Cxcl12 evolution--subfunctionalization of a ligand through altered interaction with the chemokine receptor

The active migration of primordial germ cells (PGCs) from their site of specification towards their target is a valuable model for investigating directed cell migration within the complex environment of the developing embryo. In several vertebrates, PGC migration is guided by Cxcl12, a member of the chemokine superfamily. Interestingly, two distinct Cxcl12 paralogs are expressed in zebrafish embryos and contribute to the chemotattractive landscape. Although this offers versatility in the use of chemokine signals, it also requires a mechanism through which migrating cells prioritize the relevant cues that they encounter. Here, we show that PGCs respond preferentially to one of the paralogs and define the molecular basis for this biased behavior. We find that a single amino acid exchange switches the relative affinity of the Cxcl12 ligands for one of the duplicated Cxcr4 receptors, thereby determining the functional specialization of each chemokine that elicits a distinct function in a distinct process. This scenario represents an example of protein subfunctionalization--the specialization of two gene copies to perform complementary functions following gene duplication--which in this case is based on receptor-ligand interaction. Such specialization increases the complexity and flexibility of chemokine signaling in controlling concurrent developmental processes.     

Prediction of recurrence using exfoliative cytology and melanoma‐associated antigen‐A mRNA analysis following wide excision of oral squamous cell carcinoma: short report

N. Mollaoglu, P. Metzler, J. Zenk, E. Nkenke, F. W. Neukam and J. Ries
Prediction of recurrence using exfoliative cytology and melanoma‐associated antigen‐A mRNA analysis following wide excision of oral squamous cell carcinoma: short report Background: Oral squamous cell carcinoma (OSCC) is the sixth most common cancer. The local recurrence of OSSC might result from the existence of occult cancer cells around tumour margins. Exfoliative cytology has lately gained great importance as a method for obtaining RNA samples from suspicious oral mucosal lesions in order to carry out molecular diagnosis. In addition, melanoma associated‐A antigens (MAGE‐A) are expressed in various tumours and their detection is a highly accurate sign that cancer cells are present. Objective: The prediction of a recurrence using MAGE‐A mRNA expression analysis to follow‐up OSCC cases using a newly established molecular diagnostic technique applied to cytological materials. Methods: RNA was extracted from three recurrent OSCC cases and from 20 healthy volunteers as a control group using a cytobrush. The expression of MAGE‐A3, A4, A6, A10 and A12 was investigated in these specimens using quantitative real‐time (RT‐PCR). Results: There was no expression of MAGE‐A in the specimens of normal oral mucosa. However, the expression analysis of five different MAGE‐A genes indicated a high potential for malignant change in biopsy‐proven recurrent OSCC cases. Except for MAGE‐A10, the rest of the genes were expressed in different ratios by the three recurrent cases, which had been determined on histopathology to be OSCC or carcinoma in situ. Conclusion: It is suggested that analysis of MAGE‐A expression may be used as a risk prediction method in the diagnosis of recurrence after wide excision of OSCC to enhance the accuracy of exfoliative cytology, which has limitations due to false negative and false positive results.     

Uncovering the Mechanisms of Shrimp Innate Immune Response by RNA Interference

Because of the importance of shrimp in world aquaculture, there is much interest in understanding their immune system in order to improve their resistance to pathogenic microorganisms. An effective tool in studying genes involved in the immune response in shrimp is RNA interference (RNAi). RNAi, first recognized as an antiviral response against RNA viruses, is a cellular mechanism that is triggered by double-stranded RNAs and results in the degradation of homologous genes. In this review, we describe the current studies of genes in shrimp that employed RNAi technology to elucidate or confirm their functions. We also review the potential of RNAi to elicit antiviral response in shrimp.     

Do edge responses cascade up or down a multi‐trophic food web?

Despite nearly 100?years of edge studies, there has been little effort to document how edge responses 'cascade' to impact multi-trophic food webs. We examined changes within two, four-tiered food webs located on opposite sides of a habitat edge. Based on a 'bottom-up' resource-based model, we predicted plant resources would decline near edges, causing similar declines in specialist herbivores and their associated predators, while a generalist predator was predicted to increase due to complementary resource use. As predicted, we found declines in both specialist herbivores and predators near edges, but, contrary to expectations, this was not driven by gradients in plant resources. Instead, the increase in generalist predators near edges offers one alternative explanation for the observed declines. Furthermore, our results suggest how recent advances in food web theory could improve resource-based edge models, and vice versa.     

Role of cell-to-cell variability in activating a positive feedback antiviral response in human dendritic cells

In the first few hours following Newcastle disease viral infection of human monocyte-derived dendritic cells, the induction of IFNB1 is extremely low and the secreted type I interferon response is below the limits of ELISA assay. However, many interferon-induced genes are activated at this time, for example DDX58 (RIGI), which in response to viral RNA induces IFNB1. We investigated whether the early induction of IFNBI in only a small percentage of infected cells leads to low level IFN secretion that then induces IFN-responsive genes in all cells. We developed an agent-based mathematical model to explore the IFNBI and DDX58 temporal dynamics. Simulations showed that a small number of early responder cells provide a mechanism for efficient and controlled activation of the DDX58-IFNBI positive feedback loop. The model predicted distributions of single cell responses that were confirmed by single cell mRNA measurements. The results suggest that large cell-to-cell variation plays an important role in the early innate immune response, and that the variability is essential for the efficient activation of the IFNB1 based feedback loop.     

Foraging and pollination behaviour of Xylocopa calens Lepeletier (Hymenoptera: Apidae) on Phaseolus coccineus L. (Fabaceae) flowers at Yaounde (Cameroon)

To evaluate impact of carpenter bee, Xylocopa calens, on pod and seed set of Phaseolus coccineus, its foraging and pollinating activities were studied in Yaounde, for two seasons (May–July 2008 and April–June 2009). Observations were made on 40 inflorescences per treatment. The treatments included unlimited floral access by all visitors, bagged flowers to deny all visits, and limited visits by X. calens only. In addition, all flower visitors were recorded. The carpenter bee's seasonal rhythm of activity, its foraging behavior on flowers, its pollination efficiency, the fructification rate and the number of seeds per pod were recorded. Individuals from 16 species of insects were recorded visiting flowers of P. coccineus in the 2 years. Xylocopa calens was the most frequent, followed by Chalicodoma cincta cincta and Apis mellifera. Apart from bees, wasps were also recorded as likely predators. Xylocopa calens mainly foraged for nectar resources. The mean foraging speed was 9.62 flowers/min. Flowers visited by X. calens had higher fruiting rate compared with others, while those bagged had the lowest. In addition, seed formation was higher in X. calens‐visited flowers compared with all others. The results show that this crop experiences pollination deficit even under normal circumstances, considering that flowers visited by X. calens had higher yields compared with those under unlimited access by all visitors. The fruiting rate, the number of seeds/pod and the percentage of normal seeds of unprotected inflorescences were significantly higher than those of inflorescences protected from insects. X. calens foraging resulted in a significant increment of the fruiting rate by 25.80%, as well as the number of seeds/pod by 14.97% and the percentage of normal seeds by 27.75% in 2008 and 18.39% in 2009. Conservation of X. calens nests close to P. coccineus fields could be recommended to improve pod and seed production in the region.     

Measuring chess experts' single-use sequence knowledge: an archival study of departure from 'theoretical' openings

The respective roles of knowledge and search have received considerable attention in the literature on expertise. However, most of the evidence on knowledge has been indirect--e.g., by inferring the presence of chunks in long-term memory from performance in memory recall tasks. Here we provide direct estimates of the amount of monochrestic (single use) and rote knowledge held by chess players of varying skill levels. From a large chess database, we analyzed 76,562 games played in 2008 by individuals ranging from Class B players (average players) to Masters to measure the extent to which players deviate from previously known initial sequences of moves ("openings"). Substantial differences were found in the number of moves known by players of different skill levels, with more expert players knowing more moves. Combined with assumptions independently made about the branching factor in master games, we estimate that masters have memorized about 100,000 opening moves. Our results support the hypothesis that monochrestic knowledge is essential for reaching high levels of expertise in chess. They provide a direct, quantitative estimate of the number of opening moves that players have to know to reach master level.     

Inhibition of human-type 1 3beta-hydroxysteroid deshydrogenase/Delta(5)-Delta(4)-isomerase expression using siRNA

Specific inhibition of type 1 3beta-HSD is of particular interest since it will allow us to control the formation of androgens and estrogens in peripheral target tissues without affecting type 2 3beta-HSD, which is responsible for the biosynthesis of glucocorticoids and mineralocorticoids in the adrenals. The high homology between types 1 and 2 3beta-HSD is a major difficulty in the development of specific inhibitors through classical chemical synthesis. In this report, we describe the use of small interference RNA (siRNA) to specifically inhibit human type 1 3beta-HSD. We have constructed three DNA vector-based RNAi vectors that allow us to produce three RNA duplexes of 21 nucleotides targeting three different coding regions of human type 1 3beta-HSD mRNA. The resulting constructs were co-transfected into HEK-293 cells with a vector expressing type 1 3beta-HSD. The results indicate that while the two duplexes that target sequences in the 5'-region do not have a strong inhibitory effect, the duplex that targets the 3'-region efficiently inhibits 3beta-HSD activity. Up to 98% inhibition has been observed. To our knowledge, this is the first report showing successful inhibition of steroidogenic enzymes using siRNA technology.     

Comparison of crystal structures of human type 3 3alpha-hydroxysteroid dehydrogenase reveals an "induced-fit" mechanism and a conserved basic motif involved in the binding of androgen

The aldo-keto reductase (AKR) human type 3 3alpha-hydroxysteroid dehydrogenase (h3alpha-HSD3, AKR1C2) plays a crucial role in the regulation of the intracellular concentrations of testosterone and 5alpha-dihydrotestosterone (5alpha-DHT), two steroids directly linked to the etiology and the progression of many prostate diseases and cancer. This enzyme also binds many structurally different molecules such as 4-hydroxynonenal, polycyclic aromatic hydrocarbons, and indanone. To understand the mechanism underlying the plasticity of its substrate-binding site, we solved the binary complex structure of h3alpha-HSD3-NADP(H) at 1.9 A resolution. During the refinement process, we found acetate and citrate molecules deeply engulfed in the steroid-binding cavity. Superimposition of this structure with the h3alpha-HSD3-NADP(H)-testosterone/acetate ternary complex structure reveals that one of the mobile loops forming the binding cavity operates a slight contraction movement against the citrate molecule while the side chains of many residues undergo numerous conformational changes, probably to create an optimal binding site for the citrate. These structural changes, which altogether cause a reduction of the substrate-binding cavity volume (from 776 A(3) in the presence of testosterone/acetate to 704 A(3) in the acetate/citrate complex), are reminiscent of the "induced-fit" mechanism previously proposed for the aldose reductase, another member of the AKR superfamily. We also found that the replacement of residues Arg(301) and Arg(304), localized near the steroid-binding cavity, significantly affects the 3alpha-HSD activity of this enzyme toward 5alpha-DHT and completely abolishes its 17beta-HSD activity on 4-dione. All these results have thus been used to reevaluate the binding mode of this enzyme for androgens.