Hsmar1 Transposition Is Sensitive to the Topology of the Transposon Donor and the Target

Hsmar1 is a member of the Tc1-mariner superfamily of DNA transposons. These elements mobilize within the genome of their host by a cut-and-paste mechanism. We have exploited the in vitro reaction provided by Hsmar1 to investigate the effect of DNA supercoiling on transposon integration. We found that the topology of both the transposon and the target affect integration. Relaxed transposons have an integration defect that can be partially restored in the presence of elevated levels of negatively supercoiled target DNA. Negatively supercoiled DNA is a better target than nicked or positively supercoiled DNA, suggesting that underwinding of the DNA helix promotes target interactions. Like other Tc1-mariner elements, Hsmar1 integrates into 5′-TA dinucleotides. The direct vicinity of the target TA provides little sequence specificity for target interactions. However, transposition within a plasmid substrate was not random and some TA dinucleotides were targeted preferentially. The distribution of intramolecular target sites was not affected by DNA topology.     

Working Memory in the Processing of the Iowa Gambling Task: An Individual Differences Approach

The Iowa Gambling Task (IGT) is a sequential learning task in which participants develop a tendency towards advantageous options arising from the outcomes associated with their previous decisions. The role of working memory in this complex task has been largely debated in the literature. On one hand, low working memory resources lead to a decrease in the number of advantageous decisions and make a significant part of participants unable to report explicitly which options are the most profitable. On the other hand, several studies have shown no contribution of working memory to the IGT decision patterns. In order to investigate this apparent incompatibility of results, we used an individual differences approach, which has proven an effective method to investigate the role of working memory in cognition. We compared the IGT decision patterns of participants as a function of their working memory capacity (WMC). As expected, contrary to low WMC participants, high WMC participants developed a tendency towards advantageous decisions. These findings lead us to discuss the role of WMC in decision making tasks.     

A Scalable Computational Framework for Establishing Long-Term Behavior of Stochastic Reaction Networks

Reaction networks are systems in which the populations of a finite number of species evolve through predefined interactions. Such networks are found as modeling tools in many biological disciplines such as biochemistry, ecology, epidemiology, immunology, systems biology and synthetic biology. It is now well-established that, for small population sizes, stochastic models for biochemical reaction networks are necessary to capture randomness in the interactions. The tools for analyzing such models, however, still lag far behind their deterministic counterparts. In this paper, we bridge this gap by developing a constructive framework for examining the long-term behavior and stability properties of the reaction dynamics in a stochastic setting. In particular, we address the problems of determining ergodicity of the reaction dynamics, which is analogous to having a globally attracting fixed point for deterministic dynamics. We also examine when the statistical moments of the underlying process remain bounded with time and when they converge to their steady state values. The framework we develop relies on a blend of ideas from probability theory, linear algebra and optimization theory. We demonstrate that the stability properties of a wide class of biological networks can be assessed from our sufficient theoretical conditions that can be recast as efficient and scalable linear programs, well-known for their tractability. It is notably shown that the computational complexity is often linear in the number of species. We illustrate the validity, the efficiency and the wide applicability of our results on several reaction networks arising in biochemistry, systems biology, epidemiology and ecology. The biological implications of the results as well as an example of a non-ergodic biological network are also discussed.     

Mid-Cretaceous Burmese amber pelecinid wasps (Hymenoptera,Pelecinidae) support the hypothesis of an Asian origin of the family

A new species of pelecinid wasp, Eopelecinus marechali sp. nov., is described and figured from mid-Cretaceous Burmese amber based on a single well-preserved female specimen. Contrary to Eopelecinus inopinatus Jouault et al., 2020a, unique other Eopelecinus known from this deposit, the new species is based on a complete female specimen. This discovery confirms that the Pelecinidae were highly diverse during the Cretaceous and highlights the underestimated diversity of the genus Eopelecinus in Burmese amber biota. Eopelecinus marechali sp. nov. differs from all other Eopelecinus species by its unique metasomal ratio. A summary on the fossil pelecinid species with distributions and ages is provided. Based on the particular geological history of the West Burmese Terrane and the fossil record of the family, the hypothesis of an Asian origin of the family is discussed. The records of Eopelecinus in both Laurasia and Burmese amber biota, during the mid-Cretaceous, suggest that possible transfers of fauna have taken place between these two geological blocks.     

Virtual screening on an α‐helix to β‐strand switchable region of the FGFR2 extracellular domain revealed positive and negative modulators

The secondary structure of some protein segments may vary between α‐helix and β‐strand. To predict these switchable segments, we have developed an algorithm, Switch‐P, based solely on the protein sequence. This algorithm was used on the extracellular parts of FGF receptors. For FGFR2, it predicted that β4 and β5 strands of the third Ig‐like domain were highly switchable. These two strands possess a high number of somatic mutations associated with cancer. Analysis of PDB structures of FGF receptors confirmed the switchability prediction for β5. We thus evaluated if compound‐driven α‐helix/β‐strand switching of β5 could modulate FGFR2 signaling. We performed the virtual screening of a library containing 1.4 million of chemical compounds with two models of the third Ig‐like domain of FGFR2 showing different secondary structures for β5, and we selected 32 compounds. Experimental testing using proliferation assays with FGF7‐stimulated SNU‐16 cells and a FGFR2‐dependent Erk1/2 phosphorylation assay with FGFR2‐transfected L6 cells, revealed activators and inhibitors of FGFR2. Our method for the identification of switchable proteinic regions, associated with our virtual screening approach, provides an opportunity to discover new generation of drugs with under‐explored mechanism of action. Proteins 2014; 82:2982–2997. © 2014 Wiley Periodicals, Inc.     

Functional diversification in the Nudix hydrolase gene family drives sesquiterpene biosynthesis in Rosa × wichurana

Roses use a non‐canonical pathway involving a Nudix hydrolase, RhNUDX1, to synthesize their monoterpenes, especially geraniol. Here we report the characterization of another expressed NUDX1 gene from the rose cultivar Rosa x wichurana, RwNUDX1‐2. In order to study the function of the RwNUDX1‐2 protein, we analyzed the volatile profiles of an F₁ progeny generated by crossing R. chinensis cv. ‘Old Blush’ with R. x wichurana. A correlation test of the volatilomes with gene expression data revealed that RwNUDX1‐2 is involved in the biosynthesis of a group of sesquiterpenoids, especially E,E‐farnesol, in addition to other sesquiterpenes. In vitro enzyme assays and heterologous in planta functional characterization of the RwNUDX1‐2 gene corroborated this result. A quantitative trait locus (QTL) analysis was performed using the data of E,E‐farnesol contents in the progeny and a genetic map was constructed based on gene markers. The RwNUDX1‐2 gene co‐localized with the QTL for E,E‐farnesol content, thereby confirming its function in sesquiterpenoid biosynthesis in R. x wichurana. Finally, in order to understand the structural bases for the substrate specificity of rose NUDX proteins, the RhNUDX1 protein was crystallized, and its structure was refined to 1.7 Å. By molecular modeling of different rose NUDX1 protein complexes with their respective substrates, a structural basis for substrate discrimination by rose NUDX1 proteins is proposed.     

Impairment of GABAB receptor dimer by endogenous 14-3-3ζ in chronic pain conditions

In the central nervous system, the inhibitory GABAB receptor is the archetype of heterodimeric G protein-coupled receptors (GPCRs). However, the regulation of GABAB dimerization, and more generally of GPCR oligomerization, remains largely unknown. We propose a novel mechanism for inhibition of GPCR activity through de-dimerization in pathological conditions. We show here that 14-3-3ζ, a GABAB1-binding protein, dissociates the GABAB heterodimer, resulting in the impairment of GABAB signalling in spinal neurons. In the dorsal spinal cord of neuropathic rats, 14-3-3ζ is overexpressed and weakens GABAB inhibition. Using anti-14-3-3ζ siRNA or competing peptides disrupts 14-3-3ζ/GABAB1 interaction and restores functional GABAB heterodimers in the dorsal horn. Importantly, both strategies greatly enhance the anti-nociceptive effect of intrathecal Baclofen in neuropathic rats. Taken together, our data provide the first example of endogenous regulation of a GPCR oligomeric state and demonstrate its functional impact on the pathophysiological process of neuropathic pain sensitization.     

Genetic deficiency of glycogen synthase kinase-3beta corrects diabetes in mouse models of insulin resistance

Despite treatment with agents that enhance beta-cell function and insulin action, reduction in beta-cell mass is relentless in patients with insulin resistance and type 2 diabetes mellitus. Insulin resistance is characterized by impaired signaling through the insulin/insulin receptor/insulin receptor substrate/PI-3K/Akt pathway, leading to elevation of negatively regulated substrates such as glycogen synthase kinase-3beta (Gsk-3beta). When elevated, this enzyme has antiproliferative and proapoptotic properties. In these studies, we designed experiments to determine the contribution of Gsk-3beta to regulation of beta-cell mass in two mouse models of insulin resistance. Mice lacking one allele of the insulin receptor (Ir+/-) exhibit insulin resistance and a doubling of beta-cell mass. Crossing these mice with those having haploinsufficiency for Gsk-3beta (Gsk-3beta+/-) reduced insulin resistance by augmenting whole-body glucose disposal, and significantly reduced beta-cell mass. In the second model, mice missing two alleles of the insulin receptor substrate 2 (Irs2-/-), like the Ir+/- mice, are insulin resistant, but develop profound beta-cell loss, resulting in early diabetes. We found that islets from these mice had a 4-fold elevation of Gsk-3beta activity associated with a marked reduction of beta-cell proliferation and increased apoptosis. Irs2-/- mice crossed with Gsk-3beta+/- mice preserved beta-cell mass by reversing the negative effects on proliferation and apoptosis, preventing onset of diabetes. Previous studies had shown that islets of Irs2-/- mice had increased cyclin-dependent kinase inhibitor p27(kip1) that was limiting for beta-cell replication, and reduced Pdx1 levels associated with increased cell death. Preservation of beta-cell mass in Gsk-3beta+/- Irs2-/- mice was accompanied by suppressed p27(kip1) levels and increased Pdx1 levels. To separate peripheral versus beta-cell-specific effects of reduction of Gsk3beta activity on preservation of beta-cell mass, mice homozygous for a floxed Gsk-3beta allele (Gsk-3(F/F)) were then crossed with rat insulin promoter-Cre (RIP-Cre) mice to produce beta-cell-specific knockout of Gsk-3beta (betaGsk-3beta-/-). Like Gsk-3beta+/- mice, betaGsk-3beta-/- mice also prevented the diabetes of the Irs2-/- mice. The results of these studies now define a new, negatively regulated substrate of the insulin signaling pathway specifically within beta-cells that when elevated, can impair replication and increase apoptosis, resulting in loss of beta-cells and diabetes. These results thus form the rationale for developing agents to inhibit this enzyme in obese insulin-resistant individuals to preserve beta-cells and prevent diabetes onset.