Dwi Retnowati - Academia.edu (original) (raw)
Papers by Dwi Retnowati
Genetics, 2022
Megasatellites are large tandem repeats found in all fungal genomes but especially abundant in th... more Megasatellites are large tandem repeats found in all fungal genomes but especially abundant in the opportunistic pathogen Candida glabrata. They are encoded in genes involved in cell-cell interactions, either between yeasts or between yeast and human cells. In the present work, we have been using an iterative genetic system to delete several C. glabrata megasatellite-containing genes and found that two of them were positively involved in adhesion to epithelial cells, whereas three genes negatively controlled adhesion. Two of the latter, CAGL0B05061g or CAGL0A04851g, were also negative regulators of yeast-to-yeast adhesion, making them central players in controlling C. glabrata adherence properties. Using a series of synthetic Saccharomyces cerevisiae strains in which the FLO1 megasatellite was replaced by other tandem repeats of similar length but different sequences, we showed that the capacity of a strain to flocculate in liquid culture was unrelated to its capacity to adhere to e...
BackgroundAdult male sperm whales (Physeter macrocephalus) are long distance runners of the marin... more BackgroundAdult male sperm whales (Physeter macrocephalus) are long distance runners of the marine realm, feeding in high latitudes and mating in tropical and subtropical waters where stable social groups of females and immatures live. Several areas of uncertainty still limit our understanding of their social and breeding behaviour, in particular concerning the potential existence of geographical and/or social fidelities.In this study, using underwater observation and sloughed-skin sampling, we looked for male social fidelity to a specific matrilineal sperm whale group near Mauritius. In addition, we captured a wider picture of kin relationships and genetic diversity of male sperm whales in the Indian Ocean thanks to biopsies of eight unique individuals taken in a feeding ground near the Kerguelen and Crozet Archipelagos (Southern Indian Ocean).ResultsTwenty-six adult male sperm whales, of which 13 were sampled, were identified when socializing with adult females and immatures off M...
Biology Methods and Protocols, 2018
Nucleic acid detection and quantification using a labeled DNA probe is a very common molecular bi... more Nucleic acid detection and quantification using a labeled DNA probe is a very common molecular biology procedure. Here, we describe a new method, based on commonly used laboratory solutions, for nucleic acid hybridization and detection with digoxigenin-labeled DNA probes. The protocol described is faster, more sensitive and much cheaper than a standard protocol using commercial solutions. Comparison with a classical radioactive detection method shows that the latter exhibits less background and shows a greater linear response. Hence, the proposed protocol may be routinely performed for qualitative detection of nucleic acid, but when precise signal quantitation needs to be obtained, radioactive probe hybridization associated to phosphorimaging technology is more reliable.
Biotechnology for Biofuels, 2014
Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual he... more Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant. Results: The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. Conclusions: The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications.
Serat Wulangreh adalah karya sastra Jawa karya Sri Susuhunan Pakubuwana IV yang penuh dengan ajar... more Serat Wulangreh adalah karya sastra Jawa karya Sri Susuhunan Pakubuwana IV yang penuh dengan ajaran nilai moral yang tinggi. Nilai moral yang terkandung didalamnya merupakan sumber pendidikan karakter yang berbasisi pada kearifan lokal. Serat Wulangreh pupuh Gambuh merupakan bahan ajar pada mata pelajaran Bahasa Jawa kelas VIII di tingkat SMP/MTs. Siswa kelas tersebut diduduki oleh generasi milenial. Tujuan dari penelitian ini adalah mengungkapkan nilai-nilai luhur yang terkandung di dalam serat Wulangreh pupuh Gambuh sebagai sumber pendidikan karakter bagi generasi milenial. Jenis penelitian ini adalah penelitian kualitatif dengan fokus pada pendidikan karakter yang dibangun dan diterapkan pada generasi milenial. Metode penelitian yang digunakan adalah metode deskriptif kualitatif. Analisis data dilakukan secara deskriptif. Serat Wulangreh dibongkar isinya untuk menentukan nilai-nilai luhur yang terkandung di dalamnya. Dari nilai-nilai luhur tersebut ditarik kesimpulan nilai karakt...
Genetics, 2022
Megasatellites are large tandem repeats found in all fungal genomes but especially abundant in th... more Megasatellites are large tandem repeats found in all fungal genomes but especially abundant in the opportunistic pathogen Candida glabrata. They are encoded in genes involved in cell-cell interactions, either between yeasts or between yeast and human cells. In the present work, we have been using an iterative genetic system to delete several C. glabrata megasatellite-containing genes and found that two of them were positively involved in adhesion to epithelial cells, whereas three genes negatively controlled adhesion. Two of the latter, CAGL0B05061g or CAGL0A04851g, were also negative regulators of yeast-to-yeast adhesion, making them central players in controlling C. glabrata adherence properties. Using a series of synthetic Saccharomyces cerevisiae strains in which the FLO1 megasatellite was replaced by other tandem repeats of similar length but different sequences, we showed that the capacity of a strain to flocculate in liquid culture was unrelated to its capacity to adhere to e...
BackgroundAdult male sperm whales (Physeter macrocephalus) are long distance runners of the marin... more BackgroundAdult male sperm whales (Physeter macrocephalus) are long distance runners of the marine realm, feeding in high latitudes and mating in tropical and subtropical waters where stable social groups of females and immatures live. Several areas of uncertainty still limit our understanding of their social and breeding behaviour, in particular concerning the potential existence of geographical and/or social fidelities.In this study, using underwater observation and sloughed-skin sampling, we looked for male social fidelity to a specific matrilineal sperm whale group near Mauritius. In addition, we captured a wider picture of kin relationships and genetic diversity of male sperm whales in the Indian Ocean thanks to biopsies of eight unique individuals taken in a feeding ground near the Kerguelen and Crozet Archipelagos (Southern Indian Ocean).ResultsTwenty-six adult male sperm whales, of which 13 were sampled, were identified when socializing with adult females and immatures off M...
Biology Methods and Protocols, 2018
Nucleic acid detection and quantification using a labeled DNA probe is a very common molecular bi... more Nucleic acid detection and quantification using a labeled DNA probe is a very common molecular biology procedure. Here, we describe a new method, based on commonly used laboratory solutions, for nucleic acid hybridization and detection with digoxigenin-labeled DNA probes. The protocol described is faster, more sensitive and much cheaper than a standard protocol using commercial solutions. Comparison with a classical radioactive detection method shows that the latter exhibits less background and shows a greater linear response. Hence, the proposed protocol may be routinely performed for qualitative detection of nucleic acid, but when precise signal quantitation needs to be obtained, radioactive probe hybridization associated to phosphorimaging technology is more reliable.
Biotechnology for Biofuels, 2014
Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual he... more Background: The industrially important yeast Blastobotrys (Arxula) adeninivorans is an asexual hemiascomycete phylogenetically very distant from Saccharomyces cerevisiae. Its unusual metabolic flexibility allows it to use a wide range of carbon and nitrogen sources, while being thermotolerant, xerotolerant and osmotolerant. Results: The sequencing of strain LS3 revealed that the nuclear genome of A. adeninivorans is 11.8 Mb long and consists of four chromosomes with regional centromeres. Its closest sequenced relative is Yarrowia lipolytica, although mean conservation of orthologs is low. With 914 introns within 6116 genes, A. adeninivorans is one of the most intron-rich hemiascomycetes sequenced to date. Several large species-specific families appear to result from multiple rounds of segmental duplications of tandem gene arrays, a novel mechanism not yet described in yeasts. An analysis of the genome and its transcriptome revealed enzymes with biotechnological potential, such as two extracellular tannases (Atan1p and Atan2p) of the tannic-acid catabolic route, and a new pathway for the assimilation of n-butanol via butyric aldehyde and butyric acid. Conclusions: The high-quality genome of this species that diverged early in Saccharomycotina will allow further fundamental studies on comparative genomics, evolution and phylogenetics. Protein components of different pathways for carbon and nitrogen source utilization were identified, which so far has remained unexplored in yeast, offering clues for further biotechnological developments. In the course of identifying alternative microorganisms for biotechnological interest, A. adeninivorans has already proved its strengthened competitiveness as a promising cell factory for many more applications.
Serat Wulangreh adalah karya sastra Jawa karya Sri Susuhunan Pakubuwana IV yang penuh dengan ajar... more Serat Wulangreh adalah karya sastra Jawa karya Sri Susuhunan Pakubuwana IV yang penuh dengan ajaran nilai moral yang tinggi. Nilai moral yang terkandung didalamnya merupakan sumber pendidikan karakter yang berbasisi pada kearifan lokal. Serat Wulangreh pupuh Gambuh merupakan bahan ajar pada mata pelajaran Bahasa Jawa kelas VIII di tingkat SMP/MTs. Siswa kelas tersebut diduduki oleh generasi milenial. Tujuan dari penelitian ini adalah mengungkapkan nilai-nilai luhur yang terkandung di dalam serat Wulangreh pupuh Gambuh sebagai sumber pendidikan karakter bagi generasi milenial. Jenis penelitian ini adalah penelitian kualitatif dengan fokus pada pendidikan karakter yang dibangun dan diterapkan pada generasi milenial. Metode penelitian yang digunakan adalah metode deskriptif kualitatif. Analisis data dilakukan secara deskriptif. Serat Wulangreh dibongkar isinya untuk menentukan nilai-nilai luhur yang terkandung di dalamnya. Dari nilai-nilai luhur tersebut ditarik kesimpulan nilai karakt...