MRFalign: Protein Homology Detection through Alignment of Markov Random Fields

Sequence-based protein homology detection has been extensively studied and so far the most sensitive method is based upon comparison of protein sequence profiles, which are derived from multiple sequence alignment (MSA) of sequence homologs in a protein family. A sequence profile is usually represented as a position-specific scoring matrix (PSSM) or an HMM (Hidden Markov Model) and accordingly PSSM-PSSM or HMM-HMM comparison is used for homolog detection. This paper presents a new homology detection method MRFalign, consisting of three key components: 1) a Markov Random Fields (MRF) representation of a protein family; 2) a scoring function measuring similarity of two MRFs; and 3) an efficient ADMM (Alternating Direction Method of Multipliers) algorithm aligning two MRFs. Compared to HMM that can only model very short-range residue correlation, MRFs can model long-range residue interaction pattern and thus, encode information for the global 3D structure of a protein family. Consequently, MRF-MRF comparison for remote homology detection shall be much more sensitive than HMM-HMM or PSSM-PSSM comparison. Experiments confirm that MRFalign outperforms several popular HMM or PSSM-based methods in terms of both alignment accuracy and remote homology detection and that MRFalign works particularly well for mainly beta proteins. For example, tested on the benchmark SCOP40 (8353 proteins) for homology detection, PSSM-PSSM and HMM-HMM succeed on 48% and 52% of proteins, respectively, at superfamily level, and on 15% and 27% of proteins, respectively, at fold level. In contrast, MRFalign succeeds on 57.3% and 42.5% of proteins at superfamily and fold level, respectively. This study implies that long-range residue interaction patterns are very helpful for sequence-based homology detection. The software is available for download at http://raptorx.uchicago.edu/download/. A summary of this paper appears in the proceedings of the RECOMB 2014 conference, April 2–5.     

Reductive soil disinfestation (RSD) alters gross N transformation rates and reduces NO and N2O emissions in degraded vegetable soils

Background and aims

Continuous vegetable cultivation in greenhouses can easily induce soil degradation, which considerably affects the development of sustainable vegetable production. Recently, the reductive soil disinfestation (RSD) is widely used as an alternative to chemical soil disinfestations to improve degraded greenhouse vegetable soils. Considering the importance of nitrogen (N) for plant growth and environment effect, the internal N transformation processes and rates should be well investigated in degraded vegetable soils treated by RSD, but few works have been undertaken.

Methods

Three RSD-treated and three untreated degraded vegetable soils were chosen and a ¹⁵?N tracing incubation experiment differentially labeled with ¹⁵NH₄NO₃ or NH₄ ¹⁵NO₃ was conducted at 25 °C under 50 % water holding capacity (WHC) for 96 h. Soil gross N transformation rates were calculated using a ¹⁵?N tracing model combined with Markov Chain Monte Carlo Metropolis algorithm (Müller et al. 2007), while the emissions of N₂O and NO were also measured.

Results

RSD could significantly enhance the soil microbial NH₄ ⁺ immobilization rate, the heterotrophic and autotrophic nitrification rates, and the NO₃ ^? turnover time. The ratio of heterotrophic nitrification to total inorganic N supply rate (mineralization + heterotrophic nitrification) increased greatly from 5.4 % in untreated vegetable soil to 56.1 % in treated vegetable soil. In addition, low release potential of NO and N₂O was observed in RSD-treated vegetable soil, due to the decrease in the NO and N₂O product ratios from heterotrophic and autotrophic nitrifications. These significant differences in gross N transformation rates, the supply processes and capacity of inorganic N, and the NO and N₂O emissions between untreated and treated vegetable soils could be explained by the elimination of accumulated NO₃ ^?, increased pH, and decreased electrical conductivity (EC) caused by RSD. Noticeably, the NO₃ ^? consumption rates were still significantly lower than the NO₃ ^? production rates in RSD-treated vegetable soil.

Conclusions

Except for improving soil chemical properties, RSD could significantly alter the supply processes of inorganic N and reduce the release potential of N₂O and NO in RSD-treated degraded vegetable soil. In order to retard the re-occurrence of NO₃ ^? accumulation, acidification and salinization and to promote the long-term productivity of greenhouse vegetable fields, the rational use of N fertilizer should be paid great attention to farmers in vegetable cultivation.     

Applications of Phosphorene and Black Phosphorus in Energy Conversion and Storage Devices

The successful isolation of phosphorene (atomic layer thick black phosphorus) in 2014 has currently aroused the interest of 2D material researchers. In this review, first, the fundamentals of phosphorus allotropes, phosphorene, and black phosphorus, are briefly introduced, along with their structures, properties, and synthesis methods. Second, the readers are presented with an overview of their energy applications. Particularly in electrochemical energy storage, the large interlayer spacing (0.53 nm) in phosphorene allows the intercalation/deintercalation of larger ions as compared to its graphene counterpart. Therefore, phosphorene may possess greater potential for high electrochemical performance. In addition, the status of lithium ion batteries as well as secondary sodium ion batteries is reviewed. Next, each application for energy generation, conversion, and storage is described in detail with milestones as well as the challenges. These emerging applications include supercapacitors, photovoltaic devices, water splitting, photocatalytic hydrogenation, oxygen evolution, and thermoelectric generators. Finally the fast‐growing dynamic field of phosphorene research is summarized and perspectives on future possibilities are presented calling on the efforts of chemists, physicists, and material scientists     

Na+,K+/H+ antiporters regulate the pH of endoplasmic reticulum and auxin‐mediated development

AtNHX5 and AtNHX6 are endosomal Na⁺,K⁺/H⁺ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H⁺ leak, control auxin homeostasis and auxin‐mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin‐related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the endoplasmic reticulum (ER)‐localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were colocalized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H⁺‐leak pathway provides a fine‐tuning mechanism that controls cellular auxin fluxes.     

A comparative study of the ability of recombinant oncolytic adenovirus,doxorubicin and tamoxifen to inhibit the proliferation of breast cancer cells

In this study, we compared the inhibitory effects of recombinant oncolytic adenovirus (Ad‐apoptin‐hTERTp‐E1a, Ad‐VT) with that of doxorubicin (DOX), a first‐line chemotherapy drug, and tamoxifen (TAM), an endocrine therapy drug, on the proliferation of breast cancer cells. We found that Ad‐VT could effectively inhibit the proliferation of breast cancer cells (p < 0.01); the inhibition rate of Ad‐VT on normal mammary epithelial MCF‐10A cells was less than 20%. DOX can effectively inhibit the proliferation of breast cancer cells and also has a strong inhibitory effect on MCF‐10A cells (p < 0.01). TAM also has a strong inhibitory effect on breast cancer cells, among which the oestrogen‐dependent MCF‐7 cell inhibition was stronger (p < 0.01), At higher concentrations, TAM also had a high rate of inhibition (>70%) on the proliferation of MCF‐10A cells. We also found that both recombinant adenovirus and both drugs could successfully induce tumour cell apoptosis. Further Western blot results showed that the recombinant adenovirus killed breast cancer cells through the endogenous apoptotic pathway. Analysis of the nude mouse subcutaneous breast cancer model showed that Ad‐VT significantly inhibited tumour growth (the luminescence rate of cancer cells was reduced by more than 90%) and improved the survival rate of tumour‐bearing mice (p < 0.01). Compared with DOX and TAM, Ad‐VT has a significant inhibitory effect on breast cancer cells, but almost no inhibitory effect on normal breast epithelial cells, and this inhibitory effect is mainly through the endogenous apoptotic pathway. These results indicate that Ad‐VT has significant potential as a drug for the treatment of breast cancer.     

大数据背景下北京市大型居住区通勤绿道选线研究

近年来,随着城市交通拥堵和环境污染等问题的日益凸显,自行车作为通勤出行方式的地位逐渐上升,通勤者对建立不受机动车干扰的、连续的、具备通勤功能的城市绿色道路的需求也在不断增加。绿色道路的线路建设不仅要保障空间可实施性和交通环境质量,还要与居民的通勤出行需求紧密结合,实现绿道使用的综合效益最大化。基于此,研究以北京市回龙观地区为对象,采用与居民出行行为有关的数据,识别郊区居民中短程通勤特征,划定主要通勤范围,探究基于居民真实出行的多源大数据的选线方法,通过基于通勤出行需求强度与吸引强度的绿道节点甄选与路段适宜性的评价分析。最后,通过GIS网络分析功能进行最优线路选择,并结合城市公园、绿地、河流等资源的分布情况进行修正,形成一条满足居民通勤需求的、完整互联的、安全的且具备较强实施性的绿色通道。最终达到降低居民通勤时耗、提升区域可达性、完善城市慢行系统网络的目的。     

Inferring phenotypes from substance use via collaborative matrix completion

Background

Although substance use disorders (SUDs) are heritable, few genetic risk factors for them have been identified, in part due to the small sample sizes of study populations. To address this limitation, researchers have aggregated subjects from multiple existing genetic studies, but these subjects can have missing phenotypic information, including diagnostic criteria for certain substances that were not originally a focus of study. Recent advances in addiction neurobiology have shown that comorbid SUDs (e.g., the abuse of multiple substances) have similar genetic determinants, which makes it possible to infer missing SUD diagnostic criteria using criteria from another SUD and patient genotypes through statistical modeling.

Results

We propose a new approach based on matrix completion techniques to integrate features of comorbid health conditions and individual’s genotypes to infer unreported diagnostic criteria for a disorder. This approach optimizes a bi-linear model that uses the interactions between known disease correlations and candidate genes to impute missing criteria. An efficient stochastic and parallel algorithm was developed to optimize the model with a speed 20 times greater than the classic sequential algorithm. It was tested on 3441 subjects who had both cocaine and opioid use disorders and successfully inferred missing diagnostic criteria with consistently better accuracy than other recent statistical methods.

Conclusions

The proposed matrix completion imputation method is a promising tool to impute unreported or unobserved symptoms or criteria for disease diagnosis. Integrating data at multiple scales or from heterogeneous sources may help improve the accuracy of phenotype imputation.

     

Parent-of-Origin Effects of the APOB Gene on Adiposity in Young Adults

Loci identified in genome-wide association studies (GWAS) of cardio-metabolic traits account for a small proportion of the traits'' heritability. To date, most association studies have not considered parent-of-origin effects (POEs). Here we report investigation of POEs on adiposity and glycemic traits in young adults. The Jerusalem Perinatal Family Follow-Up Study (JPS), comprising 1250 young adults and their mothers was used for discovery. Focusing on 18 genes identified by previous GWAS as associated with cardio-metabolic traits, we used linear regression to examine the associations of maternally- and paternally-derived offspring minor alleles with body mass index (BMI), waist circumference (WC), fasting glucose and insulin. We replicated and meta-analyzed JPS findings in individuals of European ancestry aged ≤50 belonging to pedigrees from the Framingham Heart Study, Family Heart Study and Erasmus Rucphen Family study (total N≅4800). We considered p<2.7x10^-4 statistically significant to account for multiple testing. We identified a common coding variant in the 4^th exon of APOB (rs1367117) with a significant maternally-derived effect on BMI (β = 0.8; 95%CI:0.4,1.1; p = 3.1x10^-5) and WC (β = 2.7; 95%CI:1.7,3.7; p = 2.1x10^-7). The corresponding paternally-derived effects were non-significant (p>0.6). Suggestive maternally-derived associations of rs1367117 were observed with fasting glucose (β = 0.9; 95%CI:0.3,1.5; p = 4.0x10^-3) and insulin (ln-transformed, β = 0.06; 95%CI:0.03,0.1; p = 7.4x10^-4). Bioinformatic annotation for rs1367117 revealed a variety of regulatory functions in this region in liver and adipose tissues and a 50% methylation pattern in liver only, consistent with allelic-specific methylation, which may indicate tissue-specific POE. Our findings demonstrate a maternal-specific association between a common APOB variant and adiposity, an association that was not previously detected in GWAS. These results provide evidence for the role of regulatory mechanisms, POEs specifically, in adiposity. In addition this study highlights the benefit of utilizing family studies for deciphering the genetic architecture of complex traits.     

The calcineurin B subunit (CnB) is a new ligand of integrin αM that mediates CnB-induced Apo2L/TRAIL expression in macrophages

We showed previously that the calcineurin B subunit (CnB) plays an important role in activation of peritoneal macrophage, but the underlying mechanism remained unknown. To examine whether there is a CnB receptor on peritoneal macrophages, we performed the radioligand binding assay of receptors. The receptor saturation binding curve demonstrated high-affinity and specific binding; the maximum binding was 1090 fmol/10(5) cells, and the K(d) was 70.59 pM. Then, we used a CnB affinity resin to trap potential receptors from highly purified peritoneal macrophage membranes. Mass spectrometry analysis showed that the binding protein was mouse integrin αM. We next performed a competition binding experiment to confirm the binding of CnB to integrin αM. This showed that FITC-CnB bound specifically to peritoneal macrophages and that binding was blocked by the addition of integrin αM Ab. We observed that CnB could induce TRAIL gene expression in peritoneal macrophages in vitro and in vivo. Integrin αM Ab blocking, RNA interference, and ligand competition experiments demonstrated that CnB-induced TRAIL expression is dependent on integrin αM. Furthermore, the tumoricidal activity of CnB-activated peritoneal macrophages is partially dependent on TRAIL. In addition, CnB treatment significantly prolongs the survival of mice bearing H22 ascites tumors, which has a positive correlation with the induction level of TRAIL. These results reveal a novel function of the CnB in innate immunity and cancer surveillance. They also point to a new signaling pathway leading to induction of TRAIL and suggest a possible application of CnB in cancer therapy.