Home Blog Page 3

Designed for Furry Success

0
otter skeleton

🦦 What does the skeleton of a highly specialized marine mammal reveal about its life?

You can find the Southern Sea #Otter (Enhydra lutris nereis), also known as the #California Sea Otter, along California’s central coast. This endangered species has:

🔵 Blunt teeth, unique for a mammal → designed for crushing shellfish and other benthic (bottom-dwelling) invertebrates common in kelp forests, estuaries, and the rocky bottom ecosystems the otters inhabit.

🔵 An intricate honeycomb-like structure inside the nasal passages → indicates an acute sense of smell that also aids in heat regulation in cold water (temperatures range from 8° C to 17° C!).

🔵 Large eye sockets → demonstrate good vision both above and below the water’s surface.

Thank you to 🇺🇸 Cecelia Azhderian, a trained visual #communicator who celebrates the collaboration of art and #science, the old and new, and bringing the outside in!
The #illustration was commissioned by SeaOtters.com, and appeared here: https://lnkd.in/eiDuzfA. The organization raises awareness about California’s threatened sea otters.

#imagenscienceadventcalendar#otters#sciart#endangered#zoology#scicomm#wildlife

otter skeleton

Sleep trouble

0
sleep apnea
Cross section of the oropharynx of a sleeping woman exhibiting obstructive sleep apnea (OSA). OSA involves repetitive partial or complete pharyngeal collapse while sleeping resulting in either apnea or hypopnea. In the section we can see the soft palette and the posterior portion of the tongue occluding the airway (indicated with blue).

Obstructive sleep apnea (OSA) is a condition consisting of repetitive partial or complete pharyngeal collapse while sleeping. This results in fragmented sleep, causing drowsiness during the day.

Illustrator Alexandra Webber says she sought to “visualize the movement of air in respiration in order to show this collapse.” Above the sleeping patient Webber referenced the data collected during a sleep test, including oxygen desaturation, sleep disruptions, brain waves, heart rate, and breathing.

When composing an image, Webber says she likes to start with a base drawing of the figure and then roughly sketch in the relevant anatomy. Once that anatomy is in place, she says, “you have a starting place to work out how to show the disruption—in this case, relaxing the tongue and soft palette until they touch the back of the throat. I draw a red circle around my area of focus to make sure it stays prominent over the hours it takes to render the final illustration.”

Thank you to 🇺🇸 Alexandra Webber is an award winning medical illustrator and owner of DNA Illustrations based in Asheville, NC. This illustration was created for a lead magazine article on obstructive sleep apnea.

sleep apnea
Cross section of the oropharynx of a sleeping woman exhibiting obstructive sleep apnea (OSA). OSA involves repetitive partial or complete pharyngeal collapse while sleeping resulting in either apnea or hypopnea. In the section we can see the soft palette and the posterior portion of the tongue occluding the airway (indicated with blue).

See the sea star?

0

A sea star (Asteroidea) has some real tricks up its…sleeves? Perhaps most bizarre is the way this echinoderm digests its food thanks to their unusual anatomy.

Sea stars:

🟠 Can ”evert” (turn inside-out) a portion of their stomach to capture prey and then pull it back into their body.

🟠 To digest their prey, such as mussels, sponges, and other small animals sea stars have hepatic caeca in their arms that release enzymes to help with digestion

🟠 Remove waste ammonia by diffusion through their feet and papulae (also called skin gills).

Thank you to 🇨🇦 Catherine Cheung is a scientific and medical illustrator based in Toronto.

sea star

Anatomy’s climbing power

0

Can you climb like a mountain goat?
Comparative anatomy is a great way to better understand our own bodies through the lens of another subject.

🐐 Up to 60% of the Rocky Mountain goat’s weight is supported by their front legs. This occurs because of the large musculature surrounding its neck and shoulder region. While one would think this would make scaling cliffs significantly more challenging, in fact it helps contribute to innate climbing abilities.

🐐 Their top heavy physique contributes to a forward centre of gravity (COG) that is key in maintaining balance as they scale vertical cliff faces and ensures that their weight is positioned over their front hooves to allow for further point precision as well as increased pressure to prevent slipping.

🧗‍♀️ Human trapezius muscle is not as developed as in mountain goats, but humans have the ability to build up incredible finger and shoulder strength!

Thank you to 🇺🇸 Tiffany Fung, a medical illustrator and passionate climber. She is one of the creators of Biotic Artlab, a medical illustration studio based in 🇳🇱 The Netherlands.
Tiffany created this comparative anatomy infographic for Ryan Lewinson at the University of Calgary in Canada.

Unveiling COVID-19’s secrets

0

We have seen the globe-sweeping reality of SARS-CoV-2.

In order to turn the tide in the pandemic, scientists are searching for the novel coronavirus’s vulnerabilities. 

This infographic illustrates targets in the replication cycle of the virus, and potential therapeutic routes. 

Of particular interest is the virus spike protein, which is:

● required for binding and fusion with the host cell membrane
● on the outer surface of the virion
● a target for the immune system and the antigen for all for vaccines reporting protection in phase 3 trials 

Downstream of entry, targeting replication via either viral proteases or RNA may be possible using anti-virals already in use or in trials. These replication events are common to RNA viruses, rather than specific to SARS-CoV-2.

Thank you to noted illustrator and The Johns Hopkins University School of Medicine Professor 🇺🇸 Jennifer E. Fairman, CMI, FAMI. Jennifer is also the Founder of Fairman Studios, LLC. The illustration was created for the “COVID-19 Special Edition” of Hopkins Bloomberg Public Health Magazine (magazine: https://lnkd.in/ePw-aRC; video: youtu.be/xRTMXvZ75dY).

The yellowtail kingfish in aquaculture

0

Who knew fish food was so important? The fast-growing aquaculture industry does. 

This illustration details the internal anatomy of a yellowtail kingfish and has been used in aquaculture and fisheries research to highlight how certain feed nutrients impact the liver and bile ducts in this fish. 

The yellowtail kingfish (Seriola lalandi) is:

🐟 commonly used in fish farming
🐟 popular in Australian cuisine and also for Japanese sashimi
🐟 a fast-growing, predatory, carnivorous fish & requires high-energy diets.

Different aquaculture feeds can impact the absorption of the lipid soluble nutrients by the biliary system of the fish, and consequently affect fish growth.

We think it’s a beautiful image, and a great way to start off our Advent Calendar Illustrator. 

Author: Thank you to 🇦🇺 Rene Campbell. René is a PhD candidate in marine ecology at @Flinders University, South Australia, and a freelance scientific illustrator specialising in ecological, environmental, and natural resources imagery.
The illustration was created in Adobe Photoshop CC and a Wacom Cintiq 24HD tablet. 

#aquaculture#science#imagenscience#zoology#marinebiology#imagenscienceAdventCalendar#sciart#scicomm#ecology#fishfarm

Not only a magazine

0

At ImagenScience, we always knew there was a disconnect between scientists and the general public. Covid-19 has only widened the gap. In the face of complex, rapidly evolving science and slow health bureaucracies with poor messaging, conversation about the virus has been marked by panic, misunderstanding, and conspiratorial thinking.

Whether or not an image is worth a thousand words, illustration combined with text can speak volumes. And so, at ImagenScience we seek to harness the power of images to clarify scientific discoveries and spread the vital work of researchers in the life sciences, our specialty, during these difficult times.

With Lit Science, we spotlight two kinds of images:

 1) Microscope images that reveal the work and capabilities of individual scientists;

 2) the creative visuals of science and medical illustrators.

 

We invite you to send us examples of your own work in these areas.

We also offer our own science communication services. And we’re always interviewing scientists on and off the bench, in academia and in industry, to keep our own knowledge and skill sets current.

Scout, evaluate, and invest: Dialogues with a VC associate

0

Scout, Evaluate, and Invest: Dialogues with a VC Associate

By Priyankaa Pitcheshwar

Just as she rounded the bend in her race for a PhD, Barbara Poinard began to ponder a career outside academia. Two little letters piqued her interest: “V” and “C.”

“Having not heard of the term ‘venture capital,’ when I chanced upon it at a conference I was intrigued,” Poinard says. She reached out to the Managing Partner of Esco Ventures X (EVX) via LinkedIn and met up for a coffee chat. Little did she know that this meeting would open doors to her future. At the end of the coffee chat EVX offered her an internship.

Just around this time, Poinard also got an opportunity to work at a talent incubator. With a thirst to explore the entrepreneurial side of science, she embarked on it, spending four months working with a co-founder, evaluating the prospects of commercialising their idea. 

“When this didn’t pan out, I reapproached EVX about job openings, and here I am,” Poinard says happily.

EVX invests in pre-seed or seed stages of a company’s funding cycle, following the model of venture creation: they build a company from the ground up. If the venture’s business model proves valid and achieves robust performance indicators, more capital is injected to scale up the venture.

Poinard first started at EVX as an analyst, performing intensive scientific due diligence and systematically reviewing huge amounts of scientific literature, another challenging part of her job. Today, having progressed to an associate in the firm, she scouts for new technologies globally, reaching out to principal investigators (PIs) to assess the potential of spinning out a company with them. 

EVX focuses on disruptive therapeutics platform technologies in areas such as gene editing, cell therapy, and gene therapy. These technologies might first be described in scientific journals or conferences, and some could be patented or might remain unpublished. In cases of patented technologies, EVX works closely with the tech transfer offices of the associated university or research institute to license out the technology into a company. 

Poinard works closely with her fellow VC Associate Akshaya Bansal. When the duo identify a promising new technology, they place an introductory call with the PI. Although nothing confidential is exchanged, the call serves as a litmus test. Should they decide to progress, deeper due diligence on the prospective venture is performed, considering its competition and evaluating risks as well as limitations. Poinard and Bansal then present their analyses to the EVX management, followed by a collective go or no-go decision. 

“We have no crystal ball,” Poinard says of EVX’s investment strategy. “But we try to estimate and see if, in three years time, it will still be a field of interest.”

“At EVX, we set up the company, lead the recruitment process, strategize ways to move the company forward, and expand the pipeline,” Poinard says. “We also think of the milestones that are necessary—perhaps key experiments and also help with planning the experiments that will be needed to proceed to a series-A funding,” whereby the business would be scaled up and its business model further optimized.

With a diverse portfolio and an expanding pipeline, EVX has made significant strides in the local biotech space. Poinard highlighted two of their current investments. The first, Carmine therapeutics, a spinoff from City University Hong Kong, was identified from a publication describing a technology to develop red blood cells’ extracellular vesicles as a gene delivery vector. “We managed to license out the intellectual property from City University Hong Kong and set up the company in Singapore,” Poinard says. The PI that spearheaded this discovery currently works at NUS and is the scientific co-founder of the company. 

The second investment, PairX Bio, from Duke-NUS, was recently incorporated and focuses on designing next-generation cancer immunotherapies.

Because the EVX team is young, with less than 10 members, Poinard says, “we have to wear many hats.” As it searches for disruptive tech, EVX also works to nurture the local biotech ecosystem in Singapore. In line with this, they host Morphosis, a talent development program designed to train high-calibre scientists and individuals passionate about translating academic findings into biotech ventures. Through a series of lectures and workshops from biotech stalwarts complemented by close mentorship from the EVX investment team, Morphosis fellows learn the nuances of successful biotech ventures. High performers are invited to join EVX or one of their portfolio companies in future.

“When applications are rolled out for Morphosis, there is a lot of marketing work: we prepare the marketing material, webinar content and get involved in the hiring process of the participants,” Poinard says. 

In addition to Morphosis, EVX recently launched their first grant call (PLATINUM Grant) in partnership with A*STAR, for PIs with promising early-stage platform technologies. Launching grants entails a good deal of marketing. Post-launch, the projects received are evaluated and a call is made on which ones can proceed to the subsequent round and receive the funding. At such times, “It is never a one person’s effort at my company,” Poinard says. “We support each other.”

What makes Poinard’s job worthwhile and fun? “When you talk to a PI, it gets exciting to see that the technology identified might have the potential to become something,” she says. “We look through so many technologies that when there is some level of interest from the team, it feels extremely rewarding, as if you have stumbled across a hidden gem.”

When asked for advice for anyone eyeing a job similar to hers, Barbara notes that “staying abreast with the latest global developments and emerging hot areas in the biotech space helps.” Also, she says, “perhaps follow newsletters focusing on the megatrends and latest deals happening in the area.”  

Poinard also volunteers for Biotech Connections Singapore (BCS) as a marketing lead. Working with two others, she sends out emails on upcoming events or job openings. “Since I am in the biotech VC space, I am sometimes more aware of what is happening in the area,” she says. Leveraging this advantage, Poinard posts relevant news on the BCS LinkedIn page, including investments or mergers happening in the local biotech space.

You can reach out to Barbara here: https://sg.linkedin.com/in/barbara-poinard

BCS: Linking scientists with Singapore’s biotech ecosystem

0

By Brian Shott

BCS began its journey in 2014 as the Singapore chapter of BCS/Oxbridge Roundtable, a global biotech and entrepreneurship network, before it rebranded itself as Biotech Connection. The group aims to promote entrepreneurship in life sciences and serves as an engagement platform for a network of academics, entrepreneurs, industry professionals, and government agencies. BCS activities center around educational events, consulting services, and communications.

Former BCS President Dr. Sau Yin Chin sat down with ImagenScience to chat about her journey with this dynamic and evolving organization. 

A beginning in consulting

Sau Yin first started volunteering with BCS as a technical consultant. Technical consultants are usually PhD students or post-docs selected based on the relevance of their domain knowledge and expertise. Most of the consulting activities at BCS involve technical due diligence for early stage investments; the rest concerns market and competitor analysis for their vendors.

For an early-stage investment in a startup, BCS volunteers assess the company’s product, the abilities of its founders, and its commercial potential. This is where mentorship from the lead consultant becomes essential—lab work alone does not typically prepare a scientist to uncover or assess relevant business data. At the end of the project the team assembles a presentation for the client with all the material they’ve scouted. Even this is a new skill, as business presentations differ markedly from scientific ones.

Sau Yin soon became a consulting lead, coordinating projects with support from a team of four or five technical consultants. Each BCS project lasts about three to six weeks.

Ten committee members run BCS, with a two-year maximum term for any one role.

Taking the helm

In 2017, Sau Yin became president of BCS. She determined that BCS needed to promote its consulting service more vigorously. “We weren’t pushing it as aggressively as we could have been,” she says. She did that through more assertive marketing and networking with potential clients about the service , and by creating a  database of 200 technical consultants so that members’ skill sets could quickly be matched to projects and consulting teams assembled. 

Project flow doubled and new clients came in. 

For scientists seeking alt-science careers, being part of a BCS consultant team gives a taste of consultancy and business, provides free mentorship, strengthens one’s CV, and comes in handy should the scientist need to speak to an industrial collaborator. It can also deepen volunteer’s interest and knowledge in business, leading to other roles in the business side of biotech, such as investing.

Increasing visibility and diversifying membership

Sau Yin made other changes to BCS, such as assembling a marketing team to improve the group’s visibility. Through digital marketing efforts via social media, the team grew BCS’s LinkedIn following from 800 to more than 2,400 in one year (the total exceeds 3,800 today). Sau Yin also focused on promoting BCS events, making sure the BCS logo was visible during the gatherings and publicizing them after the fact through photography and media. Write-ups after events, sent out to the BCS mailing list, create a track record of events and help boost sign-ups for future events.

“Our events are really relevant to the community, and they’re well attended,” Sau Yin says. 

 In early 2019, when she noticed that many BCS members were seeking new career opportunities, Sau Yin introduced a separate mailing list for members interested in information on opportunities in Singapore’s biotech sector. 

People join BCS for various reasons, Sau Yin says, and the result is a dynamic community network. Investors join to learn about new technologies and startups in Singapore; scientists who plan to stay in academia attend BCS events to find potential collaborators. In 2019, by changing the focus and topics of some BCS events, she brought more investors and clinicians into the membership. Often, Sau Yin says, researchers develop their technologies in isolation and don’t know the specific challenges clinicians face that might be addressed by new products.

Furthermore, Sau Yin says, PhDs sometimes arrive in the BCS network with ideas about industry or investing that may not be accurate. But frequently, she says, they find a rewarding, if sometimes unexpected, path better suited to their skills and desires.

BCS is “a good learning platform, to find out what you really want to do,” Sau Yin says. 

What were the challenges?

Sau Yin juggled her presidency at BCS with a full-time research job in a molecular engineering lab. What are her main challenges? Time, people, and money, she says.

When we spoke to her, she said she was devoting many hours each week to BCS, where she met with key committee members and contacts who got in touch with her through the BCS platform. The week we interviewed her, she was preparing to meet with a chamber of commerce member who reached out to her via LinkedIn. “This would never have happened if not for the ‘President of BCS’ name card I carry,” she said. For a person who calls herself an introvert, Sau Yin has extended her professional network, made important connections, and improved her networking skills. She says she enjoys BCS activities tremendously and wishes she could devote even more attention to them.

 “The experience is what you make of it,” she said. 

 In her role as president, Sau Yin said she learned how to manage different types of people who make up the team, alongside the different activities—it takes an open mind and willingness to listen to others, she said.

 Sau Yin is fiercely protective of her teammates. As she reflects on some of the past mistakes and lessons on this journey, she said she has learned to be a stronger leader and not let her team be taken advantage of—after all, she said, everyone on the BCS team volunteers their time and effort.  

 Afterword

Since we first sat down with Sau Yin she reached her maximum 2-year term as president. Since June 2020, she has taken on the role of director of research operations at a seed-funded biotech startup.

More than half of the committee members from 2017-19 have moved on to new careers after volunteering at BCS (ranging from joining industry/startups to funds that invest in biotech).

Sau Yin remains an advisor for the BCS committee and is succeeded by Natasha Ng, who has responded to the challenges of running the organization during the coronavirus pandemic by creating a wide range of webinar topics and by finding new partners and new ways to run virtual events. 

You may connect with Sau Yin at: https://www.linkedin.com/in/sau-yin-chin-ph-d-712b98136/

Chai Lean Teoh provided research assistance for this article.

Building a nexus between machine learning and super-resolution microscopy

0

by Maanasa Ravikumar

A biophysicist armed with coding expertise, Richard de Mets is deputy facility manager at the Microscopy Core at the Mechanobiology Institute (MBI) in Singapore. If you’ve ever wondered what your confocal image would look like under a super-expensive, super-resolution microscope, or you need suitable image processing codes for your research, de Mets has the right tools for the job.

Previously, de Mets worked in the Virgile Viasnoff lab at MBI for nearly four years, engaging in a wide variety of research projects and enjoying collaboration with scientists from diverse backgrounds and areas of expertise. But he knew from his early lab days in France that he did not want to be a principal investigator. The thought of being “stuck in the office to write grants and forms,” de Mets says, didn’t match his gregarious personality. Instead, he seized upon the chance to move to the Microscopy Core at MBI in September 2019.

“I want to help researchers understand their projects and teach them how to use microscopes,” de Mets says, “so they can be fully independent and, of course, bring new knowledge wherever they are.” Although he had no prior experience working in a core facility, the job responsibilities matched his outgoing personality and agile research interests. 

Currently, de Mets and the rest of the team are working to develop new algorithms to help scientists with their image processing needs. Their first algorithm is currently under testing and uses a class of machine learning systems called GAN (Generative Adversarial Network). 

I was trying to develop something capable of image restoration and improving image quality at the same time,” de Mets says. “My idea was to use a GAN to be able to link a low signal-to-noise ratio (SNR) image to a high resolution, high SNR image.” In other words, the algorithm can predict how a confocal microscopy image might look if it were taken with a super-resolution microscope (see fig 1). This image processing approach is particularly suitable for thick samples that typically cannot be imaged by super-resolution microscopy and need to be protected from photobleaching. While a super-resolution microscope may be hard to come by for most scientists, de Mets’s algorithm may be an attractive alternative!

Together with his colleagues, de Mets is also developing and adapting a plethora of other image processing codes that utilize neural networks and deep learning approaches such as Unets, CARE, Noise2Void and Noise2Noise. One such code has been configured exclusively for classification and segmentation purposes, specifically to differentiate signals and reduce background noise in images (see fig 2). De Mets says the biggest challenges in developing such image analysis methods are understanding the nature of the scientific question, evaluating which microscopy and image processing approaches can help provide answers, and pinpointing how these approaches can be improved. He describes his team’s arsenal of image analysis tools as works in progress that he is open to sharing with interested researchers, to help test and develop them further.

I am happy for people to contact me if they want to know more about our work and to discuss how we can help their research,” de Mets says.

De Mets looks back at the past year fondly, stating that he has found an ideal role where he can follow his passion for developing resources that cater to a multitude of research interests rather than a single project. He advises those looking to transition professionally from the bench to a scientific platform to keep their research interests broad, acquire basic knowledge in the platform of interest, and gain collaborative experience. In addition to technical skills, de Mets emphasizes that developing soft skills, such as effective communication and teamwork, is very important. At the end of the day, building trust in your platform’s capabilities and forging partnerships are key to working on exciting science.

Richard de Mets can be reached at mbirdm@nus.edu.sg and https://www.linkedin.com/in/richard-de-mets-1b1806103/

Image details

Fig 1

Sample PFA-fixed monolayer of primary rat hepatocytes cultured on glass bottom dishes coated with fibronectin. Cells are stained with Phalloidin-ATTO565.

Microscopy and imaging setup 

Low SNR image: Spinning disk W1 unit at 60X magnification, Photometrics Prime 95b camera with low laser power and 30ms exposure time. 

High SNR image: Spinning disk W1 unit at 60X magnification, Photometrics Prime 95b camera with high laser power and 500ms exposure time. Roper Scientific Live-SR module engaged to improve the resolution.

The first set of images exemplifies the use of a variant of the Generative Adversarial Network (GAN), called pix2pix network, dedicated to study the link between paired images for the purpose of image restoration and improvement. Both high and low signal-to-noise ratio (SNR) images were taken using the same sample and microscope. Upon training, the network was able to scan the low SNR image and provide a super-resolution image prediction that is comparable to a high SNR image taken independently.

Fig 2

Sample PFA-fixed monolayer of primary rat hepatocytes cultured on glass bottom dishes coated with fibronectin. Cells are stained with Phalloidin-ATTO565.

Microscopy and imaging setup

Spinning disk W1 unit at 60X magnification, Photometrics Prime 95b camera. Image taken 3 microns above the coverslip in order to see lumen formation between two hepatocytes

The second set of images shows the use of an algorithm dedicated to classification and segmentation, based on the Unets convolutional neural network approach. The Z-stack images show lumen formation between adjacent cells. The goal of the algorithm is to be able to differentiate signals coming from a cell junction to those from the lumen, as this cannot be performed using classical thresholding methods with a single staining. To train the algorithm, de Mets first manually demarcated masks on ImageJ to differentiate nuclei (red), junctions (green) and lumen (blue) across 20 fields of view. Using these as targets, the network was able to predict masks with 94% accuracy after just 20 minutes of training. Moreover, while the network has been trained on 2D data, it can be used for 3D segmentation purposes too, for example to estimate nuclei volumes or lumen volume.