This document summarizes the development and testing of a quorum sensing (QS)-mediated gene expression system to control bisabolene production in engineered E. coli. Researchers developed a QS system using the LuxI/R genes from Vibrio fischeri to induce expression of the bisabolene production pathway without the need for external inducers. The best QS strain, with the sensor genes integrated into the genome and an optimized response plasmid, produced 1.1 g/L of bisabolene, a 44% improvement over previous inducible systems. This QS-based system provided defined and homogeneous gene expression and production compared to inducible controls.
Metabolomic and thermodynamic analysis of C. thermocellum strains engineered ...Jordan Brown
This presentation details a preliminary integrated metabolomic and thermodynamic analysis towards the goal of improving the ethanol yield in C. thermocellum.
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.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
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.
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.
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.
1. Outcomes and Impacts
• Knocking out the gene corresponding to the RPE reaction is predicted to increase
acetate production by 6.2% according to the MoMA methodology and by 60.0% when
using the ROOM methodology. As can be seen with an RPI knockout, both MoMA and
ROOM predict a decline in acetate production.
Ando & Garcia (2018) Synthetic Metabolic Pathways: Methods and Protocols, https://doi.org/10.1007/978-1-4939-7295-1_21
Background
• Accelerating the Design–Build–Test–Learn (DBTL) cycle in synthetic biology is critical
to achieving rapid and facile bioengineering of organisms for the production of, e.g.,
biofuels and other chemicals.
• The learn (L) phase of the DBTL cycle and is, arguably, the hardest and most weakly
supported step in current metabolic engineering practice.
• The measurement of intracellular metabolic fluxes is specifically noteworthy as providing
a rapid and easy-to-understand picture of how carbon and energy flow throughout the
cell.
Approach
• Here, we present a detailed guide to performing metabolic flux analysis in the
Learn phase of the DBTL cycle, where we show how one can take the isotope labeling
data from a 13C labeling experiment and immediately turn it into a determination of
cellular fluxes that points in the direction of genetic engineering strategies that will
advance the metabolic engineering process.
• We will show how to use metabolomic data obtained from 13C labeling experiments to
generate actionable items to increase acetate production in E. coli.
• For our modeling purposes we use the Joint BioEnergy Institute (JBEI) Quantitative
Metabolic Modeling (jQMM) library, which provides an open-source, python-based
framework for modeling internal metabolic fluxes and making actionable predictions on
how to modify cellular metabolism for specific bioengineering goals.
Overview of the workflow for
13C Two-Scale Metabolic
Flux Analysis. The Test phase
of the workflow is in blue
while the Learn phase steps
are in red.
Two-scale 13C metabolic flux analysis for
metabolic engineering
2. A bacterial pioneer leaves a complex legacy
Outcomes and Impacts
• A defined community succession was observed during 15
L and 300 L cultivations at ABPDU
• Appearance of cellulase activity in the medium correlated
with relative decline of pioneer population
• This study used scaled community cultivations and
genome-resolved metagenomics to identify new cellulase
complexes distinct from cellulosomes and underscores
the importance of extracellular glycoside hydrolases as
“public goods” for biomass-deconstructing communities
Background
• In previous work at JBEI, cellulolytic consortia were used
to produce Jtherm, an thermo/IL tolerant cellulase cocktail
• Scaling of cellulolytic consortium to 300 L provided
sufficient enzyme to identify active component(s) of
Jtherm
Approach
• Time-resolved metagenomics was applied to 15 L and
300 L cultivations (14 days) to determine changes in
community structure. Genome-resolved metagenomics
was used to recover genomes in consortium. Biochemical
purification and heterologous expression were used to
characterize the active cellulases
The bacterial pioneer population is an uncultivated Firmicutes
that contains unique gene clusters with multi-domain cellulases
and LPMOs. A subset of these cellulases (CelABC) were purified
as multi-protein complexes; glycosylation appeared to be key to
complex formation and stability; the complexes provided the
majority of the activity in the Jtherm cocktail
Kolinko et al. (2017) Nature Microbiology, doi: 10.1038/s41564-017-0052-z.
3. Automated lab evolution (ALE) generates a
platform strain for IL tolerance
Outcomes and Impacts
• MG1655 and DH1 clones were obtained with tolerance
to [C2C1mim][OAc] at 6% concentration.
• Sequencing revealed common mutations in intergenic
region adjacent to mdtJI (SMR promoter-pump pair)
and coding region of yhdP (predicted transporter)
• MG1655 adapted clones significantly outperformed
JBEI IL tolerant E. coli strains established to date
• This study establishes ALE as an effective platform to
generate strains that are tolerant to ionic liquids.
Mohamed et al. (2017) Microbial Cell Factories, 16, 204, doi: 10.1186/s12934-017-0819-1
Background
• Previous work at JBEI has developed IL tolerant
E. coli strains using functional genomics and
isolating spontaneous mutants
• Automated lab evolution (ALE) is a promising
technique to adapt microbes to grow under stress
conditions (i.e. IL challenge)
Approach
• ALE was performed for 40 days on E. coli DH1
and MG1655 in the presence of increasing
amounts of [C2C1mim][OAc] and [C4C1mim]Cl
• Adapted clones were isolated, tested in
secondary screens and sequenced
Comparison of TALE evolved IL tolerant clones
MG1655#4.7 and MG1655#3.10 to previously engineered
tolerant strains JBEI-13314 and JBEI-10101 in LB (a, b)
and M9 (c, d) media containing either 300 mM of
[C2C1Im][OAc] [5.1% (w/v)] or [C4C1Im]Cl [4.4% (w/v)].
TALE evolved clones exhibited improved growth compared
to rationally-designed strains, particularly in M9, where
JBEI-13314 and JBEI-10101 were severely inhibited
4. Xylose induces cellulase production
in Thermoascus aurantiacus
Outcomes and Impacts
• Xylose was shown to specifically induce both cellulases
and xylanases in T. aurantiacus; acid hydrolysate from
biomass induced proteins to levels comparable to pure
xylose
• Xylose induction was scaled to 20 L cultures and
saccharification experiments demonstrated that dilute acid-
pretreated corn stover could be saccharified at 60 ℃
• This study demonstrates that dilute acid hydrolysate can be
used for enzyme production, which a promising biorefinery
strategy
Shüerg et al. (2017) Biotechnology for Biofuels, 10, 271, doi: 10.1186/s13068-017-0965-z
Background
• Previous work demonstrated that Thermoasucs
aurantiacus produced a highly active cellulase mixture
that saccharified biomass at 70℃
• This cellulase mixture was generated by growth on
switchgrass substrates
Approach
• To identify sugars that may induce cellulase
production, fed-batch cultures were set-up in shake
flasks and bioreactors to determine whether biomass-
derived sugars induced the expression of cellulases
Batch FB
XyloseXylan
2% 2% 0.5% 0.5%
Batch FB
GlucoseXylan
2% 2% 0.5% 0.5%
T. aurantiacus protein production with glucose and xylose
SDS-PAGE (a), protein concentration (b). Batch cultures
were performed by adding glucose and xylose at the
beginning of the cultivation and fed-batch cultures were
performed by adding the sugars continuously using a
peristaltic pump. Shift cultures with 2% beechwood xylan
as the substrate were used as positive controls for protein
production. Batch cultures are underlined in red and fed-
batch cultures in blue
5. Cascade production of lactic acid from
universal types of sugars catalyzed by La(OTf)3
Outcomes and Impacts
• We report a universal method of converting sugars to lactic with
high yield ~70%
• This is the first work to convert pyrolytic sugar into lactic acid by
chemocatalysis and also lignocellulosic sugars are converted to
lactic acid without hydrolysis
• This approach could potentially be extended to other lignocellulosic
sugars after simple removal of lignin from biomass pretreatment,
rendering moderate to high yield of lactic acid
Liu et al. (2017) ChemSusChem, doi: 10.1002/cssc.201701902
Background
• Lactic acid is on the list of the DOE’s top chemical opportunities
from carbohydrates and the market for lactic acid is increasing
rapidly due the the expanding use of lactic acid to produce plastics
• The current process of lactic acid production is dominated by
fermentation, which requires monosaccharides
• The chemocatalytic process to produce lactic acid offers high
reaction rates and simple separation process
Approach
• Universal types of sugars obtained from pyrolysis, ionic liquid
pretreatment were prepared and subjected to catalytic conversion
using La(OTf)3
Proposed mechanism of aldo sugars
conversion to lactic acid in the
presence of Lewis acid.
Lignocellulosic biomass upgrading
through thermochemical conversion
process
6. High loading solubilization and upgrading of
polyethylene terephthalate in low cost
bifunctional ionic liquid
Outcomes and Impacts
• Low cost (~$1.2/kg) biocompatible IL, cholinium phosphate
([Ch]3[PO4]) plays bifunctional roles in PET solubilization and
glycolysis degradation
• High loading of PET (10 wt%) is readily dissolved in [Ch]3[PO4] at low
temperatures (120 °C, 3h) and even in water-rich conditions
• Acid precipitation yields terephthalic acid as the dominant
depolymerized monomer with a theoretical yield of ~95%
• In the presence of ethylene glycol, [Ch]3[PO4] catalyzed glycolysis of
PET resulted in ~100% PET conversion and ~60.6% bis(2-
hydroxyethyl)terephthalate (BHET) yield
Jian et al. (2017) ChemSusChem, doi:10.1002/cssc.201701798.
Background
• Concerns on the depletion of fossil reserves, environmental pollution
and more efficient & circular carbon economies have highlighted the
importance of recycling polyethylene terephthalate (PET)
• High solubilization of PET is critical as a first step in recycling, but is
challenging in toxic solvents
• Achieving PET solubilization at high loading under mild conditions by
using relatively nontoxic and lower cost solvents is highly desirable
Approach
• Biocompatible IL was developed by changing imidazolium ring based
cation to cholinium cation
• Hydrogen bond functionalization was used to improve the activity of
IL in PET solubilization under relatively low temperature
In situ confocal fluorescence microscopy
images of PET solubilization in
[Ch]3[PO4] as a function of temperature
Proposed mechanism of PET
glycolysis catalyzed by [Ch]3[PO4]
7. Autonomous control of metabolic state by a quorum
sensing (QS)-mediated regulator for bisabolene
production in engineered E. coli
Background
• Inducible gene expression systems have disadvantages such as leaky expression, lack of dynamic control, and the prohibitively
high costs of inducers associated with large-scale production
• Quorum sensing (QS) systems in bacteria control gene expression in response to population density, and the LuxI/R system from
Vibrio fischeri is a well-studied example
• QS system could be ideal for biofuel production strains as it is self-regulated and does not require the addition of inducer
compounds, which reduce operational costs
Approach
• QS system was developed for inducer free production of the biofuel compound bisabolene from engineered E. coli.
• Seven variants of the pSensor plasmid, which carry the luxI-luxR genes, and four variants of the pResponse plasmid, which carry
bisabolene producing pathway genes under the control of the PluxI promoter
• A chromosome-integrated QS strain was engineered with the best combination of Sensor and Response plasmid
Outcomes and Impacts
• The best combination of pSensor integrated in the genome and re-engineered pResponse plasmid produced bisabolene at a titer of
1.1 g/L without addition of external inducers.
• This is a 44% improvement from our previous system
• QS strain also displayed higher homogeneity in gene expression and isoprenoid production compared to an inducible-system strain
Genome Plasmids SApSensor pResponseSummary: using QS-mediated regulator
to control bisabolene synthesis
Kim et al. (2017) Metabolic Engineering, 44:325-336, doi: 10.1016/j.ymben.2017.11.004
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