Not all pseudogenes are transcriptionally silent as previously thought. Pseudogene transcripts, although not translated, contribute to the non-coding RNA pool of the cell that regulates the expression of other genes. Pseudogene transcripts can also directly compete with the parent gene transcripts for mRNA stability and other cell factors, modulating their expression levels. Tissue-specific and cancer-specific differential expression of these "functional" pseudogenes has been reported. To ascertain potential pseudogene:gene interactions in HIV-1 infection, we analyzed transcriptomes from infected and uninfected T-cells and found that 21 pseudogenes are differentially expressed in HIV-1 infection. This is interesting because parent genes of one-third of these differentially-expressed pseudogenes are implicated in HIV-1 life cycle, and parent genes of half of these pseudogenes are involved in different viral infections. Our bioinformatics analysis identifies candidate pseudogene:gene interactions that may be of significance in HIV-1 infection. Experimental validation of these interactions would establish that retroviruses exploit this newly-discovered layer of host gene expression regulation for their own benefit.

Can people learn causal relationships about the world from someone’s emotions? We present a computational model integrating observational causal learning with emotional information, which uses emotional displays to disambiguate the beliefs, desires, and knowledge of other agents, in turn allowing causal inferences about the world. We compared our model predictions to human causal judgements on two observational learning tasks involving multiple possible causes or multiple possible outcomes. Across three studies (N = 129,127,125), emotional displays (compared to actions alone) led people to interpret agents’ beliefs differently, which in some contexts resulted in different causal inferences. Our model closely reflected these patterns of belief and causal inference and revealed new insights on how people learn causal relationships from others’ emotions.

Background

Right ventricular (RV) pacing-induced cardiomyopathy (PICM) occurs in ∼30% of patients with RV leads. This study evaluated the long-term effects of restoring antegrade conduction with a biological pacemaker in a porcine model of RV PICM.

Objectives

The goal of this study was to determine if antegrade biological pacing can attenuate RV PICM.

Methods

In pigs with complete atrioventricular (AV) block, transcription factor T-box 18 (TBX18) was injected into the His bundle region in either of 2 experimental protocols: protocol A sought to prevent PICM, and protocol B sought to reverse PICM. In protocol A, we injected adenoviral vectors expressing TBX18 (or the reporter construct green fluorescent protein) after AV node ablation, and observed the animals for 8 weeks. In protocol B, PICM was established by using AV node ablation and 4 weeks of electronic RV pacing, at which point TBX18 was injected into the His bundle region.

Results

In protocol A, TBX18 biological pacing led to superior chronotropic support (62.4 ± 3 beats/min vs. 50.4 ± 0.4 beats/min; p = 0.01), lower backup pacemaker utilization (45 ± 2.6% vs. 94.6 ± 1.4%; p = 0.001), and greater ejection fraction (58.5 ± 1.3% vs. 46.7 ± 2%; p = 0.001). In protocol B, full-blown RV PICM was evident 4 weeks after complete AV block in both groups; subsequent intervention led to higher mean heart rate (56 ± 2 beats/min vs. 50.1 ± 0.4 beats/min; p = 0.05), less backup pacemaker utilization (53 ± 8.2% vs. 95 ± 1.6%; p = 0.003), and a greater ejection fraction (61.7 ± 1.3% vs. 49 ± 1.6%; p = 0.0003) in TBX18-injected animals versus control animals.

Conclusions

In a preclinical model, pacemaker-induced cardiomyopathy can be prevented, and reversed, by restoring antegrade conduction with TBX18 biological pacing.

Neither full length genomic sequence of CRF07_BC nor that of CRF08_BC was found in any other countries since they originated in Yunnan, China, in early 1990s. Here, we first report that CRF07_BC and CRF08_BC appeared among intravenous drug users in Shan state of Myanmar bordering Yunnan, and confirmed that they spread from China to Myanmar. The introduction of CRF07_BC and CRF08_BC in northern Myanmar may forebode a changing subtype epidemic in Southeast Asia.

The on-going generation of HIV-1 intersubtype recombination has led to new circulating recombinant forms (CRFs) and unique recombinant forms (URFs) in Asia. In this study, we evaluated whether previously reported URFs were actually CRFs. All available complete or near full-length HIV-1 URF sequences from Asia were retrieved from the HIV Los Alamos National Laboratory Sequence database, and phylogenetic, transmission cluster, and bootscan analyses were performed using MEGA 6.0, Cluster Picker 1.2.1, and SimPlot3.5.1. According to the criterion of new CRFs, two new HIV-1 CRFs (CRF87_cpx and CRF88_BC) were identified from these available URFs. CRF87_cpx comprised HIV-1 subtypes B, C, and CRF01_AE, and CRF88_BC comprised subtypes B and C. HIV Blast and bootscan analysis revealed that besides the three representative strains, there were two additional CRF87_cpx strains. Furthermore, we defined seven dominant URFs (dURF01-dURF07), each of which contained two strains sharing same recombination map and can be used as sequence references to facilitate the finding of new potential CRFs in future. These results will benefit the molecular epidemiological investigation of HIV-1 in Asia.

Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.

Across six studies conducted in Mainland China and South Korea, the present research extended prior findings showing that pride is comprised of two distinct conceptual and experiential facets in the U.S.: a pro-social, achievement-oriented "authentic pride", and an arrogant, self-aggrandizing "hubristic pride". This same two-facet structure emerged in Chinese participants' semantic conceptualizations of pride (Study 1), Chinese and Koreans' dispositional tendencies to experience pride (Studies 2, 3a, and 3b), Chinese and Koreans' momentary pride experiences (Studies 3a, 3b, and 5), and Americans' pride experiences using descriptors derived indigenously in Korea (Study 4). Together, these studies provide the first evidence that the two-facet structure of pride generalizes to cultures with highly divergent views of pride and self-enhancement processes from North America.

A novel noncontact indentation system with the combination of an air jet and optical coherence tomography (OCT) was presented in this paper for the quantitative measurement of the mechanical properties of soft tissues. The key idea of this method is to use a pressure-controlled air jet as an indenter to compress the soft tissue in a noncontact way and utilize the OCT signals to extract the deformation induced. This indentation system provides measurement and mapping of tissue elasticity for small specimens with high scanning speed. Experiments were performed on 27 silicone tissue-mimicking phantoms with different Young's moduli, which were also measured by uniaxial compression tests. The regression coefficient of the indentation force to the indentation depth (N mm(-1)) was used as an indicator of the stiffness of tissue under air jet indentation. Results showed that the stiffness coefficients measured by the current system correlated well with the corresponding Young's moduli obtained by conventional mechanical testing (r = 0.89, p < 0.001). Preliminary in vivo tests also showed that the change of soft tissue stiffness with and without the contraction of the underlying muscles in the hand could be differentiated by the current measurement. This system may have broad applications in tissue assessment and characterization where alterations of mechanical properties are involved, in particular with the potential of noncontact micro-indentation for tissues.

Elucidating the temporal dynamics of arbuscular mycorrhizal (AM) fungi is critical for understanding their functions. Furthermore, research investigating the temporal dynamics of AM fungi in response to agricultural practices remains in its infancy. We investigated the effect of nitrogen fertilisation and watering reduction on the temporal dynamics of AM fungi, across the lifespan of wheat. Nitrogen fertilisation decreased AM fungal spore density (SD), extraradical hyphal density (ERHD), and intraradical colonisation rate (IRCR) in both watering conditions. Nitrogen fertilisation affected AM fungal community composition in soil but not in roots, regardless of watering conditions. The temporal analysis revealed that AM fungal ERHD and IRCR were higher under conventional watering and lower under reduced watering in March than in other growth stages at low (≤ 70 kg N ha^-1  yr^-1 ) but not at high (≥ 140) nitrogen fertilisation levels. AM fungal SD was lower in June than in other growth stages and community composition varied with plant development at all nitrogen fertilisation levels, regardless of watering conditions. This study demonstrates that high nitrogen fertilisation levels disrupt the temporal dynamics of AM fungal hyphal growth but not sporulation and community composition.