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Journal of Postdoctoral Research (JPR) - Vol. 4, No. 11, November 2016
 
EDITORIAL: How Next Generation Sequencing has Transformed Microbial Ecology
Jennifer Tsang, PhD
Microbial Ecology: Where are we now?
Lisa Boughner, PhD and Pallavi Singh, PhD
Role of L-Proline in Stabilization of Biological Membranes
Lindong Weng, PhD
OPINION : Cancer Cell Psychology: When People Behave Like Cancer Cells
Nzola De Magalhães, M.S., Ph.D., HTL(ASCP)
Shaping cancerous landscapes with microbial communities
Aditya Kulkarni, PhD
EDITORIAL : Proteins as a source for Hydrogen Fuel
Sumit O. Bajaj, PhD
Photocatalytic Hydrogen Production by Protein Systems
Sarah R. Soltau, PhD
New polymorphism of the influenza virus resistance Mx1 gene in Iberian domestic pigs
RF Godino, and AI Fernández
Unique Features of Neuronal Autophagy: Considerations for Therapeutic Targeting
José Antonio Rodríguez-Navarro, and Eloy Bejarano
Defining the cognitive enhancing properties of video games: Steps Towards Standardization and Translation
Shikha Jain Goodwin, and Derek Dziobek
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Author(s)
Jennifer Tsang, PhD
Address
Beth Israel Deaconess Medical Center, HMS, Boston, MA 02115, USA
Abstract:

In recent years, biology has steadily become a more interdisciplinary field. Advances in technology have pioneered the development of many tools that allow concepts in physics, math, computer science, and chemistry to be applied to biological problems.  As an example, next generation sequencing (NGS) technologies have been rapidly developed with these tools becoming more and more accessible to biologists.  NGS is also known as high-throughput sequencing and is an all-inclusive term used to describe modern sequencing technologies including Illumina, 454, Ion torrent, and SOLiD sequencing that can generate billions of reads.  With the advent of NGS and big data, many biological quandaries ranging from the microbiome to human population studies can now be explored in ways that were not previously possible.  


Author(s)
Lisa Boughner, PhD and Pallavi Singh, PhD
Address
Center for Microbial Ecology, and the Department of Microbiology and Molecular Genetics, MSU, E. Lansing MI 48823
Abstract:

Conventional microbiological methods have been readily taken over by newer molecular techniques due to the ease of use, reproducibility, sensitivity and speed of working with nucleic acids. These tools allow high throughput analysis of complex and diverse microbial communities, such as those in soil, freshwater, saltwater, or the microbiota living in collaboration with a host organism (plant, mouse, human, etc). For instance, these methods have been robustly used for characterizing the plant (rhizosphere), animal and human microbiome specifically the complex intestinal microbiota. The human body has been referred to as the Superorganism since microbial genes are more numerous than the number of human genes and are essential to the health of the host. In this review we provide an overview of the Next Generation tools currently available to study microbial ecology, along with their limitations and advantages. 


Author(s)
Lindong Weng, PhD
Address
BioMEMS Resource Center, MGH-HMS, 114 16th St., Charlestown, MA 02129 
Abstract:

L-proline, a natural α-amino acid, has been found useful as an osmoprotectant and antioxidant. It can prevent the denaturation of peptides and increase the survival rate of freeze-dried fungi by inhibiting the generation of intracellular reactive oxygen species. L-proline was shown to effectively preserve the structure and function of the frozen vesicles. But there is evidence showing that L-proline was able to destabilize the lamellar liquid-crystalline phases in both fully hydrated and freeze-dried lipids, which is undesirable. Given the complex role of L-proline in the stabilization of biologics, the current study conducted molecule dynamics simulations of hydrated 1, 2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) bilayers in the presence of L-proline to elucidate the interactions between L-proline and lipid bilayers. The results show that the proline molecules can slightly perturb lipid headgroups with an occasional insert of proline molecules between lipid headgroups. In the fully hydrated state, proline molecules prefer to hydrogen-bond with water molecules rather than lipids. The MD simulation results do not support the 'water replacement' hypothesis for the mechanism of membrane protection by proline.


Author(s)
Nzola De Magalhães, M.S., Ph.D., HTL(ASCP)
Address
Department of Pathology, UCSD, CA 92093, USA
Abstract:

Despite continued scientific research efforts and technological advancement to find an effective cure, Cancer remains an enigma. This article aims to propose a different scientific approach to studying the biology of Cancer by offering insights into the striking similarities between the psyche of humans and the behavior of cancer cells. Without attempting to trivialize the complexity of the disease, the article will discuss the fundamental connection between humans and cells that extend beyond just signaling pathways and molecular bonds. The discussion will introduce Cancer Cell Psychology as a new area of study that should be closely considered to further our understanding of this disease.


Author(s)
Aditya Kulkarni, PhD
Address
Department of Biochemistry, UTSMC, Dallas TX 75390, USA
Abstract:

The dynamic interplay between resident microbiota, host immunity and anti-cancer therapy has generated a captivating enigma underlying the assignment of cause-effect relationships among these factors. The diverse effects of microbes on carcinogenesis, ranging from preventing or promoting cancer to dictating therapeutic outcomes, complicates the understanding of the relationship between the microbiota and the host. Understanding how host-microbe interactions are influenced by genes and environment in carcinogenesis, and applying that knowledge for cancer detection and treatment are gathering prime interest. This review scrutinizes the host-microbe relationship in the context of cancer by discussing the latest findings involving the host-microbe-drug interaction axes. 

 


Author(s)
Sumit O. Bajaj, PhD
Address
Department of Chemistry and Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
Abstract:

To accommodate the increasing energy demands, new techniques for the production, conversion and storage of energy are required. Solar energy is a natural, free and abundant source of energy from the sun and can be converted to various forms. As hydrogen possesses '120-140 MJ/kg storage capacity and is a clean energy source, it can be studied as a future efficient and eco-friendly fuel. Studies directed towards converting solar energy for H2 production using catalysts are currently underway, but locating a fit catalyst is challenging. Dr. Soltau’s review covers emerging opportunities using natural protein structures as a booming source towards the conversion of solar energy to H2 production. 


Author(s)
Sarah R. Soltau, PhD
Address
Division of Chemical Sciences and Engineering, ANL, Argonne, IL 60439, USA
Abstract:

Integration of synthetic molecular catalysts with protein structures has emerged as a new field of study that provides novel opportunities to understand and improve on catalytic processes.  The use of proteins to develop photocatalytic biohybrid systems enhances this field by further enabling the development of direct donor-acceptor systems that utilize protein architectures to facilitate photocatalysis.  This mini-review focusses primarily on current efforts to combine protein scaffolds with homogeneous synthetic molecular catalysts and photosensitizers for photocatalytic hydrogen (H2) production, while other methods of H2 production will be briefly introduced in context. 


Author(s)
RF Godino, and AI Fernández
Address
Department of Ophthalmology, Ocular Genomics Institute-HMS, MEEI, Boston, MA. USA
Dpto Biotecnología1 y Mejora Genética2, INIA. Madrid, Spain.
Abstract:

Mx1 (Myxovirus (Influenza virus) resistance 1, interferon-inducible protein p78) gene has been implicated in the resistance to a wide range of RNA viruses including influenza A in several species such as Sus scrofa. In the present study a 28-bp deletion in exon 14 of the Mx1 gene has been identified in Iberian domestic pigs but not in other domestic breeds neither in wild boars. The mutation produces a frameshift giving a protein with 6 amino acid substitutions and the extension of the C-terminal region with additional 20 amino acids with respect to the wild type MX1 protein. The new allelic polymorphism affects the antiviral domain of the MX1 protein and therefore might impact its anti-influenza virus activity. It has been demonstrated that polymorphisms in the Mx1 murine locus, affect the survival rate of mice upon experimental infection with influenza virus. It might be possible to improve the innate resistance of pigs to influenza virus infection by determining the porcine Mx1 alleles with more potent antiviral activity and genetically selecting animals bearing such alleles.  

 


Author(s)
José Antonio Rodríguez-Navarro, and Eloy Bejarano
Address
Jean Mayer USDA Human Nutrition Research Center on Aging, 711 Washington Street Boston, MA, 02111, USA
Departamento de Investigación, Hospital Ramón y Cajal, Carretera de Colmenar, km 9,100, Madrid, Spain
Abstract:

Autophagy is an essential catabolic pathway responsible for the maintenance of organismal homeostasis. Degradation of damaged organelles and proteinaceous aggregates predominantly takes place via autophagy and a proper function of autophagy is vital for cellular surveillance. Given their post-mitotic nature, neurons are particularly vulnerable to stress and, consequently, robust housekeeping systems are required to guarantee the adequate functionality and viability of neurons. A vast literature links defective autophagic function to neurodegenerative diseases and dietary/pharmacological activation of autophagy has been proposed as potential strategy to fight these diseases. Here we summarize the recent progress on the research of neuronal autophagy highlighting the unique features of autophagy in neurons. In the last section, we discuss about therapeutic strategies modulating autophagy to preserve neuronal surveillance during aging.


Author(s)
Shikha Jain Goodwin, and Derek Dziobek
Address
Brain Sciences Center, VA Medical Center, Minneapolis MN.
Graduate Program in Neuroscience, University of Minnesota.

Abstract:

Ever since video games were available to the general public, they have intrigued brain researchers for many reasons. There is an enormous amount of diversity in the video game research, ranging from types of video games used, the amount of time spent playing video games, the definition of video gamer versus non-gamer to the results obtained after playing video games. In this paper, our goal is to provide a critical discussion of these issues, along with some steps towards generalization using the discussion of an article published by Clemenson and Stark (2005) as the starting point. The authors used a distinction between 2D versus 3D video games to compare their effects on the learning and memory in humans. The primary hypothesis of the authors is that the exploration of virtual environments while playing video games is a human correlate of environment enrichment. Authors found that video gamers performed better than the non-video gamers, and if non-gamers are trained on playing video gamers, 3D games provide better environment enrichment compared to 2D video games, as indicated by better memory scores.  The end goal of standardization in video games is to be able to translate the field so that the results can be used for greater good. 

 
     
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