piRNN: deep learning algorithm for piRNA prediction

Piwi-interacting RNAs (piRNAs) are the largest class of small non-coding RNAs discovered in germ cells. Identifying piRNAs from small RNA data is a challenging task due to the lack of conserved sequences and structural features of piRNAs. Many programs have been developed to identify piRNA from small RNA data. However, these programs have limitations. They either rely on extracting complicated features, or only demonstrate strong performance on transposon related piRNAs. Here we proposed a new program called piRNN for piRNA identification. For our software, we applied a convolutional neural network classifier that was trained on the datasets from four different species (Caenorhabditis elegans, Drosophila melanogaster, rat and human). A matrix of k-mer frequency values was used to represent each sequence. piRNN has great usability and shows better performance in comparison with other programs. It is freely available at https://github.com/bioinfolabmu/piRNN

Targeting Hepatitis B Virus with Zinc Finger Nucleases

Despite an existing effective vaccine, hepatitis B virus (HBV) remains a major public health concern. There are effective suppressive therapies for HBV, but they remain expensive and inaccessible to many, and not all patients respond well. Furthermore, HBV can persist as genomic covalently closed circular DNA (cccDNA) that remains in hepatocytes even during otherwise effective therapy and facilitates rebound in patients after treatment has stopped. Therefore, the need for an effective treatment that targets active and persistent HBV infections remains. As a novel approach to treat HBV, we have targeted the HBV genome for disruption to prevent viral reactivation and replication. We generated 3 zinc finger nucleases (ZFNs) that target sequences within the HBV polymerase, core and X genes. Upon the formation of ZFN-induced DNA double strand breaks (DSB), imprecise repair by non-homologous end joining leads to mutations that inactivate HBV genes. We delivered HBV-specific ZFNs using self-complementary adeno-associated virus (scAAV) vectors and tested their anti-HBV activity in HepAD38 cells. HBV-ZFNs efficiently disrupted HBV target sites by inducing site-specific mutations. Cytotoxicity was seen with one of the ZFNs. scAAV-mediated delivery of a ZFN targeting HBV polymerase resulted in complete inhibition of HBV DNA replication and production of infectious HBV virions in HepAD38 cells. This effect was sustained for at least 2 weeks following only a single treatment. Furthermore, high specificity was observed for all ZFNs, as negligible off-target cleavage was seen via high-throughput sequencing of 7 closely matched potential off-target sites. These results show that HBV-targeted ZFNs can efficiently inhibit active HBV replication and suppress the cellular template for HBV persistence, making them promising candidates for eradication therapy

Pulsatilla patens (Ranunculaceae), a perennial herb, is ectomycorrhizal in northeastern Poland and likely shares ectomycorrhizal fungi with Pinus sylvestris

The sharing of species of ectomycorrhizal fungi (EMF) among different co-occurring host plant species could allow the formation of common mycorrhizal networks, which can alter plant–plant interactions and succession. Such sharing of EMF among woody species is thought to be common in many forests, but very few herbaceous plants form EMF, so they are assumed to be excluded from EMF networks in forests. We studied the EMF on roots of a common coniferous tree, Pinus sylvestris, and a co-occurring rare herbaceous perennial plant, Pulsatilla patens (Ranunculaceae), in northeastern Poland. We examined roots from co-occuring P. sylvestris and P. patens, visually classified EMF into morphotypes, studied tissue sections of mycorrhizal structures using compound microscopy, and used DNA sequencing to identify the fungi. On both host plant species, we observed EMF colonization, with colonized root tips exhibiting a swollen appearance, as well as a variety of colors and textures of fungal mycelium covering and emanating from those swollen tips. Sectioning and microscopic examination of an EMF morphotype common on P. patens confirmed the presence of a mantle and Hartig net, indicating the likely presence of functional ectomycorrhizal structures. The two most frequent EMF were Cenococcum geophilum and Piloderma olivaceum, and the latter was found to associate with both host plant species. Several EMF found here only on P. patens, including C. geophilum and two Russula species, are known from previous studies to also associate with P. sylvestris and other tree species. The observation of shared EMF between a coniferous tree and an understory herb indicates the potential for common mycorrhizal networks to alter interactions between these two species and may also indicate a unique way in which the distribution and abundance of a rare herbaceous plant may be influenced by shared mutualisms with a common co-occurring woody plant

Cheaters must prosper: reconciling theoretical and empirical perspectives on cheating in mutualism.

Cheating is a focal concept in the study of mutualism, with the majority of researchers considering cheating to be both prevalent and highly damaging. However, current definitions of cheating do not reliably capture the evolutionary threat that has been a central motivation for the study of cheating. We describe the development of the cheating concept and distill a relative-fitness-based definition of cheating that encapsulates the evolutionary threat posed by cheating, i.e. that cheaters will spread and erode the benefits of mutualism. We then describe experiments required to conclude that cheating is occurring and to quantify fitness conflict more generally. Next, we discuss how our definition and methods can generate comparability and integration of theory and experiments, which are currently divided by their respective prioritisations of fitness consequences and traits. To evaluate the current empirical evidence for cheating, we review the literature on several of the best-studied mutualisms. We find that although there are numerous observations of low-quality partners, there is currently very little support from fitness data that any of these meet our criteria to be considered cheaters. Finally, we highlight future directions for research on conflict in mutualisms, including novel research avenues opened by a relative-fitness-based definition of cheating

Cheaters must prosper: reconciling theoretical and empirical perspectives on cheating in mutualism

Cheating is a focal concept in the study of mutualism, with the majority of researchers considering cheating to be both prevalent and highly damaging. However, current definitions of cheating do not reliably capture the evolutionary threat that has been a central motivation for the study of cheating. We describe the development of the cheating concept and distill a relative‐fitness‐based definition of cheating that encapsulates the evolutionary threat posed by cheating, i.e. that cheaters will spread and erode the benefits of mutualism. We then describe experiments required to conclude that cheating is occurring and to quantify fitness conflict more generally. Next, we discuss how our definition and methods can generate comparability and integration of theory and experiments, which are currently divided by their respective prioritisations of fitness consequences and traits. To evaluate the current empirical evidence for cheating, we review the literature on several of the best‐studied mutualisms. We find that although there are numerous observations of low‐quality partners, there is currently very little support from fitness data that any of these meet our criteria to be considered cheaters. Finally, we highlight future directions for research on conflict in mutualisms, including novel research avenues opened by a relative‐fitness‐based definition of cheating

Disgust sensitivity and opposition to immigration: does contact avoidance or resistance to foreign norms explain the relationship?

Past research suggests that pathogen-avoidance motives (e.g., disgust sensitivity) relate to greater opposition to immigration. Two accounts have been proposed to explain this relationship, one of which emphasizes proximally avoiding outgroups, and the other of which emphasizes adherence to traditional norms. According to the former, immigrants are perceived as being more infectious because they carry novel pathogens due to their foreign ecological origins. According to the latter, immigrants' foreign norms are perceived as posing a pathogen threat. This study aimed to disentangle these accounts. Participants (N = 975) were randomly assigned to read a description of an immigrant who had high or low contact with locals and high or low assimilation to local norms. The effect of disgust sensitivity on sentiments toward the immigrant (and immigrants like him) was compared across conditions. Results supported the traditional norms account: disgust sensitivity related to anti-immigrant sentiments when the immigrant was described as not assimilating to local norms, but not when he was described as assimilating. Contrary to the outgroup avoidance account, the relationship between disgust sensitivity and anti-immigrant sentiments did not vary across the high-contact and low-contact conditions. Results suggest that resistance to foreign norms, rather than avoidance of novel pathogens, better explains the relationship between pathogen avoidance and outgroup prejudice