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Biodiversity is a critical aspect of healthy ecosystems.

Biodiversity is a critical aspect of healthy ecosystems. This should not surprise you, since foodwebs are so interconnected, and diversity brings a sort of built in resilience to any ecosystem. However, because energy is limited, any habitat or ecosystem can only support a limited number of organisms. In any habitat or ecosystem, you can have one of two extremes on a continuum. Either there are many individuals of one species present (abundance) or there are some individuals of many species present (biodiversity). Usually, it falls somewhere in between.

One fairly constant variable is the degree of human intervention. Areas influenced and controlled by humans tend to be lower in biodiversity than natural areas. To illustrate this, you are going to do a simple ecological comparison between a natural area and a man-made area. The natural space can be anything, as long as it is not regularly mowed, watered, or managed by humans. An abandoned field will do, or a riverbank that looks “wild.” If you are unsure, check with your instructor. The manmade area can be your front lawn, a golf course, etc.

Choose your habitats, then describe them below. Include photos.

Natural Habitat:

Managed Habitat:

Area delineation: You will need to determine how you are going to define your study areas. This is important so that you can make sure that you don’t examine a larger area in one place and therefore skew one of your variables. One easy way is to take a metal coat hanger and stretch it out into a circle. Then, lay that down in each area and count the organisms you find just within that circle. Anything will work, as long as it will allow you to ensure equal study areas in each space. When you get to your area, toss the hoop or whatever your measuring device is and study the area it lands on. This will help ensure that you aren’t selecting areas more or less diverse and thus introducing an element of bias into your study.

Describe your method of measuring study space.

Calculate the study area (If using a circle, the formula for area is Πr2)

Species Tally: You will not be expected to identify species, however you can differentiate between different species just by looking at them. For instance, you may see three different types of grass. While you may not know their names, you know that one has broader leaves, one has hairier leaves, and the other has thinner spikey leaves. As you go through your study area, Fill in the table with descriptions so that you can keep your species separate in your mind. You should add more rows as necessary to each table!

**Be sure to provide data information from your worksheet on the Q&A Forum**

Natural Habitat: Species

Species # Description

Man-Made Habitat: Species

Species # Description

Individuals Tally

Natural Habitat: Species Individuals

Species # Tallies of individuals Total

B. Man-Made Habitat: Species Individuals

Species # Tallies of individuals Total

Compare and Contrast: Complete the table.

Study Area Name/Description Total # of Species Total # of Individuals

Natural Man-Made

Compare and Contrast: Write a paragraph that THOROUGHLY describes your results. Include answers to the following questions:

Which area had the greatest biodiversity? Explain.

Which area had the highest abundance of organisms? Explain.

What factors do you think lead to these differences?

Were any species found in both areas? Why do you think that is?

If the man-made area you study was to be abandoned and allowed to develop on its own, what do you think it would look like in time? Why?

Which area do you think is the most sustainable? Why?

What overall effect on biodiversity does human intervention seem to have?

A Reflection on Design and How it Promotes Inclusion and Care in the City

A Reflection on Design and How it Promotes Inclusion and Care in the City

Introduction

Buildings and urban spaces derive their quality from fulfilling peoples’ needs and demands. The design and placement of people’s homes have a significant impact on their overall quality of life and happiness. Design, planning, and management decisions have the potential to either boost or lessen people’s sense of belonging, especially in urban dwellings (Persson, Åhman, Yngling, and Gulliksen, 2015). Cities have a way of creating a sense of belonging for everyone. Designs are a two-sided sword with the ability to improve or hinder someone’s well-being include enhancing or decreasing feelings of safety and security, increasing and restricting boundaries, promoting and restricting movement, and many other things. Through the development of empathy and a giving perspective, they may be able to assist communities in overcoming actual and imagined problems.

Inclusion and Care Using Design

The purpose of inclusive design is to remove the roadblocks that create excessive effort and social isolation in people with disabilities. It gives everyone the ability to participate in everyday activities in an equitable, confident, and autonomous manner. Uncovering new views on how people interact with the built environment is made possible through a more inclusive design approach. According to Mahadevia and Lathia (2019), this opens up new avenues for putting one’s creative and problem-solving talents to good use, as well. Even after a decade of advances in accessibility, planning, and infrastructure investment, those living in poverty and other disadvantaged circumstances are still far more likely to live in substandard conditions. Planning and design must take into consideration the social, cultural, and economic inequities that are being incorporated into new developments and neighborhoods.

A collaborative effort between facilities managers, surveyors, building control surveyors, architects, planners, engineers, and access specialists is necessary to establish an inclusive workplace. Persson et al. (2015) add that the responsibility for creating an inclusive environment ultimately falls on the shoulders of developers, landlords, and service providers. Urban properties must be built, constructed, and operated in line with inclusive principles, or the owners and other shareholding agents are exposed to legal consequences. On a daily basis, these stakeholders should make it a point to comply with accessibility regulations. Human imaginations and lateral thinking should be put to use in order to come up with distinctive and imaginative solutions for real people in all their varieties, ensuring equitable access in design.

The potential of a design to generate an inclusive environment must always be considered while evaluating it. Douglas, Lennon, and Scott (2017) found that a design that does not do this is not acceptable. A good design should reflect the diversity of the people who use it rather than imposing any restrictions on a section of users. The fact that the physical environment is created and managed in an inclusive manner causes aggravation and difficulty for a large number of individuals, including disabled people, the elderly, and families with small children. When a facility is designed with inclusivity in mind, it benefits everyone who uses it.

When a single design solution is incapable of meeting the needs of all users, inclusive design steps in. An inclusive workplace does not attempt to meet every individual’s demands (Hollands, 2008), rather it does it best to ensure that overall wellbeing of all users is maintained. For example, taking into account people’s diversity, on the other hand, may help break down barriers and exclusion, and it typically results in more comprehensive solutions that benefit everyone. While handicapped people are not all alike, including their needs in the design process ensures that everyone benefits. A design embraces everyone on an equal footing by adhering to the same high design standards for all users’ access requirements (Rahim et al., 2014). Users should be motivated by an environment that goes beyond the bare necessities of technology.

The application of inclusive design results in increased flexibility. Adhering to inclusive design principles requires an understanding of how and by whom the building or space will be used (Lemaire and Kerr, 2017). Places must be built in such a manner that they can adapt to changing requirements and usage. Accessible buildings and environments are more convenient and joyful to use for everyone. For example, signage, visible lighting, visual contrast, and materials all contribute to making environments accessible to all. Building accessibility encompasses more than its architectural layout. Additionally, Mahadevia and Lathia (2019) observe that it requires individuals to possess sufficient knowledge, often prior to leave their house, in order to feel secure entering a facility or site. When guaranteeing this ‘intellectual’ and ’emotional’ access, signage, lighting, visual contrast, and materials must all be addressed. It is crucial to begin the design process by examining the transportation patterns to and within a development. Roads, parking lots, walkways, entrances to buildings, and other paths should all be considered. It is vital for visitors to be able to utilize all components of the site, including the interiors of buildings.

Care and Inclusion in City Designs: A Case of Improving Quality of Life

Perhaps, if designers build the physical environments in a more egalitarian, inclusive and cohesive manner, our communities, services, and gathering spaces will all contribute to a more equal, inclusive, and cohesive society as a result of our efforts. People’s reactions to the built environment are influenced by social, cultural, and economic variables (Rahim et al., 2014). In order for users to feel comfortable in any particular place or setting, the entire breadth of their experience must be taken into consideration.

Many cities continue to fail to take into consideration the special obstacles that persons with disabilities confront when designing their layouts and public spaces. People with disabilities will feel better integrated into society if cities are designed with their needs in mind when they are created. Anti-discrimination legislation will also have a positive impact on the housing rights of the disabled (Persson et al., 2015). By engaging more people with disabilities in the design process, designers may take into account the many different types of exclusion and barriers that people face on a daily basis. People should be able to use the spaces and structures that have been created via design and development to build strong, vibrant, and long-lasting communities. Good designs must make sure that as many people as possible are involved in the design process in order to accomplish this. The effect is that this inclusion will benefit everyone as well as increase the cohesiveness and enjoyment of society as a whole.

Good design can only be accomplished by building an environment that meets as many people’s requirements as is physically and technologically possible. It is likely that everyone, whether they are a traveler with heavy luggage, a parent with little children, an old person, or someone suffering from a medical condition, may have restricted movement at some point (Douglas et al., 2017). Identifying and addressing inclusion barriers as early as possible in the design process can help to ensure that outstanding design can overcome them. Inclusive design acknowledges and celebrates people’s differences rather than creating barriers between them. For example, Persson et al. (2015) reminds designers of a need to be considerate, ensuring to have an inclusive design for all stakeholders, something that can be achieved by using green and technologically-advanced designs. While understanding the needs of wheelchair users and individuals with mobility impairments is vital, it is also critical to understand the problems experienced by people with learning disabilities, mental illness, visual impairments, and hearing impairments.

Conclusion

The role of design is to improve the well-being of users of a facility. However, designs have the power to enhance or decrease feelings of safety and security, increase and restrict boundaries, and promote and restrict effective movement. The purpose of inclusive design is to remove the roadblocks that create excessive effort and social isolation in people with disabilities. The potential of a design to generate an inclusive environment must always be considered as an evaluation measure. Good design can only be accomplished by building an environment that meets as many people’s requirements as is physically and technologically possible through inclusion and equitable considerations.

Reference List

Douglas, O., Lennon, M. and Scott, M., 2017. Green space benefits for health and well-being: A life-course approach for urban planning, design and management. Cities, 66, pp.53-62.

Hollands, R.G., 2008. Will the real smart city please stand up? Intelligent, progressive or entrepreneurial?. City, 12(3), pp.303-320.

Lemaire, X. and Kerr, D., 2017. Inclusive Urban Planning–Promoting Equality and Inclusivity in Urban Planning Practices. https://www.researchgate.net/publication/351902692_Inclusive_Urban_Planning_-_Promoting_Equality_and_Inclusivity_in_Urban_Planning_Practices

Mahadevia, D. and Lathia, S., 2019. Women’s safety and public spaces: Lessons from the Sabarmati riverfront, India. Urban Planning, 4(2), pp.154-168.

Persson, H., Åhman, H., Yngling, A.A. and Gulliksen, J., 2015. Universal design, inclusive design, accessible design, design for all: different concepts—one goal? On the concept of accessibility—historical, methodological and philosophical aspects. Universal Access in the Information Society, 14(4), pp.505-526.

Rahim, A.A., Zen, I., Samad, N.A.A. and Rahim, C.R.C., 2014. Universal Design and Accessibility: Towards Sustainable Built Environment in Malaysia. Universal Design, pp.299-306.

BIO 332 BIOINFORMATICS

BIO 332 BIOINFORMATICS

EXERCISE 3: Retrieving and comparing amino acid sequences from different species

Name: ______________________________________

Abstract

Sequence alignment in bioinformatics is a method of arranging protein sequences to point out areas of similarity that may have resulted from functional, structural, and evolutionary relationships between several sequences. All mammals are related as they evolved from tiny creatures that were dominated by the dinosaurs but the degree of relation varies. Amino acid sequence data is used in science to infer the patterns of evolutionary relationships between species.

The methods used to infer the revolutionary relationship between Mnke whales Balaenoptera sp. Include the retrieval of amino acid sequences from GenBank (NCBI: National Center for Biotechnology Information). The amino acids sequences are then used in Multiple Sequence Alignment (MSA) to study the evolutionary relationship between sequences of three or more species and Pairwise Sequence Alignment to infer the evolutionary relationship of two protein sequences. The sequencing tool used is Tcoffee. This paper seeks to determine the level of truth in the statement multiple sequencing alignment indicate that Minke Whales are closely related to Perissodactyl through phylogenetic inference.

Introduction

Molecular evidence suggests that are closely related to hoofed mammals such as deer, cows, camels, hippos, giraffes and so forth. Today, whales alongside dolphins and porpoises make up the Cetacea group. Many features common in land mammals believe to be related to whales have changed through evolution. Although the many features of land mammals are not present in whales, their embryo grows hind limbs early on in their development but disappear as the development continues. The topic of which group is closely related to whales is still in contention but molecular biology points to the idea that artiodactyls are the closets to Cetaceans where whales belong. The hippo in this paper represents the artiodactyls. Determining the relationship between whales and Perissodactyl will require amino acid sequence alignment. A protein’s amino acid sequence is determined by the DNA sequence and so a gene shared by several closely related species should posses almost identical or just similar amino acid sequences. This is an indication that species that are found to be closely related through sequence alignment share the same ancestry and diverged from similar species or from one another fairly recently in the span of evolution. The evolutionary span is recent because the species have not had enough time to gather random mutations to their genetic codes.

Methods

The first step is retrieving the amino acid sequences of the animals under study including horse, hippopotamus, naked mole rat, minke whale, and kangaroo. The sequences were retrieved from National Center for Biotechnology Information under GenBank. The process included opening the NCBI website and typing the name of the species followed by the phrase pancreatic ribonuclease and selecting the most suitable query based on the optimum number of amino acids, roughly 150 residues. The FASTA format of the protein annotation was then copied into a sequence alignment tool by the name TCoffee. The first step was to identify regions of similarity between all the protein sequences using multiple sequence alignment. The next step was to align two protein sequences and infer the evolutionary relationships between two protein sequences.

Results

The amino-acid sequence Minke whale

Accession number

NCBI Reference Sequence: XP_007180555.1

Source Database

NCBI

>XP_007180555.1 ribonuclease pancreatic [Balaenoptera acutorostrata scammoni]

MAPKSLVLLPWLVLVLLVLGWVQPSLGRESPAMKFQRQHMDSGNSPGNNPNYCNQMMMRRKMTQGRCKPV

NTFVHESLEDVKAVCSQKNVLCKNGRTNCYESNSTMHITDCRQTGSSKYPNCAYKTSQKEKHIIVACEGD

PYVPVHFDNSV

The amino-acid sequence of kangaroo

Accession number

sp|P00686.1

Source Database

NCBI

>sp|P00686.1|RNAS1_MACRU RecName: Full=Ribonuclease pancreatic; AltName: Full=RNase 1; AltName: Full=RNase A

ETPAEKFQRQHMDTEHSTASSSNYCNLMMKARDMTSGRCKPLNTFIHEPKSVVDAVCHQENVTCKNGRTN

CYKSNSRLSITNCRQTGASKYPNCQYETSNLNKQIIVACEGQYVPVHFDAYV

The amino-acid sequence of Naked-mole rat

>EHB02901.1 Ribonuclease pancreatic [Heterocephalus glaber]

MAQKQSLVLFPLLILVLLGLVNTNYCNEMMKCRNMTERCCKLVNTFMHDPLADVQAVCFQKNVTCKNAQT

NFYQSSSNMHITGCRLTSNSKYPTCSYRTRQVERSITVACEGNPYVPGHFDALWSPPPQPEQRLISSLLR

ISTPAFPSLPPKK

The Amino-acid sequence of hippopotamus

Accession Number

>CAA06576.1

Source Database

>CAA06576.1 pancreatic ribonuclease, partial [Hippopotamus amphibius]

KETAAEKFQRQHMDTSSSLSNDSNYCNQMMVRRNMTKDRCKPVNTFVHESEADVKAVCSQKNVTCKNGQT

NCYESNSTMHITDCRETGSSKYPNCAYKTSQLQKHIIVACEGDPYV

The Amino-acid sequence of goat

Accession Number

XP_005685452.1’

Source Database

NCBI

XP_005685452.1 PREDICTED: ribonuclease K6 [Capra hircus]

MGPHLLGCSSLLLLLLGMWWSVCPLCAVPKGLTKARWFEIQHIQPRLLQCNTAMSGVNNYTRHCKPENTF

LHNFFQDVTAVCNLPNIICKNGRHNCHQSPKPVNLTQCNLIAGRYPDCRYHDDAQYKFFVVACDPPQKTD

PPYHLVPVHLDKVV

Figure 1. Result of multiple sequence alignment

CLUSTAL 2.1 Multiple Sequence Alignments

Sequence type explicitly set to Protein

Sequence format is Pearson

Sequence 1: XP_023477016.1 153 aaSequence 2: XP_007180555.1 151 aaSequence 3: sp|P00686.1|RNAS1_MACRU 122 aaSequence 4: EHB02901.1 153 aaStart of Pairwise alignments

Aligning…Sequences (1:2) Aligned. Score: 15.894

Sequences (1:3) Aligned. Score: 14.7541

Sequences (1:4) Aligned. Score: 13.0719

Sequences (2:3) Aligned. Score: 64.7541

Sequences (2:4) Aligned. Score: 47.6821

Sequences (3:4) Aligned. Score: 45.082

Guide tree file created: [clustalw.dnd]There are 3 groups

Start of Multiple Alignment

Aligning…Group 1: Sequences: 2 Score:1840

Group 2: Sequences: 3 Score:982

Group 3: Delayed

Alignment Score 1366

CLUSTAL-Alignment file created [clustalw.aln]

clustalw.aln

CLUSTAL 2.1 multiple sequence alignment

XP_007180555.1 MAPKSLVLLPWLVLVLLVLGWVQPSLGRESPAMKFQRQHMDSGNSPGNNP

sp|P00686.1|RNAS1_MACRU —————————-ETPAEKFQRQHMDTEHSTASSS

EHB02901.1 —————————MAQKQSLVLFPLLILVLLGLVNT

XP_023477016.1 -MAQAVAWLLFLQLVLEETQVVDSKLQIAIKNFRTLHIDYPMVNYPEGFQ

XP_007180555.1 NYCN–QMMMRRKMTQGRCKPVNTFVHESLEDVKAVCSQKNVLCKNGRTN

sp|P00686.1|RNAS1_MACRU NYCN–LMMKARDMTSGRCKPLNTFIHEPKSVVDAVCHQENVTCKNGRTN

EHB02901.1 NYCN–EMMKCRNMTERCCKLVNTFMHDPLADVQAVCFQKNVTCKNAQTN

XP_023477016.1 GYCNGLMAYVRDVKQSWYCPKTHYVVHAPWKAVREFCKYSESFCENYNEY

.*** . * : .:* . * .* .: *:* .

XP_007180555.1 CYESNSTMHITDCRQTGSSKYPNCAYKTSQKEKHIIVACEGDPYVPVHFD

sp|P00686.1|RNAS1_MACRU CYKSNSRLSITNCRQTGASKYPNCQYETSNLNKQIIVACEG-QYVPVHFD

EHB02901.1 FYQSSSNMHITGCRLTSNSKYPTCSYRTRQVERSITVACEGNPYVPGHFD

XP_023477016.1 CTLTHDSYPLTICSLGSIQPPTSCRYNGTLTNQRLYLLCSRKYDAEPIGI

: . :* * . . ..* *. :: : : *. .

XP_007180555.1 NSV—————————–

sp|P00686.1|RNAS1_MACRU AYV—————————–

EHB02901.1 ALWSPPPQPEQRLISSLLRISTPAFPSLPPKK

XP_023477016.1 IGLY—————————-

clustalw.dnd

(

XP_023477016.1:0.58993,

(

XP_007180555.1:0.16688,

sp|P00686.1|RNAS1_MACRU:0.18558)

:0.08060,

EHB02901.1:0.27935);

Table2. Number of identical residues in aligned ribonuclease among species of mammals

Pairwise comparison Number of identical residues between pairs of species

Horse and Minke Whale 8

Minke whale and kangaroo 9

Minke whale and naked mole rat 9

Kangaroo and naked mole rat 9

Horse and naked mole rat 8

Kangaroo and horse 8

Mink Whale and Hippopotamus 10

Table 3: Percent pairwise sequence similarity matrix

Minke Whale Kangaroo Naked Mole Rat Horse Hippopotamus

Minke Whale 100% 99% 97% 80% 100%

Kangaroo

99% 100% 99% 83% Naked Mole Rat 97% 99% 100% 86% Horse

80% 83% 86% 100% Hippopotamus 100%

Discussion

Q: Based on pairwise comparison among species, what species is most closely related to Minke whale?

The kangaroo is the species that is closely related to the Minke Whale with a score of 99

Q: Which species is most distant to the Minke whale?

The horse is the most distant relative of the minke whale with a score of 80

Phylogenetic Tree

The phylogenic tree indicates that all the four species originated from a common ancestor. However, the horse does not have a more recent common ancestor with the other three species thus is less related to not only the minke whale but the kangaroo and Naked-mole rat as well. The kangaroo shares a more recent ancestor with both the naked-mole rat and the minke whale compared to the horse. The naked-mole rat and the minke whale converge at a more recent common ancestor when we use a method where we follow the branches going backwards towards the root of the tree.