Sample Preparation Stage Research Articles

Synthesis and Characterization of a-Si<sub>x</sub>C<sub>y</sub> Thin Films Prepared by RF Magnetron Co-Sputtering Technique

Si-C based alloys have attracted much attention due to their potential applications in electronic and optical devices. In this paper, a-SixCy thin films with different Silicon (Si) content are obtained by sputtering of SiC; co-sputtering of SiC and Si targets at different deposition temperatures (Td) such as 200oC, 350oC and 500oC. It is annealed at various annealing temperature (Ta) using conventional thermal annealing (CTA) and Rapid Thermal Annealing (RTA) techniques. The effect of excess Si incorporation and the unintentional oxidation during various stages of sample preparation are discussed. Their structural and optical properties are investigated using spectroscopic ellipsometry, X-Ray Diffraction spectroscopy (XRD), and Fourier Transform Infrared spectroscopy (FTIR). The refractive index value (n1.95eV) varies between 1.6 to 3.6, suggesting the transition from porous silicon carbide to Si-rich silicon carbide or silicon oxycarbide upon increasing Td and Ta, which is also supported by the FTIR spectra. The emergence of absorption peak between ~950 cm−1 and 1100 cm−1 with the increase of Ta and excess silicon is attributed to Si-O a stretching vibration bond which is an indication of Si richness and unintentional oxidation during annealing. Detailed analysis on the process parameters and the evolution of phase transformations are discussed.

The Influence of Ionic Liquids on the Effectiveness of Analytical Methods Used in the Monitoring of Human and Veterinary Pharmaceuticals in Biological and Environmental Samples-Trends and Perspectives.

Recent years have seen the increased utilization of ionic liquids (ILs) in the development and optimization of analytical methods. Their unique and eco-friendly properties and the ability to modify their structure allows them to be useful both at the sample preparation stage and at the separation stage of the analytes. The use of ILs for the analysis of pharmaceuticals seems particularly interesting because of their systematic delivery to the environment. Nowadays, they are commonly detected in many countries at very low concentration levels. However, due to their specific physiological activity, pharmaceuticals are responsible for bioaccumulation and toxic effects in aquatic and terrestrial ecosystems as well as possibly upsetting the body’s equilibrium, leading to the dangerous phenomenon of drug resistance. This review will provide a comprehensive summary of the use of ILs in various sample preparation procedures and separation methods for the determination of pharmaceuticals in environmental and biological matrices based on liquid-based chromatography (LC, SFC, TLC), gas chromatography (GC) and electromigration techniques (e.g., capillary electrophoresis (CE)). Moreover, the advantages and disadvantages of ILs, which can appear during extraction and separation, will be presented and attention will be given to the criteria to be followed during the selection of ILs for specific applications.

The nitrate content of fresh and cooked vegetables and their health-related risks.

BackgroundVegetables are the most important source of nitrates in the human diet. During various processes in the body, nitrates are converted into nitrites, which causes various diseases, such as blue baby syndrome and cancer. This study aimed to determine the concentration of nitrates in several vegetable farms in Sanandaj city and to evaluate their health-related risks.MethodsThis descriptive cross-sectional study was conducted from October 2017 to July 2018. A total of 90 samples were taken from nine farms. Soil and water sampling was also carried out. All stages of sample preparation and extraction were carried out according to Food Standards 2–16721, and the nitrate measurements were performed using ion chromatography (Compact IC Plus 882 Model, Metrohm, Switzerland). A health risk assessment was performed using the non-carcinogenic risk assessment.ResultsThis study’s results showed that the nitrate concertation in all vegetables was less than National Iranian Vegetable Nitrate Standard. Nitrate levels in leafy vegetables were higher than in root vegetables, and the root vegetables levels were higher than those in Fruit vegetable. The nitrate level in vegetables in autumn was higher than in spring. The cooking process reduced the raw vegetables’ nitrate content from 4.094% to 13.407%, while the frying process increased the vegetables’ nitrate content from 12.46% to 29.93%. The highest health risk level in raw, cooked and fried vegetables was parsley, parsley and beet leaves, respectively, and the lowest in all categories was tomatoes. Generally, the highest health risk was related to fried beet leaves, and the lowest was raw tomatoes. In addition, each of the abovementioned relationships between vegetables’ nitrate levels and the harvest season, type of processing procedure and type of vegetables was significant (p < 0.05). The irrigation water’s nitrate concentration in all fields was between 12.36 and 33.14 mg/l. The soil contained nitrate levels of between 4.35 and 9.7 mg/kg.ConclusionBased on this study, we can conclude that the amount of nitrates in raw vegetables was lower than the standard limit’s level and that this level does not cause health problems for consumers.

Forecast of the metrological characteristics of the method of the quantitative determination of verapamil in blood in forensic chemical analysis

The aim of the work is to test theoretical prognosis of metrological characteristics of methods of quantitative determination in forensic chemical analysis on the example of method of determination of verapamil content in blood by thin layer chromatography with computer densitometry. The algorithm of prognostic determination of relative error for methods of quantitative analysis in forensic chemical examination using computer program «ChemMetrEvaluation 1.0» is offered. The implementation of the algorithm is based on a detailed analysis of error estimation of measurements at the stages of sample preparation, measuring the value of the analytical signal.

Modification of cysteine residues for mass spectrometry-based proteomic analysis: facts and artifacts

Mass spectrometric proteomic analysis at the sample preparation stage involves the artificial reduction of disulfide bonds in proteins formed between cysteine residues. Such bonds, when preserved in their native state, complicate subsequent enzymatic hydrolysis and interpretation of the research results. To prevent the re-formation of the disulfide bonds, cysteine residues are protected by special groups, most often by alkylation. In this review, we consider the methods used to modify cysteine residues during sample preparation, as well as possible artifacts of this stage. Particularly, adverse reactions of the alkylating agents with other amino acid residues are described. The most common alkylating compound used to protect cysteine residues in mass spectrometric proteomic analysis is iodoacetamide. However, an analysis of the literature in this area indicates that this reagent causes more adverse reactions than other agents used, such as chloroacetamide and acrylamide. The latter can be recommended for wider use. In the review we also discuss the features of the cysteine residue modifications and their influence on the efficiency of the search for post-translational modifications and protein products of single nucleotide substitutions.

A protocol for laser microdissection (LMD) followed by transcriptome analysis of plant reproductive tissue in phylogenetically distant angiosperms

BackgroundPlant development is controlled by the action of many, often connected gene regulatory networks. Differential gene expression controlled by internal and external cues is a major driver of growth and time specific differentiation in plants. Transcriptome analysis is the state-of-the-art method to detect spatio-temporal changes in gene expression during development. Monitoring changes in gene expression at early stages or in small plant organs and tissues requires an accurate technique of tissue isolation, which subsequently results in RNA of sufficient quality and quantity. Laser-microdissection enables such accurate dissection and collection of desired tissue from sectioned material at a microscopic level for RNA extraction and subsequent downstream analyses, such as transcriptome, proteome, genome or miRNA.ResultsA protocol for laser-microdissection, RNA extraction and RNA-seq was optimized and verified for three distant angiosperm species: Arabidopsis thaliana (Brassicaceae), Oryza sativa (Poaceae) and Eschscholzia californica (Papaveraceae). Previously published protocols were improved in processing speed by reducing the vacuum intensity and incubation time during tissue fixation and incubation time and cryoprotection and by applying adhesive tape. The sample preparation and sectioning of complex and heterogenous flowers produced adequate histological quality and subsequent RNA extraction from micro-dissected gynoecia reliably generated samples of sufficient quality and quantity on all species for RNA-seq. Expression analysis of growth stage specific A. thaliana and O. sativa transcriptomes showed distinct patterns of expression of chromatin remodelers on different time points of gynoecium morphogenesis from the initiation of development to post-meiotic stages.ConclusionHere we describe a protocol for plant tissue preparation, cryoprotection, cryo-sectioning, laser microdissection and RNA sample preparation for Illumina sequencing of complex plant organs from three phyletically distant plant species. We are confident that this approach is widely applicable to other plant species to enable transcriptome analysis with high spatial resolution in non-model plant species. The protocol is rapid, produces high quality sections of complex organs and results in RNA of adequate quality well suited for RNA-seq approaches. We provide detailed description of each stage of sample preparation with the quality and quantity measurements as well as an analysis of generated transcriptomes.

Summary of Clinical Laboratory Studies Performed During Preclinical Safety Evaluation of Medicinal Products (Part I: Haematological Studies)

Preclinical safety evaluation is an important stage in the development of medicinal products. Clinical laboratory studies, including haematological, biochemical and pathomorphological studies, are an essential part of chronic toxicity studies. A careful choice of methodological approaches to examination of toxicological characteristics of drug candidates makes it possible to assess the degree of risk associated with their subsequent clinical use, identify potential target organs, determine the extent of damage, as well as the possibility and dynamics of restoring damaged systems. Key prerequisites for obtaining adequate results of the studies are correct methodological implementation of all the stages of sample preparation and careful consideration of all factors during interpretation of the obtained data. Thus, the choice of methodological approaches to blood tests is often determined by the species, age and sex of laboratory animals, as well as by specific characteristics of the tested drug. The aim of the study was to summarise data on haematological studies performed in the Drug Toxicology Laboratory of the Federal State Budgetary Institute «Zakusov Institute of Pharmacology» when conducting chronic toxicity studies.

Understanding the contribution of operator measurement variability within Flow Cytometry data analysis for Quality Control of Cell and Gene Therapy manufacturing

Flow Cytometry is a measurement technique used in Quality Control and in-process measurements of biomanufactured Cell and Gene Therapy products. However, it contains a number of sources of measurement variation at; sample preparation, instrument setup, analysis, and post-analytical data analysis stages. The latter sees variation introduced from operator subjectivity, which is investigated here to understand what effects the interpretation of diagrammatical protocols have on inter-operator analysis.36 operators from different sites were given a series of histograms to analyse, gating a shifting peak. This was repeated with diagrammatical protocols to apply gates which reduced inter-operator variation by up to 92%. Various control limits include and exclude different results and when adjusted with a log transform differences in outlier discrimination have been found. This research supports the use of Flow Cytometry diagrammatical protocols to reduce the contribution of inter-operator variation and measurement uncertainty associated within Cell and Gene Therapy manufacturing scenarios.

The new technologies of high-throughput single-cell RNA sequencing

A wealth of genome and transcriptome data obtained using new generation sequencing (NGS) technologies for whole organisms could not answer many questions in oncology, immunology, physiology, neurobiology, zoology and other fields of science and medicine. Since the cell is the basis for the living of all unicellular and multicellular organisms, it is necessary to study the biological processes at its level. This understanding gave impetus to the development of a new direction – the creation of technologies that allow working with individual cells (single-cell technology). The rapid development of not only instruments, but also various advanced protocols for working with single cells is due to the relevance of these studies in many fields of science and medicine. Studying the features of various stages of ontogenesis, identifying patterns of cell differentiation and subsequent tissue development, conducting genomic and transcriptome analyses in various areas of medicine (especially in demand in immunology and oncology), identifying cell types and states, patterns of biochemical and physiological processes using single cell technologies, allows the comprehensive research to be conducted at a new level. The first RNA-sequencing technologies of individual cell transcriptomes (scRNA-seq) captured no more than one hundred cells at a time, which was insufficient due to the detection of high cell heterogeneity, existence of the minor cell types (which were not detected by morphology) and complex regulatory pathways. The unique techniques for isolating, capturing and sequencing transcripts of tens of thousands of cells at a time are evolving now. However, new technologies have certain differences both at the sample preparation stage and during the bioinformatics analysis. In the paper we consider the most effective methods of multiple parallel scRNA-seq using the example of 10XGenomics, as well as the specifics of such an experiment, further bioinformatics analysis of the data, future outlook and applications of new high-performance technologies.

Molecular subtyping and dna sequencing homology of Escherichia coli O157:H7 isolated from Aceh cattle

Escherichia coli (E. coli) O157:H7 is one of bacteria that recognized as pathogenic agent, both in animals and human. Several isolates of this bacteria were obtained from local livestock, such as in bali cattle and aceh cattle. However, the bacteria found in aceh cattle has not been confirmed through molecular technique. The current study was aimed to confirm the finding of E. coli strain O157:H7 in aceh cattle using molecular analysis. Three isolates of E. coli O157 (MA-35, MA-44, and MA-58) obtained from aceh cattle were extracted for the DNA using Presto™ Mini gDNA bacteria kit (Geneaid) through several processing stages of sample preparation, lysis, DNA binding, washing and elution. Then, it was continued with DNA Amplification Using Polimerase Chain Reaction (PCR). DNA sequencing homology was conducted using BLASTN program. Data of this study were analysed descriptively. The results showed that one of isolate (MA-58) was detected for the presence of genes of rfb (339 bp), fliC (401 bp), and stx2 (115 bp). Then, this isolate has a homology of 100% to 16 different strains of E. coli O157:H7 sequence in the GenBank. In conclusion, the molecular analysis of the local isolate of bacteria of MA-58 obtained from aceh cattle confirmed that it is E. coli O157:H7 and detected with the presence of genes of rfb, fliC, and stx2.

Analysis and identification of &lt;i&gt;Pseudomonas&lt;/i&gt; sp. and molds on dried anchovy (&lt;i&gt;Stelophorus&lt;/i&gt; sp) products produced by the people of Toniku Village, Halmahera Barat Regency, North Maluku Province

This research was conducted to determine the characteristics of Pseudomonas sp. and mold on dried anchovies. The sample in this study was obtained from the fishing community of Toniku Village, West Halmahera Regency, North Maluku Province. The stages carried out in this study were 3 (three) stages, namely the sample preparation stage, the analysis phase and the identification stage of Pseudomonas sp. and mold. The results showed that the characteristics of the Total Plate Count (TPC) of dried anchovy in the Toniku Village obtained a different composition from each other, with the highest log Total Plate Count (TPC) obtained, namely 5.5 or 3.2 x 105 Cfu/g or 320.000 cells bacteria, while the lowest Total Plate Count (TPC) log was obtained, 2.5 or 3.1 x 102 Cfu/g or 310 bacterial cells and for total Pseudomonas bacteria from the three sampling locations no growth was found. The highest total log fungi were obtained ie 5.6 or 3.7 x 105 Cfu/g or 370.000 mold cells, while the lowest total log fungi were obtained which were 2.4 or 2.6 x 102 Cfu/g or 260 mold cells

METHODICAL SUPPORT FOR CONTROL OVER THE CONCENTRATION OF PERSISTENT ORGANIC POLLUTANT HEXACHLOROBENZENE IN BLOOD

Introduction. Persistent organic pollutants (POP) are extremely dangerous compounds contaminating the environment and exerting the negative impact on human health. Organochlorine pesticides, including hexachlorobenzene, are a specific group among POP. Our research goal is methodological support for the hexachlorobenzene content control in human biological environments. Material and methods. We developed highly both sensitive and selective procedure for determining hexachlorobenzene in blood. Hexachlorobenzene determination in blood is based on the application of capillary gas chromatography with linear programming of a column temperature, electron capture detector (ECD), and extraction with an organic solvent at a sample preparation stage. When implementing the developed methodology, the following indices were evaluated: accuracy and error characteristics of the analysis results. The lower limit of hexachlorobenzene quantification (LOQ) in blood amounted to 0.000024 µg/cm3, with the range of detectable concentrations from 0.00015 to 0.005 (determination method error ≥ 20%), which allows to adequately diagnose chemical burden with a highly toxic persistent organic pollutant in blood. Results. The results of quantitative chemical analysis of hexachlorobenzene contents in blood had the following quality indices: precision and correctness amounted to 15.621%; repeatability - 3.45%; reproducibility - 4.65%. In the process of testing the method, concentrations of hexachlorobenzene in the range of 0.0003 ± 0.0001 ÷ 0.0007 ± 0.0001 μg/cm3 were detected in the blood of the examined group. Discussion. The high efficiency of gas chromatography determination of hexachlorobenzene in blood was achieved via selection of optimal conditions for chromatographic analysis: capillary column HP-1- 35m∙0.32mm∙0.25µm with linear programming of column temperature, carrier gas (nitrogen), electron capture detector (ECD). The developed method of the preparing a blood sample for analysis, including liquid extraction with toluene, protein denaturation by centrifuging the biological medium at 7000 rpm for 15 min at pH of 6-7 in combination with gas chromatographic analysis and an electron capture detector (ECD) made it possible to complete extraction of hexachlorobenzene from blood in an amount of 99.7%.

Determination of sources of sulfur dioxide in confectionery

Sulfur dioxide is used to ensure the safety of fruit raw materials and semi-finished products used for the production of confectionery. This preservative has allergenic properties. In accordance with the Technical Regulations of the Customs Union TR CU 022/2011 "Food products in terms of their labeling" the content of sulfur dioxide must be specified when labeling confectionery products, if its content exceeds 10 mg per kg. The definition of this preservative in raw materials, semi-finished products and confectionery in accordance with the current GOST 26811 “Confectionery. The iodometric method for determining the mass fraction of total sulfuric acid is often difficult because of the complexity of confectionery products, the formation of intensive staining of the solutions under study and the ability of sulfur dioxide to react with other components of the objects under study. Therefore, the task of developing methods with the optimization of the sample preparation stage of the samples under study, which allow one to fully determine sulfur dioxide in confectionery products, semi-finished products and raw materials, is relevant. The purpose of this work was to develop methods for determining sulfur dioxide in raw materials, semi-finished products and various names of confectionery products, as well as assessing the impact of these types of raw materials and semi-finished products on the content of sulfur dioxide in confectionery products. The results showed that sulfur dioxide is present in many raw materials. In mg per 1 kg of sugar in white sand from 1 to 9, molasses from 25 to 52, wheat flour from 9 to 15, starch from 3 to 17. In fruit raw materials from 5 to 545 mg per kg. In confectionery: marshmallow and marshmallow from 8 to 29, gingerbread from 6 to 25, biscuits from 0 to 16, chocolate from 8 to 13. Based on the data obtained, it can be concluded that the content of sulfur dioxide in raw materials and semi-finished confectionery products is a very wide range, which makes it necessary to control the quality of all raw materials entering the production. Sulfur dioxide, used as a preservative for fruit raw materials, can significantly increase the content of this allergen in confectionery made using such raw materials. Ensuring the level of sulfur dioxide less than 10 mg / kg is achieved using raw materials with low content of sulfur dioxide and technological methods.

Countercurrent Chromatography in Elemental Analysis: From Oil to High-Purity Substances

The capabilities of countercurrent chromatography (CCC) in the elemental analysis of samples with different chemical and phase compositions are demonstrated. The combination of the characteristic features of extraction chromatography and multistage extraction with separation and preconcentration processes performed in a closed system (a Teflon coiled column) opens up prospects for applying this method to the analysis of a wide range of materials from high-purity substances to oil and rocks. The use of CCC at the stage of sample preparation makes it possible to decrease the detection limits of impurity elements in high-purity materials to a pg/g level, i.e., by two or three orders of magnitude, as compared with those in the direct determination by inductively coupled plasma mass spectrometry. In the analysis of oil samples, CCC allows one to determine their complete trace element composition (including platinum group, rare, and rare earth elements) due to the concentration of trace elements in a small volume of a stationary aqueous phase retained in the column.

Determination of elements in human saliva using arc atomic emission spectrometry with MAÉS

Features of determination of trace elements in saliva samples by atomic emission spectrometry with excitation of the spectrum of the sample dry residue from the end of the carbon electrode in AC arc discharge are studied. The samples were analyzed directly after sampling, additional manipulations (including digestion) were not performed. The spectra of dried residues of the samples were recorded on a spectral device MFS-8, modernized with a MAÉS photodiode array. It was found that experimental distributions of P and Ca contents in saliva samples obey the normal law. Concentrations of Mg, Si, Fe, Ti, Mn, Al, Cu, Zn, and Cr correspond to the log-normal distribution and the geometric mean value should be used in this case as an average value of the concentration. Statistical processing of the results for Cd, Ag, and Pb was not performed, since these elements could not be detected in all the samples. The obtained data on the content of elements in 60 saliva samples of various donors are in satisfactory agreement with the literature data. The overestimated results obtained for Mg, Ca, and P can be attributed to the difference in the sample preparation stage, including preliminary centrifugation and storage of samples at negative temperatures.

Particle breakage of granular materials during sample preparation

Particle breakage is commonly observed in granular materials when subjected to external loads. It was found that particle breakage would occur during both sample preparation and loading stages. However, main attention was usually paid to the particle breakage behaviour of samples during loading stage. This study attempts to explore the breakage behaviour of granular materials during sample preparation. Triaxial samples of rockfill aggregates are prepared by layered compaction method to achieve different relative densities. Extents of particle breakage based on the gradings before and after test are presented and analysed. It is found that particle breakage during sample preparation cannot be ignored. Gradings after test are observed to shift away from the initial grading. Aggregates with larger size that appear to break are more than the smaller-sized ones. Irrespective of the initial gradings, an increase in the extent of particle breakage with the increasing relative density is observed during sample preparation.

Study of the physicochemical properties of exosome dispersions obtained by ultrafiltration

The article presents the results of studying the physicochemical properties of exosome preparations obtained by ultrafiltration, which indicate a high degree of the composition and properties dependence of the obtained product on the material of the filters used. Quantitative determination of proteins and nucleic acids in exosome samples using UPN-50 filters allows us to conclude that the content of the main impurity compounds in the preparation is significantly reduced compared to dispersions obtained using filters with pore sizes of 220 and 450 nm. Analysis of flow cytometry data made it possible to demonstrate that when using the UPN-50 filter, an increase in the contribution to the dispersion of all types of fractions of non-exosomal size was observed, the appearance of which can result from fraction destruction associated with pore size or filter material properties. drying of the dispersion was observed in the studied exosome samples. Fraction sizes ranged from 40 to 450 nm (an average of about 200 nm). Exosomes from the entire variety of membrane vesicles are fractions that have the most suitable characteristics that allow them to be used as a nanoscale drug delivery vehicle while ensuring the necessary quality control of the drug at the sample preparation stage.

An Experimental Microstructural Characterization of High-quality, Load-preserved Fabric 1-D Consolidated Kaolinite Samples

This paper describes a microstructural characterizations of high-quality, load-preserved fabric 1-D consolidated kaolinite samples, which covers from the beginning stage of clay sample preparation to the final stage of the microstructural analyses. To achieve this goal, a tailor-made oedometer is produced using the 3-D printing technique. First, a uniform kaolinite sample is prepared from a slurry state and then positioned into the 3-D printed oedometer for 1-D consolidation tests. Then, together with the applied loadings, the whole oedometer containing the consolidated kaolinite sample is submerged into the liquid nitrogen. This aims for preparing the dry sample by freeze drying, and at the same time, preserving the fabric associations for the subsequent microstructural characterizations. Afterwards, the sample is cut in half while frozen. An observation plane along the centre with the morphological information preserved is used for the scanning electron microscopy (SEM) analyses, and the remaining section is undergone the mercury intrusion porosimetry to obtain complementary information on the pore-size distribution. By ensuring the position and orientation of the SEM images taken, the number of SEM images, as well as the amount of particles and voids identified are maximized to enhance the statistical representation of the analysed results. In each sample, at least 3000 particles are identified, and the voids are segmented using proper binary images, of which their irregular shapes are further described using an equivalent ellipse. Fabric tensors are used to quantify the directional behaviour of the voids and particles. In addition, the shape evolution of the pores is examined to further understand the associated deformation mechanism. These comprehensive analyses provides quantitative evidences that the loading response of clay under 1-D consolidation is mainly governed by the inter-aggregate pores.

A Comparison of Reproducibility of Inductively Coupled Spectrometric Techniques in Soil Metal Analyses

Precise estimation of metals in samples remains a challenge as a result of analytical biases and errors, which occur at sample collection, preparation, and measurement stages. A poor understanding of the nature and occurrence of these errors further aggravates this challenge. This study aimed at comparing the effectiveness of inductively coupled plasma (ICP) mass spectrometry (MS) and optical emission spectrometry (OES) techniques in quantifying metals from contaminated soils of Roundhill landfill vicinity. Using statistical tools, the study evaluated biases of the 2 methods. High coefficients of variation were realized for V, Cr, and Pb concentrations varied at various sampling sites. Concentrations of elements obtained using the 2 methods had no significant differences using t-test analysis. Definitive agreement for the 2 methods was observed for V, Cr, Co, Ni, Cu, Zn, Sr, and Pb concentrations, whereas the concentrations of Mg, Ca, Ti, Mn, and Fe showed some deviations in their regression lines. Spectral, systematic, memory, and carry over errors could be attributable to these deviations. The errors promote chelation and adsorption of ions in samples to form insoluble compounds that cannot be quantified. Overall, ICP-MS had greater sensitivity than ICP-OES in trace elements analysis compared with major elements.

Setting Up an Ancient DNA Laboratory.

Entering into the world of ancient DNA research is nontrivial. Because the DNA in most ancient specimens is degraded to some extent, the potential is high for contamination of ancient samples, ancient DNA extracts, and genomic sequencing libraries prepared from these extracts with non-degraded DNA from the present-day environment. To minimize the risk of contamination in ancient DNA environments, experimental protocols specific to handling ancient specimens, including those that outline the design and layout of laboratory space, have been introduced. Here, we outline challenges associated with working with ancient samples, including providing guidelines for setting up a new ancient DNA laboratory. We also discuss steps that can be taken at the sample collection and preparation stage to minimize the potential for contamination of ancient DNA experiments with exogenous sources of DNA.