Metazoan parasite communities of the Pacific red snapper, Lutjanus peru (Perciformes: Lutjanidae): interannual variations in parasite communities.

Metazoan parasite communities can experience temporal structural changes related to seasonal and/or local variations in several biotic and abiotic environmental factors. However, few studies have addressed this issue in tropical regions, where changes in water temperature are less extreme than in temperate regions, so the factors or processes that can generate variations in these parasite communities are as yet unclear. We quantified and analysed the parasite communities of 421 Lutjanus peru (Nichols & Murphy, 1922) collected from Acapulco Bay in Guerrero, Mexico, over a four-year period (August 2018 to April 2021), to identify any interannual variation due to local biotic and abiotic factors influenced by natural oceanographic phenomena, such as El Niño-Southern Oscillation, or La Niña. Twenty-five metazoan parasite taxa were recovered and identified: seven Digenea species; two Monogenea; one Cestoda; one Acanthocephala; four Nematoda; and ten of Crustacea (seven Copepoda and three Isopoda). The digeneans and copepods were the best represented parasite groups. The parasite communities were characterized by a high numerical dominance of helminth larvae. Species richness at the component community level (13 to 19 species) was similar to reported richness in other Lutjanus spp. The parasite communities of L. peru had a high variability in species composition, but low aggregate variability (e.g. species diversity), suggesting that structure of these communities may be quite stable over time. A clear interannual variation pattern was not observed, suggesting that parasite species of this host may respond differently to variations in environmental factors. Interannual variations were possibly caused by a combination of biotic (i.e. host feeding behaviour and body size) and local abiotic factors (influenced by climatic anomalies) which generated notable changes in the infection levels of several component species.

Multidisciplinary guidelines for the management of paediatric tracheostomy emergencies.

Temporary and permanent tracheostomies are required in children to manage actual or anticipated long-term ventilatory support, to aid secretion management or to manage fixed upper airway obstruction. Tracheostomies may be required from the first few moments of life, with the majority performed in children < 4 years of age. Although similarities with adult tracheostomies are apparent, there are key differences when managing the routine and emergency care of children with tracheostomies. The National Tracheostomy Safety Project identified the need for structured guidelines to aid multidisciplinary clinical decision making during paediatric tracheostomy emergencies. These guidelines describe the development of a bespoke emergency management algorithm and supporting resources. Our aim is to reduce the frequency, nature and severity of paediatric tracheostomy emergencies through preparation and education of staff, parents, carers and patients.

Impact on short-lived climate forcers increases projected warming due to deforestation.

The climate impact of deforestation depends on the relative strength of several biogeochemical and biogeophysical effects. In addition to affecting the exchange of carbon dioxide (CO2) and moisture with the atmosphere and surface albedo, vegetation emits biogenic volatile organic compounds (BVOCs) that alter the formation of short-lived climate forcers (SLCFs), which include aerosol, ozone and methane. Here we show that a scenario of complete global deforestation results in a net positive radiative forcing (RF; 0.12 W m-2) from SLCFs, with the negative RF from decreases in ozone and methane concentrations partially offsetting the positive aerosol RF. Combining RFs due to CO2, surface albedo and SLCFs suggests that global deforestation could cause 0.8 K warming after 100 years, with SLCFs contributing 8% of the effect. However, deforestation as projected by the RCP8.5 scenario leads to zero net RF from SLCF, primarily due to nonlinearities in the aerosol indirect effect.

Impact on short-lived climate forcers (SLCFs) from a realistic land-use change scenario via changes in biogenic emissions.

More than one quarter of natural forests have been cleared by humans to make way for other land-uses, with changes to forest cover projected to continue. The climate impact of land-use change (LUC) is dependent upon the relative strength of several biogeophysical and biogeochemical effects. In addition to affecting the surface albedo and exchanging carbon dioxide (CO2) and moisture with the atmosphere, vegetation emits biogenic volatile organic compounds (BVOCs), altering the formation of short-lived climate forcers (SLCFs) including aerosol, ozone (O3) and methane (CH4). Once emitted, BVOCs are rapidly oxidised by O3, and the hydroxyl (OH) and nitrate (NO3) radicals. These oxidation reactions yield secondary organic products which are implicated in the formation and growth of aerosol particles and are estimated to have a negative radiative effect on the climate (i.e. a cooling). These reactions also deplete OH, increasing the atmospheric lifetime of CH4, and directly affect concentrations of O3; the latter two being greenhouse gases which impose a positive radiative effect (i.e. a warming) on the climate. Our previous work assessing idealised deforestation scenarios found a positive radiative effect due to changes in SLCFs; however, since the radiative effects associated with changes to SLCFs result from a combination of non-linear processes it may not be appropriate to scale radiative effects from complete deforestation scenarios according to the deforestation extent. Here we combine a land-surface model, a chemical transport model, a global aerosol model, and a radiative transfer model to assess the net radiative effect of changes in SLCFs due to historical LUC between the years 1850 and 2000.

Genetic inheritance of gene expression in human cell lines.

Combining genetic inheritance information, for both molecular profiles and complex traits, is a promising strategy not only for detecting quantitative trait loci (QTLs) for complex traits but for understanding which genes, pathways, and biological processes are also under the influence of a given QTL. As a primary step in determining the feasibility of such an approach in humans, we present the largest survey to date, to our knowledge, of the heritability of gene-expression traits in segregating human populations. In particular, we measured expression for 23,499 genes in lymphoblastoid cell lines for members of 15 Centre d'Etude du Polymorphisme Humain (CEPH) families. Of the total set of genes, 2,340 were found to be expressed, of which 31% had significant heritability when a false-discovery rate of 0.05 was used. QTLs were detected for 33 genes on the basis of at least one P value <.000005. Of these, 13 genes possessed a QTL within 5 Mb of their physical location. Hierarchical clustering was performed on the basis of both Pearson correlation of gene expression and genetic correlation. Both reflected biologically relevant activity taking place in the lymphoblastoid cell lines, with greater coherency represented in Kyoto Encyclopedia of Genes and Genomes database (KEGG) pathways than in Gene Ontology database pathways. However, more pathway coherence was observed in KEGG pathways when clustering was based on genetic correlation than when clustering was based on Pearson correlation. As more expression data in segregating populations are generated, viewing clusters or networks based on genetic correlation measures and shared QTLs will offer potentially novel insights into the relationship among genes that may underlie complex traits.

A new paradigm for drug discovery: integrating clinical, genetic, genomic and molecular phenotype data to identify drug targets.

Application of statistical genetics approaches to variations in mRNA transcript abundances in segregating populations can be used to identify genes and pathways associated with common human diseases. The combination of this genetic information with gene expression and clinical trait data can also be used to identify subtypes of a disease and the genetic loci specific to each subtype. Here we highlight results from some of our recent work in this area and further explore the many possibilities that exist in employing a more comprehensive genetics and functional genomics approach to the functional annotation of genomes, and in applying such methods to the validation of targets for complex traits in the drug discovery process.

Phylogeny of the Acanthocephala based on morphological characters.

Only four previous studies of relationships among acanthocephalans have included cladistic analyses, and knowledge of the phylogeny of the group has not kept pace with that of other taxa. The purpose of this study is to provide a more comprehensive analysis of the phylogenetic relationships among members of the phylum Acanthocephala using morphological characters. The most appropriate outgroups are those that share a common early cell-cleavage pattern (polar placement of centrioles), such as the Rotifera, rather than the Priapulida (meridional placement of centrioles) to provide character polarity based on common ancestry rather than a general similarity likely due to convergence of body shapes. The phylogeny of 22 species of the Acanthocephala was evaluated based on 138 binary and multistate characters derived from comparative morphological and ontogenetic studies. Three assumptions of cement gland structure were tested: (i) the plesiomorphic type of cement glands in the Rotifera, as the sister group, is undetermined; (ii) non-syncytial cement glands are plesiomorphic; and (iii) syncytial cement glands are plesiomorphic. The results were used to test an early move of Tegorhynchus pectinarius to Koronacantha and to evaluate the relationship between Tegorhynchus and Illiosentis. Analysis of the data-set for each of these assumptions of cement gland structure produced the same single most parsimonious tree topology. Using Assumptions i and ii for the cement glands, the trees were the same length (length = 404 steps, CI = 0.545, CIX = 0.517, HI = 0.455, HIX = 0.483, RI = 0.670, RC = 0.365). Using Assumption iii, the tree was three steps longer (length = 408 steps, CI = 0.539, CIX = 0.512, HI = 0.461, HIX = 0.488, RI = 0.665, RC = 0.359). The tree indicates that the Palaeacanthocephala and Eoacanthocephala both are monophyletic and are sister taxa. The members of the Archiacanthocephala are basal to the other two clades, but do not themselves form a clade. The results provide strong support for the Palaeacanthocephala and the Eoacanthocephala and the hypothesis that the Eoacanthocephala is the most primitive group is not supported. Little support for the Archiacanthocephala as a monophyletic group was provided by the analysis. Support is provided for the recognition of Tegorhynchus and Illiosentis as distinct taxa, as well as the transfer of T. pectinarius to Koronacantha.

Molecular evidence of greater selective pressure for drug resistance exerted by the long-acting antifolate Pyrimethamine/Sulfadoxine compared with the shorter-acting chlorproguanil/dapsone on Kenyan Plasmodium falciparum.

Pyrimethamine (PM) plus sulfadoxine (SD) is the last remaining affordable drug for treating uncomplicated malaria in Africa. The selective pressure exerted by the slowly eliminated combination PM/SD was compared with that exerted by the more rapidly eliminated combination chlorproguanil/dapsone (CPG/Dap) on Kenyan Plasmodium falciparum. Point mutations were analyzed in dihydrofolate reductase and dihydropteroate synthase and in the genetic diversity of 3 genes in isolates collected before and after CPG/Dap and PM/SD treatments. PM/SD was associated strongly with the disappearance of fully drug-sensitive parasites and with a significant increase in the prevalence of resistant parasites in subsequent parasitemias. However, this was not a characteristic of treatment with CPG/Dap. Moreover, most of the patients who returned with recrudescent infections were in the PM/SD-treated group. The data predict a longer useful therapeutic life for CPG/Dap than for PM/SD, and, thus, CPG/Dap is a preferable alternative for treatment of chloroquine-resistant falciparum malaria in sub-Saharan Africa.

A test for linkage and association in general pedigrees: the pedigree disequilibrium test.

Family-based tests of linkage disequilibrium typically are based on nuclear-family data including affected individuals and their parents or their unaffected siblings. A limitation of such tests is that they generally are not valid tests of association when data from related nuclear families from larger pedigrees are used. Standard methods require selection of a single nuclear family from any extended pedigrees when testing for linkage disequilibrium. Often data are available for larger pedigrees, and it would be desirable to have a valid test of linkage disequilibrium that can use all potentially informative data. In this study, we present the pedigree disequilibrium test (PDT) for analysis of linkage disequilibrium in general pedigrees. The PDT can use data from related nuclear families from extended pedigrees and is valid even when there is population substructure. Using computer simulations, we demonstrated validity of the test when the asymptotic distribution is used to assess the significance, and examined statistical power. Power simulations demonstrate that, when extended pedigree data are available, substantial gains in power can be attained by use of the PDT rather than existing methods that use only a subset of the data. Furthermore, the PDT remains more powerful even when there is misclassification of unaffected individuals. Our simulations suggest that there may be advantages to using the PDT even if the data consist of independent families without extended family information. Thus, the PDT provides a general test of linkage disequilibrium that can be widely applied to different data structures.

Removing the sampling restrictions from family-based tests of association for a quantitative-trait locus.

One strategy for localization of a quantitative-trait locus (QTL) is to test whether the distribution of a quantitative trait depends on the number of copies of a specific genetic-marker allele that an individual possesses. This approach tests for association between alleles at the marker and the QTL, and it assumes that association is a consequence of the marker being physically close to the QTL. However, problems can occur when data are not from a homogeneous population, since associations can arise irrespective of a genetic marker being in physical proximity to the QTL-that is, no information is gained regarding localization. Methods to address this problem have recently been proposed. These proposed methods use family data for indirect stratification of a population, thereby removing the effect of associations that are due to unknown population substructure. They are, however, restricted in terms of the number of children per family that can be used in the analysis. Here we introduce tests that can be used on family data with parent and child genotypes, with child genotypes only, or with a combination of these types of families, without size restrictions. Furthermore, equations that allow one to determine the sample size needed to achieve desired power are derived. By means of simulation, we demonstrate that the existing tests have an elevated false-positive rate when the size restrictions are not followed and that a good deal of information is lost as a result of adherence to the size restrictions. Finally, we introduce permutation procedures that are recommended for small samples but that can also be used for extensions of the tests to multiallelic markers and to the simultaneous use of more than one marker.

Complete genomic screen for disease susceptibility loci in nuclear families.

We performed genome-wide model dependent and independent analyses on a simulated data set of 400 families segregating for a rare disorder. Regions on chromosomes 1, 3, and 5 were consistently indicated across the various analyses performed. Follow-up analyses included stratification for locus heterogeneity and clinical phenotype and studies of gene x gene and gene x environment interaction. The region around D1G024 was most notable, showing strong association and linkage with the trait. We also identified regions D3G043-46 and D5G037-39 by strong linkage and association findings and region D1G001-09 by linkage analysis. A complex statistical interaction was suggested between D1G024, D3G046 and environmental factor 1. This report suggests that traditional methods of analysis can be implemented to analyze and describe the mechanisms that may underlie the more complex genetic disorders.

Two tests of association for a susceptibility locus for families of variable size: an example using two sampling strategies.

A two-stage approach was used to analyze Problem 2 simulated data from Genetic Analysis Workshop 11. In the first stage, we tested for linkage with the Haseman-Elston test in SIBPAL. Markers that were significant in the first stage were followed up with two types of association tests. These association tests differ in the type of family information used: 1) parental transmissions to affected children or 2) differences in marker allele frequencies between affected and unaffected siblings. We also explored how the conclusions changed when different sampling strategies were used. Of particular interest was whether the entire data set should be used to test for both linkage and association or whether the data set should be halved to allow for replication of the initial association results.

Helical structure and packing orientation of the S2 segment in the Shaker K+ channel.

Six transmembrane segments, S1-S6, cluster around the central pore-forming region in voltage-gated K+ channels. To investigate the structural characteristics of the S2 segment in the Shaker K+ channel, we replaced each residue in S2 singly with tryptophan (or with alanine for the native tryptophan). All but one of the 23 Trp mutants expressed voltage-dependent K+ currents in Xenopus oocytes. The effects of the mutations were classified as being of low or high impact on channel gating properties. The periodicity evident in the effects of these mutations supports an alpha-helical structure for the S2 segment. The high- and low-impact residues cluster onto opposite faces of a helical wheel projection of the S2 segment. The low-impact face is also tolerant of single mutations to asparagine. All results are consistent with the idea that the low-impact face projects toward membrane lipids and that changes in S2 packing occur upon channel opening. We conclude that the S2 segment is a transmembrane alpha helix and that the high-impact face packs against other transmembrane segments in the functional channel.

A comparative study of sibship tests of linkage and/or association.

Population-based tests of association have used data from either case-control studies or studies based on trios (affected child and parents). Case-control studies are more prone to false-positive results caused by inappropriate controls, which can occur if, for example, there is population admixture or stratification. An advantage of family-based tests is that cases and controls are well matched, but parental data may not always be available, especially for late-onset diseases. Three recent family-based tests of association and linkage utilize unaffected siblings as surrogates for untyped parents. In this paper, we propose an extension of one of these tests. We describe and compare the four tests in the context of a complex disease for both biallelic and multiallelic markers, as well as for sibships of different sizes. We also examine the consequences of having some parental data in the sample.

Theletrum lamothei sp. nov. (Digenea), parasite of Echidna nocturna from Cuajiniquil, Guanacaste, and other digenes of marine fishes from Costa Rica.

A new species of Theletrum is described from the intestine of two palenose morays, Echidna nocturna, collected in Cuajiniquil, Guanacaste Province, Costa Rica. The new species differs from the type species, T. fustiforme Linton, 1910 by having a subspherical pars prostatica, a subspherical seminal vesicle extending anteriorly to the anterior border of the acetabulum, by the presence of a poorly developed hermaphroditic sac, and by having a larger body size. We also report eight additional species of digeneans parasitizing marine fishes in several localities along the Atlantic and Pacific coast of Costa Rica: Bianium simonei, Didymozoinae (metacercariae), Ectenurus virgulus, Hypocreadium myohelicatum, Lecithochirium microstomum, Pseudolecithaster sp., Stephanostomum casum, and Tergestia laticollis. In addition, we present an updated list of helminth parasites of marine fish from Costa Rica and discuss the importance of including parasites as an integral part of biodiversity inventories.

Koronacantha pectinaria n. comb. (Acanthocephala: Illiosentidae) from Microlepidotus brevipinnis (Haemulidae) and redescription of Tegorhynchus brevis.

Tegorhynchus pectinarius Van Cleave, 1940, is redescribed on the basis of male and female specimens in Microlepidotus brevipinnis from the marine waters of Costa Rica and México. The elongate proboscis with a heavy cuticular coating, cuticular body spines, 8 cement glands, and the heavy, strongly recurved hooks in the shape of an inverted apostrophe with roots that are simple but exaggerated in size with a small hook blade indicate that T. pectinarius should be assigned to Koronacantha Monks and Pérez-Ponce de León, 1996. Koronacantha pectinaria n. comb. can be distinguished from Koronacantha mexicana in having strongly recurved hooks only on the dorsal side of the proboscis, a conspicuous patch devoid of normally developed hooks located just anterior to the recurved hooks, trunk spines extending from the anterior end of the trunk posteriorly over 85% of the trunk, lacking genital spines in both sexes, and by the basal comblike group of small close-set hooks made up of 5 to 7 hooks. In K. mexicana, the recurved hooks occur as a complete ring, no patchlike area devoid of hooks exists, trunk spines begin at posterior end of receptacle and extend posteriorly over rest of trunk, genital spines are present in both sexes, and the basal comblike group of small close-set hooks consists of 4 or 5 hooks. Tegorhynchus brevis Van Cleave, 1921, is redescribed based on the original specimens, and Tegorhynchus, Koronacantha, and Illiosentis are considered diagnostically distinct.

Solution structure of a polypeptide from the N terminus of the HIV protein Nef.

Nef is a 27 kDa myristylated phosphoprotein expressed early in infection by HIV. The N terminus of Nef is thought to play a vital role in the functions of this protein through its interactions with membrane structures. The solution structure of a 25-residue polypeptide corresponding to the N terminus of Nef (Nef1-25) has been investigated by 1H NMR spectroscopy. In aqueous solution at pH 4.8 and 281 K, this peptide underwent conformational averaging, with Pro13 existing in cis and trans conformations in nearly equal proportions. In methanol solution, however, the peptide adopted a well-defined alpha-helical structure from residues 6 to 22, with the N- and C-terminal regions having a less ordered structure. On the basis of a comparison of chemical shifts and NOEs, it appeared that this helical structure was maintained in aqueous trifluoroethanol (50% v/v) and to a lesser extent in a solution of SDS micelles. When the N-acetyl group was replaced by either an N-myristyl or a free ammonium group, there was little effect on the three-dimensional structure of the peptide in methanol; deamidation of the C terminus also had no effect on the structure in methanol. In water, the myristylated peptide aggregated. The similarity between the sequences of Nef1-25 and melittin is reflected in the similar structures of the two molecules, although the N-terminal helix of melittin is more defined. This similarity in structure raises the possibility that Nef1-25 not only interacts with membranes but also may be capable of disrupting them and causing cell lysis. This type of interaction could contribute at least in part to the killing of bystander cells in lymphoid tissues during HIV infection.