Miracle-dz/UniFAR-FTUs huggingface dataset:
COMPUTATIONAL APPROACH FOR IDENTIFYING THERAPEUTIC MICRO RNAs

Results: We have applied the above mentioned approach to Psoriasis. In case of Psoriasis, 29 genes are present in pharmacogenomic database and among those 29 genes only IL6, ABCC1, VDR and ABCG2 contain validated miRNAs with strong experimental evidence in miRTarBase. Binding sites were analyzed for the obtained miRNAs and it has been found that hsa-let-7a-5p, hsa-miR-26a-5p, hsa-miR-345-5p, hsa-miR-125b-5p, hsa-let-7a5p, hsa-miR-27b-3p and hsa-miR-328-3p contain 1 binding site. Similarly hsa-miR-365a-3p, hsa-miR-7-5p, hsa-miR-519c-3p and hsa-miR-520h contain 2 binding sites. and then we have identified the validated miRNA targets from miRTarBase. Finally we have found the connectivity map between the gene and validated miRNA target from miRmap and the number of binding sites were analyzed for each pair (gene-miRNA). Conclusion: Since hsa-miR-365a-3p of IL6, hsa-miR-7-5p of ABCC1, hsa-miR-519c-3p and hsa-miR-520h of ABCG2 contain two binding sites, these miRNAs have a maximum probability to become a therapeutic target of Psoriasis in future and the above mentioned methodology can also be applied for other diseases.
Genome-Wide Survey, Identification and Preliminary Analysis of Xenopus Laevis Bhlh Transcription Factors

The basic helix-loop-helix (bHLH) transcription factors play essential roles in the regulation of eukaryotic growth and development and gene transcription. In this study, we conducted a genome-wide survey using the Xenopus Laevis ongoing genome project databases, and identified 98 bHLH sequences in Xenopus Laevis genome. Phylogenetic analyses revealed those bHLH genes belong to 32 families in the super-groups (A-F) in this research. Gene Ontology (GO) enrichment statistics showed 42 significant GO annotations counted in frequency. Statistical analysis of the Gene Ontology annotations showed that these 98 bHLH proteins tend to be related to transcription regulator activity (GO: 0030528), regulation of transcription (GO: 0045449), DNA binding (GO: 0003677), transcription (GO: 0006350), DNA-dependent regulation of transcription (GO: 0006355), expected from the common GO categories of transcriptional factors. A number of bHLH genes play regulation significant role in special development or physiology processes, such as muscle organ development and eye development. This preliminary study provides useful information for further researches on Xenopus Laevis.
Molecular Evidence on Symbiotic Relationships of Bracovirus and Cotesia Species Based on PTP R Region

Bracovirus is endosymbiont to parasitoid of Braconidae as it plays an important role as immune suppressor to aid successful parasitism of the parasitoid towards the host. The association of the Bracovirus and braconids is still in vague, considering the study on Bracovirus is a new subject on biological control. In this study, clustering and genetic distance analyses of Cotesia bracovirus have been done to disclose the association between both species. PTP R region has been successfully amplified and the sequences used for the molecular evidence. Results from this study convey a highly association between endosymbiont, Bracovirus and their host, Cotesia. 
Long‐term influence of sod cutting depth on the restoration of degraded wet heaths

Temperate heaths have an unfavorable conservation status in most European biogeographical regions. Increasing nitrogen levels promote competitive grass species such as Molinia caerulea, which is a main threat to heathland conservation in Europe. This article investigates the long‐term influence of sod cutting and the resulting changes in soil properties on the heath composition, integrity, and structure. In 15 nature reserves across the northern half of Belgium, we used (1) a large number of plots (203); (2) a broad range of sod cut depths (2–40 cm), and (3) a temporal dimension that describes how long the effects of sod cutting persist (census up to 19 years after sod cutting). Multivariate analyses were used in order to explore the influence of sod cut depth and time after sod cutting on the soil and vegetation properties. There was a positive relationship between sod cut depth and soil pH and water level, and a negative relationship with Al3+, NH4+, and total organic matter (TOM). However, only a limited number of typical (target) species appeared after sod cutting, and then only weakly. Most of the time they remained a minor component of the restored vegetation. Moreover, M. caerulea reappeared and its cover significantly increased during the years following sod cutting. Although we were able to show that sod cut depth has a differential effect on soil properties and vegetation recovery, it also appeared that sod cutting does not restore wet heaths in the long term when applied in regions with high nitrogen deposition.
Long-term measurement of body temperature in the southern hairy-nosed wombat (Lasiorhinus latifrons)

The southern hairy-nosed wombat (Lasiorhinus latifrons) is a nocturnal, fossorial marsupial that has evolved a range of physiological and behavioural adaptations to its semiarid environment. This study describes long-term core body temperature (Tb) of L. latifrons in a population with opportunities for behavioural thermoregulation through burrow use. Tb was measured hourly in 12 captive L. latifrons using implanted dataloggers over a 9-month period from late winter to late autumn. Data were examined for daily patterns, seasonal changes, sex differences and the relationship with environmental conditions (ambient temperature, den temperature and relative humidity). Tb ranged from 30.9 to 38.8°C, and had a distinct nychthemeral rhythm, with peak temperatures occurring at night in line with nocturnal activity. Females had a higher mean Tb (34.9°C) than males (34.4°C). The relationship between external ambient temperature and body temperature was negative, with body temperature decreasing as ambient temperature increased. This study is an important step towards a comprehensive picture of thermoregulation in L. latifrons, which may become vulnerable in the future if environmental temperatures rise and water availability decreases.
Differential Expression of Defense-Related Genes in Sinapis alba and Brassica juncea upon the infection of Alternaria brassicae

Alternaria black spot of rapeseed mustard caused by the necrotrophic fungal pathogen Alternaria brassicae is one of the most important plant diseases in India. A comparative study on defense gene induction was undertaken to explore the signaling mechanisms that govern the defense responses of susceptible Brassica juncea and moderately resistant Sinapis alba, belonging to the family Brassicaceae, to alternaria leaf spot disease. The expression of five selected defense-related genes viz., pathogenesis related (PR)-1, PR-2, PR-3, non-expresser of PR-1(NPR-1) and plant defensin (PDF1.2) was examined after inoculation of the seedlings of B. juncea and S. alba . Transcripts of all five defense-related genes accumulated at a greater level and earlier in S. alba than in B. juncea upon challenge inoculation with A. brassicae locally as well as systemically. Although PDF1.2 is known to be induced only by jasmonic acid (JA) and PR-1 by salicylic acid (SA) in the model plant Arabidopsis thaliana belonging to the family Brassicaceae, PDF1.2 was induced also by SA and PR-1 by JA in both B. juncea and S. alba in the present study. These results suggest that defense signaling pathways in B. juncea and S. alba are different from A. thaliana, . Although JA responsive genes are predominantly induced in most crop plants and model plants against necrotrophic fungal pathogens, both JA and SA responsive genes seem to play an important role in S. alba conferring some resistance against A. brassicae .
Prevalência de Candida spp. na saliva de crianças com leucemia e a influência da lactoferrina na expressão de genes relacionados com a formação de biofilme

PINHEIRO, Raquel dos Santos. Prevalencia de Candida spp. na saliva de criancas com leucemia e a influencia da lactoferrina na expressao de genes relacionados com a formacao de biofilme / Rio de Janeiro, 2014. Tese (Doutorado em Odontologia, area de concentracao em Odontopediatria) – Faculdade de Odontologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 2014. The aim of this study was to identify and quantify Candida spp. isolated from the saliva of leukemic children and correlating the findings with the disease; also analyze in vitro the lactoferrin effect on genes related with Candida albicans biofilm formation. Saliva samples were collected from 32 children with leukemia (G1) and 32 healthy children (G2), intraoral clinical examination was performed to detect the presence of oral lesions. Saliva samples were grown on agar chromogenic. An isolate of Candida albicans of each group and a reference strain (ATCC) were used for biofilm formation . During biofilm formation two new groups were made; one group received treatment with human lactoferrin and that did not receive. For the analysis of gene expression polymerase chain reaction (PCR) was done using the follow primers: HWP1, SAP1, SAP4, SAP5 and SAP6. In G1 the mean age was 5.41 (SD = 2.74) years and 53% were girls. A high frequency of Candida spp was observed (53.10%) and most of them showed a strong CFU growth. Candida albicans was the most frequent species (82.35%). Other Candida species were found. Oral lesions during the oral exam were observed in 12.5% of the sample, and history of oral lesions was reported in 78.1%. In G2, the mean age was 5.97 (SD = 3.10) years and 53% were female. Candida spp. was found in 21.90% and Candida albicans was also the most frequent species (57.14%). There was a statistically significant difference in the colonization of Candida spp. between the groups (p <0.01, chi-square test). Regarding gene expression, all groups expressed HWP1 gene; for SAP1, the biofilm of healthy children and ATCC (10231) treated with human lactoferrin did not express this gene. For SAP 4 gene, the biofilm formed by ATCC (10231) treated with lactoferrin expressed the gene; for SAP5 only the biofilm from healthy children yeast without lactoferrin treating was expressed it. In relation to SAP6 only ATCC (10231) yeast treated with human lactoferrin did not express this gene. We conclude that children with leukemia had a higher frequency of Candida spp. compared to healthy children. It was also observed that human lactoferrin affected the thickness of the biofilm formed by Candida albicans; and that the studied genes had different expression in the groups. Key word: Candida albicans, Candida spp. , children, leukemia, PCR, lactoferrin, SAP1, SAP4, SAP5, SAP6, HWP1.
Generalized potential temperature in non-uniformly saturated atmosphere

This paper deduces the physical explanation and the conservation property of generalized potential temperature θ based on the First Law of Thermodynamics,in order to make clear of the physical basis of moist dynamics of non-uniformly saturated atmosphere.The results show that the generalized potential temperature has the same conservation property as potential temperature and equivalent potential temperature but represent the real non-uniformly saturated atmosphere better.As an application of θ,the generalized moist potential vorticity and its tendency equation has been tested theoretically on new applications.
Subspecific Variations among neotropical Anopheles Mosquitoes, and their Importance in the Transmission of Malaria.

It is gratifying that entomological research in tropical medicine is recognized to the extent of being honored with the Bailey K. Ashford award. Many entomologists, particularly those engaged in taxonomic studies, feel constrained to defend their interests when they associate with those who deal directly with the more “practical” phases of tropical medicine, such as epidemiology, treatment, and control of diseases. Although the term “species control” has become a byword among malariologists, the value of knowing exactly what mosquito one is working with has been reemphasized in recent years with the discovery by Hackett, Martini, Missiroli, and others of the so-called races or varieties of Anopheles maculipennis in Europe. In 1928 the late Dr. F. M. Root, in a paper called “The Present Status of our Knowledge of the Nyssorhynchus group of Anopheline Mosquitoes,” pointed out that only a few years prior to that date, two species were recognized in this deadly group; the forms with the hind tarsi completely white to the tip were named argyritarsis, and those with a black ring at the base of the fifth hind tarsal segment, albimanus.
Isolation and Culture of Protoplasts from Apple Callus and Cell Suspension Cultures

Protoplasts were isolated from actively growing callus and cell suspension cultures initiated from apple leaf discs. Callus and cell suspension cultures incubated in a solution of 0.7 m mannitol, 0.01 m CaCl2, 2% cellulysin, 0.5% macerase yielded protoplasts from about 75% of the callus cells and 90% of the suspension cells. Protoplast viability was 95–98% upon isolation, and 80–85% after a 2-week culture in a modified Murashige and Skoog (MS) medium. About 60% of the protoplasts regenerated cell walls, and 5–10% of the original protoplasts exhibited cell division.
TEKNIK PENGUKURAN MORFOMETRIK PADA IKAN CUCUT DI PERAIRAN SAMUDERA HINDIA

Ikan cucut atau ikan hiu (Elasmobranchii) termasuk kelompok ikan pelagis besar yang memiliki nilai ekonomis. Hampir semua bagian ikan cucut dapat diolah dan dimanfaatkan terutama siripnya yang bernilai ekonomis tinggi yaitu untuk bahan soup. Selain itu daging, tulang, kulit, hati, dan limbah (kepala dan isi perut) semuanya dapat diolah untuk dimanfaatkan. Jenis alat tangkap yang digunakan nelayan Pelabuhan Ratu dan Binuangeun untuk menangkap ikan cucut di perairan Samudera Hindia terutama pancing rawai cucut, jaring insang hanyut, dan pancing rawai tuna dan kadang-kadang tertangkap juga oleh pancing ulur dan tonda. Jenis ikan cucut hasil penelitian Balai Riset Perikanan Laut tahun 2000-2001 di Samudera Hindia teridentifikasi 43 spesies. Jenis yang dominan didaratkan di Pelabuhan Perikanan Tanjung Luar adalah Carcharhinus hemiodon, di Pelabuhan Perikanan Nusantara Cilacap didominansi oleh Alopias pelagicus, dan di Pelabuhan Perikanan Nusantara Pelabuhan Ratu Alopias superciliosis (Anonimus, 2001).
Ontogenetic profile of Antiviral Mx gene and its role in innate immunity in Mrigal, Cirrhinus mrigala (Hamilton 1822)

The aim of this study was to determine the ontogeny of antiviral Mx gene expression in different stages of development of Cirrhinus mrigala (mrigal). For this purpose, three experiments were designed; in the first experiment, Mx expression was observed in eggs, milt, poly I:C treated twitching stage and control twitching stage, and the Mx expression was maximum in eggs. In the second experiment, upregulation of Mx transcript was studied in hatchling stages of mrigal after poly I:C induction by bath treatment, while control hatchlings were studied as such. Hatchlings (both control and treated) were collected at 2-, 4-, 6- and 8-h interval after 24, 48, 72 and 96 h of poly I:C induction. The Mx gene expression showed an increasing trend up to 72 h, where it was highest 3.3-fold higher than the control and then decreased at 96 h where it was threefold higher when compared to the control. In the third experiment, expression of Mx transcript was studied in mrigal fry after intramuscular stimulation with poly I:C for a duration of 28 days. A gradual upregulation of Mx transcript was seen for the experimental period of 28 days. From the study, it is concluded that Mx gene is transmitted from egg and twitching stages and reduced in larvae and fry. Hence, ontogenically, without poly I:C induction, Mx gene is constitutively expressed at early stages indicating the antiviral defences transmitted from parents to offspring in the process of embryonic development. This indicates there is an antiviral Mx defence mechanism playing at early stages of the development for a period of 45 days.
Nanobodies as novel tools to study morphogen function "in vivo"

Nanobodies are small, monomeric antibody mimetic proteins produced by members of the camelid family (camels and llamas), that can be engineered by fusion to proteins carrying a specific function. These “functionalized” protein binders emerge as novel tools for protein manipulation in vivo. During my PhD studies I have generated scaffold-bound nanobodies (SBNs) specific to EGFP in order to interfere with gradient formation of a EGFP-tagged version of the Decapentaplegic (EGFP::Dpp) morphogen. Morphogens are secreted signaling molecules forming concentration gradients and controlling organ patterning and growth during animal development. Drosophila Decapentaplegic (Dpp) is one of the best studied morphogens, but it remains unclear how its concentration gradient is established and how it and controls patterning and growth of the Drosophila wing imaginal disc. In this PhD Thesis I summarize the development and characterization of SBNs and their applications in studying the formation and function of the Decapentaplegic morphogen gradient in the Drosophila melanogaster wing imaginal disc. In the first part of this Thesis, I will discuss how SBNs allowed us to investigate the importance of the Dpp gradient on proliferation and growth control of the wing imaginal disc. Using morphotrap, a SBN that localizes to the outer cell surface, we could completely block gradient formation and study the effect of a loss of the Dpp gradient on patterning and growth. We find that induction of Dpp target genes, and hence patterning, directly depends on the spreading of Dpp. Furthermore, we show that the Dpp gradient is crucial for growth and size control of the medial wing disc region. Moreover, we find that the Dpp gradient is not necessary for proliferation and size control of the lateral region of the wing disc. This data challenges previously published growth models, in which growth control solely depends on the signaling dynamics of Dpp. In the second part of this Thesis I investigate the mechanism of Dpp gradient formation in the wing disc. The wing disc is a complex three-dimensional structure, consisting of two contiguous epithelial layers. How the long-range Dpp gradient is established in the wing disc remains controversial. I have created different SBNs that localize to specific subcellular regions along the apicobasal axis. These SBNs allow us to reduce or block the dispersal of specific gradient subfractions and assess their contribution to wing development. We find that EGFP::Dpp disperses along three main routes: within the epithelial plane of the wing disc, in the luminal cavity between the two epithelial layers and along the basal lamina. Preliminary results suggest that these subfractions encode for different functions of Dpp. While we find that the patterning function of Dpp is encoded by the basolateral subfractions, the growth function of Dpp seems to be influenced by all three subfraction. Further experiments will investigate how target cells perceive and integrate Dpp input from these different subfractions.
Relationship between Grain Shedding and Abscission Layer in Pedicel of Japonica-Indica Hybrid Rices in Korea

In general, Japonica-Indica hybrid rices in Korea exhibit easy shedding compared with the Japonica type. To obtain detailed information on the grain shedding of Japonica-Indica hybrid rices, thc tensile breaking strength required to detach rice grain from its pedicel was examined by using unbonded gauge type transducer and automatic null balancing recorder. The abscission layer between pedicel and spikelet was investigated anatomically. Varieties Yushin and Milyang 21 of Japonica-Indica hybrid, and Jojeongjo and Akibare of Japonica type rices were used. Yushin and Jojeongjo belong to easily shedding group and other two varieties belong to medium or persistent one. The results obtained are as follows: 1. In both Yushin and Milyang 21 of Japonica-Indica hybrid, tensile breaking strength decreased with time from 1 week after heading, reached the minimum after 3 weeks, and then did not vary until the harvest time. In Japonica type rices, on the other hand, the strength of Jojeongjo decreased slightly with time after heading, while that of Akibare increased gradually with time after heading (Fig. 1). 2. Grain ripening of Japonica-Indica hybrid rice was earlier than that of Japonica type rices. In the former, grain on the upper portion of the ear became to bc almost fully ripe at 3 weeks after heading (Fig. 2). From this result and Fig. 1, it appears that in the Japonica-Indica hybrid rice the decrease in tensile breaking strength is related with its ripening. 3. In the varieties Yushin, Milyang 21 and Jojeongjo, number of grains detached from the abscission region of the pedicel gradually increased with time after heading, while in variety Akibare, number of grains detached from the bent portion of the pedicel increased (Fig. 3 and Table 1). 4. The abscission layers of Yushin and Milyang 21, Japonica-Indica hybrid rice, appear to have one to two layers of large parenchymatous cells, while that of Jojeongjo, Japonica type rice, consists of one layer of somewhat smaller parenchymatous cells with some sclerenchymatous cells. In the former, the splitting in the abscission layer was observed at three weeks after heading, but no such splitting in the abscission layer was observed in Jojeongjo even at harvest time. Furthermore, no abscission layer was observed in the Japanese cultivar, Akibare (Fig. 4). 5. From the above results, it appears that the tensile breaking strength is closely related to the width of supporting zone which is composed of central vascular tissue and sclerenchyma tissue. The occurrence of splitting in the abscission layer probably has no relationship to tensile breaking strength. 6. Based on the abscission layer characteristics, the rice varieties used in this experiment could be classified into three types; i) abscission layer exists and splitting occurs at maturity (Yushin and Milyang 21), ii) abscission layer exists but no splitting occurs until harvest time (Jojeongjo), and iii) abscission layer is absent (Akibare).