Effects of post-transcriptional regulation on phenotypic noise

ABSTRACT Cell-to-cell variations in protein abundance, called noise, give rise to phenotypic variability between isogenic cells. Studies of noise have focused on stochasticity introduced at transcription, yet the effects of post-transcriptional regulatory processes on noise remain unknown. We study the effects of RyhB, a small-RNA of Escherichia coli produced on iron stress, on the phenotypic variability of two of its downregulated target proteins, using dual chromosomal fusions to fluorescent reporters and measurements in live individual cells. The total noise of each of the target proteins is remarkably constant over a wide range of RyhB production rates despite cells being in stress. In fact, coordinate downregulation of the two target proteins by RyhB reduces the correlation between their levels. Hence, an increase in phenotypic variability under stress is achieved by decoupling the expression of different target proteins in the same cell, rather than by an increase in the total noise of each. Extrinsic noise provides the dominant contribution to the total protein noise over the total range of RyhB production rates. Stochastic simulations reproduce qualitatively key features of our observations and show that a feed-forward loop formed by transcriptional extrinsic noise, an sRNA and its target genes exhibits strong noise filtration capabilities

Opportunism or aquatic specialization? Evidence of freshwater fish exploitation at Ohalo II- A waterlogged Upper Paleolithic site.

Analysis of ca. 17,000 fish remains recovered from the late Upper Paleolithic/early Epi-Paleolithic (LGM; 23,000 BP) waterlogged site of Ohalo II (Rift Valley, Israel) provides new insights into the role of wetland habitats and the fish inhabiting them during the evolution of economic strategies prior to the agricultural evolution. Of the current 19 native fish species in Lake Kinneret (Sea of Galilee), eight species were identified at Ohalo II, belonging to two freshwater families: Cyprinidae (carps) and Cichlidae (St. Peter fish). Employing a large set of quantitative and qualitative criteria (NISP, species richness, diversity, skeletal element representation, fragmentation, color, spatial distribution, etc.), we demonstrate that the inhabitants of Ohalo II used their knowledge of the breeding behavior of different species of fish, for year-round intensive exploitation

Revisiting the species list of freshwater fish in Israel based on DNA barcoding

Abstract Israel's region forms a continental bridge; hence, the freshwater fish fauna in Israel consists of unique populations of species that originated from Africa, Asia, or Europe and are often endemic or at the edge of their distribution range. Worldwide, fish biodiversity suffers significantly from pressures and disturbances of freshwater habitats, especially in arid regions, such as in parts of Israel. Biodiversity conservation requires efficient tools for monitoring changes in populations. DNA barcoding, by complementing and enhancing species identification, provides such monitoring tools. In this study, over 200 specimens representing over 28 species were DNA barcoded and together with previously available records, a DNA barcoding database for freshwater fish of Israel was established. Of the 71 distinct barcodes generated, 37% were new, attesting to the uniqueness of fish populations in Israel. For most species, morphological and molecular species identifications agreed. However, discrepancies were found for five genera. Based on DNA barcoding, we propose Acanthobrama telavivensis as a junior synonym for Acanthobrama lissneri. In Garra spp., we propose splitting Garra nana into two species and assigning Garra rufa in the region to Garra jordanica, or possibly to two species. Israeli Pseudophoxinus kervillei is not the same species as in Syria and Lebanon. However, Pseudophoxinus syriacus might not be endangered since it is genetically very similar to Pseudophoxinus drusensis. In Israel, instead of five reported Oxynoemacheilus species, combining DNA barcoding with morphology suggests only three. Genetic and geographic separation suggested that Aphanius mento is likely a species complex. The study provides a thorough barcoding database, suggests significant species reconsiderations in the region, and highlights the Sea of Galilee and the Beit She'an valley streams as biodiversity “hotspots.” This study will therefore promote further studying of the fish species in the region and their ecology, as well as the monitoring and conservation of freshwater fish biodiversity in Israel and the region

Frequency (NISP), percentage, and survival index (SI) calculated for cranial and postcranial bones, according to the studied loci at Ohalo II.

<p>Frequency (NISP), percentage, and survival index (SI) calculated for cranial and postcranial bones, according to the studied loci at Ohalo II.</p

Correspondence analysis of taxonomic groups’ relative abundance (%) in the natural accumulation and at Loci 1, 3, 7, and 8.

<p>Correspondence analysis of taxonomic groups’ relative abundance (%) in the natural accumulation and at Loci 1, 3, 7, and 8.</p

Ohalo II fish remains taxonomic composition, species richness and diversity, by studied loci (taxonomic abundance (%) is calculated according to the different taxonomic levels: Family, genus and species, and therefore the total NISP varies).

<p>Ohalo II fish remains taxonomic composition, species richness and diversity, by studied loci (taxonomic abundance (%) is calculated according to the different taxonomic levels: Family, genus and species, and therefore the total NISP varies).</p

Comparison between diagnostic criteria of naturally accumulated fish remains vs. fish remains recovered at Ohalo II (OH), according to the studied loci (loci 1, 3, 7, 8).

<p>Comparison between diagnostic criteria of naturally accumulated fish remains vs. fish remains recovered at Ohalo II (OH), according to the studied loci (loci 1, 3, 7, 8).</p

State of bone preservation at Ohalo II, according to studied loci (chi squared test = 944.133; p = 0.0001; df = 6).

<p>State of bone preservation at Ohalo II, according to studied loci (chi squared test = 944.133; p = 0.0001; df = 6).</p

Rarefaction curves for species richness, as a function of NISP, according to the studied loci.

<p>Rarefaction curves for species richness, as a function of NISP, according to the studied loci.</p