1) Simpson's reciprocal index can be used to calculate biodiversity by taking into account both the richness and evenness of species in an ecosystem.
2) Comparing two samples with equal numbers of organisms but different distributions, Sample B was found to have slightly higher biodiversity according to the Simpson's index calculation.
3) Edge effects can impact biodiversity in forests. Abundance and richness are highest at forest edges but decrease further into the forest interior, possibly due to differences in environmental conditions.
Why and how do we evaluate ecosystems, Nature is the source of much value to us every day, and yet it mostly bypasses markets, escapes pricing and defies valuation. This lack of valuation is an underlying cause for ecological degradation and loss of biodiversity. Globally, efforts are being made to assess impact of conservation or degradation of ecological resources and a new term Green Gross Domestic Product (GGDP) has also been coined to reflect the same.
Lecture about Monitoring and Biodiversity Indices, with linkage to on-going CBD programs, and a special focus on species monitoring.Many examples, needs some formatting, hope still useful!
This slideshow was created for the VCE Environmental Science Online Course, Unit 3: Biodiversity. It explains different methods of assessing biodiversity and discusses several indices for measurement.
This Presentation Contains:
Defintion of Biodiversity
Importance
Factors Militating Against Biodiversity
Why we should conserve Biodiversity
and
How to improve Biodiversity Conservation
8.wild life and impacts of climate change on wildlifeMr.Allah Dad Khan
A series of Presentation ByMr Allah Dad Khan Special Consultant NRM , Former DG Agriculture Extension KPK Province , Visiting Professor the University of Agriculture Peshawar Pakistan allahdad52@gmail.com
Why and how do we evaluate ecosystems, Nature is the source of much value to us every day, and yet it mostly bypasses markets, escapes pricing and defies valuation. This lack of valuation is an underlying cause for ecological degradation and loss of biodiversity. Globally, efforts are being made to assess impact of conservation or degradation of ecological resources and a new term Green Gross Domestic Product (GGDP) has also been coined to reflect the same.
Lecture about Monitoring and Biodiversity Indices, with linkage to on-going CBD programs, and a special focus on species monitoring.Many examples, needs some formatting, hope still useful!
This slideshow was created for the VCE Environmental Science Online Course, Unit 3: Biodiversity. It explains different methods of assessing biodiversity and discusses several indices for measurement.
This Presentation Contains:
Defintion of Biodiversity
Importance
Factors Militating Against Biodiversity
Why we should conserve Biodiversity
and
How to improve Biodiversity Conservation
8.wild life and impacts of climate change on wildlifeMr.Allah Dad Khan
A series of Presentation ByMr Allah Dad Khan Special Consultant NRM , Former DG Agriculture Extension KPK Province , Visiting Professor the University of Agriculture Peshawar Pakistan allahdad52@gmail.com
Wildlife management techniques and methods of wildlife conservationAnish Gawande
Wildlife Conservation is the practice of protecting wild plant and animal species and their habitat. Wildlife plays an important role in balancing the environment and provides stability to different natural processes of nature. The goal of wildlife conservation is to ensure that nature will be around for future generations to enjoy and also to recognize the importance of wildlife and wilderness for humans and other species alike. Many nations have government agencies and NGO's dedicated to wildlife conservation, which help to implement policies designed to protect wildlife. Numerous independent non-profit organizations also promote various wildlife conservation causes.
Wildlife conservation has become an increasingly important practice due to the negative effects of human activity on wildlife. An endangered species is defined as a population of a living species that is in the danger of becoming extinct because the species has a very low or falling population, or because they are threatened by the varying environmental or prepositional parameters.
General Botany Group four presentation.
This presentation focus on so many biological related topics. It primarily focus on conservation of life in any biodiversity.
Wildlife management techniques and methods of wildlife conservationAnish Gawande
Wildlife Conservation is the practice of protecting wild plant and animal species and their habitat. Wildlife plays an important role in balancing the environment and provides stability to different natural processes of nature. The goal of wildlife conservation is to ensure that nature will be around for future generations to enjoy and also to recognize the importance of wildlife and wilderness for humans and other species alike. Many nations have government agencies and NGO's dedicated to wildlife conservation, which help to implement policies designed to protect wildlife. Numerous independent non-profit organizations also promote various wildlife conservation causes.
Wildlife conservation has become an increasingly important practice due to the negative effects of human activity on wildlife. An endangered species is defined as a population of a living species that is in the danger of becoming extinct because the species has a very low or falling population, or because they are threatened by the varying environmental or prepositional parameters.
General Botany Group four presentation.
This presentation focus on so many biological related topics. It primarily focus on conservation of life in any biodiversity.
Lecture note on Biodiversity conservationTalemos Seta
Describes about the concept, scope, definition of Biodiversity, threats of biodiversity, centre of Origin/diversity, Biodiversity hotspots, strartegies of BD conservation
Cobb, Seltmann, Franz. 2014. The Current State of Arthropod Biodiversity Data...taxonbytes
Cobb et al. 2014. The Current State of Arthropod Biodiversity Data: Addressing Impacts of Global Change. Presented at https://www.idigbio.org/content/collections-21st-century-symposium Program available at https://www.idigbio.org/wiki/index.php/Collections_for_the_21st_Century
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.
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.
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 .
2. Understandings Applications/Skills
An indicator species is an
organism used to assess a
specific environmental
condition.
Relative numbers of
indicator species can be
used to calculate the value
of a biotic index.
In situ conservation may
require active management
of nature reserves or
national parks.
Ex situ conservation is the
preservation of species
outside their natural
habitats.
Biogeographical factors
A: Case study of the
captive breeding and
reintroduction of an
endangered animal
species.
A: Analysis of the impact
of biogeographic factors
on diversity limited to
island size and edge
effects.
S: Analysis of the
biodiversity of two local
communities using
Simpson’s reciprocal
index of diversity.
Guidance: Simpson’s
5. Evenness vs Richness
- Both are a way to measure biological diversity
- Richness: number of different types of organisms
- Evenness: how the quantity of each organism compares to
More
species
therefore
highest
richness
Greatest
eveness as the
two populations
have similar
abundance.
http://www.nature.com/nature/journal/v405/n6783/images/405212aa.2.jpg
An ecosystem is not considered diverse if it is dominated by o
6. Simpson’s reciprocal index can be used to calculate
biodiversity.
D =
N (N - 1)
Σ n (n - 1)
Simpson’s
Reciprocal Index
total of organisms of all species
number of organisms of a
single species
the sum of (all
species)
• It takes into account both richness and evenness
• The greater the biodiversity the higher the value of D
• The lowest possible defined value of D is 1 (only one
species found)
• The maximum value is equal to the number of species
found, this only occurs if all species are equally abundant.
7. Compare the biodiversity of the two
samples:
http://www.nature.com/nature/journal/v405/n6783/images/405212aa.2.jpg
Species
*
Count
A 6
B 1
C 1
Total 8
*correct names not required
Species
*
Count
A 4
B 4
Total 8
8. D =
N (N - 1)
Σ n (n - 1)
Simpson’s Reciprocal Index
total of organisms of all species
number of
organisms of a
single species
the sum of
(all
species)
Species* Count
A 6
B 1
C 1
Total 8
Sample A
D =
8 (8 - 1)
6 (6 - 1) + 1 (1 - 1) + 1 (1 - 1)
D = 1.87
56
30 + 0 + 0
=
9. D =
N (N - 1)
Σ n (n - 1)
Simpson’s Reciprocal Index
total of organisms of all species
number of
organisms of a
single species
the sum of
(all
species)
Species* Count
A 4
B 4
Total 8
Sample B
D =
8 (8 - 1)
4 (4 - 1) + 4 (4 – 1)
D = 2.33
56
12 + 12
=
Sample B has slighter higher
biodiversity
10.
11.
12.
13. General Principles of Nature Reserves (exceptions may exist depending on
composition of local wildlife)
14.
15. Impact of the edge effect on biodiversity
1. Describe the relationship shown in the
abundance graph.
1. Deduce the edge effect upon
biodiversity in Araucaria forests.
2. Suggest a reason why both
abundance and richness is greatest at
the forest edge.
3. Suggest a reason why abundance and
richness decrease after 100 m from the
forest edge.
The graphs show changes in plant community
diversity and composition across an edge
between Araucaria forest and pasture in South
Brazil
http://www.scielo.br/scielo.php?pid=S0100-84042006000100008&script=sci_arttext
16.
17. Captive breeding
- Artificial insemination
- Embryo transfer to a surrogate mother
- Cryogenics
- Human raised young
- Keeping a pedigree
Methods
Drawbacks
- Reintroduction into the wild can spread disease
- Captive species at a disadvantage due to inexperience
18. Threats during the 1900s:
• Hunting/predator control programs
(deemed to be a pest) why?
• Destruction / alteration of habitat
U.S. Fish and Wildlife
Service initiated a
captive breeding
program enabled the
species to be
reintroduced.
The Mexican Gray Wolf
What were some of the effects of the reduction of the wolf population?
http://ultraculture.org/wp-content/uploads/2013/01/wolves1.jpg
19. Biogreographical Factors
Three factors
- Latitude gradient: the farther away from the equator, the fewer
the species
- Elevation gradient: species richness increases as you travel up
in altitude until a certain point (mid-point bulge); then it
decreases again
- Area effect: the larger the area, the more species it can support
- “island”- any very isolated area; not necessarily a literal
island
20. Impact of island size on biodiversity
http://upload.wikimedia.org/wikipedia/commons/thumb/1/13/Area_species_curve_herp
etofauna.svg/2000px-Area_species_curve_herpetofauna.svg.png
1. Describe the
relationship shown
in the graph.
1. Estimate the
number of reptile
and amphibian
species likely to be
found on an island
of 1,000 km2
Total number of reptilian and amphibian species on
seven small and large islands in the West Indies
21. Homework
Vocab
Indicator species,
biotic index, biological
diversity, evenness,
richness, restoration,
in situ conservation,
ex situ conservation,
latitude gradient,
elevation gradient,
area effect, island,
edge effect
Pg 693- challenge
yourself 27,28
Pg 694- challenge
yourself 29
Pg 695- challenge
yourself 30-32;
Exercises 10-12
