New Fisheries-related data from the Mediterranean Sea (November, 2016)

In this fourth Collective Article, with fisheries-related data from the Mediterranean, we present weight-length relationships for eight deep-sea fish species (Brama brama, Conger conger, Etmopterus spinax, Molva macrophthalma, Mora moro, Pagellus bogaraveo, Phycis blennoides) from the Eastern Ionian Sea; Scyliorhinus canicula from various locations in the Mediterranean Sea and weight-length relationships and condition factor of five Mugilidae species (Liza aurata, Liza saliens, Liza ramada, Mugil cephalus, Chelon labrosus) from a Mediterranean lagoon in the Ionian Sea. Moreover, we present otolith weight, fish length and otolith length relationships of the red mullet (Mullus barbatus) in the Aegean and Ionian Sea and otolith weight relationships in European hake (Merluccius merluccius) from the Greek Seas

Call me by my name: unravelling the taxonomy of the gulper shark genus Centrophorus in the Mediterranean Sea through an integrated taxonomic approach

The current shift of fishery efforts towards the deep sea is raising concern about the vulnerability of deep-water sharks, which are often poorly studied and characterized by problematic taxonomy. For instance, in the Mediterranean Sea the taxonomy of genus Centrophorus has not been clearly unravelled yet. Since proper identification of the species is fundamental for their correct assessment and management, this study aims at clarifying the taxonomy of this genus in the Mediterranean Basin through an integrated taxonomic approach. We analysed a total of 281 gulper sharks (Centrophorus spp.) collected from various Mediterranean, Atlantic and Indian Ocean waters. Molecular data obtained from cytochrome c oxidase subunit I (COI), 16S ribosomal RNA (16S), NADH dehydrogenase subunit 2 (ND2) and a portion of a nuclear 28S ribosomal DNA gene region (28S) have highlighted the presence of a unique mitochondrial clade in the Mediterranean Sea. The morphometric results confirmed these findings, supporting the presence of a unique and distinct morphological group comprising all Mediterranean individuals. The data strongly indicate the occurrence of a single Centrophorus species in the Mediterranean, ascribable to C. cf. uyato, and suggest the need for a revision of the systematics of the genus in the area.En prens

Conditional Gene Knockout in Human Cells with Inducible CRISPR/Cas9.

The advent of the easily programmable and efficient CRISPR/Cas9 nuclease system has revolutionized genetic engineering. While conventional gene knockout experiments using CRISPR/Cas9 are very valuable, these are not well suited to study stage-specific gene function in dynamic situations such as development or disease. Here we describe a CRISPR/Cas9-based OPTimized inducible gene KnockOut method (OPTiKO) for conditional loss-of-function studies in human cells. This approach relies on an improved tetracycline-inducible system for conditional expression of single guide RNAs (sgRNAs) that drive Cas9 activity. In order to ensure homogeneous and stable expression, the necessary transgenes are expressed following rapid and efficient single-step genetic engineering of the AAVS1 genomic safe harbor. When implemented in human pluripotent stem cells (hPSCs), the approach can be then efficiently applied to virtually any hPSC-derived human cell type at various stages of development or disease

Sexual maturity, fecundity and embryonic development of the spiny dogfish, Squalus acanthias, in the eastern Mediterranean Sea

The reproductive biology of the spiny dogfish, Squalus acanthias, was investigated throughout a year, in the eastern Mediterranean Sea. One hundred and eighty specimens were sampled of which 119 were females and 61 males, ranging from 320 to 755 mm and from 350 to 820 mm total length (TL), respectively. The minimum size of mature females was 515 mm and 470 mm TL for mature males (smaller compared with sizes in other studies). Gonadosomatic index (GSI) and hepatosomatic index (HSI) were higher during June and August in female dogfish, respectively; in males GSI had a peak in July and HSI showed its highest value in April. A total of 39 gravid females was identified with TL ranging between 570 and 755 mm. Only 28 of them were bearing embryos; candled uteri were observed in the 11 other gravid animals. A positive relationship was recorded between maternal length and litter size. Ovarian fecundity ranged between 1 and 6 (mean 2.1 1.1); uterine fecundity ranged from 1 to 6 (mean 3.3 1.2). The size of the pups varied from 72 to 220 mm TL and their weight ranged between 1.6-48.5 g (mean 11.7 8.6). The spiny dogfish was compared with fish from other study areas and was found to be smaller in size in the eastern Mediterranean Sea, reaching maturity at smaller sizes and obtaining lower fecundity than female fish in other areas

The two-faced progeria gene and its implications in aging and metabolism

Premature aging syndromes have gained much attention, not only because of their devastating symptoms but also because they might hold a key to some of the mechanisms underlying aging. The Hutchinson-Gilford progeria syndrome (HGPS) is caused by a mutation in the LMNA gene, which normally produces lamins A and C through alternative splicing. Due to this mutation, HGPS patients express an incompletely processed form of lamin A called progerin. In this issue of EMBO Reports, the Tazi group demonstrates how mice expressing different LMNA isoforms present opposite phenotypes in longevity, fat storage and mitochondrial functio

Tetracycline Antibiotics Impair Mitochondrial Function and Its Experimental Use Confounds Research

Tetracyclines, a class of antibiotics that target bacterial translation, are commonly used in research for inducible gene expression using Tet-ON/Tet-OFF systems. However, such tetracycline-inducible systems carry a risk. Given that mitochondria have a "bacterial" ancestry, these antibiotics also target mitochondrial translation and impair mitochondrial function. Indeed, treatment with doxycycline-a tetracycline derivative-disturbs mitochondrial proteostasis and metabolic activity, and induces widespread gene-expression changes. Together, this affects physiology in well-established model systems ranging from cultured cells to simple organisms and to mice and plants. These changes are observed with doxycycline doses that are widely used to regulate gene expression. In light of these findings, and bearing in mind the conserved role of mitochondria in metabolism and whole organism homeostasis, we caution against the use of tetracyclines in experimental approaches. The use of newly developed tetracycline-based systems that are more sensitive could be an alternative; however, even if no overt mitochondrial toxicity is detected, widespread changes in gene expression may sensitize cells to the intended tetracycline-controlled loss or gain of function, thereby introducing a "two-hit model." This is highly relevant for cancer research, as mitochondrial metabolism holds a central position in the reallocation of nutrients for biomass production known as the Warburg effect. (C) 2015 AACR

High levels of mislabeling in shark meat – Investigating patterns of species utilization with DNA barcoding in Greek retailers

This is the author accepted manuscript. The final version is available from Elsevier via the DOI in this record.Food authenticity has received an increasing focus due to high profile cases of substitution/mislabeling, with many investigations identifying sales of endangered or prohibited species. At the same time, the European Union (EU) has introduced one of the most progressive sets of legislation in order to promote traceability and protect consumers. This study aims to identify shark species that are sold under the commercial term “Galeos” in Greece (which officially designates Mustelus mustelus, M. punctulatus and M. asterias), using DNA barcoding. A total of 87 samples were collected from fishmongers and markets across four cities. A combination of two mitochondrial genes, the cytochrome c oxidase subunit I (COI) and the 16S ribosomal RNA (16S), were used to analyze samples, and species were identified by reference to genetic databases. The results revealed significant differences in patterns of species utilization between cities and retailers. Across the study an extremely high level of mislabeling was identified (56%). This probably relates to some degree of unintentional misidentification and confusion surrounding the designation in Greece, but highlights how consumers are unprotected from incorrect/misleading labels. Over half of products originated from species that are locally listed as threatened by the ICUN red list, and of the mislabeled products, 23% originated from species with prohibitions on landings or CITES listings. This includes large growing sharks with little resemblance to Mustelus spp. and likely demonstrates deliberate substitution. It shows how mislabeled products are providing a route for prohibited/protected sharks to enter the supply chain and be sold to consumers

COmplexome Profiling ALignment (COPAL) reveals remodeling of mitochondrial protein complexes in Barth syndrome

Motivation: Complexome profiling combines native gel electrophoresis with mass spectrometry to obtain the inventory, composition and abundance of multiprotein assemblies in an organelle. Applying complexome profiling to determine the effect of a mutation on protein complexes requires separating technical and biological variations from the variations caused by that mutation. Results: We have developed the COmplexome Profiling ALignment (COPAL) tool that aligns multiple complexome profiles with each other. It includes the abundance profiles of all proteins on two gels, using a multi-dimensional implementation of the dynamic time warping algorithm to align the gels. Subsequent progressive alignment allows us to align multiple profiles with each other. We tested COPAL on complexome profiles from control mitochondria and from Barth syndrome (BTHS) mitochondria, which have a mutation in tafazzin gene that is involved in remodeling the inner mitochondrial membrane phospholipid cardiolipin. By comparing the variation between BTHS mitochondria and controls with the variation among either, we assessed the effects of BTHS on the abundance profiles of individual proteins. Combining those profiles with gene set enrichment analysis allows detecting significantly affected protein complexes. Most of the significantly affected protein complexes are located in the inner mitochondrial membrane (mitochondrial contact site and cristae organizing system, prohibitins), or are attached to it (the large ribosomal subunit). Availability and implementation: COPAL is written in python and is available from http://github.com/cmbi/copal