Instrumental-Variable Estimation of Gravity Equations

We present an instrumental-variable approach to estimate gravity equations. Our procedure accommodates the potential endogeneity of policy variables and is fully theory-consistent. It is based on the model in levels and accounts for multilateral resistance terms by means of importer and export fixed effects. The implementation is limited-information in nature, and so is silent on the form of the mechanism that drives the actual policy decisions. The procedure spawns specification tests for the validity of the instruments used as well as a test for exogeneity. We estimate gravity equations from five cross-sections of bilateral-trade data where the policy decision of interest is the engagement in a free trade agreement. We rely on the interaction of the countries in the pair with third-party trading partners to construct a credible instrumental variable based on the substantial transitivity in the formation of trade agreements that is observed in the data. This instrument is strongly correlated with the policy variable. Our point estimate of the average impact of a free trade agreement increases over the sampling period, starting at 61% and clocking o_ at a 117% increase in bilateral trade volume. Not correcting for endogeneity yields stable estimates of around 25%

twexp and twgravity: Estimating exponential regression models with two-way fixed effects

We introduce the commands twexp and twgravity that implement the estimators developed in Jochmans (2017) for exponential regression models with two-way fixed effects. twexp is applicable to generic n x m panel data. twgravity is written for the special case where the data is a cross-section on dyadic interactions between n agents. A prime example of the latter is cross-sectional bilateral trade data, where the model of interest is a gravity equation with importer and exporter effects. Both twexp and twgravity can deal with data where n and m are large, that is, the case of many fixed effects. They make use of Mata and are very fast to execute

xtserialpm: A portmanteau test for serial correlation in a linear panel model

We introduce the command xtserialpm to perform the portmanteau test developed in Jochmans (2019). The procedure tests for serial correlation in the errors of a linear panel model after estimation of the regression coefficients by the within-group estimator. The test is different from the test of Inoue and Solon (2006) that is performed by xtistest (Wursten 2018) in that it allows for heteroskedasticity. In simulations documented below, xtserialpm is found to provide a much more powerful test than xtistest. xtserialpm can deal with unbalanced panel data

Estimation of genetic parameters in rubber progenies.

This study was designed to evaluate the genetic variability, the potential for rubber yield and secondary traits of rubber tree progenies at three locations in the state of Sao Paulo. The experiments were conducted in a randomized block design with 22 progenies and 6 replications. At the age of three years, the progenies were evaluated for rubber yield, girth growth and total number of latex vessel rings. The results showed the existence of genetic variability among progenies for each location separately as well as between locations, with differences in the progeny performance for the traits. The individual heritabilities calculated for rubber yield, girth growth and total number of latex vessel rings (0.30, 0.63 and 0.29, respectively), associated with high genetic gains with selection for the traits studied at each site, showed that the populations can be considered suitable for the rubber breeding program, provided that an appropriate selection procedure is used

Ion Torrent and lllumina, two complementary RNA-seq platforms for constructing the holm oak (Quercus ilex) transcriptome

Transcriptome analysis is widely used in plant biology research to explore gene expression across a large variety of biological contexts such as those related to environmental stress and plant-pathogen interaction. Currently, next generation sequencing platforms are used to obtain a high amount of raw data to build the transcriptome of any plant. Here, we compare Illumina and Ion Torrent sequencing platforms for the construction and analysis of the holm oak (Quercus ilex) transcriptome. Genomic analysis of this forest tree species is a major challenge considering its recalcitrant character and the absence of previous molecular studies. In this study, Quercus ilex raw sequencing reads were obtained from Illumina and Ion Torrent and assembled by three different algorithms, MIRA, RAY and TRINITY. A hybrid transcriptome combining both sequencing technologies was also obtained in this study. The RAY-hybrid assembly generated the most complete transcriptome (1,116 complete sequences of which 1,085 were single copy) with a E90N50 of 1,122 bp. The MIRAIllumina and TRINITY-Ion Torrent assemblies annotated the highest number of total transcripts (62,628 and 74,058 respectively). MIRA-Ion Torrent showed the highest number of shared sequences (84.8%) with the oak transcriptome. All the assembled transcripts from the hybrid transcriptome were annotated with gene ontology grouping them in terms of biological processes, molecular functions and cellular components. In addition, an in silico proteomic analysis was carried out using the translated assemblies as databases. Those from Ion Torrent showed more proteins compared to the Illumina and hybrid assemblies. This new generated transcriptome represents a valuable tool to conduct differential gene expression studies in response to biotic and abiotic stresses and to assist and validate the ongoing Q. ilex whole genome sequencing

Indole derivative interacts with estrogen receptor beta and inhibits human ovarian cancer cell growth

Ovarian cancer remains the leading cause of mortality among gynecological tumors. Estrogen receptor beta (ERβ) expression has been suggested to act as a tumor suppressor in epithelial ovarian cancer by reducing both tumor growth and metastasis. ERβ expression abnormalities represent a critical step in the development and progression of ovarian cancer: for these reasons, its re‐expression by genetic engineering, as well as the use of targeted ERβ therapies, still constitute an important therapeutic approach. 3‐{[2‐chloro‐1‐(4‐chlorobenzyl)‐5‐methoxy‐6-methyl‐1H‐indol‐3‐yl]methylene}‐5‐hydroxy‐6‐methyl‐1,3‐dihydro‐2H‐indol‐2‐one, referred to here as compound 3, has been shown to have cytostatic as well cytotoxic effects on various hormone-dependent cancer cell lines. However, the mechanism of its anti‐carcinogenic activity is not well understood. Here, we offer a possible explanation of such an effect in the human ovarian cancer cell line IGROV1. Chromatin binding protein assay and liquid chromatography mass spectrometry were exploited to localize and quantify compound 3 in cells. Molecular docking was used to prove compound 3 binding to ERβ. Mass spectrometry‐based approaches were used to analyze histone post‐translational modifications. Finally, gene expression analyses revealed a set of genes regulated by the ERβ/3 complex, namely CCND1, MYC, CDKN2A, and ESR2, providing possible molecular mechanisms that underline the observed antiproliferative effects

The TLQP-21 Peptide Activates the G-Protein-Coupled Receptor C3aR1 via a Folding-upon-Binding Mechanism

TLQP-21, a VGF-encoded peptide is emerging as a novel target for obesity-associated disorders. TLQP-21 is found in the sympathetic nerve terminals in the adipose tissue and targets the G-protein-coupled-receptor (GPCR) Complement-3a-Receptor1 (C3aR1). So far, the mechanisms of TLQP-21-induced receptor activation remained unexplored. Here, we report that TLQP-21 is intrinsically disordered and undergoes a disorder-to-order transition, adopting an α-helical conformation, upon targeting cells expressing the C3aR1. We determined that the hot spots for TLQP-21 are located at the C-terminus, with mutations in the last four amino acids progressively reducing the bioactivity and, a single site mutation (R21A) or C-terminal amidation abolishing its function completely. Interestingly, the human TLQP-21 sequence carrying a S20A substitution activates the human C3aR1 receptor with lower potency compared to the rodent sequence. These studies reveal the mechanism of action of TLQP-21 and provide molecular templates for designing agonists and antagonists to modulate C3aR1 functions