Log In Sign up
The largest database of trusted experimental protocols
> Chemicals & Drugs > Amino Acid > Silk

Silk

Silk is a powerful AI-driven platform that optimizes the research process.
It enables users to easily locate protocols from literature, preprints, and patents, and leverages cutting-edge AI technology to compare and identify the best protocols and products for their research needs.
Silk's intuitive tools unleash the full potential of research, empowering scientists to make informed decisions and accelerate their work.
This comprehensive platform combines the latest advancements in artificial intelligence with a user-friendly interface, making research optimization more accessible than ever before.

Most cited protocols related to «Silk»

1
Constructing Animal Social Networks
Cited 116 times
Numerous types of data can be used to construct social networks (see Chapter 3 of Whitehead 2008). A first requirement is that a substantial portion of the individuals (or each unit representing a node) in the population are uniquely identifiable. Methods for identifying individuals include using naturally occurring individual variation in coloration or morphology (Würsig & Jefferson 1990), marking individuals to make them individually identifiable (e.g. with colour‐bands McDonald 2007; Farine & Milburn 2013), or electronic tags that provide information about the location or relative distance between individuals. In addition to having individually identifiable study subjects, network analysis requires data on interactions or associations. Altmann (1974) outlined protocols for assembling raw data from direct behavioural observations, particularly focal observations, that are very relevant for animal social networks (see also Chapter 3 of Whitehead 2008).
One method frequently used to capture associations is the ‘gambit of the group’ (see Franks, Ruxton & James 2010). Gambit of the group defines all individuals within a group of animals observed at a point in time as being associated. Thus, association rates (see Section Inferring associations from data) represent the propensity for each pair of individuals to co‐occur in the same group. The fundamental assumptions of the gambit of the group are that all, or almost all, interactions of some kind take place within groups and that interactions of this type occur at a similar rate among all animals when they form groups (Whitehead & Dufault 1999; Farine et al. 2015, or that the group itself is meaningful to the animals. This method is particularly useful when groups of animals can be easily observed, and group membership changes over time (Silk et al. 2015).
Farine D.R, & Whitehead H. (2015). Constructing, conducting and interpreting animal social network analysis. The Journal of Animal Ecology, 84(5), 1144-1163.
Full text: Click here
Publication 2015
Animals Behavior Observation Techniques Silk
2
Murine Ischemia-Reperfusion Injury Protocol
Cited 38 times
This I/R injury procedure in mice is essentially the same as the procedure for inducing MI except that a slipknot is tied around the LCA 2-3 mm from its origin with a 6-0 silk suture as shown in Fig. 2A. The heart is then quickly placed back into the thoracic space followed by manual evacuation of air and the skin closing (Fig. 2B). The internal needle end of slipknot suture is cut as short as possible and the other end of the suture is approximately 0.8 cm long and remains outside of the chest (Fig. 2C). After 30 min of ischemia, the slipknot is released by pulling the long end of slipknot suture smoothly and gently until a feeling of release is sensed at which time the myocardium begins reperfusing. This outside-the-skin suture knot releasing method should only be attempted by the experienced surgeon. Alternatively, the mouse can be re-anesthetized with 2% isoflurane inhalation, the chest reopened, and the slipknot released by pulling the long end of slipknot suture smoothly and gently, and then following manual evacuation of the pneumothorax and chest closure. As above for the MI model, ventilation is recommended until times are fast enough to do this procedure without ventilation.
Gao E., Lei Y.H., Shang X., Huang Z.M., Zuo L., Boucher M., Fan Q., Chuprun J.K., Ma X.L, & Koch W.J. (2010). A Novel and Efficient Model of Coronary Artery Ligation and Myocardial Infarction in the Mouse. Circulation research, 107(12), 1445-1453.
Publication 2010
Chest Heart Inhalation Injuries Ischemia Isoflurane Mice, Laboratory Myocardium Needles Pneumothorax Silk Skin Surgeons Sutures
3
Mouse Model of Myocardial Infarction
Cited 29 times
In this new method of MI induction, mice were anesthetized with 2% isoflurane inhalation with an isoflurane delivery system (Viking Medical, Medford, NJ) but not ventilated. Of course, prior to perfecting this surgical model we recommend using ventilation in mice until the surgeon can routinely perform the LCA ligation in less than 3 min. A small skin cut (1.2cm) was made over the left chest and a purse suture was made as shown in Fig. 1A-C. After dissection and retraction of the pectoral major and minor muscle, the 4th intercostal space was exposed (Fig. 1D). A small hole was made at the 4th intercostal space with a mosquito clamp to open the pleural membrane and pericardium (Fig. 1E). With the clamp slightly open, the heart was smoothly and gently “popped out” through the hole as show in Fig. 1F. The LCA was located, sutured and ligated at a site about 3 mm from its origin using a 6-0 silk suture (Fig. 1H-I). The ligation was deemed successful when the anterior wall of the LV turned pale (Fig. 1J). After ligation, the heart was immediately placed back into the intra-thoracic space followed by manual evacuation of air and closure of muscle and the skin, by means of the previously placed purse-string suture (Fig. 1K-L). The mouse was then allowed to breathe room air and monitored during the recovery period, which was generally complete within 3-5 minutes. No artificial respiratory aid was required during the recovery time. The sham group underwent the same surgical procedure except that the LCA was not occluded. A move of this new method of MI can be found in on-line Supplemental Methods.
Gao E., Lei Y.H., Shang X., Huang Z.M., Zuo L., Boucher M., Fan Q., Chuprun J.K., Ma X.L, & Koch W.J. (2010). A Novel and Efficient Model of Coronary Artery Ligation and Myocardial Infarction in the Mouse. Circulation research, 107(12), 1445-1453.
Publication 2010
Chest Culicidae Dissection Heart Inhalation Isoflurane Ligation Mice, Laboratory Muscle Tissue Obstetric Delivery Operative Surgical Procedures Pericardium Pleura Respiration, Artificial Silk Skin Surgeons Sutures
4
Comparative RADseq Analysis in Marine Fishes
Cited 28 times
Two sample localities, each comprising 20 individuals, were chosen randomly from unpublished RADseq data sets of three different, marine fish species: red snapper (Lutjanus campechanus), red drum (Sciaenops ocellatus), and silk snapper (Lutjanus vivanus). These three species are part of ongoing RADseq projects in our laboratory, and preliminary analyses indicated high levels of nucleotide polymorphisms across all populations. Double-digest RAD libraries were prepared, generally following Peterson et al. (2012) (link). Individual DNA extractions were digested with EcoRI and MspI. A barcoded adapter was ligated to the EcoRI site of each fragment and a generic adapter was ligated to the MspI site. Samples were then equimollarly pooled and size-selected between 350 and 400 bp, using a Qiagen Gel Extraction Kit. Final library enhancement was completed using 12 cycles of PCR, simultaneously enhancing properly ligated fragments and adding an Illumina Index for additional barcoding. Libraries were sequenced on three separate lanes of an Illumina HiSeq 2000 at the University of Texas Genomic Sequencing and Analysis Facility. Raw sequence data were archived at NCBI’s Short Read Archive (SRA) under Accession SRP041032.
Demultiplexed individual reads were analyzed with dDocent (version 1.0), using three different levels of final reference contig clustering (90%, 96%, and 99% similarity) in an attempt to alter the most comparable analysis variable in dDocent to match the maximum distance between stacks parameter and the maximum distance between stacks from different individuals parameter of Stacks. The coverage cut-off for assembly was 12 for red snapper, 13 for red drum, and nine for silk snapper. All dDocent runs used mapping variables of one, three, and five for match-score value, mismatch score, and gap-opening penalty, respectively. For comparisons, complex variants were decomposed into canonical SNP and Indel representation from the raw VCF files, using vcfallelicprimitives from vcflib (https://github.com/ekg/vcflib).
For analysis with Stacks (version 1.08), reads were demultiplexed and cleaned using process_radtags, removing reads with ‘N’ calls and low-quality base scores. Because dDocent inherently uses both reads for SNP/Indel genotyping, forward reads and reverse reads were processed separately with denovo_map.pl, using three different sets of parameters. The first set had a minimum depth of coverage of two to create a stack, a maximum distance of two between stacks, and a maximum distance of four between stacks from different individuals, with both the deleveraging algorithm and removal algorithms enabled. The second set had a minimum depth of coverage of three to create a stack, a maximum distance of four between stacks, and a maximum distance of eight between stacks from different individuals, with both the deleveraging algorithm and removal algorithms enabled. The third set had a minimum depth of coverage of three to create a stack, a maximum distance of four between stacks, and a maximum distance of 10 between stacks from different individuals, with both the deleveraging algorithm and removal algorithms enabled. SNP calls were output in VCF format.
For both dDocent and Stacks runs, VCFtools was used to filter out all Indel s and SNPs that had a minor allele count of less than five. SNP calls were then evaluated at different individual-coverage levels: the total number of SNPs; the number of SNPs called in 75%, 90%, and 99% of individuals at 3X coverage; the number of SNPs called in 75% and 90% of individuals at 5X coverage; the number of SNPs called in 75% and 90% of individuals at 10X coverage; and the number of SNPS called in 75% and 90% of individuals at 20X coverage. Overall coverage levels for red snapper were lower and likely impacted by a few low-quality individuals; consequently, the number of 5X and 10X SNPs shared among 90% of individuals (after removing the bottom 10% of individuals in terms of coverage) were compared instead of SNP loci shared at 20X coverage. Results from two runs of Stacks (one using forward and one using reverse reads) were combined for comparison with dDocent, which inherently calls SNPs on both reads. All analyses and computations were performed on a 32-core Linux workstation with 128 GB of RAM.
Puritz J.B., Hollenbeck C.M, & Gold J.R. (2014). dDocent: a RADseq, variant-calling pipeline designed for population genomics of non-model organisms. PeerJ, 2, e431.
Full text: Click here
Publication 2014
Alleles Deoxyribonuclease EcoRI DNA Library Fishes Generic Drugs Genetic Polymorphism Genome INDEL Mutation Marines Nucleotides Population Group Silk Single Nucleotide Polymorphism
5
Ligature-Induced Maxillary Bone Loss
Cited 28 times

Protocol full text hidden due to copyright restrictions

Open the protocol to access the free full text link

Publication 2013
Bones Ligature Maxilla Molar Mus Osteopenia Periodontium Silk Surgical Instruments Sutures

Most recents protocols related to «Silk»

1
Lyophilized Silk Powder Formulations
Not available on PMC !

Example 19

TABLE 37
Embodiments of lyophilized silk powders
Silk SolutionTreatmentSoluble
~60 kDa silk, 6% silk, pH = 7-8lyopholize and cut withno
blender
~60 kDa silk, 6% silk, pH = 10lyopholize and cut withno
blender
~25 kDa silk, 6% silk, pH = 7-8lyopholize and cut withyes
blender
~25 kDa silk, 6% silk, pH = 10lyopholize and cut withyes
blender

The above silk solutions were transformed to a silk powder through lyophilization to remove bulk water and chopping to small pieces with a blender. pH was adjusted with sodium hydroxide. Low molecular weight silk (−25 kDa) was soluble while high molecular weight silk (−60 kDa) was not.

The lyophilized silk powder can be advantageous for enhanced storage control ranging from 10 days to 10 years depending on storage and shipment conditions. The lyophilized silk powder can also be used as a raw ingredient in the pharmaceutical, medical, consumer, and electronic markets. Additionally, lyophilized silk powder can be re-suspended in water, HFIP, or an organic solution following storage to create silk solutions of varying concentrations, including higher concentration solutions than those produced initially.

In an embodiment, aqueous pure silk fibroin-based protein fragment solutions of the present disclosure comprising 1%, 3%, and 5% silk by weight were each dispensed into a 1.8 L Lyoguard trays, respectively. All 3 trays were placed in a 12 ft2 lyophilizer and a single run performed. The product was frozen with a shelf temperature of ≤−40° C. and held for 2 hours. The compositions were then lyophilized at a shelf temperature of −20° C., with a 3 hour ramp and held for 20 hours, and subsequently dried at a temperature of 30° C., with a 5 hour ramp and held for about 34 hours. Trays were removed and stored at ambient conditions until further processing. Each of the resultant lyophilized silk fragment compositions were able to dissolve in aqueous solvent and organic solvent to reconstitute silk fragment solutions between 0.1 wt % and 8 wt %. Heating and mixing were not required but were used to accelerate the dissolving rate. All solutions were shelf-stable at ambient conditions.

In an embodiment, an aqueous pure silk fibroin-based protein fragment solution of the present disclosure, fabricated using a method of the present disclosure with a 30 minute boil, has a molecular weight of about 57 kDa, a polydispersity of about 1.6, inorganic and organic residuals of less than 500 ppm, and a light amber color.

In an embodiment, an aqueous pure silk fibroin-based protein fragment solution of the present disclosure, fabricated using a method of the present disclosure with a 60 minute boil, has a molecular weight of about 25 kDa, a polydispersity of about 2.4, inorganic and organic residuals of less than 500 ppm, and a light amber color.

US11878070B2. Silk-based moisturizer compositions and methods thereof (2024-01-23). Evolved By Nature, Inc. [US]. Inventors: Gregory H. Altman [US], Dylan S. Haas [US], Kevin T. Healy [US].
Full text: Click here
Patent 2024
Amber ARID1A protein, human Dietary Fiber Fibroins Freeze Drying Freezing Furuncles Light Pharmaceutical Preparations Powder Proteins Silk Sodium Hydroxide Solvents
2
Preservative Silk Gel Formulations
Not available on PMC !

Example 11

FIG. 93 is a table summarizing embodiments of preservative gels of the present disclosure. Silk gels were cast with standard 2% silk solution and 100 mg L-ascorbic acid/15 mL solution with the addition of a preservative and chelating agent. The preservative added was Verstatil SL by Kinetic (Water, Sodium Levulinate, Potassium Sorbate) at 1.5% and the chelating agent was Dermofeel-PA3 by Kinetic (Sodium Phytate) at 0.1%. The addition of preservatives extended gelation time to 7 days. Gel is being observed for discoloration and integrity with L-ascorbic acid and ascorbic acid-2-glucoside gel comparisons.

US11878070B2. Silk-based moisturizer compositions and methods thereof (2024-01-23). Evolved By Nature, Inc. [US]. Inventors: Gregory H. Altman [US], Dylan S. Haas [US], Kevin T. Healy [US].
Full text: Click here
Patent 2024
Ascorbic Acid ascorbic acid 2-O-glucoside CD3EAP protein, human Chelating Agents Kinetics Pharmaceutical Preservatives Silk Sodium Sodium Phytate Sorbate, Potassium
3
Green Tea Infused Silk Gel
Not available on PMC !

Example 10

Steps:
Green Tea PrepHeat 250 mL water to boil
Steep tea bag 2-3 minutes
with occasional stir
remove tea bag and let cool
Gel SolutionUse TFF-10-0047 (3.71% silk)
Prepdilute to 3% silk with water
dilute to 2% with green tea
add L-ascorbic acid
GelGelation occurred like standard
gel at room temperature
Green/yellow color
Green Tea scent
Solution Spec:2% silk solution
65 mL (35 ml of 3.71% silk, 8.3
mL water, 21.66 mL green tea)
0.43 gL-ascorbic acid

FIG. 92 is a table summarizing an embodiment of a caffeine gel of the present disclosure. A silk gel with 2% silk and 100 mg L-ascorbic acid/15 mL solution was created with the addition of 50 mg caffeine/15 mL solution. The gel has the exact appearance of standard L-ascorbic acid gels.

US11857663B2. Stable silk protein fragment compositions (2024-01-02). Evolved By Nature, Inc. [US]. Inventors: Gregory H. Altman [US], Rebecca L. Lacouture [US], Rachel Lee Dow [US], Rachel M. Lind [US], Dylan S. Haas [US].
Full text: Click here
Patent 2024
Ascorbic Acid Caffeine Fast Green FCF Furuncles Gels Green Tea Pheromone Silk STEEP1 protein, human Technique, Dilution
4
Herbal Skin Care Formulation
Not available on PMC !

Example 77

Heat applicable acids, lemongrass oil, and/or olive oil to 75° C. Dissolve NaOH in an initial aliquot of water and heat the solution to 70° C. To the alkaline solution add glycerin and silk solution, then add the blend of applicable acids, lemongrass oil, and/or olive oil. Allow the mixture to cool and then add 2M HCl followed by an ending aliquot of water. Where applicable, then add the aspen bark and/or the sodium anisate.

US11878070B2. Silk-based moisturizer compositions and methods thereof (2024-01-23). Evolved By Nature, Inc. [US]. Inventors: Gregory H. Altman [US], Dylan S. Haas [US], Kevin T. Healy [US].
Full text: Click here
Patent 2024
Acids Cascara Sagrada Glycerin Oil, Olive Silk Sodium west indian lemongrass oil
5
Formulation of Combination Cleanser
Not available on PMC !

Example 70

Heat lauric acid, stearic acid, myristic acid, oleic acid, squalene oil, rosehip oil, lemongrass oil, olive oil, and/or jojoba oil to about 75° C. Then dissolve NaOH in water (or an initial aliquot of water) and heat the solution to about 70° C. To the NaOH solution add glycerin and silk, then add the blend of lauric acid, stearic acid, myristic acid, oleic acid, squalene oil, rosehip oil, lemongrass oil, olive oil, and/or jojoba oil. Allow the mixture to cool. Where applicable, reheat the mixture and add rosehip oil, squalene oil, and/or 2M HCl. Then, where applicable, add an ending aliquot of water and/or olive oil. Finally, add aspen bark and/or sodium anisate to yield the combination cleanser.

US11878070B2. Silk-based moisturizer compositions and methods thereof (2024-01-23). Evolved By Nature, Inc. [US]. Inventors: Gregory H. Altman [US], Dylan S. Haas [US], Kevin T. Healy [US].
Full text: Click here
Patent 2024
Glycerin jojoba wax Kidney Cortex lauric acid Myristic Acid Oil, Olive Oleic Acid Rosehips Silk Sodium Squalene stearic acid west indian lemongrass oil

Top products related to «Silk»

1
Un scan it software by Silk Scientific
Sourced in United States
UN-SCAN-IT software is a data analysis tool designed for digitizing and analyzing graphical data. It provides the ability to extract numerical values from images, graphs, and charts. The software supports a variety of image formats and can be used to measure areas, lengths, and other parameters from the imported data.
2
Pentobarbital sodium by Merck Group
Sourced in United States, Germany, China, Sao Tome and Principe, United Kingdom, Japan, Italy, Canada, Hungary, Macao
Pentobarbital sodium is a laboratory chemical compound. It is a barbiturate drug that acts as a central nervous system depressant. Pentobarbital sodium is commonly used in research and scientific applications.
3
Rompun by Bayer
Sourced in Germany, France, United States, United Kingdom, Canada, Italy, Brazil, Belgium, Cameroon, Switzerland, Spain, Australia, Ireland, Sweden, Portugal, Netherlands, Austria, Denmark, New Zealand
Rompun is a veterinary drug used as a sedative and analgesic for animals. It contains the active ingredient xylazine hydrochloride. Rompun is designed to induce a state of sedation and pain relief in animals during medical procedures or transportation.
4
Un scan it by Silk Scientific
Sourced in United States
The UN-SCAN-IT is a versatile data digitizing and analysis software. It allows users to convert graphical data, such as graphs, charts, and diagrams, into numerical data that can be further analyzed and processed. The software supports a variety of input formats and provides tools for adjusting and calibrating the data.
5
Trizol reagent by Thermo Fisher Scientific
Sourced in United States, China, Japan, Germany, United Kingdom, Canada, France, Italy, Australia, Spain, Switzerland, Netherlands, Belgium, Lithuania, Denmark, Singapore, New Zealand, India, Brazil, Argentina, Sweden, Norway, Austria, Poland, Finland, Israel, Hong Kong, Cameroon, Sao Tome and Principe, Macao, Taiwan, Province of China, Thailand
TRIzol reagent is a monophasic solution of phenol, guanidine isothiocyanate, and other proprietary components designed for the isolation of total RNA, DNA, and proteins from a variety of biological samples. The reagent maintains the integrity of the RNA while disrupting cells and dissolving cell components.
6
Na2co3 by Merck Group
Sourced in United States, Germany, United Kingdom, Italy, Poland, Macao, France, Spain, Canada, India, Brazil
Na2CO3, also known as sodium carbonate or washing soda, is a chemical compound commonly used in laboratory settings. It is a white, crystalline solid that serves as a basic salt and a source of sodium ions. Na2CO3 is widely utilized in various laboratory applications due to its chemical properties and versatility.
7
Un scan it gel software by Silk Scientific
Sourced in United States
UN-SCAN-IT gel software is a data analysis tool designed to quantify and analyze gel images, such as those from electrophoresis experiments. The software provides functionality to measure band size, intensity, and other parameters from uploaded gel images.
8
Un scan it gel 6 by Silk Scientific
Sourced in United States
The UN-SCAN-IT gel 6.1 software is a tool for analyzing and quantifying data from gel electrophoresis experiments. It provides the functionality to digitize, measure, and analyze gel images.
9
6 0 silk suture by Johnson & Johnson
Sourced in United States, United Kingdom
The 6-0 silk suture is a sterile, non-absorbable surgical suture material manufactured by Johnson & Johnson. It is composed of natural silk fibers and is commonly used in ophthalmic, cardiovascular, and other delicate surgical procedures where precise suturing is required.
10
Noa 148 by Norland Products
The NOA 148 is a contact angle measurement instrument designed for determining the wettability and surface energy of solid samples. It utilizes a high-resolution camera and precise liquid dispensing system to capture and analyze the contact angle formed between a liquid and the surface of a solid material.

More about "Silk"

Discover the transformative power of Silk, the cutting-edge AI-driven platform that optimizes the research process.
Unlock the full potential of your research with Silk's intuitive tools and advanced artificial intelligence technology.
Silk enables users to easily locate and compare protocols from a vast array of sources, including literature, preprints, and patents.
Leveraging the latest advancements in AI, Silk empowers researchers to make informed decisions and accelerate their work.
Enhancing the research experience, Silk seamlessly integrates with complementary tools and technologies.
Explore the versatility of UN-SCAN-IT software, a powerful solution for analyzing data from various sources, including Pentobarbital sodium and Rompun.
Harness the capabilities of UN-SCAN-IT gel software and UN-SCAN-IT gel 6.1 software to streamline your data visualization and analysis.
Silk's comprehensive platform combines the power of AI with a user-friendly interface, making research optimization more accessible than ever before.
Elevate your research with the precision of 6-0 silk suture and the reliability of NOA 148.
Experience the future of research optimization with Silk.
Unlock new possibilities, drive innovation, and accelerate your scientific breakthroughs with this transformative AI-driven platform.