Joint modeling of linkage and association: identifying SNPs responsible for a linkage signal

Once genetic linkage has been identified for a complex disease, the next step is often association analysis, in which single-nucleotide polymorphisms (SNPs) within the linkage region are genotyped and tested for association with the disease. If a SNP shows evidence of association, it is useful to know whether the linkage result can be explained, in part or in full, by the candidate SNP. We propose a novel approach that quantifies the degree of linkage disequilibrium (LD) between the candidate SNP and the putative disease locus through joint modeling of linkage and association. We describe a simple likelihood of the marker data conditional on the trait data for a sample of affected sib pairs, with disease penetrances and disease-SNP haplotype frequencies as parameters. We estimate model parameters by maximum likelihood and propose two likelihood-ratio tests to characterize the relationship of the candidate SNP and the disease locus. The first test assesses whether the candidate SNP and the disease locus are in linkage equilibrium so that the SNP plays no causal role in the linkage signal. The second test assesses whether the candidate SNP and the disease locus are in complete LD so that the SNP or a marker in complete LD with it may account fully for the linkage signal. Our method also yields a genetic model that includes parameter estimates for disease-SNP haplotype frequencies and the degree of disease-SNP LD. Our method provides a new tool for detecting linkage and association and can be extended to study designs that include unaffected family members.     

A tribute to Shinya Inoue and innovation in light microscopy

The 2003 International Prize for Biology was awarded to Shinya Inoue for his pioneering work in visualizing dynamic processes within living cells using the light microscope. He and his scientific descendants are now pushing light microscopy even further by developing new techniques such as imaging single molecules, visualizing processes in living animals, and correlating results from light and electron microscopy.     

A standardized kinesin nomenclature

In recent years the kinesin superfamily has become so large that several different naming schemes have emerged, leading to confusion and miscommunication. Here, we set forth a standardized kinesin nomenclature based on 14 family designations. The scheme unifies all previous phylogenies and nomenclature proposals, while allowing individual sequence names to remain the same, and for expansion to occur as new sequences are discovered.     

A whole genome RNAi screen of Drosophila S2 cell spreading performed using automated computational image analysis

Recent technological advances in microscopy have enabled cell-based whole genome screens, but the analysis of the vast amount of image data generated by such screens usually proves to be rate limiting. In this study, we performed a whole genome RNA interference (RNAi) screen to uncover genes that affect spreading of Drosophila melanogaster S2 cells using several computational methods for analyzing the image data in an automated manner. Expected genes in the Scar-Arp2/3 actin nucleation pathway were identified as well as casein kinase I, which had a similar morphological RNAi signature. A distinct nonspreading morphological phenotype was identified for genes involved in membrane secretion or synthesis. In this group, we identified a new secretory peptide and investigated the functions of two poorly characterized endoplasmic reticulum proteins that have roles in secretion. Thus, this genome-wide screen succeeded in identifying known and unexpected proteins that are important for cell spreading, and the computational tools developed in this study should prove useful for other types of automated whole genome screens.     

Making more microtubules by severing: a common theme of noncentrosomal microtubule arrays?

Two related enzymes, katanin and spastin, use the energy from ATP hydrolysis to sever microtubules. Two new studies (one in this issue; see McNally et al., p. 881) show that microtubule severing by katanin provides a means for increasing microtubule density in meiotic spindles. Interestingly, loss of spastin leads to a sparser microtubule array in axons and synaptic boutons. Together, these studies hint at a wider role for microtubule-severing enzymes in the formation and organization of noncentrosomal microtubule arrays by generating new seeds for microtubule growth.     

Across‐taxa incongruence in patterns of collecting bias

If biological collections tend to be taken near accessible areas, and the number of such areas is limited, then we should expect a similar spatial distribution of collecting effort across taxa. Alternatively, if researchers working on a given taxon pick collection localities based on idiosyncratic criteria, then there should be no spatial similarity in collecting effort. This study compares the spatial distribution of collecting effort for plants and birds in Amazonia. Collection localities were transformed into a Thiessen network where polygon size works as a surrogate for collecting effort. A correlation between botanical and ornithological datasets, with an adjustment for spatial autocorrelation, showed little congruence in the spatial distribution of collecting effort between the two taxa. This incongruence of the distribution of collection effort among taxa suggests that the identification of priority areas for research, and correction for Wallacean and Linnean shortfalls based on taxon‐specific studies, should not be generalized.     

Antinociceptive and anti-inflammatory effects of electroacupuncture on experimental arthritis of the rat temporomandibular joint

This study investigated the antinociceptive and anti-inflammatory effects of electroacupuncture (EA) on zymosan-induced acute arthritis of the rat temporomandibular joint (TMJ). Male Wistar rats were injected with saline or zymosan (control group; 2?mg) into the left TMJ. Low frequency EA (10?Hz, 30?min) was performed at acupoints (LI4, LI11, ST36, ST44) or sham points 2?h after or 1?h before zymosan administration. Mechanical hypernociception was accessed by the electronic Von Frey method after zymosan administration. Rats were sacrificed 6?h after zymosan administration and the joint was removed for histopathological analysis, myeloperoxidase activity assessment, vascular permeability observations, and immunohistochemical verification of inflammatory mediators. The results showed that EA inhibited zymosan-induced hypernociception, compared with the control group and with the sham group (p?< 0.05). The results showed that EA inhibited inflammatory parameters such as neutrophil migration, vascular permeability, and tumour necrosis factor α (TNF-α), cyclooxygenase-2 (COX-2), and inducible nitric oxide synthase (iNOS) expression in the TMJ compared with the sham group (p < 0.05). Histopathological analysis showed that EA significantly inhibited edema and periarticular infiltration (p?< 0.05) compared with the control and sham groups. EA at acupoints produced antinociceptive and anti-inflammatory effects on zymosan-induced arthritis in the rat TMJ.     

Biochemical aspects of bean resistance to anthracnose mediated by silicon

This study investigated the effect of silicon (Si) on resistance of bean plants (cv. ‘Peróla’) to anthracnose, caused by Colletotrichum lindemuthianum, grown in a nutrient solution containing 0 (?Si) or 2 mmol Si L^?1 (+Si). The concentration of Si in leaf tissue and the incubation period increased by 55.2% and 14.3%, respectively, in +Si plants in relation to ?Si plants. The area under anthracnose progress curve and the severity estimated by the software QUANT significantly decreased by 32.9% and 27%, respectively, for +Si plants. Si did not affect the concentration of total soluble phenolics. Chitinases activity was higher in the advanced stages of infection by C. lindemuthianum for leaves of ?Si plants. β‐1,3‐Glucanase activity increased after C. lindemuthianum infection, but it was not enhanced by Si. Peroxidase and polyphenoloxidase activities had no apparent effect on the resistance of bean plants to anthracnose, regardless of the presence of Si. The increase in lignin concentration as well as on the phenylalanine ammonia‐lyase and lipoxygenase activities were important for the resistance of +Si plants against anthracnose. The results of this study suggest that Si may increase resistance to anthracnose in bean plants by enhancing certain biochemical mechanisms of defence as opposed to just acting as a physical barrier to penetration by C. lindemuthianum.     

Pathways of Ca²⁺ entry and cytoskeletal damage following eccentric contractions in mouse skeletal muscle

Muscles that are stretched during contraction (eccentric contractions) show deficits in force production and a variety of structural changes, including loss of antibody staining of cytoskeletal proteins. Extracellular Ca(2+) entry and activation of calpains have been proposed as mechanisms involved in these changes. The present study used isolated mouse extensor digitorum longus (EDL) muscles subjected to 10 eccentric contractions and monitored force production, immunostaining of cytoskeletal proteins, and resting stiffness. Possible pathways for Ca(2+) entry were tested with streptomycin (200 μM), a blocker of stretch-activated channels, and with muscles from mice deficient in the transient receptor potential canonical 1 gene (TRPC1 KO), a candidate gene for stretch-activated channels. At 30 min after the eccentric contractions, the isometric force was decreased to 75 ± 3% of initial control and this force loss was reduced by streptomycin but not in the TRPC1 KO. Desmin, titin, and dystrophin all showed patchy loss of immunostaining 30 min after the eccentric contractions, which was substantially reduced by streptomycin and in the TRPC1 KO muscles. Muscles showed a reduction of resting stiffness following eccentric contractions, and this reduction was eliminated by streptomycin and absent in the TRPC1 KO muscles. Calpain activation was determined by the appearance of a lower molecular weight autolysis product and μ-calpain was activated at 30 min, whereas the muscle-specific calpain-3 was not. To test whether the loss of stiffness was caused by titin cleavage, protein gels were used but no significant titin cleavage was detected. These results suggest that Ca(2+) entry following eccentric contractions is through a stretch-activated channel that is blocked by streptomycin and encoded or modulated by TRPC1.     

Three new species,four new records and an updated checklist of Habenaria (Orchidaceae) from Rio Grande do Sul,Brazil

Three new species of Habenaria (Orchidaceae) section Nudae from Rio Grande do Sul, southern Brazil, are described and illustrated: Habenaria australis, H. kleinii and H. sobraliana. These are the first records of H. sect. Nudae for the state. Based on the examination of living and dried specimens, a total of 33 species and 400 collections of Habenaria were recorded for Rio Grande do Sul. Based on this survey, an updated checklist of the genus Habenaria for Rio Grande do Sul has been compiled. Four species are known only from this state, while seven other species are restricted to southern Brazil, Argentina and Uruguay. Habenaria hieronymi, previously known only from Argentina, is recorded for the first time from Brazil, and H. brachyphyton, H. ekmaniana and H. melanopoda are new records for Rio Grande do Sul.