This document summarizes four research articles from the Office of Biological and Environmental Research.
The first article compares pretreatment processes using two ionic liquids to pretreat aspen and maple biomass for biofuel production. It finds one ionic liquid increased crystallinity while the other reduced it.
The second isolates five new Pseudomonas strains from soil that can metabolize pentose sugars, with genomes sequenced. This expands options for converting biomass into fuels and chemicals.
The third engineers poplar trees to produce less lignin using a bacterial enzyme, making the biomass easier to break down into sugars for biofuels. It reduces lignin by up to 30% while incorporating cleavable bonds into the lignin.
Induced mutational studies on saccharomyces cerevisiae for bioethanol product...eSAT Publishing House
IJRET : International Journal of Research in Engineering and Technology is an international peer reviewed, online journal published by eSAT Publishing House for the enhancement of research in various disciplines of Engineering and Technology. The aim and scope of the journal is to provide an academic medium and an important reference for the advancement and dissemination of research results that support high-level learning, teaching and research in the fields of Engineering and Technology. We bring together Scientists, Academician, Field Engineers, Scholars and Students of related fields of Engineering and Technology
Microbial Processing of Agricultural Wastes to produce Pectinase Enzyme(s) an...Meesha Singh
Production of pectinase from suitable bacterial sources using agricultural wastes and market effluents as precursors.
Optimization of the physico-chemical parameters for maximum enzyme production.
Induced mutational studies on saccharomyces cerevisiae for bioethanol product...eSAT Publishing House
IJRET : International Journal of Research in Engineering and Technology is an international peer reviewed, online journal published by eSAT Publishing House for the enhancement of research in various disciplines of Engineering and Technology. The aim and scope of the journal is to provide an academic medium and an important reference for the advancement and dissemination of research results that support high-level learning, teaching and research in the fields of Engineering and Technology. We bring together Scientists, Academician, Field Engineers, Scholars and Students of related fields of Engineering and Technology
Microbial Processing of Agricultural Wastes to produce Pectinase Enzyme(s) an...Meesha Singh
Production of pectinase from suitable bacterial sources using agricultural wastes and market effluents as precursors.
Optimization of the physico-chemical parameters for maximum enzyme production.
This pdf is about the Schizophrenia.
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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.
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.
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.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
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 .
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. Office of Biological and Environmental Research
Comparative Study on the Pretreatment of Aspen and Maple With
1-Ethyl-3-methylimidazolium Acetate and Cholinium Lysinate
Background/Objective
• Ionic liquids can be used to dissolve, fractionate, and even convert the
lignocellulosic components of biomass so it can be used a renewable carbon
resource
• The development of pretreatment processes to identify potential woody biomass
feedstock for sustainable future biorefinery and energy applications are needed.
Approach
We compared the feasibility of ionic liquid pretreatment processes for two woody
biomasses, maple and aspen, using two mechanistically distinct ionic liquids at
different pretreatment temperatures.
Results
A significant loss of crystallinity was observed for all [C2mim][OAc]-pretreated
biomasses, whereas the pretreatment with [Ch][Lys] resulted in an increase in the
crystallinity index.
Significance/Impacts
No reports exist in the literature studying the effect of temperature on the
delignification and crystallinity of aspen and maple during their pretreatment with
[C2mim][OAc] and [Ch][Lys].
Choudhary, H.., et al. (2022) Frontiers in Energy Research, doi: 10.3389/fenrg.2022.868181
Sugar yields from (A) aspen and (B) maple after IL pretreatments at
different temperatures. Glucose (dark gray bars) and xylose (light gray bars).
The percentage of lignin removal is shown in black closed circles.
2. Office of Biological and Environmental Research
Complete Genome Sequences of Five Isolated Pseudomonas Strains that Catabolize
Pentose Sugars and Aromatic Compounds Obtained from Lignocellulosic Biomass
Background/Objective
• Pseudomonas putida KT2440 is a promising host for the production of
biofuels and bio-based chemicals
• However, P. putida KT2440 lacks the native ability to metabolize
pentose sugars
Approach
• A method was developed to isolate Pseudomonas putida isolates from
soils that metabolize pentose sugars (Figure 1)
Results
• Five isolates were obtained that grew on aromatics and xylose,
two isolates also grew on arabinose
• Two isolates were had >96% amino acid identity to P. putida KT2440;
complete genomes were obtained for all five isolates
Significance/Impacts
• These isolates may provide new pentose conversion pathways and
be alternative hosts to P. putida KT2440
Park, Mee-Rye, et al Microbiology Resource Announcements (2022): e00987-21. doi.org/10.1128/mra.00987-21
Temp. = 30°C
pH = 7.0 ± 0.1
Genomic analysis
(PacBio seq. & illumina seq.)
Xylose M9 agar
Growth kinetics in M9 media
with carbon source
Environmental soil samples
collection
Pseudomonas isolation agar (PIA)
1st
Screening
p-Coumarate M9 agar
Growth test in liquid media
2nd
Screening
Xylose M9 agar
Figure 1. Isolation protocol for P. putida isolates that grow on pentose sugars
3. Office of Biological and Environmental Research
A new approach to zip-lignin: 3,4-dihydroxybenzoate
is compatible with lignification
Background/Objective
• Lignin renders plant biomass recalcitrant to enzymatic conversion into
simple sugars
• Expression of bacterial 3-dehydroshikimate dehydratase (QsuB) is known
to reduce lignin in Arabidopsis and switchgrass
Approach
QsuB was transferred to the bioenergy crop poplar to reduce lignin
Results
-> QsuB poplar trees contain up to 30% less lignin
-> DHB incorporates lignin and creates cleavable bonds (‘zips’)
-> QsuB biomass displays higher saccharification efficiency
Significance/Impacts
The improvement of poplar biomass quality via the QsuB
engineering strategy has the potential to improve the economics
of advanced bioproducts
Unda et al., 2022 New Phytol. https://doi.org/10.1111/nph.18136
QsuB
DHB E4P + PEP
3-dehydroshikimate
LIGNIN
DHB
(%
biomass)
WT QsuB-1 QsuB-2
Sugars
released
(%
biomass)
0
5
10
15
20
25
Line
1
Line
2
Line
35
Line
10
Line
15
Line
15
WT
Lignin
(%
biomass)
*p<0.05
*
* * * *
*p<0.05
Low lignin
High sugar yields
High DHB
4. Office of Biological and Environmental Research
Downregulation of Squalene Synthase Broadly
Impacts Isoprenoid Biosynthesis in Guayule
Background/Objective
• Guayule is a natural rubber-producing plant species.
• Production of natural rubber by guayule requires increased yield for economic
sustainability.
Approach
An RNAi gene silencing strategy was used to engineer isoprenoid biosynthesis by
downregulation of squalene synthase to initiate natural rubber synthesis.
Results
Downregulation of squalene synthase in guayule successfully increased natural
rubber production. Analysis of mevalonic acid and methylerythritol phosphate
pathway intermediates has provided the first evidence of cellular crosstalk between
these essential metabolic pathways in guayule.
Significance/Impacts
This study identified insights and strategies for engineering isoprenoid production in
guayule.
Placido, D., et al. (2022) Metabolites, doi: 10.3390/metabo12040303
Relative expression of metabolic and putative NR biosynthesis and structural
genes in SQSi lines’ background. Plant phenotypes for controls and SQS
lines, RT-PCR for the isoprenoid pathway, and natural rubber biosynthesis-
associated genes.
5. Office of Biological and Environmental Research
Machine-learning from 321 Gene Expression Profiles of Pseudomonas putida
KT2440 Unveils its Genome-scale Transcriptional Regulatory Network (TRN)
Approach
• We generated putidaPRECISE321, a compendium of 321 high-
quality RNA-Seq samples, and performed independent
component analysis (ICA) to analyze it.
Results
• We obtained 84 groups of independently modulated genes
(iModulons) that explain 75.7% of the total variance in the set.
• We identified the regulatory functions of 39 important TFs
(e.g., HexR), associated with iModulons.
• Complex transcriptional changes driven by utilization of different
carbon sources, the presence of stressors, and evolution-derived
mutations were explained with iModulon activity changes.
Significance/Impacts
• The structure of the P. putida TRN that governs its metabolism,
stress responses, and other cellular functions has now been revealed.
Lim et al. (2022) Metabolic Engineering, doi: 10.1016/j.ymben.2022.04.004
Background/Objective
• Elucidating the TRN is fundamental to understanding bacterial
physiology and engineering it for practical use. TRNs are poorly
understood in DOE hosts of interest such as P. putida.
6. Office of Biological and Environmental Research
Artificial Intelligence for Synthetic Biology
Background/Objective
• Biology has dramatically changed in the last two decades.
• The combination of high-throughput phenotypic data with precision DNA
editing provides a unique opportunity to link changes in DNA to phenotype.
• Artificial intelligence (AI) is ideally posed for this task.
Approach
In this article, we provide AI practitioners interested in working on
synbio an overview of:
• The potential of synthetic biology.
• Initial successes of AI in synbio.
• Main challenges faced.
Results
• Sociological, as well as technological, challenges abound.
• AI solutions that incorporate causal reasoning, interpretability, robustness, and
uncertainty estimation are needed.
• Synbio can also inspire new AI approaches.
Significance/Impacts
AI can radically enhance synbio and enable its full impact.
Eslami, Mohammed, et al. "Artificial intelligence for synthetic biology." Communications of the ACM 65.5 (2022): 88-97
8. Office of Biological and Environmental Research
Recent advances in biological activities of lignin and
emerging biomedical applications: A short review
Background/Objective
• As an abundant biopolymer, lignin gains interest owing to its renewable nature
and polyphenolic structure.
• Studies are being carried out to relate the biological activities to the
polyphenolic structures.
Approach
This review summarizes latest research results on the biological activities of lignin
and highlights potential applications exampled by selective studies.
Results
We analyzed and summarized lignin’s various applications, including antibacterial,
antiviral, and antifungal activity, antioxidant activity, drug delivery, wound healing,
antidiabetic activity, and other emerging applications.
Significance/Impacts
Lignin has various potential applications, ranging from food and cosmetics to
pharmaceuticals and biomedical applications. Further research should be performed
to highlight the potential of this biomolecule
Ullah, I., et al. (2022) International Journal of Biological Macromolecules, doi: 10.1016/j.ijbiomac.2022.03.182
Overall scheme on lignin fractionation and its antioxidant and antimicrobial
activities.
9. Office of Biological and Environmental Research
Corynebacterium glutamicum as an Efficient Omnivorous
Microbial Host for the Bioconversion of Lignocellulosic Biomass
Background/Objective
• Corynebacterium glutamicum has been successfully employed for the industrial
production of amino acids and other bioproducts
• However, several challenges still need to be overcome for efficient
bioconversion of biomass to bioproducts.
Approach
The omnivorous strain C. glutamicum ATCC 13032 was investigated for production
of mixed acids from sugars and aromatics present in lignocellulosic biomass.
Results
By using C. glutamicum as a microbial host, we demonstrate bioproduction of L-
lactate, succinate, and acetate from corn stover biomass hydrolysates with
simultaneous utilization of sugars and aromatics. This demonstrated C. glutamicum
as an efficient microbial host for utilizing diverse carbon substrates present in
biomass hydrolysates, such as glucose, arabinose, and xylose, in addition to its
natural ability to assimilate lignin-derived aromatics.
Significance/Impacts
Our findings open the door to valorize all the major carbon components of biomass
hydrolysate by using C. glutamicum as a microbial host for biomanufacturing.
Mhatre, A.., et al. (2022) Frontiers in Bioengineering and Biotechnology, doi: 10.3389/fbioe.2022.827386
Schematic representation of the overall process employed in this study. Corn
stover was subjected to deacetylation and mechanical refining (DMR) to
obtain liquid biomass hydrolysate. The hydrolysate constituting glucose,
xylose, arabinose, and aromatics was used as fermentation feedstock for C.
glutamicum to produce mixed acids having various applications.
10. Office of Biological and Environmental Research
Optimization of Heterologous Glucoraphanin Production In Planta
Background/Objective
Glucoraphanin is a plant specialized metabolite found in cruciferous vegetables that has long been
a target for production in a heterologous host because it can subsequently be hydrolyzed to form
the chemopreventive compound sulforaphane before and during consumption.
Approach
Previous studies have only been able to produce small amounts of glucoraphanin in heterologous
plant and microbial systems compared to the levels found in glucoraphanin-producing plants,
suggesting that there may be missing auxiliary genes that play a role in improving production in
planta.
Results
We leveraged transient expression in Nicotiana benthamiana to screen a
combination of previously uncharacterized coexpressed genes and
rationally selected genes alongside the glucoraphanin biosynthetic
pathway. This strategy alleviated metabolic bottlenecks, which improved
glucoraphanin production by 4.74-fold.
Significance/Impacts
Our study describes a method to systematically identify novel genes
involved in improving the yields of bioproducts in plants. This approach
can be used to further optimize production of natural products, but also
commodity chemicals and potential biofuels.
Barnum CR*, Endelman BJ*, Ornelas IJ, Pignolet RM, Shih PM. (2022) Optimization of heterologous glucoraphanin production in planta. ACS Synthetic Biology, accepted