Evaluation of Holocene pollen records from the Romanian Plain

This study is a critical review of pollen analyses carried out on Holocene sequences from 15 sites in and near the Romanian Plain. Three sites come from natural sediments, 10 sites are from anthropogenic deposits and two are from both anthropogenic and natural settings. The general reconstruction is of a steppe-forest-steppe vegetation through the Holocene. The nature of the deposits, however, casts doubts on this reconstruction. Deposits of archaeological sites generally yield pollen spectra that are influenced by human activities and thus unsuitable for vegetation reconstructions. Loess deposits are also unfavorable for pollen preservation because of high pH and porosity. Consequently, pollen spectra from loess deposits are strongly biased by selective pollen destruction. Research and experiments carried out by several authors suggest that spectra dominated by Asteraceae, Poaceae, Chenopodiaceae or Pinus pollen in soils and loess are a result of selective pollen destruction, especially if low pollen concentrations, progressive pollen deterioration or high frequencies of deteriorated or unidentifiable pollen are evidenced. The fact that pollen records from the Romanian Plain come from loess, alkaline peat or archaeological sites reduces their reliability for reconstructions of vegetation. The vegetation history of similar regions in Hungary, Bulgaria and Turkey suggests that early Holocene steppe vegetation was gradually replaced by forest or forest-steppe vegetation in the late Holocene. Records from lake sediments are required to find out whether the Holocene vegetation history of the Romanian Plain was similar.     

Metal accumulation in two contiguous eutrophic peri-urban lakes,Chivero and Manyame,Zimbabwe

Concentrations of aluminium, cadmium, chromium, cobalt, copper, iron, lead, nickel and zinc were determined in surface water, benthic sediments, and the gills, liver and stomach muscle tissues of Oreochromis niloticus and Clarias gariepinus in peri-urban lakes Chivero and Manyame, Zimbabwe. Five sites were sampled in each lake once per month in November 2015, February, May, August and November 2016. Pollution load index detected no metal contamination, whereas the geo-accumulation index reflected heavy to extreme sediment pollution, with Fe, Cd, Zn, Cr, Ni and Cu present in both lakes. Significant spatial temporal variations were detected for Al, Cr, Cu and Pb across sites within and between the two lakes. High Fe, Al and Cr concentrations in water and sediments in lakes Chivero and Manyame derive from geogenic background sources in addition to anthropogenic loads and intensity. Elevated concentrations of Al, Pb, Cu, Cd, Fe and Zn detected in gills, liver and stomach tissue of catfish corroborate concentrations in water and sediments, and pose the highest ecological and health risk for hydrobionts in lakes Chivero and Manyame. Contiguity of peri-urban lakes exposes them to similar threats, necessitating creative water management strategies, which ensure ecological continuity.     

A safe and complete algorithm for metagenomic assembly

Background

Reconstructing the genome of a species from short fragments is one of the oldest bioinformatics problems. Metagenomic assembly is a variant of the problem asking to reconstruct the circular genomes of all bacterial species present in a sequencing sample. This problem can be naturally formulated as finding a collection of circular walks of a directed graph G that together cover all nodes, or edges, of G.

Approach

We address this problem with the “safe and complete” framework of Tomescu and Medvedev (Research in computational Molecular biology—20th annual conference, RECOMB 9649:152–163, 2016). An algorithm is called safe if it returns only those walks (also called safe) that appear as subwalk in all metagenomic assembly solutions for G. A safe algorithm is called complete if it returns all safe walks of G.

Results

We give graph-theoretic characterizations of the safe walks of G, and a safe and complete algorithm finding all safe walks of G. In the node-covering case, our algorithm runs in time \(O(m^2 + n^3)\), and in the edge-covering case it runs in time \(O(m^2n)\); n and m denote the number of nodes and edges, respectively, of G. This algorithm constitutes the first theoretical tight upper bound on what can be safely assembled from metagenomic reads using this problem formulation.