MicroRNAs in the bovine ovary and placentas derived from in vivo, in vitro and nuclear transfer pregnancies

MicroRNAs are the major class of gene regulating molecules playing pivotal roles at post-transcriptional level. Identification and expression profiling are the initial steps to understand their regulation of biological processes. Despite increasing efforts in miRNAs characterization in different species, little is known in the bovine reproductive tissues especially in ovary and placenta. Two subsequent studies were carried out to the expression of miRNAs in bovine ovary and Day-50 placenta derived from different sources of pregnancy. The first study aims to identify and characterize miRNAs in bovine ovary through cloning, expression analysis and target prediction. The constructed miRNA library revealed cloning of 50 known and 24 novel miRNAs. Among these, 38 were new miRNAs which were derived from 43 distinct loci with characteristic secondary structure. Most of the miRNAs were cloned multiple times and thereby reflecting their expression level and potential role in the ovary. Analysis of identified miRNAs in different intra-ovarian structures and other tissues reveals their stage and tissue specific expression patterns. Furthermore, in silico target prediction and Gene Ontology analysis of the targets genes identified several biological processes and pathways underlying the ovarian function. Results of this study suggest the presence of miRNAs in the bovine ovary; thereby elucidate their potential role in regulating diverse mechanisms underlying the ovarian functionality. The second study aimed to elucidate the difference in expression profile of miRNAs in the placenta at day 50 derived from Somatic cell nuclear transfer (SCNT), in vitro production (IVP) and artificial insemination (AI) pregnancies by quantifying 377 miRNAs. The study reveals a massive deregulation of miRNAs which were poorly reprogrammed and affected as large chromosomal cluster as well as miRNA families in the NT and IVP placenta compared to that of AI. Furthermore, cell specific localization miRNAs in the expanded blastocysts and expression profiling in different developmental stages of embryos and placenta identified that the major deregulation of miRNAs arises at day 50 of NT and IVP pregnancies. This deregulation were found to be less dependent on global DNA methylation, rather aberrant miRNA processing molecules were evidenced. Among them, observed down regulation of AGO2 could be a reason for global down regulation of miRNAs in the NT or IVP placenta. Identified deregulation of miRNAs might associate to the abnormal placentogenesis in NT or IVP pregnancies, which are the results of aberrant genetic and epigenetic modification. Result of this study will help to move one step closer towards improving the efficiency of nuclear transfer pregnancy. Altogether, the present study has discovered miRNAs in the bovine ovary and elucidated the pattern of expression of miRNAs along with their regulatory mechanism in the placenta derived from pregnancies of various origins.Untersuchung von MicroRNAs in bovinen Ovarien und Plazenten aus geklonten, in vivo und in vitro erzeugten Trächtigkeiten MicroRNAs gehören zur großen Klasse der genregulierenden Moleküle und spielen eine bedeutende Rolle auf der posttranskriptionellen Ebene. Die Identifikation und die Erstellung von Expressionsprofilen sind die ersten Schritte für ein besseres Verständnis der miRNA und ihrer Beteiligung an der Regulierung von biologischen Prozessen. Trotz der zunehmenden Charakterisierung der miRNA in verschiedenen Spezies, sind kaum Untersuchungen in bovinen Ovarien und Plazenten bekannt. In zwei Studien wurde die miRNA Expression in bovinen Ovarien und in Plazenten am Tag 50 der Trächtigkeit, in unterschiedlich erzeugten Schwangerschaften untersucht. Das Ziel der ersten Studie war die Identifizierung und Charakterisierung von miRNAs in klonierten bovinen Ovarien, Expressionsanalysen sowie Target-Vorhersagen. Die konstruierte miRNA-Bibliothek ergab 50 bekannte und 24 neue miRNAs. Unter diesen waren 38 neue bovine miRNAs die von 43 eindeutigen Loci abgeleitet werden konnten, die eine charakteristische sekundäre Struktur zeigten. Durch die mehrfache Klonierung der meisten miRNAs, konnte ihr Expressionsniveau in den Ovarien erfasst werden. Analysen von miRNAs in unterschiedlichen intra-ovariellen Strukturen sowie anderen Geweben zeigten ihr phasen- und gewebsspezifisches Expressionsmuster. Des Weiteren konnte durch bioinformatische Auswertungen und Gen Ontology Analysen der Target Gene verschiedene biologische Prozesse und Pathways der Ovarienfunktion identifiziert werden. Die Ergebnisse dieser Studie deuten auf das Vorhandensein von miRNAs in bovinen Ovarien hin und verdeutlichen die potenzielle Bedeutung in der Regulierung diverser Mechanismen der Ovarienfunktion. Die zweite Studie sollte die Unterschiede von Expressionsprofilen von miRNAs in Plazenten am Tag 50 der Trächtigkeit von SCNT, IVP und AI Schwangerschaften durch Quantifizierung von 377 miRNAs aufklären. Die Studie zeigte eine starke reduzierte Expression und eine geringe Reprogrammierung der miRNAs in NT und IVP im Vergleich zu AI. Diese miRNAs gehören vermutlich zu einer miRNA Familie in einem chromosomalen Cluster. Des Weiteren zeigten zellspezifische Lokalisationen von miRNAs in der expandierenden Blastozyste und Expressionsprofile von unterschiedlichen Entwicklungsstadien im Embryo und in der Plazenta, dass die wichtigsten Deregulierungen von miRNAs am Tag 50 der Trächtigkeit in NT und IVP entstehen. Diese Deregulierung erwies sich als weniger abhängig von einer globalen DNA-Methylierung, vielmehr wurde eine Abweichung in den miRNA-Prozessgenen belegt. Von diesen könnte die reduzierte Expression von AGO2 die Ursache für die globale Deregulierung der miRNAs in NT oder IVP Plazenten sein. Die identifizierten Deregulationen der miRNAs könnten im Zusammenhang mit abnormaler Plazentogenese in NT oder IVP Trächtigkeiten stehen. Die Ursachen für Abnormalitäten in der Plazentogenese liegen in genetischen und epigenetischen Modifikationen. Zusammenfassend konnte durch diese Studien miRNAs in bovinen Ovarien identifiziert werden und Expressionsmustern der miRNAs sowie ihre regulierenden Mechanismen in der Plazenta von unterschiedlichen Trächtigkeiten beschrieben werden

Informed Consent and the Patients of Bangladesh

In medical practice, informed consent plays a vital role in making ethical decisions. In recent years, informed consent also appears to be a key issue in biomedical discussion. Several definitions of informed consent have already been proposed. However, the socio-economic conditions of different countries are not the same. Many countries differ culturally as well as in literacy rate. Therefore, a unified concept of informed consent might not be justified in every context. This paper discusses the importance of informed consent, different views regarding informed consent and the limitations of applying one single idea of informed consent in every context. It argues that the most plausible concept of informed consent which is achievable for developing countries, like Bangladesh, is based on care ethics. The paper concludes that informed consent could be a ‘natural outcome’ and is really not a barrier in the patient-physician relationship if the idea is seen from the perspective of care ethics

Identification, Self-Realization and Spirituality: A Comparative Study of Environmental Philosophy

Ph.DDOCTOR OF PHILOSOPH

Exploring lncRNAs associated with human pancreatic islet cell death induced by transfer of adoptive lymphocytes in a humanized mouse model

BackgroundLong noncoding RNA (lncRNA)-mediated posttranscriptional and epigenetic landscapes of gene regulation are associated with numerous human diseases. However, the regulatory mechanisms governing human β-cell function and survival remain unknown. Owing to technical and ethical constraints, studying the direct role of lncRNAs in β-cell function and survival in humans in vivo is difficult. Therefore, we utilized humanized mice with human islets to investigate lncRNA expression using whole transcriptome shotgun sequencing. Our study aimed to characterize lncRNAs that may be crucial for human islet cell function and survival.MethodsHuman β-cell death was induced in humanized mice engrafted with functional human islets. Using these humanized mice harboring human islets with induced β-cell death, we investigated lncRNA expression through whole transcriptome shotgun sequencing. Additionally, we systematically identified, characterized, and explored the regulatory functions of lncRNAs that are potentially important for human pancreatic islet cell function and survival.ResultsHuman islet cell death was induced in humanized mice engrafted with functional human islets. RNA sequencing analysis of isolated human islets, islet grafts from humanized mice with and without induced cell death, revealed aberrant expression of a distinct set of lncRNAs that are associated with the deregulated mRNAs important for cellular processes and molecular pathways related to β-cell function and survival. A total of 10 lncRNA isoforms (SCYL1-1:22, POLG2-1:1, CTRB1-1:1, SRPK1-1:1, GTF3C5-1:1, PPY-1:1, CTRB1-1:5, CPA5-1:1, BCAR1-2:1, and CTRB1-1:4) were identified as highly enriched and specific to human islets. These lncRNAs were deregulated in human islets from donors with different BMIs and with type 2 diabetes (T2D), as well as in cultured human islets with glucose stimulation and induced cell death induced by cytokines. Aberrant expression of these lncRNAs was detected in the exosomes from the medium used to culture islets with cytokines.ConclusionIslet-enriched and specific human lncRNAs are deregulated in human islet grafts and cultured human islets with induced cell death. These lncRNAs may be crucial for human β-cell function and survival and could have an impact on identifying biomarkers for β-cell loss and discovering novel therapeutic targets to enhance β-cell function and survival

Utilization of fermented wheat bran extract medium as a potential low-cost culture medium for Chlorella ellipsoidea

Microalgae, Chlorella ellipsoidea is an excellent energy source for food and biofuel production. Nevertheless, the production cost of C. ellipsoidea using Bold's Basal Medium (BBM) is expensive, which led to exploring the alternation of a low-cost medium for large-scale production. Low-cost fermented wheat bran extract medium (FWBEM), which has good nutritional properties, might be an alternative approach to mass production of C. ellipsoidea. The present study was conducted to evaluate the growth and production of C. ellipsoidea using different concentrations of FWBEM. Wheat bran was fermented at the concentration of 8.33, 6.66, and 5.00 g/L water and used as treatments for T2, T3, and T4, respectively. The BBM was used as the control medium (T1). The growth and production of C. ellipsoidea were monitored at three days intervals through cell dry weight, specific growth rate, optical cell density, chlorophyll a content, and cell numbers. Those growth data revealed that C. ellipsoidea cultured at 6.66 g/L (T3) concentration did not vary significantly with the standard inorganic BBM. However, T2 and T4 showed substantially lower cell growth and chlorophyll a content than control and T3. Compared to the BBM, a significant reduction in production cost was obtained in the FWBEM. Based on the cell biomass growth, pigmentation, and production cost, FWBEM at a 6.66 g/L could be used as an alternative medium to BBM. Therefore, FWBEM has excellent potential to be used for the low-cost production of C. ellipsoidea

Augmented Retting Effect on Kenaf Fibers Using Alkalophilic Pectinase-Producing Bacteria in Combination with Water Solvents

A degumming approach is used in this paper with alkalophilic pectinase-producing bacteria (APPB) and two sources of water solvents to address the existing conventional water retting complexities of kenaf. The incorporation of APPB was confirmed based on their retting feasibilities and multiple cell-wall-degrading enzymatic delicacy. The combinations of APPB with seawater offered retting achievements within six-day retting in non-sterile conditions. These retting niches showed maximum (14.67 U/mL) pectinase activity with fiber separation feasibilities of 4.75 Fried test score. The yielded fiber composition analysis showed a higher cellulose composition (84.65%) and the least amount of hemicellulose, pectin, and ligneous gummy substances. The transmission electron microscopy scan of the yielded fibers showed smooth fiber surfaces, 84.20 µm fiber diameter, and 7.65 g/tex fine fiber compared with uninoculated and combinations of freshwater treatments. The FTIR spectra revealed the cellulosic discrepancies of the retting treatments by monitoring O-H and C=O stretching at ~3300 cm−1 and ~1730 cm−1 wavenumbers. These findings are compelling to yield kenaf fibers of quality considering the existing retting difficulties

Identification and characterization of miRNAs expressed in the bovine ovary

<p>Abstract</p> <p>Background</p> <p>MicroRNAs are the major class of gene-regulating molecules playing diverse roles through sequence complementarity to target mRNAs at post-transcriptional level. Tightly regulated expression and interaction of a multitude of genes for ovarian folliculogenesis could be regulated by these miRNAs. Identification of them is the first step towards understanding miRNA-guided gene regulation in different biological functions. Despite increasing efforts in miRNAs identification across various species and diverse tissue types, little is known about bovine ovarian miRNAs. Here, we report the identification and characterization of miRNAs expressed in the bovine ovary through cloning, expression analysis and target prediction.</p> <p>Results</p> <p>The miRNA library (5'-independent ligation cloning method), which was constructed from bovine ovary in this study, revealed cloning of 50 known and 24 novel miRNAs. Among all identified miRNAs, 38 were found to be new for bovine and were derived from 43 distinct loci showing characteristic secondary structure. While 22 miRNAs precursor loci were found to be well conserved in more than one species, 16 were found to be bovine specific. Most of the miRNAs were cloned multiple times, in which let-7a, let-7b, let-7c, miR-21, miR-23b, miR-24, miR-27a, miR-126 and miR-143 were cloned 10, 28, 13, 4, 11, 7, 6, 4 and 11 times, respectively. Expression analysis of all new and some annotated miRNAs in different intra-ovarian structures and in other multiple tissues showed that some were present ubiquitously while others were differentially expressed among different tissue types. Bta-miR-29a was localized in the follicular cells at different developmental stages in the cyclic ovary. Bio-informatics prediction, screening and Gene Ontology analysis of miRNAs targets identified several biological processes and pathways underlying the ovarian function.</p> <p>Conclusion</p> <p>Results of this study suggest the presence of miRNAs in the bovine ovary, thereby elucidate their potential role in regulating diverse molecular and physiological pathways underlying the ovarian functionality. This information will give insights into bovine ovarian miRNAs, which can be further characterized for their role in follicular development and female fertility as well.</p

Factors Affecting Fishers’ Attitude and Willingness to use Cage Aquaculture as an Alternative Livelihood for Reducing Fishing Pressure in Haor Areas, Bangladesh

Inland capture fisheries are providing cost of livings of about 1.2 million BDT in Bangladesh. However, overexploitation causing the declination of the abundance of native fish species which adversely affects the livelihoods of haor dwellers. The present study was conducted in two haor villages (Sutarpara and Changnoagaon) of Kishoreganj, Bangladesh to explore the factors (economic and non-economic) affecting fishers’ attitude and willingness about cage aquaculture considered as livelihood alternative for reducing fishing pressure. The methodologies applied to do this study were semi-structured face-to-face interview, key informants and questionnaire survey using Likert scale (LS), focus group discussions (FGD). The result revealed that willingness to switch from traditional way of fishing to cage aquaculture activities was significantly (P<0.05) higher in those fishers’ groups that had more inclination in fishing activities. Simultaneously, non-economic factors like powerful traders and fishers, traditional belief, taking risk, launching period of cage aquaculture venture and investment duration played vital role in decisions on whether to fish or not. The economic factors were fewer in number than non-economic factors. This comparative research is significantly important for future social aquaculture researchers as well as the country policy makers for giving emphasis to gather data based on the prevailing economic and non-economic factors to innovate alternative livelihood activity concurrently