Miracle-dz/UniFAR-FTUs huggingface dataset:
Correlational networking guides the discovery of cryptic natural product biosynthetic enzymes

Bacterial natural product biosynthetic genes, canonically clustered, have been increasingly found to rely on cryptic enzymes encoded elsewhere in the genome for completion of biosynthesis. The study and application of lanthipeptides are frequently hindered by cryptic proteases required for final maturation. Here, we establish a global correlation network bridging the gap between lanthipeptide precursors and cryptic proteases. Applying our analysis to 161,954 bacterial genomes, we establish 5,209 correlations between precursors and cryptic proteases, with 91 prioritized. We use network predictions and co-expression analysis to reveal a previously missing protease for the maturation of class I lanthipeptide paenilan. We further discover widely distributed bacterial M16B metallopeptidases of previously unclear biological function as a new family of lanthipeptide proteases. We show the involvement of a pair of bifunctional M16B proteases in the production of novel class III lanthipeptides with high substrate specificity. Together, these results demonstrate the strength of our correlational networking approach to the discovery of cryptic lanthipeptide proteases and potentially other missing enzymes for natural products biosynthesis. Graphical abstract
From family to families: pushing family entrepreneurship forward

ABSTRACT The present guest editorial offers a review of the different conceptualizations of families in business used in research to date, shedding light on the unique characteristics of each type. Understanding the family through the lens of social systems theory offers a means for researchers to study contextually embedded family systems, offering a foundation for studying differences among families. We demonstrate that the family business system (ownership, business, family) is incomplete without a fourth component, that of the family in business. We then present the papers included in this special issue and highlight the collective contribution to research in the fields of family business and family entrepreneurship and provide directions for future research.
P3-MSDA: Multi-Source Domain Adaptation Network for Dynamic Visual Target Detection

Single-trial electroencephalogram detection has been widely applied in brain-computer interface (BCI) systems. Moreover, an individual generalized model is significant for applying the dynamic visual target detection BCI system in real life because of the time jitter of the detection latency, the dynamics and complexity of visual background. Hence, we developed an unsupervised multi-source domain adaptation network (P3-MSDA) for dynamic visual target detection. In this network, a P3 map-clustering method was proposed for source domain selection. The adversarial domain adaptation was conducted for domain alignment to eliminate individual differences, and prediction probabilities were ranked and returned to guide the input of target samples for imbalanced data classification. The results showed that individuals with a strong P3 map selected by the proposed P3 map-clustering method perform best on the source domain. Compared with existing schemes, the proposed P3-MSDA network achieved the highest classification accuracy and F1 score using five labeled individuals with a strong P3 map as the source domain. These findings can have a significant meaning in building an individual generalized model for dynamic visual target detection.
Identification of a New Giant Emrbryo Allele, and Integrated Transcriptomics and Metabolomics Analysis of Giant Embryo Development in Rice

Rice embryos are rich in high-quality protein, lipid, vitamins and minerals, representing the most important nutritional part of brown rice. However, the molecular mechanism of rice embryo development is poorly understood. In this study, two rice cultivars with contrasting embryo size (the giant embryo cultivar Dapeimi and the normal embryo cultivar 187R) were used to explore excellent genes controlling embryo size, and the developed near-isogenic lines (NILs) (NIL-D, which has the giant embryo phenotype, and its matching line, NIL-X) were used to explore transcript and metabolic properties in the earlier maturation stage of giant embryo development under natural conditions. The map-based cloning results demonstrated that Dapeimi is a novel allelic mutant of the rice GIANT EMBRYO (GE) gene, and the functional mutation site is a single cytosine deletion in the exon1. A total of 285 differentially accumulated metabolites (DAMs) and 677 differentially expressed genes (DEGs) were identified between NIL-D and NIL-X. The analysis of DAMs indicated that plants lacking GE mainly promoted energy metabolism, amino acid metabolism, and lipid metabolism pathways in the rice embryo. Pearson correlation coefficient showed that 300 pairs of gene-metabolites were highly correlated. Among them, OsZS_02G0528500 and OsZS_12G0013700 were considered to be key genes regulating L-Aspartic acid and L-Tryptophan content during rice giant embryo development, which are promising to be good candidate genes to improve rice nutrition. By analyzing rice embryo development through a combination of strategies, this research contributes to a greater understanding of the molecular mechanism of rice embryo development, and provides a theoretical foundation for breeding high-nutrition varieties.
An Investigation of Differences in Lower Extremity Biomechanics During Single-Leg Landing From Height Using Bionic Shoes and Normal Shoes

Bionic shoes utilizing an actual foot shape sole structure can alter lower limb’s biomechanics, which may help in the development of specific training or rehabilitation programs. The purpose of this study was to investigate the biomechanical differences in the lower limb during a single-leg landing task using bionic shoes (BS) and normal shoes (NS). Fifteen healthy male subjects participated in this study, sagittal, and frontal plane data were collected during the landing phase (drop landing from 35 cm platform). Our study showed that BS depicted a significantly greater minimum knee flexion angle at initial contact (p = 0.000), a significantly greater minimum (initial contact) hip flexion angle at initial contact (p = 0.009), a significantly smaller sagittal plane total energy dissipation (p = 0.028), a significantly smaller frontal plane total energy dissipation (p = 0.008), a significantly smaller lower limb total energy dissipation (p = 0.017) than NS during the landing phase. SPM analysis revealed that BS depicted a significantly smaller knee joint vertical reaction force during the 13.8–19.8% landing phase (p = 0.01), a significantly smaller anterior tibia shear force during the 14.2–17.5% landing phase (p = 0.024) than NS. BS appears to change lower limb kinematics at initial contact and then readjust the landing strategies for joint work and joint reaction force, thereby reducing the risk of lower limb skeletal muscle injury. BS have great potential for future development and application uses, which may help athletes to reduce lower limb injury risk.
Artificial Transcription Factors for Tuneable Gene Expression in Pichia pastoris

The non-conventional yeast Pichia pastoris (syn. Komagataella phaffii) has become a powerful eukaryotic expression platform for biopharmaceutical and biotechnological applications on both laboratory and industrial scales. Despite the fundamental role that artificial transcription factors (ATFs) play in the orthogonal control of gene expression in synthetic biology, a limited number of ATFs are available for P. pastoris. To establish orthogonal regulators for use in P. pastoris, we characterized ATFs derived from Arabidopsis TFs. The plant-derived ATFs contain the binding domain of TFs from the plant Arabidopsis thaliana, in combination with the activation domains of yeast GAL4 and plant EDLL and a synthetic promoter harboring the cognate cis-regulatory motifs. Chromosomally integrated ATFs and their binding sites (ATF/BSs) resulted in a wide spectrum of inducible transcriptional outputs in P. pastoris, ranging from as low as 1- to as high as ∼63-fold induction with only small growth defects. We demonstrated the application of ATF/BSs by generating P. pastoris cells that produce β-carotene. Notably, the productivity of β-carotene in P. pastoris was ∼4.8-fold higher than that in S. cerevisiae, reaching ∼59% of the β-carotene productivity obtained in a S. cerevisiae strain optimized for the production of the β–carotene precursor, farnesyl diphosphate, by rewiring the endogenous metabolic pathways using plant-derived ATF/BSs. Our data suggest that plant-derived regulators have a high degree of transferability from S. cerevisiae to P. pastoris. The plant-derived ATFs, together with their cognate binding sites, powerfully increase the repertoire of transcriptional regulatory modules for the tuning of protein expression levels required in metabolic engineering or synthetic biology in P. pastoris.
Loss of MAR1 Function is a Marker for Co-Selection of CRISPR-Induced Mutations in Plants

In this study, we describe the establishment of the knockout marker gene MAR1 for selection of CRISPR/Cas9-edited Arabidopsis seedlings and tomato explants in tissue culture. MAR1 encodes a transporter that is located in mitochondria and chloroplasts and is involved in iron homeostasis. It also opportunistically transports aminoglycoside antibiotics into these organelles and defects of the gene render plants insensitive to those compounds. Here, we show that mutations of MAR1 induced by the CRISPR system confer kanamycin-resistance to Arabidopsis plants and tomato tissues. MAR1 is single-copy in a variety of plant species and the corresponding proteins form a distinct phylogenetic clade allowing easy identification of MAR1 orthologs in different plants. We demonstrate that in multiplexing approaches, where Arabidopsis seedlings were selected via a CRISPR/Cas9-induced kanamycin resistance mediated by MAR1 mutation, a mutation in a second target gene was observed with higher frequency than in a control population only selected for the presence of the transgene. This so called co-selection has not been shown before to occur in plants. The technique can be employed to select for edited plants, which might be particularly useful if editing events are rare.
Impact of Seawater Temperature on Coral Reefs in the Context of Climate Change. A Case Study of Cu Lao Cham – Hoi An Biosphere Reserve

Coral reefs are a natural habitat for many species, as well as being of high economic and touristic significance. However, they represent an extremely sensitive ecosystem with a narrow ecological limit: prolonged high temperatures can lead to bleaching, in which corals expel their symbiotic algae and eventually corals will degrade and die. Based on climate change projections from the Blue Communities regional model, using linear regression, exponential regression, polynomial regression, we found that by the decades 2041–2050 and 2051–2060, whether with RCP 4.5 or RCP 8.5, the environmental temperature will change beyond the coral capacity threshold. Of particular concern is RCP 8.5, where the number of weeks per decade in which SST exceeds the threshold of coral reef bleaching is up to 55, compared to 0 at the beginning of the century. As well, the El Niño phenomenon often heats up waters to abnormally high temperatures in Cu Lao Cham and, it is projected to rise even further. Consequently, the combination of climate change and El Niño will cause abnormal increases in the seawater environment beyond the coral resistance threshold, leading to degradation of this internationally important site. Decisive and practical action must be taken to deal with climate change in this part of the world.
Molecular Characterization and Expression of Cytochrome P450 Aromatase in Atlantic Croaker Brain: Regulation by Antioxidant Status and Nitric Oxide Synthase During Hypoxia Stress

We have previously shown that nitric oxide synthase (NOS, an enzyme) is significantly increased during hypoxic stress in Atlantic croaker brains and modulated by an antioxidant (AOX). However, the influence of NOS and AOX on cytochrome P450 aromatase (AROM, CYP19a1, an enzyme) activity on vertebrate brains during hypoxic stress is largely unknown. In this study, we characterized brain AROM (bAROM, CYP19a1b) cDNA in croaker and examined the interactive effects of hypoxia and a NOS-inhibitor or AOX on AROM activity. The amino acid sequence of croaker bAROM cDNA is highly homologous (76–80%) to other marine teleost bAROM cDNAs. Both real-time PCR and Northern blot analyses showed that bAROM transcript (size: ∼2.8 kb) is highly expressed in the preoptic-anterior hypothalamus (POAH). Hypoxia exposure (dissolved oxygen, DO: 1.7 mg/L for 4 weeks) caused significant decreases in hypothalamic AROM activity, bAROM mRNA and protein expressions. Hypothalamic AROM activity and mRNA levels were also decreased by pharmacological treatment with N-ethylmaleimide (NEM, an alkylating drug that modifies sulfhydryl groups) of fish exposed to normoxic (DO: ∼6.5 mg/L) conditions. On the other hand, treatments with Nω-nitro-L-arginine methyl ester (NAME, a competitive NOS-inhibitor) or vitamin-E (Vit-E, a powerful AOX) prevented the downregulation of hypothalamic AROM activity and mRNA levels in hypoxic fish. Moreover, NAME and Vit-E treatments also restored gonadal growth in hypoxic fish. Double-labeled immunohistochemistry results showed that AROM and NOS proteins are co-expressed with NADPH oxidase (generates superoxide anion) in the POAH. Collectively, these results suggest that the hypoxia-induced downregulation of AROM activity in teleost brains is influenced by neuronal NOS activity and AOX status. The present study provides, to the best of our knowledge, the first evidence of restoration of AROM levels in vertebrate brains by a competitive NOS-inhibitor and potent AOX during hypoxic stress.
Primary Immune Responses and Affinity Maturation Are Controlled by IgD

Mature B cells co-express IgM and IgD B cell antigen receptors (BCR) on their surface. While IgM BCR expression is already essential at early stages of development, the role of the IgD-class BCR remains unclear as most B cell functions appeared unchanged in IgD-deficient mice. Here, we show that IgD-deficient mice have an accelerated rate of B cell responsiveness as they activate antibody production within 24h after immunization, whereas wildtype (WT) animals required 3 days to activate primary antibody responses. Strikingly, soluble monovalent antigen suppresses IgG antibody production induced by multivalent antigen in WT mice. In contrast, IgD-deficient mice were not able to modulate IgG responses suggesting that IgD controls the activation rate of B cells and subsequent antibody production by sensing and distinguishing antigen-valences. Using an insulin-derived peptide we tested the role of IgD in autoimmunity. We show that primary autoreactive antibody responses are generated in WT and in IgD-deficient mice. However, insulin-specific autoantibodies were detected earlier and caused more severe symptoms of autoimmune diabetes in IgD-deficient mice as compared to WT mice. The rapid control of autoimmune diabetes in WT animals was associated with the generation of high-affinity IgM that protects insulin from autoimmune degradation. In IgD-deficient mice, however, the generation of high-affinity protective IgM is delayed resulting in prolonged autoimmune diabetes. Our data suggest that IgD is required for the transition from primary, highly autoreactive, to secondary antigen-specific antibody responses generated by affinity maturation.
Understanding the Effectiveness of Genomic Prediction in Tetraploid Potato

Use of genomic prediction (GP) in tetraploid is becoming more common. Therefore, we think it is the right time for a comparison of GP models for tetraploid potato. GP models were compared that contrasted shrinkage with variable selection, parametric vs. non-parametric models and different ways of accounting for non-additive genetic effects. As a complement to GP, association studies were carried out in an attempt to understand the differences in prediction accuracy. We compared our GP models on a data set consisting of 147 cultivars, representing worldwide diversity, with over 39 k GBS markers and measurements on four tuber traits collected in six trials at three locations during 2 years. GP accuracies ranged from 0.32 for tuber count to 0.77 for dry matter content. For all traits, differences between GP models that utilised shrinkage penalties and those that performed variable selection were negligible. This was surprising for dry matter, as only a few additive markers explained over 50% of phenotypic variation. Accuracy for tuber count increased from 0.35 to 0.41, when dominance was included in the model. This result is supported by Genome Wide Association Study (GWAS) that found additive and dominance effects accounted for 37% of phenotypic variation, while significant additive effects alone accounted for 14%. For tuber weight, the Reproducing Kernel Hilbert Space (RKHS) model gave a larger improvement in prediction accuracy than explicitly modelling epistatic effects. This is an indication that capturing the between locus epistatic effects of tuber weight can be done more effectively using the semi-parametric RKHS model. Our results show good opportunities for GP in 4x potato.
Preexisting Mental Disorders Increase the Risk of COVID-19 Infection and Associated Mortality

Coronavirus disease 2019 (COVID-19), a respiratory disease of unknown origin, has a high rate of morbidity and mortality. Individuals with mental disorders may have a higher risk of infection and worse clinical outcomes because of a variety of factors such as poorer general resilience and lower immune function. However, there have been no studies to date specifically investigating the risk of COVID-19 and associated mortality in these patients. This was addressed in the present study by analyzing the data of 473,958 subjects included in the UK Biobank, 14,877 of whom tested positive for COVID-19 infection. Logistic regression analysis was performed to evaluate the associations between mental disorders and risks of COVID-19 infection and associated mortality. The results showed that subjects who were diagnosed with a mental disorder had a significantly higher risk of developing COVID-19 and a worse outcome as evidenced by higher rates of COVID-19-related mortality, with the strongest effects observed for dementia. Among dementia subtypes, Alzheimer disease patients had the highest risks of COVID-19 infection (7.39-fold increase) and associated mortality (2.13-fold increase). Late-life anxiety only increased the risk of developing COVID-19 while late-life depression not only was associated with a higher risk of infection but also a worse outcome. These findings highlight the need to prioritize patients with mental disorders-especially those who experience these disorders later in life—when implementing preventive strategies such as vaccinations.
Negative Effects of a Multimodal Inpatient CBASP Program: Rate of Occurrence and Their Impact on Treatment Outcome in Chronic and Treatment-Resistant Depression

Background: A growing number of studies indicate that the Cognitive Behavioral Analysis System of Psychotherapy (CBASP) is effective in treating chronic depression. However, there is no systematic research into possible negative effects. Therefore, the objectives of the study were to investigate the rate of occurrence of negative effects of an inpatient CBASP program and their impact on treatment response. Methods: Patients with chronic depression and treatment resistance who completed the 12-week multimodal inpatient CBASP treatment program in an open trial (N = 52) retrospectively completed the Inventory for the Assessment of Negative Effects of Psychotherapy (INEP) during follow-up data collection. Severity of depressive symptoms was assessed self- and observer-rated at admission, discharge, and 6 months follow-up. Rates of occurrence of negative effects were calculated and binary logistic regression analyses were conducted to determine the relationship to treatment outcome. Results: The results indicate that 92.3% of patients reported having experienced at least one negative effect and 45.2% indicated dependence on their therapist. Stigmatization and financial concerns as well as intrapersonal changes were reported by about one-third. Only dependence on the therapist negatively impacted treatment outcome in both outcome measures. Conclusions: While almost all patients reported at least one negative effect of a multimodal inpatient CBASP treatment program, most of the reported negative effects appear to be benign. However, dependence on the therapist seems to have a negative impact on treatment outcome. If these results can be replicated in future large-scale, randomized controlled prospective studies, CBASP therapists should be aware of possible dependence and consciously address it during treatment.
Non-palm Plant Volatile α-Pinene Is Detected by Antenna-Biased Expressed Odorant Receptor 6 in the Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae)

The majority of insects rely on a highly complex and precise olfactory system to detect various volatile organic compounds released by host and non-host plants in environments. The odorant receptors (ORs) are considered to play an important role in odor recognition and the molecular basis of ORs, particularly in coleopterans they are relatively poorly understood. The red palm weevil (RPW), Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae), is one of the most destructive pests of the global palm industry. Although feeding and egg oviposition behaviors of RPW can be repelled by some non-palm plant volatiles, such as α-pinene, geraniol, or 1-octen-3-ol, there is limited understanding of how RPW recognizes the non-host plant volatiles. In this study, three candidate RferOrs were identified from the Rfer-specific clade, and the tissue expression analysis used was mainly expressed in the antennae of both sexes. Functional characterization of RferOr6, RferOr40, and RferOr87 was analyzed by using the Xenopus oocyte expression system, and the results indicated that RferOr6/RferOrco was narrowly tuned to α-pinene. The behavioral experiment showed that α-pinene at the concentrations of 10 and 100 μg/μl can cause a significantly repelled behavioral response of RPW. In conclusion, this study reveals that RferOr6 is an antenna-biased expressed OR used by RPW to detect the volatile compound α-pinene in non-palm plants, and our results provide a foundation for further in vivo functional studies of Or6 in RPW, including in vivo knockout/knockdown and feeding/ovipositing behavioral studies of RPW and further pest control.
Durational Differences of Word-Final /s/ Emerge From the Lexicon: Modelling Morpho-Phonetic Effects in Pseudowords With Linear Discriminative Learning

Recent research has shown that seemingly identical suffixes such as word-final /s/ in English show systematic differences in their phonetic realisations. Most recently, durational differences between different types of /s/ have been found to also hold for pseudowords: the duration of /s/ is longest in non-morphemic contexts, shorter with suffixes, and shortest in clitics. At the theoretical level such systematic differences are unexpected and unaccounted for in current theories of speech production. Following a recent approach, we implemented a linear discriminative learning network trained on real word data in order to predict the duration of word-final non-morphemic and plural /s/ in pseudowords using production data by a previous production study. It is demonstrated that the duration of word-final /s/ in pseudowords can be predicted by LDL networks trained on real word data. That is, duration of word-final /s/ in pseudowords can be predicted based on their relations to the lexicon.