3,014 research outputs found
Inhibitor binding mode and allosteric regulation of Na+-glucose symporters.
Sodium-dependent glucose transporters (SGLTs) exploit sodium gradients to transport sugars across the plasma membrane. Due to their role in renal sugar reabsorption, SGLTs are targets for the treatment of type 2 diabetes. Current therapeutics are phlorizin derivatives that contain a sugar moiety bound to an aromatic aglycon tail. Here, we develop structural models of human SGLT1/2 in complex with inhibitors by combining computational and functional studies. Inhibitors bind with the sugar moiety in the sugar pocket and the aglycon tail in the extracellular vestibule. The binding poses corroborate mutagenesis studies and suggest a partial closure of the outer gate upon binding. The models also reveal a putative Na+ binding site in hSGLT1 whose disruption reduces the transport stoichiometry to the value observed in hSGLT2 and increases inhibition by aglycon tails. Our work demonstrates that subtype selectivity arises from Na+-regulated outer gate closure and a variable region in extracellular loop EL5
Complementary patterns of direct amygdala and hippocampal projections to the macaque prefrontal cortex
The projections from the amygdala and hippocampus (including subiculum and presubiculum) to prefrontal cortex were compared using anterograde tracers injected into macaque monkeys (Macaca fascicularis, Macaca mulatta). Almost all prefrontal areas were found to receive some amygdala inputs. These connections, which predominantly arose from the intermediate and magnocellular basal nucleus, were particularly dense in parts of the medial and orbital prefrontal cortex. Contralateral inputs were not, however, observed. The hippocampal projections to prefrontal areas were far more restricted, being confined to the ipsilateral medial and orbital prefrontal cortex (within areas 11, 13, 14, 24a, 32, and 25). These hippocampal projections principally arose from the subiculum, with the fornix providing the sole route. Thus, while the lateral prefrontal cortex essentially receives only amygdala inputs, the orbital prefrontal cortex receives both amygdala and hippocampal inputs, though these typically target different areas. Only in medial prefrontal cortex do direct inputs from both structures terminate in common sites. But, even when convergence occurs within an area, the projections predominantly terminate in different lamina (hippocampal inputs to layer III and amygdala inputs to layers I, II, and VI). The resulting segregation of prefrontal inputs could enable the parallel processing of different information types in prefrontal cortex
Genome-wide association study identifies _FUT8_ and _ESR2_ as co-regulators of a bi-antennary N-linked glycan A2 (GlcNAc~2~Man~3~GlcNAc~2~) in human plasma proteins
HPLC analysis of N-glycans quantified levels of the biantennary glycan (A2) in plasma proteins of 924 individuals. Subsequent genome-wide association study (GWAS) using 317,503 single nucleotide polymorphysms (SNP) identified two genetic loci influencing variation in A2: FUT 8 and ESR2. We demonstrate that human glycans are amenable to GWAS and their genetic regulation shows sex-specific effects with _FUT 8_ variants explaining 17.3% of the variance in pre-menopausal women, while _ESR2_ variants explained 6.0% of the variance in post-menopausal women
Genetic constraint at single amino acid resolution in protein domains improves missense variant prioritisation and gene discovery
: Background: One of the major hurdles in clinical genetics is interpreting the clinical consequences associated with germline missense variants in humans. Recent significant advances have leveraged natural variation observed in large-scale human populations to uncover genes or genomic regions that show a depletion of natural variation, indicative of selection pressure. We refer to this as “genetic constraint”. Although existing genetic constraint metrics have been demonstrated to be successful in prioritising genes or genomic regions associated with diseases, their spatial resolution is limited in distinguishing pathogenic variants from benign variants within genes. Methods: We aim to identify missense variants that are significantly depleted in the general human population. Given the size of currently available human populations with exome or genome sequencing data, it is not possible to directly detect depletion of individual missense variants, since the average expected number of observations of a variant at most positions is less than one. We instead focus on protein domains, grouping homologous variants with similar functional impacts to examine the depletion of natural variations within these comparable sets. To accomplish this, we develop the Homologous Missense Constraint (HMC) score. We utilise the Genome Aggregation Database (gnomAD) 125 K exome sequencing data and evaluate genetic constraint at quasi amino-acid resolution by combining signals across protein homologues. Results: We identify one million possible missense variants under strong negative selection within protein domains. Though our approach annotates only protein domains, it nonetheless allows us to assess 22% of the exome confidently. It precisely distinguishes pathogenic variants from benign variants for both early-onset and adult-onset disorders. It outperforms existing constraint metrics and pathogenicity meta-predictors in prioritising de novo mutations from probands with developmental disorders (DD). It is also methodologically independent of these, adding power to predict variant pathogenicity when used in combination. We demonstrate utility for gene discovery by identifying seven genes newly significantly associated with DD that could act through an altered-function mechanism. Conclusions: Grouping variants of comparable functional impacts is effective in evaluating their genetic constraint. HMC is a novel and accurate predictor of missense consequence for improved variant interpretation
Sex-dependent influence of endogenous estrogen in pulmonary hypertension
Rationale: The incidence of pulmonary arterial hypertension (PAH) is greater in women suggesting estrogens may play a role in the disease pathogenesis. Experimentally, in males exogenously administered estrogen can protect against PH; however in models that display female susceptibility estrogens may play a causative role.
Objectives: To clarify the influence of endogenous estrogen and gender in PH and assess the therapeutic potential of a clinically available aromatase inhibitor.
Methods: We interrogated the effect of reduced endogenous estrogen in males and females using the aromatase inhibitor, anastrozole, in two models of PH; the hypoxic mouse and Sugen 5416/hypoxic rat. We also determined the effects of gender on pulmonary expression of aromatase in these models and in lungs from PAH patients.
Results: Anastrozole attenuated PH in both models studied, but only in females. To verify this effect was due to reduced estrogenic activity we confirmed that in hypoxic mice inhibition of estrogen receptor alpha also has a therapeutic effect specifically in females. Female rodent lung displays increased aromatase and decreased BMPR2 and Id1 expression compared to male. Anastrozole treatment reversed the impaired BMPR2 pathway in females. Increased aromatase expression was also detected in female human pulmonary artery smooth muscle cells compared to male.
Conclusions: The unique phenotype of female pulmonary arteries facilitates the therapeutic effects of anastrozole in experimental PH confirming a role for endogenous estrogen in the disease pathogenesis in females and suggests aromatase inhibitors may have therapeutic potential
Pupillary light reflex circuits in the macaque monkey: the preganglionic Edinger-Westphal nucleus
The motor outfow for the pupillary light refex originates in the preganglionic motoneuron subdivision of the Edinger–
Westphal nucleus (EWpg), which also mediates lens accommodation. Despite their importance for vision, the morphology,
ultrastructure and luminance-related inputs of these motoneurons have not been fully described in primates. In macaque
monkeys, we labeled EWpg motoneurons from ciliary ganglion and orbital injections. Both approaches indicated preganglionic motoneurons occupy an EWpg organized as a unitary, ipsilateral cell column. When tracers were placed in the pretectal complex, labeled terminals targeted the ipsilateral EWpg and reached contralateral EWpg by crossing both above and
below the cerebral aqueduct. They also terminated in the lateral visceral column, a ventrolateral periaqueductal gray region
containing neurons projecting to the contralateral pretectum. Combining olivary pretectal and ciliary ganglion injections
to determine whether a direct pupillary light refex projection is present revealed a labeled motoneuron subpopulation that
displayed close associations with labeled pretectal terminal boutons. Ultrastructurally, this subpopulation received synaptic
contacts from labeled pretectal terminals that contained numerous clear spherical vesicles, suggesting excitation, and scattered dense-core vesicles, suggesting peptidergic co-transmitters. A variety of axon terminal classes, some of which may
serve the near response, synapsed on preganglionic motoneurons. Quantitative analysis indicated that pupillary motoneurons
receive more inhibitory inputs than lens motoneurons. To summarize, the pupillary light refex circuit utilizes a monosynaptic,
excitatory, bilateral pretectal projection to a distinct subpopulation of EWpg motoneurons. Furthermore, the interconnections
between the lateral visceral column and olivary pretectal nucleus may provide pretectal cells with bilateral retinal felds
Uncovering Networks from Genome-Wide Association Studies via Circular Genomic Permutation
Genome-wide association studies (GWAS) aim to detect single nucleotide polymorphisms (SNP) associated with trait variation. However, due to the large number of tests, standard analysis techniques impose highly stringent significance thresholds, leaving potentially associated SNPs undetected, and much of the trait genetic variation unexplained. Pathway- and network-based methodologies applied to GWAS aim to detect associations missed by standard single-marker approaches. The complex and non-random architecture of the genome makes it a challenge to derive an appropriate testing framework for such methodologies. We developed a rapid and simple permutation approach that uses GWAS SNP association results to establish the significance of pathway associations while accounting for the linkage disequilibrium structure of SNPs and the clustering of functionally related elements in the genome. All SNPs used in the GWAS are placed in a “circular genome” according to their location. Then the complete set of SNP association P values are permuted by rotation with respect to the genomic locations of the SNPs. Once these “simulated” P values are assigned, the joint gene P values are calculated using Fisher’s combination test, and the association of pathways is tested using the hypergeometric test. The circular genomic permutation approach was applied to a human genome-wide association dataset. The data consists of 719 individuals from the ORCADES study genotyped for ∼300,000 SNPs and measured for 51 traits ranging from physical to biochemical measurements. KEGG pathways (n = 225) were used as the sets of pathways to be tested. Our results demonstrate that the circular genomic permutations provide robust association P values. The non-permuted hypergeometric analysis generates ∼1400 pathway-trait combination results with an association P value more significant than P ≤ 0.05, whereas applying circular genomic permutation reduces the number of significant results to a more credible 40% of that value. The circular permutation software (“genomicper”) is available as an R package at http://cran.r-project.org/
Persistent starspot signals on M dwarfs: multi-wavelength Doppler observations with the Habitable-zone Planet Finder and Keck/HIRES
Young, rapidly-rotating M dwarfs exhibit prominent starspots, which create
quasiperiodic signals in their photometric and Doppler spectroscopic
measurements. The periodic Doppler signals can mimic radial velocity (RV)
changes expected from orbiting exoplanets. Exoplanets can be distinguished from
activity-induced false positives by the chromaticity and long-term incoherence
of starspot signals, but these qualities are poorly constrained for
fully-convective M stars. Coherent photometric starspot signals on M dwarfs may
persist for hundreds of rotations, and the wavelength dependence of starspot RV
signals may not be consistent between stars due to differences in their
magnetic fields and active regions. We obtained precise multi-wavelength RVs of
four rapidly-rotating M dwarfs (AD Leo, G 227-22, GJ 1245B, GJ 3959) using the
near-infrared (NIR) Habitable-zone Planet Finder, and the optical Keck/HIRES
spectrometer. Our RVs are complemented by photometry from Kepler, TESS, and the
Las Cumbres Observatory (LCO) network of telescopes. We found that all four
stars exhibit large spot-induced Doppler signals at their rotation periods, and
investigated the longevity and optical-to-NIR chromaticity for these signals.
The phase curves remain coherent much longer than is typical for Sunlike stars.
Their chromaticity varies, and one star (GJ 3959) exhibits optical and NIR RV
modulation consistent in both phase and amplitude. In general, though, we find
that the NIR amplitudes are lower than their optical counterparts. We conclude
that starspot modulation for rapidly-rotating M stars frequently remains
coherent for hundreds of stellar rotations, and gives rise to Doppler signals
that, due to this coherence, may be mistaken for exoplanets.Comment: Accepted for publication in the Astrophysical Journa
Generalized stacking fault energy surfaces and dislocation properties of aluminum
We have employed the semidiscrete variational generalized Peierls-Nabarro
model to study the dislocation core properties of aluminum. The generalized
stacking fault energy surfaces entering the model are calculated by using
first-principles Density Functional Theory (DFT) with pseudopotentials and the
embedded atom method (EAM). Various core properties, including the core width,
splitting behavior, energetics and Peierls stress for different dislocations
have been investigated. The correlation between the core energetics and
dislocation character has been explored. Our results reveal a simple
relationship between the Peierls stress and the ratio between the core width
and atomic spacing. The dependence of the core properties on the two methods
for calculating the total energy (DFT vs. EAM) has been examined. The EAM can
give gross trends for various dislocation properties but fails to predict the
finer core structures, which in turn can affect the Peierls stress
significantly (about one order of magnitude).Comment: 25 pages, 12 figure
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