Emergent digital bio-computation through spatial diffusion and engineered bacteria.

Biological computing is a promising field with potential applications in biosafety, environmental monitoring, and personalized medicine. Here we present work on the design of bacterial computers using spatial patterning to process information in the form of diffusible morphogen-like signals. We demonstrate, mathematically and experimentally, that single, modular, colonies can perform simple digital logic, and that complex functions can be built by combining multiple colonies, removing the need for further genetic engineering. We extend our experimental system to incorporate sender colonies as morphogen sources, demonstrating how one might integrate different biochemical inputs. Our approach will open up ways to perform biological computation, with applications in bioengineering, biomaterials and biosensing. Ultimately, these computational bacterial communities will help us explore information processing in natural biological systems.

Psychometric Properties of Psychosexual Functioning Survey Among Autistic and Non-autistic Adults: Adapting the Self-Report Teen Transition Inventory to the U.S. Context.

Psychosexual functioning is an important aspect of human development and relationships. A previous study investigated psychosexual functioning of autistic adolescents using the Teen Transition Inventory (TTI), but there is a lack of comprehensive measurement of psychosexual functioning among autistic and non-autistic (NA) adults. To address this gap, the current study adapted the self-report TTI to the Psychosexual Functioning Survey (PSFS) and presented it to 131 autistic (n = 59) and NA adults (n = 72) in the U.S. Comparisons of psychometric properties between the original TTI and the PSFS are shared; the developmental relevancy among some items was changed, and the alphas indicated a difference in the content of certain scales. Differences emerged between autistic and NA adults in both the intra- and interpersonal domains of psychosexual functioning, but not in sexual and intimate behaviors. The findings suggest the persistence of differences from adolescence to adulthood between autistic and NA people and highlight the importance of understanding the unique experiences of adults in psychosexual functioning relative to diagnostic status.

Children with Autism Spectrum Disorder in Times of COVID-19: Examining Emotional and Behavioral Problems, Parental Well-Being, and Resilience.

This longitudinal study assessed the impact of the COVID-19 pandemic on children with autism spectrum disorder (ASD; n = 62; Mage = 13 years) by measuring emotional and behavioral problems before and during the pandemic, and by comparing this change to a matched sample of children without ASD (n = 213; Mage = 16 years). Moreover, we examined whether indicators of parental well-being promoted resilience of children with ASD. Results showed that the mean change in problems did not differ between children with and without ASD. Importantly, some children showed an increase in problems, while others showed resilience. Parental well-being indicators were not related to resilience among children with ASD. The interindividual variability in responses, particularly among children with ASD, highlights the need for personalized support.

Adapting the Tackling Teenage Training Sex Education Program for Autistic Adults in the US: A Pilot Study.

Despite the established need for sexuality and relationship programming for autistic adults, there are extremely limited curricula for this population. This pilot study used an evidence-based sexuality and relationship education program for autistic adolescents (Tackling Teenage Training) as the basis for an adult-focused virtual psychoeducational group. Qualitative feedback, quantitative ratings of the programming, and behavioral surveys from participants were collected. Nine participants completed the program, and corresponding pre and post measures. Highly rated topics, for example gender identity and online dating, were consistent with previous research on what autistic adults want from a sexuality and relationship education program. Future programming should incorporate increased attention to themes and topics highlighted by participants, and should utilize the teaching tools (e.g., role play, peer discussions) identified as useful by the participants.

Complementing or Congruent? Desired Characteristics in a Friend and Romantic Partner in Autistic versus Typically Developing Male Adolescents.

Ideal friend and romantic partner characteristics related to self-perceived characteristics have been investigated in typically developing (TD) individuals, but not in individuals with autism spectrum disorder (ASD). Considering the autistic symptoms and challenges, investigating these concepts in autistic individuals is relevant. Given the lack of consensus, identity-first ("autistic person") and person-first ("person with autism") language are mixed throughout, to cover all preferences. This study explored (1) the association between self-perceived characteristics and desires in a friend/romantic partner, as well as (2) compare two groups (ASD and TD) in their desires for a friend/romantic partner. Two matched groups (ASD and TD) of 38 male adolescents (age 14-19 years) reported on the desire for nine characteristics (i.e., funny, popular, nice, cool, smart, trustworthy, good looking, similar interests, and being rich) in a friend/partner, and to what extent they felt they themselves possessed seven characteristics (i.e., funny, popular, nice, cool, smart, trustworthy, and good looking). Results showed both groups sought a friend and partner similar to themselves on intrinsic characteristics (e.g., trustworthiness), but less similar on extrinsic and social status characteristics (e.g., being less cool and popular). Particularly intrinsic characteristics, more than extrinsic and social status characteristics, were valued in both partners and friends, regardless of group. No significant differences were found between groups concerning to what extent characteristics were desired. Overall, adolescents with ASD desire similar characteristics as TD adolescents in their potential romantic partners and friends. There is some indication that the match between self-perception and desired characteristics is different.

Microbiome engineering: engineered live biotherapeutic products for treating human disease.

The human microbiota is implicated in many disease states, including neurological disorders, cancer, and inflammatory diseases. This potentially huge impact on human health has prompted the development of microbiome engineering methods, which attempt to adapt the composition and function of the human host-microbiota system for a therapeutic purpose. One promising method is the use of engineered microorganisms that have been modified to perform a therapeutic function. The majority of these products have only been demonstrated in laboratory models; however, in recent years more concepts have reached the translational stage. This has led to an increase in the number of clinical trials, which are designed to assess the safety and efficacy of these treatments in humans. Within this review, we highlight the progress of some of these microbiome engineering clinical studies, with a focus on engineered live biotherapeutic products.

Impact of the COVID-19 pandemic on children and adolescents with autism spectrum disorder and their families: a mixed-methods study protocol.

BACKGROUND: The COVID-19 pandemic is a challenge for everyone, particularly for children and adolescents with autism spectrum disorder (ASD). ASD is a developmental disorder characterised by limitations in social communication, repetitive behavioural patterns, and limited interests, and activities. It is expected that many families with children with ASD will experience more problems due to the COVID-19 pandemic and the related public health restrictions. At the same time, some may experience improved functioning, due to fewer expectations and social demands. METHODS/DESIGN: In a mixed-method study to identify the impact of the COVID-19 pandemic, parents of children with ASD (ages 4-21) who were in care pre-COVID-19 at one of three large mental healthcare institutions in the region of Rotterdam participated (68 for T0, 57 for T1). The aims are (1) to investigate the impact of the COVID-19 pandemic on overall functioning and autistic symptoms of the child/adolescent with ASD, as well as parental and family functioning (QUANT-QUAL), in both the short term and longer term, and (2) to investigate risk and protective factors (in light of resilience) (QUANT-qual) and (3) to investigate care and informational needs (QUAL-quant). Pre-COVID-19 baseline data will be retrieved from clinical records. Participants will fill out two surveys (one during a COVID-19 peak-January-May 2021-and one thereafter). Survey participants were invited to participate in interviews (n=27). Surveys include measures thar were included pre-COVID-19 (ie, overall functioning and autism symptoms) as well as specific measures to identify family functioning and COVID-19 impact. The semistructured interviews focus on child, parent and family functioning and care-and informational needs. ETHICS AND DISSEMINATION: The Medical Ethics Committee of the Erasmus MC has approved the study. Findings will be available to families of children with ASD, their care providers, the funders, autism societies, the government and other researchers.

Komagataeibacter Tool Kit (KTK): A Modular Cloning System for Multigene Constructs and Programmed Protein Secretion from Cellulose Producing Bacteria.

Bacteria proficient at producing cellulose are an attractive synthetic biology host for the emerging field of Engineered Living Materials (ELMs). Species from the Komagataeibacter genus produce high yields of pure cellulose materials in a short time with minimal resources, and pioneering work has shown that genetic engineering in these strains is possible and can be used to modify the material and its production. To accelerate synthetic biology progress in these bacteria, we introduce here the Komagataeibacter tool kit (KTK), a standardized modular cloning system based on Golden Gate DNA assembly that allows DNA parts to be combined to build complex multigene constructs expressed in bacteria from plasmids. Working in Komagataeibacter rhaeticus, we describe basic parts for this system, including promoters, fusion tags, and reporter proteins, before showcasing how the assembly system enables more complex designs. Specifically, we use KTK cloning to reformat the Escherichia coli curli amyloid fiber system for functional expression in K. rhaeticus, and go on to modify it as a system for programming protein secretion from the cellulose producing bacteria. With this toolkit, we aim to accelerate modular synthetic biology in these bacteria, and enable more rapid progress in the emerging ELMs community.

Engineered acetoacetate-inducible whole-cell biosensors based on the AtoSC two-component system.

Whole-cell biosensors hold potential in a variety of industrial, medical, and environmental applications. These biosensors can be constructed through the repurposing of bacterial sensing mechanisms, including the common two-component system (TCS). Here we report on the construction of a range of novel biosensors that are sensitive to acetoacetate, a molecule that plays a number of roles in human health and biology. These biosensors are based on the AtoSC TCS. An ordinary differential equation model to describe the action of the AtoSC TCS was developed and sensitivity analysis of this model used to help inform biosensor design. The final collection of biosensors constructed displayed a range of switching behaviours at physiologically relevant acetoacetate concentrations and can operate in several Escherichia coli host strains. It is envisaged that these biosensor strains will offer an alternative to currently available commercial strip tests and, in future, may be adopted for more complex in vivo or industrial monitoring applications.

Insight into Informant Discrepancies Regarding Psychosexual Functioning of Adolescents with and without Autism Spectrum Disorder.

The private nature of psychosexual functioning leads adolescents and their parents to have different perspectives, which highlights studying parent-child informant discrepancies in this domain. We investigated informant discrepancy in psychosexual functioning, using the self-report and parent report versions of the Teen Transition Inventory (TTI), of adolescents with autism spectrum disorder (ASD; 136 parent-child dyads) compared to adolescents from the general population (GP; 70 parent-child dyads). Significantly larger informant discrepancies exist in ASD dyads than GP dyads in most domains of psychosexual functioning, except for Body image, Sexual behavior, and Confidence in the future. It is important to use and pay attention to both informants, as discrepancies are relevant for both research and clinical practice regarding psychosexual functioning.

Transcriptional Terminators Allow Leak-Free Chromosomal Integration of Genetic Constructs in Cyanobacteria.

Cyanobacteria are promising candidates for sustainable bioproduction of chemicals from sunlight and carbon dioxide. However, the genetics and metabolism of cyanobacteria are less well understood than those of model heterotrophic organisms, and the suite of well-characterised cyanobacterial genetic tools and parts is less mature and complete. Transcriptional terminators use specific RNA structures to halt transcription and are routinely used in both natural and recombinant contexts to achieve independent control of gene expression and to 'insulate' genes and operons from one another. Insulating gene expression can be particularly important when heterologous or synthetic genetic constructs are inserted at genomic locations where transcriptional read-through from chromosomal promoters occurs, resulting in poor control of expression of the introduced genes. To date, few terminators have been described and characterised in cyanobacteria. In this work, nineteen heterologous, synthetic or putative native Rho-independent (intrinsic) terminators were tested in the model freshwater cyanobacterium, Synechocystis sp. PCC 6803, from which eleven strong terminators were identified. A subset of these strong terminators was then used to successfully insulate a chromosomally-integrated, rhamnose-inducible rhaBAD expression system from hypothesised 'read-through' from a neighbouring chromosomal promoter, resulting in greatly improved inducible control. The addition of validated strong terminators to the cyanobacterial toolkit will allow improved independent control of introduced genes.

Functionalizing cell-mimetic giant vesicles with encapsulated bacterial biosensors.

The design of vesicle microsystems as artificial cells (bottom-up synthetic biology) has traditionally relied on the incorporation of molecular components to impart functionality. These cell mimics have reduced capabilities compared with their engineered biological counterparts (top-down synthetic biology), as they lack the powerful metabolic and regulatory pathways associated with living systems. There is increasing scope for using whole intact cellular components as functional modules within artificial cells, as a route to increase the capabilities of artificial cells. In this feasibility study, we design and embed genetically engineered microbes (Escherichia coli) in a vesicle-based cell mimic and use them as biosensing modules for real-time monitoring of lactate in the external environment. Using this conceptual framework, the functionality of other microbial devices can be conferred into vesicle microsystems in the future, bridging the gap between bottom-up and top-down synthetic biology.

Constructing vesicle-based artificial cells with embedded living cells as organelle-like modules.

There is increasing interest in constructing artificial cells by functionalising lipid vesicles with biological and synthetic machinery. Due to their reduced complexity and lack of evolved biochemical pathways, the capabilities of artificial cells are limited in comparison to their biological counterparts. We show that encapsulating living cells in vesicles provides a means for artificial cells to leverage cellular biochemistry, with the encapsulated cells serving organelle-like functions as living modules inside a larger synthetic cell assembly. Using microfluidic technologies to construct such hybrid cellular bionic systems, we demonstrate that the vesicle host and the encapsulated cell operate in concert. The external architecture of the vesicle shields the cell from toxic surroundings, while the cell acts as a bioreactor module that processes encapsulated feedstock which is further processed by a synthetic enzymatic metabolism co-encapsulated in the vesicle.

Sense and sensitivity in bioprocessing-detecting cellular metabolites with biosensors.

Biosensors use biological elements to detect or quantify an analyte of interest. In bioprocessing, biosensors are employed to monitor key metabolites. There are two main types: fully biological systems or biological recognition coupled with physical/chemical detection. New developments in chemical biosensors include multiplexed detection using microfluidics. Synthetic biology can be used to engineer new biological biosensors with improved characteristics. Although there have been few biosensors developed for bioprocessing thus far, emerging trends can be applied in the future. A range of new platform technologies will enable rapid engineering of new biosensors based on transcriptional activation, riboswitches, and Förster Resonance Energy Transfer. However, translation to industry remains a challenge and more research into the robustness biosensors at scale is needed.

Psychosexual Functioning of Cognitively-able Adolescents with Autism Spectrum Disorder Compared to Typically Developing Peers: The Development and Testing of the Teen Transition Inventory- a Self- and Parent Report Questionnaire on Psychosexual Functioning.

To gain further insight into psychosexual functioning, including behaviors, intrapersonal and interpersonal aspects, in adolescents with Autism Spectrum Disorder (ASD), comprehensive, multi-informant measures are needed. This study describes (1) the development of a new measure of psychosexual functioning in both parent- and self-reports (Teen Transition Inventory; TTI) covering all three domains of psychosexual functioning (i.e. psychosexual socialization, psychosexual selfhood, and sexual/intimate behavior). And (2) the initial testing of this instrument, comparing adolescents with ASD (n = 79 parent-report; n = 58 self-report) to Typically Developing (TD) adolescents (n = 131 parent-report; n = 91 self-report) while taking into account gender as a covariate. Results from both informants indicate more difficulties regarding psychosexual socialization and psychosexual selfhood in the ASD group. With regard to sexual/intimate behavior, only parents reported significantly more problems in adolescents with ASD.

Comparative proteomics of Acidithiobacillus ferrooxidans grown in the presence and absence of uranium.

Acidithiobacillus ferrooxidans is an acidophile that thrives in metal-contaminated environments and tolerates high levels of uranium. To gain a better understanding of the processes involved in U(VI) resistance, comparative proteomics was used. The proteome of A. ferrooxidans was grown in the presence and absence of 0.5 mM U(VI); expression of 17 proteins was upregulated and one was downregulated. Most proteins with increased expression are part of the general stress response or are involved in reactive oxygen species detoxification. Four novel proteins showed increased expression in the presence of U(VI) and may contribute to U(VI) resistance via thiol homoeostasis and U(VI) binding.

The longitudinal relation between childhood autistic traits and psychosexual problems in early adolescence: The Tracking Adolescents' Individual Lives Survey study.

Individuals with autistic traits are considered to be prone to develop psychosexual problems due to their limited social skills and insight. This study investigated the longitudinal relation between autistic traits in childhood (T1; age 10-12 years) and parent-reported psychosexual problems in early adolescence (T2; age 12-15 years). In a general population cohort study (n = 1873; the Tracking Adolescents' Individual Lives Survey (TRAILS)), autistic traits and psychosexual problems were determined. Logistic regression analyses were used to investigate whether childhood autistic traits, in individuals displaying no psychosexual problems in childhood, predicted the presence of psychosexual problems in adolescence, while controlling for pubertal development and conduct problems. Higher levels of autistic traits at T1 significantly predicted mild psychosexual problems at T2, above and beyond pubertal development and conduct problems. Particularly two dimensions of autistic traits at T1 were significant predictors; i.e. 'reduced contact/social interest' and 'not optimally tuned to the social situation'. Children with autistic traits - especially those with limited social interest and social regulation problems - showed to have a higher risk to develop psychosexual problems, albeit mild, in early adolescence as reported by parents. Although we showed that autistic traits predict psychosexual problems, it is only one of multiple predictors.

Improving psychosexual knowledge in adolescents with autism spectrum disorder: pilot of the tackling teenage training program.

Previous studies have shown that psychosexual functioning in adolescents with autism spectrum disorder (ASD) is hampered and emphasize the need for a specialized training program tailored to their needs. Therefore, an individual training program was developed; the Tackling Teenage Training (TTT) program. The current pilot study systematically evaluated whether psychosexual knowledge increased after taking part in the TTT program, using a pre- and post-training design in 30 adolescents with ASD (77 % male, mean age = 14.80 years, mean intelligence = 96.96). Psychosexual knowledge increased significantly (pre-training total score: M = 25.74, SD = 6.20; post-training total score: M = 33.52 (SD = 2.78); F(1,29) = 65.20, p < .001). The TTT program may be useful to improve psychosexual knowledge and functioning in adolescents with ASD, yet these findings are preliminary, and a more elaborate controlled trial is needed.

Isolation and identification of cobalt- and caesium-resistant bacteria from a nuclear fuel storage pond.

One of the issues facing the nuclear power industry is how to store spent nuclear fuel which is contaminated with radionuclides produced during nuclear fission, including caesium ((134)Cs(+), (135)Cs(+) and (137)Cs(+)) and cobalt ((60)Co(2+)). In this study, we have isolated Co(2+)- and Cs(+)-resistant bacteria from water collected from a nuclear fuel storage pond. The most resistant Cs(+) and Co(2+) isolates grew in the presence of 500 mM CsCl and 3 mM CoCl2. Strain Cs67-2 is resistant to fourfold more Cs(+) than Cupriavidus metallidurans str. CH34 making it the most Cs(+)-resistant strain identified to date. The Cs(+)-resistant isolates were closely related to bacteria in the Serratia and Yersinia genera, while the Co(2+)-resistant isolates were closely related to the Curvibacter and Tardiphaga genera. These new isolates could be used for bioremediation.

Protein sliding and DNA denaturation are essential for DNA organization by human mitochondrial transcription factor A.

Mitochondria organize their genome in protein-DNA complexes called nucleoids. The mitochondrial transcription factor A (TFAM), a protein that regulates mitochondrial transcription, is abundant in these nucleoids. TFAM is believed to be essential for mitochondrial DNA compaction, yet the exact mechanism has not been resolved. Here we use a combination of single-molecule manipulation and fluorescence microscopy to show the nonspecific DNA-binding dynamics and compaction by TFAM. We observe that single TFAM proteins diffuse extensively over DNA (sliding) and, by collisions, form patches on DNA in a cooperative manner. Moreover, we demonstrate that TFAM induces compaction by changing the flexibility of the DNA, which can be explained by local denaturation of the DNA (melting). Both sliding of TFAM and DNA melting are also necessary characteristics for effective, specific transcription regulation by TFAM. This apparent connection between transcription and DNA organization clarifies how TFAM can accomplish two complementary roles in the mitochondrial nucleoid at the same time.