Comparison of fecal storage methods for steroid analysis in black rhinoceroses (Diceros bicornis)

Many field studies and conservation programs for wildlife species include noninvasive endocrine monitoring of gonadal function. Freezing fecal samples immediately after collection until further analysis is often not a viable option for researchers in remote areas. Phase 1 of this study was designed to compare different methods of preserving fecal samples over several time periods (30, 90, or 180 days) in order to determine which method provided the most accurate and reliable technique for measuring fecal progestagens. Fecal samples were collected from two female black rhinoceroses (Diceros bicornis) housed at Disney's Animal Kingdom, Lake Buena Vista, FL. We compared three storage methods: 1) storing fecal samples without processing or preservatives (untreated), 2) storing an aliquot of fecal sample in 80% methanol (MeOH), and 3) drying the fecal sample in a solar box cooker prior to storage. Control samples (day 0) were collected and extracted, and then stored at ?20°C until they were analyzed. Phase 2 of the study was designed to examine the effects of long‐term storage (up to 180 days) on fecal progestagen profiles that reflect reproductive activity (pregnancy and estrous cycles). In samples obtained from a pregnant female and stored for 30 days, there were no significant differences in fecal progestagen concentrations between the three treatment conditions. However, the mean concentrations of progestagens (± SE) in untreated samples increased significantly from 8.3 ± 0.3 µg/g wet weight feces at day 0 to 17.7 ± 5.1 µg/g feces at day 90, and 17.8 ± 4.7 µg/g feces at day 180. Samples that were collected from a pregnant female and stored in 80% MeOH or dried in the solar box correlated with controls (r=0.86 and 0.87, respectively; P<0.05) at day 180. In contrast, samples that were stored without preservatives for 180 days did not correlate with controls (r=0.35, P>0.05). Progestagen concentrations from samples of the estrous cycling female showed similar results. In conclusion, fecal samples dried in a solar box cooker or stored in 80% MeOH maintained absolute and relative progestagen concentrations for at least 180 days when they were stored outdoors and exposed to the climatic conditions of central Florida. Both methods can have significant applications for the study of reproductive events in areas where access to electricity is limited. Zoo Biol 23:291–300, 2004. © 2004 Wiley‐Liss, Inc.     

Validation of a field-friendly extraction and storage method to monitor fecal steroid metabolites in wild orangutans

Measuring hormone metabolites from feces is the most often used method to assess hormonal status in wildlife. Although immediate freezing of fecal samples collected in the field is the best method to minimize the risk of degradation of hormones over time, this is often not possible in remote field sites. Therefore, alternative storage and preservation methods for fecal samples are required in these conditions. We conducted an experiment to investigate if fecal glucocorticoid (FGCM) and progesterone metabolite (pregnanediol-3-glucuronide; PdG) levels measured from samples that were extracted with a simple, field-friendly methodology correlate with those generated from frozen samples. We also evaluated whether storing fecal samples in alcohol is a suitable alternative to preserve FGCM and PdG concentrations long-term (i.e. over a 9-month period) at locations where fecal extraction is not feasible. Finally, we tested if the hormone concentrations in unpreserved fecal samples of orangutans change over 14 h when stored at ambient conditions, representing the maximum duration between sample collection and return to the camp. FGCM and PdG levels measured from samples that were extracted with the field-friendly method showed strong correlations with those generated from frozen samples, and mean levels did not differ significantly between these methods. FGCM concentrations showed no significant change compared to control samples when fecal samples were stored for up to 6 months in alcohol at ambient temperature and PdG concentrations even remained stable for up to 9 months of storage. FGCM concentrations of fecal samples kept at ambient temperature for up to 14 h post-defecation did not significantly differ compared to control samples frozen immediately after collection. These results provide the basis for the successful monitoring of the physiological status of orangutans living in remote natural settings, like those included in the Indonesian reintroduction programs.     

不同粪便DNA提取方法比较分析北大核心CSCD

肠道微生物群落结构和多样性与人体疾病密切相关。然而,相关群落结构分析结果可能受到DNA提取质量等实验因素影响。因此,评估不同DNA提取方法对肠道特定种属的提取效果,对于全面、准确获取人体肠道微生物谱,深入探究肠道微生物群落结构具有指导意义。本研究旨在借助实时荧光定量PCR(real-time quantitative polymerase chain reaction,RT qPCR)技术,以DNA提取纯度、浓度,以及对肠道中特定种属微生物基因组DNA的提取丰度为指标,对5种DNA提取方法进行比较分析。结果表明,试剂盒Q的提取效果最佳,特别是对乳杆菌属和双歧杆菌属等革兰氏阳性菌的提取效果较好。N试剂盒的平均DNA提取浓度较Q试剂盒低,但在纯度方面,二者无显著性差异。与其他3种商用试剂盒(M、PSP、TG)相比,N方法对肠道内指定微生物基因组的提取效果仅次于Q试剂盒,位居第二。相比之下,M试剂盒提取所得DNA,质量较高,但浓度偏低,对于肠道内革兰氏阳性菌的提取效果不很理想。TG试剂盒和PSP试剂盒提取所得DNA在浓度、质量以及细菌丰度方面均不及其他验证的试剂盒。综上,Q试剂盒可作为肠道微生态研究相关实验中获取高质量基因组DNA的提取方法。本研究结果为肠道微生态研究相关实验中基因组DNA提取方法的选择提供参考依据。     

Measurement of urinary and fecal steroid metabolites during the ovarian cycle in captive and wild Japanese macaques, Macaca fuscata

We measured the concentration of steroid hormones from urine, feces, and blood samples of two captive Japanese macaques, Macaca fuscata, during nonconceptive ovarian cycles to compare the patterns of the excreted steroids with those of circulating steroids. Urine and feces were analyzed for estrone conjugates (E1C) and pregnanediol-3-glucronide (PdG) using enzyme immunoassays (EIAs), while plasma was analyzed for estradiol-17beta(E2), progesterone (P), and luteinizing hormone (LH) using radioimmunoassays (RIAs). Urinary and fecal E1C and PdG levels were approximately parallel to plasma E2 and P levels, respectively. The E1C profiles of daily urinary and fecal samples revealed a midcycle peak, followed by a sustained PdG increase lasting up to two weeks from the E1C peak. A fecal E1C peak was one day later than the urinary E1C peak. One of the captive females exhibited a discrete plasma LH peak, one indicator that ovulation has occurred, on the day following the urinary E1C peak, i.e., the same day of fecal E1C peak. We measured excreted steroids in nine wild females and determined the timing of ovulation by comparing fecal steroid profiles to those obtained in captive monkeys. Data from wild females indicated that eight of nine females conceived during their first ovulatory cycle of the sampling period, whereas the remaining female failed to conceive during the sampling period even though she ovulated. In the eight females that conceived, E1C increased again following the detected or estimated E1C peak, with levels comparable to the preovulatory peak levels, and sustained elevations of PdG for over 40 days. These data illustrate that the urinary and fecal profiles of ovarian steroid excretion obtained through the application of these noninvasive techniques provide an accurate approach for monitoring conceptive and nonconceptive ovarian cycle in captive and free-living Japanese macaques.     

Intestinal parasite infections and fecal steroid levels in wild chimpanzees

Immune-endocrine interactions have been evaluated much less frequently in nonhuman primates, and this may be due, in part, to logistical and ethical concerns regarding trapping and sampling of endangered species, especially apes. Using noninvasive fecal collection methods, the present study evaluates possible relationships between fecal steroid levels and gastrointestinal parasite infections in the Ngogo chimpanzee community in Kibale National Park, Uganda. Because both testosterone and cortisol exhibit immunosuppressive effects in vitro and in other animal models, it was hypothesized that both testosterone and cortisol would be positively associated with gastrointestinal parasite infections in these animals. When placed in a mixed model simultaneously, both testosterone (F = 4.98, df = 1, P = 0.033) and cortisol (F = 5.94, df = 1, P = 0.020) were positively associated with total (helminth and protozoan) parasite richness (the number of unique intestinal parasite species recovered from hosts' fecal samples). It is possible that androgens and corticoids alter the ability of a host to mount an effective immune response against concomitant infection with multiple parasitic species. The utility of fecal samples for assessing immune-endocrine interactions is discussed.     

植物花蜜提取、保存与检测分析方法及比较

花蜜富含多种有机物和微量元素, 不同植物花蜜的分泌量以及化学物质构成存在很大差异, 不同花蜜采集和保存方法都会影响其成分分析结果.本研究参考相关文献, 总结了常用的6种野外花蜜收集方式(注射器法、毛细管法、滤纸法、溶液稀释法、离心法和抽吸法), 6种花蜜保存方式(4℃冷藏保存、－20℃冷冻保存、－80℃超低温保存、－1...     

大鼠肠内容物细菌基因组DNA提取方法的比较

目的比较两种肠内容物前处理和两种提取方法对清洁级SD大鼠肠内容物细菌基因组DNA提取效率。方法分别选用PBS多次离心漂洗、液氮破细胞两种前处理方法和酚/氯仿抽提、试剂盒过柱法两种提取方法进行组合分析,对4份肠内容物和16份含金黄色葡萄球菌肠内容物进行随机提取。结果大鼠肠内容物细菌基因组DNA含量和纯度测定结果显示,与PBS反复离心相比,液氮研磨前处理能显著提高大鼠肠内容物基因组DNA。荧光定量PCR表明,液氮研磨前处理较PBS反复离心能更好地收集细菌基因组DNA,其Ct值最低。结论研究结果表明,采用液氮研磨试剂盒法在大鼠肠内容物DNA提取中是较为优良的方法,该方法为建立实验动物中微生物的定量PCR检测方法打下了基础。     

Testing extraction and storage parameters for a fecal hormone method

Four experiments were conducted to test different aspects of a “field‐friendly” fecal hormone extraction method that utilizes methanol extraction in the field followed by storage on C18 solid‐phase extraction cartridges. Fecal samples were collected from geladas (Theropithecus gelada) housed at the Bronx Zoo, and the experiments were conducted in a laboratory setting to ensure maximum control. The experiments were designed to either simulate the conditions to which fecal samples are subjected during fieldwork or improve on an existing protocol. The experiments tested the relationship between fecal hormone metabolite preservation/recovery and: (1) the amount of time a sample is stored at ambient temperature; (2) the number of freeze/thaw cycles a sample undergoes; (3) the effectiveness of different extraction solutions; and (4) the effectiveness of different cartridge washes. For each experiment, samples were assayed by radioimmunoassay for fecal glucocorticoid (GC) and testosterone (T) metabolites. Results for each of the experiments were as follows. First, storage at ambient temperature did not affect hormone levels until 4 weeks of storage, with significant increases for both GC and T metabolites at 4 weeks. Second, hormone levels significantly decreased in samples after two freeze/thaw cycles for GCs and six freeze/thaws cycles for T. Third, for both GCs and T, hormone extraction using various methanol solutions was significantly higher than using 100% ethanol. Finally, using a 20% methanol solution to wash cartridges significantly increased GC levels but had no effect on T levels. These results suggest that, when utilizing C18 cartridges for fecal steroid storage, researchers should consider several methodological options to optimize hormone preservation and recovery from fecal samples. Am. J. Primatol. 72:934–941, 2010. © 2010 Wiley‐Liss, Inc.     

Non-invasive collection and analysis of semen in wild macaques

Assessments of primate male fertility via semen analyses are so far restricted to captivity. This study describes a non-invasive method to collect and analyse semen in wild primates, based on fieldwork with Yakushima macaques (Macaca fuscata yakui). Over nine mating seasons between 1993 and 2010, 128 masturbatory ejaculations were recorded in 21 males of 5 study troops, and in 11 non-troop males. In 55 %, ejaculate volume was directly estimated, and in 37 %, pH-value, sperm vitality, numbers, morphology and swimming velocity could also be determined. This approach of assessing semen production rates and individual male fertility can be applied to other primate taxa, in particular to largely terrestrial populations where males masturbate frequently, such as macaques and baboons. Furthermore, since explanations of male reproductive skew in non-human primate populations have until now ignored the potential role of semen quality, the method presented here will also help to answer this question.     

Development of a field‐friendly technique for fecal steroid extraction and storage using the African wild dog (Lycaon pictus)

Hormonal analysis provides information about wildlife populations, but is difficult to conduct in the field. Our goal was to develop a rapid and effective field method for fecal steroid analysis by comparing: (1) three extraction methods (laboratory (LAB), homogenize (HO) and handshake (HS)) and (2) two storage methods (solid‐phase extraction (SPE) tubes vs. plastic tubes (PT)). Samples (n=23) from captive African wild dogs (Lycaon pictus) were thoroughly mixed, three aliquots of each were weighed (～0.5 g) and 5 ml of 90% ethanol was added. For LAB, samples were agitated (mixer setting 60; 30 min), centrifuged (1,500 rpm; 20 min) and poured into glass tubes. Or aliquots were HO (1 min) or HS (1 min) and poured through filter paper into glass tubes. Samples were split, analyzed for corticosterone (C) and testosterone (T) metabolites using enzyme immunoassays or stored in SPE or PT. Samples were stored (room temperature) for 30, 60 or 180 days, reconstituted in buffer and analyzed. Mean C and T recoveries of HO were greater (P=0.03) than HS compared with LAB, which was similar to HO (P>0.05). After 30 days <21% of C and T was recovered from SPE, but ～100% of each was recovered from HO‐PT and HS‐PT. Similarly, after 60 and 180 days, ～100% of C and T was recovered from HO‐PT and HS‐PT. Results demonstrated that, for C and T, HO was more comparable (P<0.001) to LAB than HS and PT storage was more efficient than SPE (P<0.001). Zoo Biol 29:289–302, 2010. © 2009 Wiley‐Liss, Inc.     

Comparison of six methods for the extraction of lipids from serum in terms of effectiveness and protein preservation

The present work compares six biochemical methods for extraction of lipids from human serum. Although some organic solvents were good lipid extractors, they precipitated most of the total proteins and albumin. On the other hand, methodologies using Triton X-114 and silica were efficient for extraction of lipids, while sparing the protein fraction.     

Physiological and analytical validations of fecal steroid hormone measures in black howler monkeys

The measurement of hormones in fecal samples allows for the noninvasive assessment of the endocrine status of free-ranging primates. However, procedures and techniques for hormone analysis in feces must be validated, both analytically and physiologically. Few studies have addressed the endocrinology of black howler monkeys (Alouatta pigra). Due to its conservation status, direct handling of individuals from this species and invasive sample collection are highly regulated, and therefore traditional methods for the validation of hormone assays, such as pharmacological challenges, are not allowed. As a consequence, sometimes studies of the fecal hormones of free-ranging black howler monkeys do not report physiological validations and therefore the biological reliability of such measurements cannot be assessed. In order to stimulate future research with this species, the present study aimed at providing methodological bases for fecal endocrine monitoring. Specifically, we compared the validity of two immunoassays (radioimmunoassays, RIA; solid-phase chemiluminescent enzyme immunoassay, SPCEI) performed with commercial kits to measure cortisol, testosterone, estradiol, and progesterone; and demonstrate how the physiological functions of these steroid hormones can be determined through non-pharmacological validations. We found no differences between the analytical validity of RIA and SPCEI assays to measure cortisol and testosterone, whereas for estradiol and progesterone RIA showed better results. Concerning the physiological validation of our assays, we demonstrated that: (1) comparisons between pre- and post-stress situations may be used to assess cortisol response, (2) comparisons between females and males may be used to assess variation in testosterone levels, and (3) comparisons between pregnant and non-pregnant females may be used to determine variation in estradiol and progesterone activity. The analytical and physiological validations that we performed demonstrate that there are currently commercial kits that allow for correct endocrine monitoring of this species, and that there are non-pharmacological alternatives to assess the biological validity of hormone measurements.     

Comparison of DNA extraction methods for analysis of turkey cecal microbiota

AIM: As a prelude to long-term studies to characterize the microbiota of the turkey ceca, 14 DNA isolation protocols were evaluated for their ability to reproducibly characterize microbial diversity. METHODS AND RESULTS: Eight commercially available DNA extraction kits were assessed. DNA quantity and quality were assessed and competitive PCR was used to quantify the 16S bacterial rRNA genes. The Invitrogen Easy-DNA Kit extraction method for large samples yielded over eight times more DNA than any other method (3144 +/- 873 microg g(-1) of sample, P < 0.05). Bacterial and fungal species richness was estimated by Automated Ribosomal Intergenic Spacer Analysis. The Invitrogen Easy-DNA Kit generated the greatest bacterial species richness (46 +/- 7 peaks) while Bio-Rad Aquapure yielded the highest fungal species richness (71 +/- 9.5 peaks). CONCLUSION: Cluster analysis indicated different DNA extraction methods generated different microbial community compositions using the same cecal matrix from a single donor bird. SIGNIFICANCE AND IMPACT OF THE STUDY: Optimized DNA extraction protocols Invitrogen Easy-DNA Kit extraction method for large samples and Bio-Rad Aquapure outperform other methods for extraction of DNA from poultry fecal samples, although these methods do not necessarily recover all available DNA. They will be used in future studies to monitor the dynamics of microbial communities of the avian ceca.     

Comparison of five rep-PCR genomic fingerprinting methods for differentiation of fecal Escherichia coli from humans, poultry and wild birds

The development of a methodology to identify the origin of fecal pollution is important both for assessing the degree of risk posed to public health and for developing strategies to mitigate the environmental loading of pathogens associated with waterborne disease transmission. Five rep-PCR genomic fingerprinting methods, such as rep-PCR, enterobacterial repetitive intergenic consensus (ERIC)-PCR, ERIC2-PCR, BOX-PCR and (GTG)(5)-PCR, were assessed for their potential in differentiation of 232 fecal Escherichia coli isolates obtained from humans, poultry (chicken, duck and turkey) and wild birds (Canada goose and gull). Based on the results of cluster analysis and discriminant function analysis, (GTG)(5)-PCR was found to be the most suitable method for molecular typing of fecal E. coli, followed by BOX-PCR, REP-PCR, ERIC-PCR and ERIC2-PCR. A discriminant function analysis of (GTG)(5)-PCR fingerprints showed that 94.1%, 79.8%, 80.5%, 74.4%, 86.7% and 88.6% of turkey, chicken, duck, Canada goose, gull and human E. coli isolates were classified into the correct host group, respectively. Subsequently, (GTG)(5)-PCR was tested for its ability to track the origin of 113 environmental E. coli isolated from natural pond water. In conclusion, the (GTG)(5)-PCR genomic fingerprinting method can be considered as a promising genotypic tool for epidemiological surveillance of fecal pollution in aquatic environments.     

Comparison of sampling methods for profiling cervicovaginal microbiome in rhesus macaques

Cervicovaginal bacteria cause inflammation which in turn increases HIV risk. Profiling the cervicovaginal microbiome, therefore, is instrumental for vaccine development. We show that the microbiome profile captured by cervicovaginal lavage is comparable to samples obtained by vaginal swabs. Thus, lavage may serve as a sampling strategy in NHP vaccine studies.     

Lake pigments facilitate analysis of fecal cortisol and behavior in group-housed macaques

Fecal steroid analyses are becoming more popular among both field and laboratory scientists. The benefits associated with sampling procedures that do not require restraint, anesthesia, and blood collection include less risk to both subject and investigator, as well as the potential to obtain endocrine profiles that do not reflect the influence of stress. However, the utility of the fecal steroid method has been limited in field conditions because of problems associated with sample identification. Here, we present evidence that Lake pigments are a valuable tool for the identification of individual fecal samples from group-housed female cynomolgus macaques. Further, we present data that suggest that excreted cortisol can be assayed from such samples, leading to the finding that time of day of sample collection influences cortisol concentrations, with morning samples producing higher values (t = 2.769, P = 0.024). Finally, the collection of physiological data from group-housed animals permits the evaluation of the relationship between endocrine status and behavior. This study demonstrated that morning fecal cortisol was significantly correlated with competitive and proximity behaviors, although not with rank in two stable social groups. In conclusion, the utility and validity of fecal steroid analyses continue to expand with further investigations.     

Comparison of metabolite production capability indices generated by network analysis methods

A framework of constraint-based reconstruction and analysis (COBRA) is used for modeling large-scale metabolic networks. In COBRA, extreme pathway and optimization analyses are commonly used to study the properties of networks. While the results of both methods are completely consistent, extreme pathway analysis is considered to be better because of its wider representational ability. In this study, we assessed these two methods by computational knockout experiments. We examined a simple pathway model and found that the extreme pathway method led to misguided conclusions in specific cases, while optimization analysis calculated the correct knockout effects. We also investigated the Escherichia coli metabolic pathway model, and found that these methods result in inconsistent interpretations of the network properties. IN CONCLUSION: it has been claimed that these two methods result in the same producible metabolites, but we found a difference in individual results for a biological pathway. Our results could provide helpful guidance for when to use the methods, particularly extreme pathway analysis.     

Comparison of DNA extraction methods for the PCR-single-strand-conformation polymorphism analysis of kefir

Experiments were performed to determine the influence of three DNA extraction methods (i.e. lysozyme, sonication and CTAB methods) from kefir on the microbial diversity analysis by PCR-single strand conformation polymorphism (PCR-SSCP). The results showed that the band of DNA extracted using CTAB was clearer than that using other methods. In addition, the yield and purity of DNA extracted using CTAB were the highest and reached, respectively, 915 μg/ml and 1.694.The results from the experiments indicated that the CTAB-based DNA extraction method was the most efficient method for DNA extraction from kefir. The heterogeneity of PCR products, amplified from community DNA with universal primers spanning the V3 region of 16S rRNA genes, was analysed by using SSCP. The results showed that the SSCP profile based on the sonication method gave the highest microbial diversity of kefir. One conclusion from these results was that the DNA extraction method was an important factor affecting the SSCP-based microbial diversity analysis of kefir.     

Troop composition data of wild Japanese macaques reviewed by multivariate methods

The troop composition (numbers of adult males,X ₁, adult females,X ₂, juveniles,X ₃, and infants,X ₄) of the Japanese macaque,Macaca fuscata, was examined using principal component analysis and discriminant analysis with 35 data sets from its entire distribution range.X ₂,X ₃ andX ₄ showed an equally high, positive correlation with one another. The variations of the troop composition variables were reinterpreted by a component representing the troop “size” and those representing “shape.” The data sets were sorted into three habitat zone groups from north to south. The functions discriminating between the habitat zone groups indicated thatX ₂ andX ₄ largely suffice for the discrimination. Examination ofX ₂ andX ₄ revealed that the troops in the south have a greaterX ₄/X ₂ ratio; however, further examination of this result indicated a relatively high offspring/female ratio only in the disturbed middle habitat zone but no conclusive latitudinal difference of birth rate. The results were discussed in relation to socioecology of the species. Order of authorship determined by a flip of a coin.