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Tóm tắt Đặt vấn đề Sự tiến hóa giữa các đợt đại dịch của protein hemagglutinin (HA) virus cúm A thường được coi là một hình mẫu cho sự thay đổi tiến hóa nhanh chóng dưới áp lực chọn lọc tích cực, trong đó các thay thế acid amin được cố định nhờ tác động của chúng lên tính kháng nguyên, giúp virus né tránh sự giám sát của hệ miễn dịch. Kết quả Chúng tôi đã thực hiện phân tích phát sinh chủng loại của các mẫu HA lớn và tương đối không thiên lệch được thu thập từ các mẫu virus cúm A H3N2 và H1N1 trong giai đoạn 1995–2005. Không ngờ rằng sự tiến hóa của HA H3N2 bao gồm những khoảng thời gian dài của sự tiến hóa chuỗi trung tính mà không có sự thay đổi kháng nguyên rõ ràng ("giai đoạn stasis") được đặc trưng bởi sự vượt trội của các thay thế đồng nghĩa so với các thay thế không đồng nghĩa tại mỗi vị trí, sự thiếu mối liên hệ giữa các thay thế acid amin với các vùng kháng nguyên, và sự tuyệt chủng chậm của các dòng virus đồng thời. Những khoảng thời gian stasis dài này được phân đoạn bởi những khoảng thời gian ngắn của sự tiến hóa nhanh chóng dưới áp lực chọn lọc tích cực, trong đó các dòng thống trị mới nhanh chóng thay thế những dòng đã tồn tại trước đó. Tính vượt trội của chọn lọc tích cực trong các khoảng thời gian tiến hóa nhanh được hỗ trợ bởi sự vượt trội rõ rệt của các thay thế acid amin trong các vùng kháng nguyên của HA so với các thay thế trong phần còn lại của phân tử HA. Ngược lại, các khoảng thời gian stasis cho thấy sự phân bố thay thế đồng nhất hơn nhiều trên toàn bộ phân tử HA, với sự khác biệt có ý nghĩa thống kê về tỷ lệ thay thế đồng nghĩa so với không đồng nghĩa trong các vùng kháng nguyên giữa hai chế độ tiến hóa. Một số thay thế acid amin song song - cùng một loại thay thế acid amin xảy ra độc lập ở các dòng khác nhau - cũng đã được phát hiện trong HA H3N2. Những đột biến song song này chủ yếu liên quan đến các khoảng thời gian thay đổi khả năng sống sót nhanh chóng, cho thấy có những giới hạn lớn đối với các con đường tiến hóa trong suốt sự thay đổi kháng nguyên. Phát hiện rằng stasis là hình thức chiếm ưu thế trong sự tiến hóa của H3N2 cho thấy rằng những thay đổi kháng nguyên dẫn đến sự tăng cường khả năng sống sót thường xuất phát từ các tương tác ép tích cực giữa một số thay thế acid amin trong HA và, có thể, các protein virus khác. Các chủng trở nên thống trị nhờ vào việc tăng cường khả năng sống sót xuất hiện từ các chủng có tần suất thấp, nhờ thay thế acid amin cuối cùng hoàn thiện tập hợp thay thế cần thiết để tạo ra một thay đổi kháng nguyên có ý nghĩa; không có tập hợp thay thế nào dẫn đến một thay đổi kháng nguyên có ý nghĩa sinh học và sự gia tăng khả năng sống sót tương ứng. Ngược lại với H3N2, không phát hiện thấy các khoảng thời gian rõ ràng của sự tiến hóa dưới áp lực chọn lọc tích cực đối với HA H1N1 trong cùng khoảng thời gian. Do đó, sự nổi lên của H1N1 trong một số mùa là, rất có thể, do sự giảm thiểu khả năng sống sót tương đối của các dòng H3N2 trước đó khi phần trăm chủ thể dễ bị nhiễm giảm trong các khoảng thời gian stasis.

Over the past decade, flow cytometric CFSE-labeling experiments have gained considerable popularity among experimentalists, especially immunologists and hematologists, for studying the processes of cell proliferation and cell death. Several mathematical models have been presented in the literature to describe cell kinetics during these experiments. We propose a multi-type age-dependent branching process to model the temporal development of populations of cells subject to division and death during CFSE-labeling experiments. We discuss practical implementation of the proposed model; we investigate a competing risk version of the process; and we identify the classes of cellular dependencies that may influence the expectation of the process and those that do not. An application is presented where we study the proliferation of human CD8+ T lymphocytes using our model and a competing risk branching process. The proposed model offers a widely applicable approach to the analysis of CFSE-labeling experiments. The model fitted very well our experimental data. It provided reasonable estimates of cell kinetics parameters as well as meaningful insights into the processes of cell division and cell death. In contrast, the competing risk branching process could not describe the kinetics of CD8+ T cells. This suggested that the decision of cell division or cell death may be made early in the cell cycle if not in preceding generations. Also, we show that analyses based on the proposed model are robust with respect to cross-sectional dependencies and to dependencies between fates of linearly filiated cells. This article was reviewed by Marek Kimmel, Wai-Yuan Tan and Peter Olofsson.

A dramatic increase in the prevalence of autism and Autistic Spectrum Disorders (ASD) has been observed over the last two decades in USA, Europe and Asia. Given the accumulating data on the possible role of translation in the etiology of ASD, we analyzed potential effects of rare synonymous substitutions associated with ASD on mRNA stability, splicing enhancers and silencers, and codon usage. We hypothesize that subtle impairment of translation, resulting in dosage imbalance of neuron-specific proteins, contributes to the etiology of ASD synergistically with environmental neurotoxins. A statistically significant shift from optimal to suboptimal codons caused by rare synonymous substitutions associated with ASD was detected whereas no effect on other analyzed characteristics of transcripts was identified. This result suggests that the impact of rare codons on the translation of genes involved in neuron development, even if slight in magnitude, could contribute to the pathogenesis of ASD in the presence of an aggressive chemical background. This hypothesis could be tested by further analysis of ASD-associated mutations, direct biochemical characterization of their effects, and assessment of in vivo effects on animal models. It seems likely that the synergistic action of environmental hazards with genetic variations that in themselves have limited or no deleterious effects but are potentiated by the environmental factors is a general principle that underlies the alarming increase in the ASD prevalence. This article was reviewed by Andrey Rzhetsky, Neil R. Smalheiser, and Shamil R. Sunyaev.

Ischemic stroke is a sudden and acute disease characterized by neuronal death, increment of reactive gliosis (reactive microglia and astrocytes), and a severe inflammatory process. Neuroinflammation is an early event after cerebral ischemia, with microglia playing a leading role. Reactive microglia involve functional and morphological changes that drive a wide variety of phenotypes. In this context, deciphering the molecular mechanisms underlying such reactive microglial is essential to devise strategies to protect neurons and maintain certain brain functions affected by early neuroinflammation after ischemia. Here, we studied the role of mammalian target of rapamycin (mTOR) activity in the microglial response using a murine model of cerebral ischemia in the acute phase. We also determined the therapeutic relevance of the pharmacological administration of rapamycin, a mTOR inhibitor, before and after ischemic injury. Our data show that rapamycin, administered before or after brain ischemia induction, reduced the volume of brain damage and neuronal loss by attenuating the microglial response. Therefore, our findings indicate that the pharmacological inhibition of mTORC1 in the acute phase of ischemia may provide an alternative strategy to reduce neuronal damage through attenuation of the associated neuroinflammation.

CpG dinucleotides are extensively underrepresented in mammalian genomes. It is widely accepted that genome-wide CpG depletion is predominantly caused by an elevated CpG > TpG mutation rate due to frequent cytosine methylation in the CpG context. Meanwhile the CpG content in genomic regions called CpG islands (CGIs) is noticeably higher. This observation is usually explained by lower CpG > TpG substitution rates within CGIs due to reduced cytosine methylation levels. By combining genome-wide data on substitutions and methylation levels in several human cell types we have shown that cytosine methylation in human sperm cells was strongly and consistently associated with increased CpG > TpG substitution rates. In contrast, this correlation was not observed for embryonic stem cells or fibroblasts. Surprisingly, the decreased sperm CpG methylation level was insufficient to explain the reduced CpG > TpG substitution rates in CGIs. While cytosine methylation in human sperm cells is strongly associated with increased CpG > TpG substitution rates, substitution rates are significantly reduced within CGIs even after sperm CpG methylation levels and local GC content are controlled for. Our findings are consistent with strong negative selection preserving methylated CpGs within CGIs including intergenic ones. Reviewed by: Vladimir Kuznetsov, Shamil Sunyaev, Alexey Kondrashov

Acute lung injury (ALI) is a major cause of respiratory failure in critically ill patients that results in significant morbidity and mortality. Recent studies indicate that cell-based therapies may be beneficial in the treatment of ALI. We recently demonstrated that Nrf2-overexpressing human amniotic mesenchymal stem cells (hAMSCs) reduce lung injury, fibrosis and inflammation in lipopolysaccharide (LPS)-challenged mice. Here we tested whether small extracellular vesicles (sEVs) derived from Nrf2-overexpressing hAMSCs (Nrf2-sEVs) could protect against ALI. sEVs were isolated from hAMSCs that overexpressed (Nrf2-sEVs) or silenced (siNrf2-sEVs) Nrf2. We examined the effects of sEVs treatment on lung inflammation in a mouse model of ALI, where LPS was administered intratracheally to mice, and lung tissues and bronchoalveolar lavage fluid (BALF) were analyzed 24 h later. Histological analysis, immunofluorescence microscopy, western blotting, RT-PCR and ELISA were used to measure the inflammatory response in the lungs and BALF. We found that sEVs from hAMSCs are protective in ALI and that Nrf2 overexpression promotes protection against lung disease. Nrf2-sEVs significantly reduced lung injury in LPS-challenged mice, which was associated with decreased apoptosis, reduced infiltration of neutrophils and macrophages, and inhibition of pro-inflammatory cytokine expression. We further show that Nrf2-sEVs act by inhibiting the activation of the NLRP3 inflammasome and promoting the polarization of M2 macrophages. Our data show that overexpression of Nrf2 protects against LPS-induced lung injury, and indicate that a novel therapeutic strategy using Nrf2-sEVs may be beneficial against ALI.

Long-term consumption of an excessive fat and sucrose diet (Western diet, WD) has been considered a risk factor for metabolic syndrome (MS) and cardiovascular disease. Caveolae and caveolin-1 (CAV-1) proteins are involved in lipid transport and metabolism. However, studies investigating CAV-1 expression, cardiac remodeling, and dysfunction caused by MS, are limited. This study aimed to investigate the correlation between the expression of CAV-1 and abnormal lipid accumulation in the endothelium and myocardium in WD-induced MS, and the occurrence of myocardial microvascular endothelial cell dysfunction, myocardial mitochondrial remodeling, and damage effects on cardiac remodeling and cardiac function. We employed a long-term (7 months) WD feeding mouse model to measure the effect of MS on caveolae/vesiculo-vacuolar organelle (VVO) formation, lipid deposition, and endothelial cell dysfunction in cardiac microvascular using a transmission electron microscopy (TEM) assay. CAV-1 and endothelial nitric oxide synthase (eNOS) expression and interaction were evaluated using real-time polymerase chain reaction, Western blot, and immunostaining. Cardiac mitochondrial shape transition and damage, mitochondria-associated endoplasmic reticulum membrane (MAM) disruption, cardiac function change, caspase-mediated apoptosis pathway activation, and cardiac remodeling were examined using TEM, echocardiography, immunohistochemistry, and Western blot assay. Our study demonstrated that long-term WD feeding caused obesity and MS in mice. In mice, MS increased caveolae and VVO formation in the microvascular system and enhanced CAV-1 and lipid droplet binding affinity. In addition, MS caused a significant decrease in eNOS expression, vascular endothelial cadherin, and β-catenin interactions in cardiac microvascular endothelial cells, accompanied by impaired vascular integrity. MS-induced endothelial dysfunction caused massive lipid accumulation in the cardiomyocytes, leading to MAM disruption, mitochondrial shape transition, and damage. MS promoted brain natriuretic peptide expression and activated the caspase-dependent apoptosis pathway, leading to cardiac dysfunction in mice. MS resulted in cardiac dysfunction, remodeling by regulating caveolae and CAV-1 expression, and endothelial dysfunction. Lipid accumulation and lipotoxicity caused MAM disruption and mitochondrial remodeling in cardiomyocytes, leading to cardiomyocyte apoptosis and cardiac dysfunction and remodeling.

Through the course of their evolution, viruses with large genomes have acquired numerous host genes, most of which perform function in virus reproduction in a manner that is related to their original activities in the cells, but some are exapted for new roles. Here we report the unexpected finding that protein F12, which is conserved among the chordopoxviruses and is implicated in the morphogenesis of enveloped intracellular virions, is a derived DNA polymerase, possibly of bacteriophage origin, in which the polymerase domain and probably the exonuclease domain have been inactivated. Thus, F12 appears to present a rare example of a drastic, exaptive functional change in virus evolution. Reviewers: This article was reviewed by Frank Eisenhaber and Juergen Brosius. For complete reviews, go the Reviewers’ Reports section.