Genome‐wide detection of CNVs associated with beak deformity in chickens using high‐density 600K SNP arrays

Beak deformity (crossed beaks) is found in several indigenous chicken breeds including Beijing‐You studied here. Birds with deformed beaks have reduced feed intake and poor production performance. Recently, copy number variation (CNV) has been examined in many species and is recognized as a source of genetic variation, especially for disease phenotypes. In this study, to unravel the genetic mechanisms underlying beak deformity, we performed genome‐wide CNV detection using Affymetrix chicken high‐density 600K data on 48 deformed‐beak and 48 normal birds using penncnv . As a result, two and eight CNV regions (CNVRs) covering 0.32 and 2.45 Mb respectively on autosomes were identified in deformed‐beak and normal birds respectively. Further RT‐qPCR studies validated nine of the 10 CNVRs. The ratios of six CNVRs were significantly different between deformed‐beak and normal birds (P < 0.01). Within these six regions, three and 21 known genes were identified in deformed‐beak and normal birds respectively. Bioinformatics analysis showed that these genes were enriched in six GO terms and one KEGG pathway. Five candidate genes in the CNVRs were further validated using RT‐qPCR. The expression of LRIG2 (leucine rich repeats and immunoglobulin like domains 2) was lower in birds with deformed beaks (P < 0.01). Therefore, the LRIG2 gene could be considered a key factor in view of its known functions and its potential roles in beak deformity. Overall, our results will be helpful for future investigations of the genomic structural variations underlying beak deformity in chickens.     

Nutrient levels in malformed and healthy tissues of mango (Mangifera indica L.)

Samples of malformed and healthy panicles of mango (Mangifera indica L.) as well as leaves and shoots bearing them were collected at different stages of development (fully swollen buds, bud inception, fully grown panicles prior to full bloom and at full bloom) over two consecutive years and were analysed for their macro- and micronutrient status. In addition, malformed and healthy seedlings were collected and analysed. Malformed panicles were found to be significantly higher in N at all the developmental stages except at bud inception. Phosphorus and K also tended to accumulate in malformed panicles at later stages of their development. In general, malformed panicles exhibited lower levels of P, K and Ca than healthy panicles. The differences in levels of Mg and S in malformed and healthy panicles were not significant. All micronutrients were in much lower concentrations in malformed panicles except for Mn which appears to accumulate in malformed panicles particularly at the early stages of development. The leaves on the shoots bearing malformed panicles also showed a tendency to accumulate N, while P, Mg and S were always higher in leaves on shoots bearing healthy panicles. The leaves on shoots bearing healthy panicles had lower levels of Fe, Cu and Mn, whereas levels of Zn and B tended to be higher in leaves on shoots bearing malformed panicles. The nutrient concentration differences between the two kinds of shoots were generally nonsignificant (P=0.05), except for K and S which were significantly lower in shoots bearing malformed panicles. The shoots bearing malformed panicles showed significantly (P=0.05) higher levels of almost all nutrients compared with shoots bearing healthy panicles. Vegetative malformation was found to be associated significantly (p=0.05) with higher amounts of all nutrients except Ca which was significantly higher in healthy seedlings. The present study, therefore, seems to point to lower Ca as one of the pre-disposing factors causing malformation in mango.A part of Ph.D. thesis of the senior author.A part of Ph.D. thesis of the senior author.     

Ecological aspects of a silicified bivalve fauna from the Silurian of Gotland

The silicified Wenlockian (Silurian) bivalve fauna from MÖllbos, Gotland, is part of a life assemblage. The vast number of shells show unusual phenomena, e.g. shell repair, pearl and tumour formation, etc. A number of shells contain epibionts and bored, round holes. Presumptive predators of the bivalve community are discussed. Size-frequency distribution of the two most abundant species possibly reflects age classes. The fauna, comprising eleven species, is dominated by deposit-feeders (90 %). They exhibit niche diversification, including at least three different feeding levels within the sediment.     

VEGF signalling enhances lesion burden in KRIT1 deficient mice

The exact molecular mechanisms underlying CCM pathogenesis remain a complicated and controversial topic. Our previous work illustrated an important VEGF signalling loop in KRIT1 depleted endothelial cells. As VEGF is a major mediator of many vascular pathologies, we asked whether the increased VEGF signalling downstream of KRIT1 depletion was involved in CCM formation. Using an inducible KRIT1 endothelial‐specific knockout mouse that models CCM, we show that VEGFR2 activation plays a role in CCM pathogenesis in mice. Inhibition of VEGFR2 using a specific inhibitor, SU5416, significantly decreased the number of lesions formed and slightly lowered the average lesion size. Notably, VEGFR2 inhibition also decreased the appearance of lesion haemorrhage as denoted by the presence of free iron in adjacent tissues. The presence of free iron correlated with increased microvessel permeability in both skeletal muscle and brain, which was completely reversed by SU5416 treatment. Finally, we show that VEGFR2 activation is a common downstream consequence of KRIT1, CCM2 and CCM3 loss of function, though the mechanism by which VEGFR2 activation occurs likely varies. Thus, our study clearly shows that VEGFR2 activation downstream of KRIT1 depletion enhances the severity of CCM formation in mice, and suggests that targeting VEGF signalling may be a potential future therapy for CCM.     

Elevated circulating microRNA-210 levels in patients with hereditary hemorrhagic telangiectasia and pulmonary arteriovenous malformations: a potential new biomarker

Pulmonary arteriovenous malformations (PAVMs), which can lead to life-threatening bleeding and other complications, have been reported to occur in 30–50% of patients with hereditary hemorrhagic telangiectasia (HHT). Circulating microRNAs (miRNAs) have emerged as new biomarkers for human diseases. This study was conducted to explore circulating miRNAs as biomarkers for the screening of HHT patients with PAVMs. MicroRNA array analysis revealed eight altered circulating miRNAs in patients with PAVMs. Real time RT-PCR showed that the levels of circulating miR-210 were significantly elevated in HHT patients with PAVMs but not changed in patients without PAVMs as compared with healthy controls. Circulating miR-210 therefore may be used as a new and sensitive biomarker for the screening of patients with HHT for clinically significant PAVMs.     

Cancer Risks in Parents Who had a Child with a Congenital Malformation

Cancer risk in parents may be related to congenital malformations (CMs) in their children if they share genetic susceptibility or environmental exposure that may be teratogenic and carcinogenic. We conducted a population‐based cohort study based on Danish register data. We identified 795,607 mothers and 781,424 fathers who had all their children between 1977 and 2007 in Denmark. Information on CM was obtained from the Danish Hospital Registry and information on cancer was obtained from the Danish Cancer Registry. Parents were followed from the birth of their first child until the diagnosis of cancer, death, emigration, or December 31, 2007. We used Cox regression models to estimate hazard ratios (HRs) for cancer including cancer in specific organs in mothers and fathers. Overall, 75,701 (9.5%) mothers and 72,724 (9.3%) fathers had at least one child diagnosed with CMs within the first year of life. Neither mothers (HR = 1.04; 95% CI: 0.99–1.04) nor fathers (HR = 1.03; 95% CI: 0.98–1.09) who had a child with a CM had a higher overall risk of cancer. Mothers (HR = 0.76, 95% CI: 0.58–1.00) or fathers (HR = 0.89, 95% CI: 0.66–1.19) who had a child with a chromosomal malformation had a lower overall cancer risk. The findings also showed a higher risk for some specific types of cancer in parents who had children with a CM in the specific system. Some, or perhaps all, of these findings may be due to chance caused by multiple comparisons. We present all results on paper or online to provide clues for further research and to avoid publication bias.     

First evidence of ethylene production by Fusarium mangiferae associated with mango malformation

Malformation is arguably the most crucial disease of mango (Mangifera indica L.) at present. It is receiving great attention not only because of its widespread and destructive nature but also because of its etiology and control is not absolutely understood. Recently, Fusarium mangiferae is found to be associated with mango malformation disease. There are indications that stress ethylene production could be involved in the disease. Here we have shown the first direct evidence of production of ethylene in pure culture of F. mangiferae obtained from mango. The study also revealed that all the isolates dissected from mango acquire morphological features of F. mangiferae showing most similarity to the features of species with accepted standard features. The isolates of F. mangiferae from mango were observed to produce ethylene in significant amounts, ranging from 9.28–13.66 n mol/g dry wt/day. The findings presented here suggest that F. mangiferae could contribute to the malformation of mango by producing ethylene and probably stimulating stress ethylene production in malformed tissue of mango. Ethylene might be produced through 2-oxoglutarate-dependent oxygenase-type ethylene-forming-enzyme (EFE) pathway in Fusarium sp, which needs to be investigated.     

Growth and yield of groundnut (Arachis hypogaea L.) plants in soil inoculated with Aspergillus niger Van Tieghem

Aspergillus niger, a soil-borne fungus is a causative agent of hypocotyl malformations in infected groundnut (Arachis hypogaea L.) plants, but its effect on yield is unknown. This study sought to determine its effect on growth and yield. Seeds of Chinese and JL45 varieties were sown in soil inoculated with A. niger. Fresh and dry weights of the shoots and roots were taken at 10-day intervals. Nodule count was done at 30 days after emergence and subsequently at 10-day intervals. Pods of 20 plants each from inoculated and uninoculated soils were harvested. Growth was suppressed in plants grown on A. niger inoculated soil. Eight-day old plants grown in inoculated soil developed curvatures on their hypocotyls. Nodulation was suppressed (p < 0.05) in plants grown in inoculated soil. Although growth was suppressed in plants grown on inoculated soil, yield of both varieties of groundnut was not affected.