TITLE: CRITICAL REVIEW FOR ARTICLES

Name: Mohd Fareez B Abu Hassan Metric no: 20131000478 Subject: SBF 6024 Animal Metabolism and Adaptation Lecturer: Dr. Wong Chee Fah Submission date: 31st Jan 2014

LIST OF CONTAINING AUTHOR: Denielle D Brown Roland Kays Martin Wikelski Rory Wilson Peter Klimley

ARTICLE TITLE: Observing the unwatchable through acceleration logging of animal behavior

SOURCES: http://link.springer.com/article/10.1186%2F2050-3385-1-20#page-1 accessed on 19 January 2014

DATE PUBLISHED: 2013

ABSTRACT Behavior was an important key mechanism of evolution. The experts can rarely observe animals for more than a fraction of their daily life activities and attempts to quantify behavior for modeling ecological processes. An explosion of research on remote monitoring of animal behavior using acceleration sensors occurs. Animal attached to accelerometers measure the change in velocity of the body over time and can quantify fine scale movements and body postures.It had been apply to more than 120 species of animals to date. It is used in two forms, the first is patterns of accelerometer waveforms can be used to deduce specific behaviors through animal movement and body posture. Then, the variation in accelerometer waveform measurements have been shown to correlate with energy expenditure, opening a suite of scientific questions in species which difficult to observe in the wild. There are challenges to getting the most from the accelerometers, including validation, calibration and the management analysis. This tool offers a level of detail n behavioral studies of free-ranging wild animals that has previously been impossible to achieve. It improves the understanding of the role of behavioral mechanisms in ecological and evolutionary processes.

1)

The Problem:

Is the problem clearly stated? Yes, the problems were clearly stated which is animals behavior which are in remote area were very hard to study as it have different habitat than us human. In other words, these issues underscore the need for remote measurement of animal behavior to reduce or eliminate the potential effects of observer presence while maintaining a high level of detail in data recording comparable to direct observation. Is the problem practically important? Yes, I think the problem is really important in the context of nature. The problem really urges researcher around the world to develop a new method to study animals behavior as it is one of gods creation which we need to be responsible to take care. The problem needs to be study as the aim to create a balance world. As we all know that animals play an important role in the ecosystem and basically the world. What is the purpose of the study? The purpose of the study is field biologists had developed the accelerometers to study the animals behavior using the animals attached with accelerometer to measure the change in the velocity of the body over the time and quantify fine scales movements and body postures unlimited by visibility, observer bias, or the scale of space used. What is the hypothesis? The animals behavior could be study using the accelerometer. The accelerometer could give wavelength measurement to study the animals behavior. Are the key terms defined? Yes, the key term defined in first page of the journal which are accelerometer, activity, animal behavior, bio-logging, dead reckoning, energy expenditure, ethogram, remote observation and telemetry.

2) Review of Literature Are the cited resources pertinent to the study? The cited resources are pertinent to the study because major of the resources were related to this study. These resources are said related when you review the title of all the references. Basically it is related to the journal. Is the review too broad or too narrow? I think the review is enough as the review is not too narrow or too broad as it given a lot of evidence about the research on usage of accelerometer. It also explains in brief the method or how the readings from the accelerometer were shown which is in a wavelength form. The ways to use the accelerometer and some sample of graph and diagram were shown in figure 1 and figure 2 to show how the data were presented. Are the references recent? No, the references were legible from a very long time ago and also from recent time and after reviewing the references by the years. All the books and webpage published ranging from 1934 to 2012. So, the references are coming from various period of time. This had showcased the different situation from the past and recent time. Is there any evidence bias? No, I think the evidences were correctly stated and it had portrayed the importance and effectiveness of using the accelerometer in order to study the animal behavior. The evidence stated resemble that this study as relevant to studied and no biases were stated to support this study. 3) Design and procedure

What research methodology was used? The research methodology used was quantitative research because it involves the findings of statistics and data from survey conducted served by accelerometer: body posture and body movement. In this case, is the animal behavior in the remote areas.

Was it a replica study or an original study? I think it is a replica study which serves as a continuation of what had been studied by other researcher before this. Whereas the researcher modeled the usage of the accelerometer from other studies which has been conducted before this. This study did state that the way this research conducted referred from other study in the journal itself. What measurement tools were used? The measurement tools that were used in this study are the wavelength waveform and survey questions currently served by accelerometry; body posture and body movement. Both of the measuring tools are used simultaneously to measure and monitor the animals behavior in the remote area. How were the procedures structured? The procedure were structured as it is done accordingly which shown in the journal, whereas the first thing done is the introduction or abstract written. Then, the literature review did provide support towards the procedures. Then, the data collection happens and the data were analyzed. Lastly, conclusion was made from the overall data collected. Was a pilot study conducted? No, there is no pilot study done when I read the journal. But it does refer to other study related to this topic which is the use of accelerometer in monitoring the animal behavior. What are the variables? The variables are the animals and the accelerometer wavelength which are read in waveform as a data in this study.

How was sampling performed? The sampling performed was quantitative and random sampling as 125 animals that pass through the remote area were chosen as the samples. 176 accelerometry studies will detect and provide reading in form of waveform to study the behavior of that particular animal. The habitat of the study also was separated in two. First, habitat of animals were the aquatic animals and terrestrial animals. 4) Data Analysis and presentation: How was data analyzed? Data was analysed quantitatively in the form of graph and numbers. The animals that were studied is analysed in the form of percentage. The study of their movement, body posture and position and location were presented in experimental graphs. The table of data perform the mean readings of datas of the waveform. Was data qualitative or quantitative? The data presented were quantitative in the form of mean readings from the accelerometer using wavelength in waveform. Did findings support the hypothesis and purpose? Yes, it does support and cater the hypothesis and purpose of the study. It embarks that accelerometer is the tools for fine scale observation of behavior, unlimited by animal visibility, terrain, climate, observer bias or the scale space used. Were weakness and problems discussed? No, the journal just stressed on the strength of accelerometer as the best tool to study animals behavior.

5) Conclusion and implications Are the conclusions of the study related to the original purpose? Yes, it does simplify and explain about the study in a simple manner and sum up the findings of the study which related to the original purpose of the study. Were the implications discussed? Yes, it is discussed in the subtopic of future directions. The implications of this study will help other researcher to study this topic in more depth situation so this will help to improve the life behavior of animals in the remote area. This will bring positive feedbacks towards the research in biodiversity field. Whom the results and conclusion will affect? The result will give important affect to the animals. Thus, the animals will be helped in so many ways to face their daily activities. Researcher will develop plans to help animal with problems in the remote area. This is to improve the life of the animals in order to survive in the future. As to ensure and maintain the number of life of the species What recommendations were made at the conclusion? The recommendations were made at the conclusion are the usage of this device is a good method in order to study the animal behavior in remote area. 6) Overall Assessment What is your overall assessment of the study and the articles? I think this article is an informative article that will benefit the nature especially in the aspect of studying the animal behavior in terms of their reaction towards the nature. It is best suited to explore the animals behavior in remote areas and would help more scientists to discover other undiscovered animal behavior of logging. This article also could be related to school curriculum by using more sensible explanation and the language should be more understandable.

List of the new vocabulary with meanings: 1. Cryptic- serving to camouflage an animal in its natural environment. 2. Waveform-a curve showing the shape of a wave at a given time. 3. Biotelemetry-the detection or measurement of human or animal physiological functions from a distance using a telemeter. 4. Orthogonally- extraneous: not pertinent to the matter under consideration; "an issue extraneous to the debate"; "the price was immaterial"; "mentioned several impertinent facts before finally coming to the point" 5. Piezoelectric-the generation of electricity or of electric polarity in dielectric crystals subjected to mechanical stress, or the generation of stress in such crystals subjected to an applied voltage.

LIST OF CONTAINING AUTHOR: Junhuan Xu James P Strange Dennis L Welker Rosalind R James

ARTICLE TITLE: Detoxification and stress response genes expressed in western North American Bumble Bee, Bombus Huntii (Hymenoptera: Apidae)

SOURCES: http://www.biomedcentral.com/1471-2164/14/874 accessed on 13 Jan 2014

DATE PUBLISHED: 2013

ABSTRACT

The hunt bumble bee is a holometabolous, social insect which is important as a pollinator in natural and agricultural ecosystems in western America. They spent an amount of time to foraging on a wide variety of flowering plants, posing threat in their colony. From the finding, B. Huntii atleast expressed 584 genes associated with detoxification and stress response. The expression level of some genes, cytochrome P450s, glutathione 5-transferase (GSTs) and glycosidase, vary among different life stages to a greater extent than do other genes. The number of P450s, GSTs and esterase genes expressed by B. huntii is similar to the number of these genes found in the genomes of other bees. As the conclusion, Bombus huntii has transcripts for a large number of detoxification and stress related proteins, including oxidation and reduction enzymes, conjugation enzymes, hydrolytic enzymes, ABC transporters, cadherins, and heat shock proteins. The diversity of genes expressed within some detoxification pathways varies among the life stages and castes, and we typically identified more genes in the adult females than in larvae, pupae, or adult males, for most pathways. Meanwhile, we found the numbers of detoxification and stress genes expressed by B. huntii to be more similar to other bees than to the fruit fly. Many flowering plants benefit from pollinators, and thus offer these insects rewards like nectar rather than defensive plant toxins.

7)

The Problem:

Is the problem clearly stated? Yes, I think the problem is clearly stated which basically about the detoxification and stress response of the insect. They are important to adapt allow and insects to overcome the chemical defense of the plants. During pollination activities, bees are exposed to toxic substances in the environment, such as pesticides, phytochemicals, microbial toxins, pollutant and other xenobiotics. Generally, stress response and the detoxification of xenobiotics includes three major and interrelated pathways: Oxidationreduction enzymes include alcohol dehydrogenase, aldehyde dehydrogenase,

cytochrome P450s hydroxylases and peroxidases. Is the problem practically important? In my opinion, this problem is important as it involves the cycles of food web. The problem will actually affect the ecosystem of our nature. If this problem not being resolves, in times our ecosystem will be affected in certain areas and parts of the nature which involve the bumble bee, Bombus Huntii. This bumble actually plays an important part as a primary consumer and would help to balance the ecosystem. What is the purpose of the study? The purpose of the study is to study the detoxification process and stress response genes expressed in bumble bee, Bombus huntii. The process is studied with several chemical process explained in the graphs. The processes are explained in the graph as the detoxification pathways known for insects. What is the hypothesis? The hypothesis is Bumble bee , B. huntii will express different type of genes on different life stages. These genes were determine by the hydrolysis process. The readings were presented in the form of reads per kilobase per million reads.

Are the key terms defined? The key term is defined clearly such as the word bees, bombus huntii, bumble bee, detoxification genes with transcriptome. These key terms were defined in certain chapter in paragraphs in the journal. These key terms explained in various ways to relate them with the study. This key term are really important to ensure the reader understand the basic content of the study and give an idea on the important object or nouns that symbolize the study itself.

8)

Review of Literature

Are the cited resources pertinent to the study? Yes, the study cited resources are pertinent to the study such as all the cited resources were stated in the form of pages number were that particular statement related to this study were taken. The cited resources are important in order to prove that the study is relevant enough to be carried out. Is the review too broad or too narrow? In my opinion, the review is too broad and normal people couldnt understand this journal because it contains too many scientific terms and formulae. The review also stressed on the chemical reactions and it were explained more in table forms which is hard and difficult to be understood. Are the references recent? The references are recent because the date stated in the reference section is ranging from 2005-2013. The references should be recent to ensure that the study is reliable and valid due to the change in current nature. Nature will actually change through times and evolved form one particular type and situation to another situation.

Is there any evidence bias? In my opinion, there are no evidence biases in this study related because the example and evidence stated were natural and not bias to support this study. All the evidence stated in this study are relevant they developed a cDNA database of 102, 778 contigs and singletons using pyrosequencing of mRNA extracted from the eggs, larvae, pupae, adult workers, adult males, an egglaying queen, and a diapausing queen of B. huntii. The gene experession data were examined in two ways: the number of gene detected within a class of detoxification genes (gene diversity), and the number of transcripts of a particular gene or class of genes(the expression level).

9)

Design and procedure

What research methodology was used? The research methodology used for this study was quantitative method as it involved the collecting data on numbers. The numbers of putative functions for the detoxification genes expressed in different life stages of Bombus huntii. In the forms of tables the genes were stated clearly. Then, it also stated the number of detoxification genes expressed in different life stages of the bombus huntii. The reads per kilobase per million reads (RPKM) is also stated as the normalized expression levels of possible detoxification genes in B. huntii immature, for genes in the (A) oxidation:reduction, (B) conjugation, and (C) hydrolysis groups. The procedure that were carried out was eight different stages of B. huntii were used in this analysis, eggs, early (2nd and 3rd) instar larvae, late (4th) instar larvae, pupae, adult workers, adult males, a diapausing queen and an egglaying queen. All stages were collected from a nest cultured in the lab at USDA-ARS Pollinating Insect Research Unit in Logan, UT, except for the diapausing queen, which was a sister of the egglaying queen had been held in cold storage at 4 C for three month prior to collection sequencing. The bees were reared to strange and were started from queens that were raised and mated in the laboratory.

Was it a replica study or an original study? No, it was not a replica study because it involves real process of observing and collecting data from different stages of the bee life. It also involves the process in the laboratory which include the mating and laying eggs process for the bees. It is said to be an original study because it was developed on the basis of conducting and collecting real data from the problem. The data were reported clearly with different stages and time. This involves long period of time. What measurement tools were used? The measurement tools that were used was the hydrolysis process conducted, which transfer a hydrogen atom from water to the substrate compound, and these reactions are facilitated by hydrolytic enzymes. This hydrolysis process will show the typical detoxification pathways known for insects. The data were presented in the form of tables and the readings were read as a transcriptome. How were the procedures structured? In my opinion the procedures is not structured the methods of this study which is the process of collecting data by letting the egg in their own stages were discussed in the conclusion section. Then, the other process of the mating and breeding in the laboratory was also discussed in the conclusion section. Which, it needs careful observation by the researcher in the lab. However, the data should be collected before the conclusion was made. Was a pilot study conducted? No, based on the journal there are no pilot studies conducted by the researcher. What are the variables? The variables that could be state were Bombus huntii species, the life stages of the bombus huntii, colony survival and genes expressed from the posing threat.

How was sampling performed? Sampling that were performed in this study is specific sampling because the type of species chosen were specified and breed into different life stages and they were mated and the egg laying process were observed in the laboratory.

10) Data Analysis and presentation: How was data analyzed? Data was analyzed using table forms. The tables had stated the putative functions of genes expressed in the form of detoxification genes expressed in different life stages of the Bombus huntii, based on function assigned when the gene was first isolated. Other datas that had been collected were the number of detoxification genes identified, as expressed in different life stages, as expressed in different life stages of Bombus huntii, Reads Per Kilobase million reads (RPKM) the normalized expression levels of possible detoxification genes in B. huntii Was data qualitative or quantitative? The data collected was in the form of quantitative because the data was analyzed based on the reads per kilobase per million reads (RPKM). The readings were the data perform as the normalized expression levels of possible detoxification genes in B. Huntii adults for genes in the (A) oxidation:reduction, (B) conjugation, and (C) hydrolysis groups. Did findings support the hypothesis and purpose? Yes, the findings support the hypothesis and purpose of this study where as the sequence assembly, annotation and detoxification gene identification. The gene diversity and expression levels for detoxification and stress related genes.

Were weakness and problems discussed? No, the weakness and problems were not discussed in the journal as it focused on the data collection more as its strength. 11) Conclusion and implications Are the conclusions of the study related to the original purpose? Yes, the conclusion of the study is said to be related to the original purpose because it explain the findings from the study and determined the genes expressed with stress response in the form of table as it stated about the use of transcriptome analysis of all life stages and the methods of the study were discussed in conclusion. It did state about the availability of supporting data to support the data in another website with its link. Were the implications discussed? No, the implications were not discussed. Whom the results and conclusion will affect? The result and conclusion will affect the bee species itself as the study were made on that species where the genes expressed were recognize and the level were determined. The researcher could determine the genes expressed by the B. huntii to study the stress response with increasing in foraging and feeding activity directly increase the risk of exposure to the environmental pollutant. Futhermore, increased energy demands have been shown to increase consumption rates and the formation of metabolic by-product in certain species of flowers. What recommendations were made at the conclusion? There are no recommendations were made at the conclusion as it discussed the method of the study and explain about the findings of the study.

12) Overall Assessment What is your overall assessment of the study and the articles? In my opinion, the journal is so difficult to be understood by normal people. The language that were used in this journal is so hard to be understood. The scientific terms also were advanced as it is an article written in recent time which maybe used the most advanced technology in order to study the animal adaptation of bee, B.huntii. The genes presented were also hardly heard by normal people or normal science student. This journal suited the scientist more than normal people as it will benefit them more than the normal people. I think it is a great lose of someone who can write journal that are so informative but could not be understood by the masses. List of the new vocabulary with meanings: Kilobase- (in expressing the lengths of nucleic acid molecules) 1,000 bases. Xenobiotics-substances those are foreign to the body or to an ecological system. Diapausing-(of an insect or other animal) undergo a period of suspended development. Detoxification- The process of removing toxic substances or qualities. Transcriptome-The transcriptome is the set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA produced in one or a population of cells.

Appendices