Biochar and peat amendments affect nitrogen retention, microbial capacity and nitrogen cycling microbial communities in a metal and polycyclic aromatic hydrocarbon contaminated urban soil.

Soil contaminants may restrict soil functions. A promising soil remediation method is amendment with biochar, which has the potential to both adsorb contaminants and improve soil health. However, effects of biochar amendment on soil-plant nitrogen (N) dynamics and N cycling microbial guilds in contaminated soils are still poorly understood.

RecA finds homologous DNA by reduced dimensionality search.

Homologous recombination is essential for the accurate repair of double-stranded DNA breaks (DSBs). Initially, the RecBCD complex resects the ends of the DSB into 3' single-stranded DNA on which a RecA filament assembles. Next, the filament locates the homologous repair template on the sister chromosome.

Kinetics of dCas9 target search in .

How fast can a cell locate a specific chromosomal DNA sequence specified by a single-stranded oligonucleotide? To address this question, we investigate the intracellular search processes of the Cas9 protein, which can be programmed by a guide RNA to bind essentially any DNA sequence. This targeting flexibility requires Cas9 to unwind the DNA double helix to test for correct base pairing to the guide RNA. Here we study the search mechanisms of the catalytically inactive Cas9 (dCas9) in living by combining single-molecule fluorescence microscopy and bulk restriction-protection assays.

Direct measurement of transcription factor dissociation excludes a simple operator occupancy model for gene regulation.

Transcription factors mediate gene regulation by site-specific binding to chromosomal operators. It is commonly assumed that the level of repression is determined solely by the equilibrium binding of a repressor to its operator. However, this assumption has not been possible to test in living cells.

YcbX and yiiM, two novel determinants for resistance of Escherichia coli to N-hydroxylated base analogues.

We have shown previously that lack of molybdenum cofactor (MoCo) in Escherichia coli leads to hypersensitivity to the mutagenic and toxic effects of N-hydroxylated base analogues, such as 6-N-hydroxylaminopurine (HAP). However, the nature of the MoCo-dependent mechanism is unknown, as inactivation of all known and putative E. coli molybdoenzymes does not produce any sensitivity.

The highly efficient translation initiation region from the Escherichia coli rpsA gene lacks a shine-dalgarno element.

The translational initiation region (TIR) of the Escherichia coli rpsA gene, which encodes ribosomal protein S1, shows a number of unusual features. It extends far upstream (to position -91) of the initiator AUG, it lacks a canonical Shine-Dalgarno sequence (SD) element, and it can fold into three successive hairpins (I, II, and III) that are essential for high translational activity. Two conserved GGA trinucleotides, present in the loops of hairpins I and II, have been proposed to form a discontinuous SD.