineering

Guest Editor: David Hay
Pluripotent stem cells retain the ability to form all cell types in the human body. This provides the field with renewable forms of human tissue, from defined genetic backgrounds, to model physiology ‘in the dish’ and also for clinical ap Show More

Experimental systems and methodologies for the study of axon-specific molecular events

Guest Editors: Andrew Tosolini, Giampietro Schiavo, James Sleigh, Gerardo Morfini
Axons are the main line of information transmission among neurons. Accordingly, axonal pathology represents a common pathogenic feature associated with loss of neuronal connectivity in multiple unrelated neurodegenerative diseases including Alzheimer Show More

Multi-modal approaches to study dynamic neural signals of emotion

Guest Editors: Zhaoxin Wang, Junling Gao, Qun Yang, Delin Sun
Emotions are tightly associated with human thoughts, feelings and behaviors in various ways. Abnormal emotion processing leads to excessive or insufficient reactions, and is often accompanied by mental disorders such as anxiety, depression, post Show More

Methods in dental material research


Guest Editor: Wen Zhou
Metal-ceramic restoration has remained the benchmark of prosthetic restoration for many decades, especially in high-stress occlusion surface of clinical situations. Current trends in dental research and material development have shown a preference fo Show More

Automation in radiation therapy

Guest Editor: Silvia Calusi
External beam radiotherapy consists of irradiating patients with photon, electron or particle beams that deliver a quantity of energy (radiation dose) sufficient to destroy tumor cells in a delineated target.  Dose distributions are delivered in Show More

Chloroplast research methods: probing the targeting, localization, and interactions of chloroplast proteins

Guest Editor: Paul Jarvis
Chloroplasts are the organelles that define plants. Along with many other metabolic, developmental and signalling functions, chloroplasts are responsible for photosynthesis – the process whereby sunlight energy is harnessed to power the cellula Show More

Prostate organoid research techniques and methods: three-dimensional (3D) culture, spin-down, dimpled parafilm and fusion method

Guest Editors: Sanghee Lee, Christina Jamieson
Organoids are three-dimensional (3D) ex vivo cellular structures that are believed to recapitulate and maintain the in vivo conditions of cellular viability and responsiveness to therapeutic drugs. Matrigel or collagen have been utilized as an extrac Show More

Techniques for the detection of early stage prostate cancer

Guest Editors: Huan Xu, Fubo Wang
This Methods Collection focuses on the early detection and diagnosis of prostate cancer (PCa). PCa is the second most frequently diagnosed cancer overall and is the fifth leading cause of cancer mortality in men. Prognosis is relatively positive if t Show More

Methods for studying stroke in vivo

Guest Editor: YoneJung Yoon
Stroke is the second leading cause of death and disability worldwide. Animal stroke models are important in studying the causative mechanisms of stroke as well as to investigate novel treatments. However, the different causes and biomarkers of stroke Show More

Artificial intelligence in ophthalmology

Guest Editors: Giulia Corradetti, Enrico Borrelli
The major progress achieved in ocular imaging offered to ophthalmologists worldwide the opportunity to access and analyze subclinical features. Although, the development of millions of morphological datasets raised the necessity to identify a method Show More

Current methods in cardiac regeneration research


Guest Editor: Ahmed Mahmoud
Cardiovascular diseases remain a major health and economic burden worldwide. This is a consequence to the poor regenerative ability of the adult mammalian heart to repair itself in response to injury. Understanding the cellular and molecular events t Show More

Using C. elegans to monitor proteostasis imbalances


Guest Editors: Carmen Nussbaum-Krammer, Cindy Voisine
Protein homeostasis, or ‘proteostasis’, is fundamental to cellular and organismal health. Conserved cellular processes cooperate to maintain a properly folded proteome by influencing protein synthesis, folding and clearance. Cells respond Show More

Animal behavioral paradigms and analysis methodologies in neural circuit studies of neurological dysfunctions


Guest Editor: Vania Cao
As the field of neuroscience continues to produce large and increasingly complex datasets of brain structure, physiology and function, the demand for accurate and targeted behavioral paradigms to model neurological dysfunctions continues to grow.&nbs Show More

New and improved approaches for the study of Saccharomyces cerevisiae ecology and evolution


Guest Editor: Irene Stefanini
The budding yeast Saccharomyces cerevisiae plays major roles in a broad range of environments and has relevant impacts on several biotechnological applications. It has also recently been shown to have an impact on humans and other animals he Show More

Assessment of lesion-specific transcriptional and epigenetic alterations in breast cancer

Guest Editors: Haider Hassan, Milica Krstic
Breast cancer continues to be the most commonly diagnosed cancer worldwide and represents a leading cause of cancer-related mortality among women. Next-Generation Sequencing (NGS) has played an important role in providing mechanistic insights into th Show More

Behavioral paradigms for disentangling perceptual decisions related network activity in animal models


Guest Editor: Dan Ganea
Capturing large scale neuronal activity permits the functional analysis of inter and intra-areal neuronal networks in relation to perceptual decision-making under multi-faceted behaviors. From a technological perspective, recording the function of su Show More

Breakthrough technologies for unraveling message of microRNAs

Guest Editors: Esther Zorio, Aitana Braza-Boils
miRNAs are the most studied non-coding RNAs, whose expression is tissue-specific. miRNAs post-transcriptionally modulate protein expression by degrading mRNA or blocking its translation. Increasing efforts are underway to characterize these molecules Show More

Current methods in Astyanax mexicanus research

Guest Editors: Clifford J. Tabin, Misty Rose Riddle
The Mexican Tetra, Astyanax mexicanus is an excellent model organism to study the developmental and genetic basis of evolution. This species of fish consists of a river-dwelling (surface) population and a number of cave-dwelling po Show More

Current research methods in rabies diagnosis, prevention, treatment, and control

Guest Editor: Charles E. Rupprecht
Rabies is an acute progressive encephalitis caused by a lyssavirus. The case fatality of this zoonosis is the highest for any infectious disease. Although laboratory techniques on rabies have progressed greatly over the last century, typically such i Show More

Multi-modal analytics in energy storage

Guest Editors: George J. Nelson, Leela M. R. Arava, Partha P. Mukherjee
Energy storage is a critical enabler for vehicle electrification and renewable energy integration into the electric grid. Primary challenges in lithium based intercalation (Li-ion) and conversion (e.g., Li-S) chemistries continue to remain in en Show More

New techniques and approaches for the assessment or intervention in learning disabilities and ADHD

Guest Editors: Trinidad García, Marisol Cueli, Débora Areces, Celestino Rodríguez
International classifications of mental disorders for the diagnosis of Learning Disabilities (LD) and Attention Deficit/Hyperactivity Disorders (ADHD) establish that they are not the result of other disabling conditions, although they might occur con Show More

Cellular models of neurodegeneration


Guest Editors: Manu Sharma, Jacqueline Burré
Neurodegenerative diseases including Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, amyotrophic lateral sclerosis, and frontotemporal dementia are devastating disorders with no known cure, mainly due to lack of unde Show More

Artificial oocyte activation to create parthenogenetic blastocysts.

Guest Editors: Marcos Kulmann, Adriana Bos-Mikich
Renewed interest in parthenogenetic activation of mammalian oocytes has come about for scientific, medical, and economic reasons. Germinal vesicle (GV), MI oocytes and failed to fertilize (FF) oocytes are usually discarded in human IVF cycles.  Show More

New frontiers for the production of bioactive ingredients by plant in vitro technologies

Guest Editors: Nathalie Giglioli-Guivarc'h, Bilal Abbasi, Christophe Hano
The use of plant in vitro (bio)technologies offers an attractive alternative for the production of plant-based active ingredients. Plant cells are small factories able to synthesize an exceptional variety of commercially important phytochemi Show More

Minimally invasive gynecological surgery

Guest Editor: Antonio Simone Laganà
Gynecological surgery has gone through a radical evolution during recent years, due to technological improvements and a significant shift towards a minimally invasive approach. In the current scenario, both oncological and non-oncological conditions Show More

Molecular and physiological approaches for studying plant-microbe interactions

Guest Editors: Mario Serrano, Alexandre Tromas, Oswaldo Valdés-López
Plants constantly interact with different microorganisms; some of which could be potential pathogens or symbionts. Plants need to be able to distinguish between pathogens and symbionts to activate the correct molecular responses—either eng Show More

Methods to study protein S-palmitoylation

Guest Editor: Dhrubajyoti Chowdhury
S-palmitoylation is the covalent attachment of the fatty acid palmitate to cysteine (Cys) residues of the substrate protein through thioester linkage. This universal post-translational lipid modification facilitates membrane association and therefore Show More

Methods to study human papilloma virus (HPV) in human breast samples

Guest Editor: Cristiane Cunha Frota
Human papilloma virus (HPV) plays a fundamental role in carcinogenesis of several forms of cancer by subverting an effective immune response. There are more than 100 known HPV genotypes, of which, 13 can cause cancer of the cervix and are also associ Show More

Skull base surgery - One of the most demanding disciplines in neurosurgery

Guest Editor: Ardian Hana
Performing brain surgery is a very demanding task for every neurosurgeon. In this discipline skull base surgery could be considered as the most difficult surgery to perform. Due to the geographical proximity of many vital structures of the brain Show More

Conservation and restoration of aquatic ecosystems


Guest Editors: Tony Herrera Grao, Núria Bonada, Miguel Ca?edo-Argüelles Iglesias
We are facing a global biodiversity and environmental crisis that poses serious risks to human welfare. Among the different ecosystems on Earth, aquatic ecosystems are experiencing the fastest rates in species extinction and ecosystem degradation. Gi Show More