In new study in The Crop Journal, scientists develop cutting edge vascular system image analysis pipeline for crops

This accurate, deep learning pipeline can detect the vascular system of plants with high detail, helping agricultural practices

Peer-Reviewed Publication

CACTUS COMMUNICATIONS

 

IMAGE: A DEEP-LEARNING PIPELINE BATCH-PROCESSES A SERIES OF COMPUTER TOMOGRAPHIC IMAGES OF THE MAIZE STEM TO VISUALIZE AND ANALYZE ITS VASCULAR CHARACTERISTICS. view more 

CREDIT: CHUNJIANG ZHAO VIA THE CROP JOURNAL

A plant’s vascular system is essential for maintaining stem structure, providing mechanical support, and for delivering resources to various plant organs. However, the structure and distribution of these vascular bundles varies greatly across individual plants, and this poses a great challenge in automating the process of their identification and quantification. Therefore, the ability to deliver a rapid and accurate quantitative and functional evaluation of these plant systems is vital to agricultural research.

The histological study of sectioned plant tissue (done under a microscope) is the foundation of plant anatomy and microscopy techniques. Spanning light-based, fluorescence, and electron-based techniques, this is the backbone of inner tissue plant research. However, the physical and chemical treatments during sample preparation for these methods can alter the natural structure of specimens. Micro-computed tomography (micro-CT), however, can deliver high-resolution imagery with minimal preprocessing that is non-destructive to tissue specimens. Unfortunately, some manual adjustments are necessary for CT image reconstruction which results in errors and variation introduced unwittingly by the observer.

In terms of capability, Deep Convolutional Neural Network (CNN) approach, a data-driven feature extraction technique, has only recently achieved state-of-the-art performance in detecting objects in segmented images, allowing it to be routinely used in image-based phenotyping in plant phenomics (i.e., a study of the plant’s phenotype and its evolution). Now, a group of researchers at Beijing Academy of Agriculture and Forestry Sciences (BAAFS), led by Dr. Jianjun Du, has developed a CNN based deep-learning pipeline that can rapidly produce accurate analyses of vascular bundle architecture. “We believe we can break new ground in understanding the relationship between vascular bundle architecture at the single-plant level and the traits involved in water transport,” says Dr. Chunjiang Zhao, corresponding author of a study detailing their methods and findings. The study was published online on 27 May 2022 in The Crop Journal.

The team was particularly interested in studying how plants that express plasticity in the structure of their stems can quickly adapt to their environment. It is this plasticity that allows for changing structure without hindering growth and development. To study it, they grew maize under natural and drought conditions and utilized information extracted from CT images to examine the vascular bundles for different stem internodes (which is the part of the stem between two nodes, or branching areas), evaluate architectural differences in stem structure, and investigate the relationship between flow rates and structural traits. Their pipeline processed images and detected vascular bundles in the plants, identified specific zones (the periphery, the epidermis, and the inner zones) within the bundles, categorized bundles into phenotypes based on specific traits (quality, quantity, size, and shape), and performed a statistical analysis of these traits in different stem internodes. They also conducted sap flow experiments to study the traits of vascular bundles in maize at the single-plant level to gain an insight into the water use efficiency of the different phenotypes.

“We could achieve an image processing time of three seconds, and for the first time we shed light on the thickness of the epidermis (which is the outermost layer) of the maize stem. Our pipeline is incredibly accurate too. During testing, it enumerated vascular bundles across all types of internodes and quantified size-related traits with an R2–which indicates consistency–of over 0.98,” Dr. Du explains the novelty of their study.

In addition, the sap flow experiments showed that the rate of flow was affected not only by the structure of the vascular bundles, but also by environmental and meteorological conditions.

So why are these findings so important? “We believe we have laid the foundation for deeper studies on identification of genes essential to determining water use efficiency, and development of crop breeds that can ensure national food security. The pipeline certainly allows for future work to establish the relationship between sap flow and the specific traits of vascular bundles,” says Dr. Du with a smile. Their research might lead to improved, more resilient crops in the future!         

 

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Reference

DOI: https://doi.org/10.1016/j.cj.2022.04.012

Authors: Jianjun Du, Ying Zhang, Xianju Lu, Minggang Zhang, Jinglu Wang, Shengjin Liao, Xinyu Guo, and Chunjiang Zhao

Affiliations:
Beijing Key Lab of Digital Plant, Research Center of Information Technology, Beijing Academy of Agriculture and Forestry Sciences, China

 

About Professor Chunjiang Zhao
Dr, Chunjiang Zhao, a member of the Chinese Academy of Engineering, received his Ph.D from China Agriculture University in 1993. He is currently a professor at the Beijing Academy of Agricultural and Forestry Sciences and develops technology for efficient information acquisition, quantitative analysis, diagnostic decision making, and intelligent equipment control. He has published over 400 articles and founded the International Symposium on Intelligent Information Technology in Agriculture to promote cooperation between scientists and engineers. He holds advisory roles in the Ministry of Agriculture of China, the Natural Science Foundation, and the Ministry of Science and Technology.

 

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JOURNAL

The Crop Journal

DOI

10.1016/j.cj.2022.04.012 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

A deep learning-integrated phenotyping pipeline for vascular bundle phenotypes and its application in evaluating sap flow in the maize stem

Cameras candidly capture bushmeat mammals to avert crisis

Finding the best indicators for sustainable hunting in the African rainforest

Peer-Reviewed Publication

KYOTO UNIVERSITY

 

IMAGE: USE OF CAMERA TRAPS FOR LOCALLY-BASED WILDLIFE MONITORING view more 

CREDIT: KYOTOU CAAS/YOH IZUMORI

Kyoto, Japan -- Bushmeat is not a vegan term but a commodity in crisis. With the decline of wildlife due to commercial overexploitation in the world's tropical rainforests, the bushmeat crisis is impacting biodiversity and the livelihoods of local populations.

While community participatory-based wildlife monitoring of wildlife by local people can be a solution, the challenge has been in finding indicators -- biostatistical information -- that accurately and easily estimate the total biomass of mammals targeted for bushmeat hunting abundance of bushmeat biomass.

Now, Projet Coméca, consisting of a team of researchers from Kyoto University and Cameroon, has conducted camera trap surveys in the rainforests of southeast Cameroon to predict the total biomass of large rodents and duikers, the local African forest ungulates.

"We're willing to work together empowering the locals to establish a system with the technology to take the initiative to monitor wildlife bushmeat abundance by themselves, leading to sustainable bushmeat wildlife management," says lead author Shun Hongo.

After setting up camera traps at three sites in a local forest to record videos of five target mammals, the team used the random encounter and staying time model, or REST, a statistical model to estimate spatial variation in each species' population density and corresponding the total biomass.

The research team subsequently compared the relationships between the total biomass and six indicators, which had previously been proposed by different bushmeat researchers. Based on that data, six candidate indicators were extracted, enabling the researchers to compare the relationships between the biomass totals and corresponding indicators.

Two of these -- the ratio of red duikers to blue duikers, and the ratio of all duikers to rodents -- were deemed promising as they showed positive linear correlations with total bushmeat biomass.

"Our indicators appear to be important variables tools for sustainable management of bushmeat hunting food resources," the author adds.

"Since forest ungulates and large rodents are widely distributed in rainforests worldwide, other communities in tropical areas may also be able to apply similar indicators for their local wildlife areas management.”

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The paper "Predicting bushmeat biomass from species composition captured by camera traps: implications for locally-based wildlife monitoring" appeared on 26 August 2022 in Journal of Applied Ecology, with doi: 10.1111/1365-2664.14257  

About Kyoto University

Kyoto University is one of Japan and Asia's premier research institutions, founded in 1897 and responsible for producing numerous Nobel laureates and winners of other prestigious international prizes. A broad curriculum across the arts and sciences at both undergraduate and graduate levels is complemented by numerous research centers, as well as facilities and offices around Japan and the world. For more information, please see: http://www.kyoto-u.ac.jp/en

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JOURNAL

Journal of Applied Ecology

DOI

10.1111/1365-2664.14257 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Animals

ARTICLE TITLE

Predicting bushmeat biomass from species composition captured by camera traps: implications for locally -based wildlife monitoring

ARTICLE PUBLICATION DATE

26-Aug-2022

Better wildlife observation with new counting method

Peer-Reviewed Publication

LINKÖPING UNIVERSITY

 

IMAGE: TOM LINDSTRÖM, ASSOCIATE PROFESSOR AT LINKÖPING UNIVERSITY. view more 

CREDIT: MAGNUS JOHANSSON/LINKÖPING UNIVERSITY

Are wildlife populations in Sweden increasing or decreasing? It is difficult to count wild animals, but the amount harvested through hunting gives an indication. Now, these statistics can be made clearer and more useful, thanks to a new model developed by Swedish researchers to count how many wild animals are hunted.

“We believe that this system will make the statistics clearer and more reliable. The idea is that this model is to be used from the autumn forward, for presenting official statistics about how many wild animals are harvested through hunting in Sweden”, says Tom Lindström, associate professor at the Department of Physics, Chemistry and Biology (IFM) at Linköping University, who has done the study in collaboration with Göran Bergqvist at the Swedish Association for Hunting and Wildlife Management.

Hunting is a way of getting an overview of the size of wild populations. For some species, it is the only indicator we have. Knowing how many wild animals are harvested through hunting every year is, therefore, an important part of wildlife monitoring, which needs to be adapted to changes in the ecosystem.

For example, the reporting of hunting of moose and large mammals is required by law, but for most species – everything from jays to wild boars – reporting is optional. The Swedish Association for Hunting and Wildlife Management is responsible for annual statistics around how many of these animals are harvested. Hunting teams report how much they have shot of around fifty species, and across how much land they have hunted. But because reporting is optional, and because reports are lacking for some of Sweden’s hunting grounds, statistical methods are used to calculate how many wild animals are harvested on these blind spots not covered by the hunting teams’ reports. One of the significant weaknesses with the analysis method that has been used until now is that it is very sensitive to low reporting – especially for species the hunting of which varies between hunting teams and are, generally, not so hunted. Tom Lindström gives an example:

“In 2015, the analysis appeared to show that many more beavers had been harvested than in previous years. However, when we analysed the data, it turned out that the big difference was because a single hunting team reported that they had shot a single beaver. Because this analysis method is so sensitive to single reports, it made it look like many thousands of beavers had been shot in that club.”

For this reason, the researchers developed a new analysis model which can give a better estimation as to how many wild animals of each species are harvested each year. The study, published in the journal Ecological Indicators, consists of two parts. In the first part, the researchers analysed various parameters and developed a model that is good at describing data. They then used the model to predict how many wild animals would be hunted on the area for which data were missing.

 Analyses made with the new model can contribute to insights about hunting behaviour in Sweden. In the study, the researchers saw that the hunting teams that had greater areas to hunt in generally shot fewer animals per area. The correlation was similar for all species hunted. There may have been fewer animals in those areas, so a larger area is needed in order to have a chance of catching something – or there may be other explanations. Time is another piece of the puzzle. The researchers have done something called auto-regressive modelling, which means that the analysis of the hunting volume in one area takes account of the volumes from previous years. 

This new statistical framework solves several problems.

“The model presents the uncertainty in these analyses in an honest way, and shows a range, instead of a definite figure. It is also less sensitive for individual hunting reports, and this reduces the uncertainty of the analysis”, says Tom Lindström.

The project was funded by Swedish Association of Hunting and Wildlife Management and The Swedish Environmental Protection Agency. Computation was executed on resources provided by the Swedish National Infrastructure for Computing (SNIC).

 

The article: Estimating harvest when hunting bag data are reported by area rather than individual hunters: A Bayesian autoregressive approach, Tom Lindström, Göran Bergqvist, (2022), Ecological Indicators, published online 19 June 2022, DOI: 10.1016/j.ecolind.2022.108960

For more information, contact:

Tom Lindström, associate professor, tom.lindstrom@liu.se, +4613-28 24 59

Karin Söderlund Leifler, press information officer, karin.soderlund.leifler@liu.se, +46 13 28 13 95

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DOI

10.1016/j.ecolind.2022.108960 

METHOD OF RESEARCH

Computational simulation/modeling

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Estimating harvest when hunting bag data are reported by area rather than individual hunters: A Bayesian autoregressive approach

ARTICLE PUBLICATION DATE

19-Jun-2022

COI STATEMENT

Tom Lindstrom reports financial support was provided by Swedish Association for Hunting and Wildlife Management.

Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors

Peer-Reviewed Publication

COMPUSCRIPT LTD

 

IMAGE: THE EFFECTS OF TMAO AND UREA ON THE RATE OF LABELING OF SULFHYDRYL GROUPS OF GLUTAMATE DEHYDROGENASE BY THE REAGENT 4-CHLORO-7-NITROBENZOFURAZAN (NBF-CL). CONTROL MIXTURES HAD NEITHER TMAO NOR UREA. THE STRUCTURES OF TMAO AND UREA ARE SHOWN TO THE RIGHT OF THE GRAPH. (FIGURE REDRAWN AFTER YANCEY PH, SOMERO GN (1979) COUNTERACTION OF UREA DESTABILIZATION OF PROTEIN STRUCTURE BY METHYLAMINE OSMOREGULATORY COMPOUNDS OF ELASMOBRANCH FISHES. BIOCHEM J 182:317–323) view more 

CREDIT: MLST

https://doi.org/10.1007/s42995-022-00140-3

Announcing a new publication for Marine Life Science & Technology journal. In this review article Professor George Somero, Hopkins Marine Station, Stanford University, CA, USA considers a series of adaptive changes in cellular fluids that help to enable marine organisms to cope with abiotic stresses.

A set of abiotic stressors pose multiple challenges to marine life due to their widespread influence on all classes of biochemical systems. Variations in temperature, hydrostatic pressure, and salinity have potential to disrupt structures and functions of all molecular systems on which life depends. In this article, Professor Somero focuses largely on one class of stressor effects that challenges the performance of all types of large molecular systems: proteins, nucleic acids and lipoprotein membranes. The perturbing effects of these stressors at the biochemical level often result from their potential to disrupt the fine balance that is needed between stability and flexibility of the higher-order structures of these large molecular systems, which are stabilized largely by non-covalent (weak) chemical bonds like hydrogen bonds, ionic interactions, and hydrophobic effects. Importantly, all macromolecular systems of a cell must strike this balance between flexibility and stability if an organism's physiology is to function optimally.

This physiologically important balance between stability and flexibility of structure in large molecular systems is achieved in two principal manners. First, during evolution, the abiotic conditions that an organism faces lead to genetically based adaptations in the conformational stabilities of proteins and certain types of nucleic acids, and differences in lipid compositions. These intrinsic adaptations denote that they are encoded in the genome of the organism. Second, complementing these intrinsic, sequence-based adaptations in macromolecular structure are alterations in the chemical compositions–the “micromolecular contents”–of biological solutions that bathe macromolecules and influence their stabilities and functions. Small organic solutes—organic osmolytes—play central roles in these adaptive responses. These extrinsic adaptations due to osmolytes facilitate the retention of the evolved differences in macromolecular stability under different environmental conditions.

The article develops a parallel analysis between adaptive responses to two important physical stressors of the oceans, temperature and hydrostatic pressure. For both stressors, intrinsic and extrinsic adaptive changes are vitally important. The analysis focuses on the following two questions to discuss the adaptive changes in osmolyte systems. First, does the macromolecular stabilizing power of the intracellular osmolyte pool vary with evolutionary adaptation temperature (or pressure) and with the recent thermal (or pressure) exposure of the organisms (acclimatization effects)? Second, in modulating the stabilizing power of the osmolyte pool, do adaptive changes involve alterations in the types of osmolytes used, changes in their absolute or relative concentrations, or a combination of both of these strategies?

The range of environmental tolerance of a species may depend on how effectively the osmolyte composition of its cellular fluid can be altered in the face of stress. The study draws the following four main conclusions: First, in most marine organisms, organic osmolytes can maintain (or restore) the optimal balance of macromolecular rigidity and flexibility, which is a biological key to the optimal function of macromolecules. Second, adaptive changes in the composition and concentration of the osmolyte pool may have effects on macromolecules and biofilm systems and play an important role in establishing the optimal environmental tolerance of organisms. Third, stabilizing osmolytes vary greatly in how effectively they enhance the stability of macromolecules. Fourth, the ability of osmolyte systems to fine-tune the stabilization potential of cellular fluids in the face of body temperature (or pressure) changes that occur over different time periods may help organisms withstand effects of environmental change, notably the changes in temperature occurring due to global warming.

This article not only offers marine biologists important new information on how marine life adapts to the abiotic stressors of the sea, but these investigations also teach physical biochemists critical things about the physics of water-solute interactions and, for the technologically minded, suggest new strategies for developing solutions that aid in the stabilization and preservation of biological materials.

Article reference: Somero, G.N. Solutions: how adaptive changes in cellular fluids enable marine life to cope with abiotic stressors. Mar Life Sci Technol (2022). https://doi.org/10.1007/s42995-022-00140-3

 

Keywords: Adaptation, Crowding, Extremophiles, Hydrostatic pressure, Osmolytes, Temperature

CAPTION

Fig. 2 Efficacies of differently methylated forms of glycine in offsetting salt-induced inhibition (300 mol/L NaCl) of an enzyme (malate dehydrogenase from barley). Activation rises as additional methyl groups are added. (Figure redrawn after Pollard A, Wynn-Jones RG (1979) Enzyme activities in concentrated solutions of glycinebetaine and other solutes. Planta 144:291–298)

CAPTION

Fig. 3 The efficacies of different organic osmolytes in stabilizing the structures of malate dehydrogenase (MDH) and staphylococcal nuclease (SNase). Osmolyte concentrations were 0.5 mol/L except for GGG, which was 0.4 mol/L. Chemical structures of the extremolytes, MG (mannosylglycerate), GG (glucosylglycerate), DIP (di-myo-inositol 1-3’phosphate) and GGG (α(1,6)glucosyl-α(1,2) glucosylglycerate) are shown to right of the graph. (Figure modified after Lamosa PM, Rodrigues V, Gonçalves LG, Carr J, Ventura R, Maycock C, Raven ND, Santos H (2013) Organic solutes in the deepest phylogenetic branches of the Bacteria: identification of α(1–6)glycosyl-α(1–2)glucosylglycerate in Persephonella marina. Extremophiles 17:137–146)

CREDIT

MLST

Marine Life Science & Technology (MLST) provides a platform that introduces new discoveries and theories associated with marine organisms, bioresources, and biotechnology. The journal is intended for marine scientists, biological oceanographers, conservation biologists, marine technologists, policy makers and legislators. Accordingly, we publish original research papers across a broad range of marine life sciences and technologies with an emphasis on synergistic interactions of multiple disciplines. Both theoretical and practical papers are welcome, including laboratory and field experimental studies relevant to marine life science and technology. Focused reviews, viewpoints, comments, and short communications are also accepted. As the journal’s aim is to foster multidisciplinary approaches to marine sciences, authors are encouraged to emphasise the relevance of their work in relation across the journals key-disciplines.

For more information, please visit https://www.springer.com/journal/42995/

 

Editorial Board: https://www.springer.com/journal/42995/editors

 

MLST is available on SpringerLink (https://link.springer.com/journal/42995/volumes-and-issues).

 

Submissions to MLST may be made using ScholarOne ManuscriptsTM (https://mc03.manuscriptcentral.com/mlst).

 

 

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ISSN 2662-1746

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DOI

10.1007/s42995-022-00140-3 

 

Chicken bones and snail shells help archaeologists to date more precisely

Peer-Reviewed Publication

CLUSTER OF EXCELLENCE "RELIGION AND POLITICS"

PrintEmail App

 

IMAGE: PROF. DR. ACHIM LICHTENBERGER view more 

CREDIT: WWU, UNIVERSITY OF MUENSTER

According to new research, the combined analysis of animal and plant remains, as well as written evidence, is leading to more precise dating of archaeological finds. “We can now often determine not only the year, but also the season. This allows us to reconstruct the events that produced the finds much more precisely”, says archaeologist Prof. Dr. Achim Lichtenberger from the Cluster of Excellence “Religion and Politics” at the University of Münster. “The destruction of the Greek town Tell Iẓṭabba in present-day Israel by a military campaign waged by the Hasmoneans, a Judean ruling dynasty in the 2nd and 1st centuries BC, has so far been dated to between 111 and 107 BC”, says Lichtenberger. “More recent research dates it to 108/107 BC, based on coin finds and the siege of the city of Samaria at the same time. Now, using our multi-proxy approach that makes use of several analytical methods, we can for the first time date the events with certainty to the spring of 107 BC”.

“We came across chicken leg bones in the dwellings destroyed by the Hasmoneans. Analyzing them revealed residues containing marrow that served to produce eggshells during the laying season in spring. This indicates that the chickens were slaughtered in spring”, explain Achim Lichtenberger and his colleague Prof. Oren Tal from the University of Tel Aviv. “We also discovered the shells of field snails, which were often eaten at this time of year”. Botanical examinations of the remnants of flowers on the floors of the dwellings reveal that these plants flowered in spring. Analysis of the objects is always accompanied by analysis of written evidence: “The contemporary Hebrew scroll of Megillat Ta’anit about the Hasmonean conquest, also known as the Scripture of the Fast, reports the expulsion of the inhabitants in the Hebrew month of Sivan, which corresponds to our May/June”.

“Only the multiplicity of analytical methods makes precise statements possible”

“From an archaeological point of view, this makes spring the season of destruction”, says Lichtenberger, which underlines previous findings on Hellenistic warfare, as military offensives usually took place in spring and early summer. “The individual data taken on their own would not justify determining such a clear chronology”, emphasizes Lichtenberger, who, together with his colleague Oren Tal and an interdisciplinary team comprising natural scientists, is leading a research project on the archaeology of the Hellenistic settlement Tell Iẓṭabba, in ancient Nysa-Scythopolis, an ancient conurbation in the ancient Near East. “Only by taking an overall view of the results from all analytical methods can we provide more precise information about the time of the destruction of Tell Iẓṭabba, and thus about the course of the Hasmonean campaign”. The finds must therefore be interpreted in the light of the seasons. (apo/sca)

CAPTION

Excavation Tell Iztabba

CREDIT

German-Israeli Tell Iztabba Excavation Project

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JOURNAL

Antiquity

DOI

10.15184/aqy.2022.92 

METHOD OF RESEARCH

Survey

SUBJECT OF RESEARCH

People

ARTICLE TITLE

For everything there is a season: more than a year of destruction at Seleucid Tell Iẓṭabba (Israel)