scholarly journals Deep sequencing of DNA from urine of kidney allograft recipients to estimate donor/recipient-specific DNA fractions

PLoS ONE ◽  
2021 ◽  
Vol 16 (4) ◽  
pp. e0249930
Author(s):  
Aziz Belkadi ◽  
Gaurav Thareja ◽  
Darshana Dadhania ◽  
John R. Lee ◽  
Thangamani Muthukumar ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Bacterial Infections ◽  
Human Kidney ◽  
Cost Effective ◽  
Maximum Error ◽  
Standard Test ◽  
Kidney Allograft ◽  
Cost Effective Method ◽  
In Silico Simulation ◽  
End Stage

Kidney transplantation is the treatment of choice for patients with end-stage kidney failure, but transplanted allograft could be affected by viral and bacterial infections and by immune rejection. The standard test for the diagnosis of acute pathologies in kidney transplants is kidney biopsy. However, noninvasive tests would be desirable. Various methods using different techniques have been developed by the transplantation community. But these methods require improvements. We present here a cost-effective method for kidney rejection diagnosis that estimates donor/recipient-specific DNA fraction in recipient urine by sequencing urinary cell DNA. We hypothesized that in the no-pathology stage, the largest tissue types present in recipient urine are donor kidney cells, and in case of rejection, a larger number of recipient immune cells would be observed. Extensive in-silico simulation was used to tune the sequencing parameters: number of variants and depth of coverage. Sequencing of DNA mixture from 2 healthy individuals showed the method is highly predictive (maximum error < 0.04). We then demonstrated the insignificant impact of familial relationship and ethnicity using an in-house and public database. Lastly, we performed deep DNA sequencing of urinary cell pellets from 32 biopsy-matched samples representing two pathology groups: acute rejection (AR, 11 samples) and acute tubular injury (ATI, 12 samples) and 9 samples with no pathology. We found a significant association between the donor/recipient-specific DNA fraction in the two pathology groups compared to no pathology (P = 0.0064 for AR and P = 0.026 for ATI). We conclude that deep DNA sequencing of urinary cells from kidney allograft recipients offers a noninvasive means of diagnosing acute pathologies in the human kidney allograft.

scholarly journals Deep sequencing of DNA from urine of kidney allograft recipients to estimate the donor-specific DNA fraction

2020 ◽  
Author(s):  
Aziz Belkadi ◽  
Gaurav Thareja ◽  
Darshana Dadhania ◽  
John R. Lee ◽  
Thangamani Muthukumar ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Bacterial Infections ◽  
Human Kidney ◽  
Cost Effective ◽  
Maximum Error ◽  
Standard Test ◽  
Kidney Allograft ◽  
Cost Effective Method ◽  
In Silico Simulation ◽  
End Stage

AbstractRenal transplantation is the method of choice for patients with end stage kidney failure. But transplanted allograft could be affected by viral and bacterial infections and immune rejections. The standard test for the diagnosis of acute pathologies in kidney transplants is the renal biopsy. However, noninvasive tests would be desirable. Various methods using different techniques have been developed by the transplantation community. But these methods expect improvements. We present here a cost-effective method based on estimating donor-specific DNA fraction in recipient urine based on sequencing of recipient urine DNA only. We hypothesized that in the no-pathology stage, the largest tissue types present in recipient urine are donor kidney cells and in case of rejection, a larger number of recipient immune cells would be observed. Extensive in-silico simulation was used to tune the sequencing parameters: number of variants and depth of coverage. Sequencing of DNA mixture from 2 healthy individuals showed the method high prediction accuracy (maximum error < 0.04). We then demonstrated the insignificant impact of familial relationship and ethnicity using an in-house and public database. Lastly, we performed recipient deep urine DNA sequencing in 32 samples representing two pathology groups: acute rejection (AR, 12 samples) and acute tubular injury (ATI, 11 samples) and 9 samples with no pathology. We found a significant association between the donor-specific DNA fraction in the two pathology groups compared to no pathology (P = 0.0064 for AR and P = 0.026 for ATI). We conclude that deep DNA sequencing of recipient urine offers a noninvasive means of diagnosing and prognosticating acute pathologies in the human kidney allograft.

scholarly journals A simple bioreactor-based method to generate kidney organoids from pluripotent stem cells

2017 ◽  
Author(s):  
Aneta Przepiorski ◽  
Veronika Sander ◽  
Tracy Tran ◽  
Jennifer A. Hollywood ◽  
Brie Sorrenson ◽  
...  
Keyword(s):  
Stem Cells ◽  
Pluripotent Stem Cells ◽  
Kidney Development ◽  
Kidney Tissue ◽  
Experimental System ◽  
Human Kidney ◽  
Cost Effective ◽  
Cost Effective Method ◽  
Induced Pluripotent ◽  
Kidney Organoids

SummaryKidney organoids generated from human pluripotent stem cells have the potential to revolutionize how kidney development and injury are studied. Current protocols are technically complex and suffer from poor reproducibility and high reagent costs restricting scalability. To overcome these issues, we have established a simple, inexpensive and robust method to grow kidney organoids in bulk from human induced pluripotent stem cells. Our organoids develop tubular structures by day (d) 8 and show optimal tissue morphology at d14. A comparison with fetal human kidney suggests that d14 organoid renal structures most closely resemble ‘capillary loop’ stage nephrons. We show that deletion of HNF1B, a transcription factor linked to congenital kidney defects, interferes with tubulogenesis, validating our experimental system for studying renal developmental biology. Taken together, our protocol provides a fast, efficient and cost-effective method for generating large quantities of human fetal kidney tissue, enabling the study of normal and aberrant human renal development.

scholarly journals Diagnosis of Galactosemia by Simple Technique in a Resource-Constraint Country

2020 ◽  
Vol 10 (1) ◽  
pp. 43-48
Author(s):  
Md Benzamin ◽  
Nazmul Hassan ◽  
Rono Mollika ◽  
Kaniz Fathema ◽  
Khan Lamia Nahid ◽  
...  
Keyword(s):  
Autosomal Recessive Inheritance ◽  
Cost Effective ◽  
Standard Test ◽  
Screening Methods ◽  
Neonatal Cholestasis ◽  
Dipstick Test ◽  
Disease Manifestation ◽  
Cost Effective Method ◽  
Impaired Metabolism ◽  
Milk Feeding

Galactosemia is an autosomal recessive inheritance and there is cellular deficiency of enzymes leading to defective/impaired metabolism of galactose resulting in toxic byproducts like galactilol, galactose-1-phosphate and galactonate that affect mainly liver, brain, kidneys, lens and gonads. Galactosemia appears as a rare metabolic cause of neonatal cholestasis syndrome (NCS). The classic disease manifestation after the first milk feeding varies in severity from an acute fulminant illness to a more common subacute illness beginning within the first few days of life. Neonatal sepsis is one of the presentations. Galactokinase deficiency results primarily in cataract formation and galactosuria. The preliminary diagnosis of galactosemia in sick neonates and suspected infants is made by Benedict test in several urine specimens and followed by dipstick test to exclude glycosuria. Gold standard test is demonstration of low enzyme activity in erythrocyte. Galactosemia can be detected by newborn screening methods like the Guthrie test using filterpaper blood samples. Classical form of galactosemia should be treated with an absolute galactose restricted diet without waiting for confirmation of the diagnosis. Here we report a case of a 50-dayold boy with features of neonatal cholestasis, diagnosed as galactosemia by using a simple cost effective method. J Enam Med Col 2020; 10(1): 43-48

scholarly journals Targeted Hydrolysis of β-Lactam Antibiotics in Dry Suspension Residue: A Proposed Method to Reduce Ecological Toxicity and Bacterial Resistance

Water ◽  
2021 ◽  
Vol 13 (16) ◽  
pp. 2225
Author(s):  
Arne Brahms ◽  
Christian Peifer
Keyword(s):  
Bacterial Infections ◽  
Bacterial Resistance ◽  
Sodium Hydroxide Solution ◽  
Domestic Wastewater ◽  
Cost Effective ◽  
Therapeutic Drug ◽  
Antimicrobial Drugs ◽  
River Waters ◽  
Cost Effective Method ◽  
Take Back

Within our therapeutic drug arsenal, antibiotics are of significant importance and are widely used in huge amounts to medicate, e.g., bacterial infections in humans and animals. Regarding the more than 10 types of antimicrobial drugs, the highly important orally taken β-lactams typically include dry suspension formulations. In many cases for this formulation, even after usage according to specification, residues remain in the prepared dry suspension bottle, which is often cleaned at home and the contents are flushed down into domestic wastewater. This plausible practice adds to the fact that, e.g., amoxicillin can be found in river waters, and is to be monitored in the EU, as given by resolution 2008/105/EG article 8b. When imported into the environment, β-lactam antibiotics can cause severe ecological problems, and equally importantly, therapeutic applications of these antibiotics are endangered by the forced development of pathogenic resistance. To avoid these issues, we developed and validated a fast, simple, robust, and cost-effective method using a 1 M sodium hydroxide solution to effectively hydrolyze and inactivate β-lactam residues. In this paper, we strongly propose a procedure involving pharmacists to take back residue of β-lactam dry suspension formulations. Subsequently, qualified pharmaceutical staff could inactivate β-lactam residue in the laboratory by the proposed method, and then dispose of the mixture into wastewater.

CAD Of Anticorrosive Protection Of Steel Structures

2019 ◽  
pp. 18-23
Keyword(s):  
Protective Coating ◽  
Computer Aided Design ◽  
Steel Structures ◽  
Cost Effective ◽  
Operating Conditions ◽  
Computational Tool ◽  
Protection Method ◽  
Cost Effective Method ◽  
The Cost ◽  
Aided Design

The choice of cost-effective method of anticorrosive protection of steel structures is an urgent and time consuming task, considering the significant number of protection ways, differing from each other in the complex of technological, physical, chemical and economic characteristics. To reduce the complexity of solving this problem, the author proposes a computational tool that can be considered as a subsystem of computer-aided design and used at the stage of variant and detailed design of steel structures. As a criterion of the effectiveness of the anti-corrosion protection method, the cost of the protective coating during the service life is accepted. The analysis of existing methods of steel protection against corrosion is performed, the possibility of their use for the protection of the most common steel structures is established, as well as the estimated period of effective operation of the coating. The developed computational tool makes it possible to choose the best method of protection of steel structures against corrosion, taking into account the operating conditions of the protected structure and the possibility of using a protective coating.

Monitoring effluent quality in hypertrophic wastewater reservoirs using remote sensing

1996 ◽  
Vol 33 (8) ◽  
pp. 23-29 ◽  
Author(s):  
I. Dor ◽  
N. Ben-Yosef
Keyword(s):  
Water Quality ◽  
Theoretical Model ◽  
Principal Component ◽  
Cost Effective ◽  
Operational Parameters ◽  
Effluent Quality ◽  
Optical Images ◽  
Routine Monitoring ◽  
Cost Effective Method ◽  
Wastewater Quality

About one hundred and fifty wastewater reservoirs store effluents for irrigation in Israel. Effluent qualities differ according to the inflowing wastewater quality, the degree of pretreatment and the operational parameters. Certain aspects of water quality like concentration of organic matter, suspended solids and chlorophyll are significantly correlated with the water column transparency and colour. Accordingly optical images of the reservoirs obtained from the SPOT satellite demonstrate pronounced differences correlated with the water quality. The analysis of satellite multispectral images is based on a theoretical model. The model calculates, using the radiation transfer equation, the volume reflectance of the water body. Satellite images of 99 reservoirs were analyzed in the chromacity space in order to classify them according to water quality. Principal Component Analysis backed by the theoretical model increases the method sensitivity. Further elaboration of this approach will lead to the establishment of a time and cost effective method for the routine monitoring of these hypertrophic wastewater reservoirs.

A Cost-Effective Method to Prepare Pure Vildagliptin

2013 ◽  
Vol 10 (3) ◽  
pp. 159-163 ◽  
Author(s):  
Jun Peng ◽  
Yue Feng ◽  
Zhu Tao ◽  
Yingjie Chen ◽  
Xiangnan Hu
Keyword(s):  
Cost Effective ◽  
Cost Effective Method
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