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  • 1
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 13, No. 1 ( 2022-01-10)
    Abstract: De novo mutations are known to play a prominent role in sporadic disorders with reduced fitness. We hypothesize that de novo mutations play an important role in severe male infertility and explain a portion of the genetic causes of this understudied disorder. To test this hypothesis, we utilize trio-based exome sequencing in a cohort of 185 infertile males and their unaffected parents. Following a systematic analysis, 29 of 145 rare (MAF  〈  0.1%) protein-altering de novo mutations are classified as possibly causative of the male infertility phenotype. We observed a significant enrichment of loss-of-function de novo mutations in loss-of-function-intolerant genes ( p -value = 1.00 × 10 −5 ) in infertile men compared to controls. Additionally, we detected a significant increase in predicted pathogenic de novo missense mutations affecting missense-intolerant genes ( p -value = 5.01 × 10 −4 ) in contrast to predicted benign de novo mutations. One gene we identify, RBM5 , is an essential regulator of male germ cell pre-mRNA splicing and has been previously implicated in male infertility in mice. In a follow-up study, 6 rare pathogenic missense mutations affecting this gene are observed in a cohort of 2,506 infertile patients, whilst we find no such mutations in a cohort of 5,784 fertile men ( p -value = 0.03). Our results provide evidence for the role of de novo mutations in severe male infertility and point to new candidate genes affecting fertility.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2022
    detail.hit.zdb_id: 2553671-0
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  • 2
    In: Human Reproduction, Oxford University Press (OUP), Vol. 37, No. 6 ( 2022-05-30), p. 1360-1369
    Abstract: Are there more de novo mutations (DNMs) present in the genomes of children born through medical assisted reproduction (MAR) compared to spontaneously conceived children? SUMMARY ANSWER In this pilot study, no statistically significant difference was observed in the number of DNMs observed in the genomes of MAR children versus spontaneously conceived children. WHAT IS KNOWN ALREADY DNMs are known to play a major role in sporadic disorders with reduced fitness such as severe developmental disorders, including intellectual disability and epilepsy. Advanced paternal age is known to place offspring at increased disease risk, amongst others by increasing the number of DNMs in their genome. There are very few studies reporting on the effect of MAR on the number of DNMs in the offspring, especially when male infertility is known to be affecting the potential fathers. With delayed parenthood an ongoing epidemiological trend in the 21st century, there are more children born from fathers of advanced age and more children born through MAR every day. STUDY DESIGN, SIZE, DURATION This observational pilot study was conducted from January 2015 to March 2019 in the tertiary care centre at Radboud University Medical Center. We included a total of 53 children and their respective parents, forming 49 trios (mother, father and child) and two quartets (mother, father and two siblings). One group of children was born after spontaneous conception (n = 18); a second group of children born after IVF (n = 17) and a third group of children born after ICSI combined with testicular sperm extraction (ICSI-TESE) (n = 18). In this pilot study, we also subdivided each group by paternal age, resulting in a subgroup of children born to younger fathers ( & lt;35 years of age at conception) and older fathers ( & gt;45 years of age at conception). PARTICIPANTS/MATERIALS, SETTING, METHODS Whole-genome sequencing (WGS) was performed on all parent-offspring trios to identify DNMs. For 34 of 53 trios/quartets, WGS was performed twice to independently detect and validate the presence of DNMs. Quality of WGS-based DNM calling was independently assessed by targeted Sanger sequencing. MAIN RESULTS AND THE ROLE OF CHANCE No significant differences were observed in the number of DNMs per child for the different methods of conception, independent of parental age at conception (multi-factorial ANOVA, f(2) = 0.17, P-value = 0.85). As expected, a clear paternal age effect was observed after adjusting for method of conception and maternal age at conception (multiple regression model, t = 5.636, P-value = 8.97 × 10−7), with on average 71 DNMs in the genomes of children born to young fathers ( & lt;35 years of age) and an average of 94 DNMs in the genomes of children born to older fathers ( & gt;45 years of age). LIMITATIONS, REASONS FOR CAUTION This is a pilot study and other small-scale studies have recently reported contrasting results. Larger unbiased studies are required to confirm or falsify these results. WIDER IMPLICATIONS OF THE FINDINGS This pilot study did not show an effect for the method of conception on the number of DNMs per genome in offspring. Given the role that DNMs play in disease risk, this negative result is good news for IVF and ICSI-TESE born children, if replicated in a larger cohort. STUDY FUNDING/COMPETING INTEREST(S) This research was funded by the Netherlands Organisation for Scientific Research (918-15-667) and by an Investigator Award in Science from the Wellcome Trust (209451). The authors have no conflicts of interest to declare. TRIAL REGISTRATION NUMBER N/A.
    Type of Medium: Online Resource
    ISSN: 0268-1161 , 1460-2350
    Language: English
    Publisher: Oxford University Press (OUP)
    Publication Date: 2022
    detail.hit.zdb_id: 1484864-8
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  • 3
    Online Resource
    Online Resource
    Informa UK Limited ; 2018
    In:  Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology Vol. 152, No. 2 ( 2018-03-04), p. 179-303
    In: Plant Biosystems - An International Journal Dealing with all Aspects of Plant Biology, Informa UK Limited, Vol. 152, No. 2 ( 2018-03-04), p. 179-303
    Type of Medium: Online Resource
    ISSN: 1126-3504 , 1724-5575
    Language: English
    Publisher: Informa UK Limited
    Publication Date: 2018
    detail.hit.zdb_id: 2146652-X
    SSG: 12
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  • 4
    In: Jurnal Kimia, Universitas Udayana, ( 2018-01-15), p. 50-
    Abstract: Kulit yang mengalami penuaan dini menyebabkan nilai kelembaban kulit menjadi berkurang sehingga kulit menjadi kering. Berkurangnya nilai kelembaban kulit dapat diatasi dengan memberikan perawatan terhadap kulit. Perawatan dapat dilakukan dengan sediaan topikal yang mengandung antioksidan salah satunya yaitu masker gel peel off ekstrak kulit buah manggis (Garcinia mangostana L.). Penelitian pendahuluan ini bertujuan untuk melihat nilai kelembaban kulit manusia pada pemakaian masker gel peel off ekstrak kulit buah manggis. Pengujian dilakukan dengan menggunakan 5 subjek uji masing masing dioleskan plasebo pada tangan kanan dan dioleskan masker gel peel off ekstrak kulit manggis pada tangan kiri selama 14 hari. Metode perlakuan subjek uji dilakukan secara randomized, double blind, plasebo control group design. Data yang diperoleh diuji normalitas dan homogenitasnya. Data nilai kelembaban terhadap nilai sebelum dan sesudah penelitian dibandingkan dengan uji T Berpasangan. Hasil penelitian menunjukkan bahwa pada kelompok kontrol dan perlakuan menghasilkan nilai p 〈 0,05 yang bermakna yang menunjukkan bahwa terdapat perbedaan yang bermakna sebelum dan sesudah dioleskan basis masker maupun masker yang mengandung kulit manggis. Kedua kelompok menunjukkan adanya perubahan, namun rentang peningkatan pada kelompok perlakuan lebih besar dibandingkan dengan kelompok kontrol. Dengan demikian, diketahui masker gel peel off Garcinia mangostana L. mampu meningkatkan nilai kelembaban kulit manusia lebih besar dibandingkan kelompok kontrol.
    Type of Medium: Online Resource
    ISSN: 2599-2740 , 1907-9850
    URL: Issue
    Language: Unknown
    Publisher: Universitas Udayana
    Publication Date: 2018
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  • 5
    In: IOP Conference Series: Earth and Environmental Science, IOP Publishing, Vol. 451, No. 1 ( 2020-03-01), p. 012072-
    Abstract: Water tracing was conducted at Karangbolong Karst as a rapid assessment of the Kalisirah spring hydrological characteristics. This study was conducted to determine the movement of underground flow and the estimation of the Catchment Area using the Todd Nomogram and field observations. The results of flow tracing tests conducted in Pocung Cave indicate that there is underground river network connectivity between Pocung Cave, Jeblosan Sinkhole and Kalisirah Springs. Based on topographic survey and flow tracing test, the calculation of the estimated area of the Kalisirah catchment area is 180 Ha. The results were also validate using other parameters, namely flowrate and rainfall in the research location using Todd Nomogram. The estimated area of the Kalisirah catchment area with the Todd Nomogram is 189.2 Ha. The calculation of the estimated area of Kalisirah catchment area based on topographic survey and water tracing is relevant with the estimated area with Todd Nomogram. Groundwater tracing investigation can be used to determine karst spring catchment area, as a preliminary study to understanding the karst hydrology.
    Type of Medium: Online Resource
    ISSN: 1755-1307 , 1755-1315
    Language: Unknown
    Publisher: IOP Publishing
    Publication Date: 2020
    detail.hit.zdb_id: 2434538-6
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  • 6
    In: Jurnal Kimia, Universitas Udayana, ( 2018-07-31), p. 187-
    Abstract: Jeruk limau (Citrus amblycarpa (Hassk.) Osche) merupakan tanaman endemik Indonesia yang memiliki potensi besar sebagai obat. Pendekatan kemotaksonomi terhadap daun C. amblycarpa dilakukan untuk memprediksi potensinya dalam pengobatan. Sebelum dilakukan pengujian aktivitas farmakologi, serbuk dan ekstrak yang diperoleh dari hasil ekstraksi menggunakan pelarut etanol 70% terlebih dahulu dilakukan studi pendahuluan meliputi perhitungan persentase rendemen ekstrak, pemeriksaan organoleptik dan mikroskopik serbuk, standarisasi serbuk dan ekstrak, dan skrining fitokimia untuk mengetahui kandungan metabolit sekunder dari daun C. amblycarpa. Standarisasi yang dilakukan meliputi penetapan kadar abu total, penetapan kadar abu tidak larut asam, penetapan kadar abu larut air, dan penetapan kadar air dari serbuk simpilisa dan ekstrak. Skrining fitokimia terhadap ekstrak etanol 70% daun C. amblycarpa meliputi pemeriksaan alkaloid, pemeriksaan flavonoid, pemeriksaan polifenol dan tanin, pemeriksaan glikosida, pemeriksaan steroid dan triterpenoid, pemeriksaan saponin, serta pemeriksaan minyak atsiri. Hasil skrining fitokimia menunjukkan bahwa ekstrak etanol 70% daun C. amblycarpa mengandung senyawa golongan flavonoid, polifenol dan tanin, glikosida, serta minyak atsiri. Kata Kunci: Citrus amblycarpa (Hassk.) Osche, jeruk limau, standarisasi, skrining fitokimia
    Type of Medium: Online Resource
    ISSN: 2599-2740 , 1907-9850
    URL: Issue
    Language: Unknown
    Publisher: Universitas Udayana
    Publication Date: 2018
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  • 7
    In: American Journal of Transplantation, Elsevier BV, Vol. 12, No. 4 ( 2012-04), p. 1039-1045
    Type of Medium: Online Resource
    ISSN: 1600-6135
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2012
    detail.hit.zdb_id: 2045621-9
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  • 8
    In: Investigative Opthalmology & Visual Science, Association for Research in Vision and Ophthalmology (ARVO), Vol. 60, No. 13 ( 2019-10-16), p. 4249-
    Type of Medium: Online Resource
    ISSN: 1552-5783
    Language: English
    Publisher: Association for Research in Vision and Ophthalmology (ARVO)
    Publication Date: 2019
    detail.hit.zdb_id: 2009858-3
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  • 9
    In: npj Genomic Medicine, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2021-11-18)
    Abstract: Inherited retinal diseases (IRDs) are a major cause of visual impairment. These clinically heterogeneous disorders are caused by pathogenic variants in more than 270 genes. As 30–40% of cases remain genetically unexplained following conventional genetic testing, we aimed to obtain a genetic diagnosis in an IRD cohort in which the genetic cause was not found using whole-exome sequencing or targeted capture sequencing. We performed whole-genome sequencing (WGS) to identify causative variants in 100 unresolved cases. After initial prioritization, we performed an in-depth interrogation of all noncoding and structural variants in genes when one candidate variant was detected. In addition, functional analysis of putative splice-altering variants was performed using in vitro splice assays. We identified the genetic cause of the disease in 24 patients. Causative coding variants were observed in genes such as ATXN7 , CEP78 , EYS , FAM161A , and HGSNAT . Gene disrupting structural variants were also detected in ATXN7 , PRPF31 , and RPGRIP1 . In 14 monoallelic cases, we prioritized candidate noncanonical splice sites or deep-intronic variants that were predicted to disrupt the splicing process based on in silico analyses. Of these, seven cases were resolved as they carried pathogenic splice defects. WGS is a powerful tool to identify causative variants residing outside coding regions or heterozygous structural variants. This approach was most efficient in cases with a distinct clinical diagnosis. In addition, in vitro splice assays provide important evidence of the pathogenicity of rare variants.
    Type of Medium: Online Resource
    ISSN: 2056-7944
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2021
    detail.hit.zdb_id: 2813848-X
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  • 10
    Online Resource
    Online Resource
    IOP Publishing ; 2020
    In:  IOP Conference Series: Materials Science and Engineering Vol. 742, No. 1 ( 2020-01-01), p. 012042-
    In: IOP Conference Series: Materials Science and Engineering, IOP Publishing, Vol. 742, No. 1 ( 2020-01-01), p. 012042-
    Abstract: Concerning on the dependancy of coal on electric generation wordwidely, study on fly ash, thesolid waste of fired coal electricity generation, has been comprehensively conducting, i.e. geopolymer, cenosphere, soil remediation, and adsorbent. However, only few studies dealing with the utilization of bottom ash. Having of about 53% of coal in the 2050 energy mix, Indonesia will be dealing with more than 200 million tonnes of fly ash and bottom ash (FABA). In this study, FABA was mixed in certain proportion of 50:50, 75:25, dan 100:0. The formation of geopolymer was conducted with sodium hydroxide and sodium silicate in certain concentration. Once the mixture had been homogenized, it was casted and cured in varied temperature of 30, 60, dan 90 oC with curing time of 1, 3, 5, 14, 21, dan 28 days. In each curing time, sample was then analyzed using compresive strength apparatus and FTIR in order to observed the geopolimerization of the FABA mixture. It was found that compressive strength representing the macro characteristic of the geopolymer is in line with the CORR analysis of the FTIR results showing that the formation of aluminosilicate is responsible for the mechanical strength of the geopolymer. The higher the bottom ash ratio in the mixture with decrease the strength of the geopolymer in the order of one per second. Higher temperature results higher compresive strength to the value of 42 Mpa (FABA ratio is 75:25 at temperature of 90 oC) above the Indonesian standard for concrete. From this study, kinetics of FABA geopolymerization can be generated in accordance todiffusion model with R2 of 0.9135. Thus the utilization of FABA for geopolymer is going to be a potential solution to overcome the increasing amount of FABA resulted from fired coal electrical generation in Indonesia.
    Type of Medium: Online Resource
    ISSN: 1757-8981 , 1757-899X
    Language: Unknown
    Publisher: IOP Publishing
    Publication Date: 2020
    detail.hit.zdb_id: 2506501-4
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