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Instructions:This examination is aimed at measuring your creativity, your abilities in logical thinking andwriting (including drawing schematics), and your basic knowledge in biology. We are moreinterested in understanding "how you think" as a scientist than "what you know".
Read the following story and answer Questions 1 to 4.
Please read the questions carefully. The setting of the question is basically imaginary. You arefree to choose experimental settings unless they are described, but please describe your settings
clearly in the answer sheet. When two or more possibilities can be considered for the answer toeach question, please explain them briefly, and describe the answers separately, case by case.
Even if you cannot answer a given question (or a part of a question), you may be able to answer
subsequent questions (or subsequent parts of a question).
When we evaluate the answers, we will take your research background and future researchinterests into consideration.

* Please write and draw your answers within the assigned spaces in the answer sheet. Please do
not change the size of the space. You are free to set the line spacing.
* The answer may be entered directly to the electronic file (Microsoft Word or pdf) and/or in
handwriting on a printed answer sheet. Even when your answer is a combination of typing
and handwriting, please fit them together to the assigned spaces in the same answer sheet. A
handwritten answer should be converted to an electronic file within 20 minutes after theexam.
* You may use schematics and/or tables as appropriate. If you enter your answer directly to theelectronic file, you may prepare schematics and/or tables by any software before pastingthem on the file of your answer sheet. Alternatively, you may scan handwritten schematics
and/or tables and paste them on the file of your answer sheet.
*At the end of the written exam, an electronic file of complete answer sheet should be submitted
by e-mail within 20 minutes (e-mail address: info-soken@nig.ac.jp) (before submission, a
handwritten answer should be converted to an electronic file).

1Dr. Mishima is studying Plant P and Insect I interactions in the northern (Hokkaido) andsouthern (Okinawa) populations in Japan. Within natural populations, she noted relationships
between the numbers of Insect I individuals found on plants and the numbers of flowers onPlant P. Interestingly, the relationships seem to differ in the northern and southern populations.
Individuals of Plant P and Insect I show no visible phenotypic differences between the two
populations (but genetic analysis has not been conducted).
Dr. Mishima created experimental fields in Hokkaido (northern field) and Okinawa (southernfield), respectively, to confirm this observation. She kept the plants separate (in nettedenclosures) and placed different numbers of the insects on the plants on Day 10 aftergermination (flowering occurs around Day 15). She counted the numbers of flowers on eachplant on Day 20 and the results are given in Figure 1. The numbers of Insect I on each flower
did not change during the experiment. Plant P individuals collected from the southern(Okinawa) and northern (Hokkaido) parts will be labeled P_south and P_north, respectively,
and similarly for Insects I_south and I_north.

Fig. 1. Plant P flower number vs Insect I number
Each dot represents a result for a single plant. Location of the experimental plot is given at thetop of each graph.
Q1-1 Please summarize the main patterns shown in Figure 1.
Q1-2 Propose at least two broad categories of possible explanations/mechanisms for thedifferences in the plots shown in Figure 1 panel A vs panel B. Please consider general, rather
than specific, possibilities based on only results shown in Figure 1. Your categories should
cover a wide range of plausible biological scenarios consistent with the information givenabove.

2Dr. Mishima conducted more experiments in the northern (Hokkaido) and southern (Okinawa)
experimental fields. The experimental settings for Exp. 3 and Exp. 4 were the same as for theprevious experiments, but Dr. Mishima tried different combinations of the plants and insects
originating from the northern (Hokkaido) and southern (Okinawa) populations. The four
experiments are summarized in Table 1. The results of Exp. 1 and Exp. 2 have been describedabove (Figure 1). The results for Exp. 3 and Exp. 4 are given in Figure 2.
Table 1. Experimental designs
Experiment

LocationPlant P

Insect IResultExp. 1

Southern field

P_southI_southFig. 1AExp. 2

Northern field

P_northI_northFig. 1BExp. 3

Southern field

P_northI_northFig. 2AExp. 4

Northern field

P_southI_southFig. 2BFig. 2. Plant P flower number vs Insect I number from Exp. 3 and Exp. 4
Each dot represents a result for a single plant. The location is given at the top of each graph.
Q2 Please explain the purpose or motivation for Exp. 3 and Exp. 4. What did we learn from theresults of these experiments?

3Dr. Mishima conducted four more experiments in the northern (Hokkaido) and southern(Okinawa) experimental fields. The four experiments are summarized in Table 2. The results aregiven in Figure 3.

Table 2. Experimental designs
Experiment

Location

Plant P

Insect IResultExp. 5

Southern field

P_southI_northFig. 3AExp. 6

Northern field

P_southI_northFig. 3B

Exp. 7

Southern field

P_northI_southFig. 3CExp. 8

Northern field

P_northI_southFig. 3DFig. 3. Plant P flower number vs Insect I number from Exp. 5 through 8
Each dot represents a result for a single plant. The location is given at the top of each graph.
Q3 Please explain the purpose or motivation for Exp. 5 though 8. What did we learn from theresults of these experiments?

4

Mutant strains of Insect I_south and Insect I_north are available. Each strain is homozygous fora different single gene deletion.
Dr. Mishima was interested in finding Insect I mutant strains that appear to "switch" theireffects on Plant P flower number between the I_south pattern (Fig. 1A) and the I_north pattern(Fig. 1B). Among 1,000 gene deletion strains of Insect I_south, she found three mutant strainsthat produce patterns similar to Fig. 1B. However, no deletion strains of Insect I_north produced
patterns similar to Fig. 1A. She increased the study to include 10,000 deletion strains of Insect
I_north and still found no patterns similar to Fig. 1A.
Q4-1
Propose an explanation for the difference between gene deletion effects for Insect I_south andInsect I_north. Please be sure to explain why there were no Insect I_north mutations that switch
the effects on Plant P flower number.

Dr. Mishima analyzed the three mutant strains of Insect I_south found above (mutants A, B, andC) and identified the deleted genes (genes A, B, and C) in these mutant strains. The results are
summarized in Table 3.
Table 3. Insect I_south mutant strains
StrainDeleted gene

Product of deleted gene

Effect on Plant P_south

Mutant A

Gene A

EnzymeFig. 1B-like

Mutant B

Gene B

Transcription factor

Fig. 1B-like

Mutant C

Gene CMembrane protein

Fig. 1B-like

Q4-2 Propose two models or hypotheses for Insect I_south effect on Plant P given the nature ofthe mutant strains (Table 3). Your models should explain how the products of genes A, B and C
are involved in the Insect I_south effect on Plant P (Figures 1 to 3). Please try to construct two
different proposals rather than small modifications of the same idea. If required, you can use
schematics (if it is difficult to prepare schematic drawings, you may use combinations ofarrows, other symbols, and letters).

5Dr. Mishima mutagenized the three mutant strains of Insect I_south (mutants A, B, and C) tointroduce a point mutation (a single nucleotide change) and found some phenotypic revertantmutants (referred to as "PRM") in which Insect I_south mutants have regained the wild-type
Insect I_south effects on Plant P. These strains remain homozygous for the original genedeletion (note that gene A, B or C sequence was completely deleted) but have gained a point
mutation in a non-coding region (genomic region that does not produce a protein). Although thegenotype of these double-mutant strains differs from wild-type, their phenotypes areindistinguishable from wild-type (flowering patterns are similar to Fig. 1A).
Q4-3 Under the models you proposed in Q4-2, which of the mutant strains (mutant A, B or C)
could harbor PRMs in genomic non-coding regions? Please be sure to give your reasoning andwhat kind of region(s) would have an additional point mutation for each of your models.
Q4-4 Dr. Mishima is very interested in the models you proposed in Q4-2. She would like toconduct an empirical test to distinguish between the models (the test should differ from thePRM approach discussed in Q4-3). Dr. Mishima currently does not have access to facilities for
DNA sequence analysis or "omics" (such as transcriptomic and proteomic) approaches. Pleasesuggest an experiment to test your models from Q4-2 and clearly indicate how particular results
would distinguish between your hypotheses.

6解答用紙： 受験番号
以下に各問を簡単に記載してありますが、必ず問題用紙の情報に基づいて解答して下さい。解答スペースのサイズは変更しないでください。解答スペース内の行間は自由に変更して構いません。
問 1-1 図 1 のグラフに示される結果の主な特徴を文章で説明してください。

問 1-2 図１A と B の違いが生じる理由またはメカニズムについて、それぞれ大きく異なる可能性を、2 つ以上述べてください。

1

解答用紙： 受験番号
問 2 実験 3 と実験 4 の目的を説明してください。また、これらの実験結果からどのようなことがわかるか説明してください。

問 3 実験 5~8 の目的を説明してください。また、これらの実験結果からどのようなことがわかるか説明してください。

問 4-1 昆虫 I_south と I_north の変異体探索で上記のような違いが起きた理由を説明してください。なお、植物 P に対する効果が逆転する I_north 変異体が見つからなかった理由を含めた説明をしてください。

2

解答用紙： 受験番号
問 4-2 表 3 の結果に基づいて、昆虫 I_south が植物 P に与える影響がどのような機構によるのかそれぞれ説明しうる異なる仮説モデルを 2 種類提唱してください。
モデル#1

モデル#2

3

解答用紙： 受験番号
問 4-3 あなたが問 4-2 で提唱したモデルを考慮すると、変異体 A、B または C のうち非コード領域に新たな復帰突然変異が生じ得るのはどの変異体でしょうか。それぞれのモデルに対しての答えを理由とともに述べてください。またそれぞれのモデルに対して、新たな点変異はゲノム上のどのような非コード領域に生じたのかも述べてください。

4解答用紙： 受験番号
問 4-4 2 種類のモデルのどちらが正しいか検証するためには、どのような実験をすればよいでしょうか。またどのような結果がどちらのモデルが正しいかを示すでしょうか。それぞれ説明してください。

5

Answer sheet： Application Number
Note that the exam questions are only briefly summarized in the answer sheet. Please be sure to read theexam for the full information and questions. Please do not change the size of the space. You are free to set
the line spacing in the given spaces.
Q1-1 Please summarize the main patterns shown in Figure 1.

Q1-2 Propose at least two broad categories of possible explanations/mechanisms for the differences in theplots shown in Figure 1 panel A vs panel B.

1

Answer sheet： Application Number
Q2 Please explain the purpose or motivation for Exp. 3 and Exp. 4. What did we learn from the results of theseexperiments?

Q3 Please explain the purpose or motivation for Exp. 5 though 8. What did we learn from the results of theseexperiments?

Q4-1 Propose an explanation for the difference between gene deletion effects for Insect I_south and Insect
I_north. Please be sure to explain why there were no Insect I_north mutations that switch the effects on Plant Pflower number.

2

Answer sheet： Application Number
Q4-2 Propose two models or hypotheses for the Insect I_south effect on Plant P given the nature of the mutant
strains (Table 3).
Model or hypothesis #1

Model or hypothesis #2

3

Answer sheet： Application Number
Q4-3 Under the models you proposed in Q4-2, which of the mutant strains (mutant A, B or C) could harbor
PRMs in genomic non-coding regions? Please be sure to give your reasoning and what kind of region(s) would
have an additional point mutation for each of your models.

4

Answer sheet： Application Number
Q4-4 Please suggest an experiment to test your models from Q4-2 and clearly indicate how particular results
would distinguish between your hypotheses.

5