Collection and Extraction of Saliva DNA for Next Generation Sequencing

The preferred source of DNA in human genetics research is blood, or cell lines derived from blood, as these sources yield large quantities of high quality DNA. However, DNA extraction from saliva can yield high quality DNA with little to no degradation/fragmentation that is suitable for a variety of DNA assays without the expense of a phlebotomist and can even be acquired through the mail. However, at present, no saliva DNA collection/extraction protocols for next generation sequencing have been presented in the literature. This protocol optimizes parameters of saliva collection/storage and DNA extraction to be of sufficient quality and quantity for DNA assays with the highest standards, including microarray genotyping and next generation sequencing.     

The α-test: rapid cell-free CD4 enumeration using whole saliva

There is an urgent need for affordable CD4 enumeration to monitor HIV disease. CD4 enumeration is out of reach in resource-limited regions due to the time and temperature restrictions, technical sophistication, and cost of reagents, in particular monoclonal antibodies to measure CD4 on blood cells, the only currently acceptable method. A commonly used cost-saving and time-saving laboratory strategy is to calculate, rather than measure certain blood values. For example, LDL levels are calculated using the measured levels of total cholesterol, HDL, and triglycerides. Thus, identification of cell-free correlates that directly regulate the number of CD4(+) T cells could provide an accurate method for calculating CD4 counts due to the physiological relevance of the correlates. The number of stem cells that enter blood and are destined to become circulating CD4(+) T cells is determined by the chemokine CXCL12 and its receptor CXCR4 due to their influence on locomotion. The process of stem cell locomotion into blood is additionally regulated by cell surface human leukocyte elastase (HLE(CS)) and the HLE(CS)-reactive active α(1)proteinase inhibitor (α(1)PI, α(1)antitrypsin, SerpinA1). In HIV-1 disease, α(1)PI is inactivated due to disease processes. In the early asymptomatic categories of HIV-1 disease, active α(1)PI was found to be below normal in 100% of untreated HIV-1 patients (median=12 μM, and to achieve normal levels during the symptomatic categories. This pattern has been attributed to immune inactivation, not to insufficient synthesis, proteolytic inactivation, or oxygenation. We observed that in HIV-1 subjects with >220 CD4 cells/μl, CD4 counts were correlated with serum levels of active α(1)PI (r(2)=0.93, p<0.0001, n=26) and inactive α(1)PI (r(2)=0.91, p<0.0001, n=26). Administration of α(1)PI to HIV-1 infected and uninfected subjects resulted in dramatic increases in CD4 counts suggesting α(1)PI participates in regulating the number of CD4(+) T cells in blood. With stimulation, whole saliva contains sufficient serous exudate (plasma containing proteinaceous material that passes through blood vessel walls into saliva) to allow measurement of active α(1)PI and the correlation of this measurement is evidence that it is an accurate method for calculating CD4 counts. Briefly, sialogogues such as chewing gum or citric acid stimulate the exudation of serum into whole mouth saliva. After stimulating serum exudation, the activity of serum α(1)PI in saliva is measured by its capacity to inhibit elastase activity. Porcine pancreatic elastase (PPE) is a readily available inexpensive source of elastase. PPE binds to α(1)PI forming a one-to-one complex that prevents PPE from cleaving its specific substrates, one of which is the colorimetric peptide, succinyl-L-Ala-L-Ala-L-Ala-p-nitroanilide (SA(3)NA). Incubating saliva with a saturating concentration of PPE for 10 min at room temperature allows the binding of PPE to all the active α(1)PI in saliva. The resulting inhibition of PPE by active α(1)PI can be measured by adding the PPE substrate SA(3)NA. (Figure 1). Although CD4 counts are measured in terms of blood volume (CD4 cells/μl), the concentration of α(1)PI in saliva is related to the concentration of serum in saliva, not to volume of saliva since volume can vary considerably during the day and person to person. However, virtually all the protein in saliva is due to serum content, and the protein content of saliva is measurable. Thus, active α(1)PI in saliva is calculated as a ratio to saliva protein content and is termed the α(1)PI Index. Results presented herein demonstrate that the α(1)PI Index provides an accurate and precise physiologic method for calculating CD4 counts.     

Saliva,Salivary Gland,and Hemolymph Collection from Ixodes scapularis Ticks

Ticks are found worldwide and afflict humans with many tick-borne illnesses. Ticks are vectors for pathogens that cause Lyme disease and tick-borne relapsing fever (Borrelia spp.), Rocky Mountain Spotted fever (Rickettsia rickettsii), ehrlichiosis (Ehrlichia chaffeensis and E. equi), anaplasmosis (Anaplasma phagocytophilum), encephalitis (tick-borne encephalitis virus), babesiosis (Babesia spp.), Colorado tick fever (Coltivirus), and tularemia (Francisella tularensis) ^1-8. To be properly transmitted into the host these infectious agents differentially regulate gene expression, interact with tick proteins, and migrate through the tick ^3,9-13. For example, the Lyme disease agent, Borrelia burgdorferi, adapts through differential gene expression to the feast and famine stages of the tick''s enzootic cycle ^14,15. Furthermore, as an Ixodes tick consumes a bloodmeal Borrelia replicate and migrate from the midgut into the hemocoel, where they travel to the salivary glands and are transmitted into the host with the expelled saliva ^9,16-19.As a tick feeds the host typically responds with a strong hemostatic and innate immune response ^11,13,20-22. Despite these host responses, I. scapularis can feed for several days because tick saliva contains proteins that are immunomodulatory, lytic agents, anticoagulants, and fibrinolysins to aid the tick feeding ^{3,11,20,21,23}. The immunomodulatory activities possessed by tick saliva or salivary gland extract (SGE) facilitate transmission, proliferation, and dissemination of numerous tick-borne pathogens ^3,20,24-27. To further understand how tick-borne infectious agents cause disease it is essential to dissect actively feeding ticks and collect tick saliva. This video protocol demonstrates dissection techniques for the collection of hemolymph and the removal of salivary glands from actively feeding I. scapularis nymphs after 48 and 72 hours post mouse placement. We also demonstrate saliva collection from an adult female I. scapularis tick.     

Longitudinal analysis of acute-phase proteins in saliva in pig farms with different health status

This study assesses the utility of saliva samples to monitor the time course of the acute-phase response to different viruses in pigs under field conditions by using time-resolved immunofluorometric assays (TR-IFMA). A total of 30 pigs from three different farms, located in Southeast Spain, were used. Farm 1 had outbreaks of porcine circovirus type 2, farm 2 had infections with porcine reproductive and respiratory syndrome virus and farm 3 had concomitant infections with both viruses. Serology was used to determine the time of seroconversion of pigs to two different pathogens. The levels of two acute-phase proteins (APPs), C-reactive protein (CRP) and haptoglobin (Hp), were measured in saliva and serum samples and compared with pig's serology. Kinetic curves of both APPs across the study obtained in saliva samples were similar to those of serum, with R of 0.68 and 0.78 for CRP and Hp, respectively. The median CRP and Hp concentrations in saliva were higher around the theorized time of infection, according to previous experimental studies, and at seroconversion of animals. CRP increments were apparent 1 week before the increments obtained in Hp. These findings indicate that salivary APP concentrations, by using TR-IFMA, can be used in longitudinal studies as non-invasive early indicators of health status.     

Toward a standardized saliva proteome analysis methodology

The present study aimed the evaluation of saliva sample pre-treatment, in particular the sample clearance usually performed by centrifugation, to the contribution of salivary proteome and peptidome. Using in-gel and off-gel approaches, a large content of salivary proteins was detected in the pellet fraction that is usually discarded. In addition, chaotropic/detergent treatment in combination with sonication, before the centrifugation step, resulted in salivary complex disruption and consequently in the extraction of high amounts of proteins. Based on this data, we suggest the use of urea/detergent with sonication as a standard saliva sample pre-treatment procedure. We also described a procedure to extract salivary peptides which can be performed even after saliva sample treatment with chaotropic/detergents. In overall, we reported for the first time the contribution of the pellet fraction to the whole saliva proteome. iTRAQ analysis highlighted a higher number of different peptides as well as distinct quantities of each protein class when after sample treatment with urea and sonication, acetone precipitation followed by solubilization with acetonitrile/HCl was performed.     

Growth and chemical responses of trembling aspen to simulated browsing and ungulate saliva

Aims Woody plant-browser systems represent an understudied facet of herbivory. We subjected four genotypes of trembling aspen to artificial browsing, similar to that of a large mammalian herbivore, and applied deer saliva to clipped and unclipped trees to assess: (i) the effects of artificial browsing on aspen growth and phytochemistry of leaves and stems, (ii) genotypic variation in responses and (iii) potential alterations of responses by mammalian saliva.Methods Potted aspen trees were grown outdoors on the University of Wisconsin-Madison campus. The experiment consisted of a fully-crossed, 2 × 2 × 4 randomized complete block design, with two levels of artificial browsing (unclipped and clipped), two levels of saliva application (no saliva and saliva) and four aspen genotypes. To simulate ungulate browsing damage, we removed the upper 50% of the stem of half of the trees by pinching the stem with needle-nosed pliers and then separating it by tearing. For half of the damaged trees, we immediately swabbed the wound with deer saliva. Trees in the unclipped plus saliva treatment were swabbed with saliva at the 50% height mark. To assess the effects of clipping and saliva application, we harvested all trees after 2 months and measured various growth and chemical properties. Growth measurements included height, vertical growth, mass of leaves, stems and roots, leaf number and area and bud set. Chemical parameters included defensive, nutritional and structural components of both foliage and stems.Important findings Clipping affected most of the growth parameters measured, decreasing tree height, leaf, stem, root and total tree mass and leaf area. Clipped trees had greater vertical growth, more leaves and higher specific leaf area (SLA) than unclipped trees. Deer saliva had little to no effect on plant growth response to the clipping treatment. Terminal budset was delayed by clipping and varied among genotypes but not in response to saliva application. Clipping also affected most of the phytochemical variables measured, reducing defensive compounds (phenolic glycosides and condensed tannins (CTs)) and nutrients (N), but increasing structural components (cellulose and lignin) in both leaves and stems. Saliva had very little effect on tree chemistry, causing only a slight decrease in the amount of CTs in leaves. In general, leaves contained more defensive compounds and nutrients, but much less cellulose, compared with stems. Genotypes differed for all physical and chemical indices, and in tolerance to damage as measured by vertical growth. In addition, for most of the physical and chemical variables measured, genotype interacted with the clipping treatment, suggesting that in natural stands some genotypes will resist or tolerate browsing better than others, affecting forest genetic composition and ultimately forest dynamics.     

Formulation and Evaluation of Bioadhesive Buccal Drug Delivery of Tizanidine Hydrochloride Tablets

The study aim was concerned with formulation and evaluation of bioadhesive buccal drug delivery of tizanidine hydrochloride tablets, which is extensively metabolized by liver. The tablets were prepared by direct compression using bioadhesive polymers such as hydroxylpropyl methylcellulose K4M, sodium carboxymethyl cellulose alone, and a combination of these two polymers. In order to improve the permeation of drug, different permeation enhancers like beta-cyclodextrin (β-CD), hydroxylpropyl beta-cyclodextrin (HP-β-CD), and sodium deoxycholate (SDC) were added to the formulations. The β-CD and HP-β-CD were taken in 1:1 molar ratio to drug in formulations. Bioadhesion strength, ex vivo residence time, swelling, and in vitro dissolution studies and ex vivo permeation studies were performed. In vitro release of optimized bioadhesive buccal tablet was found to be non-Fickian. SDC was taken in 1%, 2%, and 3% w/w of the total tablet weight. Stability studies in natural saliva indicated that optimized formulation has good stability in human saliva. In vivo mucoadhesive behavior of optimized formulation was performed in five healthy male human volunteers and subjective parameters were evaluated.