Biology

Bruker Launches Transformative neofleX MALDI-TOF System for Spatial Biology Mass Spec Imaging (MSI … – BioSpace

ANAHEIM, Calif.--(BUSINESS WIRE)-- At the 72nd ASMS meeting, Bruker Corporation (Nasdaq: BRKR) announced the launch of a novel, high-performance MALDI-TOF/TOF system, the neofleX Imaging Profiler for mass spectrometry-based tissue imaging. It enables facile OME-TIFF file output via the new SCiLS Scope software. The transformative neofleX MALDI-TOF/TOF MSI system now conveniently fits on a bench-top.

This press release features multimedia. View the full release here: https://www.businesswire.com/news/home/20240603327426/en/

neofleX MALDI-TOF System for Spatial Biology Mass Spec Imaging (MSI) Applications (Photo: Business Wire)

The neofleX Imaging Profiler MALDI-TOF/TOF mass spectrometer comes standard with Brukers proprietary 10 kHz smartbeam 3D laser for true pixel fidelity and with enhanced imaging detectors designed for longitudinal robustness, stability, and reproducibility in linear and reflector modes. neofleX is also available as a TOF/TOF configuration that features a reimagined fragmentation module for significantly improved TOF/TOF sensitivity, speed and sequence coverage.

Created for the unmet needs of moving from discovery imaging to translational and clinical tissue research, neofleX was used by the group of Prof. Bernd Bodenmiller at ETH and University of Zuerich to simultaneously map 116 proteins across a lung FFPE tissue section in 7 hours, using the MALDI HiPLEX-IHC workflow. Multiplexed detection with neofleX and MALDI HiPLEX-IHC technology allows increasing the number of proteins to map cellular processes without increasing MSI measurement time for a given region of interest.

In addition to MALDI HiPLEX-IHC MSI immunohistochemistry, neofleX is also compatible with the MALDI-ISH (in situ hybridization) method announced at ASMS 2024 by AmberGen, Inc. MALDI-ISH multiplexes imaging of up to 12 oligomers of interest (RNA/DNA) for multiomic spatial tissue research in neuroscience, infectious disease, and oncology.

The novel neofleX excels at providing more insight per pixel through multiomic spatial biology data from tissue sections that can positively correlate targeted proteins with glycans, metabolites, lipids, endogenous peptides, xenobiotics, and now RNA/DNA. This additional multiomics context provides important adjacency information about cellular states, function, structure, and protein activity for a range of research areas, such as oncology and neurology.

Professor Carsten Hopf of the University of Mannheim, Germany, Center for Mass Spectrometry and Optical Spectroscopy (CeMOS) commented: The innovative neofleX presents an incredibly powerful, versatile and easy-to-use mass-spec imaging system for tissue spatial biology researchers for targeted proteomics. We appreciate the value of this instrument for performance and versatility, and our clinical research collaborators welcome the translational research capabilities.

Multiomic co-localization of lipids and glycans on a tissue section allows to not only localize protein targets using MALDI HiPLEX-IHC, but also assess protein activity and function. A study performed at CeMOS on brain tissues from a transgenic mouse model demonstrated co-localization of amyloid -42 (A42) protein with a targeted membrane-bound glycosphingolipid (GM3 d36:1), yielding important structural information.

Dr. Michael L. Easterling, Vice President MSI for Brukers Life Sciences Mass Spectrometry division, commented: The neofleX offers unique combination of outstanding performance, multimodal software and workflows on the benchtop for a wide range of biopharma and clinical researchers. Additionally, neofleX brings novel capabilities to spatial biology, including spatial proteomics combined with unique multiomics correlations for developing actionable biological insights.

The neofleX is compatible with Brukers MALDI Imaging software and consumables ecosystems, such as IntelliSlides and SCiLS autopilot that simplify sample tracking, preparation, and analysis and require minimal input from users to initiate and process automated mass-spec imaging runs. For ease of collaborations, the neofleX now delivers targeted imaging data via automatically generated OME-TIFF images that can be viewed within the SCiLS environment, or easily exported into custom pipelines or digital pathology systems.

Bruker also announced extension of the SCiLS portfolio with SCiLS Scope 1.0 for collaboration around targeted, multiomic translational workflows developed for neofleX. SCiLS Scope software supports OME-TIFF datasets from targeted imaging workflows such as MALDI HiPLEX-IHC. Ion images are visualized by false-color coding of selected channels, and image processing and distance measurements can be accomplished with simple tools.

Blaine R. Roberts, Ph.D., Associate Professor in the Department of Biochemistry and Department of Neurology at Emory University in Atlanta, GA, summarized: Fast and user-friendly visualization of targets is made easy by the addition of SCiLS Scope to the MSI software lineup.

About Bruker Corporation the Emerging Leader of the Post-Genomic Era (Nasdaq: BRKR)

Bruker is enabling scientists and engineers to make breakthrough post-genomic discoveries and develop new applications that improve the quality of human life. Brukers high-performance scientific instruments and high-value analytical and diagnostic solutions enable scientists to explore life and materials at molecular, cellular, and microscopic levels. In close cooperation with our customers, Bruker is enabling innovation, improved productivity, and customer success in post-genomic life science molecular and cell biology research, in applied and biopharma applications, in microscopy and nanoanalysis, as well as in industrial and cleantech research, and next-gen semiconductor metrology in support of AI. Bruker offers differentiated, high-value life science and diagnostics systems and solutions in preclinical imaging, clinical phenomics research, proteomics and multiomics, spatial and single-cell biology, functional structural and condensate biology, as well as in clinical microbiology and molecular diagnostics. For more information, please visit http://www.bruker.com.

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Bruker Launches Transformative neofleX MALDI-TOF System for Spatial Biology Mass Spec Imaging (MSI ... - BioSpace

Biology

Fish in schools have an easier time swimming in rough waters – EurekAlert

image:

A school of pink salmon (Oncorhynchus gorbuscha) in upper Nimpkish River, British Columbia, Canada.

Credit: Fernando Lessa (CC-BY 4.0, https://creativecommons.org/licenses/by/4.0/)

Swimming through turbulent water is easier for schooling fish compared to solitary swimmers, according to a study published June 6th in the open-access journal PLOS Biology by Yangfan Zhang of Harvard University, Massachusetts, US, and colleagues.

Locomotion is key to many aspects of animal behavior, from reproduction to feeding to migration, and so many species have developed adaptations to make moving around more efficient. In this study, Zhang and colleagues propose the turbulent sheltering hypothesis, which suggests that traveling in schools allows fish to shield each other from disruptive water currents, thus making it easier to swim through rough waters.

To test this hypothesis, the researchers ran trials with giant danios (Devario aeqipinnatus), observing these fish swimming alone or in groups of eight in both turbulent and steadily flowing water. High-speed cameras allowed researchers to observe the movements of the fish as they swam, and a respirometer allowed for measurements of fish respiration rates and energy expenditure.

These trials revealed that schooling fish expended up to 79% less energy while swimming in turbulent water compared to solitary fish. Schooling fish also clustered more closely together in turbulent water compared to steady water, while solitary fish had to beat their tails much more vigorously to maintain the same speed in more turbulent currents.

These results lend support to the turbulence sheltering hypothesis, indicating that locomotion efficiency might be a driving factor behind the evolution of schooling behavior. This information is valuable for understanding fish ecology, fundamentals of hydrodynamics and it might also be applied to the design and maintenance of habitats meant to harbor protected fish species or to hinder invasive ones. The authors note that future studies might build off of these findings to explore energy dynamics of group movements in further aquatic or aerial animals.

The authors add, What is the function of schooling behaviour in fishes? We show that being in a school substantially reduces the energetic cost for fish swimming in a turbulent environment, compared to swimming alone, providing support for the hypothesis that schooling behaviour protects individual fish from the increased energetic cost associated with swimming in turbulence.

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In your coverage, please use this URL to provide access to the freely available paper in PLOS Biology: http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.3002501

Citation: Zhang Y, Ko H, Calicchia MA, Ni R, Lauder GV (2024) Collective movement of schooling fish reduces the costs of locomotion in turbulent conditions. PLoS Biol 22(6): e3002501. https://doi.org/10.1371/journal.pbio.3002501

Author Countries: United States

Funding: Funding provided by the National Science Foundation grant 1830881 (GVL), the Office of Naval Research grants N00014-21-1-2661 (GVL), N00014-16-1-2515 (GVL), 00014-22-1-2616 (GVL), and a Postdoctoral Fellowship of the Natural Sciences and Engineering Research Council of Canada (NSERC PDF - 557785 2021) followed by a Banting Postdoctoral Fellowship (202309BPF-510048-BNE-295921) of NSERC & CIHR (Canadian Institutes of Health Research) (YZ). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Experimental study

Animals

Competing interests: The authors have declared that no competing interests exist.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Fish in schools have an easier time swimming in rough waters - EurekAlert

Biology

WHS valedictorian to attend Hanover for biology | News | shelbynews.com – Shelbynews

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Biology

UK Researcher Named an Inspiring Woman in Plant Biology – Morning Ag Clips –

Aardra Kachroo, a professor in the Department of Plant Pathology in the Martin-Gatton College was nominated for her research on plant immunity and for selflessly serving to empower women in science and plant biology.

I am honored to be recognized amongst this incredible cohort of women in science and grateful for those who nominated me, said Kachroo. Our collective passion as well as that of the many plant science stalwarts not named here, offers a bright future of scientific discoveries that will improve our world and benefit all lives.

The ASPB Women in Plant Biology Committee called for nominations of remarkable women who shape the field to highlight career achievementsand celebrate their impact in plant biology.

Aardra Kachroos research at the University of Kentucky focuses on unraveling the molecular mechanisms of plant immunity, wrote one nominator. Using molecular biology and genomics, she explores how plants recognize and defend against pathogens, offering insights crucial for enhancing crop protection and global food security.

I am privileged to receive guidance from a remarkable woman who has truly been a beacon of inspiration on my journey, submitted another nominatokr.

Kachroo uses various plants and pathogens to research how primary metabolic and defense signaling pathways are connected to solve agricultural problems. Her lab focuses on systemic acquired resistance (SAR) a signaling mechanism that provides widespread plant immunity and can be passed on to other generations of plants and ones nearby.

Kachroos lab also explores SAR and the recently identified root-shoot-root signaling mechanism that regulates the associations between legumes and nitrogen-fixing bacteria on roots.

In addition to her research, Kachroo also serves on the board of the Kentucky Association of Professional African American Women while being an advocate and mentor. She also leads a biotech company that develops sustainable and environmentally friendly pest management products for plants.

Kachroo was recognized among other mid-career researchers. You can find ASPBsfull list here.

UK Martin-Gatton College of Agriculture, Food and Environment

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UK Researcher Named an Inspiring Woman in Plant Biology - Morning Ag Clips -

Biology

Man’s remains identified after nearly 40 years | Biology | kvoa.com – KVOA Tucson News

TUCSON (KVOA) - For nearly 40 years an Idaho man and his mother had no idea if their loved one was dead or alive.

The man had a suspicion and a DNA test proved his worst fears.

A DNA test proved that the man's suspicions were correct.

But, it took four decades to learn the man's fate.

They didn't know for four decades.

The remains no longer belong to John Doe they belong to John Leigh III who died in a fiery plane crash in August of 1984.

The crash site was not found until 13 years later by hikers in the Rincon Mountains. They took a picture and asked to remain anonymous.

They told News 4 "The site was very steep, brushy and difficult. The shot obviously depicts some of the wreckage among the brush."

News 4 spoke to John IV "I really want to hike up to the crash site like I've said before that's the official burial site, and I want to pay my respects up there if I can get there."

He was just 4 years old when his dad disappeared.

"It really doesn't affect me like it affects my mom, because I never knew him, and to me, the biggest part is that I know now that he didn't skip out of town and it gives me peace."

Dr. Bruce Anderson works for the Office of the Medical Examiners. He said there were the remains of four adult men who were on the plane. He had to exhume the remains when Susan Leigh and her son John IV wanted to know if their loved one John III was on that ill-fated flight.

He sent DNA samples from the bones to three different labs, but it was the California Department of Justice Missing Persons DNA Program that not only identified Leigh's DNA but the three others as well.

Anderson said, "It took a while for DNA technology to improve to where they could get DNA profiles, good quality DNA profiles, out of degraded bone like this."

Also found in the wreckage besides remains, several personal effects. such as aviator glasses, a BIC lighter, a briefcase lock, and a pocket knife.

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Man's remains identified after nearly 40 years | Biology | kvoa.com - KVOA Tucson News

Biology

Shift the Focus: Is addiction biology or psychology? – Cecil Daily

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Shift the Focus: Is addiction biology or psychology? - Cecil Daily

Physiology

Physiological responses of Atlantic cod to climate change indicate that coastal ecotypes may be better adapted to … – Nature.com

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Excerpt from:
Physiological responses of Atlantic cod to climate change indicate that coastal ecotypes may be better adapted to ... - Nature.com

Biochemistry

Scientists uncover a multibillion-year epic written into the chemistry of life – EurekAlert

image:

Metabolism is the "beating heart of the cell". New research from ELSI retraces the history of metabolism from the primordial Earth to the modern day (left to right). The history of compound discovery over time (white line) is cyclic, almost resembling an EKG.

Credit: NASA's Goddard Space Flight Center/Francis Reddy/NASA/ESA

The origin of life on Earth has long been a mystery that has eluded scientists. A key question is how much of the history of life on Earth is lost to time. It is quite common for a single species to "phase out" using a biochemical reaction, and if this happens across enough species, such reactions could effectively be "forgotten" by life on Earth. But if the history of biochemistry is rife with forgotten reactions, would there be any way to tell? This question inspired researchers from the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology, and the California Institute of Technology (CalTech) in the USA. They reasoned that forgotten chemistry would appear as discontinuities or "breaks" in the path that chemistry takes from simple geochemical molecules to complex biological molecules.

The early Earth was rich in simple compounds such as hydrogen sulfide, ammonia, and carbon dioxide molecules not usually associated with sustaining life. But, billions of years ago, early life relied on these simple molecules as a raw material source. As life evolved, biochemical processes gradually transformed these precursors into compounds still found today. These processes represent the earliest metabolic pathways.

In order to model the history of biochemistry, ELSI researchers Specially Appointed Associate Professor Harrison B. Smith, Specially Appointed Associate Professor Liam M. Longo and Associate Professor Shawn Erin McGlynn, in collaboration with Research Scientist Joshua Goldford from CalTech needed an inventory of all known biochemical reactions, to understand what types of chemistry life is able to perform. They turned to the Kyoto Encyclopedia of Genes and Genomes database, which has catalogued more than 12,000 biochemical reactions. With reactions in hand, they began to model the stepwise development of metabolism.

Previous attempts to model the evolution of metabolism in this way had consistently failed to produce the most widespread, complex molecules used by contemporary life. However, the reason was not entirely clear. Just as before, when the researchers ran their model, they found that only a few compounds could be produced. One way to circumvent this problem is to nudge the stalled chemistry by manually providing modern compounds. The researchers opted for a different approach: They wanted to determine how many reactions were missing. And their hunt led them back to one of the most important molecules in all of biochemistry: adenosine triphosphate (ATP).

ATP is the cell's energy currency because it can be used to drive reactions like building proteins that would otherwise not occur in water. ATP, however, has a unique property: The reactions that form ATP themselves require ATP. In other words, unless ATP is already present, there is no other way for today's life to make ATP. This cyclic dependency was the reason why the model was stopping.

How could this "ATP bottleneck" be resolved? As it turns out, the reactive portion of ATP is remarkably similar to the inorganic compound polyphosphate. By allowing ATP-generating reactions to use polyphosphate instead of ATP by modifying just eight reactions in total nearly all of contemporary core metabolism could be achieved. The researchers could then estimate the relative ages of all common metabolites and ask pointed questions about the history of metabolic pathways.

One such question is whether biological pathways were built up in a linear fashion in which one reaction after another is added in a sequential fashion or if the reactions of pathways emerged as a mosaic, in which reactions of vastly different ages are joined together to form something new. The researchers were able to quantify this, finding that both types of pathways are nearly equally common across all of metabolism.

But returning to the question that inspired the study how much biochemistry is lost to time? "We might never know exactly, but our research yielded an important piece of evidence: only eight new reactions, all reminiscent of common biochemical reactions, are needed to bridge geochemistry and biochemistry, says Smith." "This does not prove that the space of missing biochemistry is small, but it does show that even reactions which have gone extinct can be rediscovered from clues left behind in modern biochemistry," concludes Smith.

Reference

Joshua E. Goldford1,2,3,*,#, Harrison B. Smith3,4,#, Liam M. Longo3,4,#, Boswell A. Wing5, and Shawn Erin McGlynn3,4,6,*, Primitive purine biosynthesis connects ancient geochemistry to modern metabolism, Nature Ecology & Evolution, DOI: 10.1038/s41559-024-02361-4

#Co-first authorship

More information

Tokyo Institute of Technology (Tokyo Tech) stands at the forefront of research and higher education as the leading university for science and technology in Japan. Tokyo Tech researchers excel in fields ranging from materials science to biology, computer science, and physics. Founded in 1881, Tokyo Tech hosts over 10,000 undergraduate and graduate students per year, who develop into scientific leaders and some of the most sought-after engineers in industry. Embodying the Japanese philosophy of "monotsukuri," meaning "technical ingenuity and innovation," the Tokyo Tech community strives to contribute to society through high-impact research.

The Earth-Life Science Institute (ELSI) is one of Japan's ambitious World Premiere International research centers, whose aim is to achieve progress in broadly inter-disciplinary scientific areas by inspiring the world's greatest minds to come to Japan and collaborate on the most challenging scientific problems. ELSI's primary aim is to address the origin and co-evolution of the Earth and life.

The World Premier International Research Center Initiative (WPI) was launched in 2007 by Japan's Ministry of Education, Culture, Sports, Science and Technology (MEXT) to foster globally visible research centers boasting the highest standards and outstanding research environments. Numbering more than a dozen and operating at institutions throughout the country, these centers are given a high degree of autonomy, allowing them to engage in innovative modes of management and research. The program is administered by the Japan Society for the Promotion of Science (JSPS).

Nature Ecology & Evolution

Computational simulation/modeling

Not applicable

Primitive purine biosynthesis connects ancient geochemistry to modern metabolism

22-Mar-2024

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Scientists uncover a multibillion-year epic written into the chemistry of life - EurekAlert

Biochemistry

Scientists uncover missing link in the Chemistry of Life – Tech Explorist

In a groundbreaking study, scientists have revealed a multibillion-year epic written into the chemistry of life, shedding light on the mysterious origins of life on Earth. The study, led by researchers from the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology and the California Institute of Technology (CalTech), demonstrates that just a handful of forgotten biochemical reactions are needed to transform simple geochemical compounds into the complex molecules of life.

The research, published in a recent scientific journal, delves into the idea that certain biochemical reactions crucial to the development of life may have been forgotten over time. The team of researchers, including Specially Appointed Associate Professors Harrison B. Smith and Liam M. Longo, Associate Professor Shawn Erin McGlynn from ELSI, and Research Scientist Joshua Goldford from CalTech, embarked on a quest to unravel the missing links in the history of biochemistry.

By investigating the earliest metabolic pathways on Earth, the researchers aimed to understand how simple geochemical molecules evolved into the complex biological molecules that sustain life today. They utilized an inventory of over 12,000 known biochemical reactions from the Kyoto Encyclopedia of Genes and Genomes database to model the stepwise development of metabolism.

Previous attempts to model the evolution of metabolism had failed to produce the most widespread, complex molecules used by contemporary life. However, the researchers discovered that a few compounds could be produced due to a bottleneck caused by the cells energy currency, adenosine triphosphate (ATP). They found that the reactions that form ATP themselves require ATP, creating a cyclic dependency that hindered the models progression.

Remarkably, the researchers identified a solution to this ATP bottleneck by modifying eight reactions to allow ATP-generating reactions to use polyphosphate instead of ATP. This simple adjustment enabled the model to achieve nearly all of contemporary core metabolism, providing crucial insights into the relative ages of common metabolites and the history of metabolic pathways.

One of the studys most intriguing findings was the revelation that only eight new reactions, reminiscent of common biochemical reactions, are needed to bridge the gap between geochemistry and biochemistry. This discovery offers compelling evidence that even reactions that have gone extinct can be rediscovered from clues left behind in modern biochemistry.

The studys lead researcher, Harrison B. Smith, remarked, This does not prove that the space of missing biochemistry is small, but it does show that even reactions which have gone extinct can be rediscovered from clues left behind in modern biochemistry.

The groundbreaking insights from this study provide a deeper understanding of the history of life on Earth and open new avenues for further exploration into the origins of biochemistry and the evolution of metabolic pathways.

This remarkable research is a testament to the relentless pursuit of knowledge and the unyielding curiosity of scientists striving to unlock the secrets of lifes ancient chemistry.

Journal Reference

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Scientists uncover missing link in the Chemistry of Life - Tech Explorist

Biochemistry

Electrolyte and Biochemistry Analyzers Market Is Likely to Experience a Tremendous Growth by 2031 – openPR

Electrolyte and Biochemistry Analyzers Market

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