The document discusses several studies related to engineering plants for improved biomass composition for biofuel production. One study found that Arabidopsis plants engineered to have low lignin and xylan content showed increased drought tolerance compared to wild-type plants. The engineered plants exhibited lower water loss, up-regulation of drought response genes, and a stronger response to the plant hormone ABA. This demonstrates that modifying secondary cell walls to improve biomass composition does not necessarily compromise plant resilience to the environment.
Synthetic Biology for Plant ScientistsSachin Rawat
Tools of synthetic biology can be utilised to engineer metabolic pathways to optimize production of secondary metabolites and ligno-cellulose. The presentation describes an approach to develop an artificial positive feedback loop to increase accumulation of cell wall polysaccharides. These will decrease the cost of production of plant-based biofuels, paper and other plant products.
This pdf is about the Schizophrenia.
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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.
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.
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.
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.
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 .
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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Predicting property prices with machine learning algorithms.pdf
JBEI Research Highlights - July 2018
1. Insulator nanostructure desorption ionization
mass spectrometry
Background
• Surface-assisted laser desorption ionization (SALDI) is an
approach for gas-phase ion generation for mass spectrometry
using laser excitation on typically conductive or
semiconductive nanostructures
• Here, we introduce insulator nanostructure desorption
ionization mass spectrometry (INDIMS), a nanostructured
polymer substrate for SALDI-MS analysis of small molecules
and peptides
Approach
• INDI-MS surfaces are produced through the self-assembly of
a perfluoroalkyl silsesquioxane nanostructures in a single
chemical vapor deposition silanization step
• Used this approach to analyze a 288 compound secondary
metabolite library from Enzo life sciences, as well as glycosyl
hydrolase probes to compare the performance of two
commercial cellulase and hemicellulase enzyme cocktails
Outcomes and Impacts
• Surfaces formed from the perfluorooctyltrichlorosilane monomer
assemble semielliptical features with a 10 nm height, diameters
between 10 and 50 nm
• Self-desalting occurs passively as a sample dries with hydrophobic
molecules of interest assembling on the INDI regions and salts
depositing on the silicon
• Detected all compounds in the Enzo library and could effectively
tracked GH activity
• INDI-MS substrates represent a new SALDI surface for the analysis
of small molecules that can be used by scientists in multiple fields,
including bioenergy R&D
Duncombe et al. (2018) Analytical Chemistry, DOI: 10.1021/acs.analchem.8b01989
Insulator nanostructure desorption ionization mass spectrometry
(INDI-MS) (A) INDI substrates are generated in 20 min using silicon
oxide surface to form (III) nanostructures with a siloxane backbone
(black) decorated with fluorocarbon side groups (yellow). (B) AFM
and (C) SEM demonstrate the 10 to 50 nm diameter semielliptical
nanostructures. (D) LDI-MS is performed directly on the INDI surface
to analyze adsorbed molecules. (E) INDI-MS mass spectra of a
sample containing 250 fmols of dextromethorphan, verapamil, and
palmitoyl carnitine, 2.5 pmol mastoparan, and background.
2. A mosaic monoploid reference sequence for
the highly complex genome of sugarcane
Background
• Sugarcane (Saccharum spp.) is a major crop for sugar and
bioenergy production
• Its polyploid, aneuploid, heterozygous, and interspecific
genome poses major challenges for producing a reference
sequence
Approach
• This international team exploited colinearity with sorghum to
produce a BAC-based monoploid genome sequence of
sugarcane
• A minimum tiling path of 4660 sugarcane BAC that best
covers the gene-rich part of the sorghum genome was
selected based on whole-genome profiling, sequenced, and
assembled in a 382-Mb single tiling path of a high quality
sequence
Outcomes and Impacts
• A total of 25,316 protein-coding gene models are predicted,
17% of which display no colinearity with their sorghum
orthologs
• The two species analyzed, S. officinarum and S. spontaneum,
differ by their transposable elements and by a few large
chromosomal rearrangements, explaining their distinct
genome size and distinct basic chromosome numbers while
also suggesting that polyploidization arose in both lineages
after their divergence
• This first-ever published analysis of the sugarcane genome
provides bioenergy researchers increased knowledge that can
aid in targeted genetic engineering strategies to enhance
desired biofuel traits
Garsmeur et al. (2018) Nature Communications, DOI: : 10.1038/s41467-018-05051-5
Distribution of the 11,732 sugarcane BACs aligned onto the sorghum
genome through WGP. Sugarcane BAC clones are represented by
orange bars. Sorghum gene and transposable element densities are
represented in green and gray, respectively.
Sequencing strategy targeting the sugarcane monoploid genome
based on the overall synteny and colinearity conservation within
sugarcane homologs and with sorghum. a WGP sequence tags were
produced from R570 sugarcane BACs. b WGP sequence tags were
aligned onto the sorghum sequence. c A minimum tiling path of a
BAC (MTP) corresponding to a monoploid sugarcane genome d
Overlapping BAC sequences were trimmed to construct the single
tiling path (STP) B The STP sequence contains BAC contigs that
belong to distinct homologous chromosomes.
3. Natural variation in the multidrug efflux pump SGE1
underlies ionic liquid tolerance in yeast
Background
• Certain ionic liquids (ILs) are deconstruction solvents that
show great promise as a biomass pretreatment, but residual
solvent can be toxic to microbes and inhibit biofuel production
• The natural genetic diversity of Saccharomyces cerevisiae
isolates may help identify genes that contribute to ionic liquid
(IL) tolerance
• elucidate defense mechanisms that cells employ to improve
performance of bioconversion microbes
Approach
• Examined over 100 S. cerevisiae yeast isolates from diverse
ecological niches for growth in [C2C1im]Cl, identifying strains
with exceptional tolerance to that IL
• Screened DNA libraries from top performing strain to identify
genes that contribute to IL resistance
Outcomes and Impacts
• Two genes were associated with increased IL tolerance:
SGE1 and ILT1, encoding a multidrug efflux pump and a
predicted membrane protein, respectively
• Two major sequence variants of the SGE1 gene were found to
occur among yeast lineages that confer tolerance or sensitivity
to IL; alterations in Sge1 protein stability and cell surface
localization may impact the amount of IL that cells can pump
out of the cell
• Natural variation among diverse microbial isolates is an
important resource that can contribute to identification of
biological mechanisms of interest for biofuels conversion
Higgins et al. (2018) Genetics, DOI: 10.1534/genetics.118.301161
Schematic depiction of the multidrug efflux pump
SGE1 in the presence of ionic liquids.
BY strains containing GFP fused
to the indicated genes were
cultured in YPD medium. GFP
fluorescence (A) from
representative cells was
visualized with 100X
magnification. Insets in the lower
right corners display a single
representative cells with
additional 50% higher
magnification. ILT1 was deleted
from BY strains containing
SGE1SLS or sge1PLL alleles (B).
Resulting strains were cultured in
YPD pH 5 medium containing
62.5 mM [C2C1im]Cl. Cell growth
is reported as average cell
densities ± SEM from 3
independent biological replicates.
4. Microbial community structure and functional
potential along a hypersaline gradient
Background
• Microbial communities isolated from extreme environments
are an important source of new microbes and enzymes with
desired traits, including tolerance to salts and ionic liquids
• Salinity is one of the strongest environmental drivers of
microbial evolution and community composition
Approach
• We aimed to determine the impact of salt concentrations (2.5,
7.5, and 33.2%) on the microbial community structure of
reclaimed saltern ponds near San Francisco
• Community compositions were determined by 16S rRNA
amplicon sequencing revealing both higher richness and
evenness in the pond sediments compared to the water
columns
Outcomes and Impacts
• Functional annotation of shotgun metagenomic DNA showed
different capabilities of the microbial communities at different
salinities for methanogenesis, amino acid metabolism, and
carbohydrate-active enzymes
• There was an overall shift with increasing salinity in the
functional potential for starch degradation, and a decrease in
degradation of cellulose and other oligosaccharides
• Many of the carbohydrate-active enzymes identified have
acidic isoelectric points that have potential biotechnological
applications, including deconstruction of biofuel feedstocks
under high ionic conditions
Kimbrel et al. (2018) Frontiers in Microbiology, DOI: 10.3389/fmicb.2018.01492
OTU abundance, diversity, and phyla of sampled ponds. Pond sample
types are denoted with an “L” or “S” for water or sediment. (A) Richness
and Evenness metrics for triplicates at each sample site (Pond A23
sediments has only a single replicate) (B) Bray-Curtis Dissimilarity
dendrogram of all sample sites, color coded by sampled pond with
assignment into seven groups at a cut-off of 0.6. (C) Relative abundance
of the 8 most abundant phyla grouped by sample site.
5. Increased drought tolerance in plants engineered
for low lignin and low xylan content
Background
• We previously developed several strategies to engineer plants in order
to produce cost-efficient biofuels from plant biomass
• Engineered Arabidopsis plants with low xylan and lignin content
showed normal growth and improved saccharification efficiency under
standard growth conditions
• However, it remains to be determined whether these engineered plants
perform well under drought stress, which is the primary source of
abiotic stress in the field
Approach
• Upon exposing engineered Arabidopsis plants to severe drought, we
observed better survival rates in those with a low degree of xylan
acetylation, low lignin, and low xylan content as compared to those in
wild-type plants
• The drought tolerant plants exhibited low water loss from leaves, and
drought-responsive genes (RD29A, RD29B, DREB2A) were generally
up-regulated under drought stress, which did not occur in the well-
watered state
• When compared with the wild type, plants with low lignin showed a
stronger response to abscisic acid (ABA) in assays for seed
germination and stomatal closure
Outcomes and Impacts
• This study shows that plants engineered to accumulate less lignin or
xylan are more tolerant to drought and activate drought responses
faster than control plants
• This finding demonstrates that modification of secondary cell walls
does not necessarily render the plants less robust in the environment,
and it shows that substantial changes in biomass composition can be
achieved without compromising plant resilience.
Yan et al. (2018) Biotechnol Biofuels, DOI: 10.1186/s13068-018-1196
Plants with low xylan (XE#55 and X4) or low lignin (QsuB, W4, X4)
show increased tolerance to drought stress. Plants with secondary
cell wall galactan (W2) are not different from the Col-0 control.
Abscisic acid (ABA) is a hormone
induced by drought. The engineered
plants have normal, low ABA
content in well-watered conditions.
All the plants induce ABA in
response to drought stress, but the
low lignin plants (QsuB, W4, X4)
have much higher ABA levels after
induction. The low xylan plants
XE#55 do not show this change,
indicating an ABA-independent
improved drought tolerance in those
plants.