Engineering proteinase K using machine learning and synthetic genes

Background  

Altering a protein's function by changing its sequence allows natural proteins to be converted into useful molecular tools. Current protein engineering methods are limited by a lack of high throughput physical or computational tests that can accurately predict protein activity under conditions relevant to its final application. Here we describe a new synthetic biology approach to protein engineering that avoids these limitations by combining high throughput gene synthesis with machine learning-based design algorithms.     

Loss of cortical function in mice after decapitation, cervical dislocation, potassium chloride injection, and CO2 inhalation

Electroencephalograms (EEG) and visual evoked potentials (VEP) in mice were recorded to evaluate loss of cortical function during the first 30 s after euthanasia by various methods. Tracheal cannulae (for positive-pressure ventilation, PPV) and cortical surface electrodes were placed in mice anesthetized with inhaled halothane. Succinylcholine was used to block spontaneous breathing in the mice, which then underwent continuous EEG recording. Photic stimuli (1 Hz) were presented to produce VEPs superimposed on the EEG. Anesthesia was discontinued immediately before euthanasia. Compared with that obtained before euthanasia, EEG activity during the 30-s study period immediately after euthanasia was significantly decreased after cervical dislocation (at 5 to 10 s), 100% PPV-CO2 (at 10 to 15 s), decapitation (at 15 to 20 s), and cardiac arrest due to KCl injection (at 20 to 25 s) but not after administration of 70% PPV-CO2. Similarly, these euthanasia methods also reduced VEP amplitude, although 100% PPV-CO2 treatment affected VEP amplitude more than it did EEG activity. Thus, 100% PPV-CO2 treatment significantly decreased VEP beginning 5 to 10 s after administration, with near abolition of VEP by 30 s. VEP amplitude was significantly reduced at 5 to 10 s after cervical dislocation and at 10 to 15 s after decapitation but not after either KCl or 70% PPV-CO2 administration. The data demonstrate that 100% PPV-CO2, decapitation, and cervical dislocation lead to rapid disruption of cortical function as measured by 2 different methods. In comparison, 70% PPV-CO2 and cardiac arrest due to intracardiac KCl injection had less rapid effects on cortical function.     

The demographic consequences of mutualism: ants increase host-plant fruit production but not population growth

The impact of mutualists on a partner’s demography depends on how they affect the partner’s multiple vital rates and how those vital rates, in turn, affect population growth. However, mutualism studies rarely measure effects on multiple vital rates or integrate them to assess the ultimate impact on population growth. We used vital rate data, population models and simulations of long-term population dynamics to quantify the demographic impact of a guild of ant species on the plant Ferocactus wislizeni. The ants feed at the plant’s extrafloral nectaries and attack herbivores attempting to consume reproductive organs. Ant-guarded plants produced significantly more fruit, but ants had no significant effect on individual growth or survival. After integrating ant effects across these vital rates, we found that projected population growth was not significantly different between unguarded and ant-guarded plants because population growth was only weakly influenced by differences in fruit production (though strongly influenced by differences in individual growth and survival). However, simulations showed that ants could positively affect long-term plant population dynamics through services provided during rare but important events (herbivore outbreaks that reduce survival or years of high seedling recruitment associated with abundant precipitation). Thus, in this seemingly clear example of mutualism, the interaction may actually yield no clear benefit to plant population growth, or if it does, may only do so through the actions of the ants during rare events. These insights demonstrate the value of taking a demographic approach to studying the consequences of mutualism.     

Contrasting exotic Solenopsis invicta and native Forelius pruinosus ants as mutualists with Catalpa bignonioides, a native plant

Abstract. 1. The suitability of the red imported fire ant Solenopsis invicta Buren and a native ant Forelius pruinosus (Roger) as participants in a food-for-protection mutualism with a native nectaried tree Catalpa bignonioides Walter was compared.
2. The mean mortality of folivore larvae of Ceratomia catalpae Boisduval was similar for S. invicta and F. pruinosus although S. invicta attacked fewer caterpillar aggregations and was a devastating pupal predator. Solenopsis invicta also differed from the native ant in that it attacked the parasitoid Cotesia congregata Say, another plant mutualist, and visited extrafloral nectaries less frequently.
3. Habitats invaded by S. invicta are characterised by a scarcity of both herbivores and of beneficial insects that visit extrafloral nectaries. The plants do not require protection, and extrafloral nectaries are visited rarely. Although plants are defended incidentally by S. invicta , the insect-plant mutualism therein is greatly simplified or defunct.     

High-order SNP combinations associated with complex diseases: efficient discovery, statistical power and functional interactions

There has been increased interest in discovering combinations of single-nucleotide polymorphisms (SNPs) that are strongly associated with a phenotype even if each SNP has little individual effect. Efficient approaches have been proposed for searching two-locus combinations from genome-wide datasets. However, for high-order combinations, existing methods either adopt a brute-force search which only handles a small number of SNPs (up to few hundreds), or use heuristic search that may miss informative combinations. In addition, existing approaches lack statistical power because of the use of statistics with high degrees-of-freedom and the huge number of hypotheses tested during combinatorial search. Due to these challenges, functional interactions in high-order combinations have not been systematically explored. We leverage discriminative-pattern-mining algorithms from the data-mining community to search for high-order combinations in case-control datasets. The substantially improved efficiency and scalability demonstrated on synthetic and real datasets with several thousands of SNPs allows the study of several important mathematical and statistical properties of SNP combinations with order as high as eleven. We further explore functional interactions in high-order combinations and reveal a general connection between the increase in discriminative power of a combination over its subsets and the functional coherence among the genes comprising the combination, supported by multiple datasets. Finally, we study several significant high-order combinations discovered from a lung-cancer dataset and a kidney-transplant-rejection dataset in detail to provide novel insights on the complex diseases. Interestingly, many of these associations involve combinations of common variations that occur in small fractions of population. Thus, our approach is an alternative methodology for exploring the genetics of rare diseases for which the current focus is on individually rare variations.     

Expression levels of the human DNA repair protein metnase influence lentiviral genomic integration

We recently identified a Transposase domain protein called Metnase, which assists in repairing DNA double-strand breaks (DSB) via non-homologous end-joining (NHEJ), and is important for foreign DNA integration into a host cell genome. Since integration is essential for productive lentiviral infection we examined whether Metnase expression levels could have an influence on lentiviral genomic integration. Using cells stably transduced to either over- or under-express Metnase we determined that the expression level of Metnase did indeed correlate with live lentiviral integration. Changes in Metnase levels were accompanied by changes in the number of copies of integrated lentiviral cDNA. While Metnase levels affected lentiviral integration, it had no effect on the amount of either total cellular viral RNA, cDNA or 2-LTR circles. Therefore, Metnase enhances the integration of lentivirus DNA into the host cell genome.