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Primordial germ cells (PGCs) are the precursors of germline that are specified at the embryonic stage. Recent studies reveal that humans employ different mechanisms for PGC specification compared with model organisms such as mice. Moreover, the specific regulatory machinery remains largely unexplored, mainly due to the inaccessible nature of this complex biological process in humans. Here, we curate and integrate multi-omics data, including 581 RNA-seq, 54 ATAC-seq, 45 ChIP-seq, and 69 single-cell RNA-seq samples from different stages of human PGC development to recapitulate the precisely controlled and stepwise process, presenting an atlas in the human PGC database (hPGCdb). With these uniformly processed data and integrated analyses, we characterize the potential key transcription factors and regulatory networks governing human germ cell fate. We validate the important roles of some of the key factors in germ cell development by CRISPRi knockdown. We also identify the soma-germline interaction network and discover the involvement of SDC2and LAMA4for PGC development, as well as soma-derived NOTCH2 signaling for germ cell differentiation. Taken together, we have built a database for human PGCs (http://43.131.248.15:6882) and demonstrate that hPGCdb enables the identification of the missing pieces of mechanisms governing germline development, including both intrinsic and extrinsic regulatory programs.

Obesity is associated with the development of insulin resistance and type 2 diabetes. The pathogenesis of insulin resistance is a well-investigated area, yet the precise interplay between the molecular pathways [...], The sphingolipids sphingosine-1-phosphate (S1P) and ceramide are important bioactive lipids with many cellular effects. Intracellular ceramide accumulation causes insulin resistance, but sphingosine kinase 1 (SphK1) prevents ceramide accumulation, in part, by promoting its metabolism into S1P. Despite this, the role of SphK1 in regulating insulin action has been largely overlooked. Transgenic (Tg) mice that overexpress SphK1 were fed a standard chow or high-fat diet (HFD) for 6 weeks before undergoing several metabolic analyses. SphK1 Tg mice fed an HFD displayed increased SphK activity in skeletal muscle, which was associated with an attenuated intramuscular ceramide accumulation compared with wild-type (WT) littermates. This was associated with a concomitant reduction in the phosphorylation of c-jun amino-terminal kinase, a serine threonine kinase associated with insulin resistance. Accordingly, skeletal muscle and whole-body insulin sensitivity were improved in SphK1 Tg, compared with WT mice, when fed an HFD. We have identified that the enzyme SphK1 is an important regulator of lipid partitioning and insulin action in skeletal muscle under conditions of increased lipid supply.

Nonalcoholic fatty liver (fatty liver) is a disease characterized by lipid infiltration in hepatocytes. Fatty liver is important to identify and treat because it may progress to more severe dysfunction [...], OBJECTIVE--Exercise is an effective intervention to treat fatty liver. However, the mechanism(s) that underlie exercise-induced reductions in fatty liver are unclear. Here we tested the hypothesis that exercise requires hepatic glucagon action to reduce fatty liver. RESEARCH DESIGN AND METHODS--C57BL/6 mice were fed high-fat diet (HFD) and assessed using magnetic resonance, biochemical, and histological techniques to establish a timeline for fatty liver development over 20 weeks. Glucagon receptor null ([gcgr.sup.-/-]) and wild-type ([gcgr.sup.+/+]) littermate mice were subsequently fed HFD to provoke moderate fatty liver and then performed either 10 or 6 weeks of running wheel or treadmill exercise, respectively. RESULTS--Exercise reverses progression of HFD-induced fatty liver in [gcgr.sup.+/+] mice. Remarkably, such changes are absent in [gcgr.sup.-/-] mice, thus confirming the hypothesis that exercise-stimulated hepatic glucagon receptor activation is critical to reduce HFD-induced fatty liver. CONCLUSIONS--These findings suggest that therapies that use antagonism of hepatic glucagon action to reduce blood glucose may interfere with the ability of exercise and perhaps other interventions to positively affect fatty liver. Diabetes 60:2720-2729, 2011

The inflammatory response associated with insulin resistance may have extensive effects on extracellular matrix (ECM) remodeling and endothelial cell function. ECM adaptations that accompany insulin resistance in muscle are of [...], OBJECTIVE--The hypothesis that high-fat (HF) feeding causes skeletal muscle extracellular matrix (ECM) remodeling in C57BL/6J mice and that this remodeling contributes to diet-induced muscle insulin resistance (IR) through the collagen receptor integrin [α.sub.2]][β.sub.1] was tested. RESEARCH DESIGN AND METHODS--The association between IR and ECM remodeling was studied in mice fed chow or HF diet. Specific genetic and pharmacological murine models were used to study effects of HF feeding on ECM in the absence of IR. The role of ECM-integrin interaction in IR was studied using hyperinsulinemic-euglycemic clamps on integrin [α.sub.2][β.sub.1]-null ([itga2.sup.-/-] ), integrin ([α.sub.1][β.sub.1]-null ([itga1.sup.-/-]), and wild-type littermate mice fed chow or HF. Integrin [α.sub.2][β.sub.1] and integrin [α.sub.1][β.sub.1] signaling pathways have opposing actions. RESULTS--HF-fed mice had IR and increased muscle collagen (Col) III and ColIV protein; the former was associated with increased transcript, whereas the latter was associated with reduced matrix metalloproteinase 9 activity. Rescue of muscle IR by genetic muscle-specific mitochondria-targeted catalase overexpression or by the phosphodiesterase 5a inhibitor, sildenafil, reversed HF feeding effects on ECM remodeling and increased muscle vascularity. Collagen remained elevated in HF-fed [itga2.sup.-/-]-mice. Nevertheless, muscle insulin action and vascularity were increased. Muscle IR in HF-fed [itga1.sup.-/-] mice was unchanged. Insulin sensitivity in chow-fed [itgal.sup.-/-] and [itga2.sup.-/-] mice was not different from wild-type littermates. CONCLUSIONS--ECM collagen expansion is tightly associated with muscle IR. Studies with [itga2.sup.-/-] mice provide mechanistic insight for this association by showing that the link between muscle IR and increased collagen can be uncoupled by the absence of collagen-integrin [α.sub.2][β.sub.1] interaction. Diabetes 60:416-426, 2011

Researchers have established that rates of alcohol and illicit drug use among American Indians/Alaska Natives vary by tribe, gender, and age group, making it difficult to get an accurate estimate of the actual extent of the problem of substance abuse within this population group. Although percentage rates of alcohol consumption are higher in non-Hispanic Whites, American Indians/ Alaska Natives nevertheless have the highest alcohol-related mortality rates and rates of substance use and dependence of all ethnic groups. Alcohol-related motor vehicle accidents are especially high for American Indian/Alaska Natives. Similarly, illicit drug use is higher among American Indians/Alaska Natives across all age groups compared to non-Indians. Data indicate that American Indians/Alaska Natives have the highest rates of use for marijuana, cocaine, inhalants, hallucinogens, and non-medical use of psychotherapeutics compared to other ethnic groups. Anecdotally, use of amphetamine appears to be high within some American Indian/Alaska Native tribes and has become a serious concern for most American Indian/Alaska Native communities. The percentage of American Indian/Alaska Native women using illicit drugs is lower than that found in men, except in younger age groups, in which percentage rates of illicit drug use by women in some tribes are comparable to rates for men. KEYWORDS Alaska Native, alcoholism, American Indian, epidemiology, substance abuse

OBJECTIVE--Muscle glucose uptake (MGU) is regulated by glucose delivery to, transport into, and phosphorylation within muscle. The aim of this study was to determine the role of limitations in glucose phosphorylation in the control of MGU during either physiological insulin stimulation (4 mU x [kg.sup.-1] x [min.sup.-1]) or exercise with chow or high-fat feeding. RESEARCH DESIGN AND METHODS--C57BL/6J mice with ([HK.sup.+/-]) and without (WT) a 50% hexokinase (HK) II deletion were fed chow or high-fat diets and studied at 4 months of age during a 120-min insulin clamp or 30 rain of treadmill exercise (n = 8-10 mice/group). 2-deoxy[³H]glucose was used to measure [R.sub.g], an index of MGU. RESULTS--Body weight and fasting arterial glucose were increased by high-fat feeding and partial HK II knockout ([HK.sup.+/-]). Both high-fat feeding and partial HK II knockout independently created fasting hyperinsulinemia, a response that was increased synergistically with combined high-fat feeding and HK II knockout. Whole-body insulin action was suppressed by ~25% with either high-fat feeding or partial HK II knockout alone but by >50% when the two were combined. Insulin-stimulated [R.sub.g] was modestly impaired by high-fat feeding and partial HK II knockout independently (~15-20%) but markedly reduced by the two together (~40-50%). Exercise-stimulated [R.sub.g] was reduced by ~50% with high-fat feeding and partial HK II knockout alone and was not attenuated further by combining the two. CONCLUSIONS--In summary, impairments in whole-body metabolism and MGU due to high-fat feeding and partial HK II knockout combined during insulin stimulation are additive. In contrast, combining high-fat feeding and partial HK II knockout during exercise causes no greater impairment in MGU than the two manipulations independently. This suggests that MGU is impaired during exercise by high-fat feeding due to, in large part, a limitation in glucose phosphorylation. Together, these studies show that the high-fat-fed mouse is characterized by defects at multiple steps of the MGU system that are precipitated by different physiological conditions., The importance of limitations in muscle glucose phosphorylation capacity in insulin resistance is a point of contention. In rodent muscle, glucose phosphorylation to glucose-6-phosphate is catalyzed primarily by the hexokinase [...]

In this study, Longman et al. sought to understand how NMD regulates the stability of RNAs translated at the endoplasmic reticulum (ER), and identified a localized NMD pathway dedicated to ER-translated mRNAs. They show that NBAS, a component of the Syntaxin 18 complex involved in Golgi-to-ER trafficking, fulfills an independent function in NMD, and propose a model where NBAS recruits UPF1 to the membrane of the ER and activates an ER-dedicated NMD pathway, thus providing an ER-protective function by ensuring quality control of ER-translated mRNAs.

Gene expression profiles in homologous tissues have been observed to be different between species, which may be due to differences between species in the gene expression program in each cell type, but may also reflect differences in cell type composition of each tissue in different species. Here, we compare expression profiles in matching primary cells in human, mouse, rat, dog, and chicken using Cap Analysis Gene Expression (CAGE) and short RNA (sRNA) sequencing data from FANTOM5. While we find that expression profiles of orthologous genes in different species are highly correlated across cell types, in each cell type many genes were differentially expressed between species. Expression of genes with products involved in transcription, RNA processing, and transcriptional regulation was more likely to be conserved, while expression of genes encoding proteins involved in intercellular communication was more likely to have diverged during evolution. Conservation of expression correlated positively with the evolutionary age of genes, suggesting that divergence in expression levels of genes critical for cell function was restricted during evolution. Motif activity analysis showed that both promoters and enhancers are activated by the same transcription factors in different species. An analysis of expression levels of mature miRNAs and of primary miRNAs identified by CAGE revealed that evolutionary old miRNAs are more likely to have conserved expression patterns than young miRNAs. We conclude that key aspects of the regulatory network are conserved, while differential expression of genes involved in cell-to-cell communication may contribute greatly to phenotypic differences between species.

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1and lnc-KHDC3L-2.

Throughout the 19th and 20th centuries, aided by advances in medical imaging, discoveries in physiology and medicine have added nearly 25 years to the average life expectancy. This resounding success brings with it a need to understand a broad range of age-related health conditions, such as dementia. Today, mathematics, neuroimaging and scientific computing are being combined with fresh insights, from animal models, to study the brain and to better understand the etiology and progression of Alzheimer’s disease, the most common cause of age-related dementia in humans. In this manuscript, we offer a brief primer to the reader interested in engaging with the exciting field of mathematical modeling and scientific computing to advance the study of the brain and, in particular, human AD research.

Recommendations of geologists to architects to minimize hazard vulnerability of building sites within a potential coastal hazard area are examined.

Background: Promoters are sites of transcription initiation that harbour a high concentration of phenotype-associated genetic variation. The evolutionary gain and loss of promoters between species (collectively, termed turnover) is pervasive across mammalian genomes and may play a prominent role in driving human phenotypic diversity. Results: We classified human promoters by their evolutionary history during the divergence of mouse and human lineages from a common ancestor. This defined conserved, human-inserted and mouse-deleted promoters, and a class of functional-turnover promoters that align between species but are only active in humans. We show that promoters of all evolutionary categories are hotspots for substitution and often, insertion mutations. Loci with a history of insertion and deletion continue that mode of evolution within contemporary humans. The presence of an evolutionary volatile promoter within a gene is associated with increased expression variance between individuals, but only in the case of human-inserted and mouse-deleted promoters does that correspond to an enrichment of promoter-proximal genetic effects. Despite the enrichment of these molecular quantitative trait loci (QTL) at evolutionarily volatile promoters, this does not translate into a corresponding enrichment of phenotypic traits mapping to these loci. Conclusions: Promoter turnover is pervasive in the human genome, and these promoters are rich in molecularly quantifiable but phenotypically inconsequential variation in gene expression. However, since evolutionarily volatile promoters show evidence of selection, coupled with high mutation rates and enrichment of QTLs, this implicates them as a source of evolutionary innovation and phenotypic variation, albeit with a high background of selectively neutral expression variation.

Promoters are central to the regulation of gene expression. Changes in gene regulation are thought to underlie much of the adaptive diversification between species and phenotypic variation within populations. In contrast to earlier work emphasizing the importance of enhancer evolution and subtle sequence changes at promoters, we show that dramatic changes such as the complete gain and loss (collectively, turnover) of functional promoters are common. Using quantitative measures of transcription initiation in both humans and mice across 52 matched tissues, we discriminate promoter sequence gains from losses and resolve the lineage of changes. We also identify expression divergence and functional turnover between orthologous promoters, finding only the latter is associated with local sequence changes. Promoter turnover has occurred at the majority (>56%) of protein-coding genes since humans and mice diverged. Tissue-restricted promoters are the most evolutionarily volatile where retrotransposition is an important, but not the sole, source of innovation. There is considerable heterogeneity of turnover rates between promoters in different tissues, but the consistency of these in both lineages suggests that the same biological systems are similarly inclined to transcriptional rewiring. The genes affected by promoter turnover show evidence of adaptive evolution. In mice, promoters are primarily lost through deletion of the promoter containing sequence, whereas in humans, many promoters appear to be gradually decaying with weak transcriptional output and relaxed selective constraint. Our results suggest that promoter gain and loss is an important process in the evolutionary rewiring of gene regulation and may be a significant source of phenotypic diversification.

IMPORTANCE Hospitalist physicians face increasing pressure to maximize productivity, which may undermine the efficiency and quality of care. OBJECTIVE To determine the association between hospitalist workload and the efficiency and quality of inpatient care. DESIGN, SETTING, AND PARTICIPANTS We conducted a retrospective cohort study of 20 241 admissions of inpatients cared for by a private hospitalist group at a large academic community hospital system between February 1, 2008, and January 31, 2011. EXPOSURES Daily hospitalist workload as measured by relative value units and patient encounters from the hospitalist billing records. MAIN OUTCOMES AND MEASURES The main outcomes were length of stay (LOS), cost, rapid response team activation, in-hospital mortality, patient satisfaction, and 30-day readmission rates. Key covariates included hospital occupancy and patient-level characteristics. RESULTS The LOS increased as workload increased, particularly at lower hospital occupancy. For hospital occupancies less than 75%, LOS increased from 5.5 to 7.5 days as workload increased. For occupancies of 75% to 85%, LOS increased exponentially above a daily relative value unit of approximately 25 and a census value of approximately 15. At high occupancy (>85%), LOS was J-shaped, with significant increases at higher ranges of workload. After controlling for LOS, cost increased by $111 for each 1-unit increase in relative value unit and $205 for each 1-unit increase in census across the range of values. Changes in workload were not associated with the remaining outcomes. CONCLUSIONS AND RELEVANCE Increasing hospitalist workload is associated with clinically meaningful increases in LOS and cost. Although our findings should be validated in different clinical settings, our results suggest the need for methods to mitigate the potential negative effects of increased hospitalist workload on the efficiency and cost of care.

It is now clear that eukaryotic cells produce many thousands of non-coding RNAs. The least well-studied of these are longer than 200 nt and are known as lncRNAs (long non-coding RNAs). These loci are of particular interest as their biological relevance remains uncertain. Sequencing projects have identified thousands of these loci in a variety of species, from flies to humans. Genome-wide scans for functionality, such as evolutionary and expression analyses, suggest that many of these molecules have functional roles to play in the cell. Nevertheless, only a handful of lncRNAs have been experimentally investigated, and most of these appear to possess roles in regulating gene expression at a variety of different levels. Several lncRNAs have also been implicated in cancer. This evidence suggests that lncRNAs represent a new class of non-coding gene whose importance should become clearer upon further experimental investigation.

The article focuses compares the reconstruction plan for New Orleans, Louisiana in response to the disasters brought by Hurricane Katrina in 2005 and the Midwestern flood in 1993. The national investment in reducing future flood losses has been siphoned off in favor of local economic and political profits from exploiting the floodplain. The same scenario is now playing out in New Orleans, with city and state leaders jockeying to rebuild back to the toes of the same levees and floodwalls that failed last year.

A reef monitoring program off Roatan, Bay islands, Honduras has produced base line data for platform bathymetry, major macrofauna distribution, and sediment attributes. Because erosion accompanying accelerated island development will be increasing in the near future, measurements of total suspended solids and sedimentation rate were made. Results show TSS range from 8 to 70 mg/l in the summer and 30 to 222mg/l in the winter. Sedimentation rates in the fore reef, where finer-grained terrigenous material would potentially accumulate, are 0.14mg/cm2/day to 7.07mg/cm2/day in the summer and 41 to 71mg/cm2/day in the winter. The summer values are well within the ranges of published results from other Caribbean carbonate platforms, however winter values are up to ten times that of other localities.

Minoxidil, a long-acting vasodilating antihypertensive agent, reduces arterial blood pressure by a direct action on arteriolar smooth muscle. The present studies examined the gross anatomic, histologic and ultra-structural myocardial alterations produced by 2 daily doses of minoxidil in beagle dogs (0.5, 1, or 3 mg/kg) and miniature swine (1, 3, or 10 mg/kg). Both myocardial necroses and hemorrhages were observed in dogs and pigs 24 hr after the last dose of minoxidil. In both species, the necroses were most frequent in the left ventricular papillary muscles, particularly the posterior one, but were less severe in swine. An ischemic origin of the necroses was suggested by the location of the lesions and by the pharmacologic effects of minoxidil. Gross epicardial or endocardial hemorrhages involving the atria and, to a lesser extent, the ventricles were observed in both species but were more severe in dogs. The atrial lesions were manifested grossly by diffuse redness and microscopically by interstitial edema, extravasated erythrocytes and infiltration of mononuclear cells. Hemorrhages, occurring on the epicardial surfaces, were often associated with lesions that involved small arteries having 3–6 layers of medial smooth muscle cells and were characterized by endothelial injury, intramural accumulations of erythrocytes and platelets, periadventitial hemorrhage, fibrin deposits and an inflammatory cell reaction. These lesions preferentially involved the right atrium in dogs and the left atrium in pigs. Pretreatment of beagle dogs with pyribenzamine (3 doses of 6 mg/kg every 8 hr), cimetidine (3 doses of 15 mg/kg every 8 hr), or both, had no effect on the incidence or severity of minoxidil-induced hemorrhagic lesions. The hemorrhagic lesions may be caused by overstretching of the vascular walls due to excessive, prolonged vasodilatation.

The physical and dermatoglyphic features obtained from published reports of 128 patients with the trisomy 9p syndrome and 27 patients with the partial 9p monosomy syndrome are tabulated. This information is also provided on two new individuals with each of these chromosomal disorders. The dermal ridge patterns and palmar creases of trisomy 9p which are most helpful from a diagnostic standpoint are zygodactylous or absent palmar digital triradii, brachymesophalangy, reduced total finger ridge count, complex thenar/ID I patterns, transverse palmar ridge alignment, simian creases, distal axial triradii, and great toe and hallucal arch patterns. The characteristic features in partial 9p monosomy include dolichomesophalangy with accessory finger flexion creases, digital whorl patterns and elevated total finger ridge count, distal axial triradii, simian creases, and palmar dermal ridge dissociation.

We give an inverse construction of the stable range for general flows which may or may not admit an invariant measure. The inverse map is then shown to be a right inverse functor of the stable range functor.

Mononuclear leukocytes obtained from rabbits by cardiac puncture, and purified of erythrocytes by gravity sedimentation in a gelatin solution and of platelets and polymorphonuclear leukocytes by filtration through nylon columns, gave rise to cell strains when cultured for 2 weeks. During serial passage, the emergent strains retained a diploid number of chromosomes and displayed a morphology ranging from the fusiform to the epithelioid. Similar cell strains were also initiated by culture of cells obtained by needle biopsy simulating cardiac puncture in the thoracic region. Contrariwise, cell populations could not be established from blood drawn from the exposed femoral artery. These observations cast doubt on previous reports which suggest that stable tissue culture cell populations were derived from cells of the blood. The use of aspiration material from the chest provides a simple and reproducible method of initiating primary cell strains from rabbits.

In the human genome, most genes undergo splicing, and patterns of codon usage are splicing dependent: guanine and cytosine (GC) content is the highest within single-exon genes and within first exons of multi-exon genes. However, the effects of codon usage on gene expression are typically characterized in unspliced model genes. Here, we measured the effects of splicing on expression in a panel of synonymous reporter genes that varied in nucleotide composition. We found that high GC content increased protein yield, mRNA yield, cytoplasmic mRNA localization, and translation of unspliced reporters. Splicing did not affect the expression of GC-rich variants. However, splicing promoted the expression of AT-rich variants by increasing their steady-state protein and mRNA levels, in part through promoting cytoplasmic localization of mRNA. We propose that splicing promotes the nuclear export of AU-rich mRNAs and that codon- and splicing-dependent effects on expression are under evolutionary pressure in the human genome.

Discusses the implications of the Human Genome Project for the practice of medicine. Benefits derived from the expansion of knowledge on genetics; Development of the science of medical genetics; Problems plaguing the field; Events that converged to make community practice realistic; Organizational efforts launched.