Parallel detection of ancient pathogens via array-based DNA capture

DNA capture coupled with next generation sequencing is highly suitable for the study of ancient pathogens. Screening for pathogens can, however, be meticulous when assays are restricted to the enrichment of single organisms, which is common practice. Here, we report on an array-based DNA capture screening technique for the parallel detection of nearly 100 pathogens that could have potentially left behind molecular signatures in preserved ancient tissues. We demonstrate the sensitivity of our method through evaluation of its performance with a library known to harbour ancient Mycobacterium leprae DNA. This rapid and economical technique will be highly useful for the identification of historical diseases that are difficult to characterize based on archaeological information alone.     

Parallel declines in survival of adult Northern Fulmars Fulmarus glacialis at colonies in Scotland and Ireland

Assessing broad‐scale changes in seabird populations across the North Atlantic requires an integration of available datasets to understand the spatial extent of potential drivers and demographic change. Here, we compared survival of Northern Fulmars Fulmarus glacialis from a Scottish and an Irish colony from 1974 to 2009. Despite lower recapture probabilities of monel‐ringed Irish birds compared with colour‐ringed Scottish birds, survival probability decreased at both colonies. The extent to which the decline in survival is related to density‐dependent processes or other external drivers remains uncertain, but our results suggest that these changes in survival are possibly indicative of larger‐scale processes and are not confined to local colony dynamics.     

Blood and cloacal swab sampling for avian influenza monitoring has no effect on survival rates of free‐ranging ducks

Concerns about the spread of avian influenza viruses (AIVs) have led to cloacal swab sampling of hundreds of thousands of birds worldwide as part of AIV surveillance schemes, but the effects of cloacal swabbing have not been adequately evaluated. We tested for differences between swabbed, swabbed and bled, and non‐sampled wild ducks in terms of live re‐encounter and dead recoveries for Common Pochard Aythya ferina and Tufted Duck Aythya fuligula, and also determined re‐encounter and recovery rates for Mallard Anas platyrhynchos and Common Teal Anas crecca. No effects of sampling methods were detected, except in Teal. Re‐encounter rates were lower in sampled Teal than in controls, with annual re‐encounter probabilities being 25% and 35% lower in males and females, respectively. Teal possibly left or avoided sampling sites, or sought sites where they were less detectable after sampling. In general, no deleterious effects were found, suggesting that cloacal swabbing and blood sampling are suitable methods for conducting AIV surveillance in ducks.     

Using miniaturized radiotelemetry to discover the breeding grounds of the endangered New Zealand Storm Petrel Fregetta maoriana

Identification of breeding sites remains a critical step in species conservation, particularly in procellariiform seabirds whose threat status is of global concern. We designed and conducted an integrative radiotelemetry approach to uncover the breeding grounds of the critically endangered New Zealand Storm Petrel Fregetta maoriana (NZSP), a species considered extinct before its rediscovery in 2003. Solar‐powered automated radio receivers and hand‐held telemetry were used to detect the presence of birds on three island groups in the Hauraki Gulf near Auckland, New Zealand. At least 11 NZSP captured and radiotagged at sea were detected at night near Te Hauturu‐o‐Toi/Little Barrier Island with the detection of an incubating bird leading to the discovery of the first known breeding site for this species. In total, four NZSP breeding burrows were detected under mature forest canopy and three adult NZSP and two NZSP chicks were ringed. Telemetry data indicated NZSP showed strong moonlight avoidance behaviour over the breeding site, had incubation shifts of approximately 5 days and had a breeding season extending from February to June/July, a different season from other Procellariiformes in the region. Radiotelemetry, in combination with rigorously collected field data on species distribution, offers a valuable technique for locating breeding grounds of procellariiform seabirds and gaining insights into breeding biology while minimizing disturbance to sensitive species or damage to fragile habitat. Our study suggests an avenue for other breeding ground searches in one of the most threatened avian Orders, and highlights the general need for information on the location of breeding sites and understanding the breeding biology in data‐deficient birds.     

Assessing the short‐term effects of capture,handling and tagging of sandgrouse

Capturing and marking free‐living birds permits the study of important aspects of their biology but may have undesirable effects. Bird welfare should be a primary concern, so it is necessary to evaluate and minimize any adverse effects of procedures used. We assess short‐term effects associated with the capture, handling and tagging with backpack‐mounted transmitters of Pin‐tailed Pterocles alchata and Black‐bellied Pterocles orientalis Sandgrouse, steppe birds of conservation concern. There was a significantly higher mortality (15%) during the first week after capture than during the following weeks (< 2.5%) in Pin‐tailed Sandgrouse, but no significant temporal mortality pattern in Black‐bellied Sandgrouse. In Pin‐tailed Sandgrouse, mortality rate during the first week increased with increasing relative transmitter and harness weight regardless of season, and with increasing handling time during the breeding season. There were no significant differences in mortality rate between study areas, type of tag, sex or age or an effect of restraint time. These results suggest the use of lighter transmitters (< 3% of the bird's weight) and a reduction of handling time (< 20 min), particularly during the breeding season, as essential improvements in procedure to reduce the mortality risk associated with the capture, handling and tagging of these vulnerable species.     

Humpback whale abundance in the North Pacific estimated by photographic capture‐recapture with bias correction from simulation studies

We estimated the abundance of humpback whales in the North Pacific by capture‐recapture methods using over 18,000 fluke identification photographs collected in 2004–2006. Our best estimate of abundance was 21,808 (CV = 0.04). We estimated the biases in this value using a simulation model. Births and deaths, which violate the assumption of a closed population, resulted in a bias of +5.2%, exclusion of calves in samples resulted in a bias of ?10.5%, failure to achieve random geographic sampling resulted in a bias of ?0.4%, and missed matches resulted in a bias of +9.3%. Known sex‐biased sampling favoring males in breeding areas did not add significant bias if both sexes are proportionately sampled in the feeding areas. Our best estimate of abundance was 21,063 after accounting for a net bias of +3.5%. This estimate is likely to be lower than the true abundance due to two additional sources of bias: individual heterogeneity in the probability of being sampled (unquantified) and the likely existence of an unknown and unsampled breeding area (?8.7%). Results confirm that the overall humpback whale population in the North Pacific has continued to increase and is now greater than some prior estimates of prewhaling abundance.     

A preferred AMPK phosphorylation site adjacent to the inhibitory loop of cardiac and skeletal troponin I

5'-AMP-activated protein kinase (AMPK) is a serine/threonine protein kinase that is activated when cellular AMP to ATP ratios rise, potentially serving as a key regulator of cellular energetics. Among the known targets of AMPK are catabolic and anabolic enzymes, but little is known about the ability of this kinase to phosphorylate myofilament proteins and thereby regulating the contractile apparatus of striated muscles. Here, we demonstrate that troponin I isoforms of cardiac (cTnI) and fast skeletal (fsTnI) muscles are readily phosphorylated by AMPK. For cTnI, two highly conserved serine residues were identified as AMPK sites using a combination of high-resolution top-down electron capture dissociation mass spectrometry, (32) P-incorporation, synthetic peptides, phospho-specific antibodies, and site-directed mutagenesis. These AMPK sites in cTnI were Ser149 adjacent to the inhibitory loop and Ser22 in the cardiac-specific N-terminal extension, at the level of cTnI peptides, the intact cTnI subunit, whole cardiac troponin complexes and skinned cardiomyocytes. Phosphorylation time-course experiments revealed that Ser149 was the preferred site, because it was phosphorylated 12-16-fold faster than Ser22 in cTnI. Ser117 in fsTnI, analogous to Ser149 in cTnI, was phosphorylated with similar kinetics as cTnI Ser149. Hence, the master energy-sensing protein AMPK emerges as a possibly important regulator of cardiac and skeletal contractility via phosphorylation of a preferred site adjacent to the inhibitory loop of the thin filament protein TnI.     

实验猴身份自动识别、自动捕捉、电子芯片数据信息管理系统的研制

目的通过电子芯片植入与识别技术和计算机管理系统对接,建立每只实验猴的数据档案,其中包括遗传谱系、生理数据、实验记录。方法通过建立实验猴的电子通道,以非接触方式通过计算机管理,应用射频识别信号系统,实现实验猴身份快速自动识别、自动捕捉、数据读写、电子档案信息管理、数据远程传输的目的,减少人为因素对实验猴的干扰和引起的应激反应。结果该系统的建立极大的减少了实验和饲养实验猴过程中捕捉猴的困难,身份识别困难,减少了对工作人员和实验猴的伤害,减轻了工作量,减低了人为因素对实验结果的干扰和动物应激反应对实验数据的影响。电子档案具有终身有效,随猴携带,全球唯一序列号,不可复制,不可仿制,标签唯一性。结论实验猴身份自动识别、自动捕捉、电子芯片数据信息管理系统的研制成功,为实验动物个体电子档案建立和群体数据库的管理提供了一种高速、有效、科学、可靠的计算机管理手段,改变通道模式即可应用于大型凶猛动物或不适合人接触捕捉动物的识别和管理,具有广泛的应用前景,目前在国内外尚无同类系统。