Miracle-dz/UniFAR-FTUs huggingface dataset:
A molecular investigation of germ cell specification and migration within the tilapia Oreochromis mossambicus (Order Perciform)

This thesis reports on the investigation of gonad development in the tilapia, Oreochromis mossambicus. The project aimed to advance the field of reproductive development, aquaculture and pest management by understanding the molecular gene and protein components involved in germ cell specification and migration. Primordial germ cells (PGCs) are progenitors of the germ cell lineage, giving rise to either spermatogonia or oogonia after the completion of gonadal differentiation. Prior to this study, there was little information on the mechanism of PGCs migration leading to the formation of the primordial gonad in Perciform fish. This thesis presents the transcriptomes of ovary and testis, from which we identify the major germ cell components, including the Nanos-1, Vasa-1, Dead end, Oct-4, GFRa-1, SDF and CXCR4. Using a variety of molecular approaches, those components have been further investigated to reveal their conservation, spatial and temporal distribution within larvae and adult O. mossambicus. ; Submitted in the fulfilment of the requirements of the degree of Doctor of Philosophy, University of the Sunshine Coast, 2016.
Synergistically Controlled Stemness and Multilineage Differentiation Capacity of Stem Cells on Multifunctional Biointerfaces

Demonstrations of defined and controlled stem cell culture or differentiation advance fundamental life science research and the possibility of curing diseases. Here, the multifunctional concept of using defined matrix/interface modifications to support cell culture is demonstrated to provide synergistic coupling of concurrently immobilized fibroblast growth factor 2 and chitosan, and the resulting cell culture matrix/interface enables the proliferation of spheroids of adipose stem cells with enhanced stemness and the capacity to (trans‐)differentiate into multiple cell lineages in the mesoderm, endoderm, and ectoderm. The modification and the coimmobilization are performed using a straightforward one‐step vapor‐based coating technology applicable to a wide range of cell culture materials. The coating technology raises the important prospect of designing a material interface that incorporates effective and sustainable factors to determine stem cell fate through the use of a facile multicomponent modification approach on culture substrates.
The Role of RNF40 mediated H2B monoubiquitination in transcription

Active gene transcription is tightly correlated with the occupancy of histone H2B monoubiquitination (H2Bub1) in the transcribed region. Therefore, it is has been commonly assumed that H2Bub1 is an exclusively positively acting histone modification and that increased H2Bub1 occupancy correlates with its requirement for gene expression. In contrast, depletion of the H2B ubiquitin ligases RNF20 or RNF40 alters the expression of only a subset of genes. We show that genes occupied by low to moderate amounts of H2Bub1 are selectively regulated in response to Rnf40 deletion whereas genes marked by high levels of H2Bub1 are mostly unaffected by Rnf40 loss. Furthermore, RNF40-suppressed genes appear to play an equally important role compared to RNF40-dependent genes in the RNF40/H2Bub1 regulatory network. We show that decreased expression of RNF40-dependent genes is highly associated with widespread narrowing of H3K4me3 peaks following Rnf40 deletion. Notably, genes upregulated following Rnf40 deletion, including Foxl2, are enriched for H3K27me3, which is decreased following Rnf40 deletion due to decreased expression of the Ezh2 gene. As a consequence, increased expression of some RNF40-suppressed genes is associated with enhancer activation via FOXL2. Finally, consistent with our previous findings, H2Bub1 is essential for the activation of bivalent genes, whereby RNF40, presumably via H2Bub1, modulates bivalent gene expression via coordination of the active and repressive marks H3K4me3 and H3K27me3, respectively. Together these findings show the complexity and context-dependency whereby one histone modification can have divergent effects on gene transcription dependent upon the activity of other epigenetic regulatory proteins and histone modifications.
Lethal Haplotypes and Candidate Causal Mutations in Angus Cattle

Background If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, developmentally lethal recessive loci can be localized. This analysis comes without the need for observation of the loss-associated phenotype (e.g., failure to implant, first trimester abortion, deformity at birth). In this study, haplotypes were estimated for 3,961 registered Angus individuals using 52,545 SNP loci using findhap v2, which exploited the complex pedigree among the individuals in this population. Results Seven loci were detected to possess haplotypes that were not observed in homozygous form despite a sufficiently high frequency and pedigree-based expectation of homozygote occurrence. These haplotypes were identified as candidates for harboring autosomal recessive lethal alleles. Of the genotyped individuals, 109 were resequenced to an average 27X depth of coverage to identify putative loss-of-function alleles genome-wide and had variants called using a custom in-house developed pipeline. For the candidate lethal-harboring haplotypes present in these bulls, sequence-called genotypes were used to identify concordant variants. In addition, whole-genome sequence imputation of variants was performed into the set of 3,961 genotyped animals using the 109 resequenced animals to identify candidate lethal recessive variants at the seven loci. Conclusions Selective breeding programs could utilize the predicted lethal haplotypes associated with SNP genotypes. Sequencing and other methods for identifying the causal variants underlying these haplotypes can allow for more efficient methods of management such as gene editing. These two methods in total will reduce the negative impacts of inbreeding on fertility and maximize overall genetic gains.
Growth performance of pearl goldfish juvenile carassius auratus cultured in 3 ppt salinity with different exposure time of electric field

ABSTRACT Growth rate of pearl goldfish juvenile Carassius auratus relatively slow to reach market size which will take approximately three months. To accelerate its growth can be done by providing exposure of the fish to low-power electric fields (10 V) via 3 ppt salinity water, with the goal of providing the close isoosmotic conditions, and also to streamline the flow of electricity from the electrodes to the body of the fish. This study aims to calculate the survival and growth rate of pearl goldfish juvenile of S sizes (2‒4 cm of body length) which were maintained at 3 ppt salinity water and treated by different exposure time of electric field (zero, two, four, and six minutes before feeding) with 10 volt electric power. Fish were cultured at a density of 2 fish/L in the (20×30×20 cm3) aquaria in volume of 6 L of water. Test fish had an average body length of 4.11±0.05 cm and the average body weight of 2.89±0.05 g. Exposure time of electric field were zero, two, four, and six minutes before the fish are fed, performed every day as much as three times i.e. morning, afternoon, and evening. The research design used was completely randomized design with four treatments, namely 0, 2, 4, and 6 (time for exposure is zero/control, two, four, and six minute) with three replications. The results show test fishes exposed to 10 volt electrical field for zero, two, four, and six minutes, have no significant effect on survival rate (P>0.05). For growth performance, four minute exposure treatment gives the best results compared to controls (P 0,05). Untuk kinerja pertumbuhan, perlakuan paparan empat menit memberikan hasil yang terbaik dibandingkan kontrol (p<0,05), didukung oleh peningkatan persentase nilai rasio panjang usus terhadap panjang tubuh ikan serta nilai efisiensi pakan yang lebih tinggi. Kata kunci: lama paparan medan listrik, kinerja pertumbuhan, ikan maskoki mutiara
The weakest link A new paradigm for stabilizing the integrin-actin connection

recently shown to lack catalytic activity. 3-5 Interestingly, the pseudo-active catalytic site of ILK binds another adaptor, termed parvin, in a manner resembling a kinase– substrate interaction. 4 Parvins exist in 3 isoforms in vertebrates and are characterized by 2 in-tandem arranged calponin homology (CH) domains that constitute an actin-binding domain. The second CH domain also mediates the interaction with ILK and targets the complex to FAs, providing a direct link between integrins and the actin cytoskeleton. Consequently, ILK-deficient fibroblasts display a severe delay in the formation of FAs. Once established, the FAs are smaller in size and poorly linked to a disorganized actin cytoskeleton, highlighting the importance of ILK in regulating actin engagement downstream of integrins. 3 The integrin–actin linkage, although
clinical manifestations and hemolysis Erythrocyte density in sickle cell syndromes is associated with specific

Dense, dehydrated red blood cells (DRBCs) are a characteristic feature of sickle-cell disease (SCD). DRBCs play a role in the pathophysiology of SCD acute and chronic organ damage because of heightened tendency to undergo polymerization and sickling due to their higher HbS concentration. Relationships between red cell density (assessed with phthalate density-distribution profile method) and several hematologic, biochemical, genetic parameters and clinical manifestations were studied in a large cohort of homozygous patients. The %DRBC was significantly higher in patients who experienced skin ulcers, priapism or renal dysfunction. Presence of α -thalassemia deletions was associated with fewer DRBCs. A multivariable analysis model showed DRBCs to be positively associated with hemolytic parameters like lactate dehydrogenase and bilirubin and negatively with fetal hemoglobin. The %DRBC decreased by 34% at 6 months of hydroxycarbamide (xydroxyurea) therapy. Thus, DRBCs are associated with specific clinical manifestations and biological markers, and may be a useful addition to the biologic and clinical evaluation of SCD patients, since they can easily be measured in a hematocrit tube. the numbers of patients with a -thalassemia deletion among haplotypes. Simple linear regressions were performed for each biologic parameter to search for potential relationship with DRBC. Multiple linear regressions were used to explore models that better predicted RBC density. All the variables (except D 50 ) related to the hematologic, and biochemical profiles that were significantly correlated with DRBC with an univariate threshold ( P <.05) were considered in each model. Models were built using a forward stepwise approach. The final models included the variables that remained significantly associated with RBC density after adjustment for the other variables in the models. R-squares (r 2 ) were used as measures of variance explained by the models. Statistical significance was defined as P value less than 0.05. Correlations were established using Pearson’s correlation coefficient. Statistical analysis was conducted with SPSS 17.0, Statview 5.0 and Prism 4.
Pengaruh Umur Biak dan Posisi Daun terhadap Morfogenesis dari Daun Kentang Hitam (Solenostemon rotundifolius (POIR) JK Morton In Vitro

Plant regeneration via somatic embryogenesis or organogenesis is a key for manipulation of somatic cells in vitro. Organogenesis from leaf inoculum, petiole and stem segments of in vitro black potato (Solenostemon rotundifolius (Poir) JK Morton) is infl uenced by the balance of the concentration of BA and NAA in the culture medium. However, organogenesis could also be affected by factors inherent to the inoculums. This paper reports the infl uence of leaf position on the in vitro shoots and culture age on the formation and production of shoot adventives from leaf inoculum. Leaves excised from shoots of 3–8 week-old culture and leaf position 1-5 from apical to basal was used as inocula. The highest percentage (83.3%) of adventitious bud develops at cultures age of 5 weeks with the average number of shoots 6.1. The highest percentage of bud development occurs at leaf position number 2-4, with the percentage of buds of 83.3, 76.2 and 76.2, respectively with the average number of shoots of 3.19, 2.10 dan 2.38 respectively. Organogenesis that produces the highest shoot production of 18.6 per Petri dish was obtained from leaves derived from the 2nd leaf from apical of 5 week-old culture inoculated on MS medium enriched with 5 mg/l BA and 0.1 mg/l NAA.
Cloning, expression and characterization of an aspartate aminotransferase gene from Lactobacillus brevis CGMCC 1306

ABSTRACT An aspartate aminotransferase (AATase) gene from Lactobacillus brevis CGMCC 1306 was cloned, which contains a 1182-bp open reading frame coding for 393 amino acids (41.43 kDa). When expressed in Escherichia coli BL21 (DE3), the recombinant AATase was purified and subsequently characterized. The recombinant AATase can catalyse the conversion of L-Asp to L-Glu, and the kcat/Km was determined to be 25.5 (mmol/L)−1 s−1 for L-Asp and 207.8 m(mol/L)−1 s−1 for α-ketoglutarate. With optimum temperature as 25 ˚C, the AATase may be a novel and special psychrophilic enzyme which exhibited a good thermal stability below 55 ˚C. The conserved active site residue of AATase was identified as Lys237 by phylogenetic analysis. Secondary structure of the enzyme includes α-helix (39.2%), β-sheet (5.5%), β-turn (8.8%), and random coil (36.5%) by circular dichroism spectral analysis. Phase diagram for the fluorescence data analysis showed that guanidinium chloride-induced unfolding of AATase involved at least one intermediate.
Influence of Leaf Vein Morphology in Okra Genotypes (Malvaceae) on the Oviposition of the Leafhopper species Amrasca biguttula (Hemiptera: Cicadellidae)

Eight genotypes of okra viz., three resistant (HRB 128-1-1, HRB 118-2-1 and HRB 105-22(GS)), two moderately resistant (HRB 108-2-1 and ST 2), two susceptible (HRB 107-4-1 and HRB 121-1-1) to leafhopper, Amrasca biguttula (Ishida 1913) and one cultivated variety (Varsha Uphar) were included to study the influence of leaf vein morphology on the oviposition behaviour of this pest insect. The resistant genotypes harboured significantly (p < 0.05) less leafhopper nymphs and indicated lower visual injuries than the susceptible genotypes. Number of eggs laid per leaf was less in the resistant genotypes (156.8–174.4) than that in susce ptible ones (256.0–280.4), thereby , indicating ovipositional antixenosis. Among the leaf veins (main, lateral and sub veins), lateral veins received maximum number of eggs, except, in genotypes HRB 118-2-1 and HRB 121-1-1, in which subveins received maximum number of leafhopper eggs. The impact of trichome density on main v ein (r = – 0.80) and lateral veins (r = – 0.93) in relation to oviposition was negative and significant. Similarly, trichome length on lateral v eins (r = – 0.77) and sub veins (r = – 0.88) also sho wed a negative and significant correlation with o viposition of leafhopper. Except the thickness of sub veins (r = 0.82), which showed a positive and signif icant correlation with o viposition, the influence of length and thickness of different category of leaf veins was non-significant.
Genetic basis of melanoma: own investigations and literature review

innych nowotworów jest wypadkową działania czynników środowiskowych oraz predyspozycji genetycznych. Genetyka czerniaków jest przedmiotem intensywnych badań, prowadzonych od wielu lat przez różne ośrodki. Do tej pory udało się zidentyfikować kilka genów, których mutacje wiążą się z zachorowaniem. Są to zmiany w genach supresorowych szlaku p16(CDKN2a)-CDK4-Rb i ARF-HDM-p53 oraz mutacje aktywujące przekazywanie sygnału zidentyfikowane w onkogenach RAS i BRAF. Niestety, opisane zmiany dotyczą tylko pewnej grupy chorych i nie stanowią uniwersalnego modelu transformacji nowotworowej. Od wielu lat trwają badania nad różnymi genami, które mogły być przydatne w diagnostyce czerniaków. W pracy przedstawiono przegląd wiedzy o genetyce czerniaka na podstawie prowadzonych od wielu lat badań własnych oraz najnowszych doniesień literaturowych.
Rôle de PKC-a dans la phagocytose et les signaux detransduction médiés par les récepteurs Fe

Phagocytosis of lgG-opsonized particles by macrophages requires the activation of protein kinase C (PKC), a family of prote in serine/threonine kinases. In the present study, we have investigated the role of the PK C-a isoenzyme in FcyR-mediated phagocytosis using clones of the mouse macrophage cell Iine RA W 264.7 overexpressing a dominant-negative (DN) mutant of PK C-a. Overexpression of DN PKC-a bad no effect on the attachment of lgG-opsonized sheep red blood cells, but inhibited their intemalization. Further analysis of the signaling events induced by IgGopsonized sheep red blood cells revealed that whereas tyrosine phosphorylation of Syk was normal, phosphorylation of ERK 1/2 (p42/44) was impaired in DN PKC-a-overexpressing macrophages. These observations suggest a role for PKC-a in the regulation of FcyR-induced phagocytosis and signal transduction.
Analysis of Factors Which are Able to Influence the Admittance of BPJS Ketenagakerjaan Participants towards BPJSTK Mobile by using Technology Acceptance Model 3 (TAM 3)

: Information and Technology are rapidly evolving along with the evolution or the development of an era. BPJSTK Mobile is a service application intended for the participants as a form of expansion in BPJS Ketenagakerjaan Program information services, a medium for complaints if any discrepancy status appears, information regarding the total amount of salary and employee that can be accessed through smartphones. However, the performance of BPJSTK Mobile service is considered poor, given that it is only providing information of the employees at the Surabaya Darmo branch which amount are relatively lower than the total amount of participants who have actually registered. This research aims to analyze factors which are able to influence the admittance of BPJS Ketenagakerjaan participants at Surabaya Darmo Branch towards BPJSTK Mobile by using Technology Acceptance Model 3 (TAM 3). Variables that are used in this study are subjective norm, image, computer self-efficacy, computer/system anxiety, perceived usefulness, perceived ease of use, and intention of use (IU). Respondents chosen for the research are laborers who have not used the BPJSTK Mobile Application registered at BPJS Ketenagakerjaan of Surabaya Darmo branch. The data are gathered directly by conducting the deployment of questionnaires to 150 respondents. The sampling technique used in this research is incidental sampling . The result of the hypothesis test showed that SN or subjective norm does not have any positive effect towards intention to use (IU) and image (IMG) does not have any positive impact towards perceived usefulness (PU).
Impulsive application to design effective therapies against Cutaneous Leishmaniasis under mathematical perceptive

Leishmaniasis is one type of infectious diseases that is generated by different parasites of the Leishmania. The disease spreads in mammals (both human and animal hosts) through the bites of various infected sand fly. species. Leishmania parasites have two important developmental stages in their life cycle such as Promastigote (the proliferative form found in the lumen of the female sand fly) and another one is Amastigote (the proliferative form found inside several types of mammalian host cells). Here we have considered a mathematical model consisting susceptible (uninfected) macrophage cell, early stage infected macrophage cell (Promastigote), late stage infected macrophage cell (Amastigote) and parasite population. We have applied drugs like Sodium Stibogluconate and Meglumine Antimoniate for reducing parasite population in impulsive way under mathematical framework. Our analytical and numerical results justify that controlling parasite population by applying drugs in impulsive way gives realistic outcome. Also we have established the efficiency of the drug dose that contributes a greater effect on the system moving towards the healthy situation. https://doi.org/10.28919/cmbn/3037
Effects of dietary lysine supplementation on performance, egg quality, and development of reproductive system in egg-laying ducks

ABSTRACT This study was conducted to examine five lysine (Lys) levels (0.75, 0.80, 0.85, 0.90, and 0.95%) to estimate the optimal level of Lys for Longyan laying ducks from 22 to 38 wk of age. Nine hundred Longyan ducks aged 22 wk were assigned randomly to the 5 dietary treatments, where each treatment comprised 6 replicate pens with 30 ducks per pen. Lys had no effects on egg production, egg mass, feed conversion ratio, shape index, Haugh unit, yolk colour, yolk weight, or albumen weight, but the egg weight was improved significantly (P < 0.05) by dietary Lys supplementation, whereas the eggshell thickness, eggshell weight, and eggshell proportion decreased significantly as the Lys levels increased. Dietary supplementation of Lys did not affect the reproductive organ indices or the plasma levels of estradiol, luteinizing hormone, or follicle-stimulating hormone, whereas the plasma level of progesterone declined significantly (P < 0.01) as elevation the concentrations of Lys in the diets. In conclusion, the results indicate that the optimal Lys level in Longyan laying ducks diets is 0.80% to produce eggs with normal egg weight without adverse effects on the eggshell weight, eggshell proportion, or eggshell thickness.