Predicting mutant outcome by combining deep mutational scanning and machine learning

Deep mutational scanning provides unprecedented wealth of quantitative data regarding the functional outcome of mutations in proteins. A single experiment may measure properties (eg, structural stability) of numerous protein variants. Leveraging the experimental data to gain insights about unexplored regions of the mutational landscape is a major computational challenge. Such insights may facilitate further experimental work and accelerate the development of novel protein variants with beneficial therapeutic or industrially relevant properties. Here we present a novel, machine learning approach for the prediction of functional mutation outcome in the context of deep mutational screens. Using sequence (one-hot) features of variants with known properties, as well as structural features derived from models thereof, we train predictive statistical models to estimate the unknown properties of other variants. The utility of the new computational scheme is demonstrated using five sets of mutational scanning data, denoted “targets”: (a) protease specificity of APPI (amyloid precursor protein inhibitor) variants; (b-d) three stability related properties of IGBPG (immunoglobulin G-binding β1 domain of streptococcal protein G) variants; and (e) fluorescence of GFP (green fluorescent protein) variants. Performance is measured by the overall correlation of the predicted and observed properties, and enrichment—the ability to predict the most potent variants and presumably guide further experiments. Despite the diversity of the targets the statistical models can generalize variant examples thereof and predict the properties of test variants with both single and multiple mutations.     

Reproductive biology of the horned viper,Cerastes cerastes gasperettii in the central region of Saudi Arabia

The reproductive biology of the horned viper, Cerastes cerastes gasperettii, in Riyadh region of Saudi Arabia was investigated over a period of one year. Study of reproductive cycle of male and female C. c. gasperettii revealed that the breeding season is relatively short (April and May). Thereafter females laid eggs by mid of July and hatching probably had taken place by the end of September. No activity was observed during winter, this may indicate just a single clutch per year. Relative testis weight to body weight was drastically increased (X¯ = 0.88%) during the peak of reproductive activity (May) where maximal expansion of seminiferous tubules was also attained during April and May (X¯ = 209 μm and 191 μm, respectively). Likewise, the ovarian activity was the highest during May where ovarian parameters were greater in terms of relative ovarian weight to body weight and ova diameter being 0.46% and 2.29 mm, respectively. Fat body weight was increased drastically just before the peak of reproductive activity then started to decline during June. It could be concluded that the harsh desert conditions and similar environments certainly affect reproductive activity of Saudi Arabian reptiles including snakes.     

The importance of reproductive interference in ecology and evolution: from organisms to communities

Knowledge of species interactions is vital to understand ecological and evolutionary patterns in nature. Traditional species interactions (e.g., competition, predation, symbiosis) have received a great deal of deserved attention and their general importance in shaping the evolution of populations and structure of communities is unquestioned. Recently, reproductive interference has been receiving attention as an important species interaction. Reproductive interference is defined as interspecific reproductive activities that decrease the fitness of at least one of the species involved in the interaction. Reproductive interference has the potential to affect the evolutionary trajectories of populations and structure of communities. Here, I comment on seven papers that make up this special feature on reproductive interference. Along the way I highlight key discoveries of these studies and areas of research that may contribute to our understanding of the causes and consequences of reproductive interference.     

Functional morphology of the male caudal appendages of the damselfly Ischnura elegans (Zygoptera: Coenagrionidae)

Odonata are usually regarded as one of the most ancient extant lineages of winged insects. Their copulatory apparatus and mating behavior are unique among insects. Male damselflies use their caudal appendages to clasp the female's prothorax during both copulation and egg-laying and have a secondary copulatory apparatus for sperm transfer. Knowledge of the functional morphology of the male caudal appendages is the basis for understanding the evolution of these structures in Odonata and respective organs in other insects. However, it is still not exactly known how the zygopteran claspers work. In this study, we applied micro-computed tomography and a variety of microscopy techniques to examine the morphology, surface microstructure, cuticle material composition and muscle topography of the male caudal appendages of Ischnura elegans. The results indicate that the closing of the paraproctal claspers is mainly passive. This indirect closing mechanism is very likely supported by high proportions of the elastic protein resilin present in the cuticle of the paraproctal bases. In addition, the prothoracic morphology of the female plays an important role in the indirect closing of the male claspers. Our data indicate that both structures – the male claspers and the female prothoracic hump – function together like a snap-fastener.     

DisCons: a novel tool to quantify and classify evolutionary conservation of intrinsic protein disorder

Background

Analyzing the amino acid sequence of an intrinsically disordered protein (IDP) in an evolutionary context can yield novel insights on the functional role of disordered regions and sequence element(s). However, in the case of many IDPs, the lack of evolutionary conservation of the primary sequence can hamper the study of functionality, because the conservation of their disorder profile and ensuing function(s) may not appear in a traditional analysis of the evolutionary history of the protein.

Results

Here we present DisCons (Disorder Conservation), a novel pipelined tool that combines the quantification of sequence- and disorder conservation to classify disordered residue positions. According to this scheme, the most interesting categories (for functional purposes) are constrained disordered residues and flexible disordered residues. The former residues show conservation of both the sequence and the property of disorder and are associated mainly with specific binding functionalities (e.g., short, linear motifs, SLiMs), whereas the latter class correspond to segments where disorder as a feature is important for function as opposed to the identity of the underlying sequence (e.g., entropic chains and linkers). DisCons therefore helps with elucidating the function(s) arising from the disordered state by analyzing individual proteins as well as large-scale proteomics datasets.

Conclusions

DisCons is an openly accessible sequence analysis tool that identifies and highlights structurally disordered segments of proteins where the conformational flexibility is conserved across homologs, and therefore potentially functional. The tool is freely available both as a web application and as stand-alone source code hosted at http://pedb.vib.be/discons.     

Reproductive performance and milk traits of F1 Romanov ewes

The objective of this study was to evaluate the effect of crossbreeding Awassi and Morkaraman ewes with Romanov sires on litter size and total productivity as reflected by reproductive performance and milk production in the ewes. Twenty-three Romanov × Awassi (RA) and 19 Romanov × Morkaraman (RM) ewes were used. All of the ewes were pregnant at the start of the study, and litter size at birth and at weaning (60 days) were recorded. Milk production was recorded weekly and milk composition was estimated as dry matter and fat percentage. Litter size at birth (RM: 1.89 ± 0.18; RA: 1.62 ± 0.15) and weaning (RM: 1.67 ± 0.20; RA: 1.46 ± 0.17), dam weight at lambing (RM: 50.2 ± 2.37; RA: 44.2 ± 1.98) and total productivity (RM: 29.9 ± 3.05; RA: 24.4 ± 2.54) were not influenced by breed-type. Lactation length and milk yield was relatively but not significantly higher in RA than RM ewes. Dry matter and fat percentage of milk were found to be similar for both breed-types. Results of the present study indicate that crossbreeding of Awassi and Morkaraman ewes with Romanov rams yielded similar performance in F1 ewes. When F1 ewe performance is compared with their pure breed maternal ancestor, it is concluded that reproductive performance is improved by crossbreeding with Romanov.     

基于地理和气象要素的春玉米生育期栅格化方法

本文以黄河流域春玉米生育期和气象站点气象数据为主要数据源,采用多元逐步回归法分析了各生育期和经度、纬度、海拔高度、降水、年均温、≥10℃积温和日照时数等影响因子的关系,建立逐步回归方程,对各生育期空间栅格化方法进行了探讨,结果表明：（1）生育期空间拟合插值的统计检验说明春玉米“播种期”、“抽雄期”和“收获期”三个时期模拟效果最好,“拔节期”效果精度相对较好;（2）播种期基本满足从西南到东北延后的变化趋势,而拔节期、抽雄期和收获期基本上表现了从南北向中部、中部向东西两侧延后的现象。本研究得到的生育期与地理和气象要素之间的逐步回归方程,可为气候条件变化下作物生育期栅格化模拟试验以及农业生产应该采取的适应机制研究提供一定的依据。     

神经梅毒的诊断与治疗（附23例分析）

观察神经梅毒的临床特点,以提高对神经梅毒的诊断与治疗水平。回顾性分析哈尔滨医科大学附属第一医院2005年1月至2010年12月收治的23例神经梅毒患者的临床资料。神经梅毒患者男17例（73.9%）,女6例（26.1%）,男女比约为2.8∶1;年龄27~71岁,平均年龄43.1岁。本组首发症状：麻痹性痴呆（7例）、精神异常（3例）、急性脑梗死（3例）、癫痫（2例）、脊髓病变（2例）、颅高压（2例）、周围神经损害（2例）、脑神经损害（1例）、无症状性神经梅毒（1例）。23例患者血清及脑脊液快速血浆反应素实验及梅毒螺旋体血凝试验均呈阳性反应。颅脑电子计算机断层扫描（CT）和/或磁共振成像（MRI）检查多表现为额叶、顶叶、颞叶、基底节等多发病变。本组患者经大剂量青霉素治疗后病情有显著改善20例,死亡1例,自动出院2例。神经梅毒的临床表现复杂多样,神经系统各部位均可受累,诊断依靠病史及临床表现、实验室血清及脑脊液梅毒抗体检测,误诊率高,应早期诊断,诊断后应进行规范治疗,早期治疗效果较好。     

Wealth, status, and fitness: a historical study of Norwegians in variable environments

Wealth and status covary with lifetime reproductive success in preindustrial human populations. Local ecology is likely to modify this association, but details of this presumed relationship are not yet known. We sought to determine whether local ecology modifies the relationship between status and fitness (number of grandchildren). Our approach to the problem was to measure variation in fitness relative to status (landless or with land) and to local ecology (inland versus coastal communities). We also analyzed life history traits that might explain observed variations in fitness. Our results confirm previous findings that both status (landless=9.9 vs. with land=16.5) and ecology (inland=12.3 vs. coast=14.1) affect the number of grandchildren produced by a female in pre-industrial society. We also found that the differences in number of children between the status groups were less pronounced on the coast (landless=12.0 vs. with land=16.1) than inland (landless=7.8 vs. with land=16.8). Our findings are novel because they suggest that the fitness consequences of human status may depend on details of local ecology. We discuss four different mechanisms that could account for these fitness differences: (1) differential reproductive rate of mothers, (2) differential marriage rate of children (3) differential survival rate of children, and (4) different social practices (breastfeeding, inheritance of property and diet).     

妊娠肝内胆汁淤积症发生的分子机制研究进展

妊娠肝内胆汁淤积症（Intrahepatic cholestasis of pregnancy, ICP）是发生在妊娠中晚期,以皮肤瘙瘁、黄疸、血清胆汁酸升高,伴轻度肝功能损害为特征的妊娠并发症,严重影响母儿健康。ICP的发病机制尚未完全阐明,但有研究表明在遗传易感性妇女中,性激素及其代谢产物导致胆汁酸代谢异常与本病的发生密切相关。现就目前国内外有关ICP发病机制的研究进展做一综述,一方面为探寻更深层次的机制提供理论基础,另一方面为临床治疗ICP提供思路和方法。