Protein structure prediction assisted with sparse NMR data in CASP13

CASP13 has investigated the impact of sparse NMR data on the accuracy of protein structure prediction. NOESY and ¹⁵N-¹H residual dipolar coupling data, typical of that obtained for ¹⁵N,¹³C-enriched, perdeuterated proteins up to about 40 kDa, were simulated for 11 CASP13 targets ranging in size from 80 to 326 residues. For several targets, two prediction groups generated models that are more accurate than those produced using baseline methods. Real NMR data collected for a de novo designed protein were also provided to predictors, including one data set in which only backbone resonance assignments were available. Some NMR-assisted prediction groups also did very well with these data. CASP13 also assessed whether incorporation of sparse NMR data improves the accuracy of protein structure prediction relative to nonassisted regular methods. In most cases, incorporation of sparse, noisy NMR data results in models with higher accuracy. The best NMR-assisted models were also compared with the best regular predictions of any CASP13 group for the same target. For six of 13 targets, the most accurate model provided by any NMR-assisted prediction group was more accurate than the most accurate model provided by any regular prediction group; however, for the remaining seven targets, one or more regular prediction method provided a more accurate model than even the best NMR-assisted model. These results suggest a novel approach for protein structure determination, in which advanced prediction methods are first used to generate structural models, and sparse NMR data is then used to validate and/or refine these models.     

Established human papillomavirus type 16-expressing tumors are effectively eradicated following vaccination with long peptides

Peptide-based vaccines aimed at the induction of effective T cell responses against established cancers have so far only met with limited clinical success and clearly need to be improved. In a preclinical model of human papillomavirus (HPV)16-induced cervical cancer we show that prime-boost vaccinations with the HPV16-derived 35 amino-acid long peptide E7(43-77), containing both a CTL epitope and a Th epitope, resulted in the induction of far more robust E7-specific CD8(+) T cell responses than vaccinations with the minimal CTL epitope only. We demonstrate that two distinct mechanisms are responsible for this effect. First, vaccinations with the long peptide lead to the generation of E7-specific CD4(+) Th cells. The level of the induced E7-specific CD8(+) T cell response proved to be dependent on the interactions of these Th cells with professional APC. Second, we demonstrate that vaccination with the long peptide and dendritic cell-activating agents resulted in a superior induction of E7-specific CD8(+) T cells, even when T cell help was excluded. This suggests that, due to its size, the long peptide was preferably endocytosed, processed, and presented by professional APCs. Moreover, the efficacy of this superior HPV-specific T cell induction was demonstrated in therapeutic prime-boost vaccinations in which the long peptide admixed with the dendritic cell-activating adjuvant oligodeoxynucleotide-CpG resulted in the eradication of large, established HPV16-expressing tumors. Because the vaccine types used in this study are easy to prepare under good manufacturing practice conditions and are safe to administer to humans, these data provide important information for future clinical trials.     

关岭及相关生物群沉积与生态环境的探讨

根据近年来对黔东南至滇东关岭、兴义、贞丰和罗平等地中一晚三叠世含海生爬行动物骨架和(或)深水海百合黑色岩系(通常所称黑色页岩)化石库的研究,现将该区岩石地层单位划分.以及这些黑色岩系化石库生物组合特征、时代、分布、沉积和古地理环境概括如下:1)在关岭-兴义地区中-晚三叠世(安尼期、拉丁期和早卡尼期)地层中,至少夹有3层、甚至4层含海生爬行动物的黑色岩系化石库(或黑色"页岩"化石库),自下而上产盘县生物群、兴义生物群和关岭生物群.云南罗平地区中三叠统关岭组中新发现的"罗平生物群"与盘县生物群层位大致相当.贞丰龙场赖石科组上部新挖掘出的30m厚产创口海百合、双壳类及菊石的黑色岩系,应该是研究地区最高层位的海相三叠纪黑色岩系,时代似属晚三叠世早卡尼期晚期;2)推测这些含海生爬行动物骨架的黑色岩系化石库是在印支造山运动影响下,伴随南盘江前陆盆地隆升和闭合,在扬子克拉通台地边缘所形成的一个或几个边缘凹陷、或边缘盆地之中形成的,这些凹陷或盆地形成之初,表层水充氧,且具有很好的食物链结构,有利于各类海生生物生活;后来的海平面上升至最大海泛期,以及由此引起缺氧和含硫化氢水位的上升,导致这些凹陷逐渐变成安静、滞流的死亡之海和黑色岩系化石库;3)关岭生物群产于晚三叠世卡尼期早期小凹组下段上部黑色岩系之中,是一个典型的在滞流、缺氧且海底没有食腐动物边缘局限盆地中所形成的黑色页岩化石库,以产大量海生爬行动物和深水假浮游海百合为特征,此外还有个别的两栖类和原始龟类发现;4)产于竹杆坡组近底部黑色岩系中的兴义生物群,以产大量肿肋龙类为特点,尤以个体较小的贵州龙最为常见,共生的还有多种鱼类化石,在生物组合和产出层位上,可与阿尔卑斯南部Meride灰岩所夹黑色含沥青页岩化石库对比,时代似应归属拉丁期早或中期;大量米虾在竹杆坡组近底部含贵州龙层的发现.推测兴义生物群可能形成于台地边缘早期并不缺氧,且具有理想食物链结构的浅水、超盐的凹陷或盆地之中.由于存在浮游生物-虾-贵州龙-欧龙-虾-浮游生物所组成的生态组合和食物链结构,从而为解释以肿肋龙类为代表的兴义生物群的繁衍和多生提供了依据;接踵而来的沉积速率下降和缺氧水位的上升,以及间歇性火山作用,导致该特有生态体系的崩溃和化石库的形成.根据对贞丰挽澜竹杆坡组底部首次发现的棘皮动物的化石库的研究,指出该化石库系由海星、细小蛇尾、底栖海百合茎、海胆和海参等5类棘皮动物化石和含贵州龙骨架碎片组成,其下为8m厚夹有薄层的骨层的凝缩层沉积,后者位于硬底之上.此种沉积和埋藏模式与德国上壳灰岩早拉丁期的棘皮动物化石库类似,是在近岸海水不太浅的内陆棚的环境下,由于风暴潮作用所形成的化石库,他们与在滞流、缺氧海底、通过化石聚集所形成的化石库是不同的;5)产盘县生物群的黑色岩系化石库主要见于盘县羊件和普安青山中三叠世(安尼期)关岭组中,与云南罗平地区的"罗平生物群"在层位及生物组合上大致相当,均以含大量混鱼龙、幻龙和欧龙.以及鱼类为特点,共生的还有大量节肢动物.所不同的是后者由于靠近滨岸,故而出现大量幼年期的鱼类以及虾类和鲎类化石,推测他们形成于靠近古陆或滨岸的台缘浅水表层充氧的正常、且有时超盐的凹陷之中,时代上早于阿尔卑斯南部安尼期/拉丁期比塞娄组;其集群死亡除因后期盆地滞流、缺氧外,可能还与风暴和火山作用有关.     

Genome Analysis and Physiological Comparison of Alicycliphilus denitrificans Strains BC and K601T

The genomes of the Betaproteobacteria Alicycliphilus denitrificans strains BC and K601^T have been sequenced to get insight into the physiology of the two strains. Strain BC degrades benzene with chlorate as electron acceptor. The cyclohexanol-degrading denitrifying strain K601^T is not able to use chlorate as electron acceptor, while strain BC cannot degrade cyclohexanol. The 16S rRNA sequences of strains BC and K601^T are identical and the fatty acid methyl ester patterns of the strains are similar. Basic Local Alignment Search Tool (BLAST) analysis of predicted open reading frames of both strains showed most hits with Acidovorax sp. JS42, a bacterium that degrades nitro-aromatics. The genomes include strain-specific plasmids (pAlide201 in strain K601^T and pAlide01 and pAlide02 in strain BC). Key genes of chlorate reduction in strain BC were located on a 120 kb megaplasmid (pAlide01), which was absent in strain K601^T. Genes involved in cyclohexanol degradation were only found in strain K601^T. Benzene and toluene are degraded via oxygenase-mediated pathways in both strains. Genes involved in the meta-cleavage pathway of catechol are present in the genomes of both strains. Strain BC also contains all genes of the ortho-cleavage pathway. The large number of mono- and dioxygenase genes in the genomes suggests that the two strains have a broader substrate range than known thus far.     

Methods to quantify soft-tissue based facial growth and treatment outcomes in children: a systematic review

Context

Technological advancements have led craniofacial researchers and clinicians into the era of three-dimensional digital imaging for quantitative evaluation of craniofacial growth and treatment outcomes.

Objective

To give an overview of soft-tissue based methods for quantitative longitudinal assessment of facial dimensions in children until six years of age and to assess the reliability of these methods in studies with good methodological quality.

Data Source

PubMed, EMBASE, Cochrane Library, Web of Science, Scopus and CINAHL were searched. A hand search was performed to check for additional relevant studies.

Study Selection

Primary publications on facial growth and treatment outcomes in children younger than six years of age were included.

Data Extraction

Independent data extraction by two observers. A quality assessment instrument was used to determine the methodological quality. Methods, used in studies with good methodological quality, were assessed for reliability expressed as the magnitude of the measurement error and the correlation coefficient between repeated measurements.

Results

In total, 47 studies were included describing 4 methods: 2D x-ray cephalometry; 2D photography; anthropometry; 3D imaging techniques (surface laser scanning, stereophotogrammetry and cone beam computed tomography). In general the measurement error was below 1 mm and 1° and correlation coefficients range from 0.65 to 1.0.

Conclusion

Various methods have shown to be reliable. However, at present stereophotogrammetry seems to be the best 3D method for quantitative longitudinal assessment of facial dimensions in children until six years of age due to its millisecond fast image capture, archival capabilities, high resolution and no exposure to ionizing radiation.     

Discovery and optimization of aspartate aminotransferase 1 inhibitors to target redox balance in pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a lethal malignancy that is extremely refractory to the therapeutic approaches that have been evaluated to date. Recently, it has been demonstrated that PDAC tumors are dependent upon a metabolic pathway involving aspartate aminotransferase 1, also known as glutamate-oxaloacetate transaminase 1 (GOT1), for the maintenance of redox homeostasis and sustained proliferation. As such, small molecule inhibitors targeting this metabolic pathway may provide a novel therapeutic approach for the treatment of this devastating disease. To this end, from a high throughput screen of ～800,000 molecules, 4-(1H-indol-4-yl)-N-phenylpiperazine-1-carboxamide was identified as an inhibitor of GOT1. Mouse pharmacokinetic studies revealed that potency, rather than inherent metabolic instability, would limit immediate cell- and rodent xenograft-based experiments aimed at validating this potential cancer metabolism-related target. Medicinal chemistry-based optimization resulted in the identification of multiple derivatives with >10-fold improvements in potency, as well as the identification of a tryptamine-based series of GOT1 inhibitors.     

Direct inoculation of simian immunodeficiency virus from sooty mangabeys in black mangabeys (Lophocebus aterrimus): first evidence of AIDS in a heterologous African species and different pathologic outcomes of experimental infection

A unique opportunity for the study of the role of serial passage and cross-species transmission was offered by a series of experiments carried out at the Tulane National Primate Research Center in 1990. To develop an animal model for leprosy, three black mangabeys (BkMs) (Lophocebus aterrimus) were inoculated with lepromatous tissue that had been serially passaged in four sooty mangabeys (SMs) (Cercocebus atys). All three BkMs became infected with simian immunodeficiency virus from SMs (SIVsm) by day 30 postinoculation (p.i.) with lepromatous tissue. One (BkMG140) died 2 years p.i. from causes unrelated to SIV, one (BkMG139) survived for 10 years, whereas the third (BkMG138) was euthanized with AIDS after 5 years. Histopathology revealed a high number of giant cells in tissues from BkMG138, but no SIV-related lesions were found in the remaining two BkMs. Four-color immunofluorescence revealed high levels of SIVsm associated with both giant cells and T lymphocytes in BkMG138 and no detectable SIV in the remaining two. Serum viral load (VL) showed a significant increase (>1 log) during the late stage of the disease in BkMG138, as opposed to a continuous decline in VL in the remaining two BkMs. With the progression to AIDS, neopterin levels increased in BkMG138. This study took on new significance when phylogenetic analysis unexpectedly showed that all four serially inoculated SMs were infected with different SIVsm lineages prior to the beginning of the experiment. Furthermore, the strain infecting the BkMs originated from the last SM in the series. Therefore, the virus infecting BkMs has not been serially passaged. In conclusion, we present the first compelling evidence that direct cross-species transmission of SIV may induce AIDS in heterologous African nonhuman primate (NHP) species. The results showed that cross-species-transmitted SIVsm was well controlled in two of three BkMs for 2 and 10 years, respectively. Finally, this case of AIDS in an African monkey suggests that the dogma of SIV nonpathogenicity in African NHP hosts should be reconsidered.     

Characterization of a deep-sea microbial mat from an active cold seep at the Milano mud volcano in the Eastern Mediterranean Sea

A white, filamentous microbial mat at the Milano mud volcano in the Eastern Mediterranean Sea was sampled during the Medinaut cruise of the R/V Nadir in 1998. The composition of the mat community was characterized using a combination of phylogenetic and lipid biomarker methods. The mat sample was filtered through 0.2 and 5-microm filters to coarsely separate unicellular and filamentous bacteria. Analyses of 16S rRNA gene sequences amplified from the total community DNA from these fractions showed that similar archaeal populations were present in both fractions. However, the bacterial populations in the fractions differed from one another, and were more diverse than the archaeal ones. Lipid analysis showed that bacteria were the dominant members of the mat microbial community and the relatively low delta(13)C carbon isotope values of bulk bacterial lipids suggested the occurrence of methane- and sulfide-based chemo(auto)trophy. Consistent with this, the bacterial populations in the fractions were related to Alpha-, Gamma- and Epsilonproteobacteria, most of which were chemoautotrophic bacteria that utilize hydrogen sulfide (or reduced sulfur compounds) and/or methane. The most common archaeal 16S rRNA gene sequences were related to those of previously identified Archaea capable of anaerobic methane oxidation. Although the filamentous organisms observed in the mat were not conclusively identified, our results indicated that the Eastern Mediterranean deep-sea microbial mat community might be sustained on a combination of methane- and sulfide-driven chemotrophy.