Battle of the sexes over paternity

Reproductive behaviors have evolved through severe inter-sexual competition. We have recently described a behavior in post-mated female Drosophila melanogaster that controls ejaculate retention and sperm storage, and is a possible mechanism by which females who have mated with several partners can choose which sperm that is stored and used for fertilization. This behavior can also regulate exposure of the female to harmful effects of male SFP that are present in the ejaculate. Our study identified the neural pathway functioning in the female brain that regulates this behavior. [BMB Reports 2015; 48(5): 241-242]     

Architecture of a serine recombinase-DNA regulatory complex

An essential feature of many site-specific recombination systems is their ability to regulate the direction and topology of recombination. Resolvases from the serine recombinase family assemble an interwound synaptic complex that harnesses negative supercoiling to drive the forward reaction and promote recombination between properly oriented sites. To better understand the interplay of catalytic and regulatory functions within these synaptic complexes, we have solved the structure of the regulatory site synapse in the Sin resolvase system. It reveals an unexpected synaptic interface between helix-turn-helix DNA-binding domains that is also highlighted in a screen for synapsis mutants. The tetramer defined by this interface provides the foundation for a robust model of the synaptic complex, assembled entirely from available crystal structures, that gives insight into how the catalytic activity of Sin and other serine recombinases may be regulated.     

巨噬细胞的分类及其调节性功能的差异

巨噬细胞在固有免疫和适应性免疫反应中具有重要的作用,它可将加工后的抗原提呈给相应的T细胞,活化后的T细胞通过细胞膜上的分子或分泌的细胞介素进一步活化巨噬细胞。此时的巨噬细胞吞噬杀伤能力大大加强,并释放各种活性物质,因此巨噬细胞是主要的炎性反应调节细胞。巨噬细胞可分为经典活化和选择性活化的巨噬细胞,其在炎性反应过程中分泌不同的细胞因子、趋化因子等,然后间接或直接地参与各种炎症性疾病的反应过程。该文介绍了不同型巨噬细胞在胰岛素抵抗、HIV感染和肿瘤等疾病中的调节功能。     

Mathematical classification of regulatory logics for compound environmental changes

This paper is concerned with biological regulatory mechanisms in response to the simultaneous occurrence of a huge number of environmental changes. The restricted resources of cells strictly limit the number of their regulatory methods; hence, cells must adopt, as compensation, special mechanisms to deal with the simultaneous occurrence of environmental changes. We hypothesize that cells use various control logics to integrate information about independent environmental changes related to a cell task and represent the resulting effects of the different ways of integration by logical functions. Using the notion of equivalence classes in set theory, we describe the mathematical classification of the effects into biologically unequivalent ones realized by different control logics. Our purely mathematical and systematic classification of logical functions reveals three elementary control logics with different biological relevance. To better understand their biological significance, we consider examples of biological systems that use these elementary control logics.     

A regulatory 'landscape effect' over the HoxD cluster

Faithful expression of Hox genes in both time and space is essential for proper patterning of the primary body axis. Transgenic approaches in vertebrates have suggested that this collinear activation process is regulated in a largely gene cluster-autonomous manner. In contrast, more recently co-opted expression specificities, required in other embryonic structures, depend upon long-range enhancer sequences acting from outside the gene clusters. This regulatory dichotomy was recently questioned, since gene activation along the trunk seems to be partially regulated by signals located outside of the cluster. We investigated these alternative regulatory strategies by engineering a large inversion that precisely separates the murine HoxD complex from its centromeric neighborhood. Mutant animals displayed posterior transformations along with subtle deregulations of Hoxd genes, indicating an impact of the centromeric landscape on the fine-tuning of Hoxd gene expression. Proximal limbs were also affected, suggesting that this ‘landscape effect’ is generic and impacts upon regulatory mechanisms of various qualities and evolutionary origins.     

A way of functional classification of regulatory peptides. Parameters of divergent and convergent evolution of regulatory peptides

A mathematical method has been presented for systematization of functions of regulatory peptides (RP) and evaluation of directions of evolutionary development of RP systems. For this purpose, traditional methods of vector algebra and multi-dimensional space were used. Effects of various peptide regulators on anxiety, depression, and memory are considered by the example of the three-dimensional space. A way of the functional classification of peptides has been proposed.     

Scalable optimal Bayesian classification of single-cell trajectories under regulatory model uncertainty

Background

Biological networks describes the mechanisms which govern cellular functions. Temporal networks show how these networks evolve over time. Studying the temporal progression of network topologies is of utmost importance since it uncovers how a network evolves and how it resists to external stimuli and internal variations. Two temporal networks have co-evolving subnetworks if the evolving topologies of these subnetworks remain similar to each other as the network topology evolves over a period of time. In this paper, we consider the problem of identifying co-evolving subnetworks given a pair of temporal networks, which aim to capture the evolution of molecules and their interactions over time. Although this problem shares some characteristics of the well-known network alignment problems, it differs from existing network alignment formulations as it seeks a mapping of the two network topologies that is invariant to temporal evolution of the given networks. This is a computationally challenging problem as it requires capturing not only similar topologies between two networks but also their similar evolution patterns.

Results

We present an efficient algorithm, Tempo, for solving identifying co-evolving subnetworks with two given temporal networks. We formally prove the correctness of our method. We experimentally demonstrate that Tempo scales efficiently with the size of network as well as the number of time points, and generates statistically significant alignments—even when evolution rates of given networks are high. Our results on a human aging dataset demonstrate that Tempo identifies novel genes contributing to the progression of Alzheimer’s, Huntington’s and Type II diabetes, while existing methods fail to do so.

Conclusions

Studying temporal networks in general and human aging specifically using Tempo enables us to identify age related genes from non age related genes successfully. More importantly, Tempo takes the network alignment problem one huge step forward by moving beyond the classical static network models.

     

Phosphoregulation of the WAVE regulatory complex and signal integration

The WAVE2 regulatory complex (WRC) induces actin polymerization by activating the actin nucleator Arp2/3. Polymerizing actin pushes against the cell membrane and induces dramatic edge protrusions. In order to properly control such changes in cell morphology and function, cells have evolved multiple methods to tightly regulate WRC and Arp2/3 activity in space and time. Of these mechanisms, phosphorylation plays a fundamental role in transmitting extracellular and intracellular signals to the WRC and the actin cytoskeleton. This review discusses the phosphorylation-based regulatory inputs into the WRC. Signaling pathways that respond to growth factors, chemokines, hormones, and extracellular matrix converge upon the WAVE and ABI components of the WRC. The Abl, Src, ERK, and PKA kinases promote complex activation through a WRC conformation change that permits interaction with the Arp2/3 complex and through WRC translocation to the cell edge. The neuron-specific CDK5 and constitutively active CK2 kinases inhibit WRC activation. These regulatory signals are integrated in space and time as they coalesce upon the WRC. The combination of WRC phosphorylation events and WRC activity is controlled by stimulus, cell type, and cell cycle-specific pathway activation and via pathway cross-inhibition and cross-activation.     

Assembly of the regulatory complex of the 26S proteasome

The 19S regulatory complex (RC) of 26S proteasomes is a 900–1000 kDa particle composed of 18 distinct subunits (S1–S15) ranging in molecular mass from 25 to 110 kDa. This particle confers ATP-dependence and polyubiquitin (polyUb) recognition to the 26S proteasome. The symmetry and homogenous structure of the proteasome contrasts sharply with the remarkable complexity of the RC. Despite the fact that the primary sequences of all the subunits are now known, insight has been gained into the function of only eight subunits. The six ATPases within the RC constitute a subfamily (S4-like ATPases) within the AAA superfamily and we have shown that they form specific pairs in vitro[1]. We have now determined that putative coiled-coils within the variable N-terminal regions of these proteins are likely to function as recognition elements that direct the proper placement of the ATPases within the RC. We have also begun mapping putative interactions between non-ATPase subunits and S4-like ATPases. These studies have allowed us to build a model for the specific arrangement of 9 subunits within the human regulatory complex. This model agrees with recent findings by Glickman et al. [2] who have reported that two subcomplexes, termed the base and the lid, form the RC of budding yeast 26S proteasomes.