An Optimized Proteomics Approach Reveals Novel Alternative Proteins in Mouse Liver Development

Alternative ORFs (AltORFs) are unannotated sequences in genome that encode novel peptides or proteins named alternative proteins (AltProts). Although ribosome profiling and bioinformatics predict a large number of AltProts, mass spectrometry as the only direct way of identification is hampered by the short lengths and relative low abundance of AltProts. There is an urgent need for improvement of mass spectrometry methodologies for AltProt identification. Here, we report an approach based on size-exclusion chromatography for simultaneous enrichment and fractionation of AltProts from complex proteome. This method greatly simplifies the variance of AltProts discovery by enriching small proteins smaller than 40 kDa. In a systematic comparison between 10 methods, the approach we reported enabled the discovery of more AltProts with overall higher intensities, with less cost of time and effort compared to other workflows. We applied this approach to identify 89 novel AltProts from mouse liver, 39 of which were differentially expressed between embryonic and adult mice. During embryonic development, the upregulated AltProts were mainly involved in biological pathways on RNA splicing and processing, whereas the AltProts involved in metabolisms were more active in adult livers. Our study not only provides an effective approach for identifying AltProts but also novel AltProts that are potentially important in developmental biology.     

Bifidobacteria-mediated immune system imprinting early in life

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Cell-type-specific Hox regulatory strategies orchestrate tissue identity

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Sexual dimorphism and gonadal development of the Australian longfinned river eel

The sex and stage of gonadal development of longfinned river eels Anguilla reinhardtii , captured from nine river catchments in New South Wales, Australia, between 1999 and 2001, were determined macroscopically. Sex was verified by histology. Histology was also necessary, however, to accurately define stages of gonadal development, particularly in individuals <600 mm in total body length. Anguilla reinhardtii displayed asynchronous gamete development. The most advanced cells present in migrating male and female A. reinhardtii were spermatocytes and pre-vitellogenic oocytes, respectively. Gonadal development stages were positively correlated with body size in both sexes. Females, however, were significantly larger than males and their gonads matured over a broader size range. Size at sexual differentiation (42–60 cm for males and 50–76 cm for females) was much larger than for most other anguillids that have been studied, with the exception of the New Zealand longfinned eel Anguilla dieffenbachii . Corresponding with its large range in size at sexual differentiation was a relatively large range in size at migration for both males (44–62 cm) and females (74–142 cm).     

Evolution of avian eggshell structure

Data are presented suggesting that birds have evolved eggs with shells containing different structures (numbers of mammillae per unit of inner eggshell surface area, i.e., mammillary densities) to cope up with different calcium requirements imposed by different growth rates and modes of development. Precocial bird species grow slowly, but have high mammillary density, while altricial bird species grow rapidly, but have low mammillary density. These results suggest an adaptation associated with growth rate and mode of development and show, moreover, that the mammillary layer is indicative of the breeding biology of the bird. J. Morphol. 2012. © 2011 Wiley Periodicals, Inc.     

The controversial origin of the abdominal appendage‐like processes in immature insects: Are they true segmental appendages or secondary outgrowths? (Arthropoda hexapoda)

In this article, I review the major characteristics of different types of appendage‐like processes that develop at the abdominal segments of many immature insects, and I discuss their controversial morphological value. The main question is whether the abdominal processes are derived from segmental appendages serially homologous to thoracic legs, or whether they are “secondary” outgrowths not homologous with true appendages. Morphological and embryological data, in particular, a comparison with the structure and development of the abdominal appendages in primitive apterygote hexapods, and data from developmental genetics, support the hypothesis of appendicular origin of many of the abdominal processes present in the juvenile stages of various pterygote orders. For example, the lateral processes, such as the tracheal gills in aquatic nymphs of exopterygote insects, are regarded as derived from lateral portions of appendage primordia, homologous with the abdominal styli of apterygotan insects; these processes correspond either to rudimentary telopodites or to coxal exites. The ventrolateral processes, such as the prolegs of different endopterygote insect larvae, appear to be derived from medial portions of the appendicular primordia; they correspond to coxal endites. These views lead to the rejection of Hinton's hypothesis (Hinton [1955] Trans R Entomol Soc Lond 106:455–545) according to which all the abdominal processes of insect larvae are secondary outgrowths not derived from true appendage anlagen. J. Morphol. 2012. © 2012 Wiley Periodicals, Inc.