Diamond professorial fellowship for imaging chromosomes by coherent X-ray diffraction

Lead Research Organisation: University College London
Department Name: London Centre for Nanotechnology

Abstract

The chromosome is the repository of all genetic material in eukaryotes. Humans have 22 separate chromosomes in their karyotype plus the special X/Y sex-determining chromosome. One third of the life cycle of the chromosome, metaphase, is involved with mitosis, whereby the safe transmission of all the genetic material to progeny cells is undertaken; the remainder of the time, interphase, is when the genes are are unpacked and transcribed to operate the cellular machinery and copied to make the daughter chromosomes. Mitosis is an elaborate combination of cellular processes of which the protective packaging of the DNA into safe organized bundles - the chromosomes - is one of the fundamental steps. The first levels of organization of chromatin, the double helix, the nucleosome (DNA-histone protein complex) and the 'beads on a string' (BoS), packed into 30nm fibres with histone H1, have represented major breakthroughs in biology resulting in Nobel prizes. These levels of structure, summarized in Fig 1, are now relatively well understood, although there are still several possible models discussed for the fibre, and possibly some interesting diversity also. It is the next level of structure of the metaphase chromosome where the organisation becomes complicated and the research proposed here will begin to have impact. To protect the genes in transit though mitosis, they are packed together tightly into the familiar X-shaped chromosome pairs that separate once the cell division begins. The 30nm fibres are presumably coiled up in a regular superstructure at the next level within the chromatids; this coiling is the structure we intend to image by X-ray methods. This packing is achieved by scaffolding proteins which also protect the DNA mechanically from forces that could damage the genes. The optical refractive index of this dense complex is high enough that chromosomes are most easily visualized in metaphase. The high density also means that metaphase chromosomes can be handled under the optical microscope with micromanipulation tools that are familiar to cytogeneticists. We plan to use these same tools for sample preparation for the X-ray imaging experiments. This proposal plans to undertake a full 3D imaging of the chromosome at the 30nm resolution level. The metaphase chromosome is of necessity a compact object devoid of hanging strands or loops that would interfere with mitosis. This works well with the use of a 'support' constraint in phasing methods partly developed by the PI. The chomosome electron density is high for a biological substance because of the tightly-packed phosphorus (and counterions associated with the DNA). Staining methods might even be developed to enhance the X-ray contrast. The well-defined boundary will enable support-seeking methods such as 'shrinkwrap' to work effectively. Because they are readily manipulated, as described above, individual chromosomes can be isolated and mounted on pins or fiducialised membranes for measurement. Yet the chromosome is not expected to be a highly reproducible structure like the ribosome or certain viruses that can be solved by MX or the newer method of serial crystallography with an X-ray free-electron laser. In fact, much of the interest in cytogenetics lies in the differences between chromosomes of individuals and between copies from the same individual. All this can be contemplated and attempted in the context of the HRC.

Technical Summary

The CXD imaging will be made at I-13 in the forward ('small-angle') scattering geometry as originally used by Miao and also by Nishino. I-13 has a 250m distance from the source, so any disturbance of its wavefront by the front-end windows and collimating lenses or mirrors will be minimised. The coherence-defining aperture, clean-up slits, sample and beamstop will all be placed in vacuum to avoid parasitic scattering. The frozen sample will need an additional cryoshield to prevent sublimation. A temporary setup in air will be used while the cryo-vacuum system is under development; air dried samples will be used for this or else a 'cryostream' cooling system. The samples will be less than 5 microns in size, which is the field of view planned. The Medipix detector has 55 micron pixels, so it will have to be placed at least 1.8m away when used with 8keV X-rays. Lensless imaging, as in MX crystallography, requires phases to be determined for the recorded diffraction data. From there the image is achieved with a simple Fourier transform (FT). In Nishino's work and most of the recent work of the PI, this requires three essential steps. As pointed out by Sayre in 1953, the data must be oversampled with respect to the Shannon sampling frequency of the object; only then is the inversion problem overdetermined. This in turn implies the object being imaged must be 'compact' so that a 'support' or molecular envelope can be defined for use as a real-space constraint on the iterative FT phasing algorithm. Last, but not least, local minima must be avoided in a large-dimensional space, for which the Fienup Hybrid Input-Output (HIO) algorithm is superb. The craft of efficiently phasing the data follows from strategic use of computational tricks and alternation and recycling of methods, as is standard in MX crystallography. The PI's group has more than 10 years of experience with these phasing methods and several notable successes.

Planned Impact

A major outcome of the planned work will be a new way of looking inside the chromosome that could have widespread impact in medicine. Knowledge of the coiling and packing architecture within the metaphase chromosome could have unimaginable medical implications, for example new classes of genetic defect in the population and consequential new therapies. The Harwell Research Complex (HRC) has a wide-platform activity in Correlative Microscopy, called OCTOPUS, of which one 'leg' is X-ray imaging. Coherent Diffractive Imaging (CDI) is just one part of this activity, but potentially high-impact. Other groups at Diamond and in the UK have interest in phase contrast imaging, which, like CDI, needs the high coherence of a 3rd generation synchrotron source. Another technique is X-ray microscopy, both scanning and transmission, which will also be a big activity at Diamond. CDI is more specialized and less developed than the other imaging techniques. However the greatest impact will come about by strong interactions between these communities, which will be greatly facilitated by our on-site presence at Harwell. Dave Clarke, of the Harwell Central Laser Facility (CLF), is interested in developing a common sample mounting for Correlative Microscopy and a system of fiducials. Since optical microscopy is the starting point and frame of reference in chromosome biology, we will adopt this system, which will immediately benefit the X-ray imaging methodology. Microscopy generally will have greater impact when this is possible to apply as many imaging modes as possible to the same sample set. Similarly, we would expect to interact strongly with the users and developers of the just-ordered JEOL 200kV TEM in the HRC. X-ray to electron Correlative Microscopy would be very new and of high impact. We will develop the cryofreezing capabilities as part of the project with particular attention to encouraging the formation of vitreous ice, which is desirable to avoid spoiling the images with ice crystals (which show strong phase contrast at their boundaries). The cryofreezing methods we will need to develop can learn from the experience of Baumeister (Munich), who has developed the methodology for TEM. The CCP4 software distribution activity will be located also in the HRC. It is hoped this will be extended to cover inter-operability with imaging data. There is considerable potential impact in the development of common file formats, phasing algorithms, image segmentation methods, tomographic reconstruction etc. We have already had useful interactions with Robert Attwood of Diamond's I-12 imaging beamline, who is an expert on imaging software methods, and would hope to involve him in common activities through the HRC. Lensless imaging using X-rays (i.e. using the phasing of CXD instead of a lens) is the method to be exploited in the current proposal. The distribution of the once- developed methods by a professional organization will bring impact to all parties. In the future, there lies the exciting prospect of CDI enabling general purpose 3D imaging of biological samples, limited as always by the radiation damage. There is a lot of current excitement about collecting entire diffraction patterns in a single shot of X-rays at free-electron laser (XFEL) sources; it is estimated that samples will be immune to radiation damage at atomic resolution for 10-20 femtoseconds, which is an achievable pulse length. The further development of CDI through this proposal will have impact on XFEL science.

Publications

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Bhartiya A (2021) X-ray Ptychography Imaging of Human Chromosomes After Low-dose Irradiation. in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

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Botchway SW (2021) Contribution of advanced fluorescence nano microscopy towards revealing mitotic chromosome structure. in Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology

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Bradley RS (2017) 3D X-Ray Nanotomography of Cells Grown on Electrospun Scaffolds. in Macromolecular bioscience

 
Description We have discovered new ways to image the genetic material within chromomes
Exploitation Route Enormous potential applications of SBFSEM and FLIM methods in medicine and biology.
Sectors Education,Healthcare

URL https://www.youtube.com/watch?v=auf1gg8eGIo
 
Description Invited talks at conferences and planning meetings of facilities and institutes
First Year Of Impact 2013
Sector Education,Healthcare
Impact Types Cultural,Societal,Economic

 
Description Chair of Royal Society Conference "Real and reciprocal space X-ray imaging", 2013 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact A double event, supported as part of the Royal Society scientific meetings, was organized in February 2013 in London and at Chicheley Hall in Buckinghamshire by Dr A. Olivo and Prof. I. Robinson. The theme that joined the two events was the use of X-ray phase in novel imaging approaches, as opposed to conventional methods based on X-ray attenuation. The event in London, led by Olivo, addressed the main roadblocks that X-ray phase contrast imaging (XPCI) is encountering in terms of commercial translation, for clinical and industrial applications. The main driver behind this is the development of new approaches that enable XPCI, traditionally a synchrotron method, to be performed with conventional laboratory sources, thus opening the way to its deployment in clinics and industrial settings. The satellite meeting at Chicheley Hall, led by Robinson, focused on the new scientific developments that have recently emerged at specialized facilities such as third-generation synchrotrons and free-electron lasers, which enable the direct measurement of the phase shift induced by a sample from intensity measurements, typically in the far field. The two events were therefore highly complementary, in terms of covering both the more applied/translational and the blue-sky aspects of the use of phase in X-ray research. optics, image processing

Since Roentgen's discovery well over a century ago, X-ray imaging has been based on attenuation. While this is an effective and reliable approach, it is known to have limitations whenever objects with similar attenuation characteristics have to be distinguished, as this leads to poor image contrast. One possible solution is to generate image contrast by exploiting phase changes in the X-ray wavefront rather than attenuation: this approach is called X-ray phase contrast imaging (XPCI). Its main advantage is that the term responsible for phase effects (the unit decrement of the real part of the refractive index) is much larger than the imaginary part, responsible for attenuation. In many practical cases, this difference can be up to 1000-fold. Hence, albeit that it can be difficult to detect, phase is intrinsically a much stronger effect and can therefore lead to much higher image contrast if appropriately exploited.

The first X-ray phase contrast image dates back to 1965 and was acquired by Bonse & Hart [1] with a crystal interferometer, which has been bearing their names since. We were fortunate enough to have Prof. Hart attending our conference. Following a significant attempt by Ando & Hosoya [2] in 1972, the idea of using a crystal-based X-ray interferometer was picked up again in the 1990s, in particular by Momose's group. XPCI exploded in the mid-1990s, and, to the best of our knowledge, the first of a long series of papers published from 1995 onwards is Momose's [3], published on 1 January 1995, on results already presented in the previous year. Momose and his group continued to explore medical and biological applications of XPCI implemented with the Bonse-Hart interferometer, as reported, for example, in their 1996 Nature Medicine paper [4].

Almost simultaneously, researchers started to explore a different approach to the use of crystals in XPCI-namely the use of a perfect crystal as an 'angular analyser'. It was in fact observed that the faint distortions in the wavefront caused by phase changes translate directly into slight changes in the X-ray direction (X-ray refraction), which could therefore be picked up by a system with sufficient angular sensitivity like a perfect crystal. The fact that the refraction angle is proportional to the gradient of the phase shift gave rise to the name 'differential' XPCI, which is common to other methods listed below, such as edge-illumination and Talbot interferometry. The most famous paper pioneering this approach is the 1995 Nature letter by Davis et al. [5]. It has to be said, however, that a few known examples exist that pre-date that deservedly famous paper, where effectively the same method had been used to address specific problems, and the results were published in journals with relatively limited diffusion [6,7]. Another paper on the crystal method appeared later in the same year [8] and the method continued to be explored later, leading to some of the first simplified phase retrieval algorithms [9] and extraction of the first quantitative X-ray 'dark-field' images [10-12] (qualitative dark-field images had already been presented in [5]).

Still in 1995, a much simpler implementation, based on free-space propagation, was proposed by Snigirev et al. [13]. Through this approach, phase contrast images are acquired without the need for any additional optical element, simply by increasing the distance between sample and detector. If the source possesses enough coherence, this is sufficient to detect phase-induced interference fringes at the boundaries of the imaged objects. In the following year, Wilkins et al. [14] demonstrated that this approach works also with polychromatic radiation, something that was impossible to observe before as the use of a crystal automatically renders the beam monochromatic. Interestingly, similar images had been obtained before, but the substantially improved image contrast had not been interpreted on the basis of phase effects (e.g. [15]). Owing to its simplicity of implementation, the free-space propagation technique is still widely used, and it is the only one to date to have reached the in vivo stage for human patients [16].

A method that combines the angular selectivity principle exploited with crystal 'analysers' and the simplicity of free-space propagation, called edge-illumination XPCI, was developed in the late 1990s [17]. As the name suggests, it performs a fine selection on X-ray direction by illuminating only the physical edge of the detector pixels, and by doing so it eliminates the need for a perfect crystal, opening the way to polychromatic and divergent X-ray beams. This was later exploited to adapt the method for use with conventional X-ray sources [18], which also led to the first quantitative phase retrieval performed with incoherent illumination of the sample [19].

In the early 2000s, a further approach was introduced, based on the adaptation to X-rays of Talbot and Talbot-Lau interferometers, well-known methods among the optics community. This adaptation was made possible by novel nanofabrication techniques, which enabled the development of gratings with a pitch sufficiently small to produce Talbot 'self-images' [20] at X-ray wavelengths when coherently illuminated. The approach was first demonstrated in the 'Talbot' set-up by David et al. [21] and by Momose's group shortly afterwards [22]; a few years later, Pfeiffer et al. [23] demonstrated that the Talbot-Lau arrangement could also be implemented with X-rays, opening the way to the use of laboratory sources. In a further study, it was shown that the same set-up could also be used to obtain quantitative dark-field images [24], along the lines of what was previously done with analyser crystals [10-12]. To extract phase and dark-field signals, a technique called phase stepping is employed, in which one of the two (Talbot) or three (Talbot-Lau) gratings is scanned with respect to the others, and individual images are acquired at each scanning position. Later on, Wen et al. [25] developed a similar approach, which, however, employed a single grating, and, instead of using a phase-stepping method to isolate the different signals, did so by applying a Fourier-based analysis method to a single frame.

Quite remarkably, most of the leading figures behind the above developments agreed to participate in the conference, which meant that most of the above topics were covered in the various talks. Another interesting aspect that emerged is that the field is continuing to evolve, with new examples of implementation already being presented at this same meeting (e.g. Wen et al. [26] realized gratings with nanometric pitch which led to a hybrid between Talbot and Bonse-Hart interferometry), new implementation schemes (e.g. [27]), use of materials as common as paper to replace gratings or analysers [28] and much more. This extreme liveliness indicates a prosperous future for the area, both in terms of new methods and new applications, and definitely looks encouraging in terms of ultimately reaching the 'translation into mainstream application' goal which inspired this meeting.
Year(s) Of Engagement Activity 2013
URL http://rsta.royalsocietypublishing.org/content/372/2010/20130359
 
Description Invited talks at conferences: 20 per year 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Invitation accepted to travel to international conference, give invited talk and discuss with participants at length.
Year(s) Of Engagement Activity 2006,2007,2008,2009,2010,2011,2012,2013,2014,2015,2016,2017
URL http://www.ucl.ac.uk/~ucapikr/talk16.htm
 
Description Size Strain conference, chair 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Beams of penetrating radiation, such as X-ray photons, neutrons and electrons, provide the basis for a whole host of tools for probing material structure, composition and properties. In particular, over a century of using reciprocal space methods based on diffraction has allowed reveal- ing intricate details of complex molecules, collecting multi-scale infor- mation about different levels of structural organization, observing the course of reactions and processes, etc.
Although methods and approaches in this field are well-established, the proliferation of hardware and software tools in the recent years has led to a considerable increase in the ease of access to many techniques. This increases their attractiveness for the community, and an ever great- er number of researchers make use of large scale facilities and advanced instruments.
The 7th Size-Strain conference 'Diffraction Analysis of the Microstruc- ture of Materials' (SS-VII) was held at Oxford from 21 to 24 September 2015. The 80 participants were able to enjoy four days of college living at Trinity College, whilst all plenary conference sessions were held at the nearby Department of Engineering Science of the University of Oxford. On the final day of the conference, a half-day trip was arranged to the large scale facilities at the nearby Harwell campus, Diamond Light Source (DLS), the UK synchrotron, and ISIS neutron spallation source. The conference planning, booking and logistics were run extremely smoothly and efficiently by the DLS events team. The meeting was co- chaired by Ian Robinson (University College London) and Alexander Korsunsky (University of Oxford).
The scientific programme of the conference continued the themes set and addressed at the previous meetings in Garmisch-Partenkirchen (SS- V) and Giens (SS-VI). These address the investigation of material micro- structure and properties by diffraction methods, with a special interest in their application to polycrystalline materials, the methodologies for the study of lattice defects, residual stress and texture in thin films, nano- structures and at surfaces, line-broadening analysis, line-profile fitting, and modelling based on the fundamental parameters. In addition to the new and by now well-established topics of microbeam diffraction and co- herent diffraction introduced at SS-VI, the SS-VII saw the addition of X-ray and neutron imaging and Pair Distribution Function (PDF) analysis.
The conference was opened with an inspiring plenary talk by Cev Noyan (Columbia Uuniversity) entitled "The Anatomy of a Powder Dif- fraction Experiment", which prompted a lively discussion and set the mood for open and active exchange of views, experiences and ideas. Further invited presentations were given by Clare Grey (Cambridge) on "X-ray Diffraction Methods for Studying Structure and Dynamics in Batteries and Supercapacitors", Thomas Hansen (ILL) on "Stacking faults in ice", Felix Hofmann (Oxford) on "Probing Atomic Scale Defects", Alberto Leonardi (Indiana) on "Microstrain in nanomaterials: XRD line profile interpretation enhanced by Molecular Dynamics simulations",
http://dx.doi.org/10.1016/j.matdes.2016.10.055
0264-1275/© 2016 Elsevier Ltd. All rights reserved.
Reinhard Neder (Erlangen) on "Size and strain analysis of small highly disordered nanoparticles" and by Tobias Schulli (ESRF) on "The nanodiffraction Beamline ID01/ESRF: diffraction microscopy and coherent diffraction imaging for high resolution structural analysis". Instead of split- ting the conference into parallel sessions, the chairs took the decision to treat all participants to the opportunity to obtain a complete view of the research landscape in the field by attending all focused sessions on the key topics, including Disorder, Defects, Morphology, Nanoscience, Thin Films, Alloys, Oxides, Strain Mapping, Dynamics, and 3D Imaging.
The Virtual Special Issue of Materials and Design captures some of the interesting work presented at the conference in the form of con- tributed full length articles. Particular care has been taken by the ed- itorial team to ensure that the publications were in line with the journal scope and editorial preferences described in the editorial note [1]. This Virtual Special Issue demonstrated the wide variety of applications of advanced diffraction methodologies in modern materials science. The full details of published articles can be found at the VSI web page:
http://www.sciencedirect.com/science/journal/02641275/vsi/ 10ZD8MPKNFV.
Acknowledgements
The Special Issue Guest Editors express sincere appreciation to all authors and reviewers for their dedication in putting together a high quality body of joint work. Our gratitude is also due to the Materials & Design editorial team and technical staff for their cooperation and excel- lent service. Financial support from Diamond Light Source towards run- ning Size-Strain VII is gratefully acknowledged, as are the contributions to event organization from Zoe Cattell and Sarah Bucknall (DLS), and Eva Williams (Engineering Science). Particular thanks are due to Kevin Knott CVO, Estates Bursar of Trinity College, for the permission to use college facilities.
References
[1] A.M. Korsunsky, A.G. Gibson, G.D. Nguyen, M. Sebastiani, X. Song, T. Sui, Editorial note - on the aims & scope and priority areas in Materials & Design, Mater. Des. 88 (2015) 1377-1380.
Ian Robinson is group leader in the Condensed Matter Physics and Materials Science De- partment at Brookhaven National Laboratory, and Professor at the London Centre for Nanotechnology, University College. His research is currently focused on the development of coherent X-ray diffraction methods for image the structure of nanoparticles. His re- search makes extensive use of synchrotron radiation and Free Electron Lasers. He built a beamline at Brookhaven to develop Surface X-ray Diffraction and a second one at Argonne for Coherent X-ray Diffraction. One outcome of the work was the discovery of Crystal Truncation Rods, for which he was awarded the Surface Structure Prize in 2011 and the Gregori Aminoff Prize in 2015.
Year(s) Of Engagement Activity 2015
URL http://www.diamond.ac.uk/Home/Events/2015/Size-Strain-VII.html
 
Description UK-Japan Chromosome workshop at ACC5 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Policymakers/politicians
Results and Impact HIGH$RESOLUTION$-$FLUORESCENCE$MICROSCOPY$ Session$chair$Prof.$Hans$de$Jong$
$
1.30!
Prof.&Stanley&Botchway&
New&fluorescent?obes&for&chromosome&imaging:&FLIM?& PLIM?&beyond&
2.00!
Mr&Christophe&Lynch&
SuperRsolution&imaging&of&chromosomes&
2.15$
Ms&Rawin&Poonperm&
Study&of&KIF4&localization?&mitotic&chromosomes&
2.30$
Ms&Ana&Estandarte&
FLIMIaging&of&chromosomes&
2.45$-$3.05$BREAK$!
ELECTRON$MICROSCOPY$ Session$chair$Prof.$Yoshinori$Nishino$
3.05!
Dr&Shinichi&Ogawa&
for&imaging&of&soft&materials&such&as&chromosome?&
3.35!
Mr&Teruo&Hashimoto&&
3D&Serial&Block&face&imaging?paration?& applications&
3.55!
Mr&Kohei&Kaneyoshi&&
Inner&chromosome&structure&observed&by&FIB/SEM&&
$WORKSHOP$END$PRESENTATION$$ Session$chair$Dr$Shinichi$Ogawa!
4.10$
Prof.&Susumu&Uchiyama&
Construction&of&cell&lines&for&metaphase&chromosome& ChIP&using&CRISPR/Cas9&&system&&
4.40$
Prof.&Kiichi&Fukui&
Closing&Speech&
$4.45$-$5.10$BREAK!
5.10$- 6.00!
Prof.&Ian&Robinson/&& Prof.&Kiichi&Fukui&&
& All&welcome!
Discussion&for&future&grant˜plications?&SACLA& beamtime&
7.00$pm$onwards$-$Evening$meal$$ $ Pola$Pola$Restaurant$and$Bar$$
End$of$meeting$
2ndUK-Japan Chromosome Workshop, 1st May 2015 Venue: Kasetsart UniversityBangkok, Thailand
Programme$
Friday$1st$May$2015!
9.00!
Prof.&Ian&Robinson!
Welcome&Speech&
9.05!
Dr&Kornsorn&Srikulnath&
Introduction&to&Kasetsart&University&
X$RAY$IMAGING$$ Session$chair$Prof.$Susumu$Uchiyama$
9.15!
Prof.&Yoshinori&Nishino&!
Chromosome&structure&asRvealed&by&X?ray& Scattering&!
9.45!
Dr&Mohammed&Yusuf&!
Chromosome&sample?paration&for&X?rayIaging!
10.05!
Dr&Joerg?hwenke!
Quantitative&phase&imaging&of&human&chromosomes& and?clei&using&X?ray&diffraction!
10.25!
Dr&Bo&Chen!
A&Brief&Comparison&of&SEM?&TXMIaging&of& Human&Chromosomes&
10.45$-$11.05$BREAK!
FLUORESCENCE$MICROSCOPY! Session$chair$Prof.$Stanley$Botchway!
11.05!
Prof.&Hans&de&Jong&
Advanced&high&?&resolutionµscopy&?&status?& prospects.&An&Overview&
11.35!
Dr&Naoki&Wada&
A&hybrid&cell&line?&human?&plant&&
11.55!
Ms&Gina&Ratnasari&&
Single&chromatid&chromosome?paration&using&RNAi&
12.10$
Ms&Rinyaporn&Pengchat&
The&effect&of&calcium&ion&on&chromosome&structure&
$12.25$-$01.30$LUNCH$!
Year(s) Of Engagement Activity 2016
URL https://acc5bangkok2015.kasetsart.org/acc5/