Thoughts on stereotyping of Latina women in science

Angela Jimenez

Angela Jimenez

Recently an article in the Washington Post entitled, “Black and Latina women scientists sometimes mistaken for janitors,” was brought to my attention. The Nano-Bio blog editor and INBT science writer, Mary Spiro, asked me if I would be willing to write a response to it. After considering this topic and my experience in the States, I cannot say that I have felt stereotyped due to being a female Hispanic scientist.

Although stereotyping is a more profound issue, it is not completely unreasonable. Let me explained myself: I recently defended my PhD work at Johns Hopkins University and in the five and a half years that I have spent here, most of the janitors are blacks including a few Hispanics. When I would walk to lab, I could hear construction guys talking in Spanish all the time. Unfortunately, this stereotype is sometimes our current reality. This could be partly explained from the fact that some of us come from developing countries, and it is difficult when we come to the States to be up to speed with everyone else who has been born and raised here. This gap could be due to a variety of factors, such as the lack of education, the cultural differences, the language barrier, and even the influence of our family.

One of the reasons that I have not felt particularly stereotyped is probably because when I moved to the States 13 years ago, I came to New York City, which is known as the melting pot of this country. I went to City College of New York and out of a class of 30, there was only one person originally from the States. Everyone else was from somewhere around the world.

After arriving to the US, I was aware that I was coming from a developing country, and that I needed to work hard to succeed, which I would define as getting educated. When I decided to come here, I moved without my family and without knowing any English and I feel that the most important thing that made me succeed was the great desire and determination to learn and get educated. This determination probably made me so focus on achieving my goals that I never really thought about being stereotyped or discriminated even when this could had been the case.

Looking back, I can only say that yes, I worked really hard, but I have been extremely fortunate to be able to earn a PhD from one of the leading Universities. Now, do I think it is fair that women, in particular Blacks and Hispanics, are stereotyped or even discriminated? Of course not, but the issue here is greater than this. Stereotyping and discrimination depend on several variables. For instance, geography, demographics, education, and income all play a role.

I have Hispanic Engineer friends who work in different industries in non-traditional roles, and I have observed that the ones who work in New York City are less likely to be stereotyped or discriminated than the ones elsewhere. Do I think that as women we should support each other and create societies that inspire and help us navigate the system? Of course yes! Motivating and helping women pursue a career in the field of science will help increase the percentage of women in these challenging positions. Over time, this will lead to a greater representation of the number of blacks and Latina women scientists, and this current stereotype and discrimination will eventually vanish.

About the author: Angela Jimenez recently completed her PhD in Chemical and Biomolecular engineering in the laboratory of Denis Wirtz, associate director of INBT and Vice Provost for Research at Johns Hopkins University.

New eyes for diagnostics

Initial medical diagnoses are done based on physical examination by a health care professional. However, as the technology of optics, computing, and biology continues to advance, engineers have essentially developed “enhanced eyes” for health care professionals to see beyond the limits of our natural vision to diagnose patients. For example, with the advent of ultrasound, doctors are able to see into a pregnant mother’s womb to monitor the health of a developing baby.

Figure 1: How imaging modalities are being combined to more precisely diagnose patients. In this image high levels of cell activity are being identified to pinpoint cancer existence. Source: http://www.upmc.com/patients-visitors/education/tests/pages/petct-scan.aspx

Figure 1: How imaging modalities are being combined to more precisely diagnose patients. In this image high levels of cell activity are being identified to pinpoint cancer existence. Source: http://www.upmc.com/patients-visitors/education/tests/pages/petct-scan.aspx

New imaging techniques and machines are combining existing modalities. This improves diagnoses and combines the strengths of each imaging modality. For example, cancer diagnosis can now be achieved by scanning a patient with a dual PET/CT machine (Fig. 1). In this method, imaging specialists combine the strength of CT scans, which shows high resolution of organ location and tissue distribution, and PET scans, which determines molecular/cellular activity by introducing a radioactive molecule into the body.

These technologies have also increased our understanding of diseases and are used frequently in research to develop new theories for disease mechanisms. Nevertheless, because of the amount of technology and engineering that has gone into developing these machines, they are still very costly both to patients and researchers.

About the author: John Hickey is a second year Biomedical Engineering PhD candidate in the Jon Schneck lab researching the use of different biomaterials for immunotherapies and microfluidics in identifying rare immune cells.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

Nanodevices built with DNA origami

Did you know DNA could be used for origami?

Not actual DNA origami.

Not actual DNA origami.

The precise control and organization of nanoscale devices has shown a great potential for ultimately creating “nano-devices” that can perform nanoscale biological measurements, deliver medicine in vivo, among many other applications. A recent article from Carlos E. Castro and colleauges from The Ohio State University demonstrates the use of DNA origami with programmable complex and reversible 1D, 2D and 3D motions.

By varying the DNA origami design, they were able to observe different mechanisms for the DNA origami’s 3D motion such as the crank-slider and four bar mechanism. The research team mainly utilized transmission electron microscopy (TEM) to follow the morphology changes as the origami moves.

DNAUsing a fluorescence quenching assay (attaching a fluorescent label on one arm and a quencher on the other), they have characterized the timescale of DNA origami motion. Overall, their group sees this technology as a “foundation for developing and characterizing a library of tunable DNA origami kinematic joints and using them in more complex controllable mechanisms similar to macroscopic machines, such as manipulators to control chemical reactions, transport biomolecules, or assemble nanoscale components in real time.”

 

Shown below are some of the videos showing the motions of the DNA origami that they have reported:

About the author: Herdeline Ann M. Ardoña is a third year graduate student at Johns Hopkins University Department of Chemistry, currently working in chemistry professor J.D. Tovar’s lab and co-advised by professor Hai-Quan Mao, in materials science and engineering.

Reference: Programmable motion of DNA origami mechanisms. (Proc. Natl. Acad. Sci. U.S.A., 2015, 112, 713-718)

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

Are there problems with the peer-review process?

The pathway to publication is littered with checkpoints, reviews, and rejections. Before your paper is accepted it is read and reviewed with a few possible fates. It can be desk rejected by the editor and never reviewed or it can reach the reviewers who then decide the fate of the manuscript.

questionamarkwebSiler et al. investigated the effectiveness of the review process. They observed that top ranking journals overall have a very effective desk screening process where the best manuscripts are selected for review. However, there was one main fault; these top tier journals desk rejected the top cited manuscripts. This is likely due to the fact that their goal is to publish papers that are widely applicable and of interest to many people. This limits the ability of truly novel and exciting works to be published in these formats.

Overall, however, it was determined that the review process is helpful. Manuscripts that went to review overall had more citations than those desk rejected and resubmitted elsewhere. The results of this study were reassuring, and it was nice to see that at least a few scientists are looking into the effectiveness of the review process.

Link to article: http://www.pnas.org/content/112/2/360.abstract

About the author: Moriah Knight is a third year in the Johns Hopkins Department of Materials Science and Engineering working in Peter Searson’s lab.

Nano-bio lab course: MAPs and CD

Editor’s note: Over the next several days, we will share the student impressions of some of the techniques learned in INBT’s nano-bio laboratory course (670.621). These reports demonstrate the wide variety of techniques students trained at the Johns Hopkins Institute for NanoBioTechnology are expected to understand. Each technique is taught in a different affiliated faculty lab. More lab techniques to come.

Membrane Active Proteins (MAPs) and Circular Dichroism (CD) spectrography

During this lab, we learned a couple of techniques that I had not used before. First we synthesized liposomes and processed them, resulting in uniform liposome radius. Then we made a solution of membrane active proteins with aromatic amino acids so that their absorbance and emission could be measured.

CD_trans

circular dichroism (CD) spectrography

We ran the proteins through the fluorometer at varying wavelengths to create a profile of emission and absorbance of the protein. This was done also at varying pHs and at different liposome concentrations.

In theory the proteins should incorporate into the liposomes and there should be a change in the spectra as a result. During our lab time we had issues getting the desired results, but it was still informative on how to use the fluorometer and other new equipment. We found the spectra for two different proteins at two different pH values for each to see the effect that pH had on the emission/absorbance spectra.

We also preformed CD spectrography (circular dichroism) to determine the chirality of the proteins, that is, how are the specific molecules spatially arranged. Again the procedure did not work exactly as planned, but learning how to perform the measurement was informative, nonetheless.

About the author: Jackson DeStefano is a first year PhD candidate in the laboratory of Peter Searson, professor of materials science and engineering.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.
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How firefly research helped gene therapy

Sometimes on a calm summer or fall night, one is able to observe the beautiful dance of blinking fireflies. Scientists began to explore mechanisms to describe this unique natural phenomenon as early as the late 1800’s. After a series of experiments with solutions at different temperature with ground up abdomens of fireflies, Raphael Dubois named the enzyme luciferase and the substrate luciferin that were the cause of the light-producing reaction (1).  But it wasn’t until recently in 1985 that scientists were able to clone the gene for luciferase and express it in bacteria to produce the luciferase.

firefly

Figure 1: Picture of firefly. Source: http://www.fireflyexperience.org/photos/

Once the gene was cloned, genetic researchers realized the importance of the findings and started to use it as a reporter gene for experimental gene therapy. Gene therapies involve transfection of new genetic material into the host’s DNA and can be applied not only for therapies for diseases of genetic origin, but can be used for cancer therapy and diagnostic purposes.

By incorporating the gene for luciferase along with the gene of interest, the Hai-Quan Mao lab in the Department of Materials Science and Engineering at Johns Hopkins University can detect whether or not their nanoparticles used for gene delivery have been successful simply by adding luciferin to the cells. If the gene transfer was successful, then the luciferase will act on the substrate luciferin to emit light.

Sources

1)     Fraga, Hugo. “Firefly luminescence: A historical perspective and recent developments.” Photochemical & Photobiological Sciences 7.2 (2008): 146-158.

About the author: John Hickey is a second year Biomedical Engineering PhD candidate in the Jon Schneck lab researching the use of different biomaterials for immunotherapies and microfluidics in identifying rare immune cells.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

 

O-GlcNAc: The Sweet Side of Epigenetics

In 1992 Edmond H. Fischer and Edwin G. Krebs won the Nobel Prize in Physiology or Medicine “for their discoveries concerning reversible protein phoshorylation as a biological regulatory mechanism.” Phosphorylation of proteins can essentially be thought of as the on/off switch that regulates protein activity inside of cells.

It became increasingly clear later on, however, that protein physiology was much more complex than regulation through just a simple on/off phosphorylation switch. It was eventually discovered by Johns Hopkins’ very own Dr. Gerald Hart that a very special sugar called N-acetylglucosamine (GlcNAc) can be added to the same places on proteins where phosphorylation often occurs. The addition of GlcNAc to these sites is now known as the O-GlcNAc modification. O-GlcNAc essentially serves as another layer of control over protein physiology by acting as a sort of “cap” that must be removed before a protein can be phosphorylated. In otherwords, phosphorylation and the O-GlcNAc modification cycle between each other to regulate how many important proteins behave. One amazing feature of the O-GlcNAc modification is the fact that it is performed by only two enzymes, OGT which adds it to proteins and OGA which removes it, and that’s it. This is in stark contrast to protein phosphorylation and dephosphorylation which needs hundreds of different enzymes to perform phosphorylation mechanics.

Fig 1.  Histones are modified by O-GlcNAc.

Fig 1. Histones are modified by O-GlcNAc.

To this day O-GlcNAc cycling remains an enigma, however, emerging evidence continues to mount that illustrates the very important physiological roles for O-GlcNAc. Two of some of the most important concepts within the realm of epigenetics are the modifications of histones and the methylation of DNA. It is now known that histones, which are proteins that help package DNA into the nucleus, are modified by O-GlcNAc 1 (fig 1.). The other major type of epigenetic regulation of gene expression– methylation of DNA–silences genes, but is also a reversible process. Proteins named TETs help to remove methyl groups on DNA to reverse this silencing. Recently it has also been shown that TETs have their activity regulated by O-GlcNAc 2. In otherwords, O-GlcNAc seems to have a very important role in regulating and interacting with two very important physiological mechanisms that write the epigenetic code.

Finally, glucose is most often thought of as fuel for the cell–and this is true–however, the substrate that is required to perform the O-GlcNAc modification (GlcNAc) happens to also be a byproduct of glucose metabolism. Major diseases such as cancer, diabetes, and Alzheimer’s are often associated with altered glucose metabolism and also have profound epigenetic changes. It is quite tempting, therefore, to postulate that O-GlcNAc may be the key that links environment, stress, nutrient availability, and metabolism to changes in epigenetics. Understanding carbohydrate metabolism and O-GlcNAc regulation of epigenetics may one day open new doors that will lead to breakthroughs in regenerative medicine, understanding embryological development, tissue engineering, and treating major diseases.

About the Author: Christopher Saeui is a fourth year Biomedical Engineering PhD student in the Kevin J. Yarema Laboratory for Cell and Carbohydrate Engineering studying the epigenetic and metabolic mechanisms that alter glycosylation in cancer.

References
1. Sakabe, K., Wang, Z. & Hart, G. W. Beta-N-acetylglucosamine (O-GlcNAc) is part of the histone code. Proc. Natl. Acad. Sci. U. S. A. 107, 19915-19920 (2010).
2. Shi, F. T. et al. Ten-eleven translocation 1 (Tet1) is regulated by O-linked N-acetylglucosamine transferase (Ogt) for target gene repression in mouse embryonic stem cells. J. Biol. Chem. 288, 20776-20784 (2013).

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

Finding new tasks for the disruptive proteins in bee venom

When a bee stings you, it leaves its stinger within your body releasing a peptide toxin called melittin. Melittin is toxic to cells because it is able to insert and bind to the cell membrane, which destabilizes the membrane.

Melittin is able to interact with the hydrophobic lipid layer of the cell membrane by forming unique helixes where hydrogen bonding occurs between both peptides. Consequently, charged (polar) amino acid residues are generally not observed in such proteins and pH can change the binding affinity. Such proteins are called membrane active proteins (MAPs).

Now this is not good for your bee-stung cells, but researchers are looking to repurpose nature’s disruptive proteins as anti-microbial drugs, cancer therapeutics, and HIV drugs. Specifically, researchers in the Kalina Hristova lab in the Department of Materials Science and Engineering at Johns Hopkins are engineering proteins based off of the melittin protein.

Figure 1: Membrane Active Peptide Schematic (Source: http://ins.sjtu.edu.cn/people/jakob/)

Figure 1: Membrane Active Peptide Schematic (Source: http://ins.sjtu.edu.cn/people/jakob/)

The Hristova lab researchers study their developed MAPs by using lab-produced vesicles from phosphatidylcholine (the major component of a cell membrane). They use the natural fluorescence from tryptophan (which increases in a hydrophobic environment), and circular dichroism spectroscopy (which is able to detect the chiral structure of proteins) to verify the peptide’s interactions with the vesicles, and what affinity they will bind.

About the author: John Hickey is a second year Biomedical Engineering PhD candidate in the Jon Schneck lab researching the use of different biomaterials for immunotherapies and microfluidics in identifying rare immune cells.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.

Engineering bacteria for medical uses

According to the National Institutes of Health and Centers for Disease Control, drug resistant pathogens are responsible for 2 million illnesses, 23,000 premature deaths, and an estimated $20 billion dollars in health care costs per year (1,2). The rapid emergence of drug resistant pathogens threatens to undo nearly a century’s worth of biomedical advances, and the situation has become so dire that President Obama has recently made fighting antibiotic resistant pathogens a top national priority.

Engineering Bacteria

Figure 1. Azido modified KDO was used to metabolically glycoengineer the LPS core of E. Coli

Newly emerging molecular engineering techniques may lead the way for next generation therapies designed to attack resistant microbes. One such strategy is metabolic glycoengineering, which is using unnatural monosaccharides to intercept the metabolic machinery of a cell to artificially install chemical “handles” on the surface. These chemical handles can then be exploited by performing reactions known as “click chemistry” to connect almost anything a researcher can think of to the surface of any cell.

Some of the most important structures of bacteria such as the peptidoglycan layer, lipopolysaccharides (LPS), teichoic acids, and capsule are comprised of extensive amounts of carbohydrates. Using glycoengineering, a physician may one day be able engineer those structures with unnatural monosaccharides to disrupt the adhesive properties, directly image, or target drugs to bacteria in a species specific manner–an unprecedented level of selectivity currently unachievable with our current regimen of antibiotics (Fig. 1).

For further reading:
(1) http://www.cdc.gov/drugresistance/national-strategy/
(2) http://www.niaid.nih.gov/topics/antimicrobialResistance/understanding/Pages/quickFacts.aspx

About the Author: Christopher Saeui is a fourth year Biomedical Engineering PhD student in the Kevin J. Yarema Laboratory for Cell and Carbohydrate Engineering studying the epigenetic and metabolic mechanisms that alter glycosylation in cancer.

 

What is microfluidics?

Microfluidics continues to find applications in many fields as researchers are realizing the benefits of scaling down to micron scales. This has implications in saving money from reagents and time from completing lengthy assays.

It also means that researchers are able to control experimental parameters at the micron scale more effectively, and use the fluidic flow to provide a dynamic environment. Applications for these devices include, but are not limited to, examples such as pathogen and cancer detection from blood, forming microparticles, studying antibiotic drug-resistant bacteria, understanding nanoparticle blood transport, and observation of the kinetics of chemical reactions.

microfluidicdevice

Figure 1: A picture of a general microfluidic device. Source: http://blogs.nature.com/spoonful/2012/02/chip-promises-better-diagnosis-for-common-blood-disorder.html)

One reason that microfluidics has become so widespread is that the process to develop and create these devices is relatively simple and inexpensive. The process, called photolithography, is based off of a technology developed for the semiconductor industry in developing small features for circuits.

Photolithography uses special polymers that are reactive to certain wavelengths of light to create the forms used to make the device. Then another polymer, typically polydimethylsiloxane (PDMS), is poured into the casted photo-cured polymer mold to produce the microfluidic device. Many devices can be made from this mold and used in research and diagnostics for low-volume, high-throughput experiments.

John Hickey is a second year Biomedical Engineering PhD candidate in the Jon Schneck lab researching the use of different biomaterials for immunotherapies and microfluidics in identifying rare immune cells.

For all press inquiries regarding INBT, its faculty and programs, contact Mary Spiro, mspiro@jhu.edu or 410-516-4802.