The effect of level of straw bale provision on the behaviour and leg health of commercial broiler chickens

This study aimed to assess the effect of the number of straw bales (SBs) provided on the behaviour and leg health of commercial broiler chickens. Houses containing ~23 000 broiler chickens were assigned to one of two treatments: (1) access to 30 SBs per house, ‘30SB’ or (2) access to 45 SB per house, ‘45SB’. This equated to bale densities of 1 bale/44 m² and 1 bale/29 m² of floor space within houses, respectively. Treatments were applied in one of two houses on a commercial farm, and were replicated over six production cycles. Both houses had windows and were also artificially lit. Behaviour was observed in weeks 3 to5 of the cycle. This involved observations of general behaviour and activity, gait scores (0: perfect to 5: unable to walk) and latency to lie (measured in seconds from when a bird had been encouraged to stand). Production performance and environmental parameters were also measured. SB density had no significant effect on activity levels (P>0.05) or walking ability (P>0.05). However, the average latency to lie was greater in 30SB birds compared with 45SB birds (P<0.05). The incidence of hock burn and podo dermatitis, average BW at slaughter and levels of mortality and culling were unaffected by SB density (P>0.05). The results from this study suggest that increasing SB levels from 1 bale/44 m² to 1 bale/29 m² floor space does not lead to significant improvements in the welfare of commercial broiler chickens in windowed houses.     

An optimised version of the secretome protein enrichment with click sugars (SPECS) method leads to enhanced coverage of the secretome

The secretome, the entirety of all soluble proteins either being secreted or proteolytically released by a cell, plays a key role in inter‐cellular communication of multi‐cellular organisms. Pathological alterations contribute to diseases such as hypertension, cancer, autoimmune disorders or neurodegenerative diseases. Hence, studying disease‐related perturbations of the secretome and the secretome itself covers an important aspect of cellular physiology. We recently developed the secretome protein enrichment with click sugars (SPECS) method that enables the analysis of secretomes of in vitro cell cultures even in the presence of FCS with MS. So far, SPECS facilitated the identification of protease substrates of BACE1, SPPL3 and ADAM10. Though, the SPECS method has already enabled deep insights into secretome biology, we aimed to improve the SPECS protocol to obtain even more information from MS‐based secretome analysis and reduce the amount of input material. Here, we optimised the reaction buffer, the pH and replaced Dibenzocyclooctyne (DBCO) PEG12‐biotin with the more water‐soluble variant DBCO‐sulpho‐biotin to finally provide an optimised protocol of the recently published SPECS protocol. Overall, the number of quantified glycoproteins and their average sequence coverage was increased by 1.6‐ and 2.4‐fold, respectively. Thus, the opzimised SPECS protocol allows reducing the input material by half without losing information. These improvements make the SPECS method more sensitive and more universal applicable to cell types with limited availability.     

Wide‐scale comparative analysis of longevity genes and interventions

Hundreds of genes, when manipulated, affect the lifespan of model organisms (yeast, worm, fruit fly, and mouse) and thus can be defined as longevity‐associated genes (LAGs). A major challenge is to determine whether these LAGs are model‐specific or may play a universal role as longevity regulators across diverse taxa. A wide‐scale comparative analysis of the 1805 known LAGs across 205 species revealed that (i) LAG orthologs are substantially overrepresented, from bacteria to mammals, compared to the entire genomes or interactomes, and this was especially noted for essential LAGs; (ii) the effects on lifespan, when manipulating orthologous LAGs in different model organisms, were mostly concordant, despite a high evolutionary distance between them; (iii) LAGs that have orthologs across a high number of phyla were enriched in translational processes, energy metabolism, and DNA repair genes; (iv) LAGs that have no orthologs out of the taxa in which they were discovered were enriched in autophagy (Ascomycota/Fungi), G proteins (Nematodes), and neuroactive ligand–receptor interactions (Chordata). The results also suggest that antagonistic pleiotropy might be a conserved principle of aging and highlight the importance of overexpression studies in the search for longevity regulators.     

Differential DNA methylation and PM2.5 species in a 450K epigenome-wide association study

Although there is growing evidence that exposure to ambient particulate matter is associated with global DNA methylation and gene-specific methylation, little is known regarding epigenome-wide changes in DNA methylation in relation to particles and, especially, particle components. Using the Illumina Infinium HumanMethylation450 BeadChip, we examined the relationship between one-year moving averages of PM_2.5 species (Al, Ca, Cu, Fe, K, Na, Ni, S, Si, V, and Zn) and DNA methylation at 484,613 CpG probes in a longitudinal cohort that included 646 subjects. Bonferroni correction was applied to adjust for multiple comparisons. Bioinformatics analysis of the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment was also performed. We observed 20 Bonferroni significant (P-value < 9.4× 10^?9) CpGs for Fe, 8 for Ni, and 1 for V. Particularly, methylation at Schlafen Family Member 11 (SLFN11) cg10911913 was positively associated with measured levels of all 3 species. The SLFN11 gene codes for an interferon-induced protein that inhibits retroviruses and sensitizes cancer cells to DNA-damaging agents. Bioinformatics analysis suggests that gene targets may be relevant to pathways including cancers, signal transduction, and cell growth and death. Ours is the first study to examine the epigenome-wide association between ambient particles species and DNA methylation. We found that long-term exposures to specific components of ambient particle pollution, especially particles emitted during oil combustion, were associated with methylation changes in genes relevant to immune responses. Our findings provide insight into potential biologic mechanisms on an epigenetic level.     

CO2加富下水氮耦合对黄瓜叶片光合作用和超微结构的影响

以‘津优35号’黄瓜为试材,采用裂区-再裂区设计,研究了CO₂加富下水氮耦合对黄瓜叶片光合作用和超微结构的影响.主区设大气CO₂浓度(400 μmol·mol^-1,A)和加富CO₂浓度(800±20 μmol·mol^-1,E)2个CO₂浓度处理,裂区设无干旱胁迫(田间持水量的95%,W)和干旱胁迫(田间持水量的75%,D)2个水分处理,再裂区设施氮量450 kg·hm^-2(低氮,N₁)和900 kg·hm^-2(高氮,N₂)2个氮素处理.结果表明: 在干旱和高氮条件下,CO₂加富提高了黄瓜的株高,且使高氮下的叶面积显著增加.正常灌溉条件下,高氮处理的光合速率、气孔导度和蒸腾速率高于低氮处理,而干旱条件下则相反;CO₂加富提高了黄瓜叶片的水分利用效率,并且随着施氮量的增加,其水分利用效率提高.干旱胁迫下,黄瓜近轴面气孔密度增加,而CO₂加富和高氮却显著降低了气孔密度.高氮处理增加了黄瓜叶片叶绿体数量而减少了淀粉粒数量,干旱胁迫使叶绿体数量减少,但使淀粉粒数量呈上升趋势.干旱胁迫增加了叶绿体长度和宽度,显著增加了淀粉粒的大小,而高氮降低了叶绿体和淀粉粒的长度和宽度.CO₂加富和高氮均使基粒厚度和片层数增加(ADN₂除外),并且EDN₂处理的片层数显著高于ADN₂.综上所述,CO₂加富和适宜的水、氮条件能促进黄瓜叶片叶绿体类囊体膜系的发育,显著增加基粒厚度和基粒片层数,有效改善黄瓜的叶绿体结构,增强光合性能,提高黄瓜植株对CO₂和水、氮的吸收利用能力.     

Whole mitochondrial genome capture from faecal samples and museum‐preserved specimens

Population‐scale molecular studies of endangered and cryptic species are often limited by access to high‐quality samples. The use of noninvasively collected samples or museum‐preserved specimens reduces the pressure on modern populations by removing the need to capture and handle live animals. However, endogenous DNA content in such samples is low, making shotgun sequencing a financially prohibitive approach. Here, we apply a target enrichment method to retrieve mitochondrial genomes from 65 museum specimens and 56 noninvasively collected faecal samples of two endangered great ape species, Grauer's gorilla and the eastern chimpanzee. We show that the applied method is suitable for a wide range of sample types that differ in endogenous DNA content, increasing the proportion of target reads to over 300‐fold. By systematically evaluating biases introduced during target enrichment of pooled museum samples, we show that capture is less efficient for fragments shorter or longer than the baits, that the proportion of human contaminating reads increases postcapture although capture efficiency is lower for human compared to gorilla fragments with a gorilla‐generated bait, and that the rate of jumping PCR is considerable, but can be controlled for with a double‐barcoding approach. We succeed in capturing complete mitochondrial genomes from faecal samples, but observe reduced capture efficiency as sequence divergence increases between the bait and target species. As previously shown for museum specimens, we demonstrate here that mitochondrial genome capture from field‐collected faecal samples is a robust and reliable approach for population‐wide studies of nonmodel organisms.     

Environmental enrichment,sexual dimorphism,and brain size in sticklebacks

Evidence for phenotypic plasticity in brain size and the size of different brain parts is widespread, but experimental investigations into this effect remain scarce and are usually conducted using individuals from a single population. As the costs and benefits of plasticity may differ among populations, the extent of brain plasticity may also differ from one population to another. In a common garden experiment conducted with three‐spined sticklebacks (Gasterosteus aculeatus) originating from four different populations, we investigated whether environmental enrichment (aquaria provided with structural complexity) caused an increase in the brain size or size of different brain parts compared to controls (bare aquaria). We found no evidence for a positive effect of environmental enrichment on brain size or size of different brain parts in either of the sexes in any of the populations. However, in all populations, males had larger brains than females, and the degree of sexual size dimorphism (SSD) in relative brain size ranged from 5.1 to 11.6% across the populations. Evidence was also found for genetically based differences in relative brain size among populations, as well as for plasticity in the size of different brain parts, as evidenced by consistent size differences among replicate blocks that differed in their temperature.     

Demographic vulnerability of the clonal and endangered meadow thistle

For effective management of endangered species it is pivotal to understand why a species is endangered and which key life cycle components are involved in its response to environmental changes. Our objective was to investigate the response of rosettes of the redlisted clonal herb Cirsium dissectum to anthropogenic nutrient enrichment, which threatens its populations, and the consequences of these responses for its population dynamics. We constructed matrix population models with demographic data from three populations and four annual transitions and we decomposed the spatiotemporal variation in projected population growth rates into contributions from life cycle components. These patterns were compared with below-ground rosette dynamics in different fields, and with the below- and above-ground rosette dynamics in a garden experiment with nutrient enrichment and competing grasses. The decomposition analysis revealed that increased clonal rosette formation and decreased rosette survival were driving the spatial variation in the population growth rate. Excavating the below-ground rhizome network revealed a higher rosette turn-over in experimentally fertilized garden plots, which not only resulted in increased plot-level extinction, but also in increased spread of the clonal offspring. This supported the observed trend among field populations: rosette formation trades off with rosette survival. Surviving seedlings were only found in areas where the topsoil had been removed. The endangered C. dissectum is vulnerable when its habitat becomes more productive, because this species does not have the necessary capability to build up biomass. Small-scale disturbances such as created by sod-cutting or trampling cattle are essential for seedling establishment and necessary to render the explorative strategy of rhizomatous clonal spread successful.     

Translocation and Accumulation of Boron in Roots and Shoots of Plants Grown in Soils of Low Boron Concentration in Turkey's Keban Pb-Zn Mining Area

Boron (B) concentrations were investigated in both shoots and roots of Euphorbia macroclada, Verbascum cheiranthifolium, and Astragalus gummifer grown in soil of the Keban, Turkey, Lead–zinc–copper–fluoride mining area, which has an arid climate. Soil B concentrations were also investigated. Plants and their associated soil samples were collected and analyzed by Inductively Coupled Plasma–Mass Spectrometry (ICP-MS). Total B concentrations of soils in the study area were very low (mean: 4.97 mg kg^?1) as compared with those in surface soils in other countries. Boron concentrations of plant organs were several times higher than those in their associated soils. The mean values of B concentrations in roots of E. macroclada, V. cheiranthifolium, and A. gummifer were 25, 70, and 69 mg kg^?1, respectively, while those in shoots were 75, 115, and 77 mg kg^?1, respectively. Results indicate that roots and shoots of plants grown in soils with low B concentrations can be used both as biomonitors for environmental contamination and biogeochemical indicators for B.