Do benthic and planktonic diatoms produce equivalent effects in crustaceans?

Hippolyte inermis Leach 1814 is a benthic shrimp characterized by a peculiar mechanism of sex reversal influenced by diatom foods. In fact, the appearance of primary females in spring is due to an apoptotic early disruption of the androgenic gland and of the male gonad, triggered by still unknown compounds present in diatoms of the genus Cocconeis. The influence of diatoms on the reproductive ecology and life cycle of planktonic crustaceans has been demonstrated previously: some planktonic diatoms produce aldehydes inducing apoptosis in the embryos and in the larvae of marine copepods, reducing their viability. Both benthic and planktonic diatoms therefore produce compounds having an apoptotic effect on some tissues of target crustaceans, although the ecological significance of the two processes is different: deleterious for copepod populations, regulative for shrimps associated with Posidonia oceanica. In the present article we experimentally administered specific planktonic diatoms, their fractions and compounds known to induce apoptosis in planktonic copepods, to H. inermis postlarvae, to check whether the apoptotic effect is due to an identical family of diatom compounds, and to establish whether the processes observed in the plankton and in the benthos, respectively, are analogous or homologous, from an ecological point of view. Our results indicated that diatom compounds acting in the two systems are different, since both planktonic diatoms and their aldehydes had negligible effects on the sex ratios of cultured shrimps.     

Sequence divergence of the RNA polymerase shared subunit ABC14.5 (Rpb8) selectively affects RNA polymerase III assembly in Saccharomyces cerevisiae.

ABC14.5 (Rpb8) is a eukaryotic subunit common to all three nuclear RNA polymerases. In Saccharomyces cerevisiae, ABC14.5 (Rpb8) is essential for cell viability, however its function remains unknown. We have cloned and characterised the Schizosaccharomyces pombe rpb8(+) cDNA. We found that S.pombe rpb8, unlike the similarly diverged human orthologue, cannot substitute for S.cerevisiae ABC14. 5 in vivo. To obtain information on the function of this RNA polymerase shared subunit we have used S.pombe rpb8 as a naturally altered molecule in heterologous expression assays in S.cerevisiae. Amino acid residue differences within the 67 N-terminal residues contribute to the functional distinction of the two yeast orthologues in S.cerevisiae. Overexpression of the S.cerevisiae largest subunit of RNA polymerase III C160 (Rpc1) allows S.pombe rpb8 to functionally replace ABC14.5 in S.cerevisiae, suggesting a specific genetic interaction between the S.cerevisiae ABC14.5 (Rpb8) and C160 subunits. We provide further molecular and biochemical evidence showing that the heterologously expressed S.pombe rpb8 molecule selectively affects RNApolymerase III but not RNA polymerase I complex assembly. We also report the identification of a S.cerevisiae ABC14.5-G120D mutant which affects RNA polymerase III.     

Stature estimation in extinct Aónikenk and the myth of Patagonian gigantism

The Aónikenk were a hunter-gatherer group that inhabited the southern extreme of Patagonia at European Contact and became extinct at the end of the 19th century. The myth of Patagonian gigantism developed around these aborigines from early Spanish explorer accounts. In this study, the postcranial remains belonging to the Aónikenk (Patagonia) and the Selk'nam (Tierra del Fuego) preserved at the Instituto de la Patagonia (UMAG, Chile) have been measured, using standard metrics. Different stature estimations for these groups have been generated, by using the different regression formulae available. Aónikenk male stature appears to be between 174 and 178 cm on average, whereas the Selk'nam are considerably shorter. In addition, stature estimations from Spanish populations dating to the contact period have been compiled for comparison. While it can be concluded that the Aónikenk probably presented the highest stature values of all Meso- and South American populations, it is suggested that the perception of their gigantism could be partially attributed to the real difference in stature (probably more than 10 cm) between these aborigines and contemporaneous Europeans. Am J Phys Anthropol 105:545–551, 1998. © 1998 Wiley-Liss, Inc.     

A new species of Micragasma J. Sahlberg, 1900 (Coleoptera: Hydraenidae) from Crete

We describe a new species of Micragasma J. Sahlberg, 1900 (Coleoptera, Hydraenidae), which is here treated as a subgenus of Ochthebius Leach, 1815 Leach, W.E. (1815), ‘Entomology’, in The Edinburgh Encyclopaedia (Vol. 9), ed. D. Brewster, Balfour: Edinburgh, pp. 57–172. [Google Scholar]. The new species, O. (Micragasma) minoicus sp. n., was found at the margins of a coastal rockpool in the island of Crete. The species differs from the other two known species of Micragasma in both external and genital characters, but shares with them the presence of small setiferous tubercles on the surface of the head, pronotum and elytra, and a strong medial gibbosity on the head. In some characters, such as the structure and shape of the aedeagus, O. (M.) minoicus sp. n. is similar to other species of the genus Ochthebius, in particular of the subgenus Cobalius Rey, 1886 Rey, C. (1886), ‘Histoire naturelle des coléoptères de France (suite)’, Annales de la Société Linnéenne de Lyon, 32, 1–187, pl. 1–2.[Crossref] , [Google Scholar], typical of coastal rockpools.

http://zoobank.org/urn:lsid:zoobank.org:act:BCEAE1EE-7C5E-4017-A753-559738221502     

A framework for exhaustively mapping functional missense variants

Although we now routinely sequence human genomes, we can confidently identify only a fraction of the sequence variants that have a functional impact. Here, we developed a deep mutational scanning framework that produces exhaustive maps for human missense variants by combining random codon mutagenesis and multiplexed functional variation assays with computational imputation and refinement. We applied this framework to four proteins corresponding to six human genes: UBE2I (encoding SUMO E2 conjugase), SUMO1 (small ubiquitin‐like modifier), TPK1 (thiamin pyrophosphokinase), and CALM1/2/3 (three genes encoding the protein calmodulin). The resulting maps recapitulate known protein features and confidently identify pathogenic variation. Assays potentially amenable to deep mutational scanning are already available for 57% of human disease genes, suggesting that DMS could ultimately map functional variation for all human disease genes.     

Fingerprinting the genetic diversity of the biotin carboxylase gene (accC) in aquatic ecosystems as a potential marker for studies of carbon dioxide assimilation in the dark

We designed and tested a set of specific primers for specific PCR amplification of the biotin carboxylase subunit gene (accC) of the Acetyl CoA carboxylase (ACCase) enzyme. The primer set yielded a PCR product of c. 460 bp that was suitable for denaturing gradient gel electrophoresis (DGGE) fingerprinting followed by direct sequencing of excised DGGE bands and sequence analysis. Optimization of PCR conditions for selective amplification was carried out with pure cultures of different bacteria and archaea, and laboratory enrichments. Next, fingerprinting comparisons were done in several aerobic and anaerobic freshwater planktonic samples. The DGGE fingerprints showed between 2 and 19 bands in the different samples, and the primer set provided specific amplification in both pure cultures and natural samples. Most of the samples had sequences grouped with bacterial accC, hypothetically related to the anaplerotic fixation of inorganic carbon. Some other samples, however, yielded accC gene sequences that clustered with Crenarchaeota and were related to the 3-hydroxypropionate/4-hydroxybutyrate cycle of autotrophic crenarchaeota. Such samples came from oligotrophic high mountain lakes and the hypolimnia of a sulfide-rich lake, where crenarchaeotal populations had been previously reported by 16S rRNA surveys. This study provided a fast tool to look for presence of accC genes in natural environments as potential marker for studies of carbon dioxide assimilation in the dark. After further refinement for better specificity against archaea, the new and novel primers could be very helpful to establish a target for crenarchaeota with implications for our understanding of archaeal carbon biogeochemistry.     

Gene expression analysis of a human enterocyte cell line reveals downregulation of cholesterol biosynthesis in response to short-chain fatty acids

It has been suggested that the short-chain fatty acids (SCFAs) produced by anaerobic bacterial intestinal fermentation of soluble fiber may regulate lipid metabolism in intestine, thus reducing plasma cholesterol levels. However, the exact mechanism of action of SCFAs in lowering cholesterol levels is not fully understood. The aims of this study were to test the effects of SCFAs on gene expression in a human enterocyte cell line Caco-2/TC-7 and to validate microarray data by real-time PCR. Human Caco-2/TC-7 enterocytes were cultured on transwell filter inserts and incubated with the SCFAs acetate (Ac), propionate (Pr), and butyrate (Bu). Total RNA was then isolated for microarrays and quantitative real-time PCR analysis. Treatment of human enterocytes with Pr and Bu affects a wide variety of genes. These genes were classified according to the PANTHER classification system, and the results showed that different biological processes and metabolic pathways were modified by Pr and Bu treatment, including the intestinal cholesterol biosynthesis pathway. Differential array expression analysis showed that nine genes were downregulated in this pathway, and these results were validated by real-time PCR. This in vitro study allowed us to identify a wide variety of biological processes and metabolic pathways affected by the SCFAs tested. Importantly, our results show that the global effect of Pr and Bu is to downregulate the expression of nine key genes involved in intestinal cholesterol biosynthesis, thus possibly inhibiting this pathway.