Genome Size Changes by Duplication, Divergence, and Insertion in Caenorhabditis Worms.

Genome size has been measurable since the 1940s but we still do not understand genome size variation. Caenorhabditis nematodes show strong conservation of chromosome number but vary in genome size between closely related species. Androdioecy, where populations are composed of males and self-fertile hermaphrodites, evolved from outcrossing, female-male dioecy, three times in this group. In Caenorhabditis, androdioecious genomes are 10-30% smaller than dioecious species, but in the nematode Pristionchus, androdioecy evolved six times and does not correlate with genome size. Previous hypotheses include genome size evolution through: 1) Deletions and "genome shrinkage" in androdioecious species; 2) Transposable element (TE) expansion and DNA loss through large deletions (the "accordion model"); and 3) Differing TE dynamics in androdioecious and dioecious species. We analyzed nematode genomes and found no evidence for these hypotheses. Instead, nematode genome sizes had strong phylogenetic inertia with increases in a few dioecious species, contradicting the "genome shrinkage" hypothesis. TEs did not explain genome size variation with the exception of the DNA transposon Mutator which was twice as abundant in dioecious genomes. Across short and long evolutionary distances Caenorhabditis genomes evolved through small structural mutations including gene-associated duplications and insertions. Seventy-one protein families had significant, parallel decreases across androdioecious Caenorhabditis including genes involved in the sensory system, regulatory proteins and membrane-associated immune responses. Our results suggest that within a dynamic landscape of frequent small rearrangements in Caenorhabditis, reproductive mode mediates genome evolution by altering the precise fates of individual genes, proteins, and the phenotypes they underlie.

Acetylenotrophic and Diazotrophic Bradyrhizobium sp. Strain I71 from TCE-Contaminated Soils.

Acetylene (C2H2) is a molecule rarely found in nature, with very few known natural sources, but acetylenotrophic microorganisms can use acetylene as their primary carbon and energy source. As of 2018 there were 15 known strains of aerobic and anaerobic acetylenotrophs; however, we hypothesize there may yet be unrecognized diversity of acetylenotrophs in nature. This study expands the known diversity of acetylenotrophs by isolating the aerobic acetylenotroph, Bradyrhizobium sp. strain I71, from trichloroethylene (TCE)-contaminated soils. Strain I71 is a member of the class Alphaproteobacteria and exhibits acetylenotrophic and diazotrophic activities, the only two enzymatic reactions known to transform acetylene. This unique capability in the isolated strain may increase the genus' economic impact beyond agriculture as acetylenotrophy is closely linked to bioremediation of chlorinated contaminants. Computational analyses indicate that the Bradyrhizobium sp. strain I71 genome contains 522 unique genes compared to close relatives. Moreover, applying a novel hidden Markov model of known acetylene hydratase (AH) enzymes identified a putative AH enzyme. Protein annotation with I-TASSER software predicted the AH from the microbe Syntrophotalea acetylenica as the closest structural and functional analog. Furthermore, the putative AH was flanked by horizontal gene transfer (HGT) elements, like that of AH in anaerobic acetylenotrophs, suggesting an unknown source of acetylene or acetylenic substrate in the environment that is selecting for the presence of AH. IMPORTANCE The isolation of Bradyrhizobium strain I71 expands the distribution of acetylene-consuming microbes to include a group of economically important microorganisms. Members of Bradyrhizobium are well studied for their abilities to improve plant health and increase crop yields by providing bioavailable nitrogen. Additionally, acetylene-consuming microbes have been shown to work in tandem with other microbes to degrade soil contaminants. Based on genome, cultivation, and protein prediction analysis, the ability to consume acetylene is likely not widespread within the genus Bradyrhizobium. These findings suggest that the suite of phenotypic capabilities of strain I71 may be unique and make it a good candidate for further study in several research avenues.

Effects of collaboration on the qualities of autobiographical recall in strangers, friends, and siblings: both remembering partner and communication processes matter.

Recalling autobiographical memories with others can influence the quality of recall, but little is known about how features of the group influence memory outcomes. In two studies, we examined how the products and processes of autobiographical recall depend on individual vs. collaborative remembering and the relationship between group members. In both studies, dyads of strangers, friends, and siblings recalled autobiographical events individually (elicitation), then either collaboratively or individually (recall). Study 1 involved typing memory narratives; Study 2 involved recalling aloud. We examined shifts in vividness, emotionality, and pronoun use within memory narratives produced by different relationship types. In Study 2, we also coded collaborative dyads' "collaborative processes" or communication processes. In Study 1, all relationships showed decreased positive emotion and I-pronouns and increased negative emotion within collaboratively-produced memory narratives. In Study 2, all relationships showed increased vividness, reduced emotionality and positive and negative emotion, and increased I- and we-pronouns within collaboratively-produced memory narratives. However, strangers used collaborative processes differently from friends and siblings. Some collaborative processes were associated with memory qualities. Across studies, collaboration influenced memory quality more than did relationship type, but relationship type influenced dyads' recall dynamics. These findings indicate the complexity of social influences on memory.

Syntrophotalea acetylenivorans sp. nov., a diazotrophic, acetylenotrophic anaerobe isolated from intertidal sediments.

A Gram-stain-negative, strictly anaerobic, non-motile, rod-shaped bacterium, designated SFB93T, was isolated from the intertidal sediments of South San Francisco Bay, located near Palo Alto, CA, USA. SFB93T was capable of acetylenotrophic and diazotrophic growth, grew at 22-37 °C, pH 6.3-8.5 and in the presence of 10-45 g l-1 NaCl. Phylogenetic analyses based on 16S rRNA gene sequencing showed that SFB93T represented a member of the genus Syntrophotalea with highest 16S rRNA gene sequence similarities to Syntrophotalea acetylenica DSM 3246T (96.6 %), Syntrophotalea carbinolica DSM 2380T (96.5 %), and Syntrophotalea venetiana DSM 2394T (96.7 %). Genome sequencing revealed a genome size of 3.22 Mbp and a DNA G+C content of 53.4 %. SFB93T had low genome-wide average nucleotide identity (81-87.5 %) and <70 % digital DNA-DNA hybridization value with other members of the genus Syntrophotalea. The phylogenetic position of SFB93T within the family Syntrophotaleaceae and as a novel member of the genus Syntrophotalea was confirmed via phylogenetic reconstruction based on concatenated alignments of 92 bacterial core genes. On the basis of the results of phenotypic, genotypic and phylogenetic analyses, a novel species, Syntrophotalea acetylenivorans sp. nov., is proposed, with SFB93T (=DSM 106009T=JCM 33327T=ATCC TSD-118T) as the type strain.

Sociocultural memory development research drives new directions in gadgetry science.

Sociocultural developmental psychology can drive new directions in gadgetry science. We use autobiographical memory, a compound capacity incorporating episodic memory, as a case study. Autobiographical memory emerges late in development, supported by interactions with parents. Intervention research highlights the causal influence of these interactions, whereas cross-cultural research demonstrates culturally determined diversity. Different patterns of inheritance are discussed.

Detection of Diazotrophy in the Acetylene-Fermenting Anaerobe Pelobacter sp. Strain SFB93.

Acetylene (C2H2) is a trace constituent of the present Earth's oxidizing atmosphere, reflecting a mixture of terrestrial and marine emissions from anthropogenic, biomass-burning, and unidentified biogenic sources. Fermentation of acetylene was serendipitously discovered during C2H2 block assays of N2O reductase, and Pelobacter acetylenicus was shown to grow on C2H2 via acetylene hydratase (AH). AH is a W-containing, catabolic, low-redox-potential enzyme that, unlike nitrogenase (N2ase), is specific for acetylene. Acetylene fermentation is a rare metabolic process that is well characterized only in P. acetylenicus DSM3246 and DSM3247 and Pelobacter sp. strain SFB93. To better understand the genetic controls for AH activity, we sequenced the genomes of the three acetylene-fermenting Pelobacter strains. Genome assembly and annotation produced three novel genomes containing gene sequences for AH, with two copies being present in SFB93. In addition, gene sequences for all five compulsory genes for iron-molybdenum N2ase were also present in the three genomes, indicating the cooccurrence of two acetylene transformation pathways. Nitrogen fixation growth assays showed that DSM3426 could ferment acetylene in the absence of ammonium, but no ethylene was produced. However, SFB93 degraded acetylene and, in the absence of ammonium, produced ethylene, indicating an active N2ase. Diazotrophic growth was observed under N2 but not in experimental controls incubated under argon. SFB93 exhibits acetylene fermentation and nitrogen fixation, the only known biochemical mechanisms for acetylene transformation. Our results indicate complex interactions between N2ase and AH and suggest novel evolutionary pathways for these relic enzymes from early Earth to modern days.IMPORTANCE Here we show that a single Pelobacter strain can grow via acetylene fermentation and carry out nitrogen fixation, using the only two enzymes known to transform acetylene. These findings provide new insights into acetylene transformations and adaptations for nutrient (C and N) and energy acquisition by microorganisms. Enhanced understanding of acetylene transformations (i.e., extent, occurrence, and rates) in modern environments is important for the use of acetylene as a potential biomarker for extraterrestrial life and for degradation of anthropogenic contaminants.

"Going episodic": collaborative inhibition and facilitation when long-married couples remember together.

Two complementary approaches to the study of collaborative remembering have produced contrasting results. In the experimental "collaborative recall" approach within cognitive psychology, collaborative remembering typically results in "collaborative inhibition": laboratory groups recall fewer items than their estimated potential. In the cognitive ageing approach, collaborative remembering with a partner or spouse may provide cueing and support to benefit older adults' performance on everyday memory tasks. To combine the value of experimental and cognitive ageing approaches, we tested the effects of collaborative remembering in older, long-married couples who recalled a non-personal word list and a personal semantic list of shared trips. We scored amount recalled as well as the kinds of details remembered. We found evidence for collaborative inhibition across both tasks when scored strictly as number of list items recalled. However, we found collaborative facilitation of specific episodic details on the personal semantic list, details which were not strictly required for the completion of the task. In fact, there was a trade-off between recall of specific episodic details and number of trips recalled during collaboration. We discuss these results in terms of the functions of shared remembering and what constitutes memory success, particularly for intimate groups and for older adults.

The hows and whys of "we" (and "I") in groups.

Informed by our interdisciplinary research program on collaborative recall, we argue that Baumeister et al. should consider: (1) group success as a balance between differentiation and integration (not differentiation alone); (2) variation in constellations of people and processes within and across groups; and (3) nuanced measurement of what people bring to, do in, and get out of groups.

Cue generation and memory construction in direct and generative autobiographical memory retrieval.

Theories of autobiographical memory emphasise effortful, generative search processes in memory retrieval. However recent research suggests that memories are often retrieved directly, without effortful search. We investigated whether direct and generative retrieval differed in the characteristics of memories recalled, or only in terms of retrieval latency. Participants recalled autobiographical memories in response to cue words. For each memory, they reported whether it was retrieved directly or generatively, rated its visuo-spatial perspective, and judged its accompanying recollective experience. Our results indicated that direct retrieval was commonly reported and was faster than generative retrieval, replicating recent findings. The characteristics of directly retrieved memories differed from generatively retrieved memories: directly retrieved memories had higher field perspective ratings and lower observer perspective ratings. However, retrieval mode did not influence recollective experience. We discuss our findings in terms of cue generation and content construction, and the implication for reconstructive models of autobiographical memory.

The effect of movement kinematics on predicting the timing of observed actions.

The ability to predict the actions of other agents is vital for joint action tasks. Recent theory suggests that action prediction relies on an emulator system that permits observers to use a model of their own movement kinematics to predict the actions of other agents. If this is the case, then people should be more accurate at generating predictions about actions that are similar to their own. We tested this hypothesis in two experiments in which participants were required to predict the occurrence and timing of particular critical points in an observed action. In Experiment 1, we employed a self/other prediction paradigm in which prediction accuracy for recordings of self-generated movements was compared with prediction accuracy for recordings of other-generated movements. As expected, prediction was more accurate for recordings of self-generated actions because in this case the movement kinematics of the observer and observed stimuli are maximally similar. In Experiment 1, people were able to produce actions at their own tempo and, therefore, the results might be explained in terms of self-similarity in action production tempo rather than in terms of movement kinematics. To control for this possibility in Experiment 2, we compared prediction accuracy for stimuli that were matched in tempo but differed only in terms of kinematics. The results showed that participants were more accurate when predicting actions with a human kinematic profile than tempo-matched stimuli that moved with non-human kinematics. Finally, in Experiment 3, we confirmed that the results of Experiment 2 cannot be explained by human-like stimuli containing a slowing down phase before the critical points. Taken together, these findings provide further support for the role of motor emulation in action prediction, and they suggest that the action prediction mechanism produces output that is available rapidly and available to drive action control suggesting that it can plausibly support joint action coordination.

The collaborative emergence of group cognition.

We extend Smaldino's approach to collaboration and social organization in cultural evolution to include cognition. By showing how recent work on emergent group-level cognition can be incorporated within Smaldino's framework, we extend that framework's scope to encompass collaborative memory, decision making, and intelligent action. We argue that beneficial effects arise only in certain forms of cognitive interdependence, in surprisingly fragile conditions.

Eliminating episodic memory?

In Tulving's initial characterization, episodic memory was one of multiple memory systems. It was postulated, in pursuit of explanatory depth, as displaying proprietary operations, representations and substrates such as to explain a range of cognitive, behavioural and experiential phenomena. Yet the subsequent development of this research programme has, paradoxically, introduced surprising doubts about the nature, and indeed existence, of episodic memory. On dominant versions of the 'common system' view, on which a single simulation system underlies both remembering and imagining, there are no processes unique to memory to support robust generalizations with inductive potential. Eliminativism about episodic memory seems to follow from the claim that it has no dedicated neurocognitive system of its own. After identifying this under-noticed threat, we push back against modern eliminativists by surveying recent evidence that still indicates specialized mechanisms, computations and representations that are distinctly mnemic in character. We argue that contemporary realists about episodic memory can retain lessons of the common system approach while resisting the further move to eliminativism. This article is part of the theme issue 'Elements of episodic memory: lessons from 40 years of research'.

Identifying transgene insertions in Caenorhabditis elegans genomes with Oxford Nanopore sequencing.

Genetically modified organisms are commonly used in disease research and agriculture but the precise genomic alterations underlying transgenic mutations are often unknown. The position and characteristics of transgenes, including the number of independent insertions, influences the expression of both transgenic and wild-type sequences. We used long-read, Oxford Nanopore Technologies (ONT) to sequence and assemble two transgenic strains of Caenorhabditis elegans commonly used in the research of neurodegenerative diseases: BY250 (pPdat-1::GFP) and UA44 (GFP and human α-synuclein), a model for Parkinson's research. After scaffolding to the reference, the final assembled sequences were ∼102 Mb with N50s of 17.9 Mb and 18.0 Mb, respectively, and L90s of six contiguous sequences, representing chromosome-level assemblies. Each of the assembled sequences contained more than 99.2% of the Nematoda BUSCO genes found in the C. elegans reference and 99.5% of the annotated C. elegans reference protein-coding genes. We identified the locations of the transgene insertions and confirmed that all transgene sequences were inserted in intergenic regions, leaving the organismal gene content intact. The transgenic C. elegans genomes presented here will be a valuable resource for Parkinson's research as well as other neurodegenerative diseases. Our work demonstrates that long-read sequencing is a fast, cost-effective way to assemble genome sequences and characterize mutant lines and strains.

Mnemicity: A Cognitive Gadget?

Episodic representations can be entertained either as "remembered" or "imagined"-as outcomes of experience or as simulations of such experience. Here, we argue that this feature is the product of a dedicated cognitive function: the metacognitive capacity to determine the mnemicity of mental event simulations. We argue that mnemicity attribution should be distinguished from other metacognitive operations (such as reality monitoring) and propose that this attribution is a "cognitive gadget"-a distinctively human ability made possible by cultural learning. Cultural learning is a type of social learning in which traits are inherited through social interaction. In the case of mnemicity, one culturally learns to discriminate metacognitive "feelings of remembering" from other perceptual, emotional, action-related, and metacognitive feelings; to interpret feelings of remembering as indicators of memory rather than imagination; and to broadcast the interpreted feelings in culture- and context-specific ways, such as "I was there" or "I witnessed it myself." We review evidence from the literature on memory development and scaffolding, metacognitive learning and teaching, as well as cross-cultural psychology in support of this view before pointing out various open questions about the nature and development of mnemicity highlighted by our account.

Pancreaticoduodenectomy for the treatment of groove pancreatitis.

BACKGROUND AND AIM: Groove pancreatitis is a segmental form of chronic pancreatitis that can be treated with pancreaticoduodenectomy (PD), although outcome studies for this approach are lacking. We performed an assessment of pain symptoms, need for opioids, and weight gain following PD for symptomatic groove pancreatitis. METHODS: The study was a retrospective case series describing all patients with groove pancreatitis who underwent PD at our medical center. The primary outcome was the change in pain level and opioid use following PD. RESULTS: Five patients underwent PD for treatment of groove pancreatitis. Patients' perception of pain, using a 10-point visual analog scale, improved after surgery from 5.0 to 0.2. Opioid analgesics, as measured by oral morphine equivalents, dropped from 77.6 to 0 mg daily, with all five patients being completely free of opioids post-operatively. Weight loss ceased in all five patients, with an overall mean weight gain of 15.4 pounds post-operatively. CONCLUSIONS: PD reduces pain and opioid analgesic use in groove pancreatitis. This intervention should be considered for patients with this condition.

Assessment of Aspergillus fumigatus in guinea pig bronchoalveolar lavages and pulmonary tissue by culture and realtime polymerase chain reaction studies.

In this study we pursued a diagnostic target in Aspergillus fumigatus (AF) by using qualitative Realtime PCR combined with proprietary DNA primers and a hydrolysis probe specific for this fungal target. Qualitative Realtime PCR is a diagnostic tool that utilizes Realtime PCR technology and detects the presence or absence target specific DNA within a predetermined detection range. Respiratory tissue and fluids from experimentally infected guinea pigs were tested by extracting DNA from the samples which were amplified and detected using AF specific DNA primers and probe. This study included qualitative evaluations of all specimens for the presence of the DNA of AF. The findings in the tissues after AF infection were compared to the numbers of spores in aerosolized samples used to inoculate the animals. Results demonstrated that the specific probe and primer set could detect the presence or absence of AF DNA in the sample. The qualitative detection limit of the assay ranged from 6 × 10(4) copies to 6 copies. Since blood cultures are rarely positive for Aspergillosis, our data indicate that qualitative Realtime PCR, in combination with the appropriate DNA primers and probe can serve as an effective diagnostic tool in the early detection of fungal infections.

Complete Genome Sequence of Rhodococcus opacus Strain MoAcy1 (DSM 44186), an Aerobic Acetylenotroph Isolated from Soil.

We report the genome of Rhodococcus opacus strain MoAcy1 (DSM 44186), an aerobic soil isolate capable of using acetylene as its primary carbon and energy source (acetylenotrophy). The genome is composed of a single circular chromosome of ∼8 Mbp and two closed plasmids, with a G+C content of 67.3%.

Ageing Together: Interdependence in the Memory Compensation Strategies of Long-Married Older Couples.

People live and age together in social groups. Across a range of outcomes, research has identified interdependence in the cognitive and health trajectories of ageing couples. Various types of memory decline with age and people report using a range of internal and external, social, and material strategies to compensate for these declines. While memory compensation strategies have been widely studied, research so far has focused only on single individuals. We examined interdependence in the memory compensation strategies reported by spouses within 58 older couples. Couples completed the Memory Compensation Questionnaire, as well as an open-ended interview about their memory compensation practices. We found that internal, intra-individual memory compensation strategies were not associated within couples, but external, extra-individual strategies showed interdependence. Individuals' scores on material/technological compensation strategies were positively correlated with their partners'. Reported reliance on a spouse was higher for men and increased with age. Our open-ended interviews yielded rich insights into the complex and diverse resources that couples use to support memory in day-to-day life. Particularly evident was the extent of interaction and coordination between social and material compensation, such that couples jointly used external compensation resources. Our results suggest that individuals' reports of their compensation strategies do not tell the whole story. Rather, we propose that older couples show interdependence in their memory compensation strategies, and adopt complex systems of integrated material and social memory compensation in their day-to-day lives.

Optimizing experimental design for genome sequencing and assembly with Oxford Nanopore Technologies.

High quality reference genome sequences are the core of modern genomics. Oxford Nanopore Technologies (ONT) produces inexpensive DNA sequences, but has high error rates, which make sequence assembly and analysis difficult as genome size and complexity increases. Robust experimental design is necessary for ONT genome sequencing and assembly, but few studies have addressed eukaryotic organisms. Here, we present novel results using simulated and empirical ONT and DNA libraries to identify best practices for sequencing and assembly for several model species. We find that the unique error structure of ONT libraries causes errors to accumulate and assembly statistics plateau as sequence depth increases. High-quality assembled eukaryotic sequences require high-molecular-weight DNA extractions that increase sequence read length, and computational protocols that reduce error through pre-assembly correction and read selection. Our quantitative results will be helpful for researchers seeking guidance for de novo assembly projects.

Synchronous vs. non-synchronous imitation: Using dance to explore interpersonal coordination during observational learning.

Observational learning can enhance the acquisition and performance quality of complex motor skills. While an extensive body of research has focused on the benefits of synchronous (i.e., concurrent physical practice) and non-synchronous (i.e., delayed physical practice) observational learning strategies, the question remains as to whether these approaches differentially influence performance outcomes. Accordingly, we investigate the differential outcomes of synchronous and non-synchronous observational training contexts using a novel dance sequence. Using multidimensional cross-recurrence quantification analysis, movement time-series were recorded for novice dancers who either synchronised with (n = 22) or observed and then imitated (n = 20) an expert dancer. Participants performed a 16-count choreographed dance sequence for 20 trials assisted by the expert, followed by one final, unassisted performance trial. Although end-state performance did not significantly differ between synchronous and non-synchronous learners, a significant decline in performance quality from imitation to independent replication was shown for synchronous learners. A non-significant positive trend in performance accuracy was shown for non-synchronous learners. For all participants, better imitative performance across training trials led to better end-state performance, but only for the accuracy (and not timing) of movement reproduction. Collectively, the results suggest that synchronous learners came to rely on a real-time mapping process between visual input from the expert and their own visual and proprioceptive intrinsic feedback, to the detriment of learning. Thus, the act of synchronising alone does not ensure an appropriate training context for advanced sequence learning.