Comparison of destructive and nondestructive DNA extraction methods for the metabarcoding of arthropod bulk samples

DNA metabarcoding is routinely used for biodiversity assessment, in particular targeting highly diverse groups for which limited taxonomic expertise is available. Various protocols are currently in use, although standardization is key to its application in large-scale monitoring. DNA metabarcoding of arthropod bulk samples can be conducted either destructively from sample tissue, or nondestructively from sample fixative or lysis buffer. Nondestructive methods are highly desirable for the preservation of sample integrity but have yet to be experimentally evaluated in detail. Here, we compare diversity estimates from 14 size-sorted Malaise trap samples processed consecutively with three nondestructive approaches (one using fixative ethanol and two using lysis buffers) and one destructive approach (using homogenized tissue). Extraction from commercial lysis buffer yielded comparable species richness and high overlap in species composition to the ground tissue extracts. A significantly divergent community was detected from preservative ethanol-based DNA extraction. No consistent trend in species richness was found with increasing incubation time in lysis buffer. These results indicate that nondestructive DNA extraction from incubation in lysis buffer could provide a comparable alternative to destructive approaches with the added advantage of preserving the specimens for postmetabarcoding taxonomic work but at a higher cost per sample.     

Effect of 17β estradiol on [3H] progesterone binding in rat brain

A progesterone-binding component is reported in the cerebral hemispheres of immature female rat. [³H] progesterone binding in the brain cytosol is increased following two weeks of estradiol administration. The [³H] progesterone binding by this component can be reduced by pretreatment with unlabeled steroid. In addition, the binder from both control and estradiol-treated groups shows inter-action with ATP immobilized on columns of ATP-Sepharose.     

Dying of Gamma-Irradiated Escherichia coli Studied by the Use of Prophage

Loss of the biological activity of deoxyribonucleic acid in gamma-irradiated Escherichia coli cells was studied. The study is based on two sets of experimental data: (i) post-irradiation heat inducibility of the cells whose chromosomes were "labeled" with the thermoinducible lambdacI857ind prophage, and (ii) post-irradiation capacity of nonlysogenic cells to promote growth of the unirradiated lambdacI857ind phage. The results show that, at the beginning of incubation after irradiation, the number of plaques formed upon heat induction of lysogenic cells was much higher than the viable cell count of the nonheated culture. This high resistance of the heat inducibility gradually decreased during post-irradiation incubation. Finally, after a period of 4 h, there was no difference in sensitivity between the heat inducibility and the colony-forming ability of gamma-irradiated cells. The capacity of gamma-irradiated bacteria to support growth of unirradiated lambdacI857ind is radioresistant; this resistance, in contrast to that of heat inducibility, is much less affected during post-irradiation incubation. A continuous decrease in radioresistance of heat inducibility without a corresponding decrease in radioresistance of the capacity suggests that functional failure of initially undamaged and/or repaired parts of the chromosome gradually develops after irradiation. From the fact that after 4 h all colony formers are capable of being induced by heat, whereas no chromosomal activity can be detected in nonviable cells, two conclusions may be drawn: (i) gamma-irradiated E. coli cells destined to die reach their biological end point within 4 h of post-irradiation incubation; (ii) in most cells, functional failure of the whole chromosome is the immediate cause of death.     

An autoradiographic method of detectingA. laidlawii andM. hyorhinis in cell cultures

Summary The autoradiographic investigation of L cells and Chinese hamster cells for the presence of mycoplasmas (A. laidlawii andM. hyorhinis) using uridine/uracil (UdR/U) testing is a rapid and reliable method suitable for the serial checking of even a small number of cells. It depends on a reduced incorporation of [³H]uridine and an increased uptake of [³H]uracil into the RNA of mycoplasma-infected cells, shown in autoradiograms by the density of the grains and their distribution. Results obtained by the autoradiographic technique correspond approximately to specific activity values of RNA-infected cells after the incorporation of [³H]uridine and [³H]uracil.     

The comparison of two systems of vegetation classification of steppe communities in the Minusinskaja kotlovina basin (South Siberia)

The difference and/or similarity of both approaches, the one ofSo?ava and the one ofBraun-Blanquet, and the reciprocal transferability of the units of cartography is tested using the mapped vegetation of the Siberian steppe as an example.     

Exchange between inorganic phosphate and adenosine triphosphate in (Na+,K+)-ATPase

(Na⁺,K⁺)-ATPase is able to catalyze a continuous ATP?P_i exchange in the presence of Na⁺ and in the absence of a transmembrane ionic gradient. At pH 7.6 the Na⁺ concentration required for half-maximal activity is 85 mM and at pH 5.1 it is 340 mM. In the presence of optimal Na⁺ concentration, the rate of exchange is maximal at pH 6.0 and varies with ADP and P_i concentration in the assay medium. ATP?P_i exchange is inhibited by K⁺ and by ouabain.     

Enantioselectivity in the metabolism of mexiletine by conjugation in female patients with the arrhythmic form of chronic Chagas' heart disease

The phenomenon of enantioselectivity in the metabolism of mexiletine (MEX) conjugation was investigated in eight female patients with the arrhythmic form of chronic Chagas' heart disease treated with racemic mexiletine hydrochloride (two 100 mg capsules every 8 hr). Blood samples were collected up to 24 hr after the administration of the morning dose, with discontinuation of the subsequent doses during the study period. Plasma concentrations of N‐hydroxymexiletine glucuronide were calculated as the difference between the concentrations of unchanged and total (unchanged + conjugated) MEX enantiomers. Total plasma MEX concentrations were analyzed by HPLC after enzymatic hydrolysis with β‐glucuronidase, the formation of diastereomeric derivatives with the chiral reagent N‐acetyl‐l ‐cysteine/o‐phthalaldehyde, and fluorescence detection. The differences in the pharmacokinetic parameters of the enantiomers were evaluated by the paired t‐test. The plasma concentrations of the (+)‐(S)‐MEX did not differ before and after enzymatic hydrolysis. The pharmacokinetic parameters calculated for (−)‐(R)‐N‐hydroxymexiletine glucuronide are presented as means (95% confidence interval): maximum plasma concentration C_max = 194.0 ng · ml⁻¹ (154.3–233.7), time to maximum plasma concentration t_max = 1.4 hr (0.3–2.5), area under the plasma concentration versus time curve AUC^0–24 = 2099.2 ng · h · ml⁻¹ (1585.6–2612.6), elimination half‐life t_1/2β = 12.8 hr (9.9–15.6) and extent of conjugation of 31.6% (24.3–38.9%). The present data indicate stereospecific conjugation of (−)‐(R)‐N‐hydroxymexiletine in the female patients with the arrhythmic form of Chagas' heart disease. Chirality 11:29–32, 1999. © 1999 Wiley‐Liss, Inc.     

Enantioselective analysis of albendazole sulfoxide in plasma using the chiral stationary phase

We present a method for the enantioselective analysis of albendazole sulfoxide (ABZSO) in plasma for application in clinical pharmacokinetic studies. ABZSO enantiomers were separated on a 5-μm Chiralcel OB-H® column (4.6 × 150 mm) using hexane:ethanol (93:7, v/v) as the mobile phase and fluorescence detection. ABZSO was extracted with chloroform:isopropanol (8:2, v/v) from 500-μl aliquots of acidified plasma, with full drug recovery. The proposed method presented quantitation limits of 20 ng/ml for (−)ABZSO and 50 ng/ml for (+)ABZSO and was linear up to a concentration of 5,000 ng/ml of each enantiomer. Chirality 9:722–726, 1997. © 1997 Wiley-Liss, Inc.     

Hydrodynamic disturbance controls microbial community assembly and biogeochemical processes in coastal sediments

The microbial community composition and biogeochemical dynamics of coastal permeable (sand) sediments differs from cohesive (mud) sediments. Tide- and wave-driven hydrodynamic disturbance causes spatiotemporal variations in oxygen levels, which select for microbial generalists and disrupt redox cascades. In this work, we profiled microbial communities and biogeochemical dynamics in sediment profiles from three sites varying in their exposure to hydrodynamic disturbance. Strong variations in sediment geochemistry, biogeochemical activities, and microbial abundance, composition, and capabilities were observed between the sites. Most of these variations, except for microbial abundance and diversity, significantly correlated with the relative disturbance level of each sample. In line with previous findings, metabolically flexible habitat generalists (e.g., Flavobacteriaceae, Woeseaiceae, Rhodobacteraceae) dominated in all samples. However, we present evidence that aerobic specialists such as ammonia-oxidizing archaea (Nitrosopumilaceae) were more abundant and active in more disturbed samples, whereas bacteria capable of sulfate reduction (e.g., uncultured Desulfobacterales), dissimilatory nitrate reduction to ammonium (DNRA; e.g., Ignavibacteriaceae), and sulfide-dependent chemolithoautotrophy (e.g., Sulfurovaceae) were enriched and active in less disturbed samples. These findings are supported by insights from nine deeply sequenced metagenomes and 169 derived metagenome-assembled genomes. Altogether, these findings suggest that hydrodynamic disturbance is a critical factor controlling microbial community assembly and biogeochemical processes in coastal sediments. Moreover, they strengthen our understanding of the relationships between microbial composition and biogeochemical processes in these unique environments.Subject terms: Water microbiology, Biogeochemistry