Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathways that govern hematopoietic stem cell fate

Hematopoietic stem cells (HSCs) compose a rare population of undifferentiated cells, residing in the bone marrow of adult individuals, ensuring life-long maintenance and replenishment of the blood system. This fantastic achievement is possible owing to two special characteristics of the HSCs: their ability to make copies of themselves (self-renew), and their capacity to differentiate to all lineages of the blood system. The process of blood formation, hematopoiesis, is a dynamic and complicated process reliant on the strict balance between a large number of regulatory factors. Hematopoietic stem cell transplantation (HSCT) is currently used to treat hematological disorders such as leukemia. Cord blood is an easily accessible source of stem cells, however the number of HSCs extracted from one cord are not enough to successfully transplant adult patients. This limitation could be circumvented if we were capable of expanding stem cells outside the body. However, to reach this goal it is crucial to first understand how these cells are regulated in their natural environment. More knowledge is required to understand the interplay between different intrinsic and extrinsic factors participating in governing HSCs. Ex vivo HSC expansion would not only be beneficial for making HSCT accessible to a larger number of patients, but would also enable profound studies of HSC function and regulation. In this thesis we have identified and evaluated factors involved in the regulation of HSC fate decisions. Transforming growth factor-β (TGFβ) is one of the most potent inhibitors of hematopoietic stem and progenitor cell (HSPC) proliferation in vitro. However, the complete mechanism behind the growth inhibitory effect and the precise function of this signaling pathway in vivo, is still to be unraveled. Our results in Article I suggest that Smad4 is a limiting factor for TGFβ-mediated Smad signaling critical for long-term HSC function and demonstrate that the level of Smad4 can modulate the response to TGFβ in human cells. Furthermore, we describe a negative regulatory role of the Smad signaling pathway on human HSPCs during regeneration after transplantation - affecting self-renewal capacity but not lineage choice. In Article II, we identify a transcriptional network, consisting of important stem cell regulators, TGFβ(Smad4)/GATA2/p57, that is critical in controlling the proliferation of primitive hematopoietic cells. We further generate a database of genes that become deregulated following TGFβ stimulation, and demonstrate that GATA2 is involved in a large part of the TGFβ response. At last, in Article III, we have studied the role of Pigment epithelium-derived factor (PEDF) in murine hematopoiesis. Our findings demonstrate that PEDF is an important regulatory factor for HSC regeneration and that PEDF in vivo works in a cell-autonomous fashion. For the first time, we propose a role of PEDF in HSC biology. Taken together, the work in this thesis has contributed to the field by increased understanding of mechanisms and factors involved in the regulation of HSC fate decisions. (Less)
Characterization of Mesenchymal Stem Cells from Human Cortical Bone

Background Context: Mesenchymal stem cells (MSC) are being used for spine and orthopaedic surgical and research applications. Bone marrow and fat are the most commonly used sources of these cells. Purpose: To describe a new technique allowing the isolation and expansion of human MSC from cortical bone. Study Design: MSC from human cortical bone (vertebral lamina) were isolated, expanded, and verified in vitro. Methods: Human MSC were isolated from laminar bone obtained during surgery (decompression/laminectomy). They were then cultured and assessed using fluorescence-activated cell sorting techniques for MSC markers, colonyforming unit assays, and multilineage differentiation. Results: Isolated and cultured cells demonstrated MSC markers and trilineage differentiation confirming their stemness. International Journal of Translational Science, Vol. 2016, 71–86. doi: 10.13052/ijts2246-8765.2016. 005 c © 2016 River Publishers. All rights reserved. 72 J. S. Fernandez-Moure et al. Conclusion: A novel method for the isolation of MSC from cortical bone has been described. These cells have significant current and future application in spine and orthopaedic surgery; and both the source of the cells and particular characteristics of the cortical bone derived MSC have advantages over currently used MSC obtained from other sources.
Dinitrogen fixation in the unicellular diazotroph Crocosphaera watsonii

Crocosphaera watsonii is an abundant organism in the tropical and subtropical ocean and is considered to be an important contributor to the marine nitrogen cycle due to its ability to fix dinitrogen (N2). Light-dark cycles were used to determine the diel variation in N2 fixation and photosynthesis in the unicellular diazotrophic cyanobacterium C. watsonii WH8501. A first set of experiments showed that N2 fixation and photosynthesis were separated temporally with N2 fixation during the dark and photosynthesis during the light periods. Due to the storage of carbon reserves during the day and subsequent respiration at night, C. watsonii links its cellular nitrogen and carbon metabolism. N2 fixation and photosynthesis appear to be regulated and optimized by a circadian rhythm. Gene expression analysis demonstrated cyclic patterns of the major genes involved in nitrogen and carbon metabolism. However, the patterns of expression did not coincide with patterns of activity with the gene expression peaking several hours prior to the activity. In a second set of experiments, N2 fixation and photosynthesis were simultaneously measurable at population level in the respective dark period, i.e. an artificial light period instead of a dark period. Single-cell analysis using nanoSIMS revealed that the co-occurrence of N2 fixation and photosynthesis at population level was probably due to each individual cell’s capability of coping with the O2-sensitivity of the nitrogenase enzyme. In addition, single-cell rates showed large variability with the highest rate about six times higher than the mean rate during the normal dark N2 fixation. The experimental work with a pure culture of a diazotroph provided the opportunity for a re-assessment of the two commonly used methods for the measurement of N2 fixation in both field and laboratory studies, i.e. the 15N2-tracer addition method and the acetylene reduction assay.
PEMANFAATAN KULIT SINGKONG SEBAGAI ALTERNATIF BAHAN BAKU EDIBLE FILM

ABSTRAK Bahan makanan pada umumnya sangat sensitif dan mudah mengalami penurunan kualitas. Salah satu cara untuk mencegah atau memperlambat fenomena tersebut adalah dengan pengemasan yang tepat. Bahan pengemas dari plastik banyak digunakan dengan pertimbangan ekonomis dan memberikan perlindungan yang baik dalam pengawetan. Penggunaan material sintetis tersebut berdampak pada pencemaran lingkungan, sehingga dibutuhkan penelitian mengenai bahan pengemas yang dapat diuraikan. Alternatif penggunaan kemasan yang dapat diuraikan adalah dengan menggunakan edible film. Edible Film didefinisikan sebagai lapisan yang dapat dimakan yang ditempatkan di atas atau di antara komponen makanan, dapat memberikan alternatif bahan pengemas yang tidak berdampak pada pencemaran lingkungan karena menggunakan bahan yang dapat diperbaharui dan harganya murah. Polisakarida seperti pati dapat digunakan sebagai bahan baku pembuatan edible film menggantikan polimer plastik karena ekonomis, dapat diperbaharui, dan memberikan karakteristik fisik yang baik. Hasil Penelitian menunjukkan bahwa dengan semakin meningkatnya konsentrasi gliserol, maka semakin meningkat pula ketebalan dari edible film tersebut ( 0,097 ± 0,0029% ) pada pati kulit ubi kayu 5 gram dengan variasi gliserol 0,8 ml/gram). Daya kuat tarik yang tertinggi diperoleh pada pati kulit ubi kayu dengan variasi gliserol 0,6 ml/gram yaitu sebesar 2,0 GPa ± 0,4. Sedangkan persentase pemanjangan (elongasi) tertinggi pada pati kulit ubi kayu 5 gram dengan variasi gliserol 0,8 ml/gram yaitu 11%±4%. Penambahan gliserol tidak menunjukkan adanya penambahan gugus fungsi pada edible film, tetapi terjadi interaksi ikatan gaya Van Der Walls dan ikatan hidrogen antar molekul penyusun edible film.
Enhancement of immunological activity in exo-biopolymer from submerged culture of Lentinus edodes with rice bran

The objective of the present study was to determine the possible immune-enhancing effects of a substance extracted from a submerged culture of Lentinus edodes with rice bran (SLRB). According to the results obtained by measuring the in vitro macrophage activity of the exo-biopolymer from SLRB, it appears to exhibit activity similar to that of LPS, and this activity seems to occur in a dose-dependent manner. According to the results obtained by measuring splenocyte proliferation, the exo-biopolymer appears to induce an increase in proliferation of approximately 1.4-fold compared to the control group. We measured the proliferation of bone marrow cells in order to evaluate gut immunity and, according to our results, proliferation was increased to 109% that of the control group, and was similar to that associated with LPS. In order to characterize the enhancement of immunological activity in vivo, we orally administered the exo-biopolymer (25, 50, 250 mg/kg bw) to C3H/He mice, and then measured the macrophage activity, determining that the activity was higher than that of the controls at concentrations of 50 and 250 mg/kg. Therefore, the exo-biopolymer from SLRB can be considered to be a useful a BRM agent, as it clearly allows some protection against immunological diseases.
What is for Dinner? First Report of Human Blood in the Diet of the Hairy-Legged Vampire Bat Diphylla ecaudata

Blood-feeding is one of the most specialized foraging habits, as it demands extreme morphological, physiological, and behavioral adaptations. Three species of vampire bats (Desmodus rotundus, Diaemus youngi, and Diphylla ecaudata) rely on blood as their only food. The first two are considered less specialized, whereas D. ecaudata is frequently pointed out as a bird-specialist. We assessed what prey D. ecaudata consumes in the Caatinga dry forests of northeastern Brazil, a highly modified biome. How the species would behave in a situation of scarcity of wild birds and increase in the availability of domestic animals? Could Diphylla have been induced to include also mammals in its diet? Using PCR-amplification of DNA fragments in the feces of D. ecaudata, we detected the regular consumption of chicken blood and human blood — a novel prey for this species. Our results suggest that the diet of D. ecaudata is more flexible than expected. The record of humans as prey and the absence of blood from native species may reflect a low availability of wild birds in the study site, reinforcing the impact of human activities on local ecological processes. This also opens a range of research possibilities on vampire bats in the Caatinga, both on the species' biology and the consequences for public health, considering the potential increase in the transmission of rabies in the region.
Analysis on SSR Information in Transcriptome and Development of Molecular Markers in Rosa roxburghii

One hundred and six thousand five hundred and ninety unigenes from fruit transcriptome of Rosa roxburghii Tratt were screened using MISA software. A total of 21 711 SSRs that occurred in 18 155 unigenes were identified,and the frequency of these SSRs was 20.37% and mean distance was 1.68 kb in the unigenes. Trinucleotide,tetranucleotide and dinucleotide were major types,accounting for 26.87%,26.77% and 24.93%,respectively. AG/CT,AAG/CTT were respectively most frequent motifs in dinucleotide and trinucleotide repeats,accounting for 17.80% and 11.55%,respectively. Using the Primer 3.0,42 primers were designed and synthesized based on different dominant motifs types,and verified with R. roxburghii germplasms for validity and Rosa germplasms for transferability. The results showed that the products of 23 primers are clear and effective,23 pairs could be transferable to Rosa germplasms and 12 pairs were polymorphic among the 16 R. roxburghii germplasms. The results indicated that the unigenes generated from transcriptome sequencing in R. roxburghii can be used as an effective source to development SSR markers. The large quantities of SSR markers will provide more reliable markers for map structure,analysis of genetic polymorphism for R. roxburghii and its closely related species.
HUMAN UMBILICAL CORD TISSUE SERVES AS AN IDEAL RESERVOIR OF MESENCHYMAL STEM CELLS AS COMPARE TO THE FULL TERM UMBILICAL CORD BLOOD

Mesenchymal stem cells (MSCs) are a subset of adult stem cells that were initially found in the bone marrow along with hematopoietic stem cells (HSCs) and endothelial stem cells [1]. Likewise any other stem cells, MSCs are able to undergo selfrenewal and differentiate into not only its mesodermal lineage such as osteocytes, adipocytes, chondrocytes [2-4] and connective tissues [4, 5] but also the endodermal and ectodermal lineages such as hepatocytes [6], cardiomyocytes [7], neurons [8] and astrocytes [9]. Unlike other main stream stem cells such as embryonic stem cells and HSCs, the feasibility of acquiring MSCs for clinical therapies become more readily available not only because of their lesser ethical cues but due to their existence in many other sources such as umbilical cord tissue [10], cartilage [11], amnions [12], adipose tissue [13], umbilical cord blood [14] and peripheral blood [15].
Detection and Characterization of a Multi-drug and Multi-metal Resistant Enterobacterium Pantoea sp. from Tannery Wastewater after Secondary Treatment Process

In this study, an enterobacterium was isolated from treated tannery wastewater and characterized as gram-negative, rod shaped, motile, and lactose fermenting bacterium. Further, based on the 16S rRNA gene sequence analysis, the bacterium was identified as Pantoea sp. with accession number KJ576899. The antibiotic and heavy metal resistant property of isolated bacterium was investigated by the disk diffusion method on Muller- Hinton and nutrient agar medium amended with the increasing concentrations of various toxic metal ions, respectively. Results showed that the isolated bacterium was sensitive for amikacin, ampicillin, cefepime, cetriaxone, chloramphenicol, levofloxacin, meropenem, nalidixic acid, piperacillin and tobramycin, resistant for aztreonam, carbenicillin, cefotaxime, ceftazidime, ciprofloxacin, cotrimoxazole, imepenam, moxifloxacin, streptomycin and tetracycline, but intermediate for amoxicillin and gentamicin. In addition, the bacterium also showed the Minimum Inhibitory Concentration (MIC) values of 250, 500, 160, 190, 600, 700, 500, 380, 600 and 350 ? g ml-1 for Cu, Cr, Cd, Co, Zn, Fe, Ni, Pb, Mo and As, respectively with a plasmid DNA of 33.5 kb. This multi-drug and multi-metal resistant bacterium can be used as a potential agent for the bioremediation of metal contaminated sites.
Detection of blaNDM, blaDIM, blaIMP, blaVIM and blaCTX-M-15 beta- lactamase Genes among Pseudomonas aeruginosa and Acinetobacter baumannii Strains Isolated from Two Hospitals of Tehran, Iran

Background: In this study, we evaluated the existence of bla NDM , bla DIM , bla IMP , bla VIM , bla CTX-M-15 beta-lactamase genes among Pseudomonas aeruginosa and Acinetobacter baumannii strains isolated from hospitalized patients. M aterials and Methods: From June 2013 to May 2014, thirty-four nonduplicate nonconsecutive isolates of A. baumannii and P. aeruginosa were isolated from blood, respiratory tract, wound, sputum and urine samples of patients from hospitalized in two hospitals in Tehran, Iran. Antibiotic susceptibility test was performed by Kirby-Bauer disc diffusion method according to CLSI guidelines. In this study, the frequency of MBL (metallo-beta-lactamase) producers was evaluated by CDDT (Combined disk diffusion test) and prevalence of bla NDM , bla DIM , bla IMP , bla VIM and bla CTX-M-15 genes were evaluated by PCR and sequencing methods among P. aeruginosa and A. baumannii strains isolated from hospitalized patient of Tehran during 2013 -2014 years. Results : Of thirty-four non-fermenter isolates, 24 (70.58%) P. aeruginosa and 10 (29.41%) as A. baumannii were isolated and identified. High rate of resistance to common antibiotics were detected specially among A. baumannii isolates that showed 100% resistance to 4 of tested antibiotics. The CDDT results reveal that 4 (16.66%) of the P. aeruginosa isolates and 1 (10%) of the A.baumannii were positive for production of MBLs. The prevalence of bla CTX-M-15 gene among 10 A. baumannii isolates was 4 (40%), and for IMP-1, 2 (20%). The 𝑏𝑙𝑎 OXA-51 has been investigated and was detected in all A. baumannii isolates. Also the prevalence of bla CTX-M-15 gene among 24 P.aeruginosa isolates was 11 (45.83%), and for IMP-1, 3(12.5%). Fortunately, 𝑏𝑙𝑎 NDM , bla VIM , bla DIM gene was not detected in all isolates. C onclusion: The detection of MBL-producing A. baumannii and P. aeruginosa strains detected in this research is of great concern and highlights the need of infection control measures, including antimicrobial management and prompt detection of beta-lactamase-producing isolates.
The role of the mammalian GET pathway in the mouse liver

The correct insertion of membrane proteins is essential for the normal functioning of a eukaryotic cell, and different classes of membrane proteins employ different mechanisms of insertion into their target membrane. One of these pathways is the GET pathway, which promotes the insertion of tail-anchored proteins into the ER membrane. Tail-anchored protein substrates of this pathway are then involved in trafficking, metabolism, or protein translocation in the cell. The key players of the pathway in mammals are the cytosolic ATPase TRC40 and the heterodimeric receptor at the ER membrane consisting of CAML and WRB. Recent studies showed a second function for the yeast homologue of TRC40, Get3, to not only work in tail-anchored protein targeting, but also as an ATP-independent chaperone under oxidative stress conditions. While the pathway is not essential in yeast, loss of some of its main components results in early embryonic lethality in mice, but the reason for this is so far not fully understood. In this study, a mouse model was established to further elucidate the role of the mammalian GET pathway in vivo. The model allows a deletion of the middle exons of WRB in a hepatocyte-specific manner by using the Cre- Lox system, leading to an impairment of the pathway in the liver, a tissue that is high in secretion, protein biosynthesis and trafficking. The results obtained show that this deletion leads to severe liver damage in mice, which was evident in situ, as well is in liver enzyme levels in the blood and increasing fibrosis in the organs, shown by histological analysis. The liver damage changed from an acute state to a more chronic damage with increasing age of the animals. Furthermore, the massive damage and loss of hepatocytes led to subsequent liver regeneration. At the stage of acute liver damage, some of the substrates of the mammalian GET pathway were shown to be affected by the disturbance of the pathway. The protein levels of Syntaxin5 and Syntaxin6, two SNAREs, were decreased in hepatocytes, and Stx5 displayed a clear loss of targeting to the Golgi membrane in hepatocytes. In conclusion, the study shows that a targeted disruption of WRB in hepatocytes severely impairs liver function and integrity, and some substrates of the mammalian GET pathway show a higher susceptibility to this impairment than others.
Changes in Proximate Content of Macroalgae Ulva Sp during Co-culture with Abalone Haliotis squamata in Coastal Waters of West Timor-Indonesia

Abalone is luxurious sea food that fetches a very high price. To fulfil increasing market demand, aquaculture is a necessity. Feed is prerequisite for developing aqua culture for this species. In the absence of artificial diets, abalone growers have to depend entirely on macro algae such as Ulva sp harvested from natural population. Abalone are known to consume large amount of algal diet, thus dependence on wild algae could lead to a heavy exploitation of algae population. One of strategies to maintain the supply of Ulva sp is by culturing together with H. squamata in the same area. However, there is no information whether the cultured algae would match the nutritional quality of algae collected from the wild. This research evaluated the proximate composition of Ulva sp growing in two culture systems i.e., cage culture in open sea and recirculating aqua culture system (RAS) in land. The proximate of the cultured Ulva were compared with those freshly collected from the wild. Results showed that protein content differed significantly among the two cultured Ulva and the wild ones (P<0.05). Ulva cultured in RAS contained the highest level of protein (16.89±0.87 % dw), followed by those cultured in cage (11.29±0.31% dw), and the lowest occurred in the wild Ulva. Cultured and wild Ulva had high carbohydrate content ranged from 46.56±5.03 to 49.29±3.5% dw, but ANOVA showed no significant differences among the source of algae (P>0.05). Lipid was a minor component in Ulva with levels ranged from 0.25±0.05 to 0.9±0.31 % dw. There were significant differences in the lipid content among source of algae (P<0.05) with the highest level observed on Ulva grown in RAS, followed in decreasing order by Ulva grown in the cage and the wild ones. This study recommends that abalone growers should culture Ulva because it improves the nutritional quality of the algae and reduces dependence on the wild Ulva that could threaten the natural algal population.