Transcriptome analysis reveals the time of the fourth round of genome duplication in common carp (Cyprinus carpio)

<p>Abstract</p> <p>Background</p> <p>Common carp (<it>Cyprinus carpio</it>) is thought to have undergone one extra round of genome duplication compared to zebrafish. Transcriptome analysis has been used to study the existence and timing of genome duplication in species for which genome sequences are incomplete. Large-scale transcriptome data for the common carp genome should help reveal the timing of the additional duplication event.</p> <p>Results</p> <p>We have sequenced the transcriptome of common carp using 454 pyrosequencing. After assembling the 454 contigs and the published common carp sequences together, we obtained 49,669 contigs and identified genes using homology searches and an ab initio method. We identified 4,651 orthologous pairs between common carp and zebrafish and found 129,984 paralogous pairs within the common carp. An estimation of the synonymous substitution rate in the orthologous pairs indicated that common carp and zebrafish diverged 120 million years ago (MYA). We identified one round of genome duplication in common carp and estimated that it had occurred 5.6 to 11.3 MYA. In zebrafish, no genome duplication event after speciation was observed, suggesting that, compared to zebrafish, common carp had undergone an additional genome duplication event. We annotated the common carp contigs with Gene Ontology terms and KEGG pathways. Compared with zebrafish gene annotations, we found that a set of biological processes and pathways were enriched in common carp.</p> <p>Conclusions</p> <p>The assembled contigs helped us to estimate the time of the fourth-round of genome duplication in common carp. The resource that we have built as part of this study will help advance functional genomics and genome annotation studies in the future.</p

Efficient Serverless Function Scheduling at the Network Edge

Serverless computing is a promising approach for edge computing since its inherent features, e.g., lightweight virtualization, rapid scalability, and economic efficiency. However, previous studies have not studied well the issues of significant cold start latency and highly dynamic workloads in serverless function scheduling, which are exacerbated at the resource-limited network edge. In this paper, we formulate the Serverless Function Scheduling (SFS) problem for resource-limited edge computing, aiming to minimize the average response time. To efficiently solve this intractable scheduling problem, we first consider a simplified offline form of the problem and design a polynomial-time optimal scheduling algorithm based on each function's weight. Furthermore, we propose an Enhanced Shortest Function First (ESFF) algorithm, in which the function weight represents the scheduling urgency. To avoid frequent cold starts, ESFF selectively decides the initialization of new function instances when receiving requests. To deal with dynamic workloads, ESFF judiciously replaces serverless functions based on the function weight at the completion time of requests. Extensive simulations based on real-world serverless request traces are conducted, and the results show that ESFF consistently and substantially outperforms existing baselines under different settings

BOAT: Basic Oligonucleotide Alignment Tool

<p>Abstract</p> <p>Background</p> <p>Next-generation DNA sequencing technologies generate tens of millions of sequencing reads in one run. These technologies are now widely used in biology research such as in genome-wide identification of polymorphisms, transcription factor binding sites, methylation states, and transcript expression profiles. Mapping the sequencing reads to reference genomes efficiently and effectively is one of the most critical analysis tasks. Although several tools have been developed, their performance suffers when both multiple substitutions and insertions/deletions (indels) occur together.</p> <p>Results</p> <p>We report a new algorithm, Basic Oligonucleotide Alignment Tool (BOAT) that can accurately and efficiently map sequencing reads back to the reference genome. BOAT can handle several substitutions and indels simultaneously, a useful feature for identifying SNPs and other genomic structural variations in functional genomic studies. For better handling of low-quality reads, BOAT supports a "3'-end Trimming Mode" to build local optimized alignment for sequencing reads, further improving sensitivity. BOAT calculates an E-value for each hit as a quality assessment and provides customizable post-mapping filters for further mapping quality control.</p> <p>Conclusion</p> <p>Evaluations on both real and simulation datasets suggest that BOAT is capable of mapping large volumes of short reads to reference sequences with better sensitivity and lower memory requirement than other currently existing algorithms. The source code and pre-compiled binary packages of BOAT are publicly available for download at <url>http://boat.cbi.pku.edu.cn</url> under GNU Public License (GPL). BOAT can be a useful new tool for functional genomics studies.</p

Intravenous Busulfan-Cyclophosphamide as a Preparative Regimen Before Allogeneic Hematopoietic Stem Cell Transplantation for Adult Patients with Acute Lymphoblastic Leukemia

The use of i.v. busulfan (BU) instead of the oral formulation can improve outcomes in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) by reducing toxicity and transplantation-related mortality (TRM). There are limited reports of i.v. BU used to treat patients with acute lymphoblastic leukemia (ALL). The present study was performed to evaluate the efficacy and toxicity of i.v. BU/cyclophosphamide (CY) conditioning in adult ALL. We retrospectively analyzed 42 consecutive patients who underwent allo-HSCT with BU/CY conditioning between January 2007 and October 2010 with an HLA-matched donor (sibling, n = 18; unrelated, n = 24). Thirty-three patients were in first complete remission (CR1), 2 were in second complete remission (CR2), and 7 were in a more advanced stage. Median patient age was 28 years (range, 17∼55 years). The median follow-up was 15 months (range, 1∼48 months). Overall, 13 patients died, for a 30-month overall survival of 56.5% ± 10.6% (65.7% ± 12.5% for patients in CR1 vs 25.4% ± 15.5% for those in CR2 or beyond; P < .001). Eleven patients experienced relapse between 2 and 26 months after allo-HSCT, with a 30-month relapse rate (RR) of 40% ± 10.9% (32.0% ± 12.7% for patients in CR1 vs 71.4% ± 17.1% for those in CR2 or beyond; P = .001). The incidence of grade II-IV acute graft-versus-host disease (GVHD) was 39.2% ± 8.8%, and that of grade III-IV acute GVHD was 7.4% ± 4.1%. The incidence of chronic GVHD was 63.9% ± 11.7%, and that of extensive chronic GVHD was 19.3% ± 7.9%. Only 2 cases of clinically diagnosed veno-occlusive disease (VOD) were documented (4.7%), and 1 of these patients died of severe VOD. Other BU/CY conditioning–associated toxicities were diffuse alveolar hemorrhage in 1 patient and hemorrhagic cystitis in 8 patients. Four patients died due to TRM, for a 30-month TRM of 9.7% ± 4.6%. This study demonstrates that i.v. BU/CY can be considered a feasible conditioning regimen for adult ALL, with low incidences of VOD and TRM

Tulp1 deficiency causes early-onset retinal degeneration through affecting ciliogenesis and activating ferroptosis in zebrafish

Mutations in TUB-like protein 1 (TULP1) are associated with severe early-onset retinal degeneration in humans. However, the pathogenesis remains largely unknown. There are two homologous genes of TULP1 in zebrafish, namely tulp1a and tulp1b. Here, we generated the single knockout (tulp1a(−/−) and tulp1b(−/−)) and double knockout (tulp1-dKO) models in zebrafish. Knockout of tulp1a resulted in the mislocalization of UV cone opsins and the degeneration of UV cones specifically, while knockout of tulp1b resulted in mislocalization of rod opsins and rod-cone degeneration. In the tulp1-dKO zebrafish, mislocalization of opsins was present in all types of photoreceptors, and severe degeneration was observed at a very early age, mimicking the clinical manifestations of TULP1 patients. Photoreceptor cilium length was significantly reduced in the tulp1-dKO retinas. RNA-seq analysis showed that the expression of tektin2 (tekt2), a ciliary and flagellar microtubule structural component, was downregulated in the tulp1-dKO zebrafish. Dual-luciferase reporter assay suggested that Tulp1a and Tulp1b transcriptionally activate the promoter of tekt2. In addition, ferroptosis might be activated in the tulp1-dKO zebrafish, as suggested by the up-regulation of genes related to the ferroptosis pathway, the shrinkage of mitochondria, reduction or disappearance of mitochondria cristae, and the iron and lipid droplet deposition in the retina of tulp1-dKO zebrafish. In conclusion, our study establishes an appropriate zebrafish model for TULP1-associated retinal degeneration and proposes that loss of TULP1 causes defects in cilia structure and opsin trafficking through the downregulation of tekt2, which further increases the death of photoreceptors via ferroptosis. These findings offer insight into the pathogenesis and clinical treatment of early-onset retinal degeneration

The splicing factor DHX38 enables retinal development through safeguarding genome integrity

DEAH-Box Helicase 38 (DHX38) is a pre-mRNA splicing factor and also a disease-causing gene of autosomal recessive retinitis pigmentosa (arRP). The role of DHX38 in the development and maintenance of the retina remains largely unknown. In this study, by using the dhx38 knockout zebrafish model, wedemonstrated that Dhx38 deficiency causes severe differentiation defects and apoptosis of retinal progenitor cells (RPCs) through disrupted mitosis and increased DNA damage. Furthermore, we found a significant accumulation of R-loops in the dhx38-deficient RPCs and human cell lines. Finally, we found that DNA replication stress is the prerequisite for R-loop-induced DNA damage in the DHX38 knockdown cells. Taken together, our study demonstrates a necessary role of DHX38 in the development of retina and reveals a DHX38/R-loop/replication stress/DNA damage regulatory axis that is relatively independent of the known functions of DHX38 in mitosis control

Natural disasters, economic growth and sustainable development in China: an empirical study using provincial panel data

Using a newly developed integrated indicator system with entropy weighting, we analyzed the panel data of 577 recorded disasters in 30 provinces of China from 1985–2011 to identify their links with the subsequent economic growth. Meteorological disasters promote economic growth through human capital instead of physical capital. Geological disasters did not trigger local economic growth from 1999–2011. Generally, natural disasters overall had no significant impact on economic growth from 1985–1998. Thus, human capital reinvestment should be the aim in managing recoveries, and it should be used to regenerate the local economy based on long-term sustainable development

Atmospheric Mercury Outflow from China and Interprovincial Trade.

Mercury (Hg) is characterized by its ability to migrate between continents and its adverse effects on human health, arousing great concern around the world. The transboundary transport of large anthropogenic Hg emissions from China has attracted particular attention, especially from neighboring countries. Here, we combine an atmospheric transport model, a mass budget analysis, and a multiregional input-output model to simulate the atmospheric Hg outflow from China and investigate the impacts of Chinese interprovincial trade on the outflow. The results show outflows of 423.0 Mg of anthropogenic Hg, consisting of 65.9% of the total Chinese anthropogenic emissions, from China in 2010. Chinese interprovincial trade promotes the transfer of atmospheric outflow from the eastern terrestrial boundary (-6.4 Mg year-1) to the western terrestrial boundary (+4.5 Mg year-1) and a net decrease in the atmospheric outflow for the whole boundary, reducing the chance of risks to foreign countries derived from transboundary Hg pollution from China. These impacts of interprovincial trade will be amplified due to the expected strengthened interprovincial trade in the future. The synergistic promotional effects of interprovincial trade versus Hg controls should be considered to reduce the transboundary Hg pollution from China

Gaussian Boson Sampling with Pseudo-Photon-Number Resolving Detectors and Quantum Computational Advantage

We report new Gaussian boson sampling experiments with pseudo-photon-number-resolving detection, which register up to 255 photon-click events. We consider partial photon distinguishability and develop a more complete model for characterization of the noisy Gaussian boson sampling. In the quantum computational advantage regime, we use Bayesian tests and correlation function analysis to validate the samples against all current classical mockups. Estimating with the best classical algorithms to date, generating a single ideal sample from the same distribution on the supercomputer Frontier would take ~ 600 years using exact methods, whereas our quantum computer, Jiuzhang 3.0, takes only 1.27 us to produce a sample. Generating the hardest sample from the experiment using an exact algorithm would take Frontier ~ 3.1*10^10 years.Comment: submitted on 10 Apri

Gaussian Boson Sampling with Pseudo-Photon-Number-Resolving Detectors and Quantum Computational Advantage

We report new Gaussian boson sampling experiments with pseudo-photon-number-resolving detection, which register up to 255 photon-click events. We consider partial photon distinguishability and develop a more complete model for the characterization of the noisy Gaussian boson sampling. In the quantum computational advantage regime, we use Bayesian tests and correlation function analysis to validate the samples against all current classical spoofing mockups. Estimating with the best classical algorithms to date, generating a single ideal sample from the same distribution on the supercomputer Frontier would take ∼600 yr using exact methods, whereas our quantum computer, Jizhāng 3.0, takes only 1.27 μs to produce a sample. Generating the hardest sample from the experiment using an exact algorithm would take Frontier∼3.1×1010 yr.</p