Category Archives: Biology

Biology

Iconic savanna mammals face genetic problems due to fences and roads – EurekAlert

image:

Map showing the current distribution range of the two wildebeest species, the blue wildebeest and the black wildebeest, based on IUCN distribution data. Map prepared by Laura D. Bertola.

Credit: Laura D. Bertola

Whether by way of Attenborough, Disney or National Geographic, the iconic scene is familiar to many. The ground trembles and clouds of dust swirl as enormous hordes of large animals thunder across the African savanna, cross rivers en masse and are picked off by lions, hyena and crocodiles. The annual migration of 1.3 million wildebeest through Tanzanias Serengeti and Kenyas Masai Mara attracts hundreds of thousands of tourists, and the phenomenon has put the Serengeti on UNESCO's list of World Heritage sites. Besides its majestic sight, the migration of this emblematic species is important for the ecological functioning of ecosystems.

Unfortunately, epic annual migrations of this scale are only found in a few places on the African continent now. In some areas, roads, fences, farms and urban sprawl have fractured the historic migratory routes of wildebeest herds and prevented them from roaming far and wide in search of fresh grass and water. A new study led by researchers from the University of Copenhagen shows that the genetic health of wildebeest has suffered as a consequence.

"No one ever knew that this affected the genetics of wildebeest. But our results clearly show that wildebeest populations which no longer migrate, but have historically done so, are simply less genetically healthy than those that continue to migrate. And this weakens their chances of long-term survival," says Rasmus Heller, an associate professor at the Department of Biology and one of the new studys lead authors.

The results demonstrate that the genetic decline of non-migratory populations is reflected in several of the parameters by which genetic health is measured in nature conservation.

"Wildebeest that can no longer migrate have lower genetic diversity, are more genetically isolated and are more inbred. We expect this to lead to lower survival, reduced fertility and other negative effects on fitness," says Xiaodong Liu, one of the studys first authors and a postdoc at the Department of Biology.

Overall, this iconic savanna grazer is not currently threatened. But in the long term, wildebeest herds that can no longer migrate will likely be worse off, for example, in the face of climate change.

"The long-term consequence is that populations with low genetic diversity are less equipped to cope with the effects of environmental changes. Their evolutionary potential is reduced. So, if climatic changes continue to occur, there isnt as much genetic variation for them to work with to adapt which could ultimately threaten their survival," says Rasmus Heller.

Researchers analyzed the whole genomes of 121 wildebeest from their entire range, which spans from South Africa to Kenya. This is the first time that scientific researchers have studied the genetic effect of migration in wildebeest.

"Because we studied the genomes of many wildebeest from virtually their entire range, we have been able to make a general genetic comparison of migratory versus non-migratory populations. And because we witness a consistent difference across multiple locations, the conclusion is clear. Indeed, we can say that the overall negative effect is evident in those wildebeest that have been prevented from migrating regardless of where they live on the continent," says Xiaodong Liu.

While the total number of wildebeest remains fairly stable, many local populations have experienced steep declines and several have even collapsed in recent decades.

One hundred and fifty years ago, many wildebeest populations made great migrations. However,forty years ago, only two large intact wildebeest migrations remained in Africa: the famed Great Migration of the Serengeti-Mara and one in the Kalahari Desert of southern Africa.

"However, in Botswana in particular, fencing to protect cattle from coming into contact with migratory wild animals was put up in recent times. Botswana's Kalahari population declined from roughly 260,000 in the 1970s to fewer than 15,000 in the late 1980s. So today, the only remaining large population is that of the Serengeti-Mara. But the Serengeti-Mara migration is also threatened by plans for roads and rail corridors through the area, which worries many," says Mikkel Sinding from the Department of Biology, another of the study's first authors.

"As a species, wildebeest are dependent on migrations to support their large numbers. They can survive in resident, non-migratory populations, but their numbers simply shrink when they cannotmigrate. For example, we see this in the populations in the other parts of Kenya and Tanzania that have been prevented from migrating and whose numbers have decreased as a result," says co-author Joseph O. Ogutu, a senior statistician in the Biostatistics Unit at the University of Hohenheim, who adds:

"The migrations of wildebeest make them a keystone species in ecosystems, as their grazing keeps vegetation healthy, transports and distributes nutrients, while they themselves serve as prey for predators and carrion for scavengers. Therefore, it isnt just the iconic animal that we threaten when we prevent them from migrating but many other species as well. And to that, we might add the enormous amount of tourism revenue that benefits governments and local communities."

The researchers hope that the new results will inspire investigations into the genetic effects of reduced migration among other species. And they hope that decision-makers keep the consequences in mind:

"The study shows us that wild animal species, for whom migration is an essential part of their biology, struggle to survive in an increasingly human-dominated world, unless special attention is paid to preserving their old and natural migratory routes. As such, we hope that people will be more cautious about continuing to disrupt these routes. This concern is not just with regards to wildebeest, but also for other migratory species in Africa and elsewhere," says Rasmus Heller. He concludes:

"If we want the species to not just exist for, say, the next 50 years, but to thrive and actually survive in the much longer term, we need to halt the genetic decay caused by curtailing their natural migration routes.

The only remaining major wildebeest migration is the "Great Migration" in the Serengeti-Mara. Here, approximately 1.3 million wildebeest, accompanied by about 200,000 zebras and 400,000 gazelles, cover up to 3,000 kilometers annually in a clockwise cycle that follows seasonal rainfall patterns. But only the wildebeest and zebra from the Serengeti cross the Mara river into Kenyas Masai Mara.

Due to limited source material on African wildlife populations prior to the mid-1800s, the total number of historical wildebeest migrations is uncertain. However, it is known that migrations comparable to that of the Serengeti-Masai Mara population have been lost.

An example of this relates to two wildebeest subspecies known as the white-bearded wildebeest the Western white-bearded wildebeest, which makes up the Serengeti-Mara population, and the Eastern white-bearded wildebeest, whose migration was centered around Kenyas Kajiado County. From early European explorers and the first big game hunters, we know that both of these subspecies migrated a great deal historically. And, that they had very large populations, presumably of approximately similar size. While the Western white-bearded wildebeest was protected in the Serengeti-Mara from the early 1950s, increased human presence and activities dating back tothe early 1900s put mounting pressure on the Eastern white-bearded subspecies. Today, only 6,000-8,000 Eastern white-bearded wildebeest remain and are divided into many, small isolated populations.

Nature Communications

Introgression and disruption of migration routes have shaped the genetic integrity of wildebeest populations

12-Apr-2024

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Iconic savanna mammals face genetic problems due to fences and roads - EurekAlert

Biology

Advice to a Young Mathematical Biologist – University of Birmingham

Past and present Presidents of the Society for Mathematical Biology have pooled decades of expertise to help early career researchers get ahead in the field.

Published 10 April 20243 minute read

A group of 10 experts contributed advice on topics ranging from deciding if a career in academia is the right path, to writing grant proposals and giving lectures. Their aim was to help young researchers develop skills which are often not taught in a typical undergraduate degree. The advice is published in the Bulletin of Mathematical Biology.

The Society for Mathematical Biology was founded to support research and education at the interface of mathematical and biological sciences. Following an SMB Presidents session at the 2023 conference, held in Ohio, lead author, Dr Paul Roberts, decided to capture some of these insights in a more formal way, inspired by the inspirational biologist and writer Sir Peter Medawar, who wrote Advice to a Young Scientist in 1979.

The advice we have captured spans a real breadth of topics and challenges that mathematical biologists and indeed early career researchers in many other disciplines will face.

Dr Roberts, a mathematical biologist in the University of Birminghams Centre for Systems Modelling and Quantitative Biomedicine, said: The advice we have captured spans a real breadth of topics and challenges that mathematical biologists and indeed early career researchers in many other disciplines will face.

The aim is to offer a starting point which researchers can dip into, and explore in more depth as they wish.

Dr Roberts added: One thing we particularly emphasise is the importance of building a community, and collaborating widely outside your field. If scientists can learn to do this at the start of their careers, the next generation of researchers will truly be a force to be reckoned with.

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Advice to a Young Mathematical Biologist - University of Birmingham

Biology

New project explores warfare in animal societies – EurekAlert

image:

Mongoose warfare

Credit: Harry Marshall

A major new research project will investigate how and why groups of animals from the same species fight one another.

By focussing on warlike species mongooses and termites researchers aim to understand how evolution can lead to extreme aggression between groups, the consequences of this and the factors that can lead to peace.

The results will help to explain why violence between rival groups evolves in some species but not others, or between some groups and not others with implications for our understanding of human evolution.

The research team, led by Professor Michael Cant at the University of Exeter, includes the universities of Cambridge, York, Swansea and Bielefeld, Germany, and a field team based in Uganda.

Professor Cant and his team have been awarded a 3 million Advanced Grant by the European Research Council (ERC).

An outstanding problem in evolutionary biology is to explain how cooperative groups evolve by natural selection, said Professor Cant, from the Centre for Ecology and Conservation on Exeters Penryn Campus in Cornwall.

Classic research on this question has shown that factors that operate within the group, such as kinship and reciprocity, can select for altruism.

Yet there is now substantial evidence from humans and other social animals that conflict between groups or warfare can also exert a profound influence on social behaviour.

Intergroup conflict could in principle act as a fundamental moulding force in the evolution of animal societies, shaping not just behaviour but also life history and social organisation, but this idea has not been tested.

We will test this hypothesis through an integrated theory, field and lab study using two animal societies as model systems.

The outcome will be a significant advance in our understanding of how social life forms and societies evolve.

The researchers will study a wild population of banded mongooses in Uganda and a lab population of dampwood termites in Cornwall.

This project, entitled Intergroup conflict and the evolution of animal societies, is one of 255 included in new grants awarded by the ERC to outstanding researchers across Europe.

Iliana Ivanova, Commissioner for Innovation, Research, Culture, Education and Youth, said: "These grants will not only support leading researchers in pushing the boundaries of knowledge, but also create some 2,500 jobs for postdoctoral fellows, PhD students and other research staff across Europe.

This investment nurtures the next generation of brilliant minds.

I look forward to seeing the resulting breakthroughs and fresh advancements in the years ahead.

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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Biology

Pygmy Slow Lorises Are Born at Smithsonian’s National Zoo and Conservation Biology Institute – Smithsonian’s National Zoo and Conservation Biology…

For the first time, the Smithsonians National Zoo and Conservation Biology Institute (NZCBI) is celebrating the birth of two pygmy slow lorises, an endangered species. Small Mammal House keepers reported for duty the morning of March 21 and observed that 3-year-old mother Naga had given birth overnight and was caring for two infants. She and the babies 2-year-old father, Pabu, received a recommendation to breed from the Association of Zoos and Aquariums Species Survival Plan (SSP). These babies are the first offspring for both parents. Keepers have observed Naga carrying, grooming and nursing the babies, which appear to be healthy and strong. Animal care staff will determine the babies sexes at their first vet exam, which will take place in a few months. The family is on view at the Small Mammal House, and keepers say the babies are most active in the late morning and early afternoon.

Naga and Pabu arrived at NZCBI in August 2022 from the Brookfield Zoo in Illinois and Little Rock Zoo in Arkansas, respectively.SSP scientists determine which animals to breed by considering their genetic makeup, health and temperament, among other factors. According to keepers, Nagas personality is calm and sweet, though she tends to spook easily. She takes her time when exploring her exhibit and rests often. Pabu, on the other hand, seems to be more high energy. He is inquisitive and always the first to approach keepers and participate in training sessions and feedings. Although pygmy slow lorises reach sexual maturity around 9 months of age for females and 1.5 years of age for males, often they do not successfully reproduce until 2 to 3 years of age. Naga and Pabus howdy introductions took place in September 2023about a year after they arrivedand the pair bred soon after meeting. This species gestation is about six months.

Pygmy slow loris mothers are the primary caregivers of their offspring. In the wild and in zoos, fathers occasionally interact with offspring, depending on their personality and past experience with babies. Pabu has proved to be an attentive and patient father. Keepers have observed him grooming his family and caring for the babies when Naga leaves the nest to forage for food. Visitors may see the babies clinging to Naga as she moves around the exhibit.On occasion, she will leave the babies in their nest or on a branch while she eats or explores. Keepers look forward to watching the babies independently explore their exhibit and play with enrichment items.

Slow lorises are the only known venomous primates. They produce a venom in their brachial glands in their upper arm. Combined with enzymes in their saliva, these primates can produce a painful bite, allergic reaction and a slow-healing wound. Wild slow lorises do not use it against predators because the venom is not fast-acting. Instead, the venom is used in territorial disputes with other slow lorises. They also groom themselves with the venom to ward off parasites and warn predators to stay away.

Native to Cambodia, Lao Peoples Democratic Republic and Vietnam, pygmy slow lorises live in mixed deciduous and evergreen forests. The greatest threats facing this species are deforestation and the illegal pet trade. Much of their habitat has been cleared for the logging industry; they spend the majority of their time from 10 to 40 feet up in the forest canopy.TheInternational Union for Conservation of Natureconsiders pygmy slow lorisesendangered.

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Photo caption: The Smithsonians National Zoo and Conservation Biology Institute welcomed two pygmy slow lorises babies March 21 to mother Naga and father Pabu in the Small Mammal House. Photo credit: Kara Ingraham, Smithsonians National Zoo and Conservation Biology Institute

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Biology

VespAI: a deep learning-based system for the detection of invasive hornets | Communications Biology – Nature.com

Bait station

Bait stations consisted of a Dragon Touch Vision 1 1080p camera, suspended at a height of 210mm above a featureless detection board, shielded by an opaque baffle (Fig.4). This setup minimised background and lighting variability, thus simplifying the computational complexity of hornet detection, while ensuring that only hornets and other insects visiting the station were captured in videos. A sponge cloth impregnated with commercial vespid attractantVespaCatch (Vto-pharma) or Trappit (Agrisense)was placed in a 90mm diameter Petri dish at the centre of the bait station, thus attracting hornets to land directly beneath the camera. We used these bait stations to collect and extract an extensive training dataset, comprising images of V. velutina, V. crabro, and other insects across locations in Jersey, Portugal, France, and the UK.

To ensure dataset fidelity, resultant images of both V. velutina and V. crabro were visually identified via expert assessment of colouration, abdominal markings, and morphology. Additionally, the identity of each hornet species was confirmed through utilisation of the appropriate taxonomic keys65,66.

Data were collected in 2021 and 2022, with selected images being extracted from the raw video footage, and divided into three subsets. All training images were collected in 2021, while the final validation images were collected in 2022, ensuring complete spatiotemporal and biological novelty. Images yielded a maximum simultaneous co-occurrence of six V. velutina, this being observed in Jersey; and five V. crabro, this being recorded in the UK. As a processing step prior to training, images were letterboxedthis being the process of downsampling to 640640 for enhanced throughput performance, while maintaining a 16:9 aspect ratio and filling any residual image space with blank pixels. This then allowed for extensive image augmentation during training, producing three additional variations to supplement each original frame, and thus increasing the total number of images by a factor of four. The specific details of each training data subset are outlined in the following sections.

A collection of 1717 images for training and 430 for initial validation metrics, totalling 8,588 after augmentation. This set contained hornet images with a 50:50 split between V. velutina and V. crabro, while the number of non-target insects was intentionally limited. Data were collected from bait stations at sites in the UK and Portugal.

A collection of 2196 images for training and 549 for initial validation metrics, totalling 10,980 after augmentation. This set contained all hornet images from the HTS, in addition to 598 images of non-target insects. Images of non-target insects included a representative selection of species attracted to the bait station, with a focus on visually similar genera such as Vespula, Dolichovespula, and Polistes. All insects were identified to the genus level, utilising a combination of expert assessment and the relevant taxonomic identification resources65,67. A full list of non-target taxa is provided in (TableS1). These data were collected from bait stations at sites in the UK, Jersey, and Portugal.

A collection of 557 images for final validation only, totalling 2228 after augmentation. Of these, 433 contained instances of V. velutina and V. crabro in a 50:50 split, including multiple co-occurrences of both species and non-target insects. The remaining images contained a combination of non-target species and empty bait stations under different lighting and climatic conditions. Validation data were collected from bait stations at sites in the UK, Jersey, France, and Portugal.

Annotation was performed using the Plainsight AI (Plainsight) software interface. This allowed for expedited labelling via automated polygon selection and AI-assisted predictive annotation. Two classes of annotation were generated, corresponding to V. velutina and V. crabro, and these were then manually applied to a random selection of training frames. Polygonal masks included hornet bodies and wings, and excluded legs and antennaeas we found these to be redundant during testing. Once ~500 frames had been annotated manually, we then used this data to train an automated detection and segmentation model within the labelling interface, allowing us to more rapidly generate further annotations for training. Prior to data export, all annotations were reviewed manually, and corrections made where required. Annotations were exported in COCO format, enabling full segmentation of hornet features from the background68.

To develop a hardware-specific hornet detection and classification model, we combined our extensive image dataset with bespoke augmentations to obtain high predictive confidence. The VespAI detection algorithm is built on the YOLOv5 family of machine vision models, specifically YOLOv5sa variant optimised to run on portable processors such as the Raspberry Pi 448. As a front-end pre-filter to this, we incorporated the lightweight ViBe50 background subtraction algorithm, allowing the system to remain passive in the absence of motion (Fig.2a). Specifically, this pre-filter detects motion from the raw video input, extracts the contours of moving insects, and retains only objects within a reference size range generated from known hornet detections (Fig.2a and S1). Consequently, energy is conserved, as only relevant candidate frames are passed on to the YOLOv5 detection algorithm itself. This then applies a single fully convolutional neural network (F-CNN) to images (Fig.2b), providing superior speed, accuracy, and contextual awareness when compared to traditional regional convolutional neural networks (R-CNN)49,69.

All models were built and optimised using the PyTorch70 machine learning environment, with the aim of generating an end-to-end software package that would run on a Raspberry Pi 4. This was achieved by testing models on a range of YOLOv5 architectures, specifically YOLOv5m, YOLOv5s, and YOLOv5n; thus optimising them to include the minimum number of parametersthis being ~7 millionwhilst maintaining their performance (Fig. S2b).

Final models were trained and tested utilising a NVIDIA Tesla V100 Tensor Core GPU (NVIDIA), with a total of 200300 epochs per model, and a batch size of nine images. Model optimisation was evaluated via three loss functions; bounding box loss, this being the difference between the predicted and manually annotated bounding boxes; objectness loss, defined as the probability that bounding boxes contained target images; and cross-entropy classification loss, encompassing the probability that image classes were correctly classified (Fig. S2). In all cases, training concluded when there was no improvement in these three loss functions for a period of 50 epochs.

The prototype system was developed to provide proof-of-concept for remote detection under field-realistic conditions. The VespAI software was installed on a Raspberry Pi 4, running an Ubuntu desktop 22.04.1 LTS 64-bit operating system. This was then connected via USB to a variety of 1080p cameras, and tested using both mains and battery power supplies. These components were mounted on top of a bait station in the standard camera position, and a remote device was connected to the Pi server via the secure shell command. This allowed the hardware to be controlled remotely, and hornet detections viewed from a corresponding computer.

The setup was validated in Jersey during 2023, testing five candidate camera models and four prototype systems over a total of 55 trials at two field sites, yielding >5500 frames for analysis. Cameras were selected to test system robustness to differing lens and sensor options, while maintaining a standard resolution of 1080p across a range of cost-effective models (Fig. S5 and TableS2). Prior to testing, each camera was calibrated to a specific height, thus ensuring that the relative size of objects in frame remained constant across differences in lens angle and focal length (TableS2). Field sites were situated in Jersey to allow visits from both V. velutina, and V. crabro workers, along with a variety of common non-target insects, thus providing a rigorous test of the system under representative conditions.

Each trial consisted of a100-frame test, with the monitor capturing and analysing frames in real-time at intervals of either 5 or 30sthese being based on known hornet visitation durations (Fig. S4). Specifically, in the first 38 trials, the system was set to collect images at 5s intervals; before optimising to 30s intervals in the final 17 trials (TableS3), thus allowing for maximum power and data storage conservation, in tandem with reliable hornet detection. (Fig. S4). Results were then manually validated, and compared to the corresponding model predictions to calculate evaluation metrics.

Following field testing, the system was configured to integrate a DS3231 Real-Time Clock module, thus ensuring accurate timestamps for detections in the absence of external calibration.

To train the detection models and enable customised image augmentation, we employed the Python packages PyTorch, Torchvision, and Albumentations. Models were then evaluated via k-fold cross-validation, specifically utilising the metrics of precision, recall, box loss, objectness loss, classification loss, mean average precision (mAP), and F1 score (Fig. S2 and Table1). Cross-validation analyses employed a subsample (k) of 5, as this proved sufficient to select an optimised detection classifier that balanced model size with performance. Resultant model rankings were based on mean cross-validation scores, calculated using the Python packages scikit-learn and PaddlePaddle, and the YOLOv5 integrated validation functionality. Additional performance visualisations were generated via the packages Seaborn, Matplotlib, and NumPy. All statistical analyses were performed in SPSS (release v. 28.0.1.1) and Python (release v. 3.9.12).

Cross-validation of polygonal and box annotation techniques utilised precision, recall, box loss, objectness loss, classification loss, and mAP as response variables, and compared models with copy-paste augmentation levels of 0%, 30%, and 90%, with the former of these corresponding to box annotations.

Visualisation of training data subsets to ensure sufficient image novelty utilised frequency distribution analyses of blur, area, brightness, colour, and object density between the HTS, H/NTS, and VS.

Cross-validation of model architectures employed precision, recall, box loss, objectness loss, classification loss, and mAP as response variables, and compared models using the YOLOv5m, YOLOv5s, and YOLOv5n architectures.

Cross-validation of models trained on the hornet training subset and hornet/non-target training subset used F1 score and mAP as response variables, and compared models trained on the HTS and H/NTS, validated against the VS.

The LRP class classification model employed normalised contributions to classification decisions as a response variable, and compared same and opposite class pixel contributions. The LRP training subset classification model used normalised contributions to classification decisions as a response variable, and compared models trained on the HTS and N/HTS.

Precision and recall analyses were utilised to compare camera models, with comparisons based on median performance across test types for each metric.

Model development utilised a sample of 3302 images collected from a total of four countries, each consisting of multiple sampling sites. Data augmentation further expanded this sample to 13,208 images and provided additional variation to enhance model robustness. Analyses of the prototype system employed a sample of >5500 frames, collected across 55 field trials at two sites in Jersey. The source data underlying all figures and analyses are available within the supplementary data. Full details of statistical tests, subset sample sizes, and model selection procedures are provided in the results and statistical analyses sections.

Further information on research design is available in theNature Portfolio Reporting Summary linked to this article.

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VespAI: a deep learning-based system for the detection of invasive hornets | Communications Biology - Nature.com

Biology

Inside the new Seattle Hub for Synthetic Biology, which uses DNA to ‘record biology over time’ – GeekWire

Scientist Sundarshan Pinglay shows off a liquid handling instrument that automatically dispenses reagents, at the Seattle Hub for Synthetic Biology. (GeekWire Photo / Charlotte Schubert)

Researchers opened the doors Monday to the new Seattle Hub for Synthetic Biology, a collaboration between theAllen Institute, theChan Zuckerberg Initiativeand theUniversity of Washington.

The hub combines academic creativity with startup-style industrial execution, said Jesse Gray, senior director of scientific operations and strategy, who was previously head of discovery at gene editing startup Ascidian Therapeutics.

The hubs first main goal is to build a biological recorder mouse, enabling researchers to track biological actions such as cell divisions and molecular signaling in a live mouse across time.

Mondays tour took place at the hubs labs at Dexter Yard, a life sciences development in the South Lake Union neighborhood across from the Allen Institute, which is contributing $35 million to the hub over the next five years.

The Chan Zuckerberg Initiative is providing the same amount, and the UW is a source of foundational technology for the new hub.

The initiative leverages DNA-based technology developed in the lab of the hubs lead scientific director Jay Shendure, a UW professor of genome sciences. During the tour, he called the approach a symbolic language for longitudinally recording biology over time.

The method involves generating DNA barcodes for each cell that reflect biological activity. Scientists place a DNA tape inside a founder or stem cell. The DNA tape is edited through generations of cell division, with each edit occurring in sequential order along the tape generating a readout of the timing of cellular events.

Shendure and his colleagues introduced this DNA typewriter technique in a 2022 study published in Nature. There, they used the method to reconstruct a cell lineage tree, tracing how a single cell multiplied into thousands of cells. More recently, his lab adapted the technique to record the long-term activity of cell signals.

Ultimately, the researchers think the methods can be used to trace an even broader variety of cellular states and actions, such as metabolic status, cell-cell contact, and neuronal signaling.

The approach is foundational technology said Stephen Quake, head of science at the Chan Zuckerberg Initiative, during a fireside chat at the Allen Institute. New drugs and treatment should ultimately result from the research, he said.

Potential applications include assessing the actions of therapeutic cells and improving their design. Another application might be to track body-wide how a mouse responds over time to specific drugs or other perturbations.

Marion Pepper, professor and chair of Immunology at the UW, is excited to explore potential uses in immunotherapy.

Having these types of tools and technological developments applied to immune cells will revolutionize how we treat disease, said Pepper, who co-directs the hub with UW associate professor of genome sciences Cole Trapnell. Were going to learn so much about these cells that weve never been able to visualize or understand, added Pepper.

The Seattle Hub for Synthetic Biology, first announced in December, now has 15 staff members and plans to hire up to a dozen more by the end of next year, and around 50 within five years.

Shendure sees an opportunity to snap up talent with industry experience and the ability to spot commercial opportunities. At the same time, both the Allen Institute and the Chan Zuckerberg Initiative have a commitment to open science a culture that has also eased their collaboration, said hub leaders.

The Seattle Hub for Synthetic Biology currently occupies 3,600 square feet in Dexter Yard, and will expand to 12,000 square feet in 2025. During the tour, visitors were introduced to four research stations.

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Biology

The Biology of Kindness review: Living well and prospering – New Scientist

What is the impact of being kind on our bodies and lifespan?

Kara McWest / Stockimo / Alamy

The Biology of Kindness

Immaculata De Vivo and Daniel Lumera, translated by Fabio De Vivo

MIT Press (first published in Italian in 2020)

We tend to think about kindness as a quality that helps others, not ourselves. But a new book, The Biology of Kindness: Six daily choices for health, well-being, and longevity, unpicks the impact of being kind on our bodies and lifespan, as well as the effect of four other traits and behaviours optimism, forgiveness,

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The Biology of Kindness review: Living well and prospering - New Scientist

Biology

UND biologist explains composition of dirt to kids – UND Today – UND Blogs and E-Newsletters

Two South Dakota grade-schoolers ask, What is dirt? and in The Conversation, UNDs Brian Darby answers

Editors note:On March 25,The Conversation featured an article by Brian Darby, associate professor of Biology at UND. Since the day of its publication, the article has been read more than 3,600 times, including by readers in the United States, France, India and Germany, The Conversation reports.

Darbys story is a part of The Conversations Curious Kids feature. As UND Today readers know, The Conversation is a nonprofit, independent news organization dedicated to unlocking the knowledge of experts for the public good, asthe organizations websitestates. We publish trustworthy and informative articles written by academic experts for the general public and edited by our team of journalists.

Curious Kids publishes stories that answer questions submitted by real kids from around the world. The series explores topics across all areas of human knowledge, and the stories are written in a simple and engaging way, with the goal of appealing to children of all ages.

Darbys story answers the question, What is dirt? which was posed by Belle and Ryatt, ages 7 and 5, of Keystone, S.D.

UND faculty members and graduate students whod like to learn more about writing for The Conversation are invited to readIntroducing The Conversation, a story that appeared in UND Today in 2022, andMore than 340,000 readers worldwide, a 2023 story in which UND scholars whove written for The Conversation talk about their experiences.

****

By Brian Darby

When you think about dirt, you might picture the rock dust that gets on your pants. But theres so much more going on in the ground under our feet.

When I began studying soil, I was amazed at how much of it is actually alive. Soil is teeming with life, and not just the earthworms that you see on rainy days.

Keeping this vibrant world healthy is crucial for food, forests and flowers to grow and for the animals that live in the ground to thrive. Heres a closer look at whats down there and how it all works together.

If you scoop up a handful of dry soil, the basic dirt that you feel in your hand is actually very small pieces of weathered rock. These tiny bits eroded from larger rocks over millions of years.

The balance of these particles is important for how well soil can hold water and nutrients that plants need to thrive.

For example, sandy soil has larger rock grains, so it will be loose and can easily wash away. It wont hold very much water. Soil with mostly clay is finer and more compact, making it difficult for plants to access its moisture. In between the two in size is silt, a mix of rock dust and minerals often found in fertile flood plains.

Some of the most productive soils have a good balance of sand, clay and silt. That combination, along with the remnants of plants and animals that have died, helps the soil to retain water, allows plants to access that water and minimizes erosion from wind or rain.

Among all those rock particles is a whole world of living things, each busy doing its job.

To get a sense of just how many creatures are there, picture this: The zoo in Omaha, Nebraska, boasts over 1,000 animal species. But if you scooped up a small spoonful of soil in your backyard, it would likely contain at least 10,000 species and around a billion living microscopic cells.

Most of those species are still largely a mystery. Scientists dont know much about them or what they do in soil. In fact, most species in soil dont even have a formal scientific name. But each plays some kind of role in the vast soil ecosystem, including generating the nutrients that plants need to grow.

Imagine a leaf falling from a tree in late autumn.

Inside that leaf are a lot of nutrients that plants need, such as nitrogen, potassium and phosphorus. There is also a lot of carbon in that leaf, which holds energy that can be used by other organisms such as bacteria and fungi.

The leaf itself is too large for a plant to take up through its roots, of course. But that leaf can be broken down into smaller and smaller pieces. This process of breaking down plant and animal tissue is known as decomposition.

When the leaf first falls to the ground, arthropods such as insects, mites and collembolans break the leaf down into smaller chunks by shredding the tissue. Then, an earthworm might come along and eat one of the smaller chunks and break it down even more in its digestive tract.

Now the broken-up leaf is small enough for microbes to come in. Bacteria and fungi secrete enzymes into the soil that further break down organic material into even smaller pieces. If enough microbes are active, eventually this organic material will be broken down enough that it can dissolve in water and be taken up by plants that need it.

To aid in this process, there are many small animals, such as nematodes and amoebae, that consume bacteria and fungi. There are also predatory nematodes that feed on other nematodes to make sure they dont become too abundant, so everything remains in balance as much as possible.

Its quite a complicated food web of interacting species in a delicate balance.

While some fungi and bacteria can harm plants, there are many species that are considered beneficial. In fact, they may be the key to figuring out how to grow enough crops to feed everyone without degrading and overburdening the soil.

Scientists have named over 20,000 different types of unique soils. If youre curious about the soil and dirt in your area, the University of California, Davis has a website where you can learn more about local soils and their chemical and physical attributes.

Caring for soil to promote its living creatures benefits and minimize their harm takes work, but its essential for keeping the land healthy and growing food for the future.

****

This article is republished from The Conversation under a Creative Commons license. Read the original article.

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Biology

In the evolution of walking, the hip bone connected to the rib bones – EurekAlert

image:

New reconstruction of the skeleton of the 375-million-year-old fossil fish, Tiktaalik roseae. In a new study, researchers used Micro-CT to reveal vertebrae and ribs of the fish that were previously hidden beneath rock. The new reconstruction shows that the fishs ribs likely attached to its pelvis, an innovation thought to be crucial to supporting the body and for the eventual evolution of walking.

Credit: Thomas Stewart, Penn State

UNIVERSITY PARK, Pa. Before the evolution of legs from fins, the axial skeleton including the bones of the head, neck, back and ribs was already going through changes that would eventually help our ancestors support their bodies to walk on land. A research team including a Penn State biologist completed a new reconstruction of the skeleton of Tiktaalik, the 375-million-year-old fossil fish that is one of the closest relatives to limbed vertebrates. The new reconstruction shows that the fishs ribs likely attached to its pelvis, an innovation thought to be crucial to supporting the body and for the eventual evolution of walking.

A paper describing the new reconstruction, which used microcomputed tomography (micro-CT) to scan the fossil and reveal vertebrae and ribs of the fish that were previously hidden beneath rock, appeared April 2 in the journal Proceedings of the National Academy of Sciences.

Tiktaalik was discovered in 2004, but key parts of its skeleton were unknown, said Tom Stewart, assistant professor of biology in the Eberly College of Science at Penn State and one of the leaders of the research team. These new high-resolution micro-CT scans show us the vertebrae and ribs of Tiktaalik and allow us to make a full reconstruction of its skeleton, which is vital to understanding how it moved through the world.

Unlike most fish, which have vertebrae and ribs that are the same along the length of the trunk, the axial skeletons of limbed vertebrates show dramatic differences in the vertebrae and ribs from the head region to the tail region. The evolution of this regionalization allowed the performance of specialized functions, one of which was a mechanical linkage between ribs in the sacral region to the pelvis that enabled support of the body by the hind limbs.

The pelvic fins of fish are evolutionarily related to hind limbs in tetrapods four-limbed vertebrates, including humans. In fish, the pelvic fins and bones of the pelvic girdle are relatively small and float freely in the body. For the evolution of walking, the researchers explained, the hind limbs and pelvis became much larger and formed a connection to the vertebral column as a way of bracing the forces related to supporting the body.

Tiktaalik is remarkable because it gives us glimpses into this major evolutionary transition, Stewart said. Across its whole skeleton, we see a combination of traits that are typical of fish and life in water as well as traits that are seen in land-dwelling animals.

The original description of Tiktaalik focused on the front portion of the skeleton. Fossils were meticulously prepared to remove the surrounding matrix of rock and expose the skull, shoulder girdle and pectoral fins. The ribs in this area were large and expanded, suggesting that they may have supported the body in some way, but it was unclear exactly how they would have functioned. In 2014, the fishs pelvis, discovered in the same location as the rest of the skeleton, was also cleaned of matrix and described.

From past studies, we knew that the pelvis was large, and we had a sense that the hind fins were large too, but until now couldnt say if or how the pelvis interacted with the axial skeleton, Stewart said. This reconstruction shows, for the first-time, how it all fit together and gives us clues about how walking might have first evolved.

The researchers explained that, unlike our own hips where our bones fit tightly together, the connection between the pelvis and axial skeleton of Tiktaalik was likely a soft-tissue connection made of ligaments.

Tiktaalik had specialized ribs that would have connected to the pelvis by a ligament, Stewart said. Its astonishing really. This creature has so many traits large pair of hind appendages, large pelvis, and connection between the pelvis and axial skeleton that were key to the origin of walking. And while Tiktaalik probably wasnt walking across land, it was definitely doing something new. This was a fish that could likely prop itself up and push with its hind fin.

The new reconstruction of the skeleton also sheds light on specializations for head mobility in Tiktaalik and new details of the fishs pelvic fin anatomy.

"It's incredible to see the skeleton of Tiktaalik captured in such vivid detail, said Neil Shubin, Robert R. Bensley Distinguished Service Professor of Organismal Biology and Anatomy at the University of Chicago and one of the authors of the paper. This study sets the stage for ones that explore how the animal moved about and interacted with its environment 375 million years ago."

In addition to Stewart and Shubin, the research team includes Justin B. Lemberg, Emily J. Hillan, and Isaac Magallanes at The University of Chicago, and Edward B. Daeschler at Academy of Natural Sciences of Drexel University.

Support from the Brinson Foundation, the Biological Sciences Division of The University of Chicago, an anonymous donor to the Academy of Natural Sciences of Drexel University, and the U.S. National Science Foundation funded this research. Fieldwork was made possible by the Polar Continental Shelf Project of Natural Resources, Canada; the Department of Heritage and Culture, Nunavut; the hamlets of Resolute Bay and Grise Fiord of Nunavut; and the Iviq Hunters and Trappers of Grise Fiord.

Proceedings of the National Academy of Sciences

The axial skeleton of Tiktaalik roseae

The authors declare no competing interest.

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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In the evolution of walking, the hip bone connected to the rib bones - EurekAlert