Posted on

Tiny tech, rapid antibody mapping

A recent research paper published in Nature Biomedical Engineering shares a new way to study how the immune system battles viruses, requiring only a drop of blood and producing results in under two hours.

The technique, called microfluidic electron microscopy (mEM), is like offering scientists an extremely sleek microscope on steroids that can expose how antibodies latch onto viruses like influenza, HIV and SARS-CoV-2.

The chip, which is the size of a fingernail, requires only a single drop of serum (less than 4 microliters) and 90 minutes to complete the analysis that used to take a week, including lots of prep like cutting up antibodies and purification. It’s like a mini-lab and ultra-zoom camera all in one.

The speed isn’t the only perk. The tool is also super smart, finding more binding sites on viruses than previous methods.

This offers a more complete picture of how the immune system responds to viruses and vaccines alike. The smaller samples make it a game-changer for vaccine development by tracking immune system responses over time.

More like this: Turning the phage

Posted on

A door-opening chemo twist

A new study from the UV Center for Cancer is helping people requiring stem cell transplants safely receive stem cells from mismatched and unrelated donors. For patients with diverse backgrounds often struggling to find an ideal match, it’s great news.

The drug strategy is called post-transplant cyclophosphamide (PTCy)

Doctors used stem cells from blood (instead of bone marrow) and gave patients a powerful follow-up treatment with PTCy plus two other meds — tacrolimus and mycophenolate mofetil.

This resulted in solid survival rates a year later — about 84 percent for patients who had intense chemo, and 79 percent for those with gentler prep.

Most notably, serious cases of graft-versus-host disease — a nasty side effect where the new cells attack the patient’s body — stayed low.

Over 50 percent of patients in the study were from underrepresented racial or ethnic groups, proving this approach helps close the gap in transplant access.

The main takeaway is that a perfect match isn’t required anymore to have a strong shot at survival.

More like this: Cancer can run, but it can no longer hide

Posted on

A new form of biometrics:
We’re all ears

Previously, it took biometrics such as facial recognition, fingerprints or retinal scans to identify the unique physical characteristics of each human, but now identification might be as simple as measuring your ear.

Using ears to identify humans isn’t new, but our favorite crime shows still rely on old faithful methods — dusting for fingerprints or collecting DNA — to land a suspect. In all fairness, criminals are much more likely to touch things with their hands than rub their ears all over a crime scene.

It was, however, used in a 1997 murder trial after an investigation lifted an ear-print from the window the killer entered through. The subsequent conviction was the first using ear prints as an identifier. However, the verdict in 2004 was overturned on appeal as DNA from the ear print indicated a different suspect. It was the opinion of the expert used in the trial that solidified the guilty verdict.

That case was flawed, but recent studies show ears are just as reliable an identifier as our fingerprints.

A team of researchers from the University of Georgia in 2022 developed software that scans your ear. It was intended to serve a post-COVID world in which people wear masks — muffling voice recognition — and are conscious of what they touch.

Masks aren’t the problem they used to be, but there are other security operations in which ear identification can be instrumental.

Ears are fully formed and developed at birth. Except for the consequences of age they really don’t change over time. Each ear is unique, and your ears are even unique from each other. This makes them a reliable source of identification – even from a distance.

You can’t access someone’s fingerprints or DNA from a photo, but even a photograph of your ear can tell us who you are. And with the number of crimes recorded on video, ear biometrics can help identify the culprits.

A more recent development in ear identification came when a team of forensic and dental scientists from all over the world built on a 2011 study by Roberto Cameriere that measured the four anatomic regions of the ear and combined the measurements to produce a code that is unique to each person.

They implemented a larger specimen group and divided it across multiple ethnic groups to stretch the method and determine further accuracy. They found that when they added the codes for each person’s ears together, there were zero code repeats. This means 814 unique ear identifiers. The team concluded that “the probability of two different individuals having the same code (false-positive identification) was found to be less than .07 percent.”

So, if you’re planning to launch a crime wave, make sure to wear ear muffs. They’ll protect you from the cold and from getting caught.

But if you happen to forget, perhaps you can simply slouch your way through your criminal activity. Or not.

A team of researchers from Khalifa University suggest the factors that inhibit accurate ear identification in 2D and 3D images — posture, light and scaling — can be overcome with combining both, “To the best of our knowledge, this is the first time two-dimensional and three-dimensional ear attributes have been merged to build a detector and descriptor for matching a pair of 3D ears. Combining features from the 2D domain and features from the 3D domain considerably increased recognition efficiency.”

The team suggests that a keypoint detector and a descriptor, built from angular features of 2D ears and textures of 3D ears, can lead to more accurate ear identification. The texture and shape combined enhance the veracity of the results.

“This holistic approach culminates in the achievement of state-of-the-art results while simultaneously ensuring robustness to illumination and pose variations,” says Iyyakutti Iyappan Ganapathi. He is lead author on the study and a post-doctoral fellow in the electrical engineering and computer science department at Khalifa University.

Ganapathi says while there is comparable accuracy between other commonly used biometrics and ear identification, a lack of data is a challenge.

However, he is hopeful going forward.

“Looking ahead, it is foreseeable that, as more ear data becomes accessible, researchers will increasingly turn their attention towards ear biometrics as a viable means of human recognition. This nascent avenue holds significant promise for the future of biometric identification,” he tells KUST Review.

Posted on

Protecting your produce

When we purchase fresh produce from our local grocery store, we aren’t usually consumed with worry about whether it contains fecal matter. But the threat is real, and current testing methods are tedious and expensive. That’s why a team of researchers from Purdue University in the United States has developed a reliable and quick method to ensure the produce on our table isn’t contaminated.

Listen to the Deep Dive

But what is the threat?

A cattle farm in Arizona’s Yuma County in the United States produces 115,000 cows annually. Just three miles from the facility is a lettuce farm that is threatened by dust or irrigation water contaminated with feces. An investigation found E. coli bacteria in a nearby canal, and because Yuma County produces 90 percent of the USA’s winter lettuce, these risks need to be mitigated.

In fact, a 2018 outbreak of the same strain of E. coli killed five people after they consumed produce from the Yuma Valley.

“With changes in climate and emergence of new threats (e.g., most recently highly pathogenic avian influenza), maintaining the status quo will increase the burden of these threats,” the Purdue team’s Mohit Verma tells KUST Review.

IMAGE: Pixabay

His team’s new biosensor aims to mitigate these threats.

For a method of detection to be easily integrated, it needs to be accurate, cost effective and simple.

The biosensor detects DNA using loop-mediated isothermal amplification (LAMP), which is simpler than the polymerase chain reaction (PCR) method because it operates at a constant temperature, rather than requiring temperature changes. And to detect fecal contamination, the team uses Bacteriodales, which is an order of bacteria found in animal feces and intestines, but not usually in the surrounding environment. This makes Bacteriodales the best measure of fecal-matter presence.

CAPTION: Verma lab’s molecular tests(using loop-mediated isothermal amplification or LAMP), that can be completed with just some warm water incubation. Results can be read within one hour. IMAGE: Purdue Agricultural Communications

Small plastic sheets on wooden skewers, called collection flags, are placed around the farm and left for a week to collect samples. The flags are then collected and swabbed to transfer bioaerosols — small particles from any nearby animal operations — to the team’s biosensor, which use LAMP to amplify Bacteriodales DNA. The presence and amount of this DNA will cause a color change that can be measured instantly, detecting any level of fecal contamination ranging from safe to high-risk.

The current method of detection is typically lab-based. The biosensor, however, when compared with lab results of the lab-based quantitative polymerase chain reaction results, proved 100 percent accurate.

The team does admit, however, that the testing was done in extreme conditions (very high and very low levels in the field), but still anticipates more than 90 percent sensitivity and specificity at intermediate-level testing.

“These biosensors have the potential to serve as a site-specific risk-assessment tool. They can provide a faster response and thus help in curbing problems before they become too large. They can also help in guiding decisions quickly compared to current lab-based approaches,” Verma says.

Traditional methods of testing also require expensive equipment, expert staffing, take 24-48 hours or more to produce results, and each test runs about U.S.$50. The new biosensor, however, requires simple equipment costing about U.S.$200 and provides equally accurate results within one hour at U.S.$10 per test.

Verma says the collection flags will help producers make important decisions about where to plant and the type of crops based on biosensor results. Also, it can help farmers determine if harvest timings should be adapted due to environmental risk or changing weather patterns by providing site-specific data.

“The biosensor is designed with the end user in mind. Thus, it is meant for use by producers and food safety professionals. The biosensors come with an operation manual and the user can be trained within an hour to run the assays.”

— Mohit Verma, associate professor of agricultural and biological engineering — Purdue University

The applications are not limited to fecal detection on produce farms, however.

“These biosensors are broadly applicable because they can detect DNA or RNA. Specifically, when detecting Bacteroidales, they could be applied for measuring water quality as well. In addition, Bacteroidales can be used for microbial source tracking, i.e., determining where fecal contamination might be coming from. Thus, it applies to water safety as well,” Verma says.

Verma’s new start-up company, Krishi Inc., will develop the biosensor technology commercially and work to enhance its versatility and ease of distribution. Verma says he hopes to also target the health market for companion animals such as cats and dogs, developing biosensors to detect antimicrobial resistance in urinary-tract infections and skin and ear infections.

Bigger picture, Verma hopes to alleviate the current limitation to lab-based methods for surveillance and diagnostics. “The biosensors have the potential to overcome this bottleneck by becoming widely available, providing a rapid response and enabling use in the field,” he tells KUST Review. “Currently, our response time to microbial threats is very slow.”

Funding from the Center for Produce Safety and several other industrial partners supported the team’s work on Bacteroidales.

The 2024 paper was published in Science Direct.

Posted on

Mini 3D-printed lungs enhance
disease research

Using light-based printing, a miniature 3D-printed human lung model was created by Canadian researchers at the University of British Columbia.

The team’s tiny lung creation mimics real human airways including airway-lining cells, connective tissue cells and mini blood vessels.

The structure is printed with a special gel-like material that supports healthy cell growth and behavior. When exposed to cigarette smoke extract, it responded just like real lung tissue — releasing inflammation signals such as IL-6 and IL-8, without harming the cells.

The model also contains features like fibroblasts that move to heal soft tissue and endothelial cells forming vessel-like layers.

It’s a more realistic, customizable platform for studying lung diseases and testing treatments and offers a new tool that could help replace animal testing and improve research on asthma, COPD and more.

More like this: Immune cell sabotage