Landscape context affects the success of habitat restoration: large‐scale colonization patterns of saproxylic and fire‐associated species in boreal forests

Aim Restoration of habitats may be used as a conservation tool when ecosystems have lost their natural structure, dynamics or functioning over large areas. Controlled and planned use of fire could be an effective way to restore habitats of many threatened species in boreal forests where fire suppression has been effective. We asked whether the large‐scale landscape context affects the occurrence of rare and threatened species in forest habitats that have been burned to restore their fire‐related structures. Location Boreal forests in southern Finland. Methods We designed a large‐scale field experiment that included nine Pinus sylvestris forests (5–10 ha each) in southern Finland. Sites were located in two regions: (1) in eastern region with shorter management history and (2) in western region where intensive forestry has continued longer. We evaluated whether restoration of dead/burned wood is beneficial for rare and conservation‐dependent species and measured the recovery of pyrophilous and red‐listed insects (beetles and flatbugs) in burned forests, using standardized sampling effort. Altogether, 956 individuals of 29 red‐listed and pyrophilous species were sampled. Results Rare species colonized areas quickly, but there was a clear difference in species richness between the regions. The eastern forests harboured higher species richness after restoration. In these sites, the average species richness was 13.7 species per site, whereas in western forests it was 5.0 species per site. Similar pattern was also observed in subgroups: the corresponding numbers for pyrophilous species were 9.7 vs. 3.8, for red‐listed 8.7 vs. 2.3 and for red‐listed pyrophiles 4.7 vs. 1.2. Main conclusions Introducing fire back to boreal forests can aid in the recovery of rare species, but the landscape context considerably affects the success of restoring species. If restored habitats are located in landscapes that have lost their natural properties long ago, the success of restoration seems to be more challenging than in landscapes where habitats have been modified more recently.     

Management of a congenital tracheoesophageal fistula in a young Spanish water dog

Background

Tracheoesophageal fistula (TEF) in dogs is a rare disease with only few reports in the literature. This report aims to contribute to the current literature on suitable diagnostic methods for TEF and to provide follow-up information after successful surgical treatment.

Case presentation

A seven-month-old intact female Spanish Water Dog was presented for further investigation of recurrent respiratory symptom. Bronchoscopy revealed a small hole-like defect in the tracheal wall at the bifurcation. The finding of the contrast material swallow study under fluoroscopy was indicative of a TEF. To further evaluate the connection between the trachea and esophagus, a computed tomography scan was performed. The TEF was surgically approached by thoracotomy through the right lateral sixth intercostal space. The fistula was identified, double ligated and divided. Histopathology confirmed the process to originate from the esophagus and to be patent. The dog was re-examined two weeks and ten months after surgery, with no evidence of recurring clinical signs.

Conclusions

Contrast material swallow study using fluoroscopy was the most reliable diagnostic method. Bronchoscopy may allow the fistula to be visualized, but due to a small fistular opening it can lead to a false negative result. Surgical correction by ligation and dividing of the fistula suggests a good prognosis for early diagnosed and operated TEF.     

Consumption of crucian carp (Carassius carassius L., 1758) by restocked pike (Esox lucius L., 1758) in a lake with frequent winter hypoxia

To assess the effects of stocked pike (Esox lucius L.) on crucian carp (Carassius carassius L.) biomasses, the annual consumption of pike was estimated and compared with removal fishery catches. The studied lake, Lake Savijärvi, is a small (40 ha), shallow and eutrophicated lake in southern Finland with frequent algal blooms during summers and fish kills during winters. Until the 1980s, the fish fauna consisted of pike, perch (Perca fluviatilis L.), roach [Rutilus rutilus (L.)], crucian carp, and tench (Tinca tinca L.). Since 2003, when crucian carp were abundant in the extreme and with only a few roach and tench individuals, the lake has been biomanipulated by removal seining. To enhance the effects of seining, piscivorous pike were restocked in the spring of 2008. During the 3‐year study, the catch of crucian carp decreased from 243 to 136 kg while the catch of pike increased from 0.1 to 5.7 kg per seining hectare due to their spawning in the lake as of 2009. The total crucian carp consumption by captured pike was 588 kg during the 2008–2010 study period. When applying the number of pike estimated with the mark‐recapture method, consumption estimate increased to 917 kg, or 22.9 kg per lake hectare in 2010. Thus, pike consumption of crucian carp was about 17% of the removal catch in 2010.     

I-BAR domain proteins: linking actin and plasma membrane dynamics

Dynamic plasma membrane rearrangements occur during many cellular processes including endocytosis, morphogenesis, and migration. Actin polymerization together with proteins that directly deform membranes, such as the BAR superfamily proteins, is essential for generation of membrane invaginations during endocytosis. Importantly, recent studies revealed that direct membrane deformation contributes also to the formation of plasma membrane protrusions such as filopodia and lamellipodia. Inverse BAR (I-BAR) domain proteins bind phosphoinositide-rich membrane with high affinity and generate negative membrane curvature to induce plasma membrane protrusions. I-BAR domain proteins, such as IRSp53, MIM, ABBA, and IRTKS also harbor many protein-protein interaction modules that link them to actin dynamics. Thus, I-BAR domain proteins may connect direct membrane deformation to actin polymerization in cell morphogenesis and migration.     

Genome-wide association study in Dachshund: identification of a major locus affecting intervertebral disc calcification

Intervertebral disc calcification and herniation commonly affects Dachshund where the predisposition is caused by an early onset degenerative process resulting in disc calcification. A continuous spectrum of disc degeneration is seen within and among dog breeds, suggesting a multifactorial etiology. The number of calcified discs at 2 years of age determined by a radiographic evaluation is a good indicator of the severity of disc degeneration and thus serves as a measure for the risk of developing intervertebral disc herniation. The aim of the study was to identify genetic variants associated with intervertebral disc calcification in Dachshund through a genome-wide association (GWA) study. Based on thorough radiographic examinations, 48 cases with ≥ 6 disc calcifications or surgically treated for disc herniation and 46 controls with 0-1 disc calcifications were identified. GWA using the Illumina CanineHD BeadChip identified a locus on chromosome 12 from 36.8 to 38.6 Mb with 36 markers reaching genome-wide significance (P(genome) = 0.00001-0.026). This study suggests that a major locus on chromosome 12 harbors genetic variations affecting the development of intervertebral disc calcification in Dachshund.     

Seasonal growth and year class strength variations of perch near the northern limits of its distribution range

The effects of temperature on seasonal growth and year class strength of perch Perca fluviatilis were studied in a subarctic lake in northern Finland. Two growth models, power and von Bertalanffy, were used to estimate the growth of perch during the growing season from 1988 to 1990. Air temperature, estimated as degree-days >10° C, significantly improved both model fits. The sum of degree-days also correlated positively with the year class strength of perch. The strongest year class was born in a warm summer 1988, while the 1987 year class was totally absent, which was due to the very cold summer of that year. The backcalculation of lengths of fish caught in 1990 showed that the overall growth of perch was slow in the cold summer of 1987 and relatively rapid in the warm summer of 1988. The subsequent growth of the abundant 1988 year class was rapid, even though the summers of 1991 and 1992 were relatively cool. The improved growth could be due to the lack of competition with previous weak year classes of 1986 and 1987. This observation suggests that density-dependent factors might affect growth even near the northern limits of the distribution range of perch.     

Missing-in-metastasis and IRSp53 deform PI(4,5)P2-rich membranes by an inverse BAR domain-like mechanism

The actin cytoskeleton plays a fundamental role in various motile and morphogenetic processes involving membrane dynamics. We show that actin-binding proteins MIM (missing-in-metastasis) and IRSp53 directly bind PI(4,5)P(2)-rich membranes and deform them into tubular structures. This activity resides in the N-terminal IRSp53/MIM domain (IMD) of these proteins, which is structurally related to membrane-tubulating BAR (Bin/amphiphysin/Rvs) domains. We found that because of a difference in the geometry of the PI(4,5)P(2)-binding site, IMDs induce a membrane curvature opposite that of BAR domains and deform membranes by binding to the interior of the tubule. This explains why IMD proteins induce plasma membrane protrusions rather than invaginations. We also provide evidence that the membrane-deforming activity of IMDs, instead of the previously proposed F-actin-bundling or GTPase-binding activities, is critical for the induction of the filopodia/microspikes in cultured mammalian cells. Together, these data reveal that interplay between actin dynamics and a novel membrane-deformation activity promotes cell motility and morphogenesis.     

Allelic mapping bias in RNA-sequencing is not a major confounder in eQTL studies

Background

RNA sequencing (RNA-seq) is the current gold-standard method to quantify gene expression for expression quantitative trait locus (eQTL) studies. However, a potential caveat in these studies is that RNA-seq reads carrying the non-reference allele of variant loci can have lower probability to map correctly to the reference genome, which could bias gene quantifications and cause false positive eQTL associations. In this study, we analyze the effect of this allelic mapping bias in eQTL discovery.

Results

We simulate RNA-seq read mapping over 9.5 M common SNPs and indels, with 15.6% of variants showing biased mapping rate for reference versus non-reference reads. However, removing potentially biased RNA-seq reads from an eQTL dataset of 185 individuals has a very small effect on gene and exon quantifications and eQTL discovery. We detect only a handful of likely false positive eQTLs, and overall eQTL SNPs show no significant enrichment for high mapping bias.

Conclusion

Our results suggest that RNA-seq quantifications are generally robust against allelic mapping bias, and that this does not have a severe effect on eQTL discovery. Nevertheless, we provide our catalog of putatively biased loci to allow better controlling for mapping bias to obtain more accurate results in future RNA-seq studies.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0467-2) contains supplementary material, which is available to authorized users.     

Direct interaction of actin filaments with F‐BAR protein pacsin2

Two mechanisms have emerged as major regulators of membrane shape: BAR domain‐containing proteins, which induce invaginations and protrusions, and nuclear promoting factors, which cause generation of branched actin filaments that exert mechanical forces on membranes. While a large body of information exists on interactions of BAR proteins with membranes and regulatory proteins of the cytoskeleton, little is known about connections between these two processes. Here, we show that the F‐BAR domain protein pacsin2 is able to associate with actin filaments using the same concave surface employed to bind to membranes, while some other tested N‐BAR and F‐BAR proteins (endophilin, CIP4 and FCHO2) do not associate with actin. This finding reveals a new level of complexity in membrane remodeling processes.