Showing papers in "postdoc Journal in 2015"

Influence of environmental factors on bacterial biofilm formation in the food industry: a review

Abstract: Formation and development of bacterial biofilms in the food industry could be a cause of food contamination, compromising food safety and shelf-life. Among the factors modulating biofilm formation, this review will focus in conditions normally encountered by bacteria in food environments, especially in biofilm initiation and development. The effect of environmental factors (substratum, temperature, oxygen concentration, hydrodynamic effects, food matrix composition, and microbial interactions) on biofilm formation is multifaceted and, in many circumstances, their influence could be compensatory. A better knowledge of these factors would allow for a better control of biofilm formation, either by avoiding and/or eradicating biofilms or by defining adequate Hazard Analysis and Critical Control Point systems in the food industry.

Current Research Approaches to Target Biofilm Infections.

Abstract: This review will focus on strategies to develop new treatments that target the biofilm mode of growth and that can be used to treat biofilm infections. These approaches aim to reduce or inhibit biofilm formation, or to increase biofilm dispersion. Many antibiofilm compounds are not bactericidal but render the cells in a planktonic growth state, which are more susceptible to antibiotics and more easily cleared by the immune system. Novel compounds are being developed with antibiofilm activity that includes antimicrobial peptides, natural products, small molecules and polymers. Bacteriophages are being considered for use in treating biofilms, as well as the use of enzymes that degrade the extracellular matrix polymers to dissolve biofilms. There is great potential in these new approaches for use in treating chronic biofilm infections.

Using anti-biofilm peptides to treat antibiotic-resistant bacterial infections.

Abstract: Host defense (antimicrobial) peptides (HDPs) are produced by virtually all organisms and have an important role in protection against microbial infections. Some naturally occurring peptides such as the human cathelicidin LL-37 and the bovine peptide indolicidin have been shown to inhibit bacterial biofilm development. Rearrangement and substantial modification of the amino acid sequence of these and other HDPs has led to the identification of small synthetic peptides with increased, broad-spectrum anti-biofilm activity that is independent of activity vs. planktonic cells. Some of these peptides have also been shown to act in synergy with antibiotics commonly used in the clinic to prevent biofilm formation and eradicate pre-existing biofilms. Recently, the mechanism of action of one of these peptides (i.e., 1018) was shown to involve binding to and causing degradation of the second messenger stress response nucleotide ppGpp, which plays an important role in biofilm formation and maintenance. Here, we review recent progress in the field of anti-biofilm peptides and propose future directions to further develop these therapeutic agents.

Teacher Evaluation, Performance-related Pay, and Constructivist Instruction

Abstract: This essay highlights Liang and Akiba’s (2015) study that examined the impact of teacher performance pay on constructivist instruction in...

Is a plant's ploidy status reflected in its metabolome?

Abstract: With the enrichment of metabolomic information in a diverse number of plants, the obtained datasets reflect on important aspects of plant growth, function, physiology, productivity, and adaptation to changing biotic and abiotic environments. Many of these plant species are natural polyploids that are either model plants, crops, or are of commercial interest. Decades of efforts have resulted in artificially induced polyploids from in vitro micropropagation practices as well. Recent efforts using next generation, high throughput genome sequencing approaches have contributed to our growing understanding of their genome ploidy status and the inherent biosynthetic potentials of encoded metabolomes. However, the ever perplexing questions galore regarding the metabolic status of these polyploids across plant genomes remained. Thus we collated information on metabolomes of polyploids and asked whether they reflect the ploidy status of these plants. We conclude that polyploids, either natural or those induced artificially, demonstrate (i) enhanced primary metabolism, (ii) enhanced secondary metabolism, i.e., terpenoids, phenylpropanoids, flavonoids, and alkaloids content, and (iii) increased bioactive constituents to enable polyploids to counteract against environmental challenges in a more efficient manner in the plant species included in this review.

Professional Development and Student Achievement: International Evidence from the TIMSS Data

Abstract: This comparative study used the latest Trends in International Mathematics and Science Study (TIMSS) data sets and examined the relationship between professional development and student achievement. It found that although the national levels of access for students at the fourth and eighth grade levels to teachers who participated in professional learning in the United States were higher than the other countries, one third to one half of the fourth grades were taught by teachers who had no professional learning focusing on math instruction or curriculum. In addition, teachers’ participation in professional development was positively associated with higher student math achievement. This cross-national study provided empirical evidence highlighting the importance of investing in teacher learning for improving national educational quality.

Mechanoelectrochemical Catalysis of the Effect of Elastic Strain on a Platinum Nanofilm for the ORR Exerted by a Shape Memory Alloy Substrate

Abstract: In this research, a novel way to examine the elastic strain effect on a platinum catalysis surface during oxygen reduction...

Adeno-Associated Viral Vector Delivery to the Enteric Nervous System: A Review

Abstract: Gene therapy to the gastrointestinal tract has remarkable potential for treating gastrointestinal disorders that currently lack effective treatments. Adeno-associated viral vectors (AAVs) have been extensively applied to the central nervous system, and have repeatedly demonstrated safety and efficacy in animal models. The enteric nervous system (ENS) represents a vast collection of neurons and glial cells that may also be subject to treatment by AAV, however little work has been conducted on AAV delivery to the ENS. Challenges for gastrointestinal gene therapy include identifying gene targets, optimizing gene delivery, and target cell selection. Researchers are now beginning to tackle the later of the two challenges with AAV, and the same AAV technology can be used to identify novel gene targets in the future. Continued efforts to understand AAV delivery and improve vector design are essential for therapeutic development. This review summarizes the current knowledge about AAV delivery to the ENS.

Antibiofilm Peptide Development for Clinical and Industrial Applications

Abstract: Natural Antimicrobial peptides (AMPs) are important components of immune systems and possess immuno-modulatory and broad spectrum antimicrobial activities. These host-defense...

PI3King the right partner: unique interactions and signaling by p110β

Abstract: Phosphoinositide 3-kinases (PI3Ks) are central regulators of cellular responses to extracellular stimuli, and are involved in growth, proliferation, migration, and metabolism. The Class I PI3Ks are activated by Receptor Tyrosine Kinases (RTKs) or G Protein-Coupled Receptors (GPCRs), and their signaling is commonly deregulated in disease conditions. Among the class I PI3Ks, the p110β isoform is unique in being activated by both RTKs and GPCRs, and its ability to bind Rho-GTPases and Rab5. Recent studies have characterized these p110β interacting partners, defining the binding mechanisms and regulation, and thus provide insight into the function of this kinase in physiology and disease. This review summarizes the developments in p110β research, focusing on the interacting partners and their role in p110β-mediated signaling.

The Long-Term Impact of Performance Related Pay for Teachers: Evidence from Israel

Abstract: This research highlight reviewed the study of Lavy (2015) on the impact of performance related pay for teachers on students’ lifelong human capital outcomes.

Therapeutic potential and challenges of the CRISPR technology

Abstract: The CRISPR technology has recently received extensive attention from the research and medical community due to its remarkable genome-editing capacity....

A Brain in a Dish.

Abstract: The brain is the most sophisticated and complex organ that nature has devised. Neurons are the functional basic component of the nervous system. Cell bodies of cortical neurons are arranged in layers and each layer has complex diversity of neuronal subtypes. This complex specialization follows a coordinated temporal pattern that emerges through the specification of different subtypes of cortical neurons. This in turn populates the various cortical layers, where these neurons exhibit specific patterns of gene expression and connectivity. An organoid is a three-dimensional organ-bud that is grown in vitro. There are various types of organoid, one of which is cerebral organoid, which is a miniature organ resembling the brain. These organoid are created using human pluripotent stem cells (cells that have ability to form any adult cell type). The purpose of creating these organoids is to be able to study various disease models in a simple, variable space, free of various in-vivo limitations (especially working with humans). Some basic steps to creating cerebral organoid start with taking human pluripotent stem cells, cultivating them, inducing various nerve growth factors, fixating in a gel environment and then using bioreactor to spin. There are variety of ways to do testing of these organoid, using gene expression and functional characterization. The first demonstration of efficient generation of cortical neurons in vitro took place in 2008, where authors presented the evidence that a complex self-organized cytoarchitecture can emerge in a purely in vitro setting3,4. There has been amazing progress in the field of organoids over past few years. In a recent Nature methods paper relating to “Brains in a petri dish”, the authors developed a new streamlined method for inducing pluripotent stem cells to form cortex-like organoids (Figure 1), which include neurons supported by network of glial cells. Authors used an in vitro neural differentiation approach, where human cortical spheroids (hCSs) are maintained in floating conditions on low-attachment plates with biweekly changes of regular serum-free media. This system can be easily maintained for up to 9 months in vitro. Thus, authors were able to create functional and realistic layers of neurons that talk to each other in complex networks. Figure 1 Generation of human cortical spheroids [Image courtesy of Dr. Pasca2] Figure 1 is the schematic representation of the main stages during the process of creation of hCS. Authors used low attachment plates for the suspended colonies. Authors used both BMP and TGF signaling pathways to achieve rapid and efficient neural induction. At 6th day, EGF was added and at 25th day, BDNF was added. Medium was changed very frequently. These hCS grew to 300 microns in diameter by 2 weeks of culture and then reached 45 mm in diameter by 2.5 months. To help characterize these hCS, the authors used many functional classification techniques2. They studied the functional characterization of the neurons by using fura-2 (calcium) imaging and panels of antibodies in the human fetal cortex. This system of 3D network was also amenable to slice physiology techniques. The authors performed whole cell recordings and found that almost 80% of the cells fired action potentials in response to depolarizing current steps. There have been other techniques used in the past for developing differentiating pluripotent stem cells into cortical neurons. Some examples include neural induction in high-density monolayer cultures, embedding clusters of hiPSCs in gelatinous protein mixtures (such as Matrigel) and later culturing them in a spinning bioreactor, using embryoid bodies derived from hiPSCs that are plated on coated surfaces to generate neural progenitors2,5–7. In 2013, Lancaster et. al. in order to recapitulate features of human cortical development, namely characteristic progenitor zone organization with abundant outer radial glial stem cells, developed cerebral organoids that had similar development as in human brain6. The authors also used these cerebral organoid to model microcephaly defect (which has been difficult in model in mice) that could help explain various disease phenotypes. In 2015, Maguruma and colleagues developed a method to generate neurons of the cerebellum by 3D culture of human embryonic stem cells with sequential addition of growth factors7. In the paper on Cortical Neurogenesis (complexity emerging from simplicity)5, authors modeled spatial and temporal patterns of corticogenesis (see figure 2). These 3 D models could recapitulate similarity to in-vivo organization of cortical structure. Following paragraphs talk about the potential applications of organoid for various disease models. Figure 2 Temporal and Spatial modeling cortical neuron neurogenesis [Image courtesy of Dr. Anderson5] Timothy syndrome (TS), a development delay disorder caused by a mutation in a L-type voltage-gated calcium channel, can cause autism. The iPSC derived cortical cells from TS patient led to revelation about defects in calcium signaling and neuronal activity, and defects in the generation of specific types of neurons8. Pluripotent stem cells were used to identify the lysosomal alterations in Gaucher disease (GD) neurons (genetic disease in which fatty substances accumulate in cells and certain organs). It was found that the lysosomal alterations described were caused by the GBA1-associated neurodegeneration9. Anand and his group have already taken the application of these corticoids to Alzheimer’s and Autism research1. Authors have filed an invention disclosure and are seeking an IP, so they were unable to disclose the methods. Figure 3 shows an image of an organoid. When, I asked the author about the potential of this work and timeline, his response was “Potential is enormous. The models will accelerate research and drug discovery and more accurately predict efficacy of drugs in human clinical trials, and a lot lower cost. Timelines will vary based on the subtype of a disease under consideration (most brain diseases and disorders are syndromes with different causes, though some may converge on a pathway)”. Figure 3 Image of an organoid [Courtesy of The Ohio State University1] Gulf War illness is considered to be the outcome of the use of organophosphate pesticides [permethrin (PM) and N,Ndiethyl-m-toluamide (DEET)], daily prophylactic anti-cholinesterase pyridostigmine bromide (PB), and stress. It is also shown to cause reduction of hippocampal column and brain gray matter. Organoid can be used to evaluate the pathobiology of these noxious chemical on human brain development.

Genomic Resources of a Neotropical Orchid Opens New Avenues for Evolutionary Research of Endangered Flora in Brazil

Abstract: Next-generation sequencing (NGS) technologies have greatly reduce the cost and difficulty of sequencing partial genomes. Genome datasets are a promising...

Drawing the line â a cognitive or visual system for number extraction

Abstract: One of the most influencing theories in numerical cognition proposes a specialized cognitive system for extracting number out of visual...

Recent Developments in Antimicrobial Peptide and Bacterial Biofilm Research

Abstract: Each year, 25,000 people die in Europe as a result of antibiotic-resistant infections, costing the European Union >1.5 billion euros...

Dichloroacetate- Phase 1 Trial in Adults with Malignant Brain Tumors

Abstract: Dichloroacetate (DCA) has been used for many years as an investigational drug to treat children born with mitochondrial disorders. Through its inhibition of Pyruvate Dehydrogenase Kinase (PDK), a key component of the pyruvate dehydrogenase complex, DCA has shown promise in facilitating oxidative phosphorylation in cell mitochondria. Recently, DCA has received more attention as a possible treatment for numerous forms of cancer. In this research highlight, we will discuss a paper from Dunbar et al. in which a Phase 1 trial for DCA was run in adults with recurrent malignant brain tumors (RMBTs). These tumors often carry a poor prognosis. As DCA has the ability to pass through the blood-brain barrier, it is being investigated as a possible treatment for RMBTs. The goal of the trial was to establish dose ranges that are safe to administer to patients with recurrent malignant gliomas.

Biodegradable Comb-like Dendritic Tri-block Copolymer Promotes Nerve Cell Functions

Abstract: Novel symmetric biodegradable dendritic tri-block copolymer, consisting of a core of hydrophobic poly(Llactide) (PLLA) block and 32 poly(L-lysine) (PLL) arms, was synthesized via a facile chemistry route. The assynthesized tri-block copolymer was characterized with 1 H NMR, water contact angle measurements, GPC test, and DSC analysis. The 1 H NMR and GPC tests indicated that the tri-block copolymer, PLL-PLLA-PLL, with well-defined architecture was synthesized. The water contact angle measurements demonstrated that the incorporation of L-lysine improved prominently the hydrophilicity, and the DSC analysis indicated that the crystalline region of PLLA was slightly modified by the L-lysine component, decreasing melting temperature and crystallinity in the PLL-PLLA-PLL copolymer. NPCs and PC12 cells were seeded on PLLA, dendritic PLLA with 32 L-lysine terminals (d-PLLA-d), and PLL-PLLA-PLL films to investigate cell attachment, proliferation, and differentiation. The results strongly demonstrated that d-PLLA-d and PLL-PLLA-PLL films, especially PLL-PLLA-PLL films, dramatically promoted cell attachment, proliferation, and, more importantly, differentiation, particularly neurite outgrowth.

Smooth Muscle Cell to Macrophage Differentiation in Atherosclerosis - Remaining Limitations and Questions

Abstract: Macrophages contribute decisively to the initiation and progression of atherosclerosis. Although most studies conclude that plaque macrophages derive from circulating monocytes, there is growing evidence that vascular-resident smooth muscle cells (SMCs) may also differentiate into macrophages and contribute to the growing pool of foam cells in the atherosclerotic plaque. Understanding of SMC-to-macrophage differentiation has been clouded by inadequate fate-mapping studies and potentially inaccurate staining of SMC- or macrophage-specific markers. A new study published in Nature Medicine by Shankman et al., used a novel fate-mapping technique to label SMCs early in atherosclerosis and definitively assess their cellular fate throughout the progression of disease. The authors conclude that SMCs make up a striking number of cells in the atherosclerotic plaque, but lose several SMC-specific markers masking their inclusion in previous studies. Although this research illustrates the plasticity of SMCs and the importance of SMC retention in ameliorating atherosclerosis, it, unfortunately, does not confirm that SMCs differentiate into functional macrophages nor provide proof that SMC-to-macrophage differentiation is important for the progression of atherosclerosis.

Functional DNA repair assays with clinical and translational applications

Abstract: High-throughput RNA and DNA sequencing approaches continue to yield informative data that provides insights into genomic patterns and variations that...

Raman Spectroscopy-Based Sensing of Glycated Hemoglobin: Critical Analysis and Future Outlook

Abstract: Glycated hemoglobin is a clinically established important biomarker that provides retrospective value of blood glucose concentration over the preceding 2-3 months. Owing to the biochemical specificity and multiplexing capability, Raman spectroscopy has emerged as a promising tool for detection and quantification of blood constituents in a label-free and non-destructive manner. Here, we critically review the Raman spectroscopy-based approach to detect and quantify this important biomarker. The potential of this spectroscopy-based approach and its possible clinical translation from the current optical bench will be also briefly discussed along with the future prospects.

Designer 3D DNA polyhedra for biomedical applications

Abstract: Structural DNA nanotechnology explores various nanoscale structural and functional properties of DNA to develop probes at nanoscale for diverse applications....

A Summer Course in Cancer for High School Students - Lessons Taught and Lessons Learned

Abstract: In this discussion we present a course in cancer biology and therapeutics that we have taught for high school students...

Publish and still perish

Abstract: This opinion comments on a recent trend in science showing a proliferation of published material, while at the same time citation rate seems to drop faster than ever. It is suggested that the faster pace of scientific publication on the internet poses new challenges for the whole research community.

Structures and Infrared Spectroscopy of Metal Cation-Borazine Complexes

Abstract: Borazine (B3N3H6) is known as ‘inorganic benzene’ because of a planar B3N3 ring with equivalent B-N distance. The lone pair from N in the ring delocalize to the adjacent p-orbital of B which leads to a conjugated system. Even though metal-benzene complexes have been studied extensively as models for cation- π interactions and organometallic bonding, similar systems with borazine is relatively scarce. Here, we present a density functional study on metal cation-borazine complexes focusing on geometric and electronic structures and their effects on infrared spectra. We have chosen Al, V, Mn, and Zn cations with various d-configurations which provide models for study donor-acceptor complexes. Among these four metal complexes, Al + and Mn + prefer to bind to π-cloud on top of the borazine ring. On the other hand, V + and Zn + bind to B and N, respectively. Infrared spectra of these complexes show four major bands: N-H-, B-H stretches and B-N-B ring and scissoring modes. Interactions of Al and Mn barely shift these band positions in the respective complexes as compared to those in isolated borazine, because of less cation-π interactions. On the other hand, V + and Zn + significantly perturb the borazine ring resulting shifts in

Tracing the genetic signature of human brown adipocytes

Abstract: Until recently, a functional brown adipose tissue was thought to be restricted to rodents and human infants. The last eight years have seen a re-emergence in the presence and activity of brown adipose tissue in adult humans. This study by Shinoda and co-workers 1 characterizes the cellular origins and molecular identity of adult human brown adipose tissue. Using RNA sequencing and genome wide expression analysis, the authors characterize that the clonally derived adipocytes isolated from brown fat of adult humans carry the genetic signature of recruitable thermogenic beige adipocytes. They further identify novel molecular markers that were highly enriched in the adult human brown adipocytes and rodent beige adipocytes. This

13C saturation transfer effect of bicarbonate-carbon dioxide exchange catalyzed by extracellular carbonic anhydrase in Chlamydomonas reinhardtii

Abstract: Acetate assimilation in C. reinhardtii leads to bicarbonate and CO2aq formation in heterotrophic growth condition. Bicarbonate and CO2aq thus formed...

JAK Inhibition Induces Browning of White Adipocytes

Abstract: The global epidemic of obesity is increasing at an alarming rate, posing a severe threat to human health. The accumulation of excess white adipose tissue in obese individuals increases their risk for type 2 diabetes, cardiovascular diseases, hypertension, stoke and even cancer. Current efforts manifest the need to identify potential anti-obesity therapeutics. One promising approach is increasing the activity of ‘brown like’ adipocytes in white adipose depots, which has been shown to improve the overall metabolic phenotype of the organism. This report by Moisan and coworkers demonstrates a novel and a promising approach by inhibiting JAK kinases to induce browning in white adipose tissue.

Organelles enter the game of aging related aggregation and retention of misfolded proteins

Abstract: Aging is a degenerative process associated with several phenotypes among which are increases in accumulation of misfolded and damaged proteins. Several studies have shown associations of altered mitochondrial DNA and structure, oxidative phosphorylation function, and ROS production with aging. In this study, Zhou et al explore the role of mitochondria in regulating protein aggregate distribution during cell division. This is in fact the first account of a framework mechanism for proteome quality control and its role in aging and cell rejuvenation.