Physical enrichment research for captive fish: Time to focus on the DETAILS

Growing research effort has shown that physical enrichment (PE) can improve fish welfare and research validity. However, the inclusion of PE does not always result in positive effects and conflicting findings have highlighted the many nuances involved. Effects are known to depend on species and life stage tested, but effects may also vary with differences in the specific items used as enrichment between and within studies. Reporting fine-scale characteristics of items used as enrichment in studies may help to reveal these factors. We conducted a survey of PE-focused studies published in the last 5 years to examine the current state of methodological reporting. The survey results suggest that some aspects of enrichment are not adequately detailed. For example, the amount and dimensions of objects used as enrichment were frequently omitted. Similarly, the ecological relevance, or other justification, for enrichment items was frequently not made explicit. Focusing on ecologically relevant aspects of PE and increasing the level of detail reported in studies may benefit future work and we propose a framework with the acronym DETAILS ( D imensions, E cological rationale, T iming of enrichment, A mount, I nputs, L ighting and S ocial environment). We outline the potential importance of each of the elements of this framework with the hope it may aid in the level of reporting and standardization across studies, ultimately aiding the search for more beneficial types of PE and the development of our understanding and ability to improve the welfare of captive fish and promote more biologically relevant behaviour.     

Genomic surveillance of Nevada patients revealed prevalence of unique SARS-CoV-2 variants bearing mutations in the RdRp gene

Patients with signs of COVID-19 were tested through diagnostic RT-PCR for SARS-CoV-2 using RNA extracted from the nasopharyngeal/nasal swabs.To determine the variants of SARS-CoV-2 circulating in the state of Nevada,specimens from 200 COVID-19 patients were sequenced through our robust sequencing platform,which enabled sequencing of SARS-CoV-2 from specimens with even very low viral loads,without the need of culture-based amplification.High genome coverage allowed the identification of single and multi-nucleotide variants in SARS-CoV-2 in the community and their phylogenetic relationships with other variants present during the same period of the outbreak.We report the occurrence of a novel mutation at 323aa (314aa of orf1b) of nsp12 (RNA-dependent RNA polymerase) changed to phenylalanine(F) from proline (P),in the first reported isolate of SARS-CoV-2,Wuhan-Hu-1.This 323F variant was present at a very high frequency in Northern Nevada.Structural modeling determined this mutation in the interface domain,which is important for the association of accessory proteins required for the polymerase.In conclusion,we report the introduction of specific SARS-CoV-2 variants at very high frequency in distinct geographic locations,which is important for understanding the evolution and circulation of SARS-CoV-2variants of public health importance,while it circulates in humans.     

短期生长环境光强骤增导致典型阴生植物三七光系统受损的机制

阴生植物突然暴露在强光下造成光损伤的情况时有发生, 但其对高光敏感的潜在机制尚不十分清楚。为阐明阴生植物无法在自然全光照环境下生存的相关机制, 该研究以典型阴生植物三七(Panax notoginseng)为材料, 将遮阴环境下(10%透光率)生长的植株转移到全日光环境下3天, 研究其相对叶绿素含量(SPAD值)、光合参数以及叶绿素荧光参数的变化。结果表明, 全光环境下三七光合日变化呈现“双峰”曲线特征, 且净光合速率在处理期间逐日降低。全日光下三七叶片SPAD值、水分利用率和光能利用率显著降低; 叶片光系统I (PSI)反应中心P700最大荧光信号、光系统II (PSII)电子传递速率、暗适应下PSII最大量子效率和光下PSII最大量子效率显著低于遮阴环境下的植株, 且至傍晚不能完全恢复。而参与调节性能量耗散的量子产量、PSI受体侧限制引起的非光化学量子产量、环式电子流则显著高于遮阴环境下的三七。此外, 生长环境光照强度骤增导致荧光诱导动力学曲线发生明显变化, 并显著升高了PSII供体侧和受体侧的荧光产量。当阴生植物三七突然暴露于全光环境下时, 强烈的光照会导致PSII供体侧的放氧复合体活性受损, 抑制受体侧的电子传递, 过度还原PSI的受体侧进而引发PSI光抑制。该研究结果揭示, 全日光导致的PSII不可逆损伤和PSI光抑制可能是典型阴生植物三七为什么不能在全日照光环境下存活的重要原因。     

基因表达谱中信号通路基因集分析方法进展

微阵列技术是生物技术变革的核心,允许研究者同时监测成千上万个基的表达水平,已广泛应用医学研究.如何挖掘海量基表达信息中的有用信息并进行生物学专业解释,是基表达谱数据分析领所面临的一个重要挑战.生物信号通路研究已成为基芯片中不同表型差异表达研究的主要方法,其是以整个信号通路作为一个整体作为研究对象,此得出的研究结果更加科学和准确.在本文中我们简要描述了近10年来信号通路基集富集分析方法的发展情况,将其分为三个阶段,对每个阶段方法的基础和特点做了一些简单的总结和阐述.     

The Use of Ice to Enrich the Environment of Pigs Housed Indoors

Pigs used in research are often housed in barren environments. The effects of ice as a simple enrichment tool for newly weaned pigs were investigated. Four replicates of 120 pigs were separated into 3 groups. One group was given free access to blocks of ice (ice group), another group had access to Classic Kong toys (Kong group), and a 3rd group did not receive any enrichment (control group). The behavior of each group was observed every 5 min from 08:00 hr to 12:00 hr during 4 consecutive days. Pigs were motivated to explore the ice blocks (4.85% ± 1.34) over the Classic Kong toys (2.03% ± 0.59). No differences in other behaviors were found between treatments. Ice is an effective and easy-to-replace enrichment device. Blocks of ice can be used as enrichment devices for pigs housed in research facilities.     

Detrital diversity influences estuarine ecosystem performance

Global losses of seagrasses and mangroves, eutrophication‐driven increases in ephemeral algae, and macrophyte invasions have impacted estuarine detrital resources. To understand the implications of these changes on benthic ecosystem processes, we tested the hypotheses that detrital source richness, mix identity, and biomass influence benthic primary production, metabolism, and nutrient fluxes. On an estuarine muddy sandflat, we manipulated the availability of eight detrital sources, including mangrove, seagrass, and invasive and native algal species that have undergone substantial changes in distribution. Mixes of these detrital sources were randomly assigned to one of 12 treatments and dried detrital material was added to seventy‐two 0.25 m² plots (n = 6 plots). The treatments included combinations of either two or four detrital sources and high (60 g) or low (40 g) levels of enrichments. After 2 months, the dark, light, and net uptake of NH₄⁺, dissolved inorganic nitrogen, and the dark efflux of dissolved organic nitrogen were each significantly influenced by the identity of detrital mixes, rather than detrital source richness or biomass. However, gross and net primary productivity, average oxygen flux, and net NO_X and dissolved inorganic phosphorous fluxes were significantly greater in treatments with low than with high detrital source richness. These results demonstrate that changes in detrital source richness and mix identity may be important drivers of estuarine ecosystem performance. Continued impacts to estuarine macrophytes may, therefore, further alter detritus‐fueled productivity and processes in estuaries. Specific tests that address predicted future changes to detrital resources are required to determine the consequences of this significant environmental problem.     

Net greenhouse gas balance in response to nitrogen enrichment: perspectives from a coupled biogeochemical model

Increasing reactive nitrogen (N) input has been recognized as one of the important factors influencing climate system through affecting the uptake and emission of greenhouse gases (GHG). However, the magnitude and spatiotemporal variations of N‐induced GHG fluxes at regional and global scales remain far from certain. Here we selected China as an example, and used a coupled biogeochemical model in conjunction with spatially explicit data sets (including climate, atmospheric CO₂, O₃, N deposition, land use, and land cover changes, and N fertilizer application) to simulate the concurrent impacts of increasing atmospheric and fertilized N inputs on balance of three major GHGs (CO₂, CH₄, and N₂O). Our simulations showed that these two N enrichment sources in China decreased global warming potential (GWP) through stimulating CO₂ sink and suppressing CH₄ emission. However, direct N₂O emission was estimated to offset 39% of N‐induced carbon (C) benefit, with a net GWP of three GHGs averaging ?376.3 ± 146.4 Tg CO₂ eq yr^?1 (the standard deviation is interannual variability of GWP) during 2000–2008. The chemical N fertilizer uses were estimated to increase GWP by 45.6 ± 34.3 Tg CO₂ eq yr^?1 in the same period, and C sink was offset by 136%. The largest C sink offset ratio due to increasing N input was found in Southeast and Central mainland of China, where rapid industrial development and intensively managed crop system are located. Although exposed to the rapidly increasing N deposition, most of the natural vegetation covers were still showing decreasing GWP. However, due to extensive overuse of N fertilizer, China's cropland was found to show the least negative GWP, or even positive GWP in recent decade. From both scientific and policy perspectives, it is essential to incorporate multiple GHGs into a coupled biogeochemical framework for fully assessing N impacts on climate changes.     

Discovering lethal alleles across the turkey genome using a transmission ratio distortion approach

Deviation from Mendelian inheritance expectations (transmission ratio distortion, TRD) has been observed in several species, including the mouse and humans. In this study, TRD was characterized in the turkey genome using both allelic (specific- and unspecific-parent TRD) and genotypic (additive- and dominance-TRD) parameterizations within a Bayesian framework. In this study, we evaluated TRD for 23 243 genotyped Turkeys across 56 393 autosomal SNPs. The analyses included 500 sires, 2013 dams and 11 047 offspring (trios). Three different haplotype sliding windows of 4, 10 and 20 SNPs were used across the autosomal chromosomes. Based on the genotypic parameterizations, 14 haplotypes showed additive and dominance TRD effects highlighting regions with a recessive TRD pattern. In contrast, the allelic model uncovered 12 haplotype alleles with the allelic TRD pattern which showed an underrepresentation of heterozygous offspring in addition to the absence of homozygous animals. For regions with the allelic pattern, only one particular region showed a parent-specific TRD where the penetrance was high via the dam, but low via the sire. The gene set analysis uncovered several gene ontology functional terms, Reactome pathways and several Medical Subject Headings that showed significant enrichment of genes associated with TRD. Many of these gene ontology functional terms (e.g. mitotic spindle assembly checkpoint, DRM complex and Aneuploidy), Reactome pathways (e.g. Mismatch repair) and Medical Subject Headings (e.g. Adenosine monophosphate) are known to be related to fertility, embryo development and lethality. The results of this study revealed potential novel candidate lethal haplotypes, functional terms and pathways that may enhance breeding programs in Turkeys through reducing mortality and improving reproduction rate.     

Conspecific density and environmental complexity impact behaviour of turquoise killifish (Nothobranchius furzeri)

Fish models are essential for research in many biological and medical disciplines. With a typical lifespan of only 6 months, the Turquoise killifish (Nothobranchius furzeri) was recently established as a time- and cost-efficient model to facilitate whole-life and multigenerational studies in several research fields, including behavioural ecotoxicology. Essential information on the behavioural norm and on how laboratory conditions affect behaviour, however, is deficient. In the current study, we examined the impact of the social and structural environment on a broad spectrum of behavioural endpoints in N. furzeri. While structural enrichment affected only fish boldness and exploratory behaviour, fish rearing density affected the total body length, locomotor activity, boldness, aggressiveness and feeding behaviour of N. furzeri individuals. Overall, these results contribute to compiling a behavioural baseline for N. furzeri that increases the applicability of this new model species. Furthermore, our findings will fuel the development of improved husbandry protocols to maximize the welfare of N. furzeri in a laboratory setting.