The fushi tarazu zebra element is not required for Drosophila viability or fertility

Expression of genes in precisely controlled spatiotemporal patterns is essential for embryonic development. Much of our understanding of mechanisms regulating gene expression comes from the study of cis-regulatory elements (CREs) that direct expression of reporter genes in transgenic organisms. This reporter-transgene approach identifies genomic regions sufficient to drive expression but fails to provide information about quantitative and qualitative contributions to endogenous expression, although such conclusions are often inferred. Here we evaluated the endogenous function of a classic Drosophila CRE, the fushi tarazu (ftz) zebra element. ftz is a pair-rule segmentation gene expressed in seven stripes during embryogenesis, necessary for formation of alternate body segments. Reporter transgenes identified the promoter-proximal zebra element as a major driver of the seven ftz stripes. We generated a precise genomic deletion of the zebra element (ftzΔZ) to assess its role in the context of native chromatin and neighboring CREs, expecting large decreases in ftz seven-stripe expression. However, significant reduction in expression was found for only one stripe, ftz stripe 4, expressed at ∼25% of wild type levels in ftzΔZ homozygotes. Defects in corresponding regions of ftzΔZ mutants suggest this level of expression borders the threshold required to promote morphological segmentation. Further, we established true-breeding lines of homozygous ftzΔZ flies, demonstrating that the body segments missing in the mutants are not required for viability or fertility. These results highlight the different types of conclusions drawn from different experimental designs and emphasize the importance of examining transcriptional regulatory mechanisms in the context of the native genomic environment.

Application of Machine Learning Methods in Predicting Nuclear Receptors and their Families

Nuclear receptors (NRs) are a superfamily of ligand-dependent transcription factors that are closely related to cell development, differentiation, reproduction, homeostasis, and metabolism. According to the alignments of the conserved domains, NRs are classified and assigned the following seven subfamilies or eight subfamilies: (1) NR1: thyroid hormone like (thyroid hormone, retinoic acid, RAR-related orphan receptor, peroxisome proliferator activated, vitamin D3- like), (2) NR2: HNF4-like (hepatocyte nuclear factor 4, retinoic acid X, tailless-like, COUP-TFlike, USP), (3) NR3: estrogen-like (estrogen, estrogen-related, glucocorticoid-like), (4) NR4: nerve growth factor IB-like (NGFI-B-like), (5) NR5: fushi tarazu-F1 like (fushi tarazu-F1 like), (6) NR6: germ cell nuclear factor like (germ cell nuclear factor), and (7) NR0: knirps like (knirps, knirpsrelated, embryonic gonad protein, ODR7, trithorax) and DAX like (DAX, SHP), or dividing NR0 into (7) NR7: knirps like and (8) NR8: DAX like. Different NRs families have different structural features and functions. Since the function of a NR is closely correlated with which subfamily it belongs to, it is highly desirable to identify NRs and their subfamilies rapidly and effectively. The knowledge acquired is essential for a proper understanding of normal and abnormal cellular mechanisms. With the advent of the post-genomics era, huge amounts of sequence-known proteins have increased explosively. Conventional methods for accurately classifying the family of NRs are experimental means with high cost and low efficiency. Therefore, it has created a greater need for bioinformatics tools to effectively recognize NRs and their subfamilies for the purpose of understanding their biological function. In this review, we summarized the application of machine learning methods in the prediction of NRs from different aspects. We hope that this review will provide a reference for further research on the classification of NRs and their families.

Scambi fushi tarazu: A Musical Representation of a Drosophila Gene Expression Pattern

The term Bio-Art has entered common usage to describe the interaction between the arts and the biological sciences. Although Bio-Art implies that Bio-Music would be one of its obvious sub-disciplines, the latter term has been much less frequently used. Nevertheless, there has been no shortage of projects that have brought together music and the biological sciences. Most of these projects have allowed the biological data to dictate to a large extent the sound produced, for instance the translation of genome or protein sequences into musical phrases, and therefore may be regarded as process compositions. Here I describe a Bio-Music process composition that derives its biological input from a visual representation of the expression pattern of the gene fushi tarazu in the Drosophila embryo. An equivalent pattern is constructed from the Scambi portfolio of short electronic music fragments created by Henri Pousseur in the 1950s. This general form of the resulting electronic composition follows that of the fushi tarazu pattern, while satisfying the rules of the Scambi compositional framework devised by Pousseur. The range and flexibility of Scambi make it ideally suited to other Bio-Music projects wherever there is a requirement, or desire, to build larger sonic structures from small units.

FOXL2 down-regulates vitellogenin expression at mature stage in Eriocheir sinensis

The present study highlights that forkhead transcription factor (FOXL)2 down-regulates vitellogenin (VTG) synthesis not only through the regulation of follicular cell apoptosis with DEAD-box RNA helicase 20 (DDX20), but also may through the steroidogenic pathway with fushi tarazu factor (FTZ-F)1 at mature stage in Eriocheir sinensis.