Giovanna Noe-Wilson studied the diversity of benthic foraminifera in different elevations and seasons in Madison, Connecticut using microscopy and molecular techniques. She found that the dominant species, Arnoldiellina fluorescens, was highly abundant across most sites and seasons. Species diversity varied between sites but not clearly with elevation. Seasonality influenced species distribution and diversity. Combining morphological and molecular identification provided a better understanding of foraminiferal communities and will serve as a baseline for future climate impact studies.
Magpali et al (2020) Adaptive evolution of hearing genes in echolocating dolp...Letícia Magpali
Candidate poster for presentation at the I Meeting of Systematics, Biogeography and Evolution (SBE), in the category Phylogenomics and molecular evolution.
Magpali, L.; Freitas, L.; Ramos, E. K. S.; de Souza, E. M. S.; Nery, M. F.
University of Campinas / Biology Institute, Brazil
Seminar abstract: I will be talking about two ongoing research projects in my laboratory: (1) evolution of thermal niches in seaweeds, (2) biodiversity of endolithic algae in coral skeletons and its relationship with the environment. Using evolutionary models in an explicit phylogenetic framework, patterns of evolution in environmental traits such as the sea surface temperature (SST) affinities of species can be studied. Based on case studies in the green algae Codium and Halimeda, it is shown that lineages behave differently when it comes to their evolution of SST affinities, and that there is a strong correlation between the evolution of SST affinities and rates of species diversification. For the second part of the talk, I will focus on our recent work on environmental sequencing of coral skeletons. These feature unexpectedly high biodiversity of limestone-boring algae as well as many unknown inhabitants. Our first results indicate that the diversity of algal endoliths may be linked to environmental conditions, but this hypothesis needs further testing.
Is Dormancy an Indicator of Ecotypic Variation?CWRofUS
Miller A, Sosa C, Khoury CK, Greene S. (2016). Is Dormancy an Indicator of Ecotypic Variation?” Poster for Southern Rockies Seed Network 2016 Conference, 7 December 2016, Loveland, Colorado, USA.
Presentation by Dr. Jonathan J. Cole, Cary Institute of Ecosystem Studies
Starting in its earliest development, limnology has tended to view lakes as rather isolated from their terrestrial watersheds. This view of lakes as microcosms (Forbes 1887) proved useful in some ways, but it failed to help explain phenomena such as eutrophication which is driven by the external input of nutrients. While the study of limiting nutrients has fully embraced the watershed for decades, the study of C cycling in lakes has maintained a somewhat microcosm viewpoint. This is a viewpoint in which organic C is envisioned as being formed almost entirely by photosynthesis within the system (autochthonous sources); exogenous sources are largely ignored, downplayed, or assumed to be refractory. A number of disparate research threads in recent decades have completely overturned this view.
This slide lecture is for students seeking help regarding Metagenomics. Do remember me in your prayers.
Metagenomics Applications, Metagenomics working principles , Metagenomic libraries
, Metagenomic Techniques , Metagenomics limitations and other topics are elaborated in this Slideshare.
Magpali et al (2020) Adaptive evolution of hearing genes in echolocating dolp...Letícia Magpali
Candidate poster for presentation at the I Meeting of Systematics, Biogeography and Evolution (SBE), in the category Phylogenomics and molecular evolution.
Magpali, L.; Freitas, L.; Ramos, E. K. S.; de Souza, E. M. S.; Nery, M. F.
University of Campinas / Biology Institute, Brazil
Seminar abstract: I will be talking about two ongoing research projects in my laboratory: (1) evolution of thermal niches in seaweeds, (2) biodiversity of endolithic algae in coral skeletons and its relationship with the environment. Using evolutionary models in an explicit phylogenetic framework, patterns of evolution in environmental traits such as the sea surface temperature (SST) affinities of species can be studied. Based on case studies in the green algae Codium and Halimeda, it is shown that lineages behave differently when it comes to their evolution of SST affinities, and that there is a strong correlation between the evolution of SST affinities and rates of species diversification. For the second part of the talk, I will focus on our recent work on environmental sequencing of coral skeletons. These feature unexpectedly high biodiversity of limestone-boring algae as well as many unknown inhabitants. Our first results indicate that the diversity of algal endoliths may be linked to environmental conditions, but this hypothesis needs further testing.
Is Dormancy an Indicator of Ecotypic Variation?CWRofUS
Miller A, Sosa C, Khoury CK, Greene S. (2016). Is Dormancy an Indicator of Ecotypic Variation?” Poster for Southern Rockies Seed Network 2016 Conference, 7 December 2016, Loveland, Colorado, USA.
Presentation by Dr. Jonathan J. Cole, Cary Institute of Ecosystem Studies
Starting in its earliest development, limnology has tended to view lakes as rather isolated from their terrestrial watersheds. This view of lakes as microcosms (Forbes 1887) proved useful in some ways, but it failed to help explain phenomena such as eutrophication which is driven by the external input of nutrients. While the study of limiting nutrients has fully embraced the watershed for decades, the study of C cycling in lakes has maintained a somewhat microcosm viewpoint. This is a viewpoint in which organic C is envisioned as being formed almost entirely by photosynthesis within the system (autochthonous sources); exogenous sources are largely ignored, downplayed, or assumed to be refractory. A number of disparate research threads in recent decades have completely overturned this view.
This slide lecture is for students seeking help regarding Metagenomics. Do remember me in your prayers.
Metagenomics Applications, Metagenomics working principles , Metagenomic libraries
, Metagenomic Techniques , Metagenomics limitations and other topics are elaborated in this Slideshare.
APPLICATION OF DNA ANALYSIS APPROACH CONTRIBUTES TO THE IDENTIFICATION OF SEV...nguyenxuanhung16
DNA barcoding has been widely used to assess species diversity in a variety of ecosystems, including
temperate, subtropical, and tropical rain forests. However, due to the difficulties associated with field
exploration, most of the species in Truong Sa archipelago have never been barcoded. The purpose of this study
is to barcode five species of plants from the Truong Sa archipelago and to provide valuable evolutionary
information that will aid in future understanding of the plant community assembly on those particular islands.
Using DNA markers (ITS-rDNA), this study created a DNA barcode database for five plant species found on
the Truong Sa archipelago. We used the sequence similarity and a phylogenetic based method to the identify 15
samples from five plant species collected in Truong Sa archipelago, Vietnam. Results showed that the PCR
success rate for ITS-rDNA region was 100%. The success rate of bidirectional sequencing of PCR product was
100% for 650 bp long the ITS-rDNA region fragment. Phylogenetic analyses using maximum likelihood (ML)
indicated that five plant species (PB, BT, BV, NH and TR) had a close relationship with T. argentea, S.
taccada, B. asiatica, M. citrifolia, M. citrifolia and C. uvifera, respectively. The current study provided further
evidence for ITS-rDNA region as a useful molecular marker for species identification found on other tropical
coral islands
The presentation of the CESAB group gaspar at the 2016 french ecology conference in the FRB-CESAB session "Using a treasury of knowledge to tackle complex ecological questions." Presenter: Michel Kulbicki
A Rapid marine biodiversity assessment of the coral reefs in morales Beach, B...Innspub Net
Morales beach is one of the beaches located in the coastal town of Glan, Sarangani Province and noted for its quite enormous coral reef which is continuously degrading. This study was conducted to assess the health status of coral reef ecosystem and to evaluate the physico-chemical parameters of the area. Point Intercept Transect (PIT) method was used to monitor live coral condition and the supporting fauna at a coral reef ecosystem. Physico-chemical parameters were obtained in situ using a thermometer, refractometer, and a pH meter. The result of the study showed a very low percentage cover of hard corals, no cover percentage of soft corals and high cover percentage of other biota or substrate. The reef areas exhibited poor coral cover with an average of 15 percent live hard corals having family Acropora as the most dominant species (Shannon diversity index of 1.653). Water samples obtained were within the DENR (1990) standards suitable for the optimum growth of coral reefs. The health status of the coral reefs in Morales beach showed a partially disturbed reef due to human intervention. It is greatly recommended to constantly monitor the coral conditions in order to effectively manage and protect the increasing number of Marine Protected Areas (MPA).
(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.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
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.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
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.
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.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
1. Community diversity of
foraminifera over time,
space, and in response
to temperature
Giovanna Noe-Wilson
Undergraduate in Biology and Marine Science at Smith College
2. Hypothesis: the biodiversity of living benthic
foraminifera varies spatially (i.e. elevation) and
over time (e.g. seasonally)
5. Foraminifera are:
● Protists: single celled eukaryotes
● That have shells or tests
○ made up of calcium carbonate
(CaCO3)
● Have pseudopods
○ Arm-like projection that allows
GNW
6. My study organisms: Foraminifera
● Protists: single celled eukaryotes
● That have shells or tests
● Have pseudopods
Two main types of foraminifera:
● Planktic - mainly living in the upper water
column
● Benthic - mainly living bottom/within
sediment
They are among the most abundant shelled
organisms in marine environments
GNW
7. Molecular Perspective - importance
● Taxonomy and biodiversity of benthic foraminifera is frequently studied
● Most taxonomy is still based on morphology (physical features)
This can lead to:
● “Lumping” or “splitting” - process that results in merging of species that have
similar physical features
Problem:
Can harm and under score species diversity when studying ecological research or
when creating environmental reconstructions (where biodiversity and identification is
critical
Morphological perspective can:
Help strengthen identification of species as well as identification of new or cryptic
species
8. Methods: microscopy (some examples)
(GNW)
These three images are all benthic foraminifera - two are the same species!
Identification through morphological (physical) features:
○ can lead to errors in species taxonomy and identification
○ Can miss cryptic species
9. subtidal
tidal mudflat
low marsh
mid-marsh
High marsh
upper border & upland
(above the tidal zone)
Methods: field work
● Soil samples taken at
different months (during
low tide) in the same
location using GPS
● Only the top 1 cm of soil
was taken from the
different locations and
filtered on site. They
were placed in lysis
buffer for preservation
● Locations were chosen
based on differences in
soil/mud composition
ranging from silt to sand
● Higher elevations were
mainly dry and also
contained vegetation
● Water and air
temperature were also
taken
11. Methods: molecular work (HTS analyses of
amplicons)
Filtration
Used 100 µm
filter to filter out
large
particulates
They were then
placed in -80 ℃
freezer to help
lysis open cells
DNA/RNA
Extraction
using zymo kit
PCR amplification
with 18F and 19R
Primers
Miseq
sequencing
Assembly &
data
analysis
12. Methods: Foram-specific primers
Polymerase chain reaction (PCR) amplification - allows for amplification of specific regions of either
DNA or RNA in a specific sample
Foram specific primers (18F/19R) are used because they amplify regions that are only specific to
foraminifera and no other species in the samples
13. Methods: Foram-specific primers
● Line represents the small subunit
Ribosomal DNA
● Dark green - common to all
Eukaryotes
● Light green - inserts only found in
foraminifera
18F/19R amplify regions (shown in light
green) that are unique only to
foraminifera
14. Methods: PCR using foram primers
DNAs RNAs
● Multiple bands shown here are not errors
○ Represent different foram species
○ Showing diversity in those light green regions (shown on previous slide)
15. Elevation
● Use of LiDAR (light
detection & ranging) data
gives accurate elevation of
each site
● Accuracy led to the
discovery that all sites are
not created equal
○ Farther up tidal mudflat ≠
increase in elevation
Site 1
Map by: GNW
Site 2
16. My focus = abundant species (>100 reads)
● Smaller read numbers were not considered
○ Fewer read counts could mean transcriptional noise making it difficult to know the difference
between actual presence or instances of gene expression or randomly present gene
expression due to sequencing errors
17. Species and elevation
● No clear pattern in
the number of
species
○ Less species in
lower
elevations?
● Roughly each site
had 6 - 18 species
● The ratio of “not
active” (DNA) to
“active” (RNA)
varied between
sites
Elevation at each site
Numberofspecies
Tidal mudflat Mid-marsh High Marsh Upper marsh DNA
RNA
18. Presence/absence of species
● Compared the top 15 OTUs (OTU - my proxy for species)
First present (DNA) then active (RNA)
Black = absent (no species found or species containing less than 100 reads)
Grey = 1000 - 100 reads
White = over 1000 reads
Note:
DNA: present - species can be present in a location or
sample however, they might be dormant
RNA: active - species are active (during the time of
collection)
19. Presence absence of species - DNA
Top species:
Arnoldiellina fluorescens
Highly abundant and
found in all the locations
Trochammina sp.
Highly abundant in only
one location
20. Presence absence of species - RNA
RNA has similar trends
as DNA
Arnoldiellina fluorescens
is active mostly
everywhere all the time
Trochammina sp.
even though highly
abundant in a specific
location is not also highly
active in the same
location
21. Rank Abundance Curves
● Portray relative
abundance and
species diversity
within a
community Shows higher species
richness and higher
species evenness
Note: A lower slope
shows greater species
richness and species
evenness (shown in
red)
22. Rank Abundance of DNA
● Similar curves indicate
similar dominant trends
● Hyperdiverse sites!
● Results show
similarities in
community dynamics
by season
23. Rank abundance curve for RNA
● Rank abundance curve
shows similar curves,
indicating similar
dominance trends
● Much less variance than
DNA
24. Conclusions
● Environmental conditions play a crucial role in foraminiferal
assemblages in salt marshes of Madison, CT
● Most sites were dominated by a monothalamous species,
Arnoldiellina fluorescens
● Seasonality is an important variable that control species
distribution
○ Also affects species diversity
● Having accurate GPS locations along with species
identification help aid in future research
25. Future Work
● Onsite elevational data should be collected to assess
elevational changes at each location and with better
accuracy
● Time, space, and other variants need to be compared to
better assess differences among foraminiferal assemblages
○ Examples: salinity, sediment characteristics, temperature,
etc.
26. Take away:
Identifying spatial variation of benthic forams using
a combination of morphological & molecular data
will provide a critical baseline for studies tracking
impacts of changing climates
28. Key Literature
Burki, F., Keeling, P. J. Rhizaria. Current Biol. 24(3): R103-R107.
Cunha, Camila., Kukimodo, Isabela., Semensattoo, Decio., Foraminiferal assemblages along the intertidal zone of Itapanhau
River, Bertigoa (Brazil). South American Earth Sci. (2017)
Katz, Laura., Grattepanche, Jean., Walker, Laura M., Ott, Brittany M., Pinto, Paim., Delwiche, Charles F., Lane Christopher E.,
Microbial diversity in Eukaryotes SAR clade: Illuminating the Darkness Between Morphology and Molecular Data
BioEssays.(2018) 40, 1700198
Milker, Yvonne., Horton, Benjamin P., Nelson, Alan R., Engelhart, Simon E., Witter, Robert C., Variability of intertidal foraminiferal
assemblages in a salt marsh. Marine Micropaleontology. (2015)
Pawlowski, Jan., Holzmann, Maria., Diversity & geographic distribution of benthic foraminifera: a molecular perspective. Biodivers
Conserv (2007) 17:317-328
Nettersheim, Benjamin J., Putative Sponge Biomarkers in unicellular Rhizaria question early rise of animals. Nature Ecology &
Evolution (2019)
Prazeres, Martina., R, T.,Variation in sensitivity of large benthic Forams to the combined effects of ocean warming and local
impacts. Sci Report (2017)
T. Cavalier‐Smith, Int. J. Syst. Evol. Microbiol. 2002, 52, 297.
Photo O. opaca source: https://www.flickr.com/photos/32133972@N05/
Photo Trochammina source - http://www.marinespecies.org/aphia.php?p=taxdetails&id=114348
Editor's Notes
They can be effectively used for monitoring coastal environments (5) tracking sea-level changes 6 and be important bio-indicators of pollution like that of heavy metal. 7
Benthic are paeffectively rticularly important as they comprise 90% of deep sea biomass (source 4)
They can be used for monitoring coastal environments (5) tracking sea-level changes 6 and be important bio-indicators of pollution like that of heavy metal. 7
They live in lots of environments
Image: Giovanna Noe-Wilson - hand drawn
They have been broken down into these two types ones in the water column and and the benthics which is what I am studying
With the continuous stressors on marine and coastal habitats, taxonomy and biodiversity of benthic foraminifera is frequently studied; however, even with the increase in research done on these eukaryotes, they are still understudied (Grattepanche et al., 2018, Pawlowski & Holzmann, 2007). Most taxonomy has been, and is still, based largely on morphology classification (Grattepanche et al., 2018). The primary problem with this taxonomic approach is that it can lead to incorrect and inconsistent identification of species (Roberts et al., 2016, Saad & Wade, 2016, Pawlowski & Holzmann, 2007). Which then leads to “lumping” or “splitting,” a process that often results in a merging of species based on similar physical features; which then incorrectly groups species together. This causes erroneous foraminifera taxa or assemblages and inconsistent distribution patterns (Roberts et al., 2016, Saad & Wade, 2016 Pawlowski & Holzmann, 2007). This is extremely problematic when it comes to studying ecological research or creating environmental reconstructions where biodiversity and identification is critical (Roberts et al., 2016, Pawlowski & Holzmann, 2007)
Recently, taxonomic identification has moved away from relying solely on morphological features and focusing more heavily on a combination of morphological and molecular techniques (Grattepanche et al., 2018, Roberts et al., 2016, Pawlowski & Holzmann, 2007). Much of the molecular data has helped in the identification of new species as well as in identifying cryptic species (Roberts et al., 2016, Pawlowski & Holzmann, 2007). Molecular data enhances our understanding of the diversity of foraminifera and demonstrates the need for continued research. Recent studies which focus on bridging the gap between molecular and morphological data offer new perspectives on foraminiferal species and improved taxonomic stability (Roberts et al., 2016).
Photos taken by:
Figure 1: Rabindra
Figure 2: Elly Goetz
If you look in a microscope at these three you wouldn’t be able to differentiate or identify what species they are
They are all “snail-like” multichambered forams but this one is a genetic species
Collection location and pictures
Pictures: taken by Giovanna Noe-Wilson (using fulcrum)
Drawing hand drawn by Giovanna Noe-Wilson
Fulcrum - map!
Created by GNW
Really don’t understand the methods that much - why do we do these steps? - molecular
Kit helps amplify
The key thing is that I use foram specific primers and what means is that these primers - which means they only amplify the forams in my samples no other organisms
And the reason why I know why these are so specific is
They are amplifying the regions in light green that are unique to forams
On this green line represents the the small subunit Ribosomal DNA gene and the dark green is what all eukaryotes have and only forams have these inserts (light green)
My primers amplify two of these inserts that are unique to forams
This is a gel these are ladders for size
Here you can see bands - some or many contain multiple bands - these are not error they represent different foram species
Biologically this can come off as error but really the diversity in those light green regions
Photos provided by Laura Katz
Light Detection and Ranging—is a remote sensing method used to examine the surface of the Earth
My focus is abundant species which was species larger than 100 reads
Such few reads usually represent transcriptional noise. With so few reads it is difficult to ascertain whether these are truly actual instances of expression or randomly present due to sequencing errors. This can easily be ascertained by having multiple replicates of the same sample. If these reads are present in one, but not in other replicates then they most probably are transcriptional noise. We used this approach to ask the same question of small RNA expression library. To answer this question we used K-S statistics applied to frequency distribution plots of replicates. The rationale here was that the cut off should be the lowest number of reads where the distance between the two frequency distribution plots of replicates should be minimized. This was a valid assumption, since if the replicates were exactly the same the frequency distribution curves would overlap and the distance would be zero. Thus we defined noise as the minimum number of reads that prevents frequency distribution curves of replicates being close to each other. I am attaching the paper that describes this in more detail.
These are the actual elevations because the elevations I calculated here in the SAL lab but when we sampled we were not exact so we are in the same ecology not the same altitude
Teach the axises - that is the estimated number of species which I estimated from my molecular data
And these are my four different locations I intended to to go back but as you can see the actual altitude really varied when we did go back
3 conclusions:
1) roughly each site had 6-18 species
2) the ratio of active to quesent species varied by different sites - here we can see a site with many more active species that quesent species and here its the other way
3) there isn't a clear pattern in the number of species except for that there seems to be not many species in the lowest altitude
There is not a clear trend along the altitude???
Closely related
These are 15 of the top species found at all the locations
Here when I think about presence absence of DNA here are the top 15 species of forams
Here is the top species and it is present everywhere and all the time
There is ovammina opaca which is super abundant sometimes but not other times
And then there is other guys that
Trochammina sp - which is highly abundant at one time and place.
Photo O. opaca source: https://www.flickr.com/photos/32133972@N05/
Photo Trochammina source - http://www.marinespecies.org/aphia.php?p=taxdetails&id=114348
When we look at the RNA we can see similar trends
Arnoldiellina is still everywhere all the time
Ovammina Opaca is more patchy so it present everywhere but not active all the time
And trohcammina even though highly abundant in that specific location it is not highly active in that location
Rank Abundance curve for all DNA collection sites shows similarities in community dynamics by season. Collection sites within the season have similar curves, indicating similar dominant trends.
Talk about what a rank abundance curve is
Which plots relative abundance of species against rank in abundance
A lower slope shows greater richness and species evenness
Communities are really different
Divide into two different colors - later
I found two different kinds of communities - these a had all roughly 30 species and similar distributions and these three had 30 -50 species - what this is telling us these guys have fewer abundances and many intermediate species (june)
These are march and May and these are June
Which have the species abundance
I don’t see the same distinct patterns and trends I do for DNA
Most sites were dominated by related to a monothalamous species, Arnoldiellina fluorescens (OTU1)
In general diversity (evenness) and species richness decrease both in elevation and distance. Higher elevation along with increasing from the intertidal zone tend to have the most effect on lowering species diversity. I conclude that elevation and climate (maybe salinity ? only tested the water not the salinity of samples) are important variables controlling species distribution (which can be seen and compared with in other papers)
Environmental conditions play a crucial role in foraminiferal assemblages in Madison CT
With my research I have found a large amount of heterogeneity and so we need to look at time and space
Figure 6. Benthic foraminiferal species distribution changes with increasing water depth and distance from the shore. It is not depth per se that is the controlling factor. Availability of food (flux of organic matter out of the surface ocean) and dissolved oxygen are probably the two most important influences on benthic foraminiferal abundance and species distributions. Other factors include sunlight, substrate, temperature, and pH. From Leckie and Olson, 2003; In, Olson and Leckie, eds., Micropaleontologic Proxies for Sea-Level Change and Stratigraphic Discontinuities, SEPM Special Publication 75: 5-19.
