Jaak Simm - Academia.edu (original) (raw)

Papers by Jaak Simm

Research paper thumbnail of Macau: Scalable Bayesian Multi-relational Factorization with Side Information using MCMC

Research paper thumbnail of Changes in the Transcriptome of the Human Endometrial Ishikawa Cancer Cell Line Induced by Estrogen, Progesterone, Tamoxifen, and Mifepristone (RU486) as Detected by RNA-Sequencing

PLoS ONE, 2013

Background: Estrogen (E2) and progesterone (P4) are key players in the maturation of the human en... more Background: Estrogen (E2) and progesterone (P4) are key players in the maturation of the human endometrium. The corresponding steroid hormone modulators, tamoxifen (TAM) and mifepristone (RU486) are widely used in breast cancer therapy and for contraception purposes, respectively.

Research paper thumbnail of Observational Reinforcement Learning

We introduce an extension to standard reinforcement learning setting called observational RL (ORL... more We introduce an extension to standard reinforcement learning setting called observational RL (ORL) where additional observational information is available to the agent. This allows the agent to learn the system dynamics with fewer data samples, which is an essential feature for practical applications of RL methods. We show that ORL can be formulated as a multitask learning problem. A similarity-based and a component-based multitask learning methods are proposed for learning the transition probabilities of the ORL problem. The effectiveness of the proposed methods is evaluated in experiments of grid world.

Research paper thumbnail of Least-Squares Probabilistic Classifier: A Computationally Efficient Alternative to Kernel Logistic Regression

The least-squares probabilistic classifier (LSPC) is a computationally efficient alternative to k... more The least-squares probabilistic classifier (LSPC) is a computationally efficient alternative to kernel logistic regression (KLR). A key idea for the speedup is that, unlike KLR that uses maximum likelihood estimation for a log-linear model, LSPC uses least-squares estimation for a linear model. This allows us to obtain a global solution analytically in a classwise manner. In exchange for the speedup, however, this linear least-squares formulation does not necessarily produce a non-negative estimate. Nevertheless, consistency of LSPC is guaranteed in the large sample limit, and rounding up a negative estimate to zero in finite sample cases was demonstrated not to degrade the classification performance in experiments. Thus, LSPC is a practically useful probabilistic classifier. In this paper, we give an overview of LSPC and its extentions to covariate shift, multi-task, and multi-label scenarios. A MATLAB implementation of LSPC is available from '

Research paper thumbnail of Drell 2015

Research paper thumbnail of A computationally-efficient alternative to kernel logistic regression

2010 IEEE International Workshop on Machine Learning for Signal Processing, 2010

ABSTRACT

Research paper thumbnail of Computationally Efficient Multi-task Learning with Least-squares Probabilistic Classifiers

IPSJ Transactions on Computer Vision and Applications, 2011

Probabilistic classification and multi-task learning are two important branches of machine learni... more Probabilistic classification and multi-task learning are two important branches of machine learning research. Probabilistic classification is useful when the 'confidence' of decision is necessary. On the other hand, the idea of multi-task learning is beneficial if multiple related learning tasks exist. So far, kernelized logistic regression has been a vital probabilistic classifier for the use in multi-task learning scenarios. However, its training tends to be computationally expensive, which prevented its use in large-scale problems. To overcome this limitation, we propose to employ a recently-proposed probabilistic classifier called the least-squares probabilistic classifier in multi-task learning scenarios. Through image classification experiments, we show that our method achieves comparable classification performance to the existing method, with much less training time.

Research paper thumbnail of Differences in Gut Microbiota Between Atopic and Healthy Children

Current microbiology, Jan 14, 2015

Although gut microbiota has been studied relatively extensively in the context of allergic diseas... more Although gut microbiota has been studied relatively extensively in the context of allergic diseases, there have been several contradictions between these studies. By applying high-throughput sequencing, we aimed to analyze the differences in gut microbiota between atopic and healthy children at 5 and 12 years of age. 51 stool samples were collected from 14 atopic and 15 healthy children and analyzed with 454 pyrosequencing of the 16S rRNA gene. At the ages of 5 and 12 years, Bacteroides, Prevotella, and Dialister dominated gut microbiota in both atopic and healthy groups of children. Children in the atopic group had lower abundance and prevalence of Akkermansia in gut microbiota than their healthy counterparts. Thus, the composition of gut microbiota does not seem to be significantly different between atopic and healthy children, but lower abundance and prevalence of Akkermansia indicate that this bacterium may accompany or play a role in IgE-mediated atopic diseases.

Research paper thumbnail of Redox-Specialized Bacterioplankton Metacommunity in a Temperate Estuary

PloS one, 2015

This study explored the spatiotemporal dynamics of the bacterioplankton community composition in ... more This study explored the spatiotemporal dynamics of the bacterioplankton community composition in the Gulf of Finland (easternmost sub-basin of the Baltic Sea) based on phylogenetic analysis of 16S rDNA sequences acquired from community samples via pyrosequencing. Investigations of bacterioplankton in hydrographically complex systems provide good insight into the strategies by which microbes deal with spatiotemporal hydrographic gradients, as demonstrated by our research. Many ribotypes were closely affiliated with sequences isolated from environments with similar steep physiochemical gradients and/or seasonal changes, including seasonally anoxic estuaries. Hence, one of the main conclusions of this study is that marine ecosystems where oxygen and salinity gradients co-occur can be considered a habitat for a cosmopolitan metacommunity consisting of specialized groups occupying niches universal to such environments throughout the world. These niches revolve around functional capabilit...

Research paper thumbnail of Tree-Based Ensemble Multi-Task Learning Method for Classification and Regression

IEICE Transactions on Information and Systems, 2014

Multi-task learning is an important area of machine learning that tries to learn multiple tasks s... more Multi-task learning is an important area of machine learning that tries to learn multiple tasks simultaneously to improve the accuracy of each individual task. We propose a new tree-based ensemble multi-task learning method for classification and regression (MT-ExtraTrees), based on Extremely Randomized Trees. MT-ExtraTrees is able to share data between tasks minimizing negative transfer while keeping the ability to learn non-linear solutions and to scale well to large datasets.

Research paper thumbnail of Easy Hyperparameter Search Using Optunity

Optunity is a free software package dedicated to hyperparameter optimization. It contains various... more Optunity is a free software package dedicated to hyperparameter optimization. It contains various types of solvers, ranging from undirected methods to direct search, particle swarm and evolutionary optimization. The design focuses on ease of use, flexibility, code clarity and interoperability with existing software in all machine learning environments. Optunity is written in Python and contains interfaces to environments such as R and MATLAB. Optunity uses a BSD license and is freely available online at http://www.optunity.net.

Research paper thumbnail of High-Throughput Sequencing Approach Uncovers the miRNome of Peritoneal Endometriotic Lesions and Adjacent Healthy Tissues

PLoS ONE, 2014

Accumulating data have shown the involvement of microRNAs (miRNAs) in endometriosis pathogenesis.... more Accumulating data have shown the involvement of microRNAs (miRNAs) in endometriosis pathogenesis. In this study, we used a novel approach to determine the endometriotic lesion-specific miRNAs by high-throughput small RNA sequencing of paired samples of peritoneal endometriotic lesions and matched healthy surrounding tissues together with eutopic endometria of the same patients. We found five miRNAs specific to epithelial cells--miR-34c, miR-449a, miR-200a, miR-200b and miR-141 showing significantly higher expression in peritoneal endometriotic lesions compared to healthy peritoneal tissues. We also determined the expression levels of miR-200 family target genes E-cadherin, ZEB1 and ZEB2 and found that the expression level of E-cadherin was significantly higher in endometriotic lesions compared to healthy tissues. Further evaluation verified that studied miRNAs could be used as diagnostic markers for confirming the presence of endometrial cells in endometriotic lesion biopsy samples. Furthermore, we demonstrated that the miRNA profile of peritoneal endometriotic lesion biopsies is largely masked by the surrounding peritoneal tissue, challenging the discovery of an accurate lesion-specific miRNA profile. Taken together, our findings indicate that only particular miRNAs with a significantly higher expression in endometriotic cells can be detected from lesion biopsies, and can serve as diagnostic markers for endometriosis.

Research paper thumbnail of The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing

Gut Microbes, 2014

Objective: an increasing number of studies that are using high-throughput molecular methods are r... more Objective: an increasing number of studies that are using high-throughput molecular methods are rapidly extending our knowledge of gut microbial colonization in preterm infants whose immaturity and requirement for extensive treatment may result in altered colonization process. We aimed to describe the profile of gut microbiota in 50 extremely low birth weight (<1200 g) critically ill infants at three different time points during the first two months of life by using 16S rrNa gene specific sequencing.

Research paper thumbnail of Can microbes on skin help linking persons and crimes?

Forensic Science International: Genetics Supplement Series, 2011

... Anu Aaspõllu a , Corresponding Author Contact Information , E-mail The Corresponding Author ,... more ... Anu Aaspõllu a , Corresponding Author Contact Information , E-mail The Corresponding Author , Triin Lillsaar a , Lea Tummeleht a , b , Jaak Simm a , b , Madis Metsis a. ... Reference sequences of aligned 16S rDNA were obtained from SILVA ribosomal RNA database. ...

Research paper thumbnail of Soil sample metagenome NGS data management for forensic investigation

Forensic Science International: Genetics Supplement Series, 2013

ABSTRACT

Research paper thumbnail of Evolution of Bacterial Consortia in Spontaneously Started Rye Sourdoughs during Two Months of Daily Propagation

PLoS ONE, 2014

The evolution of bacterial consortia was studied in six semi-solid rye sourdoughs during long-ter... more The evolution of bacterial consortia was studied in six semi-solid rye sourdoughs during long-term backslopping at different temperatures. Each rye sourdough was started spontaneously in a laboratory (dough yield 200), propagated at either 20uC or 30uC, and renewed daily at an inoculation rate of 1:10 for 56 days. The changes in bacterial diversity over time were followed by both DGGE coupled with partial 16S rRNA gene sequencing and pyrosequencing of bar-coded 16S rRNA gene amplicons. Four species from the genus Lactobacillus (brevis, crustorum, plantarum, and paralimentarius) were detected in different combinations in all sourdoughs after 56 propagation cycles. Facultative heterofermentative lactic acid bacteria dominated in sourdoughs fermented at 30uC, while both obligate and facultative heterofermentative LAB were found to dominate in sourdoughs fermented at 20uC. After 56 propagation cycles, Kazachstania unispora (formerly Saccharomyces unisporus) was identified as the only yeast species that dominated in sourdoughs fermented at 20uC, while different combinations of strains from four yeast species (Kazachstania unispora, Saccharomyces cerevisiae, Candida krusei and Candida glabrata) were detected in sourdoughs propagated at 30uC. The evolution of bacterial communities in sourdoughs fermented at the same temperature did not follow the same time course and changes in the composition of dominant and subdominant bacterial communities occurred even after six weeks of backslopping.

Research paper thumbnail of Characterization of the Vaginal Micro- and Mycobiome in Asymptomatic Reproductive-Age Estonian Women

PLoS ONE, 2013

The application of high-throughput sequencing methods has raised doubt in the concept of the unif... more The application of high-throughput sequencing methods has raised doubt in the concept of the uniform healthy vaginal microbiota consisting predominantly of lactobacilli by revealing the existence of more variable bacterial community composition. As this needs to be analyzed more extensively and there is little straightforward data regarding the vaginal mycobiome of asymptomatic women we aimed to define bacterial and fungal communities in vaginal samples from 494 asymptomatic, reproductive-age Estonian women. The composition of the vaginal microbiota was determined by amplifying bacterial 16S rRNA and fungal internal transcribed spacer-1 (ITS-1) regions and subsequently sequencing them using 454 Life Sciences pyrosequencing. We delineated five major bacterial community groups with distinctive diversity and species composition. Lactobacilli were among the most abundant bacteria in all groups, but also members of genus Gardnerella had high relative abundance in some of the groups. Microbial diversity increased with higher vaginal pH values, and was also higher when a malodorous discharge was present, indicating that some of the women who consider themselves healthy may potentially have asymptomatic bacterial vaginosis (BV). Our study is the first of its kind to analyze the mycobiome that colonizes the healthy vaginal environment using barcoded pyrosequencing technology. We observed 196 fungal operational taxonomic units (OTUs), including 16 OTUs of Candida spp., which is more diverse than previously recognized. However, assessing true fungal diversity was complicated because of the problems regarding the possible air-borne contamination and bioinformatics used for identification of fungal taxons as significant proportion of fungal sequences were assigned to unspecified OTUs. Citation: Drell T, Lillsaar T, Tummeleht L, Simm J, Aaspõllu A, et al. (2013) Characterization of the Vaginal Micro-and Mycobiome in Asymptomatic Reproductive-Age Estonian Women. PLoS ONE 8(1): e54379.

Research paper thumbnail of Changes in the Transcriptome of the Human Endometrial Ishikawa Cancer Cell Line Induced by Estrogen, Progesterone, Tamoxifen, and Mifepristone (RU486) as Detected by RNA-Sequencing

PLoS ONE, 2013

Background: Estrogen (E2) and progesterone (P4) are key players in the maturation of the human en... more Background: Estrogen (E2) and progesterone (P4) are key players in the maturation of the human endometrium. The corresponding steroid hormone modulators, tamoxifen (TAM) and mifepristone (RU486) are widely used in breast cancer therapy and for contraception purposes, respectively.

Research paper thumbnail of Research Resource: Small RNA-seq of Human Granulosa Cells Reveals miRNAs in FSHR and Aromatase Genes

Molecular Endocrinology, 2013

The granulosa cells in the mammalian ovarian follicle respond to gonadotropin signaling and are i... more The granulosa cells in the mammalian ovarian follicle respond to gonadotropin signaling and are involved in the processes of folliculogenesis and oocyte maturation. Studies on gene expression and regulation in human granulosa cells are of interest due to their potential for estimating the oocyte viability and in vitro fertilization success. However, the posttranscriptional gene expression studies on micro-RNA (miRNA) level in the human ovary have been scarce. The current study determined the miRNA profile by deep sequencing of the 2 intrafollicular somatic cell types: mural and cumulus granulosa cells (MGCs and CGCs, respectively) isolated from women undergoing controlled ovarian stimulation and in vitro fertilization. Altogether, 936 annotated and 9 novel miRNAs were identified. Ninety of the annotated miRNAs were differentially expressed between MGCs and CGCs. Bioinformatic prediction revealed that TGFβ, ErbB signaling, and heparan sulfate biosynthesis were targeted by miRNAs in both granulosa cell populations, whereas extracellular matrix remodeling, Wnt, and neurotrophin signaling pathways were enriched among miRNA targets in MGCs. Two of the nine novel miRNAs found were of intronic origin: one from the aromatase and the other from the FSH receptor gene. The latter miRNA was predicted to target the activin signaling pathway. In addition to revealing the genome-wide miRNA signature in human granulosa cells, our results suggest that posttranscriptional regulation of gene expression by miRNAs could play an important role in the modification of gonadotropin signaling. miRNA expression studies could therefore lead to new prognostic markers in assisted reproductive technologies.

Research paper thumbnail of Spatial variability of winter bacterioplankton community composition in the Gulf of Finland (the Baltic Sea)

Journal of Marine Systems, 2014

The Gulf of Finland The Baltic Sea Bacterioplankton 16S rDNA 454 sequencing Community structure

Research paper thumbnail of Macau: Scalable Bayesian Multi-relational Factorization with Side Information using MCMC

Research paper thumbnail of Changes in the Transcriptome of the Human Endometrial Ishikawa Cancer Cell Line Induced by Estrogen, Progesterone, Tamoxifen, and Mifepristone (RU486) as Detected by RNA-Sequencing

PLoS ONE, 2013

Background: Estrogen (E2) and progesterone (P4) are key players in the maturation of the human en... more Background: Estrogen (E2) and progesterone (P4) are key players in the maturation of the human endometrium. The corresponding steroid hormone modulators, tamoxifen (TAM) and mifepristone (RU486) are widely used in breast cancer therapy and for contraception purposes, respectively.

Research paper thumbnail of Observational Reinforcement Learning

We introduce an extension to standard reinforcement learning setting called observational RL (ORL... more We introduce an extension to standard reinforcement learning setting called observational RL (ORL) where additional observational information is available to the agent. This allows the agent to learn the system dynamics with fewer data samples, which is an essential feature for practical applications of RL methods. We show that ORL can be formulated as a multitask learning problem. A similarity-based and a component-based multitask learning methods are proposed for learning the transition probabilities of the ORL problem. The effectiveness of the proposed methods is evaluated in experiments of grid world.

Research paper thumbnail of Least-Squares Probabilistic Classifier: A Computationally Efficient Alternative to Kernel Logistic Regression

The least-squares probabilistic classifier (LSPC) is a computationally efficient alternative to k... more The least-squares probabilistic classifier (LSPC) is a computationally efficient alternative to kernel logistic regression (KLR). A key idea for the speedup is that, unlike KLR that uses maximum likelihood estimation for a log-linear model, LSPC uses least-squares estimation for a linear model. This allows us to obtain a global solution analytically in a classwise manner. In exchange for the speedup, however, this linear least-squares formulation does not necessarily produce a non-negative estimate. Nevertheless, consistency of LSPC is guaranteed in the large sample limit, and rounding up a negative estimate to zero in finite sample cases was demonstrated not to degrade the classification performance in experiments. Thus, LSPC is a practically useful probabilistic classifier. In this paper, we give an overview of LSPC and its extentions to covariate shift, multi-task, and multi-label scenarios. A MATLAB implementation of LSPC is available from '

Research paper thumbnail of Drell 2015

Research paper thumbnail of A computationally-efficient alternative to kernel logistic regression

2010 IEEE International Workshop on Machine Learning for Signal Processing, 2010

ABSTRACT

Research paper thumbnail of Computationally Efficient Multi-task Learning with Least-squares Probabilistic Classifiers

IPSJ Transactions on Computer Vision and Applications, 2011

Probabilistic classification and multi-task learning are two important branches of machine learni... more Probabilistic classification and multi-task learning are two important branches of machine learning research. Probabilistic classification is useful when the 'confidence' of decision is necessary. On the other hand, the idea of multi-task learning is beneficial if multiple related learning tasks exist. So far, kernelized logistic regression has been a vital probabilistic classifier for the use in multi-task learning scenarios. However, its training tends to be computationally expensive, which prevented its use in large-scale problems. To overcome this limitation, we propose to employ a recently-proposed probabilistic classifier called the least-squares probabilistic classifier in multi-task learning scenarios. Through image classification experiments, we show that our method achieves comparable classification performance to the existing method, with much less training time.

Research paper thumbnail of Differences in Gut Microbiota Between Atopic and Healthy Children

Current microbiology, Jan 14, 2015

Although gut microbiota has been studied relatively extensively in the context of allergic diseas... more Although gut microbiota has been studied relatively extensively in the context of allergic diseases, there have been several contradictions between these studies. By applying high-throughput sequencing, we aimed to analyze the differences in gut microbiota between atopic and healthy children at 5 and 12 years of age. 51 stool samples were collected from 14 atopic and 15 healthy children and analyzed with 454 pyrosequencing of the 16S rRNA gene. At the ages of 5 and 12 years, Bacteroides, Prevotella, and Dialister dominated gut microbiota in both atopic and healthy groups of children. Children in the atopic group had lower abundance and prevalence of Akkermansia in gut microbiota than their healthy counterparts. Thus, the composition of gut microbiota does not seem to be significantly different between atopic and healthy children, but lower abundance and prevalence of Akkermansia indicate that this bacterium may accompany or play a role in IgE-mediated atopic diseases.

Research paper thumbnail of Redox-Specialized Bacterioplankton Metacommunity in a Temperate Estuary

PloS one, 2015

This study explored the spatiotemporal dynamics of the bacterioplankton community composition in ... more This study explored the spatiotemporal dynamics of the bacterioplankton community composition in the Gulf of Finland (easternmost sub-basin of the Baltic Sea) based on phylogenetic analysis of 16S rDNA sequences acquired from community samples via pyrosequencing. Investigations of bacterioplankton in hydrographically complex systems provide good insight into the strategies by which microbes deal with spatiotemporal hydrographic gradients, as demonstrated by our research. Many ribotypes were closely affiliated with sequences isolated from environments with similar steep physiochemical gradients and/or seasonal changes, including seasonally anoxic estuaries. Hence, one of the main conclusions of this study is that marine ecosystems where oxygen and salinity gradients co-occur can be considered a habitat for a cosmopolitan metacommunity consisting of specialized groups occupying niches universal to such environments throughout the world. These niches revolve around functional capabilit...

Research paper thumbnail of Tree-Based Ensemble Multi-Task Learning Method for Classification and Regression

IEICE Transactions on Information and Systems, 2014

Multi-task learning is an important area of machine learning that tries to learn multiple tasks s... more Multi-task learning is an important area of machine learning that tries to learn multiple tasks simultaneously to improve the accuracy of each individual task. We propose a new tree-based ensemble multi-task learning method for classification and regression (MT-ExtraTrees), based on Extremely Randomized Trees. MT-ExtraTrees is able to share data between tasks minimizing negative transfer while keeping the ability to learn non-linear solutions and to scale well to large datasets.

Research paper thumbnail of Easy Hyperparameter Search Using Optunity

Optunity is a free software package dedicated to hyperparameter optimization. It contains various... more Optunity is a free software package dedicated to hyperparameter optimization. It contains various types of solvers, ranging from undirected methods to direct search, particle swarm and evolutionary optimization. The design focuses on ease of use, flexibility, code clarity and interoperability with existing software in all machine learning environments. Optunity is written in Python and contains interfaces to environments such as R and MATLAB. Optunity uses a BSD license and is freely available online at http://www.optunity.net.

Research paper thumbnail of High-Throughput Sequencing Approach Uncovers the miRNome of Peritoneal Endometriotic Lesions and Adjacent Healthy Tissues

PLoS ONE, 2014

Accumulating data have shown the involvement of microRNAs (miRNAs) in endometriosis pathogenesis.... more Accumulating data have shown the involvement of microRNAs (miRNAs) in endometriosis pathogenesis. In this study, we used a novel approach to determine the endometriotic lesion-specific miRNAs by high-throughput small RNA sequencing of paired samples of peritoneal endometriotic lesions and matched healthy surrounding tissues together with eutopic endometria of the same patients. We found five miRNAs specific to epithelial cells--miR-34c, miR-449a, miR-200a, miR-200b and miR-141 showing significantly higher expression in peritoneal endometriotic lesions compared to healthy peritoneal tissues. We also determined the expression levels of miR-200 family target genes E-cadherin, ZEB1 and ZEB2 and found that the expression level of E-cadherin was significantly higher in endometriotic lesions compared to healthy tissues. Further evaluation verified that studied miRNAs could be used as diagnostic markers for confirming the presence of endometrial cells in endometriotic lesion biopsy samples. Furthermore, we demonstrated that the miRNA profile of peritoneal endometriotic lesion biopsies is largely masked by the surrounding peritoneal tissue, challenging the discovery of an accurate lesion-specific miRNA profile. Taken together, our findings indicate that only particular miRNAs with a significantly higher expression in endometriotic cells can be detected from lesion biopsies, and can serve as diagnostic markers for endometriosis.

Research paper thumbnail of The development of gut microbiota in critically ill extremely low birth weight infants assessed with 16S rRNA gene based sequencing

Gut Microbes, 2014

Objective: an increasing number of studies that are using high-throughput molecular methods are r... more Objective: an increasing number of studies that are using high-throughput molecular methods are rapidly extending our knowledge of gut microbial colonization in preterm infants whose immaturity and requirement for extensive treatment may result in altered colonization process. We aimed to describe the profile of gut microbiota in 50 extremely low birth weight (<1200 g) critically ill infants at three different time points during the first two months of life by using 16S rrNa gene specific sequencing.

Research paper thumbnail of Can microbes on skin help linking persons and crimes?

Forensic Science International: Genetics Supplement Series, 2011

... Anu Aaspõllu a , Corresponding Author Contact Information , E-mail The Corresponding Author ,... more ... Anu Aaspõllu a , Corresponding Author Contact Information , E-mail The Corresponding Author , Triin Lillsaar a , Lea Tummeleht a , b , Jaak Simm a , b , Madis Metsis a. ... Reference sequences of aligned 16S rDNA were obtained from SILVA ribosomal RNA database. ...

Research paper thumbnail of Soil sample metagenome NGS data management for forensic investigation

Forensic Science International: Genetics Supplement Series, 2013

ABSTRACT

Research paper thumbnail of Evolution of Bacterial Consortia in Spontaneously Started Rye Sourdoughs during Two Months of Daily Propagation

PLoS ONE, 2014

The evolution of bacterial consortia was studied in six semi-solid rye sourdoughs during long-ter... more The evolution of bacterial consortia was studied in six semi-solid rye sourdoughs during long-term backslopping at different temperatures. Each rye sourdough was started spontaneously in a laboratory (dough yield 200), propagated at either 20uC or 30uC, and renewed daily at an inoculation rate of 1:10 for 56 days. The changes in bacterial diversity over time were followed by both DGGE coupled with partial 16S rRNA gene sequencing and pyrosequencing of bar-coded 16S rRNA gene amplicons. Four species from the genus Lactobacillus (brevis, crustorum, plantarum, and paralimentarius) were detected in different combinations in all sourdoughs after 56 propagation cycles. Facultative heterofermentative lactic acid bacteria dominated in sourdoughs fermented at 30uC, while both obligate and facultative heterofermentative LAB were found to dominate in sourdoughs fermented at 20uC. After 56 propagation cycles, Kazachstania unispora (formerly Saccharomyces unisporus) was identified as the only yeast species that dominated in sourdoughs fermented at 20uC, while different combinations of strains from four yeast species (Kazachstania unispora, Saccharomyces cerevisiae, Candida krusei and Candida glabrata) were detected in sourdoughs propagated at 30uC. The evolution of bacterial communities in sourdoughs fermented at the same temperature did not follow the same time course and changes in the composition of dominant and subdominant bacterial communities occurred even after six weeks of backslopping.

Research paper thumbnail of Characterization of the Vaginal Micro- and Mycobiome in Asymptomatic Reproductive-Age Estonian Women

PLoS ONE, 2013

The application of high-throughput sequencing methods has raised doubt in the concept of the unif... more The application of high-throughput sequencing methods has raised doubt in the concept of the uniform healthy vaginal microbiota consisting predominantly of lactobacilli by revealing the existence of more variable bacterial community composition. As this needs to be analyzed more extensively and there is little straightforward data regarding the vaginal mycobiome of asymptomatic women we aimed to define bacterial and fungal communities in vaginal samples from 494 asymptomatic, reproductive-age Estonian women. The composition of the vaginal microbiota was determined by amplifying bacterial 16S rRNA and fungal internal transcribed spacer-1 (ITS-1) regions and subsequently sequencing them using 454 Life Sciences pyrosequencing. We delineated five major bacterial community groups with distinctive diversity and species composition. Lactobacilli were among the most abundant bacteria in all groups, but also members of genus Gardnerella had high relative abundance in some of the groups. Microbial diversity increased with higher vaginal pH values, and was also higher when a malodorous discharge was present, indicating that some of the women who consider themselves healthy may potentially have asymptomatic bacterial vaginosis (BV). Our study is the first of its kind to analyze the mycobiome that colonizes the healthy vaginal environment using barcoded pyrosequencing technology. We observed 196 fungal operational taxonomic units (OTUs), including 16 OTUs of Candida spp., which is more diverse than previously recognized. However, assessing true fungal diversity was complicated because of the problems regarding the possible air-borne contamination and bioinformatics used for identification of fungal taxons as significant proportion of fungal sequences were assigned to unspecified OTUs. Citation: Drell T, Lillsaar T, Tummeleht L, Simm J, Aaspõllu A, et al. (2013) Characterization of the Vaginal Micro-and Mycobiome in Asymptomatic Reproductive-Age Estonian Women. PLoS ONE 8(1): e54379.

Research paper thumbnail of Changes in the Transcriptome of the Human Endometrial Ishikawa Cancer Cell Line Induced by Estrogen, Progesterone, Tamoxifen, and Mifepristone (RU486) as Detected by RNA-Sequencing

PLoS ONE, 2013

Background: Estrogen (E2) and progesterone (P4) are key players in the maturation of the human en... more Background: Estrogen (E2) and progesterone (P4) are key players in the maturation of the human endometrium. The corresponding steroid hormone modulators, tamoxifen (TAM) and mifepristone (RU486) are widely used in breast cancer therapy and for contraception purposes, respectively.

Research paper thumbnail of Research Resource: Small RNA-seq of Human Granulosa Cells Reveals miRNAs in FSHR and Aromatase Genes

Molecular Endocrinology, 2013

The granulosa cells in the mammalian ovarian follicle respond to gonadotropin signaling and are i... more The granulosa cells in the mammalian ovarian follicle respond to gonadotropin signaling and are involved in the processes of folliculogenesis and oocyte maturation. Studies on gene expression and regulation in human granulosa cells are of interest due to their potential for estimating the oocyte viability and in vitro fertilization success. However, the posttranscriptional gene expression studies on micro-RNA (miRNA) level in the human ovary have been scarce. The current study determined the miRNA profile by deep sequencing of the 2 intrafollicular somatic cell types: mural and cumulus granulosa cells (MGCs and CGCs, respectively) isolated from women undergoing controlled ovarian stimulation and in vitro fertilization. Altogether, 936 annotated and 9 novel miRNAs were identified. Ninety of the annotated miRNAs were differentially expressed between MGCs and CGCs. Bioinformatic prediction revealed that TGFβ, ErbB signaling, and heparan sulfate biosynthesis were targeted by miRNAs in both granulosa cell populations, whereas extracellular matrix remodeling, Wnt, and neurotrophin signaling pathways were enriched among miRNA targets in MGCs. Two of the nine novel miRNAs found were of intronic origin: one from the aromatase and the other from the FSH receptor gene. The latter miRNA was predicted to target the activin signaling pathway. In addition to revealing the genome-wide miRNA signature in human granulosa cells, our results suggest that posttranscriptional regulation of gene expression by miRNAs could play an important role in the modification of gonadotropin signaling. miRNA expression studies could therefore lead to new prognostic markers in assisted reproductive technologies.

Research paper thumbnail of Spatial variability of winter bacterioplankton community composition in the Gulf of Finland (the Baltic Sea)

Journal of Marine Systems, 2014

The Gulf of Finland The Baltic Sea Bacterioplankton 16S rDNA 454 sequencing Community structure