Genes to Cells

Cover image for Vol. 19 Issue 12

Edited By: Mitsuhiro Yanagida

Impact Factor: 2.855

ISI Journal Citation Reports © Ranking: 2013: 70/165 (Genetics & Heredity); 108/185 (Cell Biology)

Online ISSN: 1365-2443

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2014
Volume 19
Issue 1Issue 2Issue 3

Wishing a prosperous new year, two horses, which carry a red and white twisted rope resembling F-actin, are galloping. This reminds us of pseudopodia that are strongly growing by the power generated from G-actin polymerization.

Mt. Fuji glows with the red tint of the rising sun. A bank of clouds is lying behind the mountain and presenting its characteristic appearance. There are lying clouds in shapes like, from the bottom, rough endoplasmic reticulum, smooth endoplasmic reticulum, and transport vesicles. There is seen above it a bank of clouds well-formed like a Golgi apparatus, and further above it smaller clouds like secretory vesicles. There may also be seen clouds like mitochondria. Wonder if it's just an illusion.

FRET (Fluorescence Resonance Energy Transfer), which is a phenomenon of energy transfer between two adjacent fluorescent molecules, has been applied to visualization of interaction between proteins in living cells and so on. To carry out high-efficiency FRET, not only the distance between two molecules must be very close (less than about 10 nm) but the relative orientation of two chromophores must also be optimized. One of the women in this picture carries the other with attention paid on how they are oriented to each other, and successfully lightens the plum blossoms just like FRET.

Issue 1 - January 2014

Issue 2 - February 2014

Issue 3 - March 2014
Issue 4Issue 5Issue 6

“Yaedatami” or an eightfold straw mat is a tatami specially prepared for use in religious services. A craftsman folds “tatamiomote” or woven soft rush straws with edging of specially designed Nishijin brocade several times over so as to perfectly align patterns of creases of the folded edgings. We use the design to schematically illustrate the somitogenesis in vertebrates. As the U-shaped presomitic mesoderm moves tailward, periodic waves of gene expression form pairs of somites one after another from the anterior end. “Oshitone” or the top cushion has a mark of an embryo woven into it. If you carefully look at the edging of “oshitone”, you can find it bears the process of segmentation in Drosophila, a species which forms all of its segments simultaneously. Cooperated by Isogaki Tatami (Kyoto, Japan)

Two artisans are heaping up lumber in the form of layers. The process where the lumber is going to be piled up perfectly in six horizontal layers reminds us of the cerebral cortex in corticogenesis. One of the artisans below, on whose back a Chinese character ‘kan’ (‘stem’) can be seen, may play the role of the neural stem cell (radial glia cell), the source of new lumber (newly created neurons), and extends a rope (radial glia fibers) upward so as to carry the lumber properly to the top layer. The other artisan above is considered to play a role similar to the cells that secrete reelin. The reelin is a protein that regulates correct migration and positioning of neurons.

A parade of “Kappore”, a dance with “nigaigasa” or double layer umbrellas. A decorative piece of cloth modeled after DNA wraps around each umbrella approximately 2 times to link one umbrella to the adjacent umbrellas. This seems to be a replication of the “beads-on-a-string” structure consisting of a DNA strand and nucleosome cores. Those who hold the “nigaigasa” are men representing the four families of core histones. If you look closely, you can find a towel printed “a-ce” on its tail hanging from one of the men's waist. This looks like the acetylation of a tail of one of the core histones. It has been found that the initiation of transcription is related to histone acetylation. If that is the case, this towel may be a sign to start dancing.

Issue 4 - April 2014

Issue 5 - May 2014

Issue 6 - June 2014

Issue 7Issue 8Issue 9

A scene of Yuzen Nagashi (a process of washing kimono silks) at a pontoon bridge over a river. This bridge actually illustrates the way a number of ribosomes (boats) are attached in a row along a single mRNA chain (a bridge) to translate in parallel, and then form a polysome. There is a grove, which is like a poly-A tail, extending from the bridge to the opposite bank of the river. The pieces of fabric form polypeptide chains synthesized by ribosomes with their edges trimmed in the shape of ‘M’ that is the abbreviation of methionine. Now, the translation processes probably have just terminated at the boats on the far end. The fabric is being folded while it is released from those boats.

Tsushima Tenno Festival has been held every summer in Tsushima city, Aichi prefecture, Japan, for the past 500 years. One of the highlights of the festival is the evening festival called Yoi-matsuri when five boats decorated hemispherically with a lot of illuminated lanterns come down the river. The distinctive shape of the hemispherical decoration reminds us of partially formed clathrin-coated vesicles (CCV). So this summer, we dare to replace the decorations with the one which looks exactly like spherical CCV after completion. On the front side of the river, we place Y-shaped structures modeled on the LDL (low-density lipoproteins) receptor that mediates CCV's capturing LDL. The reflection of the light from the lanterns which represent CCV sparkles on the water surface of the river, and creates a fantastic summer night view.

FoF1 ATPase (also known as ATP synthase) exists in mitochondrial inner membranes and bacterial plasma membranes to synthesize ATP (adenosine triphosphate) by using electrochemical gradient of protons (H+) between inside and outside of the membranes. Fo is integrated in the membranes and thought to have a rotor ring that rotates horizontally. F1 has a dome–like structure comprised of three αand three β subunits that are alternately arranged, which is anchored to the membranes to prevent rotation. Shaft–like subunit connects the center of the rotor ring of Fo and F1. As protons flow down the gradient across the membranes through Fo, the rotor ring of Fo and rotate, and the spin force of against αβ complex is used to synthesize ATP molecules. In this drawing, a waterwheel (Fo) is rotated by the gradient of water (represents proton gradient), and series of three coins (which represent ATP) are generated from the ‘apparatus’ (αβ of F1), which is made from six boards being attached to the front side of the waterwheel. A man in the back takes a role to transport protons to the outside of membranes to produce proton gradient.

Issue 7 - July 2014

Issue 8 - August 2014

Issue 9 - September 2014

     
 Issue 10  Issue 11  Issue 12

This wooden stand called “Marudai” is used for braiding a Kumihimo, a decorative belt used for tying on a kimono sash. This particular Marudai has the top surface engraved with a part of the codon table in order to translate nucleotide sequences of genes into the pattern of Kumihimo (polypeptide chain). The Marudai and bobbins actually play the role of ribosomes and tRNAs that synthesize proteins by translating mRNA sequences into amino acid sequences. The color of threads had changed depending on amino acids. The pattern of Kumihimo being braided in this drawing was obtained from the sequence of human insulin. Nothing can be as cool as gene sequences, which design the pattern of brilliantly colored Kumihimo.

An experimental procedure in behavioral neuroscience known as the Morris water maze is a method to assess the animals' ability of spatial learning and memory. In the experiment, test animals are placed in a pool filled with a pool of clouded water where they are supposed to swim, and scientists record the process how the animals find an invisible platform under the water. In this picture, two scientists are recording the behavior of mice in an experiment using the Morris water maze. It rains reminding us of dendrites of neurons. One woman puts up an umbrella over the other to prevent the recorder from being wet.

Genpaku Sugita (1733–1817) is well-known for his translation of ‘Kaitai Shinsho’ (New Text on Anatomy, in 1774) compiled based on a book of anatomy written in Dutch. This Japanese first full-blown translation from a Western language contributed to the development of medical science in Japan. The masterpiece has been accomplished while many translated terms such as “shinkei” (= nerve) were coined. Over the past 240 years since then, anatomical methods have dramatically improved. Various optical clearing agents have been invented to clear organs including the brain without difficulty. Now, those agents can make brains transparent without damaging any of the fine structures, and enable researchers to observe neurons deep inside the brain. With our great respect to Genpaku Sugita, let us give him components of the optical clearing agents: urea, detergents and aminoalcohol. Behind him stands a vase of a soapberry tree bearing fruit that used to be raw material for detergents in Edo era. A soapberry tree which used to be raw material for detergents in Edo era is now in bloom behind him.

Issue 10 - October 2014Issue 11 - November 2014Issue 12 - December 2014
2013
Volume 18
Issue 1Issue 2Issue 3

Phages have greatly contributed to flourishing of molecular biology, and even today, they remain useful tools for scientists. In this illustration, a “hikeshi” (a firefighter in Edo) is carrying a “matoi” (a standard of his firefighter team as its symbol), which is likened to a phage. Meanwhile lanterns held by firefighters in the back look like bacteria.

Kites are flying in the early spring in a town with the backdrop of Mt.Fuji. Being steered into the wind and skillfully manipulated via string, the kites look like metaphase chromosomes aligned on the equator of the cell.

A piece inspired by a fusion of traditional Japanese beauty and life sciences. There are a Japanese cosmetic brush and a hand mirror on a black board. An embryo fantastically reflected in the mirror suddenly reminds you of something: the brush is a very micropipette, and the embryo must be a subject of an experiment with it. How cleavage of a fertilized egg occurs is drawn like a family crest on a vanity bag, as if it indicates whom these cosmetic tools belong to. In the embryo, a lacZ marker transgene was driven by a connexin43 (Cx43) promoter in neural crest cells. Courtesy of Osamu Chisaka.

Issue 1 - January 2013

Issue 2 - February 2013

Issue 3 - March 2013

Issue 4 April 2013 Cover image for Volume 18 Issue 5Cover image for Volume 18 Issue 6

This month’s feature is molecular chaperones which support correct protein folding. A child represents a protein (or a polypeptide) trying to fold correctly, while a woman represents a chaperone teaching calligraphy. Pieces of paper scattered on the floor are misfolded polypeptides. In reality, accumulation of misfolded polypeptides will cause various kinds of diseases. Chaperones are essential to life.

Speaking of Japanese seasonal tradition in May, you may think of carp streamers flying high over roofs of houses. People fly the carps, wishing for healthy growth of their children. This month, we have painted each scale of a carp streamer, mimicking a mechanism known as lateral inhibition. So, how would you grade the work?

kaiA, kaiB and kaiC genes and their products constitute a core circadian oscillator in the cyanobacterium S. elongates (derived from a Japanese term “kai”, which means rotation or cycle number). KaiA stimulates autophosphorylation of KaiC, whereas KaiB promotes autodephosphorylation of KaiC. It is the particular characteristics of system of cyanobacteria that the three purified Kai proteins and ATP can reconstitute a circadian oscillation in a test tube. We overlay a diagram of this feedback loop on an armillary sphere in an Ukiyoe, which was installed at an astronomical observatory in Edo era. The pattern of roof tiles in the foreground depicts a circadian oscillation.

Issue 4 - April 2013

Issue 5 - May 2013

Issue 6 - June 2013
GTC 18:7 GTC 18:8GTC 18:9

Soma Nomaoi, Soma horse chasing festival, which used to be a religious ceremony, is now an event held in Soso District (north-eastern part of Fukushima prefecture) every July. In ancient times, Samurais captured wild horses roaming around fields, and dedicated them to Kami. Although wild horses were extinct early in Meiji era, later, the ceremony has been revived as an event in which hundreds of horsemen scramble for holy flags. In this cover art, we let warriors on horsebacks carry flags with arms of model organisms, the strongest tools for our research, to join this event. It is Arabidopsis thaliana (right foreground) what colors the field, the stage for the festival, and streamers of double helix are fluttering in the far background.

All the traditional Japanese sweets replicate the development of an early embryo from the first cleavage. Each confectionery expresses, from the back, a fertilized egg undergoing the first cleavage (made from “konashi” or kneaded sweet bean paste, coated with “kudzu” starch), a 2-cell-stage embryo (“aoume” or a green plum), an 8-cell-stage embryo (modified from “kiku” or chrysanthemum), a morula (“domyoji” or a sweet pink mochi), and a tailbud (modified from “magatama” or a claw-shaped bead).  So, which one would you like to start with?
Confectionery Coordination: Gion Narumiya, Kyoto, Japan
      

Tadataka Inou (1745-1818) was over 50 when he retired from the family business and started to learn Western astronomy. At the age of 55, he led a surveying team to travel throughout Japan islands (40,000 kilometers in total) spending 17 years, and accomplished the first Japanese actual measured map, Dai Nihon Enkai Yochi Zenzu, based on the data collected during the survey. The map created about 200 years ago was so accurate that it later amazed the western surveying teams visiting the country. This month’s cover art illustrates Tadataka Inou and his team working together to accomplish a metabolic map. Inspired by Figure 2-35 in The Molecular Biology of the Cell, 5th ed. (Alberts et al. 2008).

Issue 7 - July 2013

Issue 8 - August 2013

Issue 9 - September 2013
GTC 18:10GTC 18:11 GTC 18:12

Protruding from each side of the mountain (represented as cells) like classical cadherin cell adhesion molecules, bridge girders are mutually bound so as to link two summits (cells). This month’s cover art represents the mountain surfaces as plasma membranes, the bridge girders and trails as classical cadherins (where each of the bridge girders shows five extracellular cadherin (EC) domains and a transmembrane domain, while the trails show intracellular domains), huts along the trails as catenins, groves of trees as actin filaments, and cliffs as an intercellular space. Sealed with a word “adhesion” at lower right.

What if there had been an international academic meeting held in Edo era? It must be like this. This picture illustrates how successfully a poster session was being held.  A student-like young man on the far left is performing a presentation on a poster titled “idenshi-kara-saibou-made” (in English, “from Genes to Cells”). Another poster on the right end is the one for the 36th Annual Meeting of the Molecular Biology Society of Japan (MBSJ) (3-6 December, 2013, Kobe). Inside the floor, in the back on the right of the picture, attendees from inside and outside the country are having a discussion over snacks.

Following last month’s issue, let’s imagine what an international academic meeting was like in Edo era. No better place can be found than a Kabuki stage for the oral presentation! The presentation is full house. A presenter (probably the president of this meeting?) stands at the center of the stage, and on his left hand, the chairperson of this session is sitting on the stage. Each paper lantern hanging from the ceiling has a picture of crest imitating model organisms. There is a poster for the 36th Annual Meeting of the Molecular Biology Society of Japan (MBSJ) (3-6 December, 2013, Kobe) behind the presenter.

Issue 10 - October 2013

Issue 11 - November 2013

Issue 12 - December 2013

2012
Volume 17
Issue 1Issue 2Issue 3

Set against the backdrop of Mt. Fuji, a skilled craftsman is fixing a broken wooden barrel by excising damaged bases and then introducing new ones. We liken this to the process of DNA repair thereby recovering hydrogen bonds between each pair of bases.

A fisherman on a cliff is pulling nets as if synchronizing circadian rhythms with the help of light shining down from the sky.

A woman with a hanagasa (a traditional hat decorated with ornamental flowers) is performing a Japanese classical dance.
The ornaments on the hat actually are gap junctions, and some of them are opened and allowing small molecules to pass through.

Issue 1 - January 2012

Issue 2 - February 2012

Issue 3 - March 2012
Issue 4Issue 5Issue 6

Branched waterfalls are reminiscent of the cell lineage of the nematode Caenorhabditis elegans from a zygote to a newly hatched larva.

Regulated cell adhesion and cellular motility underlies dynamic cell rearrangement, which is essential for morphogenesis of various organs. We expressed this process using a picture of a stone levee along a canal.

The Epigenetic landscape, which was firstly depicted by C. H. Waddington in 1950's, has often been used to illustrate cellular differentiation in the process of biological development. Presented on our cover is a timeless representation of the landscape where we see worshippers of Mt. Fuji are being reprogrammed on the slope. Some are climbing high to acquire pluripotency, while others are traversing the foot, and being directly reprogrammed.

Issue 4 - April 2012

Issue 5 - May 2012

Issue 6 - June 2012

Issue 7Issue 8Issue 9

This cover depicts The Bridge in the NGS Rain where people are being exposed to torrents of genomic information, that is, fruits of next generation sequencing. The man standing in the middle of the bridge is pictured deep in thought, considering how to utilize this sequence data set of the ALDH2 gene. Another man, shown to the right with a sake bottle, is eager to know whether he is genetically predisposed with a high tolerance for alcohol or not.

Coloring the summer night sky of Japan, this firework has a theme of the half spindle of animal mitotic cells. A centrosome containing a pair of centrioles is located in the center, and astral microtubules extend to the up to the left, while polar microtubules extend to the opposite direction. Japanese technology currently produces cutting-edge fireworks, and it should not be difficult to produce such fireworks in reality.

The theme of this month is “translation”. The information in DNA is first transcribed into mRNA, which is further converted into a chain of amino acids. This conversion process is called translation and a stop codon marks the end of translation in each mRNA molecule. In the illustration, a fictitious translator on completion of his translation seals the letter with a Chinese character “stop” and amber (which is a nickname for UAG, one of the stop codons). The face of the seal depicts letters of “translation”.

Issue 7 - July 2012

Issue 8 - August 2012

Issue 9 - September 2012

     
 Issue 10  Issue 11 Issue 12

Cilia of eukaryotic cells undulate in a well-balanced motion and play a variety of roles essential to life. The cover art for this month’s issue presents movements of ciliated cells of respiratory epithelium in an analogy to Susuki glasses, a feature of autumn in Japan. The cilia beat in a given direction defined by the structure of roots. In the picture, waves to the right are generating a current. There is a goblet cell that secretes mucus being drawn at the slightly right of the center on the near side of the picture. The moon and geese are also arranged in the picture so as to evoke another feature of autumn in Japan.

The principle mechanism of skin pattern formation in vertebrates can be explained with a mathematical model proposed by Alan Turing (reaction-diffusion system, 1952). In this month's cover art, wild-type and mutant tigers are glaring to the right (at a dragon coming up in December issue). In the front of the wild-type tiger, a rock is illustrated with three peaks representing waves of activator and inhibitor that are observed in the reaction-diffusion system. Furthermore, two bamboos having four internodes represent transmembrane domains in a certain variant of connexin (a subunit of the gap junctions), which is a four-span transmembrande protein and one of the responsible genes for morphological mutation in a vertebrate. 

The cover art of this month is the second part of the series from the November issue. It describes how cellular slime molds assemble into a dragon. The cellular slime molds normally are individual of an amoeba-like unicellular organism. However, when they starve, tens of thousands of cells aggregate in one place to form a cluster. The cluster hugs the ground like a slug, searches for the right place for making spores, and forms a fluting body (lower part of the ground).
When placed in starvation conditions, the cellular slime molds begin to secrete cAMP, which stimulates nearby slime molds to secrete pulses of cAMP. Once they secrete cAMP, they become inactive for a while. As the result, waves of cAMP propagate as they swing in a spiral form (upper part of the sky). 

Issue 10 - October 2012 Issue 11 - November 2012 

Issue 12 - December 2012

2011
Volume 16
Issue 1Issue 2Issue 3

Overlooking Mount Fuji in the distance through the arching wooden bridge, reflected on the water surface, forming complete circles to resemble a pair of spectacles or a 'double helix'

Two sets of segregated chromatids during telophase are depicted as cats cuddled up comfortably beside spindle poles.

A designed family emblem of cell division blends well with traditional Japanese patterns of auspicious omens motifs as pine and bamboo, on the artwork of tiered food boxes in silver lacquer

Issue 1 - January 2011 Issue 2 - February 2011 Issue 3 - March 2011
Issue 4Issue 5Issue 6

Grand Sumo showing a YOKOZUNA or grand champion and “hands” of supporters are pulling the horizontal rope of the kesho-mawashi. They want to tie the kesho-mawashi, but simultaneously, they are making a new horizontal rope from an older vertical rope, using Holliday junction-like structure.

A beautiful woman of the Heian period is pulled by a dog and peeks out from behind a bamboo blind, which is likened to experimental data of DNase I footprint. Data: Genes to Cells 15(5), pp537-552 (2010).

A scene from a Chinese-inspired vigorous dragon dance in a festival in Kyushu, Japan. The dragon is likened to a messenger RNA (mRNA), expressing transcription with DNA template.

Issue 4 - April 2011 Issue 5 - May 2011 Issue 6 - June 2011
Issue 7 Issue 8Genes to Cells

Importance of bidirectional transportation between TOHOKU and surrounding districts. The “Kaido” expressed as a stone-pave street is designed to look like microtubules. Carts going left and pulled by bulls and messengers going right are expressions of motor proteins with cargos in eukaryote cells.

Being inspired by the similarity in the appearance, KOKESHIs are portrayed as metaphase chromosomes, which pair KOKESHIs. It deserves attention that each pair of KOKESHI is designed the same and tied with a thread at their necks (kinetochores) each other.

A huge and prestigious shrine that looks like Izumo-Taisha shrine at a glance. White zigzag paper streamers like a leucine zipper-type transcription factor are tucked in a giant sacred rope (dextrorotatory double-helix). The paper streamers probably bind to specific sequences of dsDNA expressed as a sacred rope.

Issue 7 - July 2011 Issue 8 - August 2011 Issue 9 - September 2011
Issue 10Issue 11Issue 12

Harvest time. Toreutics on a guard of a Japanese sword has a design of ears of rice and a butterfly landing on them. No, they actually are DNA winding around nucleosome.

The Thunder God is generating the action potential, which is not lightning, in a neural network. The illustration is paired with that of December Issue.

Since nerves of higher animals have myelin sheaths, an action potential is propagated rapidly (phenomenon called a saltatory conduction) like the swift wind. The wind god is likened to an action potential that conduct bounces to be propagated.

Issue 10 - October 2011 Issue 11 - November 2011 Issue 12 - December 2011

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