A standard variation file format for human genome sequences

Here we describe the Genome Variation Format (GVF) and the 10Gen dataset. GVF, an extension of Generic Feature Format version 3 (GFF3), is a simple tab-delimited format for DNA variant files, which uses Sequence Ontology to describe genome variation data. The 10Gen dataset, ten human genomes in GVF format, is freely available for community analysis from the Sequence Ontology website and from an Amazon elastic block storage (EBS) snapshot for use in Amazon's EC2 cloud computing environment.     

Diastereomeric preference in 1,4,7-tris((S)-2-hydroxy-3-phenylpropyl)-1,4,7-triazacyclononanelithium(I) and its sodium(I) analogue

In N,N-dimethylformamide (DMF), 1,4,7-tris((S)-2-hydroxy-3-phenylpropyl)-1,4,7-triazacyclononane forms metal complexes, [M(S-thppc9)]⁺, for which log K (dm³ mol⁻¹)=3.01, 2.65, 2.66, 2.65, 2.42 and 7.59 (all±0.05) where M⁺=Li⁺, Na⁺, K⁺, Rb⁺, Cs⁺ and Ag⁺, respectively. Variable temperature ¹³C{¹H} NMR spectroscopy shows that the interchange between equivalent forms of a single diastereomer occurs for [Li(S-thppc9)]⁺ and [Na(S-thppc9)]⁺ characterised by: k=43±5 and 2900±100 s⁻¹, at 298.2 K, ΔH^‡=22.5±1.6 and 33.8±1.6 kJ mol⁻¹, and ΔS^‡=−133±5 and −59±6 J K⁻¹ mol⁻¹, respectively. Gas phase ab initio modelling shows these complexes and their K⁺ analogue to preferentially form distorted trigonal prismatic Λ, Δ, and Λ diastereomers, respectively.     

<Emphasis Type="Italic">ABI3</Emphasis> and <Emphasis Type="Italic">PLCG2</Emphasis> missense variants as risk factors for neurodegenerative diseases in Caucasians and African Americans

Background

Rare coding variants ABI3_rs616338-T and PLCG2_rs72824905-G were identified as risk or protective factors, respectively, for Alzheimer’s disease (AD).

Methods

We tested the association of these variants with five neurodegenerative diseases in Caucasian case-control cohorts: 2742 AD, 231 progressive supranuclear palsy (PSP), 838 Parkinson’s disease (PD), 306 dementia with Lewy bodies (DLB) and 150 multiple system atrophy (MSA) vs. 3351 controls; and in an African-American AD case-control cohort (181 AD, 331 controls). 1479 AD and 1491 controls were non-overlapping with a prior report.

Results

Using Fisher’s exact test, there was significant association of both ABI3_rs616338-T (OR?=?1.41, p?=?0.044) and PLCG2_rs72824905-G (OR?=?0.56, p?=?0.008) with AD. These OR estimates were maintained in the non-overlapping replication AD-control analysis, albeit at reduced significance (ABI3_rs616338-T OR?=?1.44, p?=?0.12; PLCG2_rs72824905-G OR?=?0.66, p?=?0.19). None of the other cohorts showed significant associations that were concordant with those for AD, although the DLB cohort had suggestive findings (Fisher’s test: ABI3_rs616338-T OR?=?1.79, p?=?0.097; PLCG2_rs72824905-G OR?=?0.32, p?=?0.124). PLCG2_rs72824905-G showed suggestive association with pathologically-confirmed MSA (OR?=?2.39, p?=?0.050) and PSP (OR?=?1.97, p?=?0.061), although in the opposite direction of that for AD. We assessed RNA sequencing data from 238 temporal cortex (TCX) and 224 cerebellum (CER) samples from AD, PSP and control patients and identified co-expression networks, enriched in microglial genes and immune response GO terms, and which harbor PLCG2 and/or ABI3. These networks had higher expression in AD, but not in PSP TCX, compared to controls. This expression association did not survive adjustment for brain cell type population changes.

Conclusions

We validated the associations previously reported with ABI3_rs616338-T and PLCG2_rs72824905-G in a Caucasian AD case-control cohort, and observed a similar direction of effect in DLB. Conversely, PLCG2_rs72824905-G showed suggestive associations with PSP and MSA in the opposite direction. We identified microglial gene-enriched co-expression networks with significantly higher levels in AD TCX, but not in PSP, a primary tauopathy. This co-expression network association appears to be driven by microglial cell population changes in a brain region affected by AD pathology. Although these findings require replication in larger cohorts, they suggest distinct effects of the microglial genes, ABI3 and PLCG2 in neurodegenerative diseases that harbor significant vs. low/no amyloid ß pathology.

     

Effect of mechanical damage on emission of volatile organic compounds from plant leaves and implications for evaluation of host plant specificity of prospective biological control agents of weeds

Assessment of host plant specificity is a critical step in the evaluation of classical biological control agents of weeds which is necessary for avoiding possible damage to non-target plants. Volatile organic compounds (VOCs) emitted by plants likely play an important role in determining which plants attract and are accepted by a prospective arthropod agent. However, current methods to evaluate host plant specificity usually rely on empirical choice and no-choice behavioural experiments, with little knowledge about what chemical or physical attributes are stimulating the insect. We conducted experiments to measure the quantitative and qualitative effects on emission of VOCs caused by simple mechanical damage to leaves of plants known to differ in suitability and attractiveness to a prospective agent. More VOCs were detected from damaged than from undamaged leaves for all three species tested. Discriminant analysis was able to correctly distinguish the taxonomic identity of all plants based on their VOC profiles; however, the VOCs that discriminated species among undamaged leaves were completely different from those that discriminated among damaged leaves. Thus, damaged and undamaged plants present different VOC profiles to insects, which should be considered when conducting host plant specificity experiments. An unacceptable non-target plant, Centaurea cineraria, emitted all except one of the VOCs that were emitted by its preferred host plant, Centaurea solstitialis, indicating the importance of compounds that are repellant in host plant specificity. Centaurea cyanus emitted fewer VOCs than C. solstitialis, which suggests that it lacked some VOCs important for host plant recognition.     

Traces and related chemical changes in a Late Ordovician paleosol,Glossifungites ichnofacies,southern Appalachians,USA

Traces interpreted as Skolithos sp. in a Glossifungites ichnofacies occur in the upper part of the Beans Gap Claystone paleosol, in association with a Late Ordovician marine erosional surface. Paleosol color and whole‐rock chemistry are distinctly different in the vicinity of burrows, which are enveloped by olive gray mottles, 1 to 10 cm in diameter, in which total iron (measured as Fe₂O₃) is 30% lower than in grayish red, “unaltered”; claystone.

Post‐pedogenic bioturbation increased permeability locally and permitted the introduction of marine fluids and coarser sediment into the top of the paleosol. Anaerobic microbial decay of organic matter in the burrows and surrounding claystone permitted reduction (and mobilization) of formerly oxidized iron, which then combined with marine‐derived sulfate to form pyrite, both within burrows and along oxidation‐reduction fronts in the claystone proximal to burrows. Pyrite was later converted to hematite as a result of outcrop‐related oxidation by meteoric water.

Paleosols formed in coastal marine settings are especially susceptible to early diagenetic alteration related to marine hydromorphism. Differentiating these ichnologic and diagenetic effects from true pedogenic ones is essential when interpreting paleosols in paralic sequences.     

Associations between host migration and the prevalence of a protozoan parasite in natural populations of adult monarch butterflies

1. Monarch butterflies Danaus plexippus (L.) (Lepidoptera: Nymphalidae) are susceptible to infection by the obligate protozoan parasite Ophryocystis elektroscirrha (McLaughlin and Myers) (Apicomplexa: Neogregarinida). Because monarchs form resident and migratory populations in different parts of the world, this host–parasite system provides the opportunity to examine how variation in parasite prevalence relates to host movement patterns. 2. Parasite prevalence was evaluated using 14 790 adult monarchs captured between 1968 and 1997. Comparison of three populations in North America indicated that parasite prevalence is associated negatively with host dispersal distances. A continuously breeding, nonmigratory population in southern Florida showed high prevalence (over 70% heavily infected). The western population migrates moderate distances to overwintering sites on the Pacific Coast and has intermediate prevalence (30% heavily infected). The eastern migratory population, which travels the longest distance to Mexican overwintering sites, has exhibited less than 8% infection throughout the past 30 years. 3. Variation in parasite loads within North American migratory populations was investigated to determine whether the prevalence of heavy infection and average parasite loads declined during migration or overwintering. Average parasite loads of summer‐breeding adults in western North America decreased with increasing distance from overwintering sites. This suggests that heavily infected monarchs are less likely to remigrate long distances in spring. No differences in the frequency of heavily infected adults were found among eastern or western North American monarchs throughout the overwintering period, however, suggesting that this parasite does not affect overwintering mortality. 4. Changes in the prevalence of monarchs with low parasite loads demonstrate that spore transfer occurs during migration and overwintering, possibly when adult butterflies contact each other as a result of their clustering behaviour. 5. This study of geographical and temporal variation in O. elektroscirrha among populations of D. plexippus demonstrates the potential role of seasonal migration in mediating interactions between hosts and parasites, and suggests several mechanisms through which migratory behaviour may influence parasite prevalence.     

Induction of antler growth in a congenitally polled Scottish red deer stag.

A congenitally polled red deer stag was captured from a Scottish deer forest and kept in an enclosure for observations. The animal had rudimentary antler pedicles but no antlers, and during five years of study no significant antler development occurred. Amputation of the apex of one antler pedicle in May 1974 when the stat was 12 years of age resulted in the growth of a complete antler on the operated side, and this antler was subsequently cleaned and cast in the normal way and a new antler cycle was initiated. The result illustrates that the primary abnormality in this polled stag lay not in his inability to grow antler, but in his inability to develop fully formed antler pedicles from which normal antler tissue could differentiate. Traumatizing the rudimentary pedicle had the effect of stimulating growth of antler tissue, and once this was formed the process of cleaning, casting and regrowth occurred spontaneously. The incomplete development of the antler pedicles is considered to be responsible for the absence of antlers in the majority of "hummels" in Scotland, and the etiology of the condition is discussed.     

Finite state grammars for dialects of the advertising song of the savannah sparrow (PasserculusSandwichensis)

Right-linear finite state grammars were extracted for song sequences of Savannah Sparrows (Passerculus sandwichensis) from Ontario and Nova Scotia. The Nova Scotia grammar was found to be longer than the Ontario grammar (possess more rewrite statements) and allow for the production of sequences containing consecutive trills. These differences are discussed with respect to genetic and environmental factors shaping song behaviour in the two regions. Limitations of a nonstochastic finite state grammar procedure are also addressed.     

An investigation of the surface of the cuticle and associated sensory structures of the terrestrial isopod, Porcellio scaber

The exoskeletal surface of the body of the terrestrial isopod, Porcellio scaber has been examined with the scanning electron microscope as part of a study of the structural changes associated with the transition from sea to land in the Isopoda. No sexual differences are apparent. The dorsal cuticular surface is characterized by large tubercles, minute plaques and pits, separated by amorphous areas. Apart from the eyes the only structures of apparent sensory function are relatively large setae which occur near the antero-lateral and posterolateral edges of each epimeron, and sensilla squamiformia (tricorns). Tricorns are extremely numerous on the dorsal surface and appear to be formed from the fusion of a plaque and a sensillum which arises from a pit. Much of the ventral body surface is covered with closely-set plaques, tricorns being restricted to the epimera. Along the sides of the mid-ventral sternal groove occur numerous small tubercles each surmounted by a single seta. Similar, though smaller structures are found in a single row along the outer edge of the epimera. The water capillary system of this species is formed from spines which arise from plaques around the pereopodal sockets and along the junctions between the epimera and sternites. Most of the sensilla described appear to be mechanosensory and are probably associated with the thigmokinetic and proprioceptive responses of the woodlouse.