More than skin and bones: Comparing extraction methods and alternative sources of DNA from avian museum specimens

Next‐generation sequencing has greatly expanded the utility and value of museum collections by revealing specimens as genomic resources. As the field of museum genomics grows, so does the need for extraction methods that maximize DNA yields. For avian museum specimens, the established method of extracting DNA from toe pads works well for most specimens. However, for some specimens, especially those of birds that are very small or very large, toe pads can be a poor source of DNA. In this study, we apply two DNA extraction methods (phenol–chloroform and silica column) to three different sources of DNA (toe pad, skin punch and bone) from 10 historical avian museum specimens. We show that a modified phenol–chloroform protocol yielded significantly more DNA than a silica column protocol (e.g., Qiagen DNeasy Blood & Tissue Kit) across all tissue types. However, extractions using the silica column protocol contained longer fragments on average than those using the phenol–chloroform protocol, probably as a result of loss of small fragments through the silica column. While toe pads yielded more DNA than skin punches and bone fragments, skin punches proved to be a reliable alternative source of DNA and might be especially appealing when toe pad extractions are impractical. Overall, we found that historical bird museum specimens contain substantial amounts of DNA for genomic studies under most extraction scenarios, but that a phenol–chloroform protocol consistently provides the high quantities of DNA required for most current genomic protocols.     

毛梗豨莶乙酸乙酯部位化学成分及生物活性研究

毛梗豨莶草(Siegesbeckia glabresce)的乙酸乙酯萃取部位具有显著的抑制细胞坏死性凋亡(necroptosis)的活性。为明确毛梗豨莶草的活性成分,该研究采用正相硅胶柱色谱谱(二氯甲烷:甲醇20:1～0:1)、反相ODS柱色谱(30%～100% 甲醇)、Sephadex LH-20柱色谱、重结晶等方法对毛梗豨莶草乙酸乙酯萃取部位进行了化学成分分离和纯化,并根据理化性质和波谱数据进行了结构鉴定。结果表明:从毛梗豨莶乙酸乙酯部位分离并鉴定了9个化合物,分别为3,7-二甲氧基槲皮素(1)、芹菜素(2)、奥卡宁(3)、okanin-4''-O-β-D-6″-trans-p-coumaroylglucoside(4)、1H-Indole-3-carbaldehyde(5)、对羟基苯甲醛(6)、3,5-二甲氧基-4-羟基苯甲醛(7)、3,4-divanillyltetrahydrofuran(8)、buddlenol D(9)。除化合物1和化合物6外,其余7个化合物均为首次从豨莶属植物中分离得到     

黑老虎叶总黄酮提取工艺及其抗氧化活性研究

为探讨超声波辅助提取黑老虎叶总黄酮的最佳提取工艺条件及其抗氧化活性,该文以黑老虎叶为研究对象,采用超声波提取法提取黑老虎叶总黄酮,通过单因素试验研究提取时间、乙醇浓度、提取温度、料液比对黑老虎叶总黄酮提取率的影响,在单因素试验的基础上,采用正交试验优化其提取工艺条件,测试了最优条件下提取的黑老虎叶总黄酮对DPPH自由基、·OH自由基及超氧阴离子的清除能力。结果表明:黑老虎叶总黄酮超声辅助提取最佳提取条件为提取时间 35 min、乙醇浓度80%、提取温度50 ℃、料液比1:20 g·mL^-1,最佳条件下提取率为4.83%。抗氧化活性测试结果显示,黑老虎叶总黄酮表现出较好的清除DPPH自由基、·OH自由基及超氧阴离子能力,其抗氧化能力为清除DPPH自由基能力>清除超氧阴离子能力>清除·OH自由基能力。在浓度为0.8 mg·mL^-1时,黑老虎叶总黄酮清除DPPH自由基、·OH自由基及超氧阴离子的能力相当于同浓度下Vc的97.6%、82.1%、95.5%,黑老虎叶总黄酮是天然抗氧化剂的良好来源。上述结果为黑老虎叶活性成分的提取及开发利用提供了理论基础。     

生态系统的多稳态与突变

许多生态系统可能在短时间内发生难以预料的状态突变, 其中一些生态系统突变的机理可以用多稳态理论进行解释。近年来生态系统的多稳态和突变现象及其机理吸引了研究者和管理者的广泛关注。本文重点对生态系统多稳态的理论基础、识别方法及稳态转换发生的早期预警信号进行综述, 并基于典型生态系统过程对现实世界中可能观测到的稳态转换进行实例分析, 最后对多稳态概念框架和理论应用中的潜在争议进行讨论, 以期为非线性生态系统动态的理论研究、管理实践和生物多样性保护等提供参考。     

铜藻岩藻黄素提取及纯化工艺研究

为了对岩藻黄素的提取、纯化进行系统研究,进而为高纯度岩藻黄素的工业化生产提供研究基础,筛选了适用于提取铜藻（Sargassum horneri）鲜藻中岩藻黄素的有机溶剂,并通过单因素实验和正交实验确定了最佳的提取溶剂浓度、提取温度、提取时间、料液比等工艺参数。随后采用硅胶柱层析法进行纯化,并通过单因素实验确定了最佳的硅胶柱床高度、上样量和洗脱流速。最后采用制备液相法对经层析纯化的岩藻黄素进一步纯化。结果表明,有机溶剂萃取的最佳工艺条件为：甲醇浓度90%,提取温度50 ℃,提取时间1 h,料液比1∶10,此条件下岩藻黄素提取率达到(0.258 9±0.003 6) mg·g-1鲜重（FW）［(1.078 8±0.015 0) mg·g-1干重（DW）］。硅胶柱层析的最佳工艺条件为：硅胶柱床高度10 cm,上样量6 g,洗脱流速10 mL·min-1,此条件下岩藻黄素得率为0.176 5 mg·g-1FW（0.735 3 mg·g-1 DW）,纯度为87.01%±0.88%。经制备液相进一步纯化后,岩藻黄素得率为0.127 1 mg·g-1 FW（0.529 4 mg·g-1 DW）,纯度为99.27%±0.22%。研究所用工艺简单,岩藻黄素得率高,为高纯度岩藻黄素的制备提供了实验基础。     

Myocardial Infarction Detection and Localization Using Optimal Features Based Lead Specific Approach

ObjectivesObjective of this paper is to present a reliable and accurate technique for Myocardial Infarction (MI) detection and localization.Material and methodsStationary wavelet transform has been used to decompose the ECG signal. Energy, entropy and slope based features were extracted at specific wavelet bands from selected lead of ECG. k-Nearest Neighbors (kNN) with Mahalanobis distance function has been used for classification. Sensitivity (Se), specificity (Sp), positive predictivity (+P), accuracy (Acc), and area under the receiver operating characteristics curve (AUC) analyzed over 200 subjects (52 health control, 148 with MI) from Physikalisch-Technische Bundesanstalt (PTB) database has been used for performance analysis. To handle the imbalanced data adaptive synthetic (ADASYN) sampling approach has been adopted.ResultsFor detection of MI, the proposed technique has shown an AUC = 0.99, Se = 98.62%, Sp = 99.40%, PPR = 99.41% and Acc = 99.00% using 12 top ranked features, extracted from multiple leads of ECG and AUC = 0.99, Se = 98.34%, Sp = 99.77%, PPR = 99.77% and Acc = 99.05% using 12 features extracted from a single ECG lead (i.e. lead V5). For localization of MI, the proposed technique has an AUC = 0.99, Se = 98.78%, Sp = 99.86%, PPR = 98.80%, and Acc = 99.76% using 5 top ranked features from multiple leads of ECG and AUC = 0.98, Se = 96.47%, Sp = 99.60%, PPR = 96.49% and Acc = 99.28% using 8 features extracted from a single ECG lead (i.e. lead V3).ConclusionThus for MI detection and localization, the proposed technique is independent of time-domain ECG fiducial markers and can work using specific leads of ECG.     

Tracking unstable states: ecosystem dynamics in a changing world

Ecological systems can show complex and sometimes abrupt responses to environmental change, with important implications for their resilience. Theories of alternate stable states have been used to predict regime shifts of ecosystems as equilibrium responses to sufficiently slow environmental change. The actual rate of environmental change is a key factor affecting the response, yet we are still lacking a non-equilibrium theory that explicitly considers the influence of this rate of environmental change. We present a metacommunity model of predator–prey interactions displaying multiple stable states, and we impose an explicit rate of environmental change in habitat quality (carrying capacity) and connectivity (dispersal rate). We study how regime shifts depend on the rate of environmental change and compare the outcome with a stability analysis in the corresponding constant environment. Our results reveal that in a changing environment, the community can track states that are unstable in the constant environment. This tracking can lead to regime shifts, including local extinctions, that are not predicted by alternative stable state theory. In our metacommunity, tracking unstable states also controls the maintenance of spatial heterogeneity and spatial synchrony. Tracking unstable states can also lead to regime shifts that may be reversible or irreversible. Our study extends current regime shift theories to integrate rate-dependent responses to environmental change. It reveals the key role of unstable states for predicting transient dynamics and long-term resilience of ecological systems to climate change.     

Uncloaking a Lost Cause: Decolonizing ancestry estimation in the United States

Since the professionalization of US-based forensic anthropology in the 1970s, ancestry estimation has been included as a standard part of the biological profile, because practitioners have assumed it necessary to achieve identifications in medicolegal contexts. Simultaneously, forensic anthropologists have not fully considered the racist context of the criminal justice system in the United States related to the treatment of Black, Indigenous, and People of Color; nor have we considered that ancestry estimation might actually hinder identification efforts because of entrenched racial biases. Despite ongoing criticisms from mainstream biological anthropology that ancestry estimation perpetuates race science, forensic anthropologists have continued the practice. Recent years have seen the prolific development of retooled typological approaches with 21st century statistical prowess to include methods for estimating ancestry from cranial morphoscopic traits, despite no evidence that these traits reflect microevolutionary processes or are suitable genetic proxies for population structure; and such approaches have failed to critically evaluate the societal consequences for perpetuating the biological race concept. Around the country, these methods are enculturated in every aspect of the discipline ranging from university classrooms, to the board-certification examination marking the culmination of training, to standard operating procedures adopted by forensic anthropology laboratories. Here, we use critical race theory to interrogate the approaches utilized to estimate ancestry to include a critique of the continued use of morphoscopic traits, and we assert that the practice of ancestry estimation contributes to white supremacy. Based on the lack of scientific support that these traits reflect evolutionary history, and the inability to disentangle skeletal-based ancestry estimates from supporting the biological validity of race, we urge all forensic anthropologists to abolish the practice of ancestry estimation.