Comparison of transcriptomic landscapes of bovine embryos using RNA-Seq

<p>Abstract</p> <p>Background</p> <p>Advances in sequencing technologies have opened a new era of high throughput investigations. Although RNA-seq has been demonstrated in many organisms, no study has provided a comprehensive investigation of the bovine transcriptome using RNA-seq.</p> <p>Results</p> <p>In this study, we provide a deep survey of the bovine embryonic transcriptomes, the first application of RNA-seq in cattle. Embryos cultured <it>in vitro </it>were used as models to study early embryonic development in cattle. RNA amplified from limited amounts of starting total RNA were sequenced and mapped to the reference genome to obtain digital gene expression at single base resolution. In particular, gene expression estimates from more than 1.6 million unannotated bases in 1785 novel transcribed units were obtained. We compared the transcriptomes of embryos showing distinct developmental statuses and found genes that showed differential overall expression as well as alternative splicing.</p> <p>Conclusion</p> <p>Our study demonstrates the power of RNA-seq and provides further understanding of bovine preimplantation embryonic development at a fine scale.</p

Transcriptomic profiling of bovine IVF embryos revealed candidate genes and pathways involved in early embryonic development

<p>Abstract</p> <p>Background</p> <p>Early embryonic loss is a large contributor to infertility in cattle. Although genetic factors are known to affect early embryonic development, the discovery of such factors has been a serious challenge. The objective of this study was to identify genes differentially expressed between blastocysts and degenerative embryos at early stages of development.</p> <p>Results</p> <p>Using microarrays, genome-wide RNA expression was profiled and compared for in vitro fertilization (IVF) - derived blastocysts and embryos undergoing degenerative development up to the same time point. Surprisingly similar transcriptomic profiles were found in degenerative embryos and blastocysts. Nonetheless, we identified 67 transcripts that significantly differed between these two groups of embryos at a 15% false discovery rate, including 33 transcripts showing at least a two-fold difference. Several signaling and metabolic pathways were found to be associated with the developmental status of embryos, among which were previously known important steroid biosynthesis and cell communication pathways in early embryonic development.</p> <p>Conclusions</p> <p>This study presents the first direct and comprehensive comparison of transcriptomes between IVF blastocysts and degenerative embryos, providing important information for potential genes and pathways associated with early embryonic development.</p

RNA-Seq analysis uncovers transcriptomic variations between morphologically similar in vivo- and in vitro-derived bovine blastocysts

<p>Abstract</p> <p>Background</p> <p>A valuable tool for both research and industry, in vitro fertilization (IVF) has applications range from gamete selection and preservation of traits to cloning. Although IVF has achieved worldwide use, with approximately 339,685 bovine embryos transferred in 2010 alone, there are still continuing difficulties with efficiency. It is rare to have more than 40% of fertilized in vitro cattle oocytes reach blastocyst stage by day 8 of culture, and pregnancy rates are reported as less than 45% for in vitro produced embryos. To investigate potential influences in-vitro fertilization (IVF) has on embryonic development, this study compares in vivo- and in vitro-derived bovine blastocysts at a similar stage and quality grade (expanded, excellent quality) to determine the degree of transcriptomic variation beyond morphology using RNA-Seq.</p> <p>Results</p> <p>A total of 26,906,451 and 38,184,547 fragments were sequenced for in vitro and in vivo embryo pools, respectively. We detected expression for a total of 17,634 genes, with 793 genes showing differential expression between the two embryo populations with false discovery rate (FDR) < 0.05. There were also 395 novel transcribed units found, of which 45 were differentially expressed (FDR < 0.05). In addition, 4,800 genes showed evidence of alternative splicing, with 873 genes displaying differential alternative splicing between the two pools (FDR < 0.05). Using GO enrichment analysis, multiple biological pathways were found to be significantly enriched for differentially expressed genes (FDR < 0.01), including cholesterol and sterol synthesis, system development, and cell differentiation.</p> <p>Conclusions</p> <p>Thus, our results support that IVF may influence at the transcriptomic level and that morphology is limited in full characterization of bovine preimplantation embryos.</p

Learning without contingencies induces higher order asynchrony in brain networks in schizophrenia

Schizophrenia (SCZ) is characterized by both cognitive and reward impairments. A recent study suggests that SCZ is associated with a loss of synchrony between learning and reward circuits (Robison et al., 2019) and higher levels of dis-organization of functional brain networks may underpin failures in learning that characterize SCZ (Hütt et al., 2014). Therefore, here we examined inter-group (HC ≠ SCZ) 4th order differences in statistical regularity across a connectome of cognition and reward brain circuits. The analyses were conducted on fMRI time series data from a previous learning paradigm (Stanley et al., 2017) with periods of Encoding and Retrieval. 75 participants (46 SCZ, 18 Age 50) consented for fMRI. Time Series were extracted from eight bilateral a priori nodes (across learning and reward sub-networks). 2nd order undirectional functional connectivity was characterized across all nodal pairs during Encoding, Retrieval, and their subsequent rest periods. From this, a 4th order cross-correlation matrix was produced within each group and condition. Significant 4th order differences were projected to chords in the 4th order connectomic rings for Encoding and Retrieval (Figure 1). Two effects are evident: 1) SCZ are characterized by a massive loss of 4th order synchrony during both Encoding and Retrieval and 2) Retrieval evokes a greater loss in 4th order statistical synchrony than does Encoding. These results appear to validate the idea the SCZ is characterized by a loss of synergy between cognition and reward circuits, and that this loss of synergy is evident at higher order scales

Health Risk Associated with Some Trace and Some Heavy Metals Content of Harvested Rainwater in Yatta Area, Palestine

Rainwater is considered a dependable source for domestic purposes within rural areas in Palestine. Harvested rainwater stored in cisterns is used to leverage deficits from municipal water supplies. Harvested rainwater in areas surrounded with industrial and agricultural activities is usually contaminated with heavy and trace metals. To study the effects of human exposure to heavy and trace metals, 74 harvested rainwater samples of rain-fed cisterns were collected from different localities in the Yatta area of Palestine in the months of January and February of 2016. The water samples were analysed for Ca, Mg, Al, Fe, K, Na, Ag, Li, Co, Ba, Bi, Sr, Ga, V, Rb, Mo, Beand Tl elements utilizing ICP-MS (inductively coupled plasma mass spectrometry). The selected trace metals were found within the concentration limits of the acceptable values, in accordance with WHO and Palestinian standards, except for K and Al, which were found above the allowed limits. The potential risks of the selected trace metals on the health of the local residents, as well as the possible sources of such heavy metals, were also studied. The Chronic daily intake (CDI) of each metal and health risk indexes (HRI) were calculated for both adults and children residents. The oral ingestion pathway was studied, including exposure via drinking water. The values for CDI were found in the descending order of: Ca > Mg > Na > K > Sr > Fe > Al > Ba > Li > V > Rb > Ag > Mo > Ga > Co > Bi > TI > Be. The values of HRI were below 1 for most of the selected heavy metals, expect for Li for children, indicating potential health risk. The study also predicted that the local residents have a higher chance of developing cancer in their lifetime, especially children, with respect to the carcinogenic risk (CRing) values for Na, Mg, Al, Ba, K, Ca, Fe and Sr, which were greater than standardized limits (>106). The rest of the selected elements were within the acceptable limit in the five different studied locations. Furthermore, univariate, multivariate and statistical analysis depending on one-way ANOVA, inter-metal correlation, cluster analysis (CA) and principal component analysis (PCA) results revealed that geogenic and anthropogenic activities were major sources of drinking water contamination by heavy metals in the Yatta area.The authors would like to thank Yatta municipality for helping in samples collection, the households that facilitated our sampling, and Al-Quds University where water samples were analysed

Activation of slag through a combination of NaOH/NaS alkali for transforming it into geopolymer slag binder mortar – assessment the effects of two different Blaine fines and three different curing conditions

This study investigates the effects of two different Blaine fineness and three distinct curing conditions on the physico-mechanical properties of a geopolymer-ground granulated blast furnace slag (GGBFS) binder mortar activated through a combination of NaOH/NaS alkalis. By ensuring constant curing and mixing conditions, geopolymer mortar (GPM) specimens were prepared and evaluated to determine their capillary water sorption, capillarity coefficient, and change in unit weight, alongside their compressive strength and flexural strength 3, 7, 28, and 56 d after production. It was found that the capillary water sorption decreased by approximately 50% as the curing temperature of the water increased from ambient temperature to 22 °C. The coefficient of capillarity remained constant across the geopolymer materials, irrespective of the Blaine fineness of the GGBFS. Furthermore, the increase in the unit weight, owing to the variation in the Blaine fineness of GGBFS, results in a reduction in the water sorption properties of GPMs. The GGBFS and alkali-based binders imparted a continuous increase in the compressive and flexural strengths. The results revealed that a Blaine fineness of 6000 cm2/g in the GGBFS under water-curing conditions imparted the most significant advantageous effect on the physico-mechanical properties of a GGBFS binder mortar activated through a combination of NaOH/NaS alkalis

The Technical and Design Characteristics of Traditional Natural Lighting Methods in Islamic Architecture

Lighting is an important element to carry out life activities within architectural spaces. Every life activity depends on the level of lighting in the vacuum. This level varies according to the activities and the size of the interior space. The pursuit of lighting spaces in a way that is compatible with the functional and aesthetic dimensions in the interior Islamic design is one of the controversies worthy of research and study, as it is possible to establish patterns of lighting in the modern interior design follow the principles of lighting used in Islamic architecture, where patterns of natural and industrial lighting have both functional and aesthetic objectives. The importance of this research is to study the effect of traditional lighting patterns used in Islamic architecture on the lighting of internal spaces, and how to influence the formation and structure of modern and contemporary spaces by studying the impact of these patterns in controlling the quantity and efficiency of natural and industrial lighting in the vacuum through an analytical study of the performance of these patterns. Keywords: Architecture, Tourism, Interior Design, Traditional Lighting, History of Islamic Art DOI: 10.7176/JTHS/41-07 Publication date:May 31st 201

The Four Symmetries "A Study of the Shape Characteristics and Expressive Connotations of the Dwelling"

This study seeks to study the relations and the shape characteristics and expressive connotations of the house through following it based on the relationship between shape and meaning and their association with human existence. Because it is related to his body and his idea of these relations, which are formed in his consciousness through his movement and locomotion between the blocks and the interior spaces of the house, therefore, what we see in front of us is really what we think, which gives us a sense of surprise and harmony, which explains the close relationship between the visible and the invisible in the things in front of us. The house and the sense of it is ultimately not abstract; but it carries a broad philosophical content, and that its study from this angle, specifically (phenomenal), give it its true meaning in this world, here is the gap that the study seeks to research, in terms of experience living and sense of place and the interaction of the individual with the place and specifically housing and the internal vacuum of the place. This study concluded that the dwelling is inseparable from the self in terms of the visual formation of the blocks and shapes; rather, the house and the body are intertwined with memories. The sight of familiarity and feeling of residence is not only born of childhood memories; but this feeling may be generated by what the dwelling impose on us of the data in the phenomenal shape of it, and therefore what the shape of the rooms achieved by central concentrates, the harmony of shape, color and texture are the ones that motivate us to enjoy the dwelling and thus can be formulated and arranged in harmony and correspondence to achieve familiarity. The availability of shape characteristics of certain patterns and systems and the provision of sufficient internal spaces contribute to a kind of affinity between the self and the subject as a whole (between the inhabitant and the inhabited), which is a necessary objective for realizing the idea of housing awareness. Keywords: Dwelling, Shape, Sense, Place, Interior design. DOI: 10.7176/ADS/73-05 Publication date:May 31st 201