Microbial residence time is a controlling parameter of the taxonomic composition and functional profile of microbial communities.

A remaining challenge within microbial ecology is to understand the determinants of richness and diversity observed in environmental microbial communities. In a range of systems, including activated sludge bioreactors, the microbial residence time (MRT) has been previously shown to shape the microbial community composition. However, the physiological and ecological mechanisms driving this influence have remained unclear. Here, this relationship is explored by analyzing an activated sludge system fed with municipal wastewater. Using a model designed in this study based on Monod-growth kinetics, longer MRTs were shown to increase the range of growth parameters that enable persistence, resulting in increased richness and diversity in the modeled community. In laboratory experiments, six sequencing batch reactors treating domestic wastewater were operated in parallel at MRTs between 1 and 15 days. The communities were characterized using both 16S ribosomal RNA and non-target messenger RNA sequencing (metatranscriptomic analysis), and model-predicted monotonic increases in richness were confirmed in both profiles. Accordingly, taxonomic Shannon diversity also increased with MRT. In contrast, the diversity in enzyme class annotations resulting from the metatranscriptomic analysis displayed a non-monotonic trend over the MRT gradient. Disproportionately high abundances of transcripts encoding for rarer enzymes occur at longer MRTs and lead to the disconnect between taxonomic and functional diversity profiles

Clinical case seminar - Hypogonadotropic hypogonadism as a presenting feature of late-onset X-linked adrenal hypoplasia congenita

Mutations in the orphan nuclear receptor DAX-1 cause X-linked adrenal hypoplasia congenita. Affected boys usually present with primary adrenal failure in early infancy or childhood. Impaired sexual development because of hypogonadotropic hypogonadism becomes apparent at the time of puberty. We report adult-onset adrenal hypoplasia congenita in a patient who presented with hypogonadism at 28 yr of age. Although he had no clinical evidence of adrenal dysfunction, compensated primary adrenal failure was diagnosed by biochemical testing. Semen analysis showed azoospermia, and he did not achieve fertility after 8 months of treatment with gonadotropins. A novel Y380D DAX-1 missense mutation, which causes partial loss of function in transient gene expression assays, was found in this patient. This case demonstrates that partial loss-of-function mutations in DAX1 can present with hypogonadotropic hypogonadism and covert adrenal failure in adulthood. Further, an important role for DAX-1 in spermatogenesis in humans is confirmed, supporting findings in the Dax1 (Ahch) knockout mouse

Homozygous disruption of P450 side-chain cleavage (CYP11A1) is associated with prematurity, complete 46,XY sex reversal, and severe adrenal failure

Disruption of the P450 side-chain cleavage cytochrome (P450scc) enzyme due to deleterious mutations of the CYP11A1 gene is thought to be incompatible with fetal survival because of impaired progesterone production by the fetoplacental unit. We present a 46, XY patient with a homozygous disruption of CYP11A1.The child was born prematurely with complete sex reversal and severe adrenal insufficiency. Laboratory data showed diminished or absent steroidogenesis in all pathways. Molecular genetic analysis of the CYP11A1 gene revealed a homozygous single nucleotide deletion leading to a premature termination at codon position 288. This mutation will delete highly conserved regions of the P450scc enzyme and thus is predicted to lead to a nonfunctional protein. Both healthy parents were heterozygous for this mutation.Our report demonstrates that severe disruption of P450scc can be compatible with survival in rare instances. Furthermore, defects in this enzyme are inherited in an autosomal-recessive fashion, and heterozygote carriers can be healthy and fertile. The possibility of P450scc-independent pathways of steroid synthesis in addition to the current concept of luteoplacental shift of progesterone synthesis in humans has to be questioned

The spectrum of phenotypes associated with mutations in steroidogenic factor 1 (SF-1, NR5A1, Ad4BP) includes severe penoscrotal hypospadias in 46,XY males without adrenal insufficiency

OBJECTIVE. Hypospadias is a frequent congenital anomaly but in most cases an underlying cause is not found. Steroidogenic factor 1 (SF-1, NR5A1, Ad4BP) is a key regulator of human sex development and an increasing number of SF-1 (NR5A1) mutations are reported in 46,XY disorders of sex development (DSD). We hypothesized that NR5A1 mutations could be identified in boys with hypospadias. DESIGN AND METHODS. Mutational analysis of NR5A1 in 60 individuals with varying degrees of hypospadias from the German DSD network. RESULTS. Heterozygous NR5A1 mutations were found in three out of 60 cases. These three individuals represented the most severe end of the spectrum studied as they presented with penoscrotal hypospadias, variable androgenization of the phallus and undescended testes (three out of 20 cases (15%) with this phenotype). Testosterone was low in all three patients and inhibin B/anti-Müllerian hormone (AMH) were low in two patients. Two patients had a clear male gender assignment. Gender re-assignment to male occurred in the third case. Two patients harbored heterozygous nonsense mutations (p.Q107X/WT, p.E11X/WT). One patient had a heterozygous splice site mutation in intron 2 (c.103-3A/WT) predicted to disrupt the main DNA-binding motif. Functional studies of the nonsense mutants showed impaired transcriptional activation of an SF-1-responsive promoter (Cyp11a). To date, adrenal insufficiency has not occurred in any of the patients. CONCLUSIONS. SF-1 (NR5A1) mutations should be considered in 46,XY individuals with severe (penoscrotal) hypospadias, especially if undescended testes, low testosterone, or low inhibin B/AMH levels are present. SF-1 mutations in milder forms of idiopathic hypospadias are unlikely to be common

Automatic detection of microsleep episodes with deep learning

Brief fragments of sleep shorter than 15 s are defined as microsleep episodes (MSEs), often subjectively perceived as sleepiness. Their main characteristic is a slowing in frequency in the electroencephalogram (EEG), similar to stage N1 sleep according to standard criteria. The maintenance of wakefulness test (MWT) is often used in a clinical setting to assess vigilance. Scoring of the MWT in most sleep-wake centers is limited to classical definition of sleep (30-s epochs), and MSEs are mostly not considered in the absence of established scoring criteria defining MSEs but also because of the laborious work. We aimed for automatic detection of MSEs with machine learning, i.e. with deep learning based on raw EEG and EOG data as input. We analyzed MWT data of 76 patients. Experts visually scored wakefulness, and according to recently developed scoring criteria MSEs, microsleep episode candidates (MSEc), and episodes of drowsiness (ED). We implemented segmentation algorithms based on convolutional neural networks (CNNs) and a combination of a CNN with a long-short term memory (LSTM) network. A LSTM network is a type of a recurrent neural network which has a memory for past events and takes them into account. Data of 53 patients were used for training of the classifiers, 12 for validation and 11 for testing. Our algorithms showed a good performance close to human experts. The detection was very good for wakefulness and MSEs and poor for MSEc and ED, similar to the low inter-expert reliability for these borderline segments. We provide a proof of principle that it is feasible to reliably detect MSEs with deep neuronal networks based on raw EEG and EOG data with a performance close to that of human experts. Code of algorithms ( https://github.com/alexander-malafeev/microsleep-detection ) and data ( https://zenodo.org/record/3251716 ) are available

The growth hormone receptor gene deleted for exon three (GHRd3) polymorphism is associated with birth and placental weight.

Human growth hormone receptor (GHR) transcripts have two isoforms, full-length (GHRfl) or exon 3 deleted (GHRd3). An association of these isoforms has been found with small for gestational age (SGA) infants but does not influence adult height. The role of this polymorphism in the birth size spectrum in the general population is unclear

Analysis of the Temporal Organization of Sleep Spindles in the Human Sleep EEG Using a Phenomenological Modeling Approach

The sleep electroencephalogram (EEG) is characterized by typical oscillatory patterns such as sleep spindles and slow waves. Recently, we proposed a method to detect and analyze these patterns using linear autoregressive models for short (≈ 1 s) data segments. We analyzed the temporal organization of sleep spindles and discuss to what extent the observed interevent intervals correspond to properties of stationary stochastic processes and whether additional slow processes, such as slow oscillations, have to be assumed. We have found evidence for such an additional slow process, most pronounced in sleep stage 2

Sterol O-Acyltransferase 1 (SOAT1, ACAT) Is a Novel Target of Steroidogenic Factor-1 (SF-1, NR5A1, Ad4BP) in the Human Adrenal

Context: Steroidogenic factor-1 (SF-1, NR5A1, Ad4BP) is a master regulator of adrenal development and steroidogenesis. Defects in several known targets of SF-1 can cause adrenal disorders in humans.Objective: We aimed to identify novel targets of SF-1 in the human adrenal. These factors could be important regulators of adrenal development and steroidogenesis and potential candidates for adrenal dysfunction.Design: A gene discovery strategy was developed based on bidirectional manipulation of SF-1. Overexpression or knockdown of SF-1 in NCI-H295R human adrenocortical cells was used to identify a subset of positively-regulated SF-1 targets.Results: This approach identified well-established SF-1 target genes (STAR, CYP11A) and several novel genes (VSNL1, ZIM2, PEG3, SOAT1, and MTSS1). Given its role in cholesterol metabolism, sterol O-acyltransferase 1 (SOAT1, previously referred to as acyl-Coenzyme A: cholesterol acyltransferase 1, ACAT) was studied further and found to be expressed in the developing human fetal adrenal cortex. We hypothesized that impaired SOAT1 activity could result in adrenal insufficiency through reduced cholesteryl ester reserves or through toxic destruction of the adrenal cells during development. Therefore, mutational analysis of SOAT1 in a cohort of 43 patients with unexplained adrenal insufficiency was performed but failed to reveal significant coding sequence changes.Conclusions: Our reverse discovery approach led to the identification of novel SF-1 targets and defined SOAT1 as an important factor in human adrenal steroidogenesis. SF-1-dependent upregulation of SOAT1 may be important for maintaining readily-releasable cholesterol reserves needed for active steroidogenesis and during episodes of recurrent stress. (J Clin Endocrinol Metab 96: E663-E668, 2011

Implications of the Cosmic Background Imager Polarization Data

We present new measurements of the power spectra of the E-mode of CMB polarization, the temperature T, the cross-correlation of E and T, and upper limits on the B-mode from 2.5 years of dedicated Cosmic Background Imager (CBI) observations. Both raw maps and optimal signal images in the uv-plane and real space show strong detections of the E-mode (11.7 sigma for the EE power spectrum overall) and no detection of the B-mode. The power spectra are used to constrain parameters of the flat tilted adiabatic Lambda-CDM models: those determined from EE and TE bandpowers agree with those from TT, a powerful consistency check. There is little tolerance for shifting polarization peaks from the TT-forecast locations, as measured by the angular sound crossing scale theta = 100 ell_s = 1.03 +/- 0.02 from EE and TE cf. 1.044 +/- 0.005 with the TT data included. The scope for extra out-of-phase peaks from subdominant isocurvature modes is also curtailed. The EE and TE measurements of CBI, DASI and BOOMERANG are mutually consistent, and, taken together rather than singly, give enhanced leverage for these tests.Comment: 15 pages, 9 figures, submitted to ApJ -- Accepted version. The fine-bin spectrum, covariance matrix, and window functions are now available on the web (suitable for use in COSMOMC) at: http://www.astro.caltech.edu/~tjp/CBI/data2006/index.html The pipeline in the previous version inadvertently omitted one antenna, so the new spectrum contains ~15% more data. We emphasize that previous results were in no way biased, and that the (small) changes to the spectrum solely reflect the inclusion of the additional data. Numbers and figures in the paper have been updated correspondingly. All maps now have color bar