Identification of sparse neural functional connectivity using penalized likelihood estimation and basis functions

One key problem in computational neuroscience and neural engineering is the identification and modeling of functional connectivity in the brain using spike train data. To reduce model complexity, alleviate overfitting, and thus facilitate model interpretation, sparse representation and estimation of functional connectivity is needed. Sparsities include global sparsity, which captures the sparse connectivities between neurons, and local sparsity, which reflects the active temporal ranges of the input-output dynamical interactions. In this paper, we formulate a generalized functional additive model (GFAM) and develop the associated penalized likelihood estimation methods for such a modeling problem. A GFAM consists of a set of basis functions convolving the input signals, and a link function generating the firing probability of the output neuron from the summation of the convolutions weighted by the sought model coefficients. Model sparsities are achieved by using various penalized likelihood estimations and basis functions. Specifically, we introduce two variations of the GFAM using a global basis (e.g., Laguerre basis) and group LASSO estimation, and a local basis (e.g., B-spline basis) and group bridge estimation, respectively. We further develop an optimization method based on quadratic approximation of the likelihood function for the estimation of these models. Simulation and experimental results show that both group-LASSO-Laguerre and group-bridge-B-spline can capture faithfully the global sparsities, while the latter can replicate accurately and simultaneously both global and local sparsities. The sparse models outperform the full models estimated with the standard maximum likelihood method in out-of-sample predictions.     

Extensive Phylogenetic Analysis of a Soil Bacterial Community Illustrates Extreme Taxon Evenness and the Effects of Amplicon Length,Degree of Coverage,and DNA Fractionation on Classification and Ecological Parameters

To thoroughly investigate the bacterial community diversity present in a single composite sample from an agricultural soil and to examine potential biases resulting from data acquisition and analytical approaches, we examined the effects of percent G+C DNA fractionation, sequence length, and degree of coverage of bacterial diversity on several commonly used ecological parameters (species estimation, diversity indices, and evenness). We also examined variation in phylogenetic placement based on multiple commonly used approaches (ARB alignments and multiple RDP tools). The results demonstrate that this soil bacterial community is highly diverse, with 1,714 operational taxonomic units demonstrated and 3,555 estimated (based on the Chao1 richness estimation) at 97% sequence similarity using the 16S rRNA gene. The results also demonstrate a fundamental lack of dominance (i.e., a high degree of evenness), with 82% of phylotypes being encountered three times or less. The data also indicate that generally accepted cutoff values for phylum-level taxonomic classification might not be as applicable or as general as previously assumed and that such values likely vary between prokaryotic phyla or groups.Efforts to describe bacterial species richness and diversity have long been hampered by the inability to cultivate the vast majority of bacteria from natural environments. New methods to study bacterial diversity have been developed in the last two decades (32), many of which rely on PCR-based procedures and phylogenetic comparison of 16S rRNA gene sequences. However, PCR using complex mixtures of templates (as in the case of total microbial community DNA) is presumed to preferentially amplify certain templates in the mixture (23) based on their primary sequence, percent G+C (hereafter GC) content, or other factors, resulting in so-called PCR bias. Moreover, the amplification of template sequences depends on their initial concentration and tends to skew detection toward the most abundant members of the community (23). To further complicate matters, subsequent random cloning steps on amplicon mixtures are destined to result in the detection of numerically dominant sequences, especially where relative abundance can vary over orders of magnitude. Indeed, any analysis based on random encounter is destined to primarily detect numerically dominant populations. This is especially of concern where limited sampling is performed on highly complex microbial communities exhibiting mostly even distribution of populations with only a few showing any degree of dominance, as typically perceived for soils (17). These artifacts and sampling limitations represent major hurdles in bacterial community diversity analysis, since the vast majority of bacterial diversity probably lies in “underrepresented minority” populations (24, 30). This is important because taxa that are present only in low abundance may still perform important ecosystem functions (e.g., ammonia-oxidizing bacteria). Of special concern is that biases in detection might invalidate hypothesis testing on complex communities where limited sampling is performed (5).Recently, there has been a concerted effort toward addressing problems impeding comprehensive bacterial diversity studies (7, 13, 24, 26, 28). In recent years, studies have increased sequencing efforts, with targeted 16S rRNA gene sequence libraries approaching 2,000 clones (11) and high-throughput DNA-sequencing efforts (e.g., via 454 pyrosequencing and newer-generation high-throughput approaches) of up to 149,000 templates from one or a few samples (25, 30). These technological advances have come as researchers recognize that massive sequencing efforts are required to accurately assess the diversity of populations that comprise complex microbial communities (29, 30). Alternatively, where fully aligned sequence comparisons need to be made, novel experimental strategies that allow more-comprehensive detection of underrepresented bacterial taxa can be applied. One such approach involves the application of prefractionation of total bacterial community genomic DNA based on its GC content (hereafter GC fractionation) prior to subsequent molecular manipulations of total community DNA (14). This strategy has been successfully applied in combination with denaturing gradient gel electrophoresis (13) and 16S rRNA gene cloning (2, 21) to study microbial communities. This approach separates community genomic DNA, prior to any PCR, into fractions of similar percent GC content, effectively reducing the overall complexity of the total community DNA mixture by physical separation into multiple fractions. This facilitates PCR amplification, cloning, and detection of sequences in fractions with relatively low abundance in the community, thereby enhancing the detection of minority populations (13). Collectively, this strategy reduces the biases introduced by PCR amplification and random cloning of the extremely complex mixtures of templates of different GC content, primary sequence, and relative abundance present in total environmental genomic DNA.Any large molecular survey that relies on sequencing further requires the analysis of large amounts of data that must be catalogued into phylogenetically relevant groups. This is usually done using high-throughput methods like RDP Classifier or Sequence Match (6) or a tree-based method like Greengenes (8) or ARB (18). Two major pitfalls that are encountered using these former approaches are the presence of huge numbers of unclassified sequences in databases and the lack of representative sequences from all phyla. This leads to most surveys having large portions of their phylotypes designated as unclassified. The latter tree-based approaches, although better suited for classification schemes, are also dependent on having a comprehensive database with well-classified sequences for reproducible results. This reproducibility becomes especially important when trying to compare data across different studies, especially those that utilize different approaches and study systems.In the current study, we analyzed an extensive (∼5,000 clones) partial 16S rRNA gene library from a single soil sample that was generated using very general primers and GC-fractionated DNA. Total DNA was extracted from soil at a cultivated treatment plot at the National Science Foundation Long Term Ecological Research (NSF-LTER) site at the Kellogg Biological Station (KBS) in mid-Michigan (http://www.kbs.msu.edu/lter). To test the effect of GC fractionation on recovery of 16S rRNA gene sequences, we conducted a direct comparison with a nonfractionated library generated from the same soil sample. Using the GC-fractionated library, we also calculated several measures of bacterial diversity and examined the effects of sampling size and sequence length on Shannon-Weaver diversity index, Simpson''s reciprocal index (1/D, where D is the probability that two randomly selected individuals from a sample belong to the same species), evenness, and Chao1 richness estimation. The results show that GC fractionation is a powerful tool to help mitigate limitations of random PCR- and cloning-based analyses of total microbial community diversity, resulting in the recovery of underrepresented taxa and, in turn, reducing the sampling size needed for accurate estimations of bacterial richness. The results also provided evidence for the need to expand the typical scale of sequence-based survey efforts, particularly in environments where evenness abounds or where minority bacterial populations may have important effects on community function and processes. We suggest that there is a need for the establishment of standardized approaches for the analysis of sequence data from community diversity studies in order to maximize data comparisons across independent studies and show examples of software programs developed to facilitate comparative analysis of large sequence datasets.     

Ca2+-surfactant interactions affect enzyme stability in detergent solutions

Detergent proteases and amylases generally bind Ca(2+) ions. These bound ions enhance enzyme stability, reducing the rates of degradative reactions such as unfolding and proteolysis. Thus, surfactant aggregates, such as micelles, affect protease and amylase stability indirectly, by competing with the enzymes for Ca(2+) ions. Dissociation constants for Ca(2+) interactions with anionic surfactant micelles are in the 10(-3) to 10(-2) M range. These interactions are weak relative to enzyme-Ca(2+) interactions (K(d) of order 10(-6) M). However, surfactant is typically present at much higher concentration than enzyme, and it is the Ca(2+)-micelle equilibrium that largely determines the amount of free Ca(2+) available for binding to enzymes. The problem of surfactant-mediated Ca(2+) removal from enzymes can be avoided by adding calcium to a detergent formulation in an amount such that the concentration of free Ca(2+) is around 10(-5)M.     

Consequences of a Government-Controlled Agricultural Price Increase on Fishing and the Coral Reef Ecosystem in the Republic of Kiribati

Background

Economic development policies may have important economic and ecological consequences beyond the sector they target. Understanding these consequences is important to improving these policies and finding opportunities to align economic development with natural resource conservation. These issues are of particular interest to governments and non-governmental organizations that have new mandates to pursue multiple benefits. In this case study, we examined the direct and indirect economic and ecological effects of an increase in the government-controlled price for the primary agricultural product in the Republic of Kiribati, Central Pacific.

Methods/Principal Findings

We conducted household surveys and underwater visual surveys of the coral reef to examine how the government increase in the price of copra directly affected copra labor and indirectly affected fishing and the coral reef ecosystem. The islands of Kiribati are coral reef atolls and the majority of households participate in copra agriculture and fishing on the coral reefs. Our household survey data suggest that the 30% increase in the price of copra resulted in a 32% increase in copra labor and a 38% increase in fishing labor. Households with the largest amount of land in coconut production increased copra labor the most and households with the smallest amount of land in coconut production increased fishing the most. Our ecological data suggests that increased fishing labor may result in a 20% decrease in fish stocks and 4% decrease in coral reef-builders.

Conclusions/Significance

We provide empirical evidence to suggest that the government increase in the copra price in Kiribati had unexpected and indirect economic and ecological consequences. In this case, the economic development policy was not in alignment with conservation. These results emphasize the importance of accounting for differences in household capital and taking a systems approach to policy design and evaluation, as advocated by sustainable livelihood and ecosystem-based management frameworks.     

Use and value of serologic tests for the diagnosis of systemic candidiasis in cancer patients: A prospective study of 146 patients

Sera from 146 cancer patients at risk for disseminated candidiasis were studied prospectively with immunodiffusion (ID), counterelectrophoresis (CEP), and latex agglutination (LA) tests to determine their diagnostic value in the detection of antibodies to theCandida species. Serial serum samples, cultures, and clinical data were obtained after a malignancy was diagnosed. Patients were classified into three groups (I, II, and III) on the basis of cultural, histological, and clinical evidence for superficial (Group I) versus disseminated (Group III)Candida infection. Thirty-two of 78 patients (41%) in Group I had positive ID, CEP, and LA titers. In Group II, those patients lacking histological confirmation of disseminated infection, 16 of 18 (89%) had positive titers. Thirty-six of 50 (72%) in Group III were positive by all three tests. Heavy colonization of the gastrointestinal tract, without evidence of tissue invasion, produced positive test results. Negative serologic tests were encountered in immunosuppressed patients with rapidly progressive candidiasis.C. krusei infections produced specific antibody titers detected by the homologous antigen but not byC. albicans antigen. Stable or decreasing LA titers were correlated with clinical improvement in patients receiving effective antifungal therapy.     

ATP25, a new nuclear gene of Saccharomyces cerevisiae required for expression and assembly of the Atp9p subunit of mitochondrial ATPase

We report a new nuclear gene, designated ATP25 (reading frame YMR098C on chromosome XIII), required for expression of Atp9p (subunit 9) of the Saccharomyces cerevisiae mitochondrial proton translocating ATPase. Mutations in ATP25 elicit a deficit of ATP9 mRNA and of its translation product, thereby preventing assembly of functional F(0). Unlike Atp9p, the other mitochondrial gene products, including ATPase subunits Atp6p and Atp8p, are synthesized normally in atp25 mutants. Northern analysis of mitochondrial RNAs in an atp25 temperature-sensitive mutant confirmed that Atp25p is required for stability of the ATP9 mRNA. Atp25p is a mitochondrial inner membrane protein with a predicted mass of 70 kDa. The primary translation product of ATP25 is cleaved in vivo after residue 292 to yield a 35-kDa C-terminal polypeptide. The C-terminal half of Atp25p is sufficient to stabilize the ATP9 mRNA and restore synthesis of Atp9p. Growth on respiratory substrates, however, depends on both halves of Atp25p, indicating that the N-terminal half has another function, which we propose to be oligomerization of Atp9p into a proper size ring structure.     

The price of insulation: costs and benefits of feather delivery to nests for male tree swallows Tachycineta bicolor

Many species of birds line their nests with feathers, and it has been hypothesized that this functions to provide a thermally stable microenvironment for the development of eggs and nestlings. Feathers in the nest may also function as a mechanism for parasite control, providing a physical barrier that protects nestlings from ectoparasites. We tested these hypotheses by performing a feather removal and addition experiment in tree swallows Tachycineta bicolor, a species well‐known for lining their nests with feathers. While we found no evidence that quantity of feathers in nests influenced the ability of females to produce and incubate eggs, offspring in well‐feathered nests had longer flight feathers and were structurally larger just prior to fledging that those in nests with fewer feathers. Furthermore, we also demonstrated a positive correlation between feathers and the abundance of larval blow flies Protocalliphora spp. in nests, a result opposite to that predicted by the anti‐parasite hypothesis. While our study provides strong support for the insulation hypothesis, we also discuss the possibility that devoting time to feather gathering may result in males losing paternity in their nests, although manipulative studies will be necessary to fully evaluate this idea.     

Structure and mutagenesis of the parainfluenza virus 5 hemagglutinin-neuraminidase stalk domain reveals a four-helix bundle and the role of the stalk in fusion promotion

Paramyxovirus entry into cells requires the fusion protein (F) and a receptor binding protein (hemagglutinin-neuraminidase [HN], H, or G). The multifunctional HN protein of some paramyxoviruses, besides functioning as the receptor (sialic acid) binding protein (hemagglutinin activity) and the receptor-destroying protein (neuraminidase activity), enhances F activity, presumably by lowering the activation energy required for F to mediate fusion of viral and cellular membranes. Before or upon receptor binding by the HN globular head, F is believed to interact with the HN stalk. Unfortunately, until recently none of the receptor binding protein crystal structures have shown electron density for the stalk domain. Parainfluenza virus 5 (PIV5) HN exists as a noncovalent dimer-of-dimers on the surface of cells, linked by a single disulfide bond in the stalk. Here we present the crystal structure of the PIV5-HN stalk domain at a resolution of 2.65 Å, revealing a four-helix bundle (4HB) with an upper (N-terminal) straight region and a lower (C-terminal) supercoiled part. The hydrophobic core residues are a mix of an 11-mer repeat and a 3- to 4-heptad repeat. To functionally characterize the role of the HN stalk in F interactions and fusion, we designed mutants along the PIV5-HN stalk that are N-glycosylated to physically disrupt F-HN interactions. By extensive study of receptor binding, neuraminidase activity, oligomerization, and fusion-promoting functions of the mutant proteins, we found a correlation between the position of the N-glycosylation mutants on the stalk structure and their neuraminidase activities as well as their abilities to promote fusion.     

MC4R Variant Is Associated With BMI but Not Response to Resistance Training in Young Females

Recently, a genome‐wide association study (GWAS) that identified eight single‐nucleotide polymorphisms (SNPs) associated with BMI highlighted a possible neuronal influence on the development of obesity. We hypothesized these SNPs would govern the response of BMI and subcutaneous fat to resistance training in young individuals (age = 24 years). We genotyped the eight GWAS‐identified SNPs in the article by Willer et al. in a cohort (n = 796) that undertook a 12‐week resistance‐training program. Females with a copy of the rare allele (C) for rs17782313 (MC4R) had significantly higher BMIs (CC/CT: n = 174; 24.70 ± 0.33 kg/m², TT: n = 278; 23.41 ± 0.26 kg/m², P = 0.002), and the SNP explained 1.9% of overall variation in BMI. Males with a copy of the rare allele (T) for rs6548238 (TMEM18) had lower amounts of subcutaneous fat pretraining (CT/TT: n = 65; 156,534 ± 7,415 mm³, CC: n = 136; 177,825 ± 5,139 mm³, P = 0.019) and males with a copy of the rare allele (A) for rs9939609 (FTO) lost a significant amount of subcutaneous fat with exercise (AT/AA: n = 83; ?798.35 ± 2,624.30 mm³, TT: n = 47; 9,435.23 ± 3,494.44 mm³, P = 0.021). Females with a copy of the G allele for a missense variant in the SH2B1 (rs7498665) was associated with less change of subcutaneous fat volume with exercise (AG/GG: n = 191; 9,813 ± 2,250 mm³ vs. AA: n = 126; 770 ± 2,772 mm³; P = 0.011). These data support the original finding that there is an association between measures of obesity and a variant near the MC4R gene and extends these results to a younger population and implicates FTO, TMEM18, and SH2B1 polymorphisms in subcutaneous fat regulation.     

A Potential Role for 5‐Androstene‐3β,7β,17β‐triol in Obesity and Metabolic Syndrome

Metabolic syndrome is marked by perturbed glucocorticoid (GC) signaling, systemic inflammation, and altered immune status. Dehydroepiandrosterone (DHEA), a major circulating adrenal steroid and dietary supplement, demonstrates antiobesity, anti‐inflammatory, GC‐opposing and immune‐modulating activity when administered to rodents. However, plasma DHEA levels failed to correlate with metabolic syndrome and oral replacement therapy provided only mild benefits to patients. Androstene‐3β,7β,17β‐triol (β‐AET) an anti‐inflammatory metabolite of DHEA, also exhibits GC‐opposing and immune‐modulating activity when administered to rodents. We hypothesized a role for β‐AET in obesity. We now report that plasma levels of β‐AET positively correlate with BMI in healthy men and women. Together with previous studies, the observations reported here may suggest a compensatory role for β‐AET in preventing the development of metabolic syndrome. The β‐AET structural core may provide the basis for novel pharmaceuticals to treat this disease.