Sufu defines the balance of hindbrain progenitor cells maintenance and differentiation

Suppressor of fused (Sufu) was identified as a regulator in Hedgehog signalling. Study shown that Sufu knockout mice were embryonic lethal at E9.5, exhibiting cephalic deformities, open neural tube and ventralized spinal cord resulting from ectopic Shh signalling, implying indispensable role of Sufu during development of central nervous system. Aiming to investigate the functions of Sufu in hindbrain neurogenesis, we used B2‐r4‐Cre to knock‐out Sufu in rhombomere4 (r4). We observed significant enlargement of mutant r4 size from E10.5, exhibiting more profound expansion in the dorsal region at E12.5. Accordingly, BrdU pulse labelling and sox2 staining showed region specific increased accumulation of proliferative progenitor cells, indicating differential maintenance of progenitor pools along the dorsoventral axis of r4. Tuj1 staining also showed impaired differentiation of the ectopic progenitor cells. Further analysis revealed dramatic dorsal expansion of pMN and p2 progenitor domains in mutant r4. Surprisingly, the FoxA2 positive floor plate, and the dorsal p0 domain were not severely affected, suggesting a novel domain specific regulation of neural progenitor pools by Sufu. Intriguingly, we observed spatial upregulation Gli1 and Gli2 transcription factors, selectively at the region that resides highly proliferative cells, implying that the increased cell proliferation could be caused by the changes of Gli transcription factors. Indeed, concomitant deletion of Gli2 in the Sufu mutant largely rescued the aberrant phenotypes. These findings clearly showed the requirement of Sufu to suppress Gli2 to conduct a domain specific regulation of hindbrain progenitor maintenance and differentiation. Our study demonstrates novel function of Sufu to ensure a tightly controlled progenitor pools maintenance and differentiation, mainly achieve by suppressing Gli2 activation.postprin

MMP14 regulates the lineage progression of hypertrophic chondrocytes

It is traditionally believed that chondrocytes and osteoblasts are two separate lineages with hypertrophic chondrocytes (HCs) being the terminal stage of chondrocyte differentiation, culminating in apoptosis. However, we have shown that HCs can contribute to the full osteoblast (Obs) lineage in vivo. MMP14 is a transmembrane matrix metalloproteinase responsible for matrix remodeling that is highly expressed at the chondro‐osseous junction which coincides with the transition from HCs to Obs. Knockout of Mmp14 in mice results in impaired endochondral ossification. To test whether loss of MMP14 has an impact on the HC to Obs transition, we have employed a genetic recombination approach to track and compare the fate of HCs in wild‐type and Mmp14 conditional and total null mutants. Both complete and conditional deletion of MMP14 activity results in increased number of HC‐descendent cells in the trabecular bone. Surprisingly, conditional knockout of Mmp14 in HC‐descendent cells results in increased trabecular bone formation. Our results suggest that MMP14 in general negatively regulates HC to Obs transition.postprin

Kinesin-1 is involved in chondrocytes adhesion to extracellular matrix and motility

Intercalation movement of proliferative chondrocytes is crucial for their columnar organization which is essential for proper function of growth plate cartilage. The conventional motor protein kinesin‐1 directionally transporting various cargos along microtubules might be involved in this polarized cell movement. Kinesin‐1 is suggested to transport unknown cargo(s) modulating focal adhesion (FA) turnover which is a key step in cell movement. To investigate kinesin‐1’s role in chondrocytes intercalation, we generate kinesin‐1 heavy chain (Kif5b) knockout mouse. In the growth plate of KIF5B deficient mouse, we observed abnormal cell morphology and disrupted columnar structure. Isolated mutant chondrocytes show reduced motility and adhesion ability to ECM proteins. Vinculin, the key regulator of focal adhesions, is found as a potential protein associated with KIF5B in mouse chondrocytes. Further study will investigate whether KIF5B affects chondrocytes motility and adhesion via FAs modulation.postprin

Identification and characterization of long-range SOX9 enhancers in limb development

The transcription factor Sox9 is a master regulator of skeletogenesis. Heterozygous mutations of human SOX9 result in Campomelic Dysplasia (CD), in which affected individuals display distinct abnormalities in limbs and other skeletal assemblies. Recently, chromosomal translocations and deletions at >1Mb from SOX9 have been detected in some CD patients, suggesting the requirement of long‐range regulatory elements in mediating both spatiotemporal and dosage of Sox9 during limb development. To this end, we exploited several published ChIP‐Seq data, and identified nine, evolutionarily conserved, putative limb enhancers of SOX9, namely E1Sox9 to E9Sox9. Transgenic mouse embryos carrying E1Sox9‐driven LacZ reporter showed discrete transgene expression at the pre‐scapular domain where endogenous Sox9 is also expressed. Bioinformatic analyses on our candidate enhancers result in the identification of several signaling effector binding motifs, and indeed, we revealed that BMP‐Smad and Shh‐Gli pathways are possible upstream regulatory networks that govern the spatiotemporal and dosage of limb Sox9 expression via our predicted enhancers, respectively. Our results unveil the underlying molecular control in governing the complex patterning of Sox9 expression in the developing limb, and provide new molecular insight to the etiology of CD syndrome.postprin

The roles of Irx3 and Irx5 in mammalian inner ear development

Iroquois genes encode a family of transcription factors containing TALE class homeodomain. They are regarded as prepatterning genes in Drosophila sensory organ development. There are six members (Irx1Irx6) of Iroquois genes in mouse and human. Irx3 and Irx5 are linked genes on mouse chromosome 8, which are involved in many mammalian developmental processes. However, the roles of Irx3 and Irx5 in mammalian hearing loss are poorly understood. To identify the function of these two genes in inner ear development, we have investigated two reporter knock‐in mouse mutants: Irx3lacZ, Irx5EGFP, and a double knock‐out mutant: Irx3/5‐/‐. Irx3 and Irx5 have overlapping expression domains in the developing inner ear. Physiological tests indicated that the Irx3lacZ and Irx5EGFP mutant mice displayed hearing defect, while Irx3/5‐/‐ mice were embryonic lethal. Although paint filling analysis showed the normal cochlea morphology of Irx3lacZ and Irx5EGFP mutant mice, ectopic inner hair cells have been discovered in the organ of Corti. Interestingly, the cochlear duct of Irx3/5‐/‐ mice was enlarged and shortened, and the basal part of the cochlea was fused with the saccule. There were also numerous vestibular‐like ectopic hair cells surrounded by ectopic Sox2‐positive cells in the greater epithelial ridge of cochlea. The organ of Corti was malformed with neither hair cell differentiation nor supporting cell differentiation at E16.5. In summary, our results indicate that Irx3 and Irx5 cooperatively pattern the boundary between the vestibule and the cochlea and they are important for the cochlear sensory neural cell specification.postprin

Ontologies and Computational Methods for Traditional Chinese Medicine

Perinteinen kiinalainen lääketiede (PKL) on tuhansia vuosia vanha hoitomuoto, jonka tarkoituksena on terveyden ylläpito, tautien ennaltaehkäisemisen ja terveydellisten ongelmien hoito. Useat vuosittain julkaistavat tutkimukset tukevat hoitojen tehokkuutta ja PKL onkin jatkuvasti kasvattamassa suosiotaan maailmanlaajuisesti. Kiinassa PKL ollut suosittu hoitomuoto jo pitkään ja nykyään sitä harjoitetaan rinnakkain länsimaisen lääketieteen kanssa. Viime vuosikymmeninä tapahtuneen tietotekniikan kehityksen ja yleistymisen myötä myös PKL:n menetelmät ovat muuttuneet ja tietotekniikkaa on alettu hyödyntämään PKL:n tutkimuksessa. PKL:n tietoa on tallennettu digitaaliseen muotoon, minkä seurauksena on syntynyt suuri määrä erilaisia tietokantoja. Tieto on jakautunut eri tietokantoihin, joiden terminologia ei ole yhtenevää. Tämä aiheuttaa ongelmia tiedon löytämisessä ja tietoa hyödyntävien sovellusten kehittämisessä. Tässä työssä selvitetään, mitä PKL on, ja mikä sen asema on nykyään Kiinassa ja muualla maailmalla. Työn tarkoituksena on tutkia PKL:n tietoteknisten sovelluksen kehittämistä ja siihen liittyviä haasteita. Työssä perehdytään PKL:n ontologioiden ja semanttisten työkalujen toimintaan, sekä PKL:n laskennallisiin menetelmiin ja niiden tarjoamiin mahdollisuuksiin. Lisäksi kerrotaan uusimmista kansainvälisesti merkittävistä projekteista ja pohditaan tulevaisuuden näkymiä. Jo kehitetyt PKL:n tietotekniset sovellukset tarjoavat uusia mahdollisuuksia tiedon etsimiseen ja parantavat tutkijoiden mahdollisuutta jakaa tietoa ja tehdä yhteistyötä. Tietokoneavusteiset diagnoosityökalut ja asiantuntijajärjestelmät tarjoavat mahdollisuuksia lääkärin tekemän diagnoosin varmistamiseen. Tulevaisuudessa laskennallisia menetelmiä hyödyntäen voitaisiin tarjota terveyttä ja hyvinvointia edistäviä palveluja verkossa.Traditional Chinese Medicine (TCM) has been used for thousands of years in China for the purposes of health maintenance, disease prevention and treatment of health problems. Several published studies support the effectiveness of TCM treatments and the global use of TCM is constantly increasing. In China, Western and Chinese medicine are practiced in parallel. During the past few decades, the use of information technology in medicine has increased rapidly. The development of information technology has opened up new possibilities for information storage and sharing, as well as communication and interaction between people. Along with the growing use of information technology, a wide variety of patient databases and other electronic sources of information have emerged. However, the information is fragmented and dispersed, and the terminology is ambiguous. The objective of the thesis is to examine the position of TCM today, and to find out what changes and new opportunities the modern information technology brings for different aspects of TCM. This study describes how ontologies and semantic tools can be utilized when collecting existing knowledge and combining different databases. Also different computational methods and TCM expert systems are introduced. Finally, the most recent projects in the field of TCM are discussed and the future challenges are reflected. The computational methods for TCM, such as diagnostic tools and expert systems, could be very useful in anticipating and preventing health problems. E-science and knowledge discovery offer new ways for knowledge sharing and cooperation. TCM expert systems can be used to generate diagnosis or automatic clinical alerts. In the future, a comprehensive and easily accessible online health service system could be developed and used to improve the health and well-being of people

Network Pharmacology Approaches for Understanding Traditional Chinese Medicine

Traditional Chinese medicine (TCM) has obvious efficacy on disease treatments and is a valuable source for novel drug discovery. However, the underlying mechanism of the pharmacological effects of TCM remains unknown because TCM is a complex system with multiple herbs and ingredients coming together as a prescription. Therefore, it is urgent to apply computational tools to TCM to understand the underlying mechanism of TCM theories at the molecular level and use advanced network algorithms to explore potential effective ingredients and illustrate the principles of TCM in system biological aspects. In this thesis, we aim to understand the underlying mechanism of actions in complex TCM systems at the molecular level by bioinformatics and computational tools. In study Ⅰ, a machine learning framework was developed to predict the meridians of the herbs and ingredients. Finally, we achieved high accuracy of the meridians prediction for herbs and ingredients, suggesting an association between meridians and the molecular features of ingredients and herbs, especially the most important features for machine learning models. Secondly, we proposed a novel network approach to study the TCM formulae by quantifying the degree of interactions of pairwise herb pairs in study Ⅱ using five network distance methods, including the closest, shortest, central, kernel, as well as separation. We demonstrated that the distance of top herb pairs is shorter than that of random herb pairs, suggesting a strong interaction in the human interactome. In addition, center methods at the ingredient level outperformed the other methods. It hints to us that the central ingredients play an important role in the herbs. Thirdly, we explored the associations between herbs or ingredients and their important biological characteristics in study III, such as properties, meridians, structures, or targets via clusters from community analysis of the multipartite network. We found that herbal medicines among the same clusters tend to be more similar in the properties, meridians. Similarly, ingredients from the same cluster are more similar in structure and protein target. In summary, this thesis intends to build a bridge between the TCM system and modern medicinal systems using computational tools, including the machine learning model for meridian theory, network modelling for TCM formulae, as well as multipartite network analysis for herbal medicines and their ingredients. We demonstrated that applying novel computational approaches on the integrated high-throughput omics would provide insights for TCM and accelerate the novel drug discovery as well as repurposing from TCM.Perinteinen kiinalainen lääketiede (TCM) on ilmeinen tehokkuus taudin hoidoissa ja on arvokas lähde uuden lääkkeen löytämiseen. TCM: n farmakologisten vaikutusten taustalla oleva mekanismi pysyy kuitenkin tuntemattomassa, koska TCM on monimutkainen järjestelmä, jossa on useita yrttejä ja ainesosia, jotka tulevat yhteen reseptilääkkeeksi. Siksi on kiireellistä soveltaa Laskennallisia työkaluja TCM: lle ymmärtämään TCM-teorioiden taustalla oleva mekanismi molekyylitasolla ja käyttävät kehittyneitä verkkoalgoritmeja tutkimaan mahdollisia tehokkaita ainesosia ja havainnollistavat TCM: n periaatteita järjestelmän biologisissa näkökohdissa. Tässä opinnäytetyössä pyrimme ymmärtämään monimutkaisten TCM-järjestelmien toimintamekanismia molekyylitasolla bioinformaattilla ja laskennallisilla työkaluilla. Tutkimuksessa kehitettiin koneen oppimiskehystä yrttien ja ainesosien meridialaisista. Lopuksi saavutimme korkean tarkkuuden meridiaaneista yrtteistä ja ainesosista, mikä viittaa meridiaaneihin ja ainesosien ja yrtteihin liittyvien molekyylipiirin välillä, erityisesti koneen oppimismalleihin tärkeimmät ominaisuudet. Toiseksi ehdoimme uuden verkon lähestymistavan TCM-kaavojen tutkimiseksi kvantitoimisella vuorovaikutteisten yrttiparien vuorovaikutuksen tutkimuksessa ⅱ käyttämällä viisi verkkoetäisyyttä, mukaan lukien lähin, lyhyt, keskus, ydin sekä erottaminen. Osoitimme, että ylä-yrttiparien etäisyys on lyhyempi kuin satunnaisten yrttiparien, mikä viittaa voimakkaaseen vuorovaikutukseen ihmisellä vuorovaikutteisesti. Lisäksi Center-menetelmät ainesosan tasolla ylittivät muut menetelmät. Se vihjeitä meille, että keskeiset ainesosat ovat tärkeässä asemassa yrtteissä. Kolmanneksi tutkimme yrttien tai ainesosien välisiä yhdistyksiä ja niiden tärkeitä biologisia ominaisuuksia tutkimuksessa III, kuten ominaisuudet, meridiaanit, rakenteet tai tavoitteet klustereiden kautta moniparite-verkoston yhteisön analyysistä. Löysimme, että kasviperäiset lääkkeet samoilla klusterien keskuudessa ovat yleensä samankaltaisia ominaisuuksissa, meridiaaneissa. Samoin saman klusterin ainesosat ovat samankaltaisempia rakenteissa ja proteiinin tavoitteessa. Yhteenvetona tämä opinnäytetyö aikoo rakentaa silta TCM-järjestelmän ja nykyaikaisten lääkevalmisteiden välillä laskentatyökaluilla, mukaan lukien Meridian-teorian koneen oppimismalli, TCM-kaavojen verkkomallinnus sekä kasviperäiset lääkkeet ja niiden ainesosat Osoitimme, että uusien laskennallisten lähestymistapojen soveltaminen integroidulle korkean suorituskyvyttömiehille tarjosivat TCM: n näkemyksiä ja nopeuttaisivat romaanin huumeiden löytöä sekä toistuvat TCM: stä

The Quality Control of Puerariae Lobatae Radix and Puerariae Thomsonii Radix

Puerariae Lobatae Radix (PLR) and Puerariae Thomsonii Radix (PTR) are traditional Chinese medicines used interchangeably in clinical practice, even though they possess significantly different chemical profiles. The aim of this thesis was to differentiate PLR from PTR using various analytical instruments coupled with chemometrics. Morphological results illustrate PLR possessed distinct macroscopic and microscopic features as compared to PTR. UPLC results reveal isoflavonoids were the major chemical constituents in both species, with the content of puerarin in PLR significantly greater than in PTR. PLS-DA models demonstrate both UPLC and HPTLC chromatographic fingerprints were effective in differentiating PLR from PTR. PLSR coupled with Raman spectra was able to predict the TPC and antioxidant capacities of PLR and PTR. The pharmacological results illustrate PLR possessed significantly greater anti-diabetic, cytoprotective and anti-cancer activities as compared to PTR. In summary, the results reveal the chemical fingerprints coupled with chemometrics was effective in differentiating PLR from PTR, and PLR was morphologically, chemically and pharmacologically different from PTR. This thesis provided further insight into the comprehensive nature of the quality control of two similar species and recommends changes to their descriptions in the pharmacopoeias. This will ultimately improve the quality, safety and efficacy of herbal products

ZHENG-Omics Application in ZHENG Classification and Treatment: Chinese Personalized Medicine

With the hope to provide an effective approach for personalized diagnosis and treatment clinically, traditional chinese medicine (TCM) is being paid increasing attention as a complementary and alternative medicine. It performs treatment based on ZHENG (TCM syndrome) classification, which could be identified clinical special phenotypes by symptoms and signs of patients even if they have a different disease. However, it caused controversy because ZHENG classification only depends on observation, knowledge, and clinical experience of TCM practitioners, which lacks objectivity and repeatability. Although researchers and scientists of TCM have done some work with a lot of beneficial methods, the results could not reach satisfactory with the shortcomings of generalizing the entire state of the body or ignoring the patients' feelings. By total summary, mining, and integration of existing researches, the present paper attempts to introduce a novel macro-microconcept of ZHENG-omics, with the prospect of bright future in providing an objective and repeatable approach for Chinese personalized medicine in an effective way. In this paper, we give the brief introduction and preliminary validation, and discuss strategies and system-oriented technologies for achieving this goal

Perception of mathematics game’s design for primary school: based on teachers’ opinions

Unmistakable methods can be used for learning, and they can be looked at in a few viewpoints, particularly those identified with learning results. In this paper, we introduce an examination with a specific end goal to think about the design adequacy and development’s requirement of a game based learning (GBL) approach that is about to be used in LINUS screening for mathematics subject in primary school. The approach includes multiple interaction forms regarding addition and subtraction operation in mathematics based on LINUS constructs. Ten teachers from three different school located in Batu Pahat have participated in the study. The investigations involving survey activity by using questionnaire as the instrument. While breaking down the results, the outcomes demonstrated that the kids observed the amusement to be all the more fulfilling if there are less levels and more colours. Since the survey were conducted to a very common type of school in Malaysia, we believe game that is about to be built based on opinion gained could be utilized as an effective instrument in primary schools to strengthen pupils' lessons