Overexpression of four previously uncharacterized poplar transcription factors produced enhanced saccharification of plant biomass in poplar. Two transcription factors, PtxtERF123 and PtxtZHD14, significantly improved both glucan and xylan release from plant cell walls. These transcription factors regulate groups of genes involved in xylem cell wall biosynthesis and are potential targets for improving biomass digestibility in poplar and other bioenergy feedstocks.
Plants are continually exposed to harsh environmental conditions which is life- threatening for their survival. Drought is one of the major environmental constraints that highly affect plant growth and productivity worldwide. Osmotic stress due to limited availability of water during drought lead to the inhibition of photosynthesis which ultimately affect plant growth, yield and productivity. As sessile in nature, plants cannot escape from such adverse situations. Hence, to cope up with these adverse situations, plants have developed a complex array of adaptive strategies including intricate regulation of cellular, physiological, biochemical and metabolic processes to avoid or tolerate cellular dehydration. Under limited water availability, stomata plays an essential role to check water loss due to transpiration. In addition, upon perception of stress signal, a wide range of signaling cascade has been activated which ultimately initiates the expression of stress-responsive genes in a timely and coordinated manner. Abscisic acid (ABA), the universal stress hormone, highly accumulated under stress condition, also plays an important role in stress adaptation including stomatal closure and expression of stress-responsive genes. In recent times, whole genome sequencing analysis of different plants reveals that a large family of genes is expressed under different types of abiotic stresses that are involved in defense-related pathways. These genes can be grouped into three categories, genes involving recognition of osmotic stress, signal perception, and transduction and production of stress-adaptive components for physiological responses.
A number of developments have been made in the molecular biology of oat (Avena spp.) in recent years. Many of these were recently described at the Fourth International Oat Conference, held on 18 to 23 October, in Adelaide, South Australia. These advances include a report of oat transformation and regeneration, the characterisation of J3-glucanase genes in oat, the further development of a molecular genetic map in oats, and the characterisation of genes encoding novel oat grain proteins. A technique for assessing pedigrees in the oat and other cereal crops has been reported using a modified electrophoretic technique.
Abstract— Storage roots are important for the growth and development in plants because they provide nutrients, water, and energy storage. Storage roots are also modulating growth direction, disease resistance, and root formation at the cellular and molecular level through interactions of genes and gene networks. However, molecular mechanisms regulating storage root formation in plants are not fully understood. In this review, we have overviewed transcriptional regulation of storage root formation, proteomic regulation of storage root formation, ethylene regulation of storage root formation, auxin regulation of storage root formation, gene expression regulation of storage root formation, and metabolism regulation of storage root formation. We have reviewed the basic regulatory principles of storage root formation from the network of genomics to proteomics and metabolism in plants that will be valuable to research work in storage root growth and development regulation at the molecular level.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
1. Plant Biosystems Design Research Roadmap 1.0
Background
• Various plants have been genetically improved mostly through
breeding, along with limited modification via genetic engineering,
yet they are still not able to meet the ever-increasing needs, in
terms of both quantity and quality, resulting from the rapid increase
in world population and expected standards of living.
Approach
• This review highlights how plant biosystems design seeks to
accelerate plant genetic improvement using genome editing and
genetic circuit engineering or create novel plant systems through
de novo synthesis of plant genomes.
Outcomes and Impacts
• We highlight current challenges, future opportunities, and research
priorities, along with a framework for international collaboration,
towards rapid advancement of this emerging interdisciplinary area
of research.
• We discuss the importance of social responsibility in utilizing plant
biosystems design and suggest strategies for improving public
perception, trust, and acceptance.
Yang et al. (2020) BioDesign Research, doi: 10.34133/2020/8051764
2. Genome sequencing adds to the synthetic biology
“parts list”
Background
• Ochratoxin (OTA) is a secondary metabolite produced by
Aspergillus species
• This study focuses on the characterization of a novel cyclase
involved in tailoring the polyketide synthase backbone of OTA
Approach
• JBEI’s Whole Aspergillus Genus Genome Sequencing project aims
to sequence one strain from every Aspergillus species (~300) in
order to uncover new biomass deconstruction enzymes and
biochemical pathways
Outcomes and Impacts
• Comparative genomic analysis identified an additional gene
encoding a cyclase putatively needed for the biosynthesis of
ochratoxin, a polyketide
• Polyketides and other secondary metabolites have potential as
enzymes to produce bioproducts or biofuel molecules
• Understanding the biosynthetic pathway, including tailoring
enzymes such as the cyclase uncovered here, adds to the
synthetic biology “parts list” needed for design and synthetis of
biofuel and bioproduct molecules
https://doi.org/10.3389/fmicb.2020.581309
The ochratoxin biosynthetic gene cluster is found in several
species of Aspergillus. Comparative genomic analysis of these
clusters revealed the presence of an novel polyketide cyclase
encoding gene.
3. The TaCslA12 gene expressed in the wheat grain
endosperm synthesizes wheat-like mannan when
expressed in yeast and Arabidopsis
Background
• Mannan is a class of cell wall polysaccharides ubiquitous in the
plant kingdom. Mannan structure and properties vary according to
species and organ.
• The cell walls of cereal grains have been extensively studied due
to their role in cereal processing and to their beneficial effect as
dietary fiber.
• Recently, we showed that mannan in wheat (Triticum
aestivum) grain endosperm has a linear structure of β-1,4-linked
mannose residues.
Approach
• The aim of this work was to study the biosynthesis and function of
wheat grain mannan.
• We showed that mannan is deposited in the endosperm early
during grain development, and we identified candidate mannan
biosynthetic genes expressed in the endosperm.
• The mannan synthase genes were expressed in heterologous
systems to study their activity.
Outcomes and Impacts
• The endosperm-specific TaCslA12 gene expressed in Pichia
pastoris and in an Arabidopsis thaliana mutant depleted in
glucomannan led to the production of wheat-like linear mannan
lacking glucose residues and with moderate acetylation.
• Different mannan synthases produce pure mannans or
glucomannans. The product is not determined by substrate
availability as previously thought.
• Mannan synthases may be useful to increase the C6/C5 sugar
ratio in bioenergy crops.
Verhertbruggen et al. (2021) Plant Science, doi: 10.1016/j.plantsci.2020.110693
Subcellular localization in tobacco leaves show that wheat
CslA12 colocalizes with the Golgi marker, as expected for an
enzyme involved in hemicellulose biosynthesis
(A) Wheat TaCSLA12 is active when expressed in Pichia.
AkCSLA3 is a positive control from konjac. (B) Linkage analysis
shows that the mannan synthesized by the wheat enzyme is
pure mannan, unlike the glucomannan synthesized by the
konjac homolog. Expression in Arabidopsis confirmed these
results (not shown)
4. Cell Wall β-1,4-galactan Regulated by BPC1/BPC2-
GALS1 Module Aggravates Salt Sensitivity
in Arabidopsis thaliana
Background
• Salinity severely reduces plant growth and limits agricultural
productivity.
• Dynamic changes and rearrangement of the plant cell wall is an
important response to salt stress, but relatively little is known
about the biological importance of specific cell wall components in
the response.
Approach
• Salt stress induced the accumulation of β-1,4-galactan in root cell
walls by up-regulating the expression of GALACTAN SYNTHASE
1 (GALS1), which encodes β-1,4-galactan synthase.
• The role of GALS1 in salt response was investigated in mutants
and overexpressors.
• A yeast-1-hybrid screen was used to identify transcription factors
controlling GALS1 expression in response to salt stress.
Outcomes and Impacts
• Exogenous application of D-galactose causes an increase in β-
1,4-galactan levels in plants, especially in GALS1 overexpressors,
which correlated with the aggravated salt hypersensitivity.
• Further analysis revealed that the BPC1 and BPC2 transcription
factors affected the salt tolerance by repressing GALS1
expression and β-1,4-galactan accumulation.
• Our results reveal a new regulatory mechanism where β-1,4-
galactan regulated by BPC1/BPC2-GALS1 module aggravates salt
sensitivity in Arabidopsis thaliana.
• The study may help to identify tools to increase salt tolerance of
bioenergy crops, which is especially important on some marginal
lands.
Yan et al. (2020) Molecular Plant, doi: 10.1016/j.molp.2020.11.023
GALS1 expression is increased in response to NaCl treatment.
NaCl suppresses root growth in wild type. Mutants gals1
respond much less, whereas GALS1 overexpressors respond
more strongly
Galactan in the root affects
cellulose content as shown with a
fluorescence assay. Salt treatment
reduces cellulose synthesis, but
less so in gals1 mutants and more
so in GALS1 overexpressors
Schematic model of the interaction between BPC1/2, GALS1
and cellulose synthase. Decreased cellulose synthesis during
salt stress is likely the direct cause of decreased root growth.
5. Identifying transcription factors that reduce wood
recalcitrance and improve enzymatic degradation of
xylem cell wall in Populus
Background
• Fast growing Populus spp. (poplar) trees are promising sources
of woody biomass for the production of biofuels and bioproducts
• The biomass is highly recalcitrant, and efforts to improve
saccharification efficiency by altering the activity of single
metabolic enzymes has had limited success.
Approach
• Here, in work led by Hokkaido University researchers, we
overexpressed 33 poplar transcription factors (TFs, proteins
which control the expression of groups of genes) in hybrid aspen
(Populus tremula × Populus tremuloides) that were predicted to
have a role in regulating xylem cell wall biosynthesis.
Outcomes and Impacts
• Of the 33, four previously uncharacterized transcription factors
produced enhanced saccharification in the initial screen of
material grown in tissue culture.
• Lines of the two best performing TFs (PtxtERF123 and
PtxtZHD14) were grown to maturity in the greenhouse.
• Lines showed both increased glucan release as well as xylose
from xylan release.
• These TFs are widely distributed in angiosperms, and so are a
breeding target in other woody biomass species, such as willow
and eucalyptus
Hori et al. (2020) Sci Reports, doi: 10.1038/s41598-020-78781-6
Fig. 1: Gene expression and saccharification data from
the transformed poplar generated in this study