KaKs＿Calculator 3.0: Calculating Selective Pressure on Coding and Non-coding Sequences

KaKs＿Calculator 3.0 is an updated toolkit that is capable of calculating selective pressure on both coding and non-coding sequences. Similar to the nonsynonymous/synonymous substitution rate ratio for coding sequences, selection on non-coding sequences can be quantified as the ratio of non-coding nucleotide substitution rate to synonymous substitution rate of adjacent coding sequences. As testified on empirical data, KaKs＿Calculator 3.0 shows effectiveness to detect the strength and mode of sele...     

以thyA基因为选择压力非抗性质粒载体的构建

以干酷乳杆菌L.casei34103染色体DNA为模板,利用PCR技术扩增胸苷酸合成酶（Thymidylatesynthase,thyA)基因,回收纯化,选择以红霉素抗性为选择压力的可以在大肠杆菌和乳酸菌中穿梭表达的质粒pW425e为基本质粒,以thyA基因取代红霉素基因,获得重组载体并鉴定,此重组载体可以对thyA基因缺陷的大肠杆菌E.coli X51和嗜酸乳杆菌DOMLaS 107进行功能弥补,进而构建了以thyA基因为地选择压力的非抗生素抗性穿梭表达载体,其大小为3716bp,并命名为pW425t。     

Selective consumption of acorns by the Japanese wood mouse according to tannin content: a behavioral countermeasure against plant secondary metabolites

We examined the presence of selective consumption against tannins in acorns as a pre-ingestive countermeasure to plant secondary metabolites by using the Japanese wood mouse (Apodemus speciosus) and acorns of Quercus serrata, which contained ca. 6.4% tannins on a dry weight basis. In addition, the presence of selective consumption against proteins was also examined. In the acorn-feeding experiment, 18 wood mice were allocated to two groups: the experienced group (N = 9), which had previous experience in feeding on acorns, and the inexperienced group (N = 9), which had no experience. Mice of both groups were fed only acorns for 3 nights. Selectivity against tannins (an index estimated from the tannin content in control, remaining, and ingested acorns) was significantly positive in the experienced group, indicating the presence of selective consumption against tannins. In contrast, mice in the inexperienced group did not show significant selectivity against tannins. Comparing the selectivity indices directly between two groups, however, they did not differ significantly. Selective consumption against proteins rather than that for proteins also occurred in the experienced group, but it was thought to be a byproduct resulted from the selectivity against tannins. Selective consumption against tannins can mitigate the negative effects of tannins by decreasing tannin intake.     

Mean-field analysis of selective persistent activity in presence of short-term synaptic depression

Mean-Field theory is extended to recurrent networks of spiking neurons endowed with short-term depression (STD) of synaptic transmission. The extension involves the use of the distribution of interspike intervals of an integrate-and-fire neuron receiving a Gaussian current, with a given mean and variance, in input. This, in turn, is used to obtain an accurate estimate of the resulting postsynaptic current in presence of STD. The stationary states of the network are obtained requiring self-consistency for the currents—those driving the emission processes and those generated by the emitted spikes. The model network stores in the distribution of two-state efficacies of excitatory-to-excitatory synapses, a randomly composed set of external stimuli. The resulting synaptic structure allows the network to exhibit selective persistent activity for each stimulus in the set. Theory predicts the onset of selective persistent, or working memory (WM) activity upon varying the constitutive parameters (e.g. potentiated/depressed long-term efficacy ratio, parameters associated with STD), and provides the average emission rates in the various steady states. Theoretical estimates are in remarkably good agreement with data “recorded” in computer simulations of the microscopic model. Action Editor: Karen Sigvardt     

Spatial single cell metabolomics: Current challenges and future developments

Single cell metabolomics is a rapidly advancing field of bio-analytical chemistry which aims to observe cellular biology with the greatest detail possible. Mass spectrometry imaging and selective cell sampling (e.g. using nanocapillaries) are two common approaches within the field. Recent achievements such as observation of cell–cell interactions, lipids determining cell states and rapid phenotypic identification demonstrate the efficacy of these approaches and the momentum of the field. However, single cell metabolomics can only continue with the same impetus if the universal challenges to the field are met, such as the lack of strategies for standardisation and quantification, and lack of specificity/sensitivity. Mass spectrometry imaging and selective cell sampling come with unique advantages and challenges which, in many cases are complementary to each other. We propose here that the challenges specific to each approach could be ameliorated with collaboration between the two communities driving these approaches.     

Oxalate utilisation is widespread in the actinobacterial genus Kribbella

The type strains of all 33 species in the genus Kribbella were tested for growth on oxalate (^?OOC-COO^?) as sole carbon source. Media were initially formulated to contain sodium oxalate, but even a concentration as low as 7.5 mM oxalate prevented growth. A modified medium based on calcium oxalate was very successful in characterising oxalate utilisation by Kribbella strains (metabolism of oxalate by oxalotrophic bacteria results in visible zones of clearing around the growth streaks on the opaque plates). To assess the variability of oxalate utilisation in Kribbella species, we also tested eight non-type strains for their ability to use oxalate. Thirty of 33 type strains (90.9%) and six of eight non-type strains (75%) were able to use oxalate as a sole carbon source. Based on these results, we propose that oxalate would be an excellent carbon source for the selective isolation of Kribbella strains. Based on the oxalate-utilisation phenotype and analyses of the 19 publicly available Kribbella type-strain genome sequences, we propose a pathway for oxalate metabolism in Kribbella. This pathway is significantly different from those previously proposed for oxalate metabolism in other bacteria, involving the indirect catabolism of oxalate to formate. Formate production is proposed to be involved in energy generation and to be crucial for oxalate import via an oxalate:formate antiporter. To our knowledge, this is the first report of an oxalate:formate antiporter in an aerobic, Gram-positive bacterium.     

TNIP1 inhibits selective autophagy via bipartite interaction with LC3/GABARAP and TAX1BP1

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Novel selective inhibitors of aminopeptidases that generate antigenic peptides

Endoplasmic reticulum aminopeptidases, ERAP1 and ERAP2, as well as Insulin regulated aminopeptidase (IRAP) play key roles in antigen processing, and have recently emerged as biologically important targets for manipulation of antigen presentation. Taking advantage of the available structural and substrate-selectivity data for these enzymes, we have rationally designed a new series of inhibitors that display low micromolar activity. The selectivity profile for these three highly homologous aminopeptidases provides a promising avenue for modulating intracellular antigen processing.     

Activity of Ca2+/Calmodulin-Dependent Protein Kinase II Following Ischemia: A Comparison Between CA1 and Dentate Gyrus in a Hippocampal Slice Model

Abstract: Both CA1 and dentate gyrus regions of the hippocampal slice exhibit an irreversible loss of synaptic transmission after exposure to in vitro ischemic conditions (buffer without oxygen and glucose). However, after shorter durations of ischemia (8–10 min) the CA1 region shows an irreversible loss of synaptic responses, whereas the dentate gyrus region completely recovers synaptic responses upon reoxygenation. To determine biochemical mechanisms underlying this differential susceptibility, we have examined changes in Ca²⁺/calmodulin-dependent protein kinase II (CaM-KII) and cyclic AMP-dependent protein kinase activities in homogenates from CA1 and dentate gyrus regions of the hippocampal slice after increasing durations of in vitro ischemia. Time-dependent changes in CaM-KII activities were correlated with changes in electrophysiological responses. CA1 homogenates from slices exposed to 1 min of ischemia showed significant increases in CaM-KII activity, whereas there was no significant change in kinase activity in dentate homogenates after 1 min of ischemia. However, after longer durations of ischemia (5, 10, and 20 min) we found a time-dependent reduction in CaM-KII activity in both CA1 and dentate gyrus regions, whereas no change was detected in cyclic AMP-dependent protein kinase activity. Irreversible depression of CaM-KII activity was seen at shorter durations of ischemia (10 min) in the CA1 region than in dentate region (20 min), which correlated with irreversible effects on synaptic responses. Immunoblot analysis showed that the decrease in CaM-KII activity was not due to degradation of CaM-KII protein. However, the microtubule-associated protein MAP2, known to be a substrate for the Ca²⁺-dependent proteases (calpains), showed extensive proteolysis evident after 90 min of reoxygenation after ischemia.