Jenny Liang

Annotated Source List

Leips, Jeff. Personal interview. N.d.
Our research is focused on understanding the genetic basis of natural variation in
life history traits using the fruit fly, Drosophila melanogaster, as a model
organism. We are particularly interested in identifying genes that control
age-specific changes in traits that directly contribute to senescence and ultimately
limit life span. These traits include age-specific reproduction, immune response and
energy storage. We are also actively studying the ecology of natural populations of
Drosophila to identify the agents of selection acting on genes controlling these
traits. Our goal is to combine knowledge of the natural history of this species with an
understanding of the genetic architecture of these traits to help explain the
maintenance of genetic variation in age-related changes in fitness in natural
populations.

FlyBase. N.p., n.d. Web. 8 Oct. 2015. <http://flybase.org>.

I can find a lot of useful information to help me with my research on this website.
It contains tons of information on fly genome and the details of each gene, such as the
function of the specific gene. Also related articles are presented on the website for
further information. The website allows me to find related information more quickly
and precisely.

Durham, Mary F. "A Genomic Approach to Identify the Genetic Basis of Natural
Variation in Lifespan and Age Specific Fecundity and Their Plastic
Responses to Diet in Drosophila Melanogaster." 2013. Digital file.
In this article, the author mainly discussed the influences that the gene acts on
natural variation in lifespan and reproduction, and how these genes interact with
environmental variables. The researcher used the Drosophila melanogaster Genetic
Reference Panel (DGRP), to complete a genome-wide association (GWA) study on
lifespan, age specific fecundity, lifetime fecundity and the plastic response of
these traits.The result suggests that individual genes influence lifespan and fecundity
in a diet specific manner.
I think this article is useful for me because it contains the methods he used to test
and also the hypothesis being tested is related to my topic. The description on the
methods may help me with my experimental design and how I will conduct it. The
data provided in the article can be helpful to my experiment.

Mackay, Trudy F. C., Stephen Richards, and Eric A. Stone. "The Drosophila
Melanogaster Genetic Reference Panel." Nature 482.7384 (2012): 173-78.
Print.
The article mainly explains the Drosophila melanogaster Genetic Reference Panel
(DGRP) which is a community resource charting the molecular and phenotypic
variation in 168 fully sequenced fruitfly strains derived from a single outbred natural
population. The analyses of DGRP data introduce the genomic landscape of genetic
variation, positive and negative selection, and rapid evolution of the X chromosome.
The results also reveal many low frequency variants in novel loci that are associated
with quantitative traits, and explain a large fraction of the phenotypic variance.
This source is useful for me because its content explain the DGRP which is also
mentioned in the methods used off the experiments in the last source. The explanation
helped me with understanding of the last source.

V, Deepa Parvathi, Akshaya Amritha S, and Solomon FD Paul. "Wonder Animal

Model for Genetic Studies- Drosophila Melanogaster- Its Life Cycle and
Breeding Methods- a Review." Sri Ramachandra Journal of Medicine II.2.33
(2009): n. pag. Print.
In this article the author talks about the basic information of Drosophila
Melanogaster. The life circle of the Drosophila is explained in detail and the
mechanisms involved are also explained. The features to determine the sex of adult
fly are also stated in the article. Also the approach for culturing is explained in the
article.
The article is extremely useful for me because it explained the basic information
of Drosophila Melanogaster and the methods that I will be using in the lab. Since I am
completed new to this topic, this provides me an introduction of the big idea of the
Drosophila, and how its lab works. The information in this article can help me with
identifying the stage of a fruit fly and also help me with the lab practical part.

Roff, Derek A. The Evolution of Life History. N.p.: n.p., 1992. Print.
In this book, the basic theory and methods of life histories are explained. It
includes examinations of genetic and optimization approach, the broad scope of life
history, the concept of fitness, the mathematical tools for prediction, the factor
affecting age and so on. It provides a big picture of the theory of life history and
explains it in details.
The explanation of the life history theory and its approaches are very thorough in
this book. The understanding of this theory will help me with the research on the
genetic basis of natural variation of the drosophila.

Adams, Mark D., et al. "The Genome Sequence of Drosophila Melanogaster."

Science 24 Mar. 2000: 2185-95. Print.
In this article, the researchers reported their examination of the genome of
Drosophila Melanogaster, which is one of the most intensively studied organisms in
biology and serve as a model system for investigation of many develomental and
cellular processes. They have determined the nucleotide sequence of nearly all of
the~120-megabase euchromatic portion of the Drosophila genome using a
whole-genome shotgun sequencing strategy supported by extensive clone-based
sequence and a high-quality bacterial artificial chromosome physical map. As a result,
they found out that the genome encodes ~13,600 genes.
I think this article is useful for me because it evaluated the genome of the
Drosophila. In my research, the gene is very important since we research on the genes
that have effects on the natural variation, so the data provided in this article can be
really helpful when it comes to identify the genes.

Giot, L., et al. "A Protein Interaction Map of Drosophila Melanogaster."

Science 302.5651 (2003): 1727-36. Print.
In the article, the researchers present a two-hybridbased protein-interaction map
of the fly proteome. During the experiment, a total of 10,623 predicted transcripts
were isolated and screened against standard and normalized complementary DNA
libraries to produce a draft map of 7048 proteins and 20,405 interactions. They used a
computational method of rating two-hybrid interaction confidence to refine this draft
map to a higher confidence map of 4679 proteins and 4780 interactions. The map
serves as a starting point for a systems biology modeling of multicellular organisms,
including humans.
The protein interaction map can that is provided by this article can help me
identify the usage of these proteins. What is more, the proteins are coded by the genes,
therefore I can find the genes that express in certain ways which is stated in the map
and do some further research on the gene. This is also a great source for me to identify
specific interactions happening in the drosophila, which can help me with better
understanding of the organism.

Elbashir, Sayda M., et al. "Functional Anatomy of siRNAs For Mediating

Efficient RNAi in Drosophila Melanogaster Embryo Lysate." The EMBO
Journal 20.23 (2001): 6877-88. Print.
In the research, synthetic, short interfering RNAs (siRNAs) were examined
in Drosophila melanogaster embryo lysate for their requirements regarding length,

structure, chemical composition and sequence in order to mediate efficient RNAi. I

was found that duplexes of 21 nt siRNAs with 2 nt 3 overhangs were the most
efficient triggers of sequencespecific mRNA degradation. Substitution of one or
both siRNA strands by 2deoxy or 2Omethyl oligonucleotides abolished
RNAi, although multiple 2deoxynucleotide substitutions at the 3 end of siRNAs
were tolerated.
The results provide a rational basis for the design of siRNAs in future gene
targeting experiments and this is helpful for me because I will be examine the genetic
cues of the Drosophila Melanogaster. Also, the article helps me with better
understanding of the siRNA of the drosophila.

Sohal, Rajindar S., et al. "Simultaneous Overexpression of Copper- and

Zinc-containing Superoxide Dismutase and Catalase Retards Age-related
Oxidative Damage and Increases Metabolic Potential in Drosophila
Melanogaster." The Journal of Biological Chemistry: 15671-74. Print.
In this article, the focus of the research is to elucidate the nature of the
mechanisms by which overexpression of copper- and zinc-containing superoxide
dismutase (Cu,Zn-SOD) and catalase extends life span of Drosophila melanogaster.
Experiment is conducted by comparing experimental flies containing single extra
doses of Drosophila Cu,Zn-SOD and catalase genes with appropriate controls at
different ages. It is found that overexpression of Cu,Zn-SOD and catalase caused a
retardation in the accumulation of 8-hydroxydeoxyguanosine during aging and in
response to the exposure of live flies to x-rays. The results of this study indicate that
overexpression of Cu,Zn-SOD and catalase ameliorates the age-related accumulation
of molecular oxidative damage and susceptibility to such damage in response to acute
oxidative stress while prolonging the metabolic life of flies. The concept that
oxidative stress is a causal factor in the aging process is supported.
I think this article is useful to me because I want to research on the genetic
influences on life span. Though this is a research on the environmental factors that
influence the aging process, I can still use this as a reference, because there may be a
kind of gene which its expression has the similar influence as the Drosophila Cu,
Zn-SOD does. Also, its methods is an example that I can look into and imitate.

Cho, Irene, et al. "Age- and Diet-specific Effects of Variation at S6 Kinase on

Life History, Metabolic, and Immune Response Traits in Drosophila
Melanogaster." DNA and Cell Biology (2010): 473-85. Print.
The research was focused on a candidate gene S6 kinase (S6k) which a recent
mapping study identified as affecting lipid storage in Drosophila. S6k is in the target
of rapamycin pathway, which regulates cell growth in response to nutrient availability
and has also been implicated to influence many life history traits from fecundity to

life span. In this article, researchers used quantitative complementation tests to

examine the effect of allelic variation at S6k on a range of phenotypes associated with
metabolism and fitness in an age-, diet-, and sex-specific manner. It is found that
alleles of S6k have pleiotropic effects on total protein levels, glycogen storage, life
span, and the immune response and demonstrate that these allelic effects are age, diet,
and sex specific. As many of the genes in the target of rapamycin pathway are
evolutionarily conserved, our data suggest that genes in this pathway could play a
pivotal role in life history evolution in a wide range of taxa.
This article is helpful for me because it provides an important information on the
life history theory. The success study of S6 kinase provides me a modal for other
candidate genes study. The methods mentioned in the article can be helpful for me to
use. Also it helps me know what kind of factors I want to find to conduct the
experiment.

"Age Specificity of Inbreeding Load in Drosophila Melanogaster and Implications

for the Evolution of Late-Life Mortality Plateaus." Genetics (2007):
587-95. Print.
The article argued that current evolutionary theories that explain the origin of
aging as a byproduct of the decline in the force of natural selection with age seems
inconsistent with the late-life mortality plateaus, since under traditional evolutionary
models mortality rates should increase monotonically after sexual maturity. The
researchers tested the degree of age specificity of segregating alleles affecting fitness
in Drosophila melanogaster, assessed age specificity by measuring the homozygous
fitness effects of segregating alleles across the adult life span and calculated genetic
correlations of these effects across age classes. For both males and females, it is found
that allelic effects are age specific with effects extending over 12 weeks across all
age classes, consistent with modified mutation-accumulation theory.
The results indicate that a modified mutation-accumulation theory can both
explain the origin of senescence and predict late-life mortality plateaus, which is
helpful for me because I may research on the genetic influence on aging process.

Attrill, Helen, et al. "FlyBase: Establishing a Gene Group Resource for

Drosophila Melanogaster." Nucleic Acid Research 43.18 (2015): n. pag. Print.
The article mainly described the FlyBase which is a tool for searching the
genome of flies.Many publications describe sets of genes or gene products that share a
common biology. They think it is useful for such gene collections to be presented as
discrete lists within the appropriate Model Organism Database (MOD) so that
researchers can readily access these data alongside other relevant information. They
argue that this new resource will enable researchers with diverse backgrounds and

interests to easily view and analyse acknowledged D. melanogaster gene sets and
compare them with those of other species.
I think this source is helpful for me because I will be using the FlyBase for
searching the genetic sequence, the function of the protein, or the chemical formula of
the gene. This article helps me with how to use the website and where to find the
information I want in the database.

Jennings, Barbara H. "Drosophila a Versatile Model in Biology & Medicine."

Materials Today 14.5 (2011): 190-95. Print.
In the article, the author stated that the fruit fly Drosophila melanogaster is a
versatile model organism that has been used in biomedical research for over a century
to study a broad range of phenomena. Using Drosophila has many technical
advantages over vertebrate models; they are easy and inexpensive to culture in
laboratory conditions, have a much shorter life cycle, they produce large numbers of
embryos and they can be genetically modified in numerous ways. Research
using Drosophila has made key advances in our understanding of regenerative biology
and will no doubt contribute to the future of regenerative medicine in many different
ways.
In the article, the advantages of using a drosophila as a model system in many
biological researches are being explained. I think it is useful because it gives me an
idea of why we are using the drosophila instead of other organisms, and how it would
help us to advance in our technology.

Berman, Gordon J., et al. "Mapping the Stereotyped Behaviour of Freely Moving
Fruit Flies." Interface (2014): n. pag. Print.
In this article, the researchers introduce a method for mapping an animal's actions,
relying only upon the underlying structure of postural movement data to organize and
classify behaviours.They applied this method to the ground-based behaviour of the
fruit fly, Drosophila melanogaster, where they found that flies perform stereotyped
actions roughly 50% of the time, discovering over 100 distinguishable, stereotyped
behavioural states. These include multiple modes of locomotion and grooming. they
used the resulting measurements as the basis for identifying subtle sex-specific
behavioural differences and revealing the low-dimensional nature of animal motions.
This article is helpful for me because it tested the behavior of the drosophila
melanogaster. I can understand the behaviors of the fruit flies with the data provided
in this article.

Carnes, Megan Ulmer, et al. "The Genomic Basis of Postponed Senescence in

Drosophila Melanogaster." PLoS One 10.9 (2015): n. pag. Print.

In the article, the researchers assessed the genetic divergence between

five Drosophila melanogaster lines selected for postponed senescence for over 170
generations (O lines) and five lines from the same base population maintained at a
two week generation interval for over 850 generations (B lines). They performed
population sequencing of pools of individuals from all B and O lines and identified
6,394 genetically divergent variants in or near 1,928 genes at a false discovery rate of
0.068. They found a number of candidate genes affecting postponed senescence.
While several of these genes have been previously associated
with Drosophila lifespan, most are novel and constitute a rich resource for future
functional validation.
This source is helpful for me because a number of candidate genes in females
affecting postponed senescence and increased lifespan are identified. This is
significant because I will be identify the specific genes that will influence on lifespan
and the data from this article will provide me the potential genes that I can look into,
and safe a lot of time for me.

Reeve, Eric C. R., and Isobel Black. Encyclopedia of Genetics. N.p.: Taylor &
Francis, 2001. Print.
The Encyclopedia includes 125 entries, beginning with the origins of genetics,
and progressing to the structure of DNA and modern theories such as selfish genes.
All branches of genetics are covered, including the genetics of bacteria, viruses,
insects, animals and plants, as well as humans. Important topical issues such as the
human genome project are fully surveyed. There is also a section on techniques and
biotechnology includes modern methods of analysis.
This book is helpful for me because I can get a big picture of what is discussed in
the genetic study. Genetic information of the Drosophila Melanogaster is also
discussed in detail in the book.The section where several methods of analysis is
explained may help me with how I will design my experiment.

Halligan, Daniel L., and Peter D. Keightley. "Ubiquitous Selective Constraints

in the Drosophila Genome Revealed by a Genome-wide Interspecies
Comparison." Genome Research 16.7 (2006): 875-84. Print.
In this research, the researchers have compared the complete D.
melanogaster and Drosophila simulans genome sequences to estimate mean selective
constraint (the fraction of mutations that are eliminated by selection) in coding and
non-coding DNA by standardizing to substitution rates in putatively unconstrained
sequences. They infer that there is more than three times as much functional
non-coding DNA as protein-coding DNA in the Drosophila genome. Most deleterious

mutations therefore occur in non-coding DNA, and these may make an important
contribution to a wide variety of evolutionary processes.
This article is useful for me because it studied the non-coding DNA in drosophila.
It is more likely to cause a mutation occur in non-coding since there are more of the
non-coding ones than the coding ones. The mutation can be a factor of a different
lifespan from other drosophila, and this is related to my research topic.

Berkeley Drosophila Genome Project. Berkeley Drosophila Genome Project. N.p.,

n.d. Web. 25 Oct. 2015. <http://www.fruitfly.org/>.
This site is very helpful for me because it contains a lot of projects I can look into,
as well as the methods, tools, and materials concerning with my projects. The data
posted on the website can help me get what I want to use quickly and accurately. Also
the tools provided can help me analyze the data after I collect them.

Sasamura, Takeshi, Kenji Matsuno, and Mark E. Fortini. "Disruption of Drosophila

Melanogaster Lipid Metabolism Genes Causes Tissue Overgrowth Associated
with Altered Developmental Signaling." PLOS Genetics (2013): n. pag. Print.
In a forward genetic screen for mutations that alter intracellular Notch receptor
trafficking in Drosophila melanogaster, the researchers recovered mutants that disrupt
genes encoding serine palmitoyltransferase and acetyl-CoA carboxylase. Both
mutants cause Notch, Wingless, the Epidermal Growth Factor Receptor (EFGR), and
Patched to accumulate abnormally in endosomal compartments. In mosaic animals,
mutant tissues exhibit an unusual non-cell-autonomous effect whereby mutant cells
are functionally rescued by secreted activities emanating from adjacent wildtype
tissue. Strikingly, both mutants display prominent tissue overgrowth phenotypes that
are partially attributable to altered Notch and Wnt signaling. The analysis of the
mutants demonstrates genetic links between abnormal lipid metabolism, perturbations
in developmental signaling, and aberrant cell proliferation.
This source talks about the lipid metabolism genes of the Drosophila
Melanogaster that its disruption can cause tissue overgrowth with atered
developmental signaling. This is helpful for me because it is associated with genes
and its effect on the phenotype of the flies. The expression of the gene can change the
fitness of the fly in its environment. So I can link this article to what I want to
research by its focus on the genetic expression influencing the pheonotype.

Cingolani, Pablo, et al. "A Program for Annotating and Predicting the Effects of
Single Nucleotide Polymorphisms, SnpEff." Fly 10.4161 (2012): 80-92. Print.

The researchers describe a new computer program, SnpEff, for rapidly

categorizing the effects of variants in genome sequences. Once a genome is
sequenced, SnpEff annotates variants based on their genomic locations and predicts
coding effects. Annotated genomic locations include intronic, untranslated region,
upstream, downstream, splice site, or intergenic regions. Coding effects such as
synonymous or non-synonymous amino acid replacement, start codon gains or losses,
stop codon gains or losses, or frame shifts can be predicted.
This source is helpful for me because the program described in this article can
help me categorize the effect of variants in genome sequence that are used in my
experiment. The program will decrease the time that a person will spend to categorize.

Ren, Xingjie, et al. "Optimized Gene Editing Technology for Drosophila

Melanogaster Using Germ Line-specific Cas9." CrossMark 110.47 (2013):
19012-17. Print.
The researchers report an effective and inexpensive method for genome DNA
editing in Drosophila melanogaster whereby plasmid DNAs encoding short sgRNAs
under the control of the U6b promoter are injected into transgenic flies in which Cas9
is specifically expressed in the germ line via the nanos promoter. They evaluate the
off-targets associated with the method and establish a Web-based resource, along with
a searchable, genome-wide database of predicted sgRNAs appropriate for genome
engineering in flies. Finally, they discuss the advantages of our method in comparison
with other recently published approaches.
I think this source is useful because a method of experiment is tested and
evaluated. I may use this technique when I am conducting the experiment. The
evaluation from this article is critical for me to decide whether or not this method is
suitable for my experiment.

Pandey, Udai Bhan, and Charles D. Nichols. "Human Disease Models in Drosophila
Melanogaster and the Role of the Fly in Therapeutic Drug Discovery."
Pharmacological Reviews 63.2 (2011): 411-36. Print.
In the article, the author mainly discussed the common fruit fly, Drosophila
melanogaster as a well studied and highly tractable genetic model organism for
understanding molecular mechanisms of human diseases. Many basic biological,
physiological, and neurological properties are conserved between mammals and D.
melanogaster, and nearly 75% of human disease-causing genes are believed to have a
functional homolog in the fly. They review the basic biology of the fly and discuss
models of human diseases and opportunities for therapeutic discovery for central
nervous system disorders, inflammatory disorders, cardiovascular disease, cancer, and
diabetes. They also provide information and resources for those interested in pursuing

fly models of human disease, as well as those interested in using D. melanogaster in

the drug discovery process.
I think this source is helpful for me because it explains why Drosophila
melanogaster is a good model system for studying in human disease. The discussion
involved in this article helps me understand the importance of studying the drosophila
and how much impact it would make for us.

Schrider, Daniel R., et al. "Rates and Genomic Consequences of Spontaneous

Mutational Events in Drosophila Melanogaster." Genetics 194.4 (2013):
937-54. Print.
The researchers sequenced eight genomes produced by a mutation-accumulation
experiment in Drosophila melanogaster. Their analysis reveals that point mutation and
small indel rates vary significantly between the two different genetic backgrounds
examined. Results suggest that, at least in inbred lines like those examined here,
mutational pressures may result in net growth rather than contraction of
the Drosophila genome, and ~99% of duplications and deletions are
deleteriousmaking them 10 times more likely to be removed by selection than
nonsynonymous mutations. Our results illuminate not only the rates of new small- and
large-scale mutations, but also the selective forces that they encounter once they arise.
The data presented in the article is helpful for me because the rate of the
mutational events are tested in this experiment. Mutation is an important cause of a
extremely long lifespan for a drosophila. So it is helpful for my research on the
elongated lifespan of drosophila.

Berezikov, Eugene, et al. "Deep Annotation of Drosophila Melanogaster MicroRNAs

Yields Insights into Their Processing, Modification, and Emergence."
Genome Research (2011): 203-15. Print.
In this article, the researchers report a meta-analysis of short RNA data
from Drosophila melanogaster, aggregating published libraries with 76 data sets that
we generated for the modENCODE project. They elucidated several features of
known miRNA loci, including multiple phased byproducts of cropping and dicing,
abundant alternative 5 termini of certain miRNAs, frequent 3 untemplated additions,
and potential editing events. They also identified 49 novel genomic locations of
miRNA production, and 61 additional candidate loci with limited evidence for
miRNA biogenesis. Altogether, this study lays a comprehensive foundation for the
study of miRNA diversity and evolution in a complex animal model.
The data that is included in the article is helpful for me because the loci that are
related to miRNA synthesis is described. It may help me with my research in a way to
identify the loci that are specific to a certain miRNA. The data will help me find the
loci faster and it will safe me a lot of time to research on my own.

Langley, Charles H., et al. "Genomic Variation in Natural Populations of

Drosophila Melanogaster." Genetics (2012): n. pag. Print.
In this article, the researchers compared the two natural populations of
Drosophila melanogaster since the determination of both of their independent genome
sequences. Evidence of interactions between natural selection and linkage is abundant
not only in the centromere- and telomere-proximal regions, but throughout the
euchromatic arms. Comparative analysis of the variation among these genomes to
genomes from D. simulana suggests that many targets of directional selection may be
shared between these species.
This source is helpful for me because in the article two natural populations are
compared. The comparison will give me a clue on the genetic variation of both
species and I can link it with my project by the natural selection of certain genes that
express the phenotype that provides fitness for the fly in its environment.

Campbell, Sarah. E-mail interview. 25 Oct. 2015.

Initially, I attended Marietta College in Ohio for my freshman year, then
transferred to University of Maryland, Baltimore County, from which I graduated
with a Bachelors of Science Degree in Biological Sciences. UMBC proved to be an
excellent university for my pursuits as a STEM major, with a wide array of rigorous
science courses and opportunities for research. UMBC also has a student/ community
symphony orchestra that I could participate in as a violinist (obtained a music minor,
as well).
I studied biological sciences because I am interested in understanding how simple
and complex organisms function, particularly as it pertains to human health and
disease. Eventually, I would like to focus my attention on biomedical research,
studying a specific disease at the molecular and genetic level to elucidate the
molecular mechanisms and physiological functions within the human body.