A Brief Review: The Z-curve Theory and its Application in Genome Analysis

In theoretical physics, there exist two basic mathematical approaches, algebraic and geometrical methods, which, in most cases, are complementary. In the area of genome sequence analysis, however, algebraic approaches have been widely used, while geometrical approaches have been less explored for a long time. The Z-curve theory is a geometrical approach to genome analysis. The Z-curve is a three-dimensional curve that represents a given DNA sequence in the sense that each can be uniquely reconstructed given the other. The Z-curve, therefore, contains all the information that the corresponding DNA sequence carries. The analysis of a DNA sequence can then be performed through studying the corresponding Z-curve. The Z-curve method has found applications in a wide range of areas in the past two decades, including the identifications of protein-coding genes, replication origins, horizontally-transferred genomic islands, promoters, translational start sides and isochores, as well as studies on phylogenetics, genome visualization and comparative genomics. Here, we review the progress of Z-curve studies from aspects of both theory and applications in genome analysis.     

How marginality leads to inclusion: insights from mobilizations of Chinese female migrants in Paris

ABSTRACT

This article examines the collective actions undertaken by two groups of Chinese female migrants in Paris: sex workers who opposed a new law on prostitution, and manicurists who joined trade unions and went on strike. These women share similar geographical origins and migration projects; many came to France alone, and thus have much weaker social capital than other Chinese migrants in Paris, which pushed them to choose professional sectors viewed as marginal or even stigmatized. Despite their precarious situation, their marginal position has created conditions for collective action, enabling them to develop strong sense of collective belonging and receive support from organizations outside the community. These findings show how a marginal position in an ethnic community can be a triggering factor for migrants’ inclusion and political engagement in the host society.     

Contact Matters: Local People’s Perceptions of <Emphasis Type="Italic">Hapalemur alaotrensis</Emphasis> and Implications for Conservation

Understanding factors that influence local community support for conservation projects is critical to their success. Perceptions of wildlife are particularly important in countries where people rely heavily on natural resources for their survival, as is the case in Madagascar. Renowned as one of the “hottest” regions for global biodiversity, Madagascar hosts an exceptional assemblage of lemurs. Yet little is known concerning the knowledge and perceptions of local people toward lemurs. The Lake Alaotra gentle lemur (Hapalemur alaotrensis) is classified as Critically Endangered on the IUCN Red List and restricted to marsh habitat in the Lake Alaotra New Protected Area. Habitat destruction and hunting have brought the lemur to the brink of extinction. In this study we characterize local people’s knowledge, awareness, and perceptions of Hapalemur alaotrensis. We conducted an initial survey with 180 participants in 6 villages with varying distance to Park Bandro, a high-priority conservation zone. During a second survey, we interviewed 50 people in the village adjacent to the park. Our findings demonstrate that fishers are the most knowledgeable local resource users despite having the lowest education levels, and they also are the most concerned with the endemic lemur’s decline. There is a link between environmental awareness and distance in both a literal and figurative sense; the more often people encounter Hapalemur alaotrensis, the more they know about it, and the more likely they are to be concerned about its future. Our study further shows that despite this concern, subsistence is prioritized over conservation in the Alaotra region. Ecological knowledge in the fishers’ communities is a valuable resource that can benefit the conservation of Hapalemur alaotrensis and its marshland habitat if conservation planning and management can align the resource users’ concerns and livelihood needs with biodiversity values.     

Sex pheromone composition of Ascotis selenaria (Lepidoptera: Geometridae) and its regional variation in Korea

This study was conducted to investigate sex pheromone composition of Ascotis selenaria (Lepidoptera: Geometridae) in Korea. Two sex pheromone compounds such as (Z,Z)-6,9-cis-3,4-epoxynonadecadiene (6Z,9Z-cis-3,4-epoxy-19:H) and (Z,Z,Z)-3,6,9-nonadecatriene (3Z,6Z,9Z-19:H) were identified in the glands of A. selenaria females by gas chromatography–mass spectrometry analysis. However, the component 3Z,6Z,9Z-19:H neither elicited an electroantennogram response nor increased the attractiveness for A. selenaria males in the field. The role of 3Z,6Z,9Z-19:H seems to be as an antagonistic signal for mating behavior of A. selenaria males.The blend ratios of two 6Z,9Z-cis-3,4-epoxy-19:H isomers such as, 6Z,9Z-cis-3R,4S-epoxy-19:H and 6Z,9Z-cis-3S,4R-epoxy-19:H, were critical to attract A. selenaria males. The blend ratios of the two isomers showing peak catch of A. selenaria males had large variations among the locations investigated. A. selenaria populations in Gunwi showed peak activity at ratios of 0.9:0.1 and 0.8:0.2, whereas the populations in Goheung, Yeongam, and Jeju (Aewol and Harye) showed peak activity at a 0.5:0.5 ratio. In Changnyeong, the peak activity occurred in a bimodal form at ratios of 0.7:0.3 and 0.4:0.6. Such variation was partially explained by geographical isolation due to mountain ranges. Consequently, the results of our study should be useful for designing a region-specific pheromone lure for successful A. selenaria monitoring.     

Sex pheromone composition of the variegated cutworm,Peridroma saucia (Lepidoptera: Noctuidae), in Korea

This study was conducted to investigate the sex pheromone composition of the variegated cutworm (Peridroma saucia Hübner) in Korea. The sex pheromone components of P. saucia were identified as (Z)-9-tetradecenyl acetate (Z9-14:Ac) and (Z)-11-hexadecenyl acetate (Z11-16:Ac) through GC-EAD and GC–MS analysis. EAG tests of the male antennae revealed that the Z9-14:AC exerted significantly larger responses than other compounds. The female moths primarily called and copulated between 6 h and 7 h after the lights off, and the ratio of two pheromone components, Z9-14:Ac and Z11-16:Ac, in the sex pheromone gland during this period was 1:2.1 to 1:2.4. In the field trapping studies, a large number of male moths were caught in the traps baited with the mixtures of Z9-14:Ac and Z11-16:Ac at the ratios ranging from 2.3:1 to 1:4, with the highest trap catches at 1:1 to 1:2.3 ratios of the two components. The seasonal flight activities of P. saucia monitored by using pheromone lures revealed complicated patterns in Korea. Specifically, the first flight period was spread over a long period and irregular, while the second flight period differed among the localities examined.     

Exclusion through acculturation? Comparing first- and second-generation European Muslims’ perceptions of discrimination across four national contexts

ABSTRACT

Negative attitudes towards Muslims have increased substantially in Europe, but European Muslims’ perceptions of discrimination vary across national contexts. Three separate approaches explain perceptions of discrimination: social psychological theories at the micro-level, migration theories at the social structural level, and citizenship theories at the macro-level. We know less about how these approaches fit together to explain variation in perceptions of discrimination across national contexts. To evaluate this question, this article combines survey data of European Muslims (n?=?1,618) with indices of policy commitments to immigrant integration in four countries. Contrary to hypothesized findings, this article identifies a striking puzzle: (1) Muslims report more experiences of discrimination in more inclusive contexts and (2) native-born Muslims are more likely to perceive societal hostility than Muslim immigrants in more inclusive contexts. To make sense of this puzzle, I offer an integrated approach that explains how macro-level contexts condition individual-level perceptions of exclusion through cultural knowledge.     

Binding properties of pheromone-binding protein 1 from the common cutworm Spodoptera litura

Pheromone-binding proteins (PBPs) were formerly thought to act as passive pheromone carriers. However, recent studies, particularly in Drosophila melanogaster, suggest that PBPs are involved in the recognition of semiochemicals, thus making ligand-binding studies more meaningful. Previously, we cloned three PBPs from Spodoptera litura (Slit), and showed that SlitPBP1 is much more abundant than the other two, particularly in male antennae. To investigate the ligand specificity of SlitPBP1, we expressed the protein in a bacterial system and performed binding experiments with the three components of the specific sex pheromones (Z9-14:Ac, Z9,E11-14:Ac and Z9,E12-14:Ac), as well as with 26 volatile ligands. The results indicated that SlitPBP1 bound all three sex pheromone components with dissociation constants between 0.6 and 1.1 μM. The same protein also bound with comparable affinities several pheromone analogs, but not plant volatiles. The presence of a double bond was the most important element for a strong binding, while its position and configuration also affected the affinity. Finally, the binding of pheromone components is strongly affected by pH, showing a critical pH value corresponding to isoelectric point of the protein. This suggests that a pH-dependent conformational mechanism might exist in SlitPBP1 for pheromone binding and release.     

Glyceroglycolipids,a novel class of platelet-activating factor antagonists from Kalimeris indica

The bioassay-guided purification of chloroform extracts of Kalimeris indica (Linn) Schultz-Bip led to the isolation of three diacylglycerols: 1-O-(9Z,12Z,15Z-octadecatrienoyl)-2-O-hexadecanoylglycerol (1), 1-O-(9Z,12Z,15Z-octadecatrienoyl)-2-O-hexadecanoyl-3-O-α-(6-sulfoquinovopyranosyl)glycerol (2), 1-O-(9Z,12Z,15Z-octadecatrienoyl)-2-O-hexadecanoyl-3-O-[α-d-galactopyranosyl(1 → 6)-O-β-d-galactopyranosyl]glycerol (3). Their structures were established on the basis of spectral and chemical methods. The glyceroglycolipids 2 and 3 exhibited significant PAF receptor binding inhibitory activities. Our studies have identified diacylglycolipids as a novel class of potent PAF antagonist.     

Neighborhood influences on perceived social support among parents: findings from the project on human development in Chicago neighborhoods

Background

Social support is frequently linked to positive parenting behavior. Similarly, studies increasingly show a link between neighborhood residential environment and positive parenting behavior. However, less is known about how the residential environment influences parental social support. To address this gap, we examine the relationship between neighborhood concentrated disadvantage and collective efficacy and the level and change in parental caregiver perceptions of non-familial social support.

Methodology/Principal Findings

The data for this study came from three data sources, the Project on Human Development in Chicago Neighborhoods (PHDCN) Study''s Longitudinal Cohort Survey of caregivers and their offspring, a Community Survey of adult residents in these same neighborhoods and the 1990 Census. Social support is measured at Wave 1 and Wave 3 and neighborhood characteristics are measured at Wave 1. Multilevel linear regression models are fit. The results show that neighborhood collective efficacy is a significant (ß = .04; SE = .02; p = .03), predictor of the positive change in perceived social support over a 7 year period, however, not of the level of social support, adjusting for key compositional variables and neighborhood concentrated disadvantage. In contrast concentrated neighborhood disadvantage is not a significant predictor of either the level or change in social support.

Conclusion

Our finding suggests that neighborhood collective efficacy may be important for inducing the perception of support from friends in parental caregivers over time.     

Application of the Marcus theory for analysis of the temperature dependence of the reactions leading to photosynthetic water oxidation: results and implications

The temperature dependence of donor side reactions was analysed within the framework of the Marcus theory of nonadiabatic electron transfer. The following results were obtained for PS II membrane fragments from spinach: (1) the reorganisation energy of P680^+? reduction by Y_Z is of the order of 0.5?eV in samples with a functionally fully competent water oxidising complex (WOC); (2) destruction of the WOC by Tris-washing gives rise to a drastic increase of λ to values of the order of 1.6?eV; (3) the reorganisation energies of the oxidation steps in the WOC are dependent, on the redox states S _i with values of about 0.6?eV for the reactions Y_Z ^OX S ₀→Y_Z S ₁ and Y_Z ^OX S ₁→Y_Z S ₂, 1.6?eV for the reaction Y_Z ^OX S ₂→Y_Z S ₃ and 1.1?eV (above a characteristic temperature u_c of about 6??°C) for the reaction Y_Z ^OX S ₃→→Y_Z S ₀+O₂. Using an empirical rate constant-distance relationship, the van der Waals distance between Y_Z and P680 was found to be about 10?Å, independent of the presence or absence of the WOC, whereas the distance between Y_Z and the manganese cluster in the WOC was ≥15?Å. Based on the calculated activation energies the environment of Y_Z is inferred to be almost "dry" and hydrophobic when the WOC is intact but becomes enriched with water molecules after WOC destruction. Furthermore, it is concluded that the transition S ₂→S ₃ is an electron transfer reaction gated by a conformational change, i.e. it comprises significant structural changes of functional relevance. Measurements of kinetic H/D isotope exchange effects support the idea that none of these reactions is gated by the break of a covalent O-H bond. The implications of these findings for the mechanism of water oxidation are discussed.     

Essential oil variation of Tagetes minuta in South Africa – A chemometric approach

Tagetes minuta L., generally known as wild marigold and locally as “Kakiebos”, has been used traditionally for medicinal purposes in many countries around the world. South Africa is currently the major producer of Tagetes essential oil which is used in perfumery, cosmetics and aromatherapy. The organoleptic and therapeutic properties of an essential oil are dependent upon the chemical profile of the oil. Tagetes essential oil from India, Egypt and the United Kingdom has been reported to be highly variable. In this study, possible chemotypic variation of South African Tagetes oil was explored. Eighty-three individual plants were collected from twenty-one different localities in South Africa. Essential oils were obtained by hydrodistillation using a Clevenger-type apparatus and the oil yield obtained ranged between 0.38 and 1.52%. The essential oils were analysed by gas chromatography coupled to mass spectrometry with flame ionisation detector (GC–MS‒FID) and the major compounds accounting for >85% of the total composition were identified as: (Z)-β-ocimene (27.9–56.0%), (E)-ocimenone (7.4–37.2%), (Z)-tagetone (1.4–24.9%), dihydrotagetone (n.d.−23.4%), (Z)-ocimenone (4.5–13.9%), limonene (n.d.−6.5%) and (E)-tagetone (n.d.−3.2%). Untargeted analysis of GC–MS data using MarkerLynx^® and hierarchical clustering analysis (HCA) revealed two major chemotypes. Further analysis of the two chemotypes using orthogonal projections to latent structures-discriminant analysis (OPLS-DA) identified (E)-tagetone, dihydrotagetone and (Z)-tagetone as characteristic marker constituents for chemotype 1, while chemotype 2 was characterised by (Z)-β-ocimene, (E)-ocimenone and (Z)-ocimenone.     

Prostaglandin synthases: Molecular characterization and involvement in prostaglandin biosynthesis

Prostaglandins (PGs) belong to a subclass of eicosanoids and are classified based on the structures of the cyclopentane ring and their number of double bonds in their hydrocarbon structures. PGs are important lipid mediators that are involved in inflammatory response. The biosynthesis of diverse PGs from unsaturated C20 fatty acids containing at least three double bonds such as dihomo-γ-linoleic acid (20:3^Δ8Z,11Z,14Z), arachidonic acid (20:4^{Δ5Z,8Z,11Z,14Z}), and eicosapentaenoic acid (20:5^{Δ5Z,8Z,11Z,14Z,17Z}) is enables by various PG synthases, including prostaglandin H synthase (PGHS), 15-hydroxyprostaglandin dehydrogenase (15-HPGD), PGES, PGDS, PGFS, PGIS, and thromboxane A synthase (TXAS). This review summarizes the biochemical properties, reaction mechanism, and active site details of PG synthases. Because PGs are involved in the immune system, an understanding of PG synthases is important in the design of new anti-inflammatory drugs. The biosynthesis of PGs in various organisms, such as mammals, corals, florideae (a class of red algae), yeast, and fungi, is also introduced. The expression of PG synthases in the microbial systems for the synthesis of PGs is discussed. Now, the biosynthesis of PGs from glucose or glycerol is possible using metabolically engineered cells expressing both unsaturated fatty acid-producing enzymes and PG synthases.     

Local Ecological Knowledge and Scientific Data Reveal Overexploitation by Multigear Artisanal Fisheries in the Southwestern Atlantic

In the last decades, a number of studies based on historical records revealed the diversity loss in the oceans and human-induced changes to marine ecosystems. These studies have improved our understanding of the human impacts in the oceans. They also drew attention to the shifting baseline syndrome and the importance of assessing appropriate sources of data in order to build the most reliable environmental baseline. Here we amassed information from artisanal fishermen''s local ecological knowledge, fisheries landing data and underwater visual census to assess the decline of fish species in Southeastern Brazil. Interviews with 214 fishermen from line, beach seine and spearfishing revealed a sharp decline in abundance of the bluefish Pomatomus saltatrix, the groupers Epinephelus marginatus, Mycteroperca acutirostris, M. bonaci and M. microlepis, and large parrotfishes in the past six decades. Fisheries landing data from a 16-year period support the decline of bluefish as pointed by fishermen''s local knowledge, while underwater visual census campaigns show reductions in groupers'' abundance and a sharp population decline of the Brazilian endemic parrotfish Scarus trispinosus. Despite the marked decline of these fisheries, younger and less experienced fishermen recognized fewer species as overexploited and fishing sites as depleted than older and more experienced fishermen, indicating the occurrence of the shifting baseline syndrome. Here we show both the decline of multigear fisheries catches – combining anecdotal and scientific data – as well as changes in environmental perceptions over generations of fishermen. Managing ocean resources requires looking into the past, and into traditional knowledge, bringing historical baselines to the present and improving public awareness.     

Electroantennogram and field responses of Korean population of the rice leaf folder,Cnaphalocrocis medinalis (Lepidoptera: Crambidae), to sex attractant candidates

A series of studies was conducted to determine the optimum sex attractant for monitoring the rice leaf folder, Cnaphalocrocis medinalis, in Korea, based on the previously reported pheromone composition in this species. (Z)-13-Octadecenal (Z13-18:Al) was most active in electroantennogram (EAG) and field tests. (Z)-11-Hexadecenal (Z11-16:Al), (Z)-11-octadecenal (Z11-18:Al), (Z)-11-hexadecenyl acetate (Z11-16:Ac), (Z)-13-octadecenyl acetate (Z13-18:Ac) and (Z)-13-octadecenol (Z13-18:OH) individually elicited significant EAG responses, but were not individually attractive in field trials. (Z)-11-Octadecenol (Z11-18:OH) alone was inactive in both EAG and field tests. The addition of Z11-18:OH and Z13-18:OH to the binary mixture of Z11-18:Al and Z13-18:Al, as the previously reported composition of the Japanese blend, significantly increased the trap catches of males in field trials. In contrast, the Philippine and Indian blends were not attractive to this species. Interestingly, when Z13-18:Ac alone was added to the binary mixture of Z11-18:Al and Z13-18:Al, the trap catch number was the same as that of the Japanese blend. The present study indicates that the four-component blend (Z11-18:Al/Z13-18:Al/Z11-18:OH/Z13-18:OH = 11/100/24/36) and the three-component blend (Z11-18:Al/Z13-18:Al/Z13-18:Ac = 11/100/11) can be used as sex attractants for monitoring the Korean populations of C. medinalis.     

高温胁迫对不同种源希蒙得木叶片生理特性的影响

利用人工气候室模拟高温环境,研究了不同程度高温处理对3个不同种源(Z1:会东可河;Z2:澳大利亚肯多伯冷;Z3:美国菲尼克斯)希蒙得木叶片相对含水量(LRWC)、叶片光合特性、渗透调节、抗氧化保护酶、膜脂过氧化的影响.结果表明,3个种源希蒙得木幼苗LRWC、净光合速率(Pn)和蒸腾速率(Tr)均随高温胁迫强度的加剧呈极显著下降趋势,叶绿素含量(Chl)、可溶性糖含量显著降低;脯氨酸(Pro)含量呈极显著上升趋势;丙二醛(MDA)含量和相对电导率(REC)均随高温胁迫强度的加剧而显著增加;高温胁迫对希蒙得木幼苗叶片过氧化物酶(POD)活性和超氧化物歧化酶(SOD)活性的影响因种源不同而有所差异,Z1、Z2的POD活性随高温胁迫程度的增加而持续上升,Z3的POD活性呈先上升后降低趋势;Z1、Z3的SOD活性随高温胁迫程度的增加而持续上升,Z2的SOD活性呈先降低后上升趋势.以隶属函数法综合分析各种源希蒙得木幼苗抗高温能力的结果表明,3个种源希蒙得木幼苗的抗高温能力由强到弱依次为:Z1、Z3和Z2.结果表明,长期生长在金沙江干热河谷的Z1可能已经适应当地的生态环境,表现出较好的抵御高温的能力,不同种源耐高温能力的差异可能是通过种源所在地的气候、土壤、海拔等因子综合作用,经过漫长的系统发育,产生不同的变异结果.     

Identification and behavioral evaluation of sex pheromone components of the Chinese pine caterpillar moth, Dendrolimus tabulaeformis

Background

The Chinese pine caterpillar moth, Dendrolimus tabulaeformis Tsai and Liu (Lepidoptera: Lasiocampidae) is the most important defoliator of coniferous trees in northern China. Outbreaks occur over enormous areas and often lead to the death of forests during 2–3 successive years of defoliation. The sex pheromone of D. tabulaeformis was investigated to define its chemistry and behavioral activity.

Methodology/Principal Findings

Sex pheromone was collected from calling female D. tabulaeformis by headspace solid phase microextraction (SPME) and by solvent extraction of pheromone glands. Extracts were analyzed by coupled gas chromatography/mass spectrometry (GC-MS) and coupled GC-electroantennographic detection (GC-EAD), using antennae from male moths. Five components from the extracts elicited antennal responses. These compounds were identified by a combination of retention indices, electron impact mass spectral matches, and derivatization as (Z)-5-dodecenyl acetate (Z5-12:OAc), (Z)-5-dodecenyl alcohol (Z5-12:OH), (5Z,7E)-5,7-dodecadien-1-yl acetate (Z5,E7-12:OAc), (5Z,7E)-5,7-dodecadien-1-yl propionate (Z5,E7-12:OPr), and (5Z,7E)-5,7-dodecadien-1-ol (Z5,E7-12:OH). Behavioral assays showed that male D. tabulaeformis strongly discriminated against incomplete and aberrant blend ratios. The correct ratio of Z5,E7-12:OAc, Z5,E7-12:OH, and Z5,E7-12:OPr was essential for optimal upwind flight and source contact. The two monoenes, Z5-12:OAc and Z5-12:OH, alone or binary mixtures, had no effect on behavioral responses when added to the optimal three-component blend.

Conclusions/Significance

The fact that deviations from the optimal ratio of 100∶100∶4.5 of Z5,E7-12:OAc, Z5,EZ7-12:OH, and Z5,E7-12:OPr resulted in marked decreases in male responses suggests that biosynthesis of the pheromone components is precisely controlled. The optimal blend of the sex pheromone components of D. tabulaeformis worked out in this study should find immediate use in monitoring this pest in Chinese forests.     

Planar Cell Polarity Signaling in Collective Cell Movements During Morphogenesis and Disease

Collective and directed cell movements are crucial for diverse developmental processes in the animal kingdom, but they are also involved in wound repair and disease. During these processes groups of cells are oriented within the tissue plane, which is referred to as planar cell polarity (PCP). This requires a tight regulation that is in part conducted by the PCP pathway. Although this pathway was initially characterized in flies, subsequent studies in vertebrates revealed a set of conserved core factors but also effector molecules and signal modulators, which build the fundamental PCP machinery. The PCP pathway in Drosophila regulates several developmental processes involving collective cell movements such as border cell migration during oogenesis, ommatidial rotation during eye development, and embryonic dorsal closure. During vertebrate embryogenesis, PCP signaling also controls collective and directed cell movements including convergent extension during gastrulation, neural tube closure, neural crest cell migration, or heart morphogenesis. Similarly, PCP signaling is linked to processes such as wound repair, and cancer invasion and metastasis in adults. As a consequence, disruption of PCP signaling leads to pathological conditions. In this review, we will summarize recent findings about the role of PCP signaling in collective cell movements in flies and vertebrates. In addition, we will focus on how studies in Drosophila have been relevant to our understanding of the PCP molecular machinery and will describe several developmental defects and human disorders in which PCP signaling is compromised. Therefore, new discoveries about the contribution of this pathway to collective cell movements could provide new potential diagnostic and therapeutic targets for these disorders.