Miracle-dz/UniFAR-FTUs huggingface dataset:
Differences between conventional breeding and genetic engineering: An assessment of the statement made by the Group of Chief Scientific Advisors’ (SAM)

Testbiotech became aware of the ‘Statement by the Group of Chief Scientific Advisors’ (SAM), titled: “A Scientific Perspective on the Regulatory Status of Products Derived from Gene Editing and the Implications for the GMO Directive” (SAM 2018). After detailed analysis, we concluded that this statement needs to be revised. Many of the arguments used in the SAM (2018) statement are insufficiently science-based. Some of them appear to be less than scientific and rather more political; they may even be considered biased and populist.
Implementing telemetry on new species in remote areas: recommendations from a large-scale satellite tracking study of African waterfowl

We provide recommendations for implementing telemetry studies on waterfowl on the basis of our experience in a tracking study conducted in three countries of sub-Saharan Africa. The aim of the study was to document movements by duck species identified as priority candidates for the potential spread of avian influenza. Our study design included both captive and field test components on four wild duck species (Garganey, Comb Duck, White-faced Duck and Fulvous Duck). We used our location data to evaluate marking success and determine when signal loss occurred. The captive study of eight ducks marked with non-working transmitters in a zoo in Montpellier, France, prior to fieldwork showed no evidence of adverse effects, and the harness design appeared to work well. The field study in Malawi, Nigeria and Mali started in 2007 on 2 February, 6 February and 14 February, and ended on 22 November 2007 (288 d), 20 January 2010 (1 079 d), and 3 November 2008 (628 d), respectively. The field study indicated that 38 of 47 (81%) of the platform transmitter terminals (PTTs) kept transmitting after initial deployment, and the transmitters provided 15 576 locations. Signal loss during the field study was attributed to three main causes: PTT loss, PTT failure and mortality (natural, human-caused and PTT-related). The PTT signal quality varied by geographic region, and interference caused signal loss in the Mediterranean Sea region. We recommend careful attention at the beginning of the study to determine the optimum timing of transmitter deployment and the number of transmitters to be deployed per species. These sample sizes should be calculated by taking into account region-specific causes of signal loss to ensure research objectives are met. These recommendations should be useful for researchers undertaking a satellite tracking program, especially when working in remote areas of Africa where logistics are difficult or with poorly-known species.
Grass litter is a natural seed trap in long‐term undisturbed grassland

Questions Litter quantity in grasslands is highly affected by disturbance regime and influences seed recruitment of constituent species through different mechanisms. Does litter act as a mechanical barrier to burial of freshly shed seeds, and does seed morphology affect this? How is the fate and mobility of seeds affected by litter compared to that of seeds in the seed bank? Location Transylvanian Lowland, Romania. Methods We analysed the seed content of litter and underlying soil collected from six dry grassland sites having different disturbance histories, ranging from sites that are currently grazed to those that have been long abandoned. We related seed content of litter to the litter quantity, seed morphology and the seed content of soil, and the estimated seed production of the above-ground vegetation. Results Grass litter represented a natural trap for seeds; we identified significant quantities of seeds of a large number of species (37) within litter samples, and there was a mass effect in the seed trapping by litter – higher litter quantities trapped more seeds. As a long-term consequence, we expected that seed bank stores would be gradually depleted in abandoned grassland due to the elimination of seeds by litter, but this was not the case. The higher seed production of the above-ground vegetation in undisturbed sites very probably compensated for seed losses through litter. Seeds retained in the litter were larger, more rounded and had appendages than those in soil. Especially for seeds meeting any of these criteria, litter represents a hazardous medium, since the seeds may fail or have delayed germination. Conclusions The role of litter as a seed trap is more relevant in grasslands that have not been disturbed for a long time, where litter seed entrapment can exert a selective pressure on certain species, and thus drive community assembly in grasslands.
A new generation of bioproduction systems

Currently, nearly everyone in the biotech community is thinking about and taking action towards a new generation of bioproduction systems. Cell-free reactions and synthetic biotechnology seem to promise an overcome of some of the classical biotechnology handicaps. These are, for instance, the facts that life is only possible with water and that living beings are mutable. What is fantasy and what is a real promise for the biotechnology of the 21 century? I am convinced that biology and hence biotechnology will not work in abiotic systems – this branch of science yet has a name: chemistry. Nevertheless, new ideas are emerging and combining the -omics technologies with engineering sciences which build the basis to new and economically efficient bioproduction systems. In the first issue of this 13 volume of Engineering in Life Sciences, several reviews present recent developments and future prospects in the field of new and unconventional bioproduction systems. Guterl and Sieber (Technische Universität München, Germany) review and discuss novel bioproduction strategies with a special focus on bulk chemical synthesis or power generation [1]. Enzyme cascade reactions for bulk productions represent an exciting and highly explorative field of research. The authors postulate the expectation that future results from this field will certainly display influence on the production of high-value products in the first. Much developmental work has to be done before standardized cascade reactions can enter the market for bulk chemicals. Next generation bioproduction systems are the topics of Rupp ́s (Fraunhofer IGB Stuttgart, Germany) review too [2]. Especially the development of new cell-free bioreactors for protein production containing integrated energy regeneration systems are in the focus of this paper. The author addresses the question if and how membranes are necessary in efficient cell free systems and discusses future developments like expanding a genetic code and amino acids with new functions.
Learning a Concept Hierarchy from Multi-labeled Documents

While topic models can discover patterns of word usage in large corpora, it is difficult to meld this unsupervised structure with noisy, human-provided labels, especially when the label space is large. In this paper, we present a model—Label to Hierarchy (L2H)—that can induce a hierarchy of user-generated labels and the topics associated with those labels from a set of multi-labeled documents. The model is robust enough to account for missing labels from untrained, disparate annotators and provide an interpretable summary of an otherwise unwieldy label set. We show empirically the effectiveness of L2H in predicting held-out words and labels for unseen documents.
Suppression of Thielaviopsis basicola by two fungicides applied to sandy loam soils in New Mexico.

HSI, D. C. H. , and M. ORTIZ, JR. 1980. Suppression of Thielaviopsis basicola by two fungicides applied to sandy loam soils in New Mexico. Plant Disease 64:1011-1012. Populations of Thielaviopsis basicola in soil were suppressed by adding benomyl (1.7 kg a.i./ ha) or thiophanate-methyl (3.2 kg a.i./ha) to alkaline sandy loam soils near Portales, NM. Both fungicides suppressed T basicola but not Fusarium spp. Recoveries of T. basicola did not differ by month during the growing season. There was also no appreciable seasonal buildup of inoculum in any of the four fields during 1974-1976. Populations of T. basicola were higher in 1975 and 1976 than in 1974, but those of Fusarium spp. did not differ during the 3 yr. The incidence of blackhull (defined as more than 25% of the shell area discolored) was reduced from 55% to 16-31% in 1974 and from 28-44% to 10-25% in 1975 and 1976 by treatment with the fungicides. The hulls of Valencia peanut plants (Arachis hypogaea L. subsp. fastigiata Waldron var. fastigiata) growing near Portales in eastern New Mexico have commonly been discolored since 1963 (3,7). Isolations from the affected fruit have repeatedly and predominantly yielded Thielaviopsis basicola (Berk. & Br.) Ferraris and Fusarium spp. (3,7). Applications of benomyl or thiophanatemethyl to the planting row during seeding have been effective against the black root rot of citrus, tobacco, poinsettia, and beans and the blackhull of peanuts (1,2,4,6,8-10). Papavizas et al (8) found that several fungicides were effective against black root rot of beans and tobacco. In their tests (8) MSNB (2methylsulfonyl-VI-nitrobonzothiazole) Journal Article 752, New Mexico State University Agricultural Experiment Station. Research supported in part by a grant from the New Mexico Peanut Commission. 0191-2917/80/11101102/$03.00/0 © 1980 American Phytopathological Society reduced the inoculum potential of the pathogen in soil, but benomyl did not change its density appreciably. Although considerable work has been done with benomyl and thiabendazole on other pathogens, little if anything is known of the mechanism of these materials on T. basicola. Determination of the persistence of T. basicola in the fruiting zone of peanuts is essential to understanding the incidence of infection. Furthermore, such understanding of population dynamics of T. basicola is helpful in predicting disease losses. The purpose of this work was to determine the persistence of T basicola in field soil where peanuts are grown and to evaluate the role of benomyl and thiophanate-methyl in suppressing T. basicola populations and the occurrence
Genetic transformation system of Cytospora chrysosperma, the causal agent of poplar canker

[Objective] To explore the molecular pathogenic mechanism of C. chrysosperma, a protoplast preparation and transformation method is established, and the transformation efficiency and the stability of transformants are analyzed. [Methods] In this study, strain CFCC 89981 served as the recipient. The protoplasts were prepared using cell wall degrading enzymes, and transformed by gGFP plasmid mediated by PEG. PCR amplification, Southern blot and fluorescent observation were used to confirm the transformation efficiency and the genetic stability of GFP-tagged transformants. [Results] High-quality protoplasts with excellent regeneration efficiency (63.74%±9.73%) were generated using Driselase and Lysing enzyme digesting fresh mycelium with 1.2 mol/L KCl in pH 5.5 for 4 h and transformed with the gGFP plasmid using PEG. A total of 304 hygromycin B resistant transformants was obtained though added 4 μg DNA. FDA staining results showed that 98% of protoplasts exhibited high activity. The GFP fragments were detectable in the genomes of transformants by both PCR amplification and Southern blot analysis, and the fluorescence detection results also indicated that the GFP gene had been integrated and was stably expressed in the C. chrysosperma genome. Highly intense green fluorescence was observed in single-spore purified transformants. The GFP gene and hph gene were stably expressed after subculturing in PDA plates without hygromycin B resistant. [Conclusion] The high quality and viable protoplast of C. chrysosperma preparation and transformation system are established, it will provide a solid foundation and greatly facilitate the future studies on functional genomics and pathogenic molecular mechanism in C. chrysosperma.
The determinants of groundwater demand for industrial uses. Application to an urban environment

Designing policies to contribute to the sustainability of water resources requires an appropriate understanding of the use of the different sources of water and their determining factors. This work analyses the determinants of the demand for water captured underground for the industries (self-supply) in an urban environment with availability of water from the municipal network (publicly-supply). We apply a hurdle model using microdata for companies located in Zaragoza (Spain). We observe that self-supplied and publicly-supplied water are substitutes, so pricing policies focusing only on the latter have limited effectiveness for water conservation, confirming the need for integrated management. The variable cost of self-supply does not determine groundwater demand since there is no a groundwater volumetric tariff in Spain.
Binary to Bushy: Bayesian Hierarchical Clustering with the Beta Coalescent

Discovering hierarchical regularities in data is a key problem in interacting with large datasets, modeling cognition, and encoding knowledge. A previous Bayesian solution—Kingman's coalescent—provides a probabilistic model for data represented as a binary tree. Unfortunately, this is inappropriate for data better described by bushier trees. We generalize an existing belief propagation framework of Kingman's coalescent to the beta coalescent, which models a wider range of tree structures. Because of the complex combinatorial search over possible structures, we develop new sampling schemes using sequential Monte Carlo and Dirichlet process mixture models, which render inference efficient and tractable. We present results on synthetic and real data that show the beta coalescent outperforms Kingman's coalescent and is qualitatively better at capturing data in bushy hierarchies.
βl integrin and organized actin filaments facilitate cardiomyocyte‐specific RhoA‐dependent activation of the skeletal α‐actin promoter

Activation of RhoA GTPase causes actin filament bundling into stress fibers, integrin clustering, and focal adhesion formation through its action on actin cytoskeleton organization. RhoA also regulates transcriptional activity of serum response factor (SRF). Recent studies in NIH 3T3 fibroblasts have shown that SRF activation by RhoA does not require an organized cytoskeleton and may be regulated by G‐actin level. In cardiac myocytes, the organization of actin fibers into myofibrils is one of the primary characteristics of cardiac differen¬tiation and hypertrophy. The primary purpose of this study was to examine if RhoA regulates SRF‐dependent gene expression in neonatal cardiomyocytes in a manner different from that observed in fibroblasts. Our results show that RhoA‐dependent skeletal α‐actin promoter ac¬tivation requires βl integrin and a functional cytoskeleton in cardiomyocytes but not in NIH 3T3 fibroblasts. Activa¬tion of the α‐actin promoter by RhoA is greatly potenti¬ated (up to 15‐fold) by co‐expression of the integrin βlA or βlD isoform but is significantly reduced by 70% with a co‐expressed dominant negative mutant of βl integrin. Furthermore, clustering of βl integrin with anti‐βl integrin antibodies potentiates synergistic RhoA and βl integrin activation of the α‐actin promoter. Cytochalasin D and latrunculin B, inhibitors of actin polymerization, significantly reduced RhoA‐induced activation of the α‐actin promoter. Jasplakinolide, an actin polymerizing agent, mimics the synergistic effect of RhoA and βl integrin on the actin promoter. These observations sup¬port the concept that RhoA regulates SRF‐dependent cardiac gene expression through cross‐talk with βl integrin signal pathway via an organized actin cytoskeleton. — Wei, L. , Wang, L. , Carson, J. A. , Agan, J. E. , ImanakaYoshida, K. , and Schwartz, R. J. βl integrin and organized actin filaments facilitate cardiomyocyte‐specific RhoA‐de¬pendent activation of the skeletal α‐actin promoter. FASEBJ. 15, 785‐796 (2001)
Identification of Drought Tolerant Sorghum Genotypes in Aweil (Nyamliel, Gog Machar) and Tonj South Rain fed Areas of South Sudan

These studies were conducted for two seasons (dry and rain seasons) during 2016/2017cropping season at Nyamliel Agricultural Demonstration and Learning Centre, NADLC and the University of Juba. The objectives were to identify stress tolerant/ or resistant traditional sorghum land races to both drought and high moisture conditions that are locally cultivated in Tonj South: GPS coordinates N 070 18.328'; and E 028045.533'), Nyamliel and Gog Machar (Aweil). Eight sorghum genotypes 5 from Nyamliel evaluated at (Aweil) and 3 from Tonjplus the 5 from Aweil evaluated at the University of Juba namely, Rapchol, Yar, Rapheir (Contrl-1), Malwal, Luel, Aher (Contrl-2), AdhalRwuait and Acholkol. These genotypes were evaluated under five irrigation regimes of: 2DI (two day intervals); 7DI; 10DI; 15DI and 30DI, respectively. Results showed sorghum genotypes namely, Yar, Malwal, Rapher and Aher as superior and out yielded genotypes Luel and Acholkol and the other entries at (P<0.05) under drought conditions. Conversely, under water-logged conditions the yields of all eight tested genotypes were not significantly different from each other (P<0.05). The study concluded that in the areas covered by the study namely, Aweil (Nyamliel and Gog Machar), and Tonj South within the traditional sorghum germplasm there are materials with good traits that are tolerant to both excess (high) and (low) levels of moisture stress. Furthermore, the study recommends another similar exercise to include an extended range of sorghum genotypes in this and neighboring areas so as to widen the spectrum of tolerant genotypes/ varieties to high/low moisture stresses and the introduction of exotic high yielding genotypes from similar environments as tools to build resilience and adapt to the effects of climate change and improve crop productivity thus, striving to build and maintain resilient and food secure communities in South Sudan.
Short‐chain fatty acid content and pH in caecum of rats given various sources of carbohydrates

The caecal content of short‐chain fatty acids (SCFA; acetic, propionic and butyric acid), caecal pH, fermentability and dry matter digestibility (DMD) were examined through balance experiments in rats fed 11 various indigestible carbohydrates. The following carbohydrate sources were incorporated into test diets: cellulose, oat husk, wheat bran, oat bran, pea fibre, linseed fibre, low methoxylated (LM)‐pectin, guargum, β‐glucans, neosugar and raffinose. The indigestible carbohydrates, except for those in wheat bran, oat husk and cellulose, were highly fermented, ie > 90%. Caecal pH varied between 5·6 and 7·8, with neosugar and raffinose causing the lowest pH and the fibre‐free diet and the diet with oat husk the highest. The caecal pool sizes of SCFA were highest with raffinose, β‐glucans, LM‐pectin, guargum and linseed fibre (335‐400 μmol) while pea fibre, wheat bran, oat bran and neosugar gave intermediate levels (137–227 μmol). The pool size with oat husk and cellulose was similar as with the basal diet (45–64 μmol). A high proportion of propionic acid was obtained with guargum and linseed fibre, whereas acetic acid was the predominant product in case of LM‐pectin. On the other hand, linseed fibre gave a remarkably low proportion of butyric acid. The quantity fermented and caecal pH correlated well to the amount of SCFA with most materials (r = 0·96 and r = −0·87, respectively), an exception was neosugar and in case of fermentability also oat bran. DMD values with most of the easily fermented carbohydrates were high (>96%). Exceptions were diets with β‐glucans and oat bran which caused low DMD values, about 93%. It is concluded that indigestible carbohydrates may differ in ability to lower caecal pH and to form SCFA during fermentation. (Less)
Higher BMI, but not obesity-related genetic polymorphisms, correlates with reduced structural connectivity of the reward network

Background: Obesity is of complex origin, involving genetic and neurobehavioral factors. Most consistently, polymorphisms in the fat-and-obesity associated gene (FTO) may increase the risk for developing obesity by modulating dopaminergic signaling in the brain. Dopamine-dependent behaviors, such as reward processing, are crucial for eating behavior and are altered in obesity. Yet, few studies have investigated the association of obesity, related genetic variants and structural connectivity of the dopaminergic reward network. Methods: We analyzed 378 participants (age range: 20 - 59 years, BMI range: 17 - 38 kg/m2) of the LIFE-Adult Study. Genotyping for the single nucleotid polymorphisms rs1558902 (FTO) and rs1800497 (near dopamine D2 receptor) was performed on a micro-array. Structural connectivity of the reward network was derived from diffusion-weighted magnetic resonance imaging at 3 Tesla using deterministic tractography of Freesurfer-derived regions of interest. Using graph metrics, we extracted summary measures of clustering coefficient and connectivity strength between frontal and striatal brain regions, normalized for global connectivity. We applied linear regression models to test the association of BMI, risk alleles of both variants and reward network connectivity. Results: Higher BMI was significantly associated with reduced connectivity strength for fractional anisotropy ({beta}= -0.0011, 95%-C.I. [-0.0019, -0.0003], p= 0.0062) and number of streamlines ({beta} = -0.0026, 95%-C.I.:[-0.004,-0.0009], p= 0.0024), but not clustering coefficient. Strongest associations were found for right accumbens, right lateral orbitofrontal cortex and left putamen. As expected, the polymorphism rs1558902 in FTO was associated with higher BMI (F=7.9, p<0.001). None of the genetic variants was associated with reward network structural connectivity. Conclusions: Here, we provide evidence that higher BMI correlates with reduced reward network structural connectivity. This result is in line with previous findings of obesity-related decline in white matter microstructure. We did not find any association of variants in FTO or near DRD2 receptor and reward network structural connectivity, indicating that the genetic influence of these variants is small or non-existent. Future research should investigate the behavioral implications of structural connectivity differences in the fronto-striatal network and incorporate larger sample sizes with longitudinal designs in order to gain further insight into the genetic determinants of obesity in the brain.