Methodological advances enabled by the construction of a synthetic yeast genome.

The international Synthetic Yeast Project (Sc2.0) aims to construct the first synthetic designer eukaryote genome. Over the past few years, the Sc2.0 consortium has achieved several significant milestones by synthesizing and characterizing all 16 nuclear chromosomes of the yeast Saccharomyces cerevisiae, as well as a 17thde novo neochromosome containing all nuclear tRNA genes. In this commentary, we discuss the recent technological advances achieved in this project and provide a perspective on how they will impact the emerging field of synthetic genomics in the future.

Chromosome-scale assembly of the streamlined picoeukaryote Picochlorum sp. SENEW3 genome reveals Rabl-like chromatin structure and potential for C4 photosynthesis.

Genome sequencing and assembly of the photosynthetic picoeukaryotic Picochlorum sp. SENEW3 revealed a compact genome with a reduced gene set, few repetitive sequences, and an organized Rabl-like chromatin structure. Hi-C chromosome conformation capture revealed evidence of possible chromosomal translocations, as well as putative centromere locations. Maintenance of a relatively few selenoproteins, as compared to similarly sized marine picoprasinophytes Mamiellales, and broad halotolerance compared to others in Trebouxiophyceae, suggests evolutionary adaptation to variable salinity environments. Such adaptation may have driven size and genome minimization and have been enabled by the retention of a high number of membrane transporters. Identification of required pathway genes for both CAM and C4 photosynthetic carbon fixation, known to exist in the marine mamiellale pico-prasinophytes and seaweed Ulva, but few other chlorophyte species, further highlights the unique adaptations of this robust alga. This high-quality assembly provides a significant advance in the resources available for genomic investigations of this and other photosynthetic picoeukaryotes.

Killer yeasts: expanding frontiers in the age of synthetic biology.

Killer yeasts secrete protein toxins that are selectively lethal to other yeast and filamentous fungi. These exhibit exceptional genetic and functional diversity, and have several biotechnological applications. However, despite decades of research, several limitations hinder their widespread adoption. In this perspective we contend that technical advances in synthetic biology present an unprecedented opportunity to unlock the full potential of yeast killer systems across a spectrum of applications. By leveraging these new technologies, engineered killer toxins may emerge as a pivotal new tool to address antifungal resistance and food security. Finally, we speculate on the biotechnological potential of re-engineering host double-stranded (ds) RNA mycoviruses, from which many toxins derive, as a safe and noninfectious system to produce designer RNA.

Debugging and consolidating multiple synthetic chromosomes reveals combinatorial genetic interactions.

The Sc2.0 project is building a eukaryotic synthetic genome from scratch. A major milestone has been achieved with all individual Sc2.0 chromosomes assembled. Here, we describe the consolidation of multiple synthetic chromosomes using advanced endoreduplication intercrossing with tRNA expression cassettes to generate a strain with 6.5 synthetic chromosomes. The 3D chromosome organization and transcript isoform profiles were evaluated using Hi-C and long-read direct RNA sequencing. We developed CRISPR Directed Biallelic URA3-assisted Genome Scan, or "CRISPR D-BUGS," to map phenotypic variants caused by specific designer modifications, known as "bugs." We first fine-mapped a bug in synthetic chromosome II (synII) and then discovered a combinatorial interaction associated with synIII and synX, revealing an unexpected genetic interaction that links transcriptional regulation, inositol metabolism, and tRNASerCGA abundance. Finally, to expedite consolidation, we employed chromosome substitution to incorporate the largest chromosome (synIV), thereby consolidating >50% of the Sc2.0 genome in one strain.

Design, construction, and functional characterization of a tRNA neochromosome in yeast.

Here, we report the design, construction, and characterization of a tRNA neochromosome, a designer chromosome that functions as an additional, de novo counterpart to the native complement of Saccharomyces cerevisiae. Intending to address one of the central design principles of the Sc2.0 project, the ∼190-kb tRNA neochromosome houses all 275 relocated nuclear tRNA genes. To maximize stability, the design incorporates orthogonal genetic elements from non-S. cerevisiae yeast species. Furthermore, the presence of 283 rox recombination sites enables an orthogonal tRNA SCRaMbLE system. Following construction in yeast, we obtained evidence of a potent selective force, manifesting as a spontaneous doubling in cell ploidy. Furthermore, tRNA sequencing, transcriptomics, proteomics, nucleosome mapping, replication profiling, FISH, and Hi-C were undertaken to investigate questions of tRNA neochromosome behavior and function. Its construction demonstrates the remarkable tractability of the yeast model and opens up opportunities to directly test hypotheses surrounding these essential non-coding RNAs.

Synthetic yeast chromosome XI design provides a testbed for the study of extrachromosomal circular DNA dynamics.

We describe construction of the synthetic yeast chromosome XI (synXI) and reveal the effects of redesign at non-coding DNA elements. The 660-kb synthetic yeast genome project (Sc2.0) chromosome was assembled from synthesized DNA fragments before CRISPR-based methods were used in a process of bug discovery, redesign, and chromosome repair, including precise compaction of 200 kb of repeat sequence. Repaired defects were related to poor centromere function and mitochondrial health and were associated with modifications to non-coding regions. As part of the Sc2.0 design, loxPsym sequences for Cre-mediated recombination are inserted between most genes. Using the GAP1 locus from chromosome XI, we show that these sites can facilitate induced extrachromosomal circular DNA (eccDNA) formation, allowing direct study of the effects and propagation of these important molecules. Construction and characterization of synXI contributes to our understanding of non-coding DNA elements, provides a useful tool for eccDNA study, and will inform future synthetic genome design.

Parallel laboratory evolution and rational debugging reveal genomic plasticity to S. cerevisiae synthetic chromosome XIV defects.

Synthetic chromosome engineering is a complex process due to the need to identify and repair growth defects and deal with combinatorial gene essentiality when rearranging chromosomes. To alleviate these issues, we have demonstrated novel approaches for repairing and rearranging synthetic Saccharomyces cerevisiae genomes. We have designed, constructed, and restored wild-type fitness to a synthetic 753,096-bp version of S. cerevisiae chromosome XIV as part of the Synthetic Yeast Genome project. In parallel to the use of rational engineering approaches to restore wild-type fitness, we used adaptive laboratory evolution to generate a general growth-defect-suppressor rearrangement in the form of increased TAR1 copy number. We also extended the utility of the synthetic chromosome recombination and modification by loxPsym-mediated evolution (SCRaMbLE) system by engineering synthetic-wild-type tetraploid hybrid strains that buffer against essential gene loss, highlighting the plasticity of the S. cerevisiae genome in the presence of rational and non-rational modifications.

Visioning synthetic futures for yeast research within the context of current global techno-political trends.

Yeast research is entering into a new period of scholarship, with new scientific tools, new questions to ask and new issues to consider. The politics of emerging and critical technology can no longer be separated from the pursuit of basic science in fields, such as synthetic biology and engineering biology. Given the intensifying race for technological leadership, yeast research is likely to attract significant investment from government, and that it offers huge opportunities to the curious minded from a basic research standpoint. This article provides an overview of new directions in yeast research with a focus on Saccharomyces cerevisiae, and places these trends in their geopolitical context. At the highest level, yeast research is situated within the ongoing convergence of the life sciences with the information sciences. This convergent effect is most strongly pronounced in areas of AI-enabled tools for the life sciences, and the creation of synthetic genomes, minimal genomes, pan-genomes, neochromosomes and metagenomes using computer-assisted design tools and methodologies. Synthetic yeast futures encompass basic and applied science questions that will be of intense interest to government and nongovernment funding sources. It is essential for the yeast research community to map and understand the context of their research to ensure their collaborations turn global challenges into research opportunities.

Assessing acceptance and effects of child feeding counselling on nutritional status of children aged 6-23 months in a semi-urban community.

In Bangladesh, only 34 % of the children aged 18-23 months old are given minimum acceptable diets of complementary foods. Objective of the study was to find the effects of complementary feeding counselling on nutritional status among 6-23 months old children of poor families. This was a community-based randomised control trial. A total of 192 children in two groups were randomly selected. Nutrition education was given for a period of 4 months with post-intervention follow-up for 2 months. After 4 months of intervention, the difference in height for age Z score, weight for height Z score and weight for age Z score were significantly higher in the intervention group than in the control group (1·01 ± 0·31 v. 0·19 ± 0·01, P =< 0·001; 1·34 ± 0·15 v 0·72 ± 0·11, P =< 0·001; 1·5 ± 0·24 v. 0·62 ± 0·04, P =< 0·001). Mid-upper arm circumference Z score also improved in the intervention group than in the control group (0·95 ± 0·03 v. 0·57 ± 0·12, P =< 0·001). Morbidity of the children in the intervention group significantly reduced than in the control group (49 % v 80·20 %, P =< 0·001). Higher feeding frequency (3-4 times) (71·9 % v. 45·8 %) and energy intake increased in the intervention group than in the control group. Promotion of complementary feeding from the family foods can improve the nutritional status of 6-23 months old children of poor families within a short period.

Effectiveness of home-based "egg-suji" diet in management of severe acute malnutrition of Rohingya refugee children.

BACKGROUND: Prevalence of severe acute malnutrition (SAM) among Rohingya children aged 6-59 months who took shelter in refugee camp in Cox's Bazar District, Bangladesh, was found to be 7.5%. OBJECTIVE: To measure the effectiveness of homemade diet in the management of severe acute malnutrition of Rohingya refugee children. METHODS: In total, 645 SAM children (MUAC < 11.5 cm) aged 6-59 months were selected and fed the homemade diet for 3 months by their caregivers and followed up for next 2 months. Nutrition counseling, demonstration of food preparation and the ingredients of food (rice powder, egg, sugar and oil) were provided to the families for 3 months to cook "egg-suji" diet to feed the children. RESULTS: The study children were assessed for nutritional status. After intervention, energy intake from diet increased from 455.29 ± 120.9 kcal/day to 609.61 ± 29.5 kcal/day (P = 0.001) in 3 months. Frequency of daily food intake improved from 4.89 ± 1.02 to 5.94 ± 0.26 (P = 0.001). The body weight of children increased from 6.3 ± 1.04 kg to 9.93 ± 1.35 kg (P = 0.001), height increased from 67.93 ± 6.18 cm to 73.86 ± 0.35 (P = 0.001) cm, and MUAC improved from 11.14 ± 1.35 cm to 12.89 ± 0.37 cm (P = 0.001). HAZ improved from - 3.64 ± 1.35 to - 2.82 ± 1.40 (P = 0.001), WHZ improved from - 2.45 ± 1.23 to 1.03 ± 1.17 (P = 0.001), WAZ improved from - 3.8 ± 0.61 to - 0.69 ± 0.78, and MUACZ improved from - 3.32 ± 0.49 to 1.8 ± 0.54 (P = 0.001) from the beginning to the end of observation. Morbidity was found in 5.12% children in the first month which reduced to 0.15% at the end of follow-up. CONCLUSIONS: Nutritional counseling and supply of food ingredients at refugee camps resulted in complete recovery from severe malnutrition for all children which was sustainable.

Efficacy of Low-Level Laser Therapy in Management of Temporomandibular Joint Pain: A Double Blind and Placebo Controlled Trial.

Background: Stomatognathic system is an interaction of the muscles of mastication, dentition, neural component, and temporomandibular joint. Any dysfunction in this system may lead to temporomandibular disorders (TMDs). Various non-surgical modalities have been employed for treating TMDs. Aim and objectives: The aim of the study was to objectively evaluate the effects of low-level laser therapy (LLLT) in treatment of patients with TMDs. Materials and Methods: Sixty individuals diagnosed with TMDs were divided randomly into two groups (Group I-placebo and Group II -LLLT). A series of 20 sessions of LLLT applied both in closed mouth and maximum mouth opening position were given over a period of 08 weeks. Assessment was done in terms of improvement in mouth opening, pain, clicking, and deviation of mandible. The data collected were analyzed statistically. Results: The results showed improvement in the pain reduction, improvement in the maximum mouth opening, reduction in deviation, and clicking in both groups but better treatment outcome in the low-level laser group. Conclusion: Though conservative measures improved the symptoms in TMD but LLLT has shown better results in comparison with the placebo group. Being non-surgical can be employed in combination with other modes for effectively treating such disorders. Keywords: Pain, Dysfunction, Temporomandibular joint disorders (TMDs), Low-level laser therapy (LLLT).

The Shishu Pushti Trial-Extended Peer Counseling for Improving Feeding Practices and Reducing Undernutrition in Children Aged 0-48 Months in Urban Bangladesh: Protocol for a Cluster-Randomized Controlled Trial.

BACKGROUND: The aim of this study is to assess if peer counseling of women improves breastfeeding, complementary feeding practices, and child growth, and thus reduces the prevalence of undernutrition in children up to 4 years of age. OBJECTIVE: Lack of exclusive breastfeeding and inappropriate complementary feeding are critical factors in reducing child undernutrition, morbidity, and mortality. There are reported trials of peer counseling to improve breastfeeding; however, they did not examine the efficacy of peer counseling to improve complementary feeding or the long-term impacts on child growth and development. METHODS: This study has used a community-based, cluster-randomized controlled trial with a superiority design and 2 parallel treatment arms. It is assessing the impact of peer counseling, starting in late pregnancy up to 1 year after delivery, on child feeding practices, growth, and development with follow-up until 48 months of age. The study site was Mirpur, a densely populated area in Dhaka. Using satellite maps and geographic information system mapping, we constructed 36 clusters with an average population of 5000 people. We recruited pregnant women in the third trimester aged 16-40 years, with no more than 3 living children. Trained peer counselors visited women at home twice before delivery, 4 times in the first month, monthly from 2 to 6 months, and again at 9 and 12 months. Trained research assistants collected anthropometric measurements. The primary outcome will be differences in child stunting and mean length for age at 6, 12, 15, and 18 months. Secondary outcomes will be differences in the percentage of women exclusively breastfeeding in the mean duration of any breastfeeding and in the percentage of children at 6 and 9 months of age who receive solid, semisolid, or soft foods; and the percentage of children consuming foods from 4 or more food groups at 9, 12, 15, and 18 months. We will assess the mean cognitive function scores from the Ages and Stages Questionnaire (9 and 18 months) and Bayley tests (24 and 36 months). RESULTS: We identified 65,535 people in mapped residences, from which we defined 36 clusters and randomly allocated them equally to intervention or control groups stratified by cluster socioeconomic status. From July 2011 to May 2013, we identified 1056 pregnant women and 993 births in the intervention group and 994 pregnancies and 890 births in the control group. At 18 months, 692 children remained in the intervention group and 551 in the control group. From January 2015 to February 2017, we conducted the long-term follow-up of the cohort. We have now completed the data collection and processing and have started analyses. CONCLUSIONS: This study will help fill the evidence gap about the short- and long-term impact of peer counseling on improving infant feeding, preventing childhood undernutrition, and enhancing child cognitive development. TRIAL REGISTRATION: ClinicalTrials.gov NCT01333995; https://clinicaltrials.gov/ct2/show/NCT01333995. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/31475.

Synthetic biology for the engineering of complex wine yeast communities.

Wine fermentation is a representation of complex higher-order microbial interactions. Despite the beneficial properties that these communities bring to wine, their complexity poses challenges in predicting the nature and outcome of fermentation. Technological developments in synthetic biology enable the potential to engineer synthetic microbial communities for new purposes. Here we present the challenges and applications of engineered yeast communities in the context of a wine fermentation vessel, how this represents a model system to enable novel solutions for winemaking and introduce the concept of a 'synthetic' terroir. Furthermore, we introduce our vision for the application of control engineering.

Perceived stress, eating behavior, and overweight and obesity among urban adolescents.

BACKGROUND: WHO estimated 20% of adolescents (10-19 years) have mental health problems. We examined the prevalence and associated risk predictors of overweight/obesity and perceived stress using eating behaviors and physical activity among school-and-college-going urban adolescents in Bangladesh. METHODS: A cross-sectional study with a multistage sampling technique was employed to select 4609 adolescent students, aged 13-19 years, from all eight Bangladesh divisions during January-June 2019. Data were collected using a self-administered questionnaire containing Turconi Physical Activity Questionnaire (PAQ), Adolescent Stress Questionnaire (ASQ), Dutch Eating Behavior Questionnaire (DEBQ), and Anthropometric measurements. Logistic regression and different association measures assessed relationships among adolescent characteristics. RESULTS: The major 61.5% of adolescents were in moderate-to-extremely-severe levels of stress, 28.2% were overweight/obese, only 2.7% had a very active lifestyle, and 30.5% had a sedentary lifestyle. Perceived stress was positively and significantly correlated with eating behaviors and body mass index, whereas physical activity was significantly associated with the prevalence of overweight/obesity and high stress. The prevalence of overweight/obesity (53.8%) and high stress (52.5%) was higher in males. Adolescents' obesity was 2.212 times more likely who had a sedentary lifestyle (95% CI 1.377-3.552), 1.13 times more likely for those who had experienced stress due to school/leisure conflict (95% CI 1.051-1.222), and 1.634 times more likely for those who were tempted by restrained eating behavior (95% CI 1.495-1.786). CONCLUSION: Stress on secondary school-and-college-going students needs to be recognized, and strategies need to be developed to improve adolescents' mental health.

Enhancing Yeast Alcoholic Fermentations.

The production of ethanol by yeast fermentation represents the largest of all global biotechnologies. Consequently, the yeast Saccharomyces cerevisiae is the world's premier industrial microorganism, which is responsible not only for the production of alcoholic beverages, including beer, wine, and distilled spirits, but also for the billions of liters of bioethanol produced annually for use as a renewable transportation fuel. Although humankind has exploited the fermentative activities of yeasts for millennia, many aspects of alcohol fermentation remain poorly understood. This chapter will review some of the key considerations in optimizing industrial alcohol fermentations with a particular emphasis on enhancement opportunities involving cell physiology and strain engineering of the major microbial ethanologen, the yeast S. cerevisiae.

Applications of Yeast Synthetic Biology Geared towards the Production of Biopharmaceuticals.

Engineered yeast are an important production platform for the biosynthesis of high-value compounds with medical applications. Recent years have witnessed several new developments in this area, largely spurred by advances in the field of synthetic biology and the elucidation of natural metabolic pathways. This minireview presents an overview of synthetic biology applications for the heterologous biosynthesis of biopharmaceuticals in yeast and demonstrates the power and potential of yeast cell factories by highlighting several recent examples. In addition, an outline of emerging trends in this rapidly-developing area is discussed, hinting upon the potential state-of-the-art in the years ahead.

No yield penalty under favorable conditions paving the way for successful adoption of flood tolerant rice.

Flooding is one of the major constraints for rice production in rainfed lowlands, especially in years and areas of high rainfall. Incorporating the Sub1 (Submergence1) gene into high yielding popular varieties has proven to be the most feasible approach to sustain rice production in submergence-prone areas. Introgression of this QTL into popular varieties has resulted in considerable improvement in yield after flooding. However, its impact under non-flooded conditions or years have not been thoroughly evaluated which is important for the farmers to accept and adopt any new version of their popular varieties. The present study was carried out to evaluate the effect of Sub1 on grain yield of rice in different genetic backgrounds, under non-submergence conditions, over years and locations. The study was carried out using head to head trials in farmer's fields, which enable the farmers to more accurately compare the performance of Sub1 varieties with their recurrent parents under own management. The data generated from different head to head trials revealed that the grain yield of Sub1 varieties was either statistically similar or higher than their non-Sub1 counterparts under non-submergence conditions. Thus, Sub1 rice varieties show no instance of yield penalty of the introgressed gene.

Identification of mega-environments and rice genotypes for general and specific adaptation to saline and alkaline stresses in India.

In the present study, a total of 53 promising salt-tolerant genotypes were tested across 18 salt-affected diverse locations for three years. An attempt was made to identify ideal test locations and mega-environments using GGE biplot analysis. The CSSRI sodic environment was the most discriminating location in individual years as well as over the years and could be used to screen out unstable and salt-sensitive genotypes. Genotypes CSR36, CSR-2K-219, and CSR-2K-262 were found ideal across years. Overall, Genotypes CSR-2K-219, CSR-2K-262, and CSR-2K-242 were found superior and stable among all genotypes with higher mean yields. Different sets of genotypes emerged as winners in saline soils but not in sodic soils; however, Genotype CSR-2K-262 was the only genotype that was best under both saline and alkaline environments over the years. The lack of repeatable associations among locations and repeatable mega-environment groupings indicated the complexity of soil salinity. Hence, a multi-location and multi-year evaluation is indispensable for evaluating the test sites as well as identifying genotypes with consistently specific and wider adaptation to particular agro-climatic zones. The genotypes identified in the present study could be used for commercial cultivation across edaphically challenged areas for sustainable production.

Opportunities for strengthening infant and young child feeding policies in South Asia: Insights from the SAIFRN policy analysis project.

BACKGROUND: South Asian countries experience some of the highest levels of child undernutrition in the world, strongly linked to poor infant and young child feeding (IYCF) practices. Strong and responsive policy support is essential for effective interventions to improve IYCF. This study aimed to identify opportunities for strengthening the policy environment in the region to better support appropriate infant and young child feeding. METHODS: We mapped policies relevant to infant and young child feeding in India, Pakistan, Bangladesh, Sri Lanka and Nepal, based on a common matrix. The matrix described potentially relevant policies ranging from high-level strategic policy documents to implementation-level guidelines. We analyzed the data based on themes focused on caregiver interactions with IYCF interventions: provision of correct information to mothers, training of frontline workers, enabling mothers to engage with service providers and strategic support for IYCF. RESULTS: Policy support for IYCF was present in relation to each of the themes assessed. In all countries, there was support for nutrition in National Development Plans, and all countries had some level of maternity protection and restrictions on marketing of breast milk substitutes. Sectoral and implementation-level policy documents contained provisions for system strengthening for IYCF and for training of frontline workers. CONCLUSIONS: The key opportunities for strengthening IYCF policy support were in relation to translating strategic directives into implementation level documents; improving multi-sectoral support and coordination; and increased clarity regarding roles and responsibilities of frontline workers interacting with mothers. These findings can support efforts to strengthen IYCF policy at the national and regional level.

Obstructive jaundice: a clinical review for the UK armed forces.

Obstructive jaundice is a clinical condition that indicates the possibility of a significant underlying disease process. This clinical review considers the pathophysiology, investigation and management of patients with obstructive jaundice and considers the particular challenges that medical personnel may face when deployed away from the United Kingdom (UK). It aims to give guidance with regard to the short- and long-term investigation and management of such patients.