Evaluation of the ISO Standard 11063 DNA Extraction Procedure for Assessing Soil Microbial Abundance and Community Structure

Soil DNA extraction has become a critical step in describing microbial biodiversity. Historically, ascertaining overarching microbial ecological theories has been hindered as independent studies have used numerous custom and commercial DNA extraction procedures. For that reason, a standardized soil DNA extraction method (ISO-11063) was previously published. However, although this ISO method is suited for molecular tools such as quantitative PCR and community fingerprinting techniques, it has only been optimized for examining soil bacteria. Therefore, the aim of this study was to assess an appropriate soil DNA extraction procedure for examining bacterial, archaeal and fungal diversity in soils of contrasting land-use and physico-chemical properties. Three different procedures were tested: the ISO-11063 standard; a custom procedure (GnS-GII); and a modified ISO procedure (ISOm) which includes a different mechanical lysis step (a FastPrep ®-24 lysis step instead of the recommended bead-beating). The efficacy of each method was first assessed by estimating microbial biomass through total DNA quantification. Then, the abundances and community structure of bacteria, archaea and fungi were determined using real-time PCR and terminal restriction fragment length polymorphism approaches. Results showed that DNA yield was improved with the GnS-GII and ISOm procedures, and fungal community patterns were found to be strongly dependent on the extraction method. The main methodological factor responsible for differences between extraction procedure efficiencies was found to be the soil homogenization step. For integrative studies which aim to examine bacteria, archaea and fungi simultaneously, the ISOm procedure results in higher DNA recovery and better represents microbial communities.     

The loss of an electrostatic contact unique to AMPA receptor ligand binding domain 2 slows channel activation

Ligand-gated ion channels undergo conformational changes that transfer the energy of agonist binding to channel opening. Within ionotropic glutamate receptor (iGluR) subunits, this process is initiated in their bilobate ligand binding domain (LBD) where agonist binding to lobe 1 favors closure of lobe 2 around the agonist and allows formation of interlobe hydrogen bonds. AMPA receptors (GluAs) differ from other iGluRs because glutamate binding causes an aspartate-serine peptide bond in a flexible part of lobe 2 to rotate 180° (flipped conformation), allowing these residues to form cross-cleft H-bonds with tyrosine and glycine in lobe 1. This aspartate also contacts the side chain of a lysine residue in the hydrophobic core of lobe 2 by a salt bridge. We investigated how the peptide flip and electrostatic contact (D655-K660) in GluA3 contribute to receptor function by examining pharmacological and structural properties with an antagonist (CNQX), a partial agonist (kainate), and two full agonists (glutamate and quisqualate) in the wildtype and two mutant receptors. Alanine substitution decreased the agonist potency of GluA3(i)-D655A and GluA3(i)-K660A receptor channels expressed in HEK293 cells and differentially affected agonist binding affinity for isolated LBDs without changing CNQX affinity. Correlations observed in the crystal structures of the mutant LBDs included the loss of the D655-K660 electrostatic contact, agonist-dependent differences in lobe 1 and lobe 2 closure, and unflipped D(A)655-S656 bonds. Glutamate-stimulated activation was slower for both mutants, suggesting that efficient energy transfer of agonist binding within the LBD of AMPA receptors requires an intact tether between the flexible peptide flip domain and the rigid hydrophobic core of lobe 2.     

The TP53INP2 Protein Is Required for Autophagy in Mammalian Cells

Using a bioinformatic approach, we identified a TP53INP1-related gene encoding a protein with 30% identity with tumor protein 53-induced nuclear protein 1 (TP53INP1), which was named TP53INP2. TP53INP1 and TP53INP2 sequences were found in several species ranging from Homo sapiens to Drosophila melanogaster, but orthologues were found neither in earlier eukaryotes nor in prokaryotes. To gain insight into the function of the TP53INP2 protein, we carried out a yeast two-hybrid screening that showed that TP53INP2 binds to the LC3-related proteins GABARAP and GABARAP-like2, and then we demonstrated by coimmunoprecipitation that TP53INP2 interacts with these proteins, as well as with LC3 and with the autophagosome transmembrane protein VMP1. TP53INP2 translocates from the nucleus to the autophagosome structures after activation of autophagy by rapamycin or starvation. Also, we showed that TP53INP2 expression is necessary for autophagosome development because its small interfering RNA-mediated knockdown strongly decreases sensitivity of mammalian cells to autophagy. Finally, we found that interactions between TP53INP2 and LC3 or the LC3-related proteins GABARAP and GABARAP-like2 require autophagy and are modulated by wortmannin as judged by bioluminescence resonance energy transfer assays. We suggest that TP53INP2 is a scaffold protein that recruits LC3 and/or LC3-related proteins to the autophagosome membrane by interacting with the transmembrane protein VMP1. It is concluded that TP53INP2 is a novel gene involved in the autophagy of mammalian cells.     

Measurements of left ventricular myocardial longitudinal systolic displacement using spectral and colour tissue Doppler: time for a reassessment?

Background

Echocardiographic measurements of left ventricular (LV) myocardial displacement may produce different results depending on the choice of employed modality and subjective adjustments during data acquisition and analysis.

Methods

In this study, left ventricular longitudinal systolic displacement was quantified in 57 patients (31 women and 26 men, 50 ± 16 years) using colour (colour TD) and spectral tissue Doppler (spectral TD) before and after temporal filtering (30 to 70 milliseconds in 20-millisecond steps) and changed offline gain saturation (0%, 50% and 100%), respectively. The results were compared with those obtained with anatomic M-mode.

Results

Whereas only minor differences occurred between the results of colour TD and anatomic M-mode measurements, spectral TD significantly overestimated the results obtained with both these methods. However, the limits of agreement between the results produced by all three studied methods were not clinically acceptable in any of the cases. The spectral TD displacement values increased along with increasing offline gain saturation whereas the effect of temporal filtering on colour Doppler measurements was insignificant.

Conclusion

Measurements of LV myocardial longitudinal displacement employing spectral TD, colour TD or anatomic M-mode produce different results, thus discouraging interchangeable use of these modalities. Whereas the results of spectral TD measurements can be significantly altered by changing offline gain setting, the effect of temporal filtering on colour TD measurements is insignificant, a fact that increases clinical practicality of the latter method.     

Exposure to Thiodan results in lipofuscin accumulation in hepatocytes of the freshwater catfish Tandanus tandanus

We investigated the effect of time after pulse exposure to 1.0 microg l(-1) endosulfan (applied as Thiodan) on endosulfan residues in the liver and ultrastructural changes in the hepatocytes of the freshwater catfish Tandanus tandanus. Time after exposure did not affect the mean residue level in the liver. After exposure to endosulfan, residues in the liver were 227.47 microg kg(-1) after 1 d and 282.83 microg kg(-1) after 28 d; residues in the bile were 313.97 microg kg(-1) after 1 d and 334.53 microg kg(-1) after 28 d. At the end of 28 d exposure, lipofuscin was present in up to 69% of hepatocytes of fish containing residues of endosulfan, but absent from control fish. There was a statistically significant increase in the percentage of pyknotic nuclei and altered rough endoplasmic reticulum 28 d after exposure. The mean percentage of cells with altered endoplasmic reticulum ranged from 12.93% (Day 1) to 7.50% (Day 28) for control fish, while for exposed fish it increased from 14.30% (Day 1) to 35.00% (Day 28). The mean percentage of cells with pyknotic nuclei increased from 1.1 to 2.1% in control fish and from 3.8 to 9.6% in exposed fish. Other ultrastructural changes included increased ultrastructural heterogeneity, progressive vacuolation and fractionation of rough endoplasmic reticulum, accumulation of lysosomes and residual bodies, intranuclear inclusions and pseudoinclusions, membrane whorls and myelinated bodies. Protracted senescence was one of the main features of endosulfan toxicity to T. tandanus hepatocytes.     

Competitive exclusion and coexistence of universal grammars

Universal grammar (UG) is a list of innate constraints that specify the set of grammars that can be learned by the child during primary language acquisition. UG of the human brain has been shaped by evolution. Evolution requires variation. Hence, we have to postulate and study variation of UG. We investigate evolutionary dynamics and language acquisition in the context of multiple UGs. We provide examples for competitive exclusion and stable coexistence of different UGs. More specific UGs admit fewer candidate grammars, and less specific UGs admit more candidate grammars. We will analyze conditions for more specific UGs to outcompete less specific UGs and vice versa. An interesting finding is that less specific UGs can resist invasion by more specific UGs if learning is more accurate. In other words, accurate learning stabilizes UGs that admit large numbers of candidate grammars.