Environmental DNA metabarcoding for benthic monitoring: A review of sediment sampling and DNA extraction methods.

Environmental DNA (eDNA) metabarcoding (parallel sequencing of DNA/RNA for identification of whole communities within a targeted group) is revolutionizing the field of aquatic biomonitoring. To date, most metabarcoding studies aiming to assess the ecological status of aquatic ecosystems have focused on water eDNA and macroinvertebrate bulk samples. However, the eDNA metabarcoding has also been applied to soft sediment samples, mainly for assessing microbial or meiofaunal biota. Compared to classical methodologies based on manual sorting and morphological identification of benthic taxa, eDNA metabarcoding offers potentially important advantages for assessing the environmental quality of sediments. The methods and protocols utilized for sediment eDNA metabarcoding can vary considerably among studies, and standardization efforts are needed to improve their robustness, comparability and use within regulatory frameworks. Here, we review the available information on eDNA metabarcoding applied to sediment samples, with a focus on sampling, preservation, and DNA extraction steps. We discuss challenges specific to sediment eDNA analysis, including the variety of different sources and states of eDNA and its persistence in the sediment. This paper aims to identify good-practice strategies and facilitate method harmonization for routine use of sediment eDNA in future benthic monitoring.

Correction to: JNK-NQO1 axis drives TAp73-mediated tumor suppression upon oxidative and proteasomal stress.

Correction to: Cell Death Dis. 5, e1484 (2014); https://doi.org/10.1038/cddis.2014.408 ; published online 23 October 2014.

JNK-NQO1 axis drives TAp73-mediated tumor suppression upon oxidative and proteasomal stress.

Hyperproliferating cancer cells produce energy mainly from aerobic glycolysis, which results in elevated ROS levels. Thus aggressive tumors often possess enhanced anti-oxidant capacity that impedes many current anti-cancer therapies. Additionally, in ROS-compromised cancer cells ubiquitin proteasome system (UPS) is often deregulated for timely removal of oxidized proteins, thus enabling cell survival. Taken that UPS maintains the turnover of factors controlling cell cycle and apoptosis--such as p53 or p73, it represents a promising target for pharmaceutical intervention. Enhancing oxidative insult in already ROS-compromised cancer cells appears as an attractive anti-tumor scenario. TAp73 is a bona fide tumor suppressor that drives the chemosensitivity of some cancers to cisplatin or γ-radiation. It is an important drug target in tumors where p53 is lost or mutated. Here we discovered a novel synergistic mechanism leading to potent p73 activation and cancer cell death by oxidative stress and inhibition of 20S proteasomes. Using a small-molecule inhibitor of 20S proteasome and ROS-inducer--withaferin A (WA), we found that WA-induced ROS activates JNK kinase and stabilizes phase II anti-oxidant response effector NF-E2-related transcription factor (NRF2). This results in activation of Nrf2 target--NQO1 (NADPH quinone oxidoreductase), and TAp73 protein stabilization. The observed effect was ablated by the ROS scavenger--NAC. Concurrently, stress-activated JNK phosphorylates TAp73 at multiple serine and threonine residues, which is crucial to ablate TAp73/MDM2 complex and to promote TAp73 transcriptional function and induction of robust apoptosis. Taken together our data demonstrate that ROS insult in combination with the inhibition of 20S proteasome and TAp73 activation endows synthetic lethality in cancer cells. Thus, our results may enable the establishment of a novel pharmacological strategy to exploit the enhanced sensitivity of tumors to elevated ROS and proteasomal stress to kill advanced tumors by pharmacological activation of TAp73 using molecules like WA.

Genetic transformation of Salvia austriaca by Agrobacterium rhizogenes and diterpenoid isolation.

Hairy roots of Salvia austriaca Jacq. transformed with Agrobacterium rhizogenes strain A4 were obtained and transgenic status of the roots was confirmed by polymerase chain reaction (PCR) using rolB and rolC specific primers. The root cultures growing in half-strength Gamborg (1/2 B5) liquid medium supplemented with sucrose (30 g L(-1)) under light conditions (photoperiod: 16 h light/8 h dark) were examined for their ability to produce diterpenoids. From n-hexane extract the abietane-type diterpenoids royleanone, 15-deoxyfuerstione and taxodione were isolated and identified. This is the first report on the genetic transformation of S. austriaca.

Catalytic adsorptive stripping voltammetry versus electrothermal atomic absorption spectrometry in the determination of trace cobalt and chromium in human urine.

Two methods of the determination of cobalt and chromium in human urine of non-occupationally exposed populations-highly sensitive catalytic adsorptive stripping voltammetry (CAdSV) and electrothermal atomic absorption spectrometry (ET-AAS)-are evaluated and compared. The CAdSV methods are based on adsorptive accumulation of a cobalt-nioxime (1,2-cyclohexanedione dioxime) or a chromium-DTPA (diethylenetriammine-N,N,N',N'',N''-pentaacetic acid) complexes on a hanging mercury drop electrode, followed by a stripping voltammetric measurement of the catalytic reduction current of the adsorbed complex in the presence of sodium nitrite in case of cobalt or in the presence of sodium nitrate in case of chromium determination. In the CAdSV procedure UV-photolysis was used for the sample pre-treatment; the ET-AAS determination did not require any separate preliminary decomposition of the analyte urine samples. The accuracy of the procedures was checked by the analysis of commercially available quality control urine samples. The detection limits (3sigma) were 0.13mugl(-1) for Co and 0.18mugl(-1) for Cr in ET-AAS determination and 0.007mugl(-1) for Co and 0.002mugl(-1) for Cr in CAdSV measurements. Precision (R.S.D.) was less than 5% for both methods. The study has shown that the CAdSV is a more reliable and sensitive technique for the determination of very low cobalt and chromium contents in urine, the detection of which is not possible when using the AAS technique.

Stimulation of furanochromone accumulation in callus cultures of Ammi visnaga L. by addition of elicitors.

In order to check the possibility of producing secondary metabolites, in vitro cultures of A. visnaga callus were established. The best growth of A. visnaga callus was obtained on Murashige and Skoog medium (MS) containing 6-benzyladenine (BA) and alpha-naphtaleneacetic acid (NAA). The study was concentrated on the induction of production of secondary metabolites by exposing callus to abiotic elicitors: benzo(1,2,3)-thiadiazole-7-carbothionic acid S-methyl ester (BION) and a suspension of silica (SiO2) and biotic elicitors: autoclaved lysates of Enterobacter sakazaki and scleroglucan. GC analysis indicated that not-elicited callus of A. visnaga grown in darkness accumulated 2 times more visnagin than the one which was grown under a 16-h photoperiod. The highest accumulation of visnagin was observed in the callus culture elicited with scleroglucan or BION. Scleroglucan induced also the accumulation of khellin in A. visnaga callus. The presented work shows that biosynthesis of pharmacologically important secondary metabolites in A. visnaga cultures could be stimulated by application of elicitors.

Establishment of hairy root cultures of Ammi majus.

Axenically grown Ammi majus plantlets were inoculated with seven different Agrobacterium rhizogenes strains. Hairy root lines were established only after inoculation with the two agropine strains: A4 and LBA9402. The growth rate of hairy root cultures was about thirty times faster than that of callus and cell suspension cultures. Polymerase chain reaction with primers for the genes rolB and rolC confirmed the integration of the T-DNA fragment of Ri plasmid of A. rhizogenes to the genome of hairy roots obtained after transformation by both Agrobacterium strains. The furanocoumarins (psoralen, xanthotoxine, bergapten and imperatorin) usually found in seeds of A. majus were not detected in callus, cell suspension and hairy root cultures using Gas chromatography-mass spectrometry (GC-MS). However, umbelliferone, a precursor of furanocoumarins, was detected in callus, cell suspension and hairy root cultures. The umbelliferone content in extracts of hairy root cultures, obtained after transformation by A4, was similar to that determined in A. majus seeds (19 µg/g DW) and higher than those obtained for cell suspension and callus cultures (2 and 9 µg/g DW, respectively).