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American Journal of Human Genetics Apr 2021Each human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity,...
Each human genome includes de novo mutations that arose during gametogenesis. While these germline mutations represent a fundamental source of new genetic diversity, they can also create deleterious alleles that impact fitness. Whereas the rate and patterns of point mutations in the human germline are now well understood, far less is known about the frequency and features that impact de novo structural variants (dnSVs). We report a family-based study of germline mutations among 9,599 human genomes from 33 multigenerational CEPH-Utah families and 2,384 families from the Simons Foundation Autism Research Initiative. We find that de novo structural mutations detected by alignment-based, short-read WGS occur at an overall rate of at least 0.160 events per genome in unaffected individuals, and we observe a significantly higher rate (0.206 per genome) in ASD-affected individuals. In both probands and unaffected samples, nearly 73% of de novo structural mutations arose in paternal gametes, and we predict most de novo structural mutations to be caused by mutational mechanisms that do not require sequence homology. After multiple testing correction, we did not observe a statistically significant correlation between parental age and the rate of de novo structural variation in offspring. These results highlight that a spectrum of mutational mechanisms contribute to germline structural mutations and that these mechanisms most likely have markedly different rates and selective pressures than those leading to point mutations.
Topics: Aging; Autistic Disorder; Bias; DNA Copy Number Variations; DNA Mutational Analysis; Family; Female; Genome, Human; Germ Cells; Germ-Line Mutation; Humans; Male; Mutation Rate; Paternal Age; Point Mutation
PubMed: 33675682
DOI: 10.1016/j.ajhg.2021.02.012 -
International Journal of Molecular... Feb 2023Food enzymes have an important role in the improvement of certain food characteristics, such as texture improvement, elimination of toxins and allergens, production of... (Review)
Review
Food enzymes have an important role in the improvement of certain food characteristics, such as texture improvement, elimination of toxins and allergens, production of carbohydrates, enhancing flavor/appearance characteristics. Recently, along with the development of artificial meats, food enzymes have been employed to achieve more diverse functions, especially in converting non-edible biomass to delicious foods. Reported food enzyme modifications for specific applications have highlighted the significance of enzyme engineering. However, using direct evolution or rational design showed inherent limitations due to the mutation rates, which made it difficult to satisfy the stability or specific activity needs for certain applications. Generating functional enzymes using de novo design, which highly assembles naturally existing enzymes, provides potential solutions for screening desired enzymes. Here, we describe the functions and applications of food enzymes to introduce the need for food enzymes engineering. To illustrate the possibilities of using de novo design for generating diverse functional proteins, we reviewed protein modelling and de novo design methods and their implementations. The future directions for adding structural data for de novo design model training, acquiring diversified training data, and investigating the relationship between enzyme-substrate binding and activity were highlighted as challenges to overcome for the de novo design of food enzymes.
Topics: Protein Engineering; Functional Food; Proteins; Enzymes
PubMed: 36835238
DOI: 10.3390/ijms24043827 -
Clinical Kidney Journal Apr 2023Acute kidney injury (AKI) is often iatrogenic and potentially preventable. Reduced renal nicotinamide adenine dinucleotide (NAD) is reported to increase the...
BACKGROUND
Acute kidney injury (AKI) is often iatrogenic and potentially preventable. Reduced renal nicotinamide adenine dinucleotide (NAD) is reported to increase the susceptibility of AKI. The present study explored the predictive value of urinary NAD synthetic metabolites for AKI using two independent cohorts.
METHODS
The expression of NAD synthetic enzymes in human kidney was examined by immunohistochemistry and single-cell transcriptomes. Urine samples were collected from two independent cohorts: the methotrexate (MTX) cohort with high-dose MTX treatment for lymphoma ( = 189) and the liver transplantation cohort with orthotopic liver transplantation ( = 49). Urinary metabolomics study of NAD synthesis was performed by liquid chromatography with mass spectrometry, screening for AKI predictive biomarkers. Nephroseq database and immunohistochemistry were used to analyze kidney NAD synthetic enzymes expression in AKI-susceptible conditions.
RESULTS
Human proximal tubule was the main structure in the kidney that expressed the necessary enzymes for NAD synthesis. In the MTX cohort, the urinary quinolinic acid (QA)/3-hydroxyanthranilic acid (3-OH AA) ratio before chemotherapy was significantly lower in those who developed AKI after chemotherapy compared with those who did not. This finding was consistent in the liver transplantation cohort. The area under the receiver-operating characteristic curve (AUC) of urinary QA/3-OH AA for AKI prediction was 0.749 and 0.729 in two cohorts, respectively. 3-Hydroxyanthranilic acid dioxygenase (HAAO), the enzyme catalyzing QA synthesis from 3-OH AA, decreased in AKI-susceptible diabetic kidneys.
CONCLUSIONS
The human proximal tubules were important source of NAD from the pathway. Reduced urinary QA/3-OH AA ratio, which possibly suggested decreased HAAO activity, could be a potential AKI predictive biomarker.
PubMed: 37007695
DOI: 10.1093/ckj/sfac262 -
Journal of Genetics and Genomics = Yi... Dec 2022The major histocompatibility complex (MHC) is closely associated with numerous diseases, but its high degree of polymorphism complicates the discovery of...
The major histocompatibility complex (MHC) is closely associated with numerous diseases, but its high degree of polymorphism complicates the discovery of disease-associated variants. In principle, recombination and de novo mutations are two critical factors responsible for MHC polymorphisms. However, direct evidence for this hypothesis is lacking. Here, we report the generation of fine-scale MHC recombination and de novo mutation maps of ∼5 Mb by deep sequencing (> 100×) of the MHC genome for 17 MHC recombination and 30 non-recombination Han Chinese families (a total of 190 individuals). Recombination hotspots and Han-specific breakpoints are located in close proximity at haplotype block boundaries. The average MHC de novo mutation rate is higher than the genome-wide de novo mutation rate, particularly in MHC recombinant individuals. Notably, mutation and recombination generated polymorphisms are located within and outside linkage disequilibrium regions of the MHC, respectively, and evolution of the MHC locus was mainly controlled by positive selection. These findings provide insights on the evolutionary causes of the MHC diversity and may facilitate the identification of disease-associated genetic variants.
Topics: Humans; Recombination, Genetic; Mutation; Major Histocompatibility Complex; Polymorphism, Genetic; Linkage Disequilibrium
PubMed: 35358716
DOI: 10.1016/j.jgg.2022.03.006 -
Medicina (Kaunas, Lithuania) Jul 2021: Development of hepatitis-B is considered a serious complication after liver transplantation. HBV de novo infection is a rather rare phenomenon, however it deserves...
: Development of hepatitis-B is considered a serious complication after liver transplantation. HBV de novo infection is a rather rare phenomenon, however it deserves attention in the era of donor organ shortage. The aim of the present analysis was to examine its course in liver transplant patients. : Prevalence of de novo HBV-infections was extracted from our local transplant data base. Analysis focused on the moment of HBV-detection and on the long-term follow-up in terms of biochemical and histological changes over 30 years. : 46 patients were identified with the diagnosis of de novo hepatitis B. Median time from liver transplantation to diagnosis was 397 days (7-5505). 39 patients received antiviral therapy. No fibrosis progression could be detected, whereas the grade of inflammation significantly lessened from the moment of HBV detection to the end of histological follow-up over a median of 4344 days (range 123-9490). Patients with a poor virological control demonstrated a significantly poorer overall survival. : De novo hepatitis B in liver transplant patients is a condition that can be controlled very well without significant fibrosis progression or graft loss if recognized on time within a regular transplant follow-up schedule.
Topics: Follow-Up Studies; Hepatitis B; Hepatitis B virus; Humans; Liver Transplantation; Retrospective Studies; Transplants
PubMed: 34440973
DOI: 10.3390/medicina57080767 -
Thyroid : Official Journal of the... Oct 2020The prevalence and clinical significance of detection of anti-thyroglobulin antibodies (TgAbs) during the follow-up of patients with differentiated thyroid cancer...
The prevalence and clinical significance of detection of anti-thyroglobulin antibodies (TgAbs) during the follow-up of patients with differentiated thyroid cancer (DTC) is unknown. We utilized the National Thyroid Cancer Treatment Cooperative Study registry (1987-2012). Patients registered after 1996 ( = 3318) were analyzed. We identified 1545 subjects who had available TgAb status (TgAb cohort) between years 1996 and 2012, of whom 1325 were TgAb negative at first postoperative follow-up testing. From this initial TgAb-negative group, we excluded 513 patients: 423 patients who had less than 3 years of follow-up and/or fewer than three follow-up visits, 86 patients with persistent disease after initial treatment, and 4 patients with data entry errors. The remaining 812 patients were included for analysis, comprising the TgAb persistently negative group (defined as TgAb negative for at least 3 consecutive follow-up visits and at least 3 years of follow-up) ( = 772) and the TgAb-positive group in whom TgAbs became detectable ( = 40). We then assessed whether appearance of TgAb was associated with DTC structural recurrence by using the Kaplan-Meier method. The detection of TgAb occurred in 5% of DTC patients. Recurrence of DTC in the TgAb persistently negative group compared with the TgAb-positive group did not differ significantly (9.6% vs. 15.0%, = 0.23). Baseline characteristics, histology, history of radiation exposure, staging, and median duration of follow-up were similar between the two groups. Interestingly, in all six patients who suffered a recurrence in the TgAb-positive group, the TgAbs were negative at the time of recurrence detection and became positive at a median of 2.1 (0.7-8.7) years after the structural recurrence. Utilizing a large North American DTC registry, we found the prevalence of TgAb detection to be 5% among initially TgAb-negative patients. We did not find a statistically significant association between TgAb development and DTC structural recurrence. Larger prospective studies are required to confirm these findings and further assess the significance of TgAb detection in the follow-up of DTC.
Topics: Adult; Autoantibodies; Cell Differentiation; Female; Follow-Up Studies; Humans; Male; Middle Aged; Neoplasm Recurrence, Local; North America; Prospective Studies; Registries; Thyroglobulin; Thyroid Gland; Thyroid Neoplasms
PubMed: 32228151
DOI: 10.1089/thy.2019.0791 -
Protein Science : a Publication of the... Jun 2024De novo protein design expands the protein universe by creating new sequences to accomplish tailor-made enzymes in the future. A promising topology to implement diverse...
De novo protein design expands the protein universe by creating new sequences to accomplish tailor-made enzymes in the future. A promising topology to implement diverse enzyme functions is the ubiquitous TIM-barrel fold. Since the initial de novo design of an idealized four-fold symmetric TIM barrel, the family of de novo TIM barrels is expanding rapidly. Despite this and in contrast to natural TIM barrels, these novel proteins lack cavities and structural elements essential for the incorporation of binding sites or enzymatic functions. In this work, we diversified a de novo TIM barrel by extending multiple βα-loops using constrained hallucination. Experimentally tested designs were found to be soluble upon expression in Escherichia coli and well-behaved. Biochemical characterization and crystal structures revealed successful extensions with defined α-helical structures. These diversified de novo TIM barrels provide a framework to explore a broad spectrum of functions based on the potential of natural TIM barrels.
Topics: Models, Molecular; Escherichia coli; Crystallography, X-Ray; Protein Folding; Protein Engineering; Proteins
PubMed: 38723111
DOI: 10.1002/pro.5001 -
Research and Reports in Urology 2021Pubovaginal sling is an efficient and safe procedure for stress urinary incontinence without the complications of synthetic sling. Urine retention and de novo urgency...
INTRODUCTION
Pubovaginal sling is an efficient and safe procedure for stress urinary incontinence without the complications of synthetic sling. Urine retention and de novo urgency are bothersome aftermath of this procedure. We aim to identify potential risk factors for de novo urgency after autologous pubovaginal sling.
METHODS
From 2013 to 2016, 347 patients underwent autologous pubovaginal sling. Age, BMI, pelvic irradiation, use of anticholinergic medication, previous vaginal related surgical histories, "over-tight" technique, and concomitant surgeries were examined for potential risk factors. De novo urgency/urge incontinence was defined as treatment (medication, botulinum toxin injection, sacral neuromodulation) for urge postoperatively and was not noted before surgery. Chi-square and fisher's exact tests were used as statistical analysis.
RESULTS
A total of 109 patients underwent autologous rectus fascia pubovaginal sling, after excluding status post urethral diverticulectomy, concomitant diverticulectomy, and concomitant abdominal surgery. Twenty-three (21.1%) patients were treated for de novo urge/urge incontinence, 18 (78.2%) with anticholinergic, 4 (17.3%) with botox injection and 2 (8.69%) with sacral neuromodulation. None but prior pelvic organ prolapse surgery was associated with developing de novo urge/urge incontinence (p=0.026).
DISCUSSION
Patients with prior pelvic organ prolapse surgery were more likely to be at risk of de novo urgency after autologous pubovaginal sling. This study provided more information for preoperative consultation for patients undergoing incontinence surgery.
PubMed: 34422706
DOI: 10.2147/RRU.S321955 -
Annals of Translational Medicine May 2021With the exponential increase of worldwide obesity, the number of bariatric surgery (BaS) procedures have equally risen. The surgical management of obesity has been... (Review)
Review
With the exponential increase of worldwide obesity, the number of bariatric surgery (BaS) procedures have equally risen. The surgical management of obesity has been widely established as the standard of care for sustained weight reduction, resolution, and improvement of associated comorbidities. However, BaS itself can have postoperative deleterious effects, including gastroesophageal reflux disease (GERD) and upper gastrointestinal motility disorders. The modified anatomy resulting from BaS, due to either a restrictive or hypoabsorptive component, gives this disorder a multifactorial etiology. The overall management of GERD should focus on three primordial approaches: Non-surgical, endoluminal, and surgical. Even in the absence of GERD following primary or secondary BaS, said disorder should be closely monitored and therapy should be catered in a case-by-case approach. Consequently, treatment strategies have been developed on this principle as to adequately resolve GERD. Despite the presence of multiple and suitable treatment modalities, the operating surgeon should perform them in the best interest of the patient. Short-, medium-, and long-term outcomes should be taken into consideration prior to proceed with any type of preferred management option. This article herein presents an update on the surgical management of GERD following BaS and current practical innovations.
PubMed: 34164533
DOI: 10.21037/atm-20-5890 -
International Journal of Molecular... Feb 2024The worldwide agricultural system confronts a significant challenge represented by the increasing demand for food in the face of a growing global population. This... (Review)
Review
The worldwide agricultural system confronts a significant challenge represented by the increasing demand for food in the face of a growing global population. This challenge is exacerbated by a reduction in cultivable land and the adverse effects of climate change on crop yield quantity and quality. Breeders actively embrace cutting-edge omics technologies to pursue resilient genotypes in response to these pressing issues. In this global context, new breeding techniques (NBTs) are emerging as the future of agriculture, offering a solution to introduce resilient crops that can ensure food security, particularly against challenging climate events. Indeed, the search for domestication genes as well as the genetic modification of these loci in wild species using genome editing tools are crucial steps in carrying out de novo domestication of wild plants without compromising their genetic background. Current knowledge allows us to take different paths from those taken by early Neolithic farmers, where crop domestication has opposed natural selection. In this process traits and alleles negatively correlated with high resource environment performance are probably eradicated through artificial selection, while others may have been lost randomly due to domestication and genetic bottlenecks. Thus, domestication led to highly productive plants with little genetic diversity, owing to the loss of valuable alleles that had evolved to tolerate biotic and abiotic stresses. Recent technological advances have increased the feasibility of de novo domestication of wild plants as a promising approach for crafting optimal crops while ensuring food security and using a more sustainable, low-input agriculture. Here, we explore what crucial domestication genes are, coupled with the advancement of technologies enabling the precise manipulation of target sequences, pointing out de novo domestication as a promising application for future crop development.
Topics: Domestication; Plant Breeding; Crops, Agricultural; Agriculture; Gene Editing
PubMed: 38397047
DOI: 10.3390/ijms25042374