Sampling Human Indigenous Saliva Peptidome Using a Lollipop-Like Ultrafiltration Probe: Simplify and Enhance Peptide Detection for Clinical Mass Spectrometry

Although human saliva proteome and peptidome have been revealed ^1-2 they were majorly identified from tryptic digests of saliva proteins. Identification of indigenous peptidome of human saliva without prior digestion with exogenous enzymes becomes imperative, since native peptides in human saliva provide potential values for diagnosing disease, predicting disease progression, and monitoring therapeutic efficacy. Appropriate sampling is a critical step for enhancement of identification of human indigenous saliva peptidome. Traditional methods of sampling human saliva involving centrifugation to remove debris ^3-4 may be too time-consuming to be applicable for clinical use. Furthermore, debris removal by centrifugation may be unable to clean most of the infected pathogens and remove the high abundance proteins that often hinder the identification of low abundance peptidome.Conventional proteomic approaches that primarily utilize two-dimensional gel electrophoresis (2-DE) gels in conjugation with in-gel digestion are capable of identifying many saliva proteins ^5-6. However, this approach is generally not sufficiently sensitive to detect low abundance peptides/proteins. Liquid chromatography-Mass spectrometry (LC-MS) based proteomics is an alternative that can identify proteins without prior 2-DE separation. Although this approach provides higher sensitivity, it generally needs prior sample pre-fractionation ⁷ and pre-digestion with trypsin, which makes it difficult for clinical use. To circumvent the hindrance in mass spectrometry due to sample preparation, we have developed a technique called capillary ultrafiltration (CUF) probes ^8-11. Data from our laboratory demonstrated that the CUF probes are capable of capturing proteins in vivo from various microenvironments in animals in a dynamic and minimally invasive manner ^8-11. No centrifugation is needed since a negative pressure is created by simply syringe withdrawing during sample collection. The CUF probes combined with LC-MS have successfully identified tryptic-digested proteins ^8-11. In this study, we upgraded the ultrafiltration sampling technique by creating a lollipop-like ultrafiltration (LLUF) probe that can easily fit in the human oral cavity. The direct analysis by LC-MS without trypsin digestion showed that human saliva indigenously contains many peptide fragments derived from various proteins. Sampling saliva with LLUF probes avoided centrifugation but effectively removed many larger and high abundance proteins. Our mass spectrometric results illustrated that many low abundance peptides became detectable after filtering out larger proteins with LLUF probes. Detection of low abundance saliva peptides was independent of multiple-step sample separation with chromatography. For clinical application, the LLUF probes incorporated with LC-MS could potentially be used in the future to monitor disease progression from saliva.     

Differences in saliva collection location and disparities in baseline and diurnal rhythms of alpha-amylase: A preliminary note of caution

Identified in the early 1980s as a surrogate marker of the sympathetic nervous system component of the stress response, there has been renewed interest in measuring salivary alpha-amylase (sAA) to test biosocial models of stress vulnerability. This brief report presents studies that document that oral fluids from the parotid and submandibular gland areas had higher sAA values than did whole saliva specimens, and sAA values in whole saliva were higher than levels measured in oral fluids from the sublingual gland area. sAA in oral fluids from the parotid and submandibular gland areas showed the highest and more pronounced diurnal variation than levels in whole saliva, and sAA in sublingual saliva showed the lowest and shallowest diurnal variation. When this source of inherent variability in sAA activity levels is not controlled for by collecting oral fluids consistently from specific gland areas, the detection of individual differences, associations between sAA and “behavioral” variables, and intra-individual change in sAA levels may be compromised. Awareness, and management, of this ubiquitous source of measurement error in sAA are essential to ensure the success of future research on the correlates and concomitants of sAA levels, stress-related reactivity and recovery, and diurnal variation.     

Differences in saliva collection location and disparities in baseline and diurnal rhythms of alpha-amylase: a preliminary note of caution

Identified in the early 1980s as a surrogate marker of the sympathetic nervous system component of the stress response, there has been renewed interest in measuring salivary alpha-amylase (sAA) to test biosocial models of stress vulnerability. This brief report presents studies that document that oral fluids from the parotid and submandibular gland areas had higher sAA values than did whole saliva specimens, and sAA values in whole saliva were higher than levels measured in oral fluids from the sublingual gland area. sAA in oral fluids from the parotid and submandibular gland areas showed the highest and more pronounced diurnal variation than levels in whole saliva, and sAA in sublingual saliva showed the lowest and shallowest diurnal variation. When this source of inherent variability in sAA activity levels is not controlled for by collecting oral fluids consistently from specific gland areas, the detection of individual differences, associations between sAA and “behavioral” variables, and intra-individual change in sAA levels may be compromised. Awareness, and management, of this ubiquitous source of measurement error in sAA are essential to ensure the success of future research on the correlates and concomitants of sAA levels, stress-related reactivity and recovery, and diurnal variation.     

Diurnal Rhythms of Plasma Ions and Metabolites Levels in Thoroughbred Racehorses

The purposes of this study were to observe the presence of diurnal rhythms in plasma ions and metabolites levels in Thoroughbred racehorses under physical training, and to determine the time of blood sampling in clinical investigations. Plasma calcium, phosphorus, potassium, sodium, chloride, magnesium, iron, glucose, cholesterol, triglycerides, and total proteins levels were studied over a 72-h period. Blood samples were taken every 4 hours from five male and five female Thoroughbred racehorses under physical training. COSINOR analyses (P = 0.05) were done. Plasma potassium and triglycerides showed significant diurnal rhythms, with its acrophases occurring at dark period. No significant diurnal rhythms of other variables were found. It was concluded that, in Thoroughbred racehorses, the optimum time for potassium, and triglycerides sampling seems to be light period. And for other variables, time of diagnosis is not important.     

Diurnal Rhythms of Plasma Ions and Metabolites Levels in Thoroughbred Racehorses

The purposes of this study were to observe the presence of diurnal rhythms in plasma ions and metabolites levels in Thoroughbred racehorses under physical training, and to determine the time of blood sampling in clinical investigations. Plasma calcium, phosphorus, potassium, sodium, chloride, magnesium, iron, glucose, cholesterol, triglycerides, and total proteins levels were studied over a 72-h period. Blood samples were taken every 4 hours from five male and five female Thoroughbred racehorses under physical training. COSINOR analyses (P = 0.05) were done. Plasma potassium and triglycerides showed significant diurnal rhythms, with its acrophases occurring at dark period. No significant diurnal rhythms of other variables were found. It was concluded that, in Thoroughbred racehorses, the optimum time for potassium, and triglycerides sampling seems to be light period. And for other variables, time of diagnosis is not important.     

Dynamic proteome changes of Shigella flexneri 2a during transition from exponential growth to stationary phase

Shigella flexneri is an infectious pathogen that causes dysentery to human, which remains a serious threat to public health, particularly in developing countries. In this study, the global protein expression patterns of S. flexneri during transition from exponential growth to stationary phase in vitro were analyzed by using 2-D PAGE combined with MALDI-TOF MS. In a time-course experiment with five time points, the relative abundance of 49 protein spots varied significantly. Interestingly, a putative outer membrane protein YciD （OmpW） was almost not detected in the exponential growth phase but became one of the most abundant proteins in the whole stationary-phase proteome. Some proteins regulated by the global regulator FNR were also significantly induced （such as AnsB, AspA, FrdAB, and KatG） or repressed （such as AceEF, OmpX, SodA, and SucAB） during the growth phase transition. These proteins may be the key effectors of the bacterial cell cycle or play important roles in the cellular maintenance and stress responses. Our expression profile data provide valuable information for the study of bacterial physiology and form the basis for future proteomic analyses of this pathogen.     

Detection and quantitation of forty eight cytokines, chemokines, growth factors and nine acute phase proteins in healthy human plasma, saliva and urine

Cytokines, chemokines, growth factors (CCGFs) and other low abundance proteins/peptides in human body fluids or in tissues are potential biomarkers. Human body fluids such as plasma, saliva, urine, etc. are being analyzed more frequently than tissues primarily because of ease of sample collection. However, available information on concentrations of a large number of CCGFs in various body fluids of the same healthy individuals and gender-specific CCGFs is limited. In this work concentrations of 48 CCGFs were measured using multiplex bead assays and compared between plasma, saliva and urine collected from 20 male and female healthy volunteers. Forty three CCGFs were detected at least in one sample type of which 37 were in plasma, 41 were in saliva, and 34 were in urine; five CCGFs were not detected in any sample. Concentrations of detected CCGFs differed significantly between sample types but similar between gender groups. Gender-specific CCGFs were also observed. Concentrations of nine acute phase proteins were also measured from plasma, saliva and urine to determine general health conditions of the volunteers. This work will provide an idea of which CCGFs are detectable and their relative concentrations in healthy human plasma, saliva and urine and which CCGFs are gender-specific.     

Speed and Cardiac Recovery Variables Predict the Probability of Elimination in Equine Endurance Events

Nearly 50% of the horses participating in endurance events are eliminated at a veterinary examination (a vet gate). Detecting unfit horses before a health problem occurs and treatment is required is a challenge for veterinarians but is essential for improving equine welfare. We hypothesized that it would be possible to detect unfit horses earlier in the event by measuring heart rate recovery variables. Hence, the objective of the present study was to compute logistic regressions of heart rate, cardiac recovery time and average speed data recorded at the previous vet gate (n-1) and thus predict the probability of elimination during successive phases (n and following) in endurance events. Speed and heart rate data were extracted from an electronic database of endurance events (80–160 km in length) organized in four countries. Overall, 39% of the horses that started an event were eliminated—mostly due to lameness (64%) or metabolic disorders (15%). For each vet gate, logistic regressions of explanatory variables (average speed, cardiac recovery time and heart rate measured at the previous vet gate) and categorical variables (age and/or event distance) were computed to estimate the probability of elimination. The predictive logistic regressions for vet gates 2 to 5 correctly classified between 62% and 86% of the eliminated horses. The robustness of these results was confirmed by high areas under the receiving operating characteristic curves (0.68–0.84). Overall, a horse has a 70% chance of being eliminated at the next gate if its cardiac recovery time is longer than 11 min at vet gate 1 or 2, or longer than 13 min at vet gates 3 or 4. Heart rate recovery and average speed variables measured at the previous vet gate(s) enabled us to predict elimination at the following vet gate. These variables should be checked at each veterinary examination, in order to detect unfit horses as early as possible. Our predictive method may help to improve equine welfare and ethical considerations in endurance events.     

Fecal dehydroepiandrosterone (DHEA) immunoreactivity as a noninvasive index of circulating DHEA activity in young male laboratory rats

Evidence suggests that dehydroepiandrosterone (DHEA) plays a key role in stress and coping responses. Fecal sampling permits assessment of hormone-behavior interactions reliably and effectively, but no previous study has compared circadian- or stress-dependent alterations between serum DHEA and its fecal metabolites. In the current study, young (28 d of age) male rats were assigned to either an experimental (n = 6) or control (n = 6) group. Rats in the experimental group were exposed to a forced swim test to assess their behavioral and physiologic response to an environmental stressor; blood samples were drawn before the test (baseline), immediately after the test, and at 2 later time points. Only fecal samples were collected from control animals. Fecal DHEA and corticosterone metabolites were monitored in all animals for 24 h. DHEA metabolites in control rats exhibited significant diurnal variation, showing a similar temporal pattern as that of corticosterone metabolites. In addition, fecal and serum DHEA levels were highly correlated. Significant peaks in both DHEA and corticosterone metabolite levels were detected. These data suggest that measures of fecal DHEA can provide a complementary, noninvasive method of assessing adrenal gland function in rats.     

Changes in the diurnal rhythms of cortisol,melatonin, and testosterone after 2, 4, and 7 consecutive night shifts in male police officers

Night work is associated with a large range of acute health problems and possibly also health consequences in the long run. Yet, only very few field studies specifically investigate the effects of consecutive night shift on key physiological regulatory systems. In this field study, we investigated the effects of consecutive night shifts on three hormones, melatonin, cortisol, and testosterone, among police officers at work. More specifically, the aim was to investigate how the diurnal rhythms of melatonin, cortisol, and testosterone responded to two, four, and seven consecutive night shifts and a corresponding number of days for recovery. The study was part of the “In the Middle of the Night” project and included 73 male police officers from five different police districts. The participants were exposed to three intervention conditions: “2+2”: two consecutive night shifts followed by two consecutive day recovery days; “4+4”: four consecutive night shifts followed by four consecutive recovery days; “7+7”: seven consecutive night shifts followed by seven consecutive recovery days. On the last day with night shift and the last recovery day in each intervention, the participants collected saliva samples every 4th hour when awake. The diurnal rhythms of melatonin, cortisol, and testosterone were all affected differently by an increasing number of consecutive night shifts: the amplitude of the melatonin rhythm was suppressed by 4.9% per day (95% CI 1.4–8.2% per day; p = 0.006). The diurnal rhythm of cortisol phase was delayed with an increasing number of night shifts by 33 min/day (95% CI 18–48 min per day; p ≤ 0.001), but did not show any changes in amplitude. For the diurnal rhythm of testosterone, there was no effect of the number of consecutive night shifts and the diurnal rhythm completely followed the sleep/wake cycle. We found that there were no differences in the rhythms of melatonin, cortisol, and testosterone after 2, 4, and 7 recovery days, respectively. In conclusion, we found signs of desynchronization in terms of suppressed amplitude of melatonin and phase delay of salivary cortisol as a consequence of the increasing number of consecutive night shifts among police officers at work. Lack of synchronization has been suggested as a possible mechanism linking night work to disease, but this remains to be determined.     

Diurnal variation of salivary cortisol in captive African elephants (Loxodonta africana) under routine management conditions and in relation to a translocation event

The present study assessed the diurnal variation in salivary cortisol in captive African elephants during routine management (baseline) and in relation to a potential stressor (translocation) to evaluate to what extent acute stress may affect diurnal cortisol patterns. Under baseline conditions, we collected morning and afternoon saliva samples of 10 animals (three zoos) on different days in two study periods (n = 3–10 per animal, daytime and period). Under stress conditions, we sampled the transported cow (newcomer) and the two cows of the destination zoo before and after the transport in the morning and afternoon (n = 3–9 per animal, daytime and transport phase), as well as after the first introduction of the newcomer to the bull (n = 1 per animal). Cortisol was measured in unextracted samples by enzyme immunoassay. Under baseline conditions, we observed the expected diurnal variation with higher cortisol levels in the morning than in the afternoon. Under stress conditions, neither a significant difference between pre- and posttransport, nor between morning and afternoon levels was found. The percentage difference between morning and afternoon cortisol after the transport, however, was remarkably lower than before the transport in the newcomer potentially indicating a stress response to familiarization. Saliva samples taken immediately after the introduction of the newcomer to the bull revealed a marked cortisol increase. Our findings indicate that stressors may disturb the diurnal cortisol rhythm. Furthermore, provided that samples can be collected promptly, salivary cortisol is a useful minimally invasive measure of physiological stress in the African elephant.     

西藏南部岗巴地区晚白垩世Cenomanian—Turonian集群灭绝事件后有孔虫动物群的复苏

西藏南部岗巴地区Cenomanian-Turonian界线附近发生过一次与大洋缺氧事件有关的集群灭绝事件。其后,随着海水中溶解氧含量的逐渐增加,海洋中微体古生物,尤其是有孔虫逐渐得到了恢复以至繁盛。从Turonian早期至Santonian晚期,有孔虫动物群的复苏过程经历了三个时期：残存期,复苏期及辐射期,其复苏的型式为渐变式复苏。     

Changes in rain forest butterfly diversity following major ENSO-induced fires in Borneo

Aims Throughout South‐East Asia, droughts associated with ENSO (El Niño Southern Oscillation) events have resulted in large‐scale fires affecting millions of hectares of rain forest. However, the long‐term impacts of these fires on the rain forest faunas are only poorly understood. Our aim was to study the recovery of rain forest butterfly assemblages following the 1997–98 ENSO event, which resulted in the largest‐scale fires in the recorded history of the region. Location A 420‐km² area in the Balikpapan‐Samarinda region of East Kalimantan, Indonesian Borneo. Methods Four landscapes were assessed after the 1997–98 ENSO event, including one landscape that was assessed prior to the event. Comparisons of species richness, species composition and guild abundance were made among landscapes and years. The relative importance of environment, geographical distance between sampling sites, and time between sampling years was quantified during the succession phase using a variance partitioning technique. Results The fires dramatically altered the butterfly community and resulted in a major decline in observed species richness within the landscape surveyed prior to the ENSO event. Following fires in 1998, butterfly assemblages in all landscapes were dominated by large‐winged generalist species. During 1999 and 2000, assemblages became increasingly dominated by smaller specialist species. Species endemic to Borneo that were present before fires were absent in 2000, despite intensive sampling over enhanced spatial and environmental scales. Community similarity was significantly dependent upon local environmental variables, geographical distance between sampling sites, and time between sampling years. Together, these explained over 52% of the observed variation in samples. Conclusions The importance of geographical distance between sampling sites indicates that recovery was dependent upon colonization from proximate habitats. Despite an apparent trend of return to pre‐ENSO community structure, low species richness throughout the survey area indicates that full recovery had not taken place by 2000.     

Diurnal rhythms of free estradiol and cortisol during the normal menstrual cycle in women with major depression

To investigate whether depression is accompanied by changes in diurnal rhythms of free estradiol and cortisol in different phases of the menstrual cycle, we measured these two hormone levels in saliva samples collected every 2 h for 24 h from 15 healthy normally cycling women and 12 age-matched normally cycling women suffering from major depression taking antidepressants. The assessments were repeated four times over one menstrual cycle: during menstruation and in the late follicular/peri-ovulating, early to mid-luteal and late luteal phases, respectively. Quantification with a nonlinear periodic regression model revealed distinct diurnal rhythms in free estradiol and free cortisol in all subjects. For the diurnal cortisol rhythm, significant differences were found in the peak-width and ultradian amplitude among different menstrual phases, both in controls and depressed patients, while no significant differences were found between the two groups. The diurnal estradiol rhythm, on the other hand, was quite consistent among different menstrual phases within both groups, while the depressed patients had overall larger amplitudes than controls, which is negatively correlated with disease duration. Significant positive correlations between the two hormone rhythms were found for 24-h mean level (mesor), peak, and trough in late luteal phase, and for ultradian harmonics in early to mid-luteal phase in controls, but only for ultradian harmonics in late follicular/peri-ovulating phase and for acrophase in the menstruation phase in depressed patients. A sub-analysis was also performed in patients who received Fluoxetine (n = 7). The findings implicate a close correlation between the hypothalamic-pituitary-adrenal axis and the hypothalamic-pituitary-gonadal axis, both of which may be involved in depression.     

枯草芽孢杆菌J-15抗大丽轮枝菌次生代谢产物对棉田土壤真菌多样性的影响

【背景】目前利用拮抗菌进行作物病害防治的研究较多,但拮抗菌次生代谢产物如何影响棉花根际土壤微生物群落相关的研究较少。【目的】探讨枯草芽孢杆菌J-15抗大丽轮枝菌次生代谢产物对棉田土壤真菌多样性的影响,为利用枯草芽孢杆菌J-15及其次生代谢产物防治棉花黄萎病的土壤微生物生态安全进行评估。【方法】以新疆北部玛纳斯地区棉田为土壤采样点,随机选取10个点进行采样后混合,经枯草芽孢杆菌J-15抗大丽轮枝菌次生代谢产物处理一定时间后,提取土样总DNA,利用Illumina HiSeq高通量技术,对样品中真菌ITS1-ITS2区进行高通量测序,分析J-15抗大丽轮枝菌次生代谢产物处理对土样真菌多样性的影响。【结果】在97%相似度水平下,处理10、30d后,样品中真菌的OTU数量、Chao1和ACE丰度指数均分别高于相同时间放置的未处理的对照组,而Simpson指数低于其对照组。从群落组成分析来看,与对照组相比,受J-15次生代谢产物处理的土壤样品,子囊菌门(Ascomycota)的盘菌属(Tricharina)和被孢霉门(Mortierellomycota)的被孢霉属(Mortierella)等优势真菌相对丰度提高,而丰度高于1%的2类病原真菌轮枝孢属(Verticillium)、镰孢霉属(Fusarmm)的丰度显著降低。【结论】J-15抗大丽轮枝菌次生代谢产物对棉田土壤真菌群落及丰度有显著影响,但不改变影响农业生产的土壤真菌群落的结构。