Stability and variability of synapses in the adult molluskan CNS

Synaptic transmission was examined between identified neurons in the central nervous system (CNS) of the freshwater mollusk, Lymnaea stagnalis. Four identified neurons were used: Right Pedal Dorsal one (RPeD1; a dopaminergic respiratory interneuron), Visceral Dorsal two and three (VD2/3), and Visceral Dorsal four (VD4; a cardiorespiratory interneuron). Neuron RPeD1 synapses onto both VD2/3 and VD4, while VD4 makes a reciprocal synapse onto RPeD1. When compared from animal to animal, the connections were variable in sign. Previously, we demonstrated that, in a given animal, the RPeD1 --> VD4 synapse could be either inhibitory, biphasic, or undetectable. The present study now expands this concept of variability by showing that the RPeD1 --> VD2/3 synapse was either excitatory or undetectable from animal to animal, while the synapse from VD4 to RPeD1 was observed as inhibitory, biphasic, depolarizing, excitatory, or undetectable. Next, we used 1-day organ culture to determine if the variability observed between animals is a product of ongoing change to the sign of these identified synapses and whether or not the extent of change could be influenced by the culture conditions. Changes to the sign of transmission occurred within minutes and, more commonly, after 24-h organ culture. All three synapses were investigated before and after 1-day organ culture, in either defined medium (DM) or brain-conditioned medium (CM). Regardless of culture conditions, the RPeD1 --> VD2/3 synapse showed no change of sign, i.e., it was relatively stable. However, the synapses between RPeD1 and VD4 did change sign, and when cultured in CM, the VD4 --> RPeD1 synapse changed significantly more than in DM. These data indicate that variability of some synapses reflects changes at these synapses. This is the first report that specific synapses in an adult CNS can change sign, and that the sign of transmission can be modulated by environmental conditions.     

Structure and Function of Human Xylulokinase,an Enzyme with Important Roles in Carbohydrate Metabolism

d-Xylulokinase (XK; EC 2.7.1.17) catalyzes the ATP-dependent phosphorylation of d-xylulose (Xu) to produce xylulose 5-phosphate (Xu5P). In mammals, XK is the last enzyme in the glucuronate-xylulose pathway, active in the liver and kidneys, and is linked through its product Xu5P to the pentose-phosphate pathway. XK may play an important role in metabolic disease, given that Xu5P is a key regulator of glucose metabolism and lipogenesis. We have expressed the product of a putative human XK gene and identified it as the authentic human d-xylulokinase (hXK). NMR studies with a variety of sugars showed that hXK acts only on d-xylulose, and a coupled photometric assay established its key kinetic parameters as K_m(Xu) = 24 ± 3 μm and k_cat = 35 ± 5 s⁻¹. Crystal structures were determined for hXK, on its own and in complexes with Xu, ADP, and a fluorinated inhibitor. These reveal that hXK has a two-domain fold characteristic of the sugar kinase/hsp70/actin superfamily, with glycerol kinase as its closest relative. Xu binds to domain-I and ADP to domain-II, but in this open form of hXK they are 10 Å apart, implying that a large scale conformational change is required for catalysis. Xu binds in its linear keto-form, sandwiched between a Trp side chain and polar side chains that provide exquisite hydrogen bonding recognition. The hXK structure provides a basis for the design of specific inhibitors with which to probe its roles in sugar metabolism and metabolic disease.     

Mobster: accurate detection of mobile element insertions in next generation sequencing data

Mobile elements are major drivers in changing genomic architecture and can cause disease. The detection of mobile elements is hindered due to the low mappability of their highly repetitive sequences. We have developed an algorithm, called Mobster, to detect non-reference mobile element insertions in next generation sequencing data from both whole genome and whole exome studies. Mobster uses discordant read pairs and clipped reads in combination with consensus sequences of known active mobile elements. Mobster has a low false discovery rate and high recall rate for both L1 and Alu elements. Mobster is available at http://sourceforge.net/projects/mobster.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0488-x) contains supplementary material, which is available to authorized users.     

Identifying protein domains by global analysis of soluble fragment data

The production and analysis of individual structural domains is a common strategy for studying large or complex proteins, which may be experimentally intractable in their full-length form. However, identifying domain boundaries is challenging if there is little structural information concerning the protein target. One experimental procedure for mapping domains is to screen a library of random protein fragments for solubility, since truncation of a domain will typically expose hydrophobic groups, leading to poor fragment solubility. We have coupled fragment solubility screening with global data analysis to develop an effective method for identifying structural domains within a protein. A gene fragment library is generated using mechanical shearing, or by uracil doping of the gene and a uracil-specific enzymatic digest. A split green fluorescent protein (GFP) assay is used to screen the corresponding protein fragments for solubility when expressed in Escherichia coli. The soluble fragment data are then analyzed using two complementary approaches. Fragmentation “hotspots” indicate possible interdomain regions. Clustering algorithms are used to group related fragments, and concomitantly predict domain location. The effectiveness of this Domain Seeking procedure is demonstrated by application to the well-characterized human protein p85α.     

Ambivalent moralities of cooperation and corruption: Local explanations for (under)development on a Philippine island

Concepts of development are inevitably loaded with value judgements concerning what constitutes ‘proper’ social and economic organisation. Focusing on the cultural politics of development on Siquijor, an island in the Central Visayas region of the Philippines, this paper explores these often tacit ideals. It considers one of the key idioms Siquijodnon use in explaining how development is brought about—cooperation—and some of its locally perceived opposites—‘crab mentality’, politicking and corruption—which contain powerful moral critiques of self and society. On Siquijor, local discourses of development have it that widespread poverty in the Philippines demonstrates a failing of Filipinos to live up to supposedly universal norms of ethical socio‐economic conduct. However, I argue that attention to local norms of moral economy reveal the ambivalence underlying these notions of development, particularly in relation to the roles of individualism and reciprocity in socio‐economic organisation.     

Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

Linking variation in quantitative traits to variation in the genome is an important, but challenging task in the study of life-history evolution. Linkage maps provide a valuable tool for the unravelling of such trait−gene associations. Moreover, they give insight into recombination landscapes and between-species karyotype evolution. Here we used genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, of over 2000 individuals to produce high-density linkage maps of the great tit (Parus major), a passerine bird that serves as a model species for ecological and evolutionary questions. We created independent maps from two distinct populations: a captive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom (UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and 1917 cM for the NL and UK populations, respectively, and were similar in size and marker order. Subtle levels of heterochiasmy within and between chromosomes were remarkably consistent between the populations, suggesting that the local departures from sex-equal recombination rates have evolved. This key and surprising result would have been impossible to detect if only one population was mapped. A comparison with zebra finch Taeniopygia guttata, chicken Gallus gallus and the green anole lizard Anolis carolinensis genomes provided further insight into the evolution of avian karyotypes.     

Concerning Constructions of Self and Other: Auto-racism and Imagining Amerika in the Christian Philippines

The term ‘colonial mentality’ is popularly used among many Filipinos to refer to a tendency to compare themselves negatively to Amerikanos. This paper explores the everyday form such deprecating self/other constructions take on the island of Siquijor in the Central Visayas region of the archipelago. It sheds light on how these constructions are socially situated, deployed and reproduced, their limits and their effects. It shows that comparisons between categories of Filipino and Amerikano must be understood in relation to local hierarchies. On Siquijor, local imaginings of Amerikano lifestyles and bodies not only serve as reference points for ideals of affluence and beauty, but act as markers of prestige in competitions for status between neighbours and kin, sustaining a sense of Amerikano superordinancy. While, on Siquijor, superordinancy presumes neither innate nor moral superiority (and, indeed, there exists ambivalence towards the relative moral status of Amerikanos and Filipinos), there is a strong presumption specifically that the ‘failure’ of the Philippines to achieve similar levels of affluence to the US is due to moral deficiencies of the Filipino self. Thus, outward-looking desire is contained by inward-looking discontent, the latter keeping the former from spilling over into demands for change to a global status quo.     

Neuronal plasticity in the adult invertebrate nervous system

This essay provides a brief overview of neuronal plasticity in adult invertebrate nervous systems. Our discussion focuses on the factors which influence sprouting by adult neurons, i.e., (1) the nature of the neuron itself, (2) axon integrity, (3) the presence of targets, (4) diffusible factors, and (5) ageing. Evidence that the neurites of some adult neurons exhibit a dynamic equilibrium of expansion and retraction is presented, a topic which prompted us to speculate on the significance of such plasticity in altered behavioral states. We conclude with some suggestions as to specific questions that need to be addressed by future studies in this challenging area.