Phosphoproteomics: unraveling the signaling web

In recent years, phosphoproteomic technologies have increased our understanding of cellular signaling networks. Here, we frame recent phosphoproteomics-based advances in the context of the DNA damage response and ErbB receptor family signaling and offer a perspective on how the molecular insights arising from the integration of such proteomic approaches might be used for clinical applications.     

Seeing is believing: Applications for nanotechnology in medical imaging and drug discovery

In recent years, progress has been made on in both micro- and nano-sized materials. At the same time, the advances in biology, specifically in genomics, have provided us with a wealth of information that can now be put into research applications and hopefully clinical practice. In our research center in Niskayuna, NY, we have been working on advanced technologies and novel approaches in both areas. Here we show several examples of how we have addressed different topics in our research. In addition, we will show, how we are combining nanotechnology with advanced biology. In particular, we will show examples of using nanoparticles for different applications in vitro and in vivo. We will also show the context for both technology areas and the applications of strategic importance.     

Modelling emotion,perfecting heart: disassembling technologies of affect with an android bodhisattva in Japan

As part of a surge in technologies with so-called ‘artificial emotional intelligence’, robotics engineers and Buddhist monks in Japan have developed an android bodhisattva to deliver teachings at a popular Zen temple. Like many recent robots in Japan, the android is designed to impact visitors’ feelings. For this reason, it can be called a ‘technology of affect’. In order to communicate how new affective technologies are facilitating intimacy in human-machine relations in Japan, we employ the concept of ‘disassembling’. By conceptually disassembling technologies of affect and placing them in performative contexts, we show how technologies of affect also disassemble established associations between artificial agents and the feelings they evoke in popular imaginaries. We argue that identifying these disassembling processes helps demonstrate how emerging AI technologies can engender social change at the level of affect through evocative depictions of machine emotion.     

Cell patterning technologies for organotypic tissue fabrication

Bottom-up tissue engineering technologies address two of the main limitations of top-down tissue engineering approaches: the control of mass transfer and the fabrication of a controlled and functional histoarchitecture. These emerging technologies encompass mesoscale (e.g. cell sheets, cell-laden hydrogels and 3D printing) and microscale technologies (e.g. inkjet printing and laser-assisted bioprinting), which are used to manipulate and assemble cell-laden building blocks whose thicknesses correspond to the diffusion limit of metabolites, and present the capacity for cell patterning with microscale precision, respectively. Here, we review recent technological advances and further discuss how these technologies are complementary, and could therefore be combined for the biofabrication of organotypic tissues either in vitro, thus serving as realistic tissue models, or within a clinic setting.     

Emerging frontiers in immuno- and gene therapy for cancer

Background aimsThe field of cell and gene therapy in oncology has moved rapidly since 2017 when the first cell and gene therapies, Kymriah followed by Yescarta, were approved by the Food and Drug Administration in the United States, followed by multiple other countries. Since those approvals, several new products have gone on to receive approval for additional indications. Meanwhile, efforts have been made to target different cancers, improve the logistics of delivery and reduce the cost associated with novel cell and gene therapies. Here, we highlight various cell and gene therapy-related technologies and advances that provide insight into how these new technologies will speed the translation of these therapies into the clinic.ConclusionsIn this review, we provide a broad overview of the current state of cell and gene therapy-based approaches for cancer treatment – discussing various effector cell types and their sources, recent advances in both CAR and non-CAR genetic modifications, and highlighting a few promising approaches for increasing in vivo efficacy and persistence of therapeutic drug products.     

Novel Genomic Tools and Modern Genetic and Breeding Approaches for Crop Improvement

In recent past, genomic tools especially molecular markers have been extensively used for understanding genome dynamics as well for applied aspects in crop breeding. Several new genomics technologies such as next generation sequencing (NGS), high-throughput marker genotyping, -omics technologies have emerged as powerful tools for understanding genome variation in crop species at DNA, RNA as well as protein level. These technologies promise to provide an insight into the way gene(s) are expressed and regulated in cell and to unveil metabolic pathways involved in trait(s) of interest for breeders not only in model-/major- but even for under-resourced crop species which were once considered “orphan” crops. In parallel, genetic variation for a species present not only in cultivated genepool but even in landraces and wild species can be harnessed by using new genetic approaches such as advanced-backcross QTL (AB-QTL) analysis, introgression libraries (ILs), multi-parent advanced generation intercross (MAGIC) population and association genetics. The gene(s) or genomic regions, responsible for trait(s) of interest, identified either through conventional linkage mapping or above mentioned approaches can be introgressed or pyramided to develop superior genotypes through molecular breeding approaches such as marker-assisted back crossing (MABC), marker assisted recurrent selection (MARS) and genome wide selection (GWS). This article provides an overview on some recent genomic tools and novel genetic and breeding approaches as mentioned above with a final aim of crop improvement.     

Imaging of the host/parasite interplay in cutaneous leishmaniasis

An understanding of host-parasite interplay is essential for the development of therapeutics and vaccines. Immunoparasitologists have learned a great deal from ‘conventional’ in vitro and in vivo approaches, but recent developments in imaging technologies have provided us (immunologists and parasitologists) with the ability to ask new and exciting questions about the dynamic nature of the parasite-immune system interface. These studies are providing us with new insights into the mechanisms involved in the initiation of a Leishmania infection and the consequent induction and regulation of the immune response. Here, we review some of the recent developments and discuss how these observations can be further developed to understand the immunology of cutaneous Leishmania infection in vivo.     

Targeted and Untargeted Proteomics Approaches in Biomarker Development

An enormous amount of research effort has been devoted to biomarker discovery and validation. With the completion of the human genome, proteomics is now playing an increasing role in this search for new and better biomarkers. Here, what leads to successful biomarker development is reviewed and how these features may be applied in the context of proteomic biomarker research is considered. The “fit‐for‐purpose” approach to biomarker development suggests that untargeted proteomic approaches may be better suited for early stages of biomarker discovery, while targeted approaches are preferred for validation and implementation. A systematic screening of published biomarker articles using MS‐based proteomics reveals that while both targeted and untargeted technologies are used in proteomic biomarker development, most researchers do not combine these approaches. i) The reasons for this discrepancy, (ii) how proteomic technologies can overcome technical challenges that seem to limit their translation into the clinic, and (iii) how MS can improve, complement, or replace existing clinically important assays in the future are discussed.     

“The state of the heart”: Recent advances in engineering human cardiac tissue from pluripotent stem cells

The pressing need for effective cell therapy for the heart has led to the investigation of suitable cell sources for tissue replacement. In recent years, human pluripotent stem cell research expanded tremendously, in particular since the derivation of human-induced pluripotent stem cells. In parallel, bioengineering technologies have led to novel approaches for in vitro cell culture. The combination of these two fields holds potential for in vitro generation of high-fidelity heart tissue, both for basic research and for therapeutic applications. However, this new multidisciplinary science is still at an early stage. Many questions need to be answered and improvements need to be made before clinical applications become a reality. Here we discuss the current status of human stem cell differentiation into cardiomyocytes and the combined use of bioengineering approaches for cardiac tissue formation and maturation in developmental studies, disease modeling, drug testing, and regenerative medicine.     

Classifying by colors: FISH-based genome analysis

In recent years a fascinating evolution of different multicolor fluorescence in situ hybridization (FISH) technologies could be witnessed. The various approaches to cohybridize multiple DNA probes in different colors opened new avenues for FISH-based automated karyotyping or the simultaneous analysis of multiple defined regions within the genome. These developments had a remarkable impact on microscopy design and the usage of highly sensitive area imagers. In addition, they led to the introduction of new fluorochromes with appropriate filter combinations, refinements of hybridization protocols, novel probe sets, and innovative software for automated chromosome analysis. This paper attempts to summarize the various multicolor approaches and discusses the application of the individual technologies.     

Model-organism genomics in veterinary parasite drug-discovery

A recent article about genomic filtering highlights exciting new opportunities for antiparasitic drug discovery resulting from major advances in genomic technologies. In this article, we discuss several approaches in which model-organism genomics and proteomics could be applied to the identification and validation of novel targets for antiparasitic drug discovery in veterinary medicine.     

Acoustic-based chemical tools for profiling the tumor microenvironment

Acoustic-based imaging modalities (e.g. ultrasonography and photoacoustic imaging) have emerged as powerful approaches to noninvasively visualize the interior of the body due to their biocompatibility and the ease of sound transmission in tissue. These technologies have recently been augmented with an array of chemical tools that enable the study and modulation of the tumor microenvironment at the molecular level. In addition, the application of ultrasound and ultrasound-responsive materials has been used for drug delivery with high spatiotemporal control. In this review, we highlight recent advances (in the last 2–3 years) in acoustic-based chemical tools and technologies suitable for furthering our understanding of molecular events in complex tumor microenvironments.     

Genomics in a changing arctic: critical questions await the molecular ecologist

Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox. These questions include understanding (i) the mechanisms of plant acquisition and uptake of N in cold soils, (ii) how these processes are mediated by root traits, (iii) the role played by the plant microbiome in cycling C and nutrients within high‐latitude ecosystems and (iv) plant adaptation to extreme Arctic climates. We highlight how contributions can be made in these areas through studies that target model and nonmodel organisms and emphasize that the sequencing of the Populus and Salix genomes provides a valuable resource for scientific discoveries related to the plant microbiome and plant adaptation in the Arctic. Moreover, there exists an exciting role to play in model development, including incorporating genetic and evolutionary knowledge into ecosystem and Earth System Models. In this regard, the molecular ecologist provides a valuable perspective on plant genetics as a driver for community biodiversity, and how ecological and evolutionary forces govern community dynamics in a rapidly changing climate.     

Into the wild—WAMBAM goes to Canada

The sixth Wild Animal Models Bi‐Annual Meeting was held in July 2017 in Québec, with 42 participants. This report documents the evolution of questions asked and approaches used in evolutionary quantitative genetic studies of wild populations in recent decades, and how these questions and approaches were represented at the recent meeting. We explore how ideas from previous meetings in this series have developed to their present states, and consider how the format of the meetings may be particularly useful at fostering the rapid development and proliferation of ideas and approaches.