scholarly journals Extraction Methods, Characterization and Biomedical Applications of Collagen: a Review

2021 ◽  
Vol 11 (5) ◽  
pp. 13587-13613
Keyword(s):  
Tissue Engineering ◽  
Extraction Method ◽  
Biomedical Applications ◽  
Extraction Procedure ◽  
Extraction Methods ◽  
Collagen Types ◽  
Advantages And Disadvantages ◽  
Native Collagen ◽  
Isolation Methods ◽  
Different Tissues

It is difficult to develop a standard extraction method for all types of collagen from different tissues due to the extreme diversity of collagen types. Some procedures are based on the isolation of acid, pepsin, and enzymatic soluble collagen, showing certain advantages and disadvantages. Other methods were also optimized to partially purify collagen and extract it easier than the methods currently used. Indeed, this review describes some advantages and disadvantages of these isolation methods. Moreover, major biomedical applications of collagen were reported. Given the great importance of biocompatible matrices in tissue engineering, the availability of native collagen should be investigated by refining the collagen extraction procedure.

scholarly journals Toward standards in clinical microbiome studies: comparison of three DNA extraction methods and two bioinformatic pipelines

2019 ◽  
Author(s):  
Q.R. Ducarmon ◽  
B.V.H. Hornung ◽  
A.R. Geelen ◽  
E.J. Kuijper ◽  
R.D. Zwittink
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Bacterial Biomass ◽  
Extraction Methods ◽  
Rrna Gene ◽  
Method Choice ◽  
Advantages And Disadvantages ◽  
Dna Extraction Method ◽  
Dna Extraction Methods ◽  
Negative Controls

ABSTRACTWhen studying the microbiome using next generation sequencing, DNA extraction method, sequencing procedures and bioinformatic processing are crucial to obtain reliable data. Method choice has been demonstrated to strongly affect the final biological interpretation. We assessed the performance of three DNA extraction methods and two bioinformatic pipelines for bacterial microbiota profiling through 16S rRNA gene amplicon sequencing, using positive and negative controls for DNA extraction and sequencing, and eight different types of high- or low-biomass samples. Performance was evaluated based on quality control passing, DNA yield, richness, diversity and compositional profiles. All DNA extraction methods retrieved the theoretical relative bacterial abundance with maximum three-fold change, although differences were seen between methods, and library preparation and sequencing induced little variation. Bioinformatic pipelines showed different results for estimating richness, but diversity and compositional profiles were comparable. DNA extraction methods were successful for feces and oral swabs and variation induced by DNA extraction methods was lower than inter-subject (biological) variation. For low-biomass samples, a mixture of genera present in negative controls and sample-specific genera, possibly representing biological signal, were observed. We conclude that the tested bioinformatic pipelines perform equally with pipeline-specific advantages and disadvantages. Two out of three extraction methods performed equally well, while one method was less accurate regarding retrieval of compositional profiles. Lastly, we demonstrate the importance of including negative controls when analyzing low bacterial biomass samples.IMPORTANCEMethod choice throughout the workflow of a microbiome study, from sample collection to DNA extraction and sequencing procedures, can greatly affect results. This study evaluated three different DNA extraction methods and two bioinformatic pipelines by including positive and negative controls, and various biological specimens. By identifying an optimal combination of DNA extraction method and bioinformatic pipeline use, we hope to contribute to increased methodological consistency in microbiome studies. Our methods were not only applied to commonly studied samples for microbiota analysis, e.g. feces, but also for more rarely studied, low-biomass samples. Microbiota composition profiles of low-biomass samples (e.g. urine and tumor biopsies) were not always distinguishable from negative controls, or showed partial overlap, confirming the importance of including negative controls in microbiome studies, especially when low bacterial biomass is expected.

scholarly journals Current Nucleic Acid Extraction Methods and Their Implications to Point-of-Care Diagnostics

2017 ◽  
Vol 2017 ◽  
pp. 1-13 ◽  
Author(s):  
Nasir Ali ◽  
Rita de Cássia Pontello Rampazzo ◽  
Alexandre Dias Tavares Costa ◽  
Marco Aurelio Krieger
Keyword(s):  
Nucleic Acid ◽  
Extraction Method ◽  
Point Of Care ◽  
Extraction Methods ◽  
Vital Role ◽  
Acid Extraction ◽  
Nucleic Acid Extraction ◽  
Advantages And Disadvantages ◽  
Point Of Care Diagnostics ◽  
Working Principle

Nucleic acid extraction (NAE) plays a vital role in molecular biology as the primary step for many downstream applications. Many modifications have been introduced to the original 1869 method. Modern processes are categorized into chemical or mechanical, each with peculiarities that influence their use, especially in point-of-care diagnostics (POC-Dx). POC-Dx is a new approach aiming to replace sophisticated analytical machinery with microanalytical systems, able to be used near the patient, at thepoint of careorpoint of need. Although notable efforts have been made, a simple and effective extraction method is still a major challenge for widespread use of POC-Dx. In this review, we dissected the working principle of each of the most common NAE methods, overviewing their advantages and disadvantages, as well their potential for integration in POC-Dx systems. At present, it seems difficult, if not impossible, to establish a procedure which can be universally applied to POC-Dx. We also discuss the effects of the NAE chemicals upon the main plastic polymers used to mass produce POC-Dx systems. We end our review discussing the limitations and challenges that should guide the quest for an efficient extraction method that can be integrated in a POC-Dx system.

scholarly journals Toward Standards in Clinical Microbiota Studies: Comparison of Three DNA Extraction Methods and Two Bioinformatic Pipelines

mSystems ◽  
2020 ◽  
Vol 5 (1) ◽  
Author(s):  
Q. R. Ducarmon ◽  
B. V. H. Hornung ◽  
A. R. Geelen ◽  
E. J. Kuijper ◽  
R. D. Zwittink
Keyword(s):  
Dna Extraction ◽  
Extraction Method ◽  
Bacterial Biomass ◽  
Extraction Methods ◽  
Rrna Gene ◽  
Method Choice ◽  
Advantages And Disadvantages ◽  
Dna Extraction Method ◽  
Dna Extraction Methods ◽  
Negative Controls

ABSTRACT When studying the microbiome using next-generation sequencing, the DNA extraction method, sequencing procedures, and bioinformatic processing are crucial to obtain reliable data. Method choice has been demonstrated to strongly affect the final biological interpretation. We assessed the performance of three DNA extraction methods and two bioinformatic pipelines for bacterial microbiota profiling through 16S rRNA gene amplicon sequencing, using positive and negative controls for DNA extraction and sequencing and eight different types of high- or low-biomass samples. Performance was evaluated based on quality control passing, DNA yield, richness, diversity, and compositional profiles. All DNA extraction methods retrieved the theoretical relative bacterial abundance with a maximum 3-fold change, although differences were seen between methods, and library preparation and sequencing induced little variation. Bioinformatic pipelines showed different results for observed richness, but diversity and compositional profiles were comparable. DNA extraction methods were successful for feces and oral swabs, and variation induced by DNA extraction methods was lower than intersubject (biological) variation. For low-biomass samples, a mixture of genera present in negative controls and sample-specific genera, possibly representing biological signal, were observed. We conclude that the tested bioinformatic pipelines perform equally, with pipeline-specific advantages and disadvantages. Two out of three extraction methods performed equally well, while one method was less accurate regarding retrieval of compositional profiles. Lastly, we again demonstrate the importance of including negative controls when analyzing low-bacterial-biomass samples. IMPORTANCE Method choice throughout the workflow of a microbiome study, from sample collection to DNA extraction and sequencing procedures, can greatly affect results. This study evaluated three different DNA extraction methods and two bioinformatic pipelines by including positive and negative controls and various biological specimens. By identifying an optimal combination of DNA extraction method and bioinformatic pipeline use, we hope to contribute to increased methodological consistency in microbiota studies. Our methods were applied not only to commonly studied samples for microbiota analysis, e.g., feces, but also to more rarely studied, low-biomass samples. Microbiota composition profiles of low-biomass samples (e.g., urine and tumor biopsy specimens) were not always distinguishable from negative controls, or showed partial overlap, confirming the importance of including negative controls in microbiota studies, especially when low bacterial biomass is expected.

scholarly journals Revisiting chlorophyll extraction methods in biological soil crusts – methodology for determination of chlorophyll <i>a</i> and chlorophyll <i>a</i> + <i>b</i> as compared to previous methods

2018 ◽  
Vol 15 (5) ◽  
pp. 1415-1424 ◽  
Author(s):  
Jennifer Caesar ◽  
Alexandra Tamm ◽  
Nina Ruckteschler ◽  
Anna Lena Leifke ◽  
Bettina Weber
Keyword(s):  
Chlorophyll Content ◽  
Extraction Method ◽  
Biological Soil Crust ◽  
Extraction Procedure ◽  
Extraction Methods ◽  
Intermediate Step ◽  
Green Algal ◽  
Chlorophyll Extraction ◽  
The Impact

Abstract. Chlorophyll concentrations of biological soil crust (biocrust) samples are commonly determined to quantify the relevance of photosynthetically active organisms within these surface soil communities. Whereas chlorophyll extraction methods for freshwater algae and leaf tissues of vascular plants are well established, there is still some uncertainty regarding the optimal extraction method for biocrusts, where organism composition is highly variable and samples comprise major amounts of soil. In this study we analyzed the efficiency of two different chlorophyll extraction solvents, the effect of grinding the soil samples prior to the extraction procedure, and the impact of shaking as an intermediate step during extraction. The analyses were conducted on four different types of biocrusts. Our results show that for all biocrust types chlorophyll contents obtained with ethanol were significantly lower than those obtained using dimethyl sulfoxide (DMSO) as a solvent. Grinding of biocrust samples prior to analysis caused a highly significant decrease in chlorophyll content for green algal lichen- and cyanolichen-dominated biocrusts, and a tendency towards lower values for moss- and algae-dominated biocrusts. Shaking of the samples after each extraction step had a significant positive effect on the chlorophyll content of green algal lichen- and cyanolichen-dominated biocrusts. Based on our results we confirm a DMSO-based chlorophyll extraction method without grinding pretreatment and suggest the addition of an intermediate shaking step for complete chlorophyll extraction (see Supplement S6 for detailed manual). Determination of a universal chlorophyll extraction method for biocrusts is essential for the inter-comparability of publications conducted across all continents.

scholarly journals Revisiting chlorophyll extraction methods in biological soil crusts – methodology for determination of chlorophyll a and chlorophyll a + b as compared to previous methods

2017 ◽  
Author(s):  
Jennifer Caesar ◽  
Alexandra Tamm ◽  
Nina Ruckteschler ◽  
Bettina Weber
Keyword(s):  
Chlorophyll Content ◽  
Chlorophyll A ◽  
Extraction Method ◽  
Extraction Procedure ◽  
Extraction Methods ◽  
Intermediate Step ◽  
Green Algal ◽  
Chlorophyll Extraction ◽  
The Impact

Abstract. Chlorophyll concentrations of biological soil crust (biocrust) samples are commonly determined to quantify the relevance of photosynthetically active organisms within these surface soil communities. Whereas chlorophyll extraction methods for freshwater algae and leaf tissues of vascular plants are well established, there is still some uncertainty regarding the optimal extraction method for biocrusts, where organism composition is highly variable and samples comprise major amounts of soil. In this study we analyzed the efficiency of two different chlorophyll extraction solvents, the effect of grinding the soil samples prior to the extraction procedure and the impact of shaking as an intermediate step during extraction. The analyses were conducted on four different types of biocrusts. Our results show, that for all biocrust types chlorophyll contents obtained with ethanol were significantly lower than those obtained with dimethyl sulfoxide (DMSO) as solvent. Grinding of biocrust samples prior to analysis caused a highly significant decrease in chlorophyll content for green algal lichen- and cyanolichen-dominated biocrusts, and a tendency towards lower values for moss- and algae-dominated biocrusts. Shaking of the samples after each extraction step had a significant positive effect on the chlorophyll content of green algal lichen- and cyanolichen-dominated biocrusts. Based on our results we confirm a DMSO-based chlorophyll extraction method without grinding pretreatment and suggest to insert an intermediate shaking step for complete chlorophyll extraction (see supplement S6 for detailed manual). Determination of a universal chlorophyll extraction method for biocrusts is essential for the inter-comparability of studies conducted across all continents.

HPLC analysis and activity to determine the effect of drying and extraction on Ficus benghalensis leaves

2020 ◽  
Vol 9 (1) ◽  
pp. 6-10
Author(s):  
Nithyakalyani K
Keyword(s):  
Extraction Method ◽  
Chemical Constituents ◽  
Extraction Procedure ◽  
Chemical Constituent ◽  
Chemical Components ◽  
Drying Method ◽  
Ultrasound Assisted Extraction ◽  
Critical Stage ◽  
Ficus Benghalensis ◽  
Assisted Extraction

Ficus benghalensis is one of those taboo plants in India, which was claimed to be possessed and have weird effects on human health. Apart from this ficus species has a great variety of chemical constituents and an abundant amount of antioxidants. Drying is the most critical stage of improving the activity or preventing the loss of chemical components from a drug. There is another stage of ensuring high chemical constituent content in the plant and that is the extraction procedure. So the point of focus in the current research is to find the effect of extraction method and drying on the anti-inflammatory potential of the plant. The result of the extraction method and drying method of the plant was investigated and found that the ultrasound-assisted extraction of the shade dried leaves was found to give the highest yield of flavonoids and activity.

Graphene and Graphene-Based Materials in Biomedical Applications

2019 ◽  
Vol 26 (38) ◽  
pp. 6834-6850 ◽  
Author(s):  
Mohammad Omaish Ansari ◽  
Kalamegam Gauthaman ◽  
Abdurahman Essa ◽  
Sidi A. Bencherif ◽  
Adnan Memic
Keyword(s):  
Tissue Engineering ◽  
Thermal Properties ◽  
Gene Delivery ◽  
Regenerative Medicine ◽  
Biomedical Research ◽  
Biomedical Applications ◽  
Biomedical Application ◽  
Two Dimensional ◽  
Drug And Gene Delivery ◽  
Biomedical Fields

: Nanobiotechnology has huge potential in the field of regenerative medicine. One of the main drivers has been the development of novel nanomaterials. One developing class of materials is graphene and its derivatives recognized for their novel properties present on the nanoscale. In particular, graphene and graphene-based nanomaterials have been shown to have excellent electrical, mechanical, optical and thermal properties. Due to these unique properties coupled with the ability to tune their biocompatibility, these nanomaterials have been propelled for various applications. Most recently, these two-dimensional nanomaterials have been widely recognized for their utility in biomedical research. In this review, a brief overview of the strategies to synthesize graphene and its derivatives are discussed. Next, the biocompatibility profile of these nanomaterials as a precursor to their biomedical application is reviewed. Finally, recent applications of graphene-based nanomaterials in various biomedical fields including tissue engineering, drug and gene delivery, biosensing and bioimaging as well as other biorelated studies are highlighted.

3D Printing & Pharmaceutical Manufacturing: Opportunities and Challenges

2016 ◽  
Vol 5 (01) ◽  
pp. 4723 ◽  
Author(s):  
Bhusnure O. G.* ◽  
Gholve V. S. ◽  
Sugave B. K. ◽  
Dongre R. C. ◽  
Gore S. A. ◽  
...  
Keyword(s):  
Drug Delivery ◽  
Tissue Engineering ◽  
3D Printing ◽  
Computer Aided Design ◽  
Patient Specific ◽  
Computer Design ◽  
3D Scaffolds ◽  
Engineering Research ◽  
Advantages And Disadvantages ◽  
Computer Aided

Many researchers have attempted to use computer-aided design (C.A.D) and computer-aided manufacturing (CAM) to realize a scaffold that provides a three-dimensional (3D) environment for regeneration of tissues and organs. As a result, several 3D printing technologies, including stereolithography, deposition modeling, inkjet-based printing and selective laser sintering have been developed. Because these 3D printing technologies use computers for design and fabrication, and they can fabricate 3D scaffolds as designed; as a consequence, they can be standardized. Growth of target tissues and organs requires the presence of appropriate growth factors, so fabrication of 3Dscaffold systems that release these biomolecules has been explored. A drug delivery system (D.D.S) that administrates a pharmaceutical compound to achieve a therapeutic effect in cells, animals and humans is a key technology that delivers biomolecules without side effects caused by excessive doses. 3D printing technologies and D. D. Ss have been assembled successfully, so new possibilities for improved tissue regeneration have been suggested. If the interaction between cells and scaffold system with biomolecules can be understood and controlled, and if an optimal 3D tissue regenerating environment is realized, 3D printing technologies will become an important aspect of tissue engineering research in the near future. 3D Printing promises to produce complex biomedical devices according to computer design using patient-specific anatomical data. Since its initial use as pre-surgical visualization models and tooling molds, 3D Printing has slowly evolved to create one-of-a-kind devices, implants, scaffolds for tissue engineering, diagnostic platforms, and drug delivery systems. Fuelled by the recent explosion in public interest and access to affordable printers, there is renewed interest to combine stem cells with custom 3D scaffolds for personalized regenerative medicine. Before 3D Printing can be used routinely for the regeneration of complex tissues (e.g. bone, cartilage, muscles, vessels, nerves in the craniomaxillofacial complex), and complex organs with intricate 3D microarchitecture (e.g. liver, lymphoid organs), several technological limitations must be addressed. Until recently, tablet designs had been restricted to the relatively small number of shapes that are easily achievable using traditional manufacturing methods. As 3D printing capabilities develop further, safety and regulatory concerns are addressed and the cost of the technology falls, contract manufacturers and pharmaceutical companies that experiment with these 3D printing innovations are likely to gain a competitive edge. This review compose the basics, types & techniques used, advantages and disadvantages of 3D printing

scholarly journals How to Improve Physico-Chemical Properties of Silk Fibroin Materials for Biomedical Applications?—Blending and Cross-Linking of Silk Fibroin—A Review

Materials ◽  
2021 ◽  
Vol 14 (6) ◽  
pp. 1510
Author(s):  
Sylwia Grabska-Zielińska ◽  
Alina Sionkowska
Keyword(s):  
Silk Fibroin ◽  
Biomedical Applications ◽  
Magnetic Particles ◽  
Chemical Properties ◽  
Ternary Mixtures ◽  
Cross Linking ◽  
Advantages And Disadvantages ◽  
Physico Chemical ◽  
Binary And Ternary Mixtures ◽  
To Receive

This review supplies a report on fresh advances in the field of silk fibroin (SF) biopolymer and its blends with biopolymers as new biomaterials. The review also includes a subsection about silk fibroin mixtures with synthetic polymers. Silk fibroin is commonly used to receive biomaterials. However, the materials based on pure polymer present low mechanical parameters, and high enzymatic degradation rate. These properties can be problematic for tissue engineering applications. An increased interest in two- and three-component mixtures and chemically cross-linked materials has been observed due to their improved physico-chemical properties. These materials can be attractive and desirable for both academic, and, industrial attention because they expose improvements in properties required in the biomedical field. The structure, forms, methods of preparation, and some physico-chemical properties of silk fibroin are discussed in this review. Detailed examples are also given from scientific reports and practical experiments. The most common biopolymers: collagen (Coll), chitosan (CTS), alginate (AL), and hyaluronic acid (HA) are discussed as components of silk fibroin-based mixtures. Examples of binary and ternary mixtures, composites with the addition of magnetic particles, hydroxyapatite or titanium dioxide are also included and given. Additionally, the advantages and disadvantages of chemical, physical, and enzymatic cross-linking were demonstrated.

scholarly journals Evaluation of DNA Extraction Methods Developed for Forensic and Ancient DNA Applications Using Bone Samples of Different Age

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 146
Author(s):  
Catarina Xavier ◽  
Mayra Eduardoff ◽  
Barbara Bertoglio ◽  
Christina Amory ◽  
Cordula Berger ◽  
...  
Keyword(s):  
Dna Extraction ◽  
Ancient Dna ◽  
Extraction Method ◽  
Fragment Size ◽  
Molecular Genetic ◽  
Extraction Methods ◽  
Degraded Dna ◽  
Size Analysis ◽  
Dna Fragments ◽  
Dna Amount

The efficient extraction of DNA from challenging samples, such as bones, is critical for the success of downstream genotyping analysis in molecular genetic disciplines. Even though the ancient DNA community has developed several protocols targeting small DNA fragments that are typically present in decomposed or old specimens, only recently forensic geneticists have started to adopt those protocols. Here, we compare an ancient DNA extraction protocol (Dabney) with a bone extraction method (Loreille) typically used in forensics. Real-time quantitative PCR and forensically representative typing methods including fragment size analysis and sequencing were used to assess protocol performance. We used four bone samples of different age in replicates to study the effects of both extraction methods. Our results confirm Loreille’s overall increased gain of DNA when enough tissue is available and Dabney’s improved efficiency for retrieving shorter DNA fragments that is beneficial when highly degraded DNA is present. The results suggest that the choice of extraction method needs to be based on available sample, degradation state, and targeted genotyping method. We modified the Dabney protocol by pooling parallel lysates prior to purification to study gain and performance in single tube typing assays and found that up to six parallel lysates lead to an almost linear gain of extracted DNA. These data are promising for further forensic investigations as the adapted Dabney protocol combines increased sensitivity for degraded DNA with necessary total DNA amount for forensic applications.

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