Searching behaviour of an omnivorous predator for novel and native host plants of its herbivores: a study on arthropod colonization of eucalyptus in Brazil

Adaptation to novel host plants is a much‐studied process in arthropod herbivores, but not in their predators. This is surprising, considering the attention that has been given to the role of predators in host range expansion in herbivores; the enemy‐free space hypothesis suggests that plants may be included in the host range of herbivores because of lower predation and parasitism rates on the novel host plants. This effect can only be important if natural enemies do not follow their prey to the novel host plant, at least not immediately, thus allowing the herbivores to adapt to the novel host plant. Hence, depending on the speed with which natural enemies follow their prey to a new host plant, enemy‐free space on novel host plants may only exist for a limited period. This situation may presently be occurring in a system consisting of the herbivorous moth Thyrinteina arnobia Stoll (Lepidoptera: Geometridae) that attacks various species of Myrtaceae, such as guava (Psidium guajava L.) and jaboticaba (Myrciaria spp.), in Brazil. Since the introduction of eucalyptus (Myrtaceae) species into this country some 100 years ago, the moth has included this plant species in its host range and frequently causes outbreaks, a phenomenon that does not occur on the native host plant species. This suggests that the natural enemies that attack the herbivore on native species are not very effective on the novel host. We tested this hypothesis by studying the searching behaviour of one of the natural enemies, the omnivorous predatory bug Podisus nigrispinus (Dallas) (Heteroptera: Pentatomidae). When offered a choice between plants of the two species, the predators (originally collected in eucalyptus plantations) preferred guava to eucalyptus when both plant species were clean, infested with herbivores, or damaged by herbivores but with herbivores removed prior to the experiments. The bugs preferred herbivore‐damaged to clean guava, and showed a slight preference for damaged to clean eucalyptus. These results may explain the lack of impact of predatory arthropods on herbivore populations on eucalyptus and suggests that eucalyptus may offer an enemy‐free space for herbivores.     

APOBEC3G cytosine deamination hotspots are defined by both sequence context and single-stranded DNA secondary structure

Apolipoprotein B mRNA-editing, enzyme-catalytic, polypeptide-like 3G (i.e., APOBEC3G or A3G) is an evolutionarily conserved cytosine deaminase that potently restricts human immunodeficiency virus type 1 (HIV-1), retrotransposons and other viruses. A3G has a nucleotide target site specificity for cytosine dinucleotides, though only certain cytosine dinucleotides are ‘hotspots’ for cytosine deamination, and others experience little or no editing by A3G. The factors that define these critical A3G hotspots are not fully understood. To investigate how A3G hotspots are defined, we used an in vitro fluorescence resonance energy transfer-based oligonucleotide assay to probe the site specificity of A3G. Our findings strongly suggest that the target single-stranded DNA (ssDNA) secondary structure as well as the bases directly 3′ and 5′ of the cytosine dinucleotide are critically important A3G recognition. For instance, A3G cannot readily deaminate a cytosine dinucleotide in ssDNA stem structures or in nucleotide base loops composed of three bases. Single-stranded nucleotide loops up to seven bases in length were poor targets for A3G activity unless cytosine residues flanked the cytosine dinucleotide. Furthermore, we observed that A3G favors adenines, cytosines and thymines flanking the cytosine dinucleotide target in unstructured regions of ssDNA. Low cytosine deaminase activity was detected when guanines flanked the cytosine dinucleotide. Taken together, our findings provide the first demonstration that A3G cytosine deamination hotspots are defined by both the sequence context of the cytosine dinucleotide target as well as the ssDNA secondary structure. This knowledge can be used to better trace the origins of mutations to A3G activity, and illuminate its impact on processes such as HIV-1 genetic variation.     

Cyst bank life-history model for a fairy shrimp from ephemeral ponds

1. Ephemeral wetland habitats provide a useful model system for studying how life‐history patterns enable populations to persist despite high environmental variation. One important life‐history trait of both plants and crustaceans in such habitats involves hatching/germination of only some of the eggs/seeds at any time. This bet‐hedging leads to the development of a bank composed of dormant propagules of many ages. 2. The San Diego fairy shrimp, Branchinecta sandiegonensis (Crustacea: Anostraca), a dominant faunal element of ephemeral ponds in San Diego, California, is a suitable organism for studying the consequences of highly fluctuating environmental conditions. As a result of large‐scale habitat loss, the species is also endangered, and this motivated our specific study towards understanding the hatching dynamics of its egg bank for planning conservation efforts such as pool restoration and re‐creation. 3. We formulated a matrix population model using egg age within the bank to study the relationship between adult survival and reproduction, and survival in and hatching from the egg bank. As vital rates for fairy shrimp are only poorly known, we generated 48 matrices with parameters encompassing ranges of likely values for the vital rates of B. sandiegonensis. We calculated population growth rates and eigenvalue elasticities both for a static model and a model with periodic reproductive failure. 4. The model shows that in good filling events, population growth rate is very high and the egg bank is increased dramatically. While population growth rate is insensitive to long‐term survival in the egg bank in our static deterministic model, it becomes sensitive to survival in the egg bank when a regime of periodically failed reproductive events is imposed. 5. Under favourable conditions, it was best for shrimp to hatch from eggs as soon as possible. However, under a regime where failed reproductive events were common, it was best to hatch after several pool fillings. Because conditions change from favourable to unfavourable unpredictably, variation in age within the egg bank appears to be critical for the persistence of the population. This attribute needs to be carefully considered when restoring or creating new pools for conservation purposes.     

Autism spectrum disorder detection from semi-structured and unstructured medical data

Autism spectrum disorder (ASD) is a developmental disorder that significantly impairs patients’ ability to perform normal social interaction and communication. Moreover, the diagnosis procedure of ASD is highly time-consuming, labor-intensive, and requires extensive expertise. Although there exists no known cure for ASD, there is consensus among clinicians regarding the importance of early intervention for the recovery of ASD patients. Therefore, to benefit autism patients by enhancing their access to treatments such as early intervention, we aim to develop a robust machine learning-based system for autism detection by using Natural Language Processing techniques based on information extracted from medical forms of potential ASD patients. Our detecting framework involves converting semi-structured and unstructured medical forms into digital format, preprocessing, learning document representation, and finally, classification. Testing results are evaluated against the ground truth set by expert clinicians and the proposed system achieve a 83.4% accuracy and 91.1% recall, which is very promising. The proposed ASD detection framework could significantly simplify and shorten the procedure of ASD diagnosis.     

Thyroid Hormone Signaling In Vivo Requires a Balance between Coactivators and Corepressors

Resistance to thyroid hormone (RTH), a human syndrome, is characterized by high thyroid hormone (TH) and thyroid-stimulating hormone (TSH) levels. Mice with mutations in the thyroid hormone receptor beta (TRβ) gene that cannot bind steroid receptor coactivator 1 (SRC-1) and Src-1^−/− mice both have phenotypes similar to that of RTH. Conversely, mice expressing a mutant nuclear corepressor 1 (Ncor1) allele that cannot interact with TRβ, termed NCoRΔID, have low TH levels and normal TSH. We hypothesized that Src-1^−/− mice have RTH due to unopposed corepressor action. To test this, we crossed NCoRΔID and Src-1^−/− mice to create mice deficient for coregulator action in all cell types. Remarkably, NCoR^ΔID/ΔID Src-1^−/− mice have normal TH and TSH levels and are triiodothryonine (T₃) sensitive at the level of the pituitary. Although absence of SRC-1 prevented T₃ activation of key hepatic gene targets, NCoR^ΔID/ΔID Src-1^−/− mice reacquired hepatic T₃ sensitivity. Using in vivo chromatin immunoprecipitation assays (ChIP) for the related coactivator SRC-2, we found enhanced SRC-2 recruitment to TR-binding regions of genes in NCoR^ΔID/ΔID Src-1^−/− mice, suggesting that SRC-2 is responsible for T₃ sensitivity in the absence of NCoR1 and SRC-1. Thus, T₃ targets require a critical balance between NCoR1 and SRC-1. Furthermore, replacement of NCoR1 with NCoRΔID corrects RTH in Src-1^−/− mice through increased SRC-2 recruitment to T₃ target genes.     

Accumulation of “Old Proteins” and the Critical Need for MS‐based Protein Turnover Measurements in Aging and Longevity

Aging and age‐related diseases are accompanied by proteome remodeling and progressive declines in cellular machinery required to maintain protein homeostasis (proteostasis), such as autophagy, ubiquitin‐mediated degradation, and protein synthesis. While many studies have focused on capturing changes in proteostasis, the identification of proteins that evade these cellular processes has recently emerged as an approach to studying the aging proteome. With advances in proteomic technology, it is possible to monitor protein half‐lives and protein turnover at the level of individual proteins in vivo. For large‐scale studies, these technologies typically include the use of stable isotope labeling coupled with MS and comprehensive assessment of protein turnover rates. Protein turnover studies have revealed groups of highly relevant long‐lived proteins (LLPs), such as the nuclear pore complexes, extracellular matrix proteins, and protein aggregates. Here, the role of LLPs during aging and age‐related diseases and the methods used to identify and quantify their changes are reviewed. The methods available to conduct studies of protein turnover, used in combination with traditional proteomic methods, will enable the field to perform studies in a systems biology context, as changes in proteostasis may not be revealed in studies that solely measure differential protein abundances.