Miracle-dz/UniFAR-FTUs huggingface dataset:
Clonal Diversity in Differently-Aged Populations of the Pseudo-Annual Clonal Plant Circaea lutetiana L.

: In many clonal plant species seedling recruitment is restricted to short colonization episodes early in the development of the population, and clonal diversity (i.e., genet diversity) in the population is expected to decrease with increasing population age. In established populations of the pseudo-annual Circaea lutetiana seedling recruitment has previously not been observed. Therefore, we expected established populations to have low clonal diversities. We analysed number and frequency of genets and spatial distribution of genets in six differently-aged C. lutetiana populations with the use of four informative RAPD primers. We found relatively low clonal diversities in young populations but very high clonal diversities in established populations. Therefore, the hypothesis was rejected that seedling recruitment does not occur in established populations. Moreover, we did not find large genet size asymmetries in established populations. Genet size differences can be caused by stochastic processes or by fitness related traits, such as differences in vegetative reproduction. Because vegetative propagation of ramets is dependent on ramet size, and the number of ramets and the size of each ramet determine genet size, we expected that large genets produced, on average, large ramets. However, this was not the case, suggesting that stochastic processes caused genet size differences. Genet size may also be bounded if spatial distribution of genets is affected by micro-habitat differences. For this we expected to find a clumped spatial distribution of ramets of the same genet. However, ramets of large genets were always found intermingled with ramets belonging to other genets.
Anti-CS1 × Anti-CD3 Bispecific Antibody (BiAb)-Armed Anti-CD3 Activated T Cells (CS1-BATs) Kill CS1+ Myeloma Cells and Release Type-1 Cytokines

Background: Multiple myeloma (MM) remains incurable despite significant advances in chemotherapy, targeted therapies, and immunotherapy. Bispecific antibody (BiAb)-armed activated T cells (BATs) have been developed for targeting and treatment of solid and hematologic malignancies. BATs are serial killers of tumor cells, secrete Th1 cytokines, and induce adaptive cellular and humoral immune responses in patients (pts). This study provides preclinical data using bispecific anti-CS1 (elotuzumab) × anti-CD3 (OKT3) antibody (CS1Bi)-armed activated T cells (CS1- BATs) that provide a strong rationale for applying CS1-BATs to pts with MM. Methods: CS1-BATs and unarmed activated T cells (ATC) were incubated with MM cell targets at various effector to target ratios (E:T) in a quantitative flow cytometry-based assay to determine the degree of cell loss relative to target cells incubated without ATC. ATC from up to 8 normal donors were armed with various concentrations of CS1 BiAb and tested against 5 myeloma cells lines for CS1-BATs-mediated killing and release of Th1 cytokines, chemokines and granzyme B. Results: CS1-BATs from normal donors killed each of 5 MM cell lines proportional to E:T ratios ranging between 1:1 and 10:1 and arming concentrations of 12.5 to 50 ng/million ATC, which was accompanied by release of Th1 cytokines, chemokines and granzyme B. CS1-BATs prepared from MM pts' peripheral blood mononuclear cells (PBMC) showed increasing cytotoxicity and T cell expansion over time against ARH77 MM cells. The optimal arming dose of CS1Bi is 50 ng/106 ATC. Conclusions: These data demonstrate the therapeutic potential of CS1-BATs-mediated cytotoxicity and Th1 cytokines release at low E:T and support advancing their clinical development in pts with MM.
Recent Advances in Metabolically Engineered Microorganisms for the Production of Aromatic Chemicals Derived From Aromatic Amino Acids

Aromatic compounds derived from aromatic amino acids are an important class of diverse chemicals with a wide range of industrial and commercial applications. They are currently produced via petrochemical processes, which are not sustainable and eco-friendly. In the past decades, significant progress has been made in the construction of microbial cell factories capable of effectively converting renewable carbon sources into value-added aromatics. Here, we systematically and comprehensively review the recent advancements in metabolic engineering and synthetic biology in the microbial production of aromatic amino acid derivatives, stilbenes, and benzylisoquinoline alkaloids. The future outlook concerning the engineering of microbial cell factories for the production of aromatic compounds is also discussed.
The Effect of Intermittent Light on Carcass Quality, Feed Efficiency, and Growth of Broilers

Abstract A total of 2400 broiler chicks of both sexes and of two commercial strains were reared in an environment of either intermittent lighting (IL) of 1 hr light:3 hr dark or extended lighting (EL) of 23.5 hr light:. 5 hr dark from 15 to 48 or 55 days of age. The IL significantly (P
Physical Connectivity Between the NE Atlantic Seamounts

Within the Portuguese Exclusive Economic Zone, the Great Meteor and Madeira-Tore complexes are highly productive areas, which are likely to be classified as marine protected areas (MPAs) due to their ecological vulnerability. This was the main focus of the BIOMETORE project and, framed on it, the aim of the present study was to investigate the physical connectivity between both seamount complexes. Using the HYbrid Coordinate Ocean Model coupled with the Connectivity Modeling System (CMS) (a Lagrangian tool), a series of experiments was conducted in order to determine the influence of the main oceanographic phenomena governing the area in: (i) the origin of the particles that reach each complex, (ii) their capacity to capture and retain incoming particles, and (iii) the physical connectivity between them as well as the intra-connectivity within each seamount system. Due to the geographical location of both groups of seamounts, the Azores Current (AzC) and its associated eddies were identified as the main transport pathways, its influence being stronger at intermediate waters and decreasing with depth. Notwithstanding, the Great Meteor and the Madeira-Tore were mainly affected by the AzC southward and eastward branches, respectively, resulting in a non-significant connectivity between the two groups. Meanwhile, the inter-connectivity between seamounts slightly varied with depth at the Great Meteor complex while increasing at Madeira-Tore. In addition, the Plateau, Irving, and Cruiser (PIC) seamounts from the Great Meteor complex and Gorringe and Coral from the Madeira-Tore complex proved to incorporate the regional connectivity routes. Although containing the three smallest seamounts, Madeira-Tore showed the higher capturing capacity per square kilometer, highlighting the influence of the “sticky water effect. ” In the Great Meteor complex, the “seamount effect” seems to be the main phenomenon responsible for the greater retention and self-recruitment abilities of these seamounts. The presented results provide valuable information for the design of a MPA to preserve these vulnerable habitats.
Geometrical model explains multiple preferred escape trajectories of fish

To evade predators, many prey perform rapid escape movements. The resulting escape trajectory (ET) – measured as the angle of escape direction relative to the predator’s approach path – plays a major role in avoiding predation. Previous geometrical models predict a single ET; however, many animals (fish and other animal taxa) show highly variable ETs with multiple preferred directions. Although such a high ET variability may confer unpredictability, preventing predators from adopting counter-strategies, the reasons why animals prefer specific multiple ETs remain unclear. Here, we constructed a novel geometrical model in which Tdiff (the time difference between the prey entering the safety zone and the predator reaching that entry point) is expected to be maximized. We tested this prediction by analyzing the escape responses of Pagrus major attacked by a dummy predator. At each initial body orientation of the prey relative to the predator, our model predicts a multimodal ET with an optimal ET at the maximum Tdiff (Tdiff,1) and a suboptimal ET at a second local maximum of Tdiff (Tdiff,2). Our experiments show that when Tdiff, 1–Tdiff, 2 is negligible, the prey uses optimal or suboptimal ETs to a similar extent, in line with the idea of unpredictability. The experimentally observed ET distribution is consistent with the model, showing two large peaks at 110–130° and 170–180° away from the predator. Because various animal taxa show multiple preferred ETs similar to those observed here, this behavioral phenotype may result from convergent evolution that combines maximal Tdiff with a high level of unpredictability.Animals from many taxa escape from suddenly approaching threats, such as ambush predators, by using multiple preferred escape trajectories. However, the reason why these multiple preferred escape trajectories are used is still unknown. By fitting a newly constructed model to the empirical escape response data, we show that the seemingly complex multiple preferred escape trajectories can arise from a simple geometrical rule which maximizes the time difference between when the prey enters the safety zone and when the predator reaches that entry point. Our results open new avenues of investigation for understanding how animals choose their escape trajectories from behavioral and neurosensory perspectives.
Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation

Translational control shapes the proteome in normal and pathophysiological conditions. Current high-throughput approaches reveal large differences in mRNA-specific translation activity but cannot identify the causative mRNA features. We developed direct analysis of ribosome targeting (DART) and used it to dissect regulatory elements within 5′ untranslated regions that confer thousand-fold differences in ribosome recruitment in biochemically accessible cell lysates. Using DART, we identified novel translational enhancers and silencers, determined a functional role for most alternative 5′ UTR isoforms expressed in yeast, and revealed a general mode of increased translation via direct binding to a core translation factor. DART enables systematic assessment of the translational regulatory potential of 5′ UTR variants, whether native or disease-associated, and will facilitate engineering of mRNAs for optimized protein production in various systems. Highlights DART illuminates thousand-fold differences in 5′ UTR-specific translation activity SNPs and alternative 5′ UTR isoforms affect ribosome recruitment significantly Inhibitory effects of RNA structures are highly dependent on 5′ UTR context 5′ UTR motifs bind initiation factors directly, broadly stimulating translation
Breakdown of Self-incompatibility in Brassica by the Antisense RNA of the SLG Gene

The self incompatibility (SI) system of Brassica is sporophytically controlled by multiallenic genes at an S-locus. Two genes, SLG (S-locus glycoprotein) and SRK(S-receptor protein kinase), on the S-locus are thought to play an important role in recognition of the self pollen, though there is no direct evidence. We introduced the antisense SLG gene to self incompatible Brassica species through Agrobacterium-mediated transformation. We found that a transgenic plant of B. raga (syn. B. campestris) could set seeds after self pollination, and that no SLG protein was detectable in a gel blot analysis of the transgenic plant. These observations provide strong evidence that SLG and/or SRK are directly involved in the pollen-stigma recognition of SI.
Field-deployable molecular diagnostic platform for arbovirus and Wolbachia detection in Aedes aegypti

Background Surveillance of mosquito infection status is critical for planning and deployment of proper mosquito control initiatives. Concurrently, Wolbachia is being widely used as a control method for arboviral transmission. Point-of-care (POC) detection assays are necessary for monitoring the infection prevalence and geographic range of viruses as well as Wolbachia in mosquito vector populations. We therefore assessed the novel qPCR bCUBE molecular diagnostic system as a tool for virus and Wolbachia detection. Results We developed a reliable, specific, and sensitive diagnostic assay for detecting Zika virus and dengue virus serotype 2 using the real-time qPCR platform bCUBE. With bCUBE-based qRT-PCR, both Wolbachia bacterium and virus RNA could be reliably detected in individually infected Ae. aegypti mosquitoes and in pools of 5, 10, or 15 mosquitoes. Conclusions The portable qPCR bCUBE diagnostic platform is capable of detecting Zika and dengue virus as well as Wolbachia in mosquitoes and therefore has potential as a practical field-deployable diagnostic test for vector-borne disease surveillance programs.
Ecological processes underlying the emergence of novel enzootic cycles—arboviruses in the neotropics as a case study

Pathogens originating from wildlife (zoonoses) pose a significant public health burden, comprising the majority of emerging infectious diseases. Efforts to control and prevent zoonotic disease have traditionally focused on animal-to-human transmission, or “spillover”. However, in the modern era, increasing international mobility and commerce facilitate the spread of infected humans, non-human animals (hereafter animals), and their products worldwide, thereby increasing the risk that zoonoses will be introduced to new geographic areas. Imported zoonoses can potentially ‘spill back’ to infect local wildlife—a danger magnified by urbanization and other anthropogenic pressures that increase contacts between human and wildlife populations. In this way, humans can function as vectors, dispersing zoonoses from their ancestral enzootic systems to establish reservoirs elsewhere in novel animal host populations. Once established, these enzootic cycles are largely unassailable by standard control measures and have the potential to feed human epidemics. Understanding when and why translocated zoonoses establish novel enzootic cycles requires disentangling ecologically complex and stochastic interactions between the zoonosis, the human population, and the natural ecosystem. We address this challenge by delineating potential ecological mechanisms affecting each stage of enzootic establishment—wildlife exposure, enzootic infection, and persistence—applying existing ecological concepts from epidemiology, invasion biology, and population ecology. We ground our study in the neotropics, where four arthropod-borne viruses (arboviruses) of zoonotic origin—yellow fever, dengue, chikungunya, and Zika viruses—have separately been introduced into the human population. This paper is a step towards developing a framework for predicting and preventing novel enzootic cycles in the face of zoonotic translocations.
DNA damage independent inhibition of NF-κB transcription by anthracyclines

Anthracyclines are among the most used and effective anticancer drugs. Their activity has been attributed to DNA double-strand breaks resulting from topoisomerase II poisoning and to eviction of histones from select sites in the genome. Here we show that the extensively used anthracyclines Doxorubicin, Daunorubicin and Epirubicin, decrease the transcription of nuclear factor kappa B (NF-κB)-dependent gene targets, but not interferon responsive genes. Using an NMR-based structural approach, we demonstrate that anthracyclines disturb the complexes formed between the NF-κB subunit RelA and its DNA binding sites. The variant anthracyclines Aclarubicin, Doxorubicinone and the newly developed Dimethyl-doxorubicin, which share anticancer properties with the other anthracyclines but do not induce DNA damage, also suppressed inflammation, thus uncoupling DNA damage from the effects on inflammation. These findings have implications for anticancer therapy and for the development of novel anti-inflammatory drugs with limited side effects for life-threatening conditions such as sepsis.
Contrasting effects of commercial and native arbuscular mycorrhizal fungal inoculants on plant biomass allocation, nutrients and phenolics

As the global population increases, the need to feed more people must be met while simultaneously conserving the long-term sustainability of our agroecosystems. There is mounting interest and discussion around the application of arbuscular mycorrhizal fungal (AMF) inoculants to enhance crop growth, nutrient uptake and pest resistance. However, the effects of AMF inoculation are variable and context dependent. This study shows the stronger effects of an AMF inoculant with greater number of fungal species, but that these effects are no better than re-inoculating plants with a field-sourced native AMF inoculant.
Epistatic interactions between PHOTOPERIOD1, CONSTANS1 and CONSTANS2 modulate the photoperiodic response in wheat

In Arabidopsis, CONSTANS (CO) integrates light and circadian clock signals to promote flowering under long days (LD). In the grasses, a duplication generated two paralogs designated as CONSTANS 1 (CO1) and CONSTANS 2 (CO2). Here we show that in tetraploid wheat plants grown under LD, combined loss-of-function mutations in the A and B-genome homeologs of CO1 and CO2 (co1 co2) result in a small (3 d) but significant (P<0.0001) acceleration of heading time both in PHOTOPERIOD1 (PPD1) sensitive (Ppd-A1b) and insensitive (Ppd-A1a) backgrounds. Under short days (SD), co1 co2 mutants headed 13 d earlier than the wild type (P<0.0001) in the presence of Ppd-A1a. However, in the presence of Ppd-A1b, spikes from both genotypes failed to emerge by 180 d. These results indicate that CO1 and CO2 operate mainly as weak heading time repressors in both LD and SD. By contrast, in the absence of functional PPD1 alleles (ppd1), Co1 accelerated heading time >60 d relative to co1 under LD. We detected significant genetic interactions among CO1, CO2 and PPD1 alleles on heading time, which were reflected in complex interactions among these genes at the transcriptional and protein levels. Loss-of-function mutations in PPD1 had a stronger effect on heading time than combined co1 co2 mutations and, more importantly, PPD1 was able to perceive and respond to differences in photoperiod in the absence of functional CO1 and CO2 genes. Similarly, CO1 was able to accelerate heading time in response to LD in the absence of a functional PPD1. Taken together, these results indicate that PPD1 and CO1 are able to respond to photoperiod in the absence of each other, and that interactions between these two photoperiod pathways at the transcriptional and protein levels are important to fine-tune the flowering response in wheat. Author summary An understanding of the mechanisms involved in the regulation of wheat heading time is required to engineer more productive varieties better adapted to new or changing environments. A large proportion of wheat’s natural variation in heading time is determined by differences in genes controlling the photoperiodic response. In this study, we show that the wheat PHOTOPERIOD1 (PPD1) gene has a stronger effect on heading time than CONSTANS1 (CO1) and CO2 in the regulation of the photoperiodic response, and that complex genetic interactions among these genes are important to fine-tune heading time. Using loss-of-function mutants for both CO1 and CO2, we demonstrate that these genes are not required for PPD1 to perceive differences in photoperiod and regulate heading time. Similarly, we show that in the absence of PPD1, CO1 can accelerate heading time more than 60 days in response to long days. Our results indicate that each of these two wheat photoperiod pathways can respond to differences in photoperiod even in the absence of the other one. Differences in the relative importance of these two pathways and in their epistatic interactions have contributed to the diversity of photoperiodic responses observed in different grass species.
Gut expressed vitellogenin is hijacked by a virus to facilitate its spread

Insect vitellogenin (Vg) has been considered to be synthesized in the female fat body, secreted into hemolymph, and taken up by developing oocytes to serve as nutrition for embryo development. However, the expression and function of Vg in other tissues are largely unknown. Here, we show that Vg is expressed in the whitefly midgut epithelial cells and secreted into gut lumen where it binds to the microvillar membrane. Furthermore, we find that the midgut expressed Vg is hijacked by Tomato yellow leaf curl virus to facilitate the movement of virus crossing the midgut wall. Silencing of Vg or immune-blocking the interaction between viral coat protein and midgut Vg inhibited virus movement across the midgut wall and decreased virus transmission. Our findings show possession of functional Vg in the midgut of an insect, and reveal a novel mechanism involved in the movement of virus crossing the midgut barrier of vector insect.
Placental microRNA Expression Associates with Birthweight through Control of Adipokines: Results from Two Independent Cohorts

MicroRNAs are non-coding RNAs that regulate gene expression post-transcriptionally. In the placenta, the master regulator of fetal growth and development, microRNAs shape the basic processes of trophoblast biology and specific microRNA have been associated with fetal growth. To comprehensively assess the role of microRNAs in placental function and fetal development, we have performed small RNA sequencing to profile placental microRNAs from two independent mother-infant cohorts: the Rhode Island Child Health Study (n=225) and the New Hampshire Birth Cohort Study (n=317). We modeled microRNA counts on infant birthweight percentile (BWP) in each cohort, while accounting for race, sex, parity and technical factors, using negative binomial generalized linear models. We identified microRNAs that were differentially expressed (DEmiRs) with BWP at false discovery rate (FDR) less than 0.05 in both cohorts. hsa-miR-532-5p (miR-532) was positively associated with BWP in both cohorts. By integrating parallel whole transcriptome and small RNA sequencing in the RICHS cohort, we identified putative targets of miR-532. These targets are enriched for pathways involved in adipogenesis, adipocytokine signaling, energy metabolism and hypoxia response, and included Leptin, which we further demonstrated to have decreasing expression with increasing BWP, particularly in male infants. Overall, we have shown a robust and reproducible association of miR-532 with BWP, which could influence BWP through regulation of adipocytokines Leptin and Adiponectin.
Forecasting the Short-term Price Trend of Taiwan Stocks with Deep Neural Network

The relationship between technical indicators and prices in stock market has always been an important topic of concern for the academic and financial communities. Many literatures suggest that it is feasible to use technical analysis to estimate the future price of stocks. The use of machine learning to estimate stock prices has also gradually become mainstream in the financial market. This study aims to explore the feasibility of using deep network and technical analysis indicators to estimate short-term price movements of stocks. The subject of this study is TWSE 0050, which is the most traded ETF in Taiwan's stock exchange. We use Long Short Term Memory (LSTM) to construct a deep network stock estimation model and conduct experiments on the Taiwan Stock Exchange's open data from 2019/01 to 2019/10. Experimental results show that LSTM model obtained an average of 75% accuracy on TWSE 0050 ETF.