Miracle-dz/UniFAR-FTUs huggingface dataset:
Diversity of yeast strains isolated from the “magnan’’ a traditional ferment used for the production of “attiéké” a cassava food in Côte d'Ivoire

Objective: This study aimed to identify the yeasts in the traditional fermented cassava root called ''magnan'', used for fermentation of cassava dough for “attieke: a fermented cassava food product’’ production in Cote d'Ivoire. Methodology and results: ‘magnan'' is a fermented cassava root used as a traditional starter and “attieke’’ is a fermented cassava food product. This study involved 99 samples of ''magnan'' taken from different production areas in eleven (11) communes in the District of Abidjan (Abobo, Adjame, Anyama, Attecoube, Bingerville, Cocody, Koumassi, Marcory, Port-Bouet, Songon and Yopougon). Samples of ‘’magnan’’ were collected and carried to the Biotechnology Laboratory of the Felix Houphouet-Boigny University, during sixmonth (May - November 2017) and treated separately on MYPG medium (malt extract, yeast extract, peptone, glucose, and chloramphenicol). One hundred and six (106) pure yeast cultures were identified at genus and species level by MALDI-TOF mass spectrometry at the bio-bank laboratory of the Pasteur Institute of Cote d’Ivoire. A total of 83 yeast isolates were clearly identified (78.30 %) and showed five genus: Candida, Saccharomyces, Trichosporon, Kloeckera, and Millerozyma. The major species included C. krusei (30.12 %), C. tropicalis (28.92 %), and S. cerevisiae (20.50 %) followed by a low proportion of C. kefyr (6.02 %), C. guilliermondii (3.61 %), T. asahii (3.61 %), K. apis (2.41 %), C. pararugosa (1.20 %), M. farinosa (1.20 %) and C. albicans (1.20 %). Conclusion and application of the results: This study showed the traditional cassava ferment ''magnan'' used for the fermentation of cassava dough for the production of “attieke ’’ on the sampled sites was colonized by several yeasts genera including Candida, Saccharomyces, Trichosporon, Kloeckera and Millerozyma in varying proportions. The frequently isolated species were composed by C. krusei, C. tropicalis and S. cerevisiae. The results obtained will constitute a database on the diversity of yeasts for the selection of starter strains for producing of “attieke ’’. In perspective, the techno-functional properties (enzyme production: amylase, cellulase, pectinase, phytase, tannase and β-glucosidase) of each strain will be determined for their impact on the fermenting process of the cassava dough. And the starter strains will be used by producers to optimize and standardize the quality of “attieke ’’. Keywords: yeast strains, traditional ferment, “attieke ’’, ‘’magnan’’
Records of Culturable Endophytic Fungi Inhabiting Rhizome of Elettaria in Hutan Sibayak, North Sumatera

Endophytic microorganisms are microbial associates living in various part of host, yet expressing benefits to healthy plants. Existence of species-specific endophytes, endophytic fungi is still poorly studied especially in Zingiberaceae. In this study, we reported several endophytic fungal species isolated from rhizome of Elettaria through isolative efforts and molecular evidence. Host plant, Elettaria sp. was sampled from representative natural area, i.e. Hutan Sibayak which is known as biodiversity spot for Zingiberaceae in North Sumatera. Molecular identification revealed the identity of five isolated fungal strains collected from rhizomes of Elettaria, namely Trichoderma atroviride, Curvularia lunata, Schizophyllum commune, Trichoderma harzianum and Pholiota multicingulata. Phylogenetic tree is constructed based on Neighbor-joining method in a bootstrap test (1000x replication) with outgroup and database retrieved from NCBI GenBank. From our perspective, this is the first report on finding fungal endophytes from rhizomes of Elettaria sp. yet further investigation is needed to evaluate their future bioprospectives.
Geographical differentiation and cryptic diversity in the monocled cobra, Naja kaouthia (Elapidae), from Thailand

South‐East Asia has an exceptionally high diversity of snakes, with more than 250 snake species currently recorded from Thailand. This diversity likely reflects the diverse range of geographical and climatic conditions under which they live, but the evolutionary history and population genetics of many snake species in South‐East Asia have been little investigated in comparison with morphological studies. Here, we investigated genetic variation in the monocled cobra, Naja kaouthia, Lesson, 1831, across its distribution range in Thailand using mitochondrial DNA (cytochrome b, control region) for ~100 individuals and the nuclear DNA gene (C‐mos) for a small subset. Using population genetic and phylogenetic methods, we show high levels of genetic variation between regional populations of this non‐spitting cobra, including the north‐eastern, north‐central and southern regions, in addition to a population on Pha‐ngan Island, 150 km offshore from the southern peninsula. Moreover, inclusion of the north‐eastern population renders N. kaouthia paraphyletic in relation to other regional Naja species. The north‐eastern population is therefore probably specifically distinct. Given that these cobras are otherwise undifferentiated based on colour and general appearance to the “typical” cobra type of this region, they would represent a cryptic species. As has been shown in other animal groups from Thailand, it is likely that the geographical characteristics and/or tectonic alteration of these regions have facilitated high levels of population divergence of N. kaouthia in this region. Our study highlights the need for dense sampling of snake populations to reveal their systematics, plan conservation and facilitate anti‐snake venom development.
Fall Age-Ratio Survey Design for Eastern Population Greater Sandhill Cranes

For migratory birds, wildlife managers can use the recruitment rate of young into an adult population to model population dynamics, manage harvest, or evaluate habitat. Few recruitment estimates exist for Eastern Population greater sandhill cranes Antigone canadensis tabida, and estimates are outdated and local in scale. Wildlife managers can use age ratios as an index to recruitment, and surveying at fall staging areas is efficient and cost effective. We created a systematic survey design for surveying eastern population crane age ratios in the Kankakee River valley (2013–2015) in northwestern Indiana and the south-central counties of Michigan (2014–2015). Using logistic regression, we investigated factors that may cause spatial and temporal variation in age ratios, including flock size, timing within season, state, year, random vs. incidental survey routes, and observer. We stratified our selection of survey routes using a core area of high crane abundance, but do not recommend stratifying due to the added complexity and low utility. Observers determined the age of 53,371 cranes and found that the proportion of juveniles in Eastern Population crane flocks (π = 0.113, 95% CI: 0.105 – 0.122) was similar to previous estimates for the population. Proportion of juveniles was greater for south-central Michigan than for the Kankakee River valley, decreased with flock size, increased with lateness in the season, and varied among observers. Our design accounted for both ecological sources of variation in age ratios as well as nuisance variation. We recommend that future surveys use our design as part of a monitoring plan for Eastern Population cranes to support harvest management of the population and ensure that future survey results are comparable across years.
Towards the Foundations of Diversity-Aware Node Summarisation on Knowledge Graphs

This paper aims at initiating a discussion of the foundations of the notion of diversity in a novel problem of computing graphical node summarisations in knowledge multi-graphs (equivalently viewed as RDF-graphs). As it reports an ongoing work, it proposes a general framework of basic concepts and adaptations of two diversity-aware evaluation measures previously studied in the context of information retrieval to the studied problem and brieﬂy discusses them.
Effects of thinning on canopy transpiration of a dense Moso bamboo stand in Western Japan

ABSTRACT Bamboos tend to become abundant associated with human activities and possibly affect ecosystem dynamics including vegetation water cycles. We examined the effects of thinning on canopy transpiration (Ec) for a dense, unmanaged (i.e. unthinned) Moso bamboo stand based on sap flow measurements. We unselectively thinned 45% of the culms during summer in a study plot (i.e. the first thinning). During the next spring, many new culms were generated in the plot and a comparable number of culms were thinned (i.e. the second thinning). After the first thinning, mean stand sap flux (Js) increased immediately by approximately 60% at a given potential evaporation (Ep); therefore, the Ec of the thinned stand reached 90% that of the pre-thinning condition. During the next year, after the second thinning, the Js of the current year culms was generally more than twice that of the pre-thinning stand at a given Ep, whereas the Js of the older culms decreased again to the level of the pre-thinning condition. The overall Ec was 78% that of the pre-thinning condition. Our results suggest that moderate thinning of dense Moso bamboo stands may not have major effects on Ec; thus, intensive thinning is required when the aim is to control water loss from bamboo stands. The relative insensitivity of water use in bamboo stands after thinning resulted from dynamic changes in water use in the individual culms. These processes might be related to the clonal nature of bamboo where culms are structurally and physiologically interconnected.
Biological control of powdery mildew on Cornus florida using endophytic Bacillus thuringiensis

Abstract Powdery mildew (Erysiphe pulchra) is a devastating disease in nursery production of flowering dogwood (Cornus florida L.). Disease management relies heavily on season-long use of chemical fungicides and there is a demand for alternative strategies. An endophytic bacterium IMC8 was isolated from disease-free C. florida stem tissue, and was shown to be an effective biological control agent against E. pulchra in growth chamber, greenhouse and shadehouse environments. This isolate, identified as Bacillus thuringiensis, exhibited normal growth in NaCl concentrations up to 6%, pH 5 to 11, and temperatures up to 50°C. It was compatible with the conventional fungicide thiophanate methyl and clarified hydrophobic extract of neem seed oil at label recommended concentrations. The isolate IMC8 produced volatile compounds identified by GC/MS, which included antifungal and antibacterial compounds and suggested antibiosis as a mode of action. Scanning electron microscopy revealed lysis of powdery mildew spores and hyphae, which suggested parasitism as a second mode of action. These observations suggested that the isolate IMC8 has potential as a biological control agent in the management of powdery mildew on C. florida, and would tolerate a wide range of salinity, pH and high temperature conditions. It could be included as a component of integrated pest management in rotation or tank mix with lower levels of conventional fungicides, or used with clarified hydrophobic extract of neem seed oil.
PHYTOCHEMICAL SCREENING, TOTAL PHENOLIC AND FLAVONOIDS CONTENTS AND ANTIOXIDANT ACTIVITIES OF CITRULLUS COLOCYNTHIS L. AND CANNABIS SATIVA L.

Citrullus colocynthis L. and Cannabis sativa L. are well known herbs for their curative value and farming applications. Thus, extraction was performed to examine yield, total phenolic, flavonoids content and antioxidant activities for farming exertions. Qualitative analyses were conducted to scrutinize alkaloids, glycosides, terpenoids, flavonoids, flavones, steroids, tannins, phenols, saponins and quantitative analysis for total phenolic and flavonoids content was assessed by Folin-Ciocalteu and aluminium chloride colourimetric method respectively, while antioxidant activities was assessed by using 1, 1-Diphenyl-1-picrylhydrazyl. Results showed that distilled water afforded the maximum extract yield followed by methanol and ethanol thus, coefficient of determination (R) of extract yield present a positive correlation compared to root mean square error (RMSE). Phytoconstituents except terpenoids from C. sativa and C. colocynthis leaves were reported while, in contrast, steroids, tannins and phenols were absent in C. colocynthis roots. The methanol derived maximum phenolic contents from C. sativa and C. colocynthis leaves were 36.42 and 37.69 mg gallic acid equivalent GAE/g respectively. However, total flavonoids registered from C. sativa leaves and C. colocynthis leaves and roots were 59.03, 50.58 and 43.32 mg quercetin equivalent QE/g respectively. Interestingly, C. colocynthis leaves produced the highest flavonoids 119.63 mg QE/g using ethyl acetate extract. DPPH inhibition (%) was high in acetone 55.57, hexane 45.98 and distilled water 35.5% from C. sativa, C. colocynthis leaves and roots respectively. Our findings suggest that studied plants contain phytochemicals, reasonable quantity of phenol and flavonoids content confer to the potential antioxidant activity responsible for insecticidal properties as safer alternatives of synthetic pesticides.
Changes in brain microRNAs are associated with social evolution in bees

Evolutionary transitions to a social lifestyle in insects are associated with lineage-specific changes in gene expression, but the key nodes that drive these regulatory changes are largely unknown. We tested the hypothesis that changes in gene regulation associated with social evolution are facilitated by lineage-specific function of microRNAs (miRNAs). Genome scans across 12 bee species showed that miRNA copy-number is mostly conserved and not associated with sociality. However, deep sequencing of small RNAs in six bee species revealed a substantial proportion (20-35%) of detected miRNAs had lineage-specific expression in the brain, 24-72% of which did not have homologs in other species. Lineage-specific miRNAs disproportionately target lineage-specific genes, and have lower expression levels than shared miRNAs. The predicted targets of lineage-specific miRNAs are enriched for genes related to social behavior in social species, but they are not enriched for genes under positive selection. Together, these results suggest that novel miRNAs may contribute to lineage-specific patterns of social evolution. Our analyses also support the hypothesis that many new miRNAs are purged by selection due to deleterious effects on mRNA targets, and suggest genome structure is not as influential in regulating bee miRNA evolution as has been shown for mammalian miRNAs.
Engineering of Chimeric Antigen Receptor T Cells with integrin αEβ7 Results in Augmented Therapeutic Efficacy against E-cadherin positive tumor

Integrin αEβ7 (CD103) can interact with E-cadherin and promote T cell retention in epithelial tissue. However, whether the expression of CD103 on chimeric antigen receptor (CAR)-T cells may augment T cell anti-tumor activity remains unknown. Using a preclinical model, we demonstrate that CD103 engineering of human CAR-T cells significantly improves their therapeutic effects on eliminating pre-established E-cadherin expressing tumor cells in immune deficient NOD.scid. Il2Rγcnull (NSG) mice. Human T cells that were engineered with CAR containing 4-1BB and CD3zeta intracellular signaling domains (named BBz) expressed reduced level of CD103 in mice model. Ex vivo assays confirmed the effect of 4-1BB on repressing CD103 expression in CAR-T cells. On the other hand, we generated CD103 expressing CAR-T cells by introducing the αE gene into the CAR structure (named CD103-BBz CAR-T cells). As compared to BBz CAR-T cells, CD103-BBz CAR-T cells produced higher levels of IL-2 and underwent greater expansion in cultures and acquired greater capacity to control the growth and metastasis of E-cadherin expressing lymphoma cells in NSG mice. This effect of CD103-BBz CAR-T cells was associated with their increased capacity to infiltrate into the tumor and persist in vivo, leading to significantly improved overall survival of lymphoma mice. Our findings suggest that engineering tumor-reactive T cells with CD103 may represent a novel strategy to improve adoptive T cells anti-tumor efficacy, and this strategy may have broad implication in the epithelial solid tumor treatment. Highlights CAR-T cells with 4-1BB costimulatory domain express reduced level of CD103 4-1BB signaling antagonist TGF-β1 induced CD103 expression Ectopically expression of CD103 on CAR-T cells enhanced their anti-E-cadherin positive tumor capacity Graphical Abstract: Graphic Summary: The co-stimulatory molecule 4-1BB within the CAR protein potently suppresses CD103 expression. Engineering CAR-T cells with CD103 significantly enhances their capacity to proliferate and infiltrate into the solid tumor, leading to augmented anti-tumor immunity.
Efficient RNP-directed human gene targeting reveals SPDEF is required for IL-13-induced mucostasis

Primary human bronchial epithelial cell (HBEC) cultures are a useful model for studies of lung health and major airway diseases. However, mechanistic studies have been limited by our ability to selectively disrupt specific genes in these cells. Here we optimize methods for gene targeting in HBECs by direct delivery of single guide RNA (sgRNA) and recombinant Cas9 (rCas9) complexes by electroporation, without a requirement for plasmids, viruses, or antibiotic selection. Variations in the method of delivery, sgRNA and rCas9 concentrations, and sgRNA sequences all had effects on targeting efficiency, allowing for predictable control of the extent of gene targeting and for near complete disruption of gene expression. To demonstrate the value of this system, we targeted SPDEF, which encodes a transcription factor previously shown to be essential for the differentiation of MUC5AC-producing goblet cells in mouse models of asthma. Targeting SPDEF led to proportional decreases in MUC5AC expression in HBECs stimulated with IL-13, a central mediator of allergic asthma. Near-complete targeting of SPDEF abolished IL-13-induced MUC5AC expression and goblet cell differentiation. In addition, targeting of SPDEF prevented IL-13-induced impairment of mucociliary clearance, which is likely to be an important contributor to airway obstruction, morbidity, and mortality in asthma. We conclude that direct delivery of sgRNA and rCas9 complexes allows for predictable and efficient gene targeting and enables mechanistic studies of disease-relevant pathways in primary HBECs.
Sphingomyelin suppresses Hedgehog signaling by restricting cholesterol accessibility at the ciliary membrane

Transmission of the Hedgehog signal across the plasma membrane by Smoothened is proposed to be triggered by its direct interaction with cholesterol. But how is cholesterol, an abundant lipid, regulated tightly enough to control a signaling system that can cause birth defects and cancer? Using toxin-based sensors that distinguish between distinct pools of cholesterol, we find here that Smoothened activation and Hedgehog signaling are driven by a biochemically defined fraction of membrane cholesterol, termed accessible cholesterol. Increasing accessible cholesterol levels by depletion of sphingomyelin, which sequesters cholesterol in complexes, potentiates Hedgehog signaling. By inactivating the transporter-like protein Patched 1, Hedgehog ligands trigger an increase in cholesterol accessibility in the ciliary membrane, the subcellular location for Smoothened signaling. Thus, compartmentalization of Hedgehog signaling in the primary cilium may allow cholesterol accessibility to be used as a second messenger to mediate the communication between Patched 1 and Smoothened, without causing collateral effects on other cellular processes.
Effects of exogenous nitric oxide on cadmium toxicity in black poplar (Populus nigra): physiological approaches

Abstract Cadmium (Cd) is a highly toxic metallic contaminant that negatively affects plant metabolism and causes reductions in productivity. Nitric oxide (NO) is a signaling molecule that regulates various physiological processes and is involved in response to biotic/abiotic stresses. This work investigated the effects of exogenous sodium nitroprusside (SNP), a nitric oxide (NO) donor, application on Cd toxicity in black poplar (Populus nigra). Black poplars were exposed to individual/combined CdCl2 and SNP treatments for 21 days by complete randomized design with three replications. Cd concentrations increased in leaves, bark, and roots at Cd treatments, whereas Cd + SNP applications had alleviative effects on Cd exposures, except for leaves. Photosynthetic pigments (chlorophyll a, b, a + b and carotenoids) reduced with Cd treatments in leaves, while they increased in Cd + SNP applications. Similarly, plant biomass was reduced with Cd treatments, but Cd + SNP application prevented these reductions. SNP also alleviated malondialdehyde (MDA) and hydrogen peroxide (H2O2) accumulation in leaves under Cd treatments. Catalase (CAT, EC 1.11.1.6) and ascorbate peroxidase (APX, EC 1.11.1.11) activities were also affected by Cd and Cd + SNP applications. Cd exposure also decreased Zn2+, Fe2+ and Mn2+ levels in leaves, bark and roots, while it increased Cu2+ level in leaves and roots. This study concludes that Cd toxicity caused a reduction of plant growth and mineral nutrition parameters. However, SNP indicates great potentials for improving the growth under Cd toxicity in P. nigra.