Significant Comparative Characteristics between Orphan and Nonorphan Genes in the Rice (Oryza sativa L.) Genome

Microsatellites are short tandem repeats of one to six bases in genomic DNA. As microsatellites are highly polymorphic and play a vital role in gene function and recombination, they are an attractive subject for research in evolution and in the genetics and breeding of animals and plants. Orphan genes have no known homologs in existing databases. Using bioinformatic computation and statistical analysis, we identified 19,26 orphan genes in the rice (Oryza sativa ssp. Japanica cv. Nipponbare) proteome. We found that a larger proportion of orphan genes are expressed after sexual maturation and under environmental pressure than nonorphan genes. Orphan genes generally have shorter protein lengths and intron size, and are faster evolving. Additionally, orphan genes have fewer PROSITE patterns with larger pattern sizes than those in nonorphan genes. The average microsatellite content and the percentage of trinucleotide repeats in orphan genes are also significantly higher than in nonorphan genes. Microsatellites are found less often in PROSITE patterns in orphan genes. Taken together, these orphan gene characteristics suggest that microsatellites play an important role in orphan gene evolution and expression

1-[Morpholino(phen­yl)meth­yl]-2-naphthol

There are two independent mol­ecules in the asymmetric unit of the title compound, C21H21NO2, which was synthesized by the one-pot reaction of 2-naphthol, morpholine and benzaldehyde. The dihedral angles between the naphthalene ring systems and the benzene rings are 84.03 (7) and 75.76 (8)° in the two mol­ecules and an intra­molecular O—H⋯N hydrogen bond occurs in each independent mol­ecule

A yeast's eye view of mammalian reproduction: cross-species gene co-expression in meiotic prophase

<p>Abstract</p> <p>Background</p> <p>Meiotic prophase is a critical stage in sexual reproduction. Aberrant chromosome recombination during this stage is a leading cause of human miscarriages and birth defects. However, due to the experimental intractability of mammalian gonads, only a very limited number of meiotic genes have been characterized. Here we aim to identify novel meiotic genes important in human reproduction through computational mining of cross-species and cross-sex time-series expression data from budding yeast, mouse postnatal testis, mouse embryonic ovary, and human fetal ovary.</p> <p>Results</p> <p>Orthologous gene pairs were ranked by order statistics according to their co-expression profiles across species, allowing us to infer conserved meiotic genes despite obvious differences in cellular synchronicity and composition in organisms. We demonstrated that conserved co-expression networks could successfully recover known meiotic genes, including homologous recombination genes, chromatin cohesion genes, and genes regulating meiotic entry. We also showed that conserved co-expression pairs exhibit functional connections, as evidenced by the annotation similarity in Gene Ontology and overlap with physical interactions. More importantly, we predicted six new meiotic genes through their co-expression linkages with known meiotic genes, and subsequently used the genetically more amenable yeast system for experimental validation. The deletion mutants of all six genes showed sporulation defects, equivalent to a 100% validation rate.</p> <p>Conclusions</p> <p>We identified evolutionarily conserved gene modules in meiotic prophase by integrating cross-species and cross-sex expression profiles from budding yeast, mouse, and human. Our co-expression linkage analyses confirmed known meiotic genes and identified several novel genes that might be critical players in meiosis in multiple species. These results demonstrate that our approach is highly efficient to discover evolutionarily conserved novel meiotic genes, and yeast can serve as a valuable model system for investigating mammalian meiotic prophase.</p

Type IIs restriction based combinatory modulation technique for metabolic pathway optimization

Additional file 1: Table S1. Oligonucleotides used in this study

Adversarial Noise Layer: Regularize Neural Network By Adding Noise

In this paper, we introduce a novel regularization method called Adversarial Noise Layer (ANL) and its efficient version called Class Adversarial Noise Layer (CANL), which are able to significantly improve CNN's generalization ability by adding carefully crafted noise into the intermediate layer activations. ANL and CANL can be easily implemented and integrated with most of the mainstream CNN-based models. We compared the effects of the different types of noise and visually demonstrate that our proposed adversarial noise instruct CNN models to learn to extract cleaner feature maps, which further reduce the risk of over-fitting. We also conclude that models trained with ANL or CANL are more robust to the adversarial examples generated by FGSM than the traditional adversarial training approaches

Are Coiled-Coils of Dimeric Kinesins Unwound during Their Walking on Microtubule?

Dimeric kinesin motor proteins such as homodimeric kinesin-1, homodimeric Ncd and heterodimeric Kar3/Vik1are composed of two head domains which are connected together by a rod-shaped, coiled-coil stalk. Despite the extensive and intensive studies on structures, kinetics, dynamics and walking mechanism of the dimers, whether their coiled-coils are unwound or not during their walking on the microtubule is still an unclear issue. Here, we try to clarify this issue by using molecular dynamics simulations. Our simulation results showed that, for Ncd, a large change in potential of mean force is required to unwind the coiled-coil by only several pairs of residues. For both Ncd and kinesin-1, the force required to initiate the coiled-coil unwinding is larger than that required for unfolding of the single -helix that forms the coiled-coil or is larger than that required to unwind the DNA duplex, which is higher than the unbinding force of the kinesin head from the microtubule in strong microtubule-binding states. Based on these results and the comparison of the sequence between the coiled-coil of Kar3/Vik1 and those of Ncd and kinesin-1, it was deduced that the coiled-coil of the Kar3/Vik1 should also be very stable. Thus, we concluded that the coiled-coils of kinesin-1, Ncd and Kar3/Vik1 are almost impossible to unwind during their walking on the microtubule

Constructivist Perspective on Developing a Multidimensional Blended Teaching Model Fostering Deep Learning

To promote high-quality development of higher education, it is imperative to facilitate students’ transition from surface learning to deep learning. Compared with surface learning that focuses on rote memorization, deep learning emphasizes meaningful learning based on understanding and transfer. It involves three progressively advanced cognitive stages of knowing: "learning for understanding," "learning for application," and "learning for innovation," which ultimately enable the internalization, transfer, and creative application of knowledge. How to foster deep learning in students has been an urgent issue of higher education. This study, grounded in constructivist learning theory, explores a multidimensional blended teaching model fostering deep learning. It also develops an evaluation system assessing learning outcomes from the perspectives of ideological, political and moral education, knowledge, and competencies. We conducted an empirical study to test the effectiveness of this multidimensional blended teaching model. Findings will provide theoretical and practical implications for teaching reforms of similar courses

Clinical significance of SOX9 in human non-small cell lung cancer progression and overall patient survival

<p>Abstract</p> <p>Background</p> <p>Sex determining region Y (SRY)-related high mobility groupbox 9 (SOX9) is an important transcription factor required for development, which regulates the expression of target genes in the associated pathway. The aim of this study was to describe the expression of SOX9 in human non-small cell lung cancer (NSCLC) and to investigate the association between SOX9 expression and progression of NSCLC.</p> <p>Methods</p> <p>SOX9 protein and mRNA expression in normal human pneumonocytes, lung cancer cell lines, and eight pairs of matched lung cancer tissues and their adjacent normal lung tissues were detected by Western blotting and real-time reverse transcription-polymerase chain reaction (RT-PCR). Immunohistochemistry was used to determine SOX9 protein expression in 142 cases of histologically characterized NSCLC. Statistical analyses were applied to test for prognostic and diagnostic associations.</p> <p>Results</p> <p>SOX9 in lung cancer cell lines was upregulated at both mRNA and protein levels, and SOX9 mRNA and protein were also elevated in NSCLC tissues compared with levels in corresponding adjacent non-cancerous lung tissues. Immunohistochemical analysis demonstrated a high expression of SOX9 in 74/142 (52.1%) paraffin-embedded archival lung cancer biopsies. Statistical analysis indicated that upregulation of SOX9 was significantly correlated with the histological stage of NSCLC (<it>P </it>= 0.017) and that patients with a high SOX9 level exhibited a shorter survival time (<it>P </it>< 0.001). Multivariate analysis illustrated that SOX9 upregulation might be an independent prognostic indicator for the survival of patients with NSCLC.</p> <p>Conclusions</p> <p>This work shows that SOX9 may serve as a novel and prognostic marker for NSCLC, and play a role during the development and progression of the disease.</p