Replicated high-density genetic maps of two great tit populations reveal fine-scale genomic departures from sex-equal recombination rates

Linking variation in quantitative traits to variation in the genome is an important, butchallenging task in the study of life-history evolution. Linkage maps provide a valuabletool for the unravelling of such trait−gene associations. Moreover, they giveinsight into recombination landscapes and between-species karyotype evolution. Here weused genotype data, generated from a 10k single-nucleotide polymorphism (SNP) chip, ofover 2000 individuals to produce high-density linkage maps of the great tit (Parusmajor), a passerine bird that serves as a model species for ecological andevolutionary questions. We created independent maps from two distinct populations: acaptive F2-cross from The Netherlands (NL) and a wild population from the United Kingdom(UK). The two maps contained 6554 SNPs in 32 linkage groups, spanning 2010 cM and1917 cM for the NL and UK populations, respectively, and were similar in size andmarker order. Subtle levels of heterochiasmy within and between chromosomes wereremarkably consistent between the populations, suggesting that the local departures fromsex-equal recombination rates have evolved. This key and surprising result would have beenimpossible to detect if only one population was mapped. A comparison with zebra finchTaeniopygia guttata, chicken Gallus gallus and the green anole lizardAnolis carolinensis genomes provided further insight into the evolution ofavian karyotypes.     

A histological and immunohistochemical study of the effects of N-acetyl cysteine on retinopathy of prematurity by modifying insulin-like growth factor-1

Retinopathy of prematurity (ROP) is a vasoproliferative disorder that occurs in premature infants and may lead to permanent visual impairment. We investigated both the possible protective role of N-acetyl cysteine (NAC) for preventing ROP and the role of IGF-1 in the disorder. Forty-five newborn rats were divided into three groups. Group 1 was raised in room air as controls. Group 2 was exposed to 60% oxygen for 14 days after birth, then transferred to room air. Group 3 was exposed to the same conditions as group 2, but received intraperitoneal injections of NAC on postnatal days 7–17. After 35 days, both eyes of all rats were processed for histology. Some sections were stained with hematoxylin and eosin to assess structural changes and other sections were immunostained to determine the location of IGF-1. Frozen sections also were prepared and stained for adenosine triphosphatase to detect retinal blood vessels. Compared to the controls, more blood vessels, many of which were abnormal, and increased IGF-1 expression were observed in group 2. In group 3, abnormal blood vessels and IGF-1 expression were less evident. NAC appeared to be an effective vascular-protective agent for ROP by decreasing IGF-1 expression.     

AMIGO is an auxiliary subunit of the Kv2.1 potassium channel

Kv2.1 is a potassium channel α-subunit abundantly expressed throughout the brain. It is a main component of delayed rectifier current (I(K)) in several neuronal types and a regulator of excitability during high-frequency firing. Here we identify AMIGO (amphoterin-induced gene and ORF), a neuronal adhesion protein with leucine-rich repeat and immunoglobin domains, as an integral part of the Kv2.1 channel complex. AMIGO shows extensive spatial and temporal colocalization and association with Kv2.1 in the mouse brain. The colocalization of AMIGO and Kv2.1 is retained even during stimulus-induced changes in Kv2.1 localization. AMIGO increases Kv2.1 conductance in a voltage-dependent manner in HEK cells. Accordingly, inhibition of endogenous AMIGO suppresses neuronal I(K) at negative membrane voltages. In conclusion, our data indicate AMIGO as a function-modulating auxiliary subunit for Kv2.1 and thus provide new insights into regulation of neuronal excitability.     

Automatically extracting functionally equivalent proteins from SwissProt

Background  

There is a frequent need to obtain sets of functionally equivalent homologous proteins (FEPs) from different species. While it is usually the case that orthology implies functional equivalence, this is not always true; therefore datasets of orthologous proteins are not appropriate. The information relevant to extracting FEPs is contained in databanks such as UniProtKB/Swiss-Prot and a manual analysis of these data allow FEPs to be extracted on a one-off basis. However there has been no resource allowing the easy, automatic extraction of groups of FEPs – for example, all instances of protein C.     

Naturally occurring human autoantibodies recognize a fetal brain antigen identified as microtubulus associated protein 1B

We have recently reported naturally occurring autoantibodies against a large fetal brain antigen (FBA). Now we describe the process of purification and identification of this particular FBA. The brains of newborn rabbits were solubilized and purified with preparative gel electrophoresis. The protein fractions were concentrated and desalted and the fractions were tested by a known positive serum. On membrane digestion of the FBA-band gave a twelve amino acid sequence that resulted in best identity score for mouse, rat and human microtubule-associated protein (MAP) 1B: a member of the microtubule-associated protein family. Monoclonal anti-MAP1B recognized a band in immunoblots of the brain homogenate and of the partially purified fractions with the same electrophoretic mobility as that recognized by a known anti-FBA positive serum. When adult rabbit brain was used as an antigen, the anti-MAP1B failed to recognize any bands on immunoblots. MAP lB has not been previously known as an autoantigen, even though many structural proteins of the neuronal cytoskeleton are known to be targets of naturally occurring autoantibodies. MAP 1B is a functionally important regulatory protein in the developing brain; thus autoantibodies against MAP1B may affect the normal development.     

Improved genome assembly and evidence-based global gene model set for the chordate Ciona intestinalis: new insight into intron and operon populations

Background

The draft genome sequence of the ascidian Ciona intestinalis, along with associated gene models, has been a valuable research resource. However, recently accumulated expressed sequence tag (EST)/cDNA data have revealed numerous inconsistencies with the gene models due in part to intrinsic limitations in gene prediction programs and in part to the fragmented nature of the assembly.

Results

We have prepared a less-fragmented assembly on the basis of scaffold-joining guided by paired-end EST and bacterial artificial chromosome (BAC) sequences, and BAC chromosomal in situ hybridization data. The new assembly (115.2 Mb) is similar in length to the initial assembly (116.7 Mb) but contains 1,272 (approximately 50%) fewer scaffolds. The largest scaffold in the new assembly incorporates 95 initial-assembly scaffolds. In conjunction with the new assembly, we have prepared a greatly improved global gene model set strictly correlated with the extensive currently available EST data. The total gene number (15,254) is similar to that of the initial set (15,582), but the new set includes 3,330 models at genomic sites where none were present in the initial set, and 1,779 models that represent fusions of multiple previously incomplete models. In approximately half, 5'-ends were precisely mapped using 5'-full-length ESTs, an important refinement even in otherwise unchanged models.

Conclusion

Using these new resources, we identify a population of non-canonical (non-GT-AG) introns and also find that approximately 20% of Ciona genes reside in operons and that operons contain a high proportion of single-exon genes. Thus, the present dataset provides an opportunity to analyze the Ciona genome much more precisely than ever.     

Annual and seasonal variation of sap flow and conductance of pine trees grown in elevated carbon dioxide and temperature

Measurements of sap flow, crown structure, and microclimate were used to estimate the transpiration of individual 30-year-old Pinus sylvestris L. trees grown in elevated temperature and CO2. The trees were enclosed in closed-top chambers and exposed either to current ambient conditions (CON), or elevated CO2 (+350 micromol mol(-1); EC), or elevated temperature (+2 to +6 degrees C; ET) or a combination of EC and ET (ECT) since 1996, and the measurements were made from 1999 to 2001. EC significantly increased annual sap flow per tree (Ft.m) by 14% in 1999, but reduced it by 13% in 2000 and 16% in 2001. The CO2-induced increase in Ft.m in 1999 was due to a large increase in foliage area of trees, which more than compensated for a small decrease in crown conductance (Gc). The CO2-induced decreases in Ft.m in 2000 and 2001 resulted from a pronounced decline in Gc, which was much greater than the increase in foliage area. The CO2-induced increase in sensitivity of Gc at high vapour pressure deficit (VPD) did not alter the general response of sap flow to CO2 enrichment, but it did affect the diurnal courses of sap flow on some days during the main growing season (days 150-240). ET increased Ft.m by 53%, 45%, and 57% in 1999, 2000, and 2001, respectively, attributable to the combined effects of greater foliage area and maximum crown conductance, lower stomatal sensitivity to high VPD, and higher transpiration demand relative to the control treatments. There was no significant interaction between CO2 and temperature on sap flow, because ECT entailed approximately similar patterns of sap flow to ET, suggesting that the temperature played a dominate role in the case of ECT under boreal climate conditions.     

Design of reference populations for genomic selection in crossbreeding programs

Background

In crossbreeding programs, genomic selection offers the opportunity to make efficient use of information on crossbred (CB) individuals in the selection of purebred (PB) candidates. In such programs, reference populations often contain genotyped PB animals, although the breeding objective is usually more focused on CB performance. The question is what would be the benefit of including a larger proportion of CB individuals in the reference population.

Methods

In a deterministic simulation study, we evaluated the benefit of including various proportions of CB animals in a reference population for genomic selection of PB animals in a crossbreeding program. We used a pig breeding scheme with selection for a moderately heritable trait and a size of 6000 for the reference population.

Results

Applying genomic selection to improve the performance of CB individuals, with a genetic correlation between PB and CB performance (r_PC) of 0.7, selection accuracy of PB candidates increased from 0.49 to 0.52 if the reference population consisted of PB individuals, it increased to 0.55 if the reference population consisted of the same number of CB individuals, and to 0.60 if the size of the CB reference population was twice that of the reference population for each PB line. The advantage of using CB rather than PB individuals increased linearly with the proportion of CB individuals in the reference population. This advantage disappeared quickly if r_PC was higher or if the breeding objective put some emphasis on PB performance. The benefit of adding CB individuals to an existing PB reference population was limited for high r_PC.

Conclusions

Using CB rather than PB individuals in a reference population for genomic selection can provide substantial advantages, but only when correlations between PB and CB performances are not high and PB performance is not part of the breeding objective.     

Meningococcal disease in Scandinavia.

Scandinavia (Denmark, Finland, Iceland, Norway, and Sweden) comprises with mutual borders and 22.3 million inhabitants an area where the socioeconomic and cultural conditions are similar. Epidemic diseases, such as meningococcal infection, might therefore be expected to be uniformly distributed. An epidemiological study in the 10-year period 1970-9 shows, however, remarkable differences in the incidence, age, and serogroup and type distribution, as well as in the general dynamics of the disease. Three epidemics, two caused by different serotypes of group B (Norway and Iceland) and one by group A (Finland) occurred within the observation period. The annual overall incidence was generally around 3/100 000 but increased from fivefold (Finland) to eightfold (northern Norway) during epidemics. The epidemic strains caused infection in over 3000 patients and the loss of at least 250 lives. The overall case fatality rate was 8.6% (range 4.1-13.7%). Men were more susceptible and had a worse prognosis than women of the same age group. The group A epidemic in Finland was influenced by a large vaccination campaign, but this possibility was not feasible in the two other epidemics.