Conserved Motifs and Domains in Members of Pospiviroidae

In 1985, Keese and Symons proposed a hypothesis on the sequence and secondary structure of viroids from the family : their secondary structure can be subdivided into five structural and functional domains and “viroids have evolved by rearrangement of domains between different viroids infecting the same cell and subsequent mutations within each domain”; this article is one of the most cited in the field of viroids. Employing the pairwise alignment method used by Keese and Symons and in addition to more recent methods, we tried to reproduce the original results and extent them to further members of which were unknown in 1985. Indeed, individual members of consist of a patchwork of sequence fragments from the family but the lengths of fragments do not point to consistent points of rearrangement, which is in conflict with the original hypothesis of fixed domain borders.

Syntax-semantics interactions – seeking evidence from a synchronic analysis of 38 languages

The notion that, to facilitate processing, as semantic complexity increases, syntactic complexity decreases, follows from various linguistic theories. This brief report presents the results of testing that notion, by analysing synchronic data from 38languages and correlating canonical measures of semantic and syntactic difficulty. We expected an overall positive tendency. However, the results came out mixed to negative. There is a notable degree of variation and there are no clear tendencies within language families. After detailing the theoretic and cognitive reasons that support the original hypothesis, we conclude with a short discussion about the potential causes and implications of our findings. A possible interpretation is that the interaction we are looking for is more subtle than one might have assumed.

Electron microscopy reveals novel external specialized organs housing bacteria in eagle ray tapeworms

Nutritionally-based mutualisms with bacteria are known to occur in a wide array of invertebrate phyla, although less commonly in the Platyhelminthes. Here we report what appears to be a novel example of this type of association in two geographically disparate and phylogenetically distant species of tapeworms of eagle rays—the lecanicephalidean Elicilacunosus dharmadii off the island of Borneo and the tetraphyllidean Caulobothrium multispelaeum off Senegal. Scanning and transmission electron microscopy revealed that the grooves and apertures on the outer surfaces of both tapeworms open into expansive cavities housing concentrations of bacteria. This led us to reject the original hypothesis that these structures, and their associated mucopolysaccharides, aid in attachment to the host mucosa. The cavities were found to be specialized in-foldings of the tapeworm body that were lined with particularly elongate filitriches. Given tapeworms lack a gut and employ filitriches to assist in nutrient absorption, enhanced nutrient uptake likely occurs in the cavities. Each tapeworm species appeared to host different bacterial monocultures; those in E. dharmadii were coccoid-like in form, while those in C. multispelaeum were bacillus-like. The presence of bacteria in a specialized structure of this nature suggests the structure is a symbiotic organ. Tapeworms are fully capable of obtaining their own nutrients, and thus the bacteria likely serve merely to supplement their diet. Given the bacteria were also extracellular, this structure is more consistent with a mycetome than a trophosome. To our knowledge, this is not only the first evidence of an external symbiotic organ of any type in a nutritionally-based mutualism, but also the first description of a mycetome in a group of invertebrates that lacks a digestive system. The factors that might account for the independent evolution of this unique association in these unrelated tapeworms are unclear—especially given that none of their closest relatives exhibit any evidence of the phenomenon.

Many Labs 5: Registered Replication of Albarracín et al. (2008), Experiment 5

In Experiment 5 of Albarracín et al. (2008), participants primed with words associated with action performed better on a subsequent cognitive task than did participants primed with words associated with inaction. A direct replication attempt by Frank, Kim, and Lee (2016) as part of the Reproducibility Project: Psychology (RP:P) failed to find evidence for this effect. In this article, we discuss several potential explanations for these discrepant findings: the source of participants (Amazon’s Mechanical Turk vs. traditional undergraduate-student pool), the setting of participation (online vs. in lab), and the possible moderating role of affect. We tested Albarracín et al.’s original hypothesis in two new samples: For the first sample, we followed the protocol developed by Frank et al. and recruited participants via Amazon’s Mechanical Turk ( n = 580). For the second sample, we used a revised protocol incorporating feedback from the original authors and recruited participants from eight universities ( n = 884). We did not detect moderation by protocol; patterns in the revised protocol resembled those in our implementation of the RP:P protocol, but the estimate of the focal effect size was smaller than that found originally by Albarracín et al. and larger than that found in Frank et al.’s replication attempt. We discuss these findings and possible explanations.

Pragmatic Markers in the Aspect of Communicative Alignmen

The article presents a model of communicative alignment in pragmatic markers (PM) use in Russian everyday dialogical communication. The main objectives are to check whether speakers coordinate their linguistic behavior not just with the use of lexemes or grammar forms or constructions, but also with PMs and how this actually works. We suppose that the use of PM by one of the speakers in the dialogue may increase the chances that the same PM will be used by the other speaker. In a Russian speech corpus "One Day of Speech" there were found 57 macro-episodes of communication where the PM koroche / koroche govorya was used by multiple speakers (46 episodes with 2 speakers using the PM, 11 – with 3 speakers). The analysis of PM use applying the system of quantitative parameters, worked out by the authors, has enabled them to note, that medium frequency of PM use rises when the number of speakers increases. PM used by speaker 1 is repeated by speaker 2, thus inducing speaker 3 to use the same PM, which influences the speech of the first two speakers respectively. The data analysis allows us to conclude that the original hypothesis of alignment in PMs has been proved for the marker we studied.

English Mnemonic Lexicon: Constituent Structure and Verbalization Potential

This paper presents a study of the system of lexical devices used by English speakers to verbalize their personal memory experiences. The approach presented in the paper presupposes inclusion of non-narrative structures into the spectrum of language forms conveying mnemonic meanings and extends the latter so as to encompass the meanings of encoding, storage, retrieval and loss. The research is based on the hypothesis that lexical units expressing memory-related meanings in English constitute a specifically organized system. A variety of communicative contexts representing mnemonic situations are analyzed as to develop a typology of memory verbalizers in English, estimate their functional potential and role in objectifying personal memory experiences on the lexical level. The results confirm the original hypothesis and suggest that mnemonic lexicon as a linguistic reflection of the mnemonic faculty is an important and largely understudied element of the language – memory system.

The recent report by Liu and Zhang Claiming “No support for the adaptive hypothesis of lagging-strand encoding in bacterial genomes” is factually incorrect

In their manuscript1 entitled “No support for the adaptive hypothesis of lagging-strand encoding in bacterial genomes”, Liu and Zhang attempt to refute the findings of our 2018 Nature Communications paper2. Here, we demonstrate that multiple key claims made by Liu and Zhang are factually incorrect, and that their overall conclusions, including the title of their paper, are invalid. We show that multiple existing controls already preclude the null hypothesis proposed by Liu and Zhang. We also show that the authors falsely claim that we did not publish key data, when in fact, these data were presented in our manuscript. Similarly, we point out that the authors falsely claim that we made comparisons and logical arguments we never made. Furthermore, the authors claim that they reanalyzed our data when in fact they did not. Therefore, they could not, by definition, have identified errors in our data. Our reanalysis of the Liu and Zhang data reveals that the main problem is that the authors simply do not understand the meaning of the term “inversion”. This caused them to misjudge the limitations of both their own inversion detection technique and ours. In fact, we find that the Liu and Zhang method cannot, specifically, identify inversions. Lastly, we provide new empirical evidence demonstrating further that our method works properly as described in our original manuscript. We conclude that Liu and Zhang’s manuscript has no rational basis, and that our original hypothesis meets the criteria for acceptance based on their own standards.

Rethinking power, production, and social reproduction: Toward variegated social reproduction

This special issue introduces new work, new perspectives, and engages in a dialogue to revisit, extend and go beyond the original central hypothesis of Power, Production and Social Reproduction (2003). That volume and its primary hypothesis focused upon the unfolding contradiction between the global accumulation of capital and the provision of stable and progressive conditions of social reproduction. It hypothesized a growing contradiction between the intensified power of capital and many life-making/sustaining processes, including the condition of bodies and the biosphere. Our original hypothesis conceptualized capital accumulation and social reproduction as interlinked although within different and contradictory moments in the same system or totality. We add to this here the concept of variegated social reproduction which refers to the historical and ontological variability of social reproduction - and its specific differentiations and varieties in contemporary globalized capitalism - stemming from concrete social, cultural, ecological and material practices and structures. Indeed, as the articles in the special issue reflect, the neoliberalization and commodification of social reproduction remains incomplete and not all-encompassing or determinant. As such, the introduction and the special issue also suggest new research agendas.

Not all saponins have a greater antiprotozoal activity than their related sapogenins

ABSTRACT The antiprotozoal effect of saponins varies according to both the structure of the sapogenin and the composition and linkage of the sugar moieties to the sapogenin. The effect of saponins on protozoa has been considered to be transient as it was thought that when saponins were deglycosilated to sapogenins in the rumen they became inactive; however, no studies have yet evaluated the antiprotozoal effect of sapogenins compared to their related saponins. The aims of this study were to evaluate the antiprotozoal effect of eighteen commercially available triterpenoid and steroid saponins and sapogenins in vitro, to investigate the effect of variations in the sugar moiety of related saponins and to compare different sapogenins bearing identical sugar moieties. Our results show that antiprotozoal activity is not an inherent feature of all saponins and that small variations in the structure of a compound can have a significant influence on their biological activity. Some sapogenins (20(S)-protopanaxatriol, asiatic acid and madecassic acid) inhibited protozoa activity to a greater extent than their corresponding saponins (Re and Rh1 and asiaticoside and madecassoside), thus the original hypothesis that the transient nature of the antiprotozoal action of saponins is due to the deglycosilation of saponins needs to be revisited.