The document summarizes geology fieldwork conducted in the San Bernardino Mountains. It describes the formation of the mountains due to tectonic plate movement along the San Andreas Fault. It details the local geology, including metamorphic and sedimentary rocks observed in Lytle Creek. Native plants, animals and trees of the area are also discussed, along with their fossil and evolutionary histories.
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.
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 .
(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.
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.
2. SAN BERNARDINO AND SAN GABRIEL MOUNTAINS
• The San Bernardino and San Gabriel Mountains are part of the eastern Transverse
Ranges in Southern California. It is part of a mountain chain that was formed by
the shifting of the North American tectonic plate past the Pacific tectonic plate
along the San Andreas Fault.
• The San Andreas fault cuts through the mountains near Gorgonio Pass and along
the southern base of the mountains approaching Cajon Pass.
Lytle Creek, south fork
3. SAN BERNARDINO
MOUNTAINS
• The San Bernardino Mountain
(SBM) range stretches for 55 miles
rising to a height of 11,499 feet at
San Gorgonio Mountain.
• The SBM consists of high elongate
block that his been uplifted to its
present elevation during the last
few million years (USGS)
• Geologic materials of the San
Bernardino Mountains mainly are
ancient basement rocks that have
been uplifted to their current
elevations.
San Gorgonio Mountain peak
4. SAN BERNARDINO
MOUNTAINS TODAY
•The modern landscape of the San Bernardino
Mountains is a product of erosional dissection by
streams and rivers that are gradually stripping away
rock products and carrying them downstream to
basins at the base of the range.
•Cities within the San Bernardino Mountains total a
population of about 44,000.
•The SBM are home to many ski resorts such as Big
Bear, Snow Summit and Mountain High.
Bonita Falls Lytle Creek
5. LYTLE CREEK, CA
•My field report was conducted at
this location marked by the
green/black dot. I hiked along the
south fork of Lytle Creek.
6. ECOLOGY
•Southern California has a Mediterranean
climate. The weather is warm and dry in the
summer and cool and wet in the winter.
•The SBM are well known for their lush forests
of tall pine trees, chaparral bushes, manzanitas,
scrub oak and wild lilac. They are often joined
by yucca plants and native succulents.
•Grizzly Bears once lived in great abundance in
the SBM, but were hunted during the pioneer
days. They are now extinct in California.
Dudleya cymosa Photo Credit: S. Avila
Sahara mustard, Photo Credit: S.Avila
7. NATIVE PLANT LIFE
An evergreen leaf succulent. It has one or few reddish
stalks bearing red to yellow flowers growing from a
basal rosette of thick grayish-green leaves. The
rootstock penetrates rock crevices only found naturally
in California. Dudleya cymosa is in the class of
angiosperms. It flowers in the early spring and
produces a seed-filled fruit. It shares many physical and
physiological similarities to cacti. Dudleya cymosa can
be found at elevations ranging from 300 feet up to
8000 feet (Jepson). It is considered a xerophyte
because it grows in arid climates, they survive low
precipitation and high temperatures (Stern).
Dudleya cymosa
8. EVOLUTION OF CANYON
LIVE FOREVER PLANT
Like all flowering seed angiosperms, Dudleya
cymosa’s evolutionary record is difficult to trace. It
appeared abruptly in the fossil record 120 MYA
during the Cretaceous period. Scientists use its
characteristics to to determine its beginnings. There
is speculation that succulents evolved during periods
of low carbon dioxide levels because it has an ability
to conserve CO2.
9. BIGHORN SHEEP
•Ovis canadensis is in the mammalia class. During the Tertiary Period,
65mya, mammals spread through the world.
•Bighorn sheelp belong to the Bovidae family. Bovidae fossils appeard in
the Miocene epoch. They have unbranched horns. Family members
consist of gazelle, mountain goats, buffalo, yaks, cattle and sheep.
•A fossil record for Ovis canadensis appeared 100,000 years ago in
North America.
•American forms of Ovis evolved in the absence of goats, and are short
legged and broad chested and inhabit rocky cliffs devoid of goat
competition.
Bighorn sheep, Wiki
Bighorn sheep, Lytle Creek
Ovis canadensis
10. CALIFORNIA SYCAMORE
TREE
Platanus racemosa
The California sycamore tree is native to California and
Baja California where it grows in canyons, floodplains,
and along streams. The bark has areas of white,
pinkish gray and pale tan, with older bark becoming
darker and peeling away.
11. CALIFORNIA SYCAMORE
HISTORY
The plant family containing the
California sycamore is the
Platanaceae. Although it is a very
small family comprised of the
single genus Plantus, it has an
interesting prehistory. Its fossil
record is 10s of million of years
older than the maples, elms, oaks
and ashes that it associates with.
Fossil leaves and even fruit
impressions are quite common in
the fossil record from the later
part of the Cretaceous Period
(Paratley,n.d).
12. This rock was found in the dry river bed.
METAMORPHIC ROCK
Gneiss
Foliated rock identified by its bands and lenses of
varying composition. These bands are usually light
in color and alternate between dark and light.
Gneisses are composed of granular materials such
as quartz, and feldspar. These minerals compose
the light-colored bands(Monroe, 2012).
Gneiss can from from igneous rocks such as granite
or older metamorphic rock.
It is characterized by its medium to coarse grain. It
is hardy and difficult to break. Generally rough to
the touch.
13. Slate is a low grade metamorphic rock
generally formed by the metamorphosis
of mudstone/shale under low pressure.
Slate is made up of parallel foliated
plates.
Clay minerals in the rock metamorphose
into mica minerals which are aligned
along foliation planes perpendicular to
the direction of pressure (slate, n.d.)
It is characterized by its hardiness and
brittleness. It is smooth to the touch. It
is valued for its ability to break into thin
plates.
METAMORPHIC ROCK
Slate
14. METAMORPHIC ROCK
Schist is a medium grade metamorphic rock
formed by the metamorphosis of
mudstone/shale. It has been subjected to
higher temperatures and pressures.
The green color of the minerals and their
platy habit cause the rocks to be greenish.
They have a high luster and are generally
hard.
Smooth to the touch. There are many
varieties of schist, and are named by the
dominant mineral comprising the rock. Eg.
Greenschist.
Schist
Green schist rock
15. LAW OF ORIGINAL
HORIZONTALITY
•This rock is curved, or folded. It
appears in layers. This type of folding
occurs when rock is near a fault.
• The Law of Original Horizontality
states that layers of sediment were
originally deposited horizontally
under the action of gravity.
•Any rock layers that are now folded,
have since been altered by outside
sources.
17. References
• Geology of the San Bernardino Mountains. (n.d.). Retrieved June 5, 2018, from
https://geomaps.wr.usgs.gov/archive/socal/geology/transverse_ranges/san_bernardino_mtns/index.html
• Hickman, J. C. (editor) 1993. The Jepson manual: higher plants of California. Berkeley, CA. University of
California Press.
• Stern, K.R. 1988. Introductory Plant Biology. Dubuque, IA. Wm. C. Brown Publishers.
• Matti, J. C. (2000). Geologic setting, San Bernardino National Forest. Retrieved from USFS
• Bighorn Sheep. (n.d.). Retrieved June 6, 2018, from https://www.desertusa.com/bighorn/bighorn-sheep.html
• Monroe, J. S., & Wicander, R. (2012). The changing earth: Exploring geology and evolution. Belmont, CA:
Brooks/Cole.
• Slate. (n.d.). Retrieved from https://flexiblelearning.auckland.ac.nz/rocks_minerals/rocks/slate.html
• Paratley, R. (n.d.). Economic Botany & Cultural History: Sycamore. Retrieved June 14, 2018, from
https://ufi.ca.uky.edu/treetalk/ecobot-sycamore
• Small, D. (2013, August 21). California sycamore / Platanus racemosa. Retrieved June 16, 2018, from
https://deborahsmall.wordpress.com/2008/07/24/sycamore-plantanus-racemosa/
