Miracle-dz/UniFAR-FTUs huggingface dataset:
Antibacterial activity, optimal culture conditions and cultivation of the medicinal Ganoderma australe, new to Thailand

Ganoderma is a well-known genus of medicinal mushrooms that belongs to the order Polyporales. Many members of this genus are extensively used in traditional Asian medicines. Herein we report a new strain of Ganoderma australe collected in Thailand and identified using macro- and micro-morphological characteristics as well as phylogenetic analysis. The optimal conditions for mycelia growth were 25-30 degrees C at pH 7-8, while sorghum and barley were found to be the best grain media for spawn production. The best medium for mycelia growth was Potato Dextrose Agar (PDA) medium. Para rubber sawdust with organic and inorganic additives is used as a standard cultivation substrate in Thailand. The mycelia were fully distributed throughout the sawdust substrate after being incubated at 30 degrees C, 60-75% relative humidity for 18 days. The first primordia were observed three days after the bags were opened. Three fruiting cycles were obtained, although the weight of mushrooms produced decreased each time (115.04 +/- 48.85 g kg(-1), 72.01 +/- 6.00 g kg(-1) and 36.47 +/- 9.04 g kg(-1), respectively). Extracts of G. australe inhibited Micrococcus luteus, Bacillus subtilis, Staphylococcus aureus and Salmonella typhimurium bacteria however, the extracts were not effective against Escherichia coli and Pseudomonas aeruginosa. This is the first report of the antimicrobial activities observed in G. australe.
Prevalence and Antibiotic Resistance of Escherichia coli O157:H7 Isolated from Raw Meat Samples of Ruminants and Poultry

Escherichia coli O157:H7 is one of the most dangerous zoonotic pathogens of meat. The present investigation was done to study the prevalence and antibiotic resistance of E. coli O157:H7 strains isolated from raw meat samples. A total of 458 meat samples were collected. Samples were cultured using what? After which sorbitol negative isolates were analyzed for rfbO157 and flicH7 genes. Thirty-six out of 458 meat samples were positive for sorbitol negative strains of E. coli (7.86%). All of the sorbitol negative strains were also positive for rfbO157 and flicH7 genes. Prevalence of E. coli O157:H7 strains were 7.86%. The prevalence of E. coli O157:H7 in chicken meat was higher than the other samples (16.25%). The genes that encode resistance to ampicillin (CITM) (100%), gentamicin (aac(3)-IV) (94.44%) and tetracycline (tetA) (61.11%) had the highest prevalence. Escherichia coli O157:H7 strains from raw meat samples from ruminants and poultry had the highest resistance to ampicillin (100%), tetracycline (83.33%) and gentamicin (83.33%) respectively. Strains of antibiotic resistant E. coli 0157:H7 found in this present study are of public health importance.
Seasonal shift in community pattern of planktonic diatoms and environmental drivers in Jiaozhou Bay, northern China

Diatoms are a primary producer and play an important role in the functioning of microbial food webs. Temporal variations in community patterns of planktonic diatom assemblages were studied during a 1-year cycle (June 2007–May 2008) in Jiaozhou Bay, northern China. Samples were collected biweekly at a depth of 1 m from five sampling stations. A total of 75 diatom species representing 40 genera, 28 family, 19 orders and three classes were recorded. Of these species, 11 distributed in all four seasons, while 27, 35, 56 and 28 forms occurred only in spring, summer, autumn and winter season, respectively. The species number and total abundance peaked in autumn, with minimum values in May. All three species biodiversity measures (Shannon diversity, Pielou's evenness and Marglef's richness) peaked in spring and autumn. There was a significant difference in diatom community patterns among seasons, except the pair of spring and winter. The environmental variables, especially temperature and the nutrients, could significantly drive the seasonal variation in diatom community patterns. Of 11 dominant species, four (Paralia sulcata, Skeletonema costatum, Guinardia delicatula and Nitzschia lorenziana) were significantly related with temperature, pH and/or nutrients. These findings suggest that the seasonal shift in community pattern of planktonic diatoms was driven by both temperature and nutrients in this eutrophic basin ecosystem.
Characterization of Enterobacteries Genus in Intestinal Microbiota of Celiac Children

The imbalance of the intestinal microbiota is link, by several diseases such as celiac disease, which causes inflammation in the small intestine. This inflammation is due by the digestion of gluten present in some type of cereals. In this work, fecal and duodenal biopsy samples were collected to characterize by conventional culture technique the composition of the Enterobacteries group in intestinal mirobiota of celiac children and were compared with control children. A significant difference detected in the intestinal flora of celiac children compared to controls children concerning the Enterobacteries group. We found an increase of E.coli, Enterobacter aerogeneses, and Klebsiella with presence of Salmonella sp, Shigella sp in biopsy and fecal samples of celiac children and a relationship between the increase of Enterobacter cloacea and the presence of positive anti-transglutaminase value.
Modulation of mutagen-induced genotoxicity by vitamin C and medicinal plants in Allium cepa L.

Abstract Three concentrations (mg ml−1) of extracts of the medicinal plants Xysmalobium undulatum (XU) roots (0.125, 0.25, 0.50), leaves of Helichrysum caespititum (HC) (0.00625, 0.0125, 0.025) and ascorbic acid (AA) (0.125, 0.25, 0.50) were assessed for cytotoxicity (CT), genotoxicity (GT) and modulation of cyclophosphamide- and EMS-induced GT using the Allium cepa assay following 24 h treatment. CP (1.00 mg ml−1) and EMS (0.0375 mg ml−1) were not cytotoxic but genotoxic. CT was measured by the mitotic index (MI). GT was the number of aberrant cells per 100 mitotic cells. The MI and GT of test groups were compared with the negative control group using t-test. The modulatory effect (ME), calculated as (B – C) – (A – C)/(A – C) gave the number of times of the mutagen-induced GT by which the GT of the mutagen was reduced (anti-GT) or increased (synergism). One or more concentrations of AA, XU and HC and their mixtures with CP or EMS were cytotoxic and genotoxic. Mixtures of AA, XU and HC with CP were significantly more genotoxic than CP alone which indicated a synergistic interaction. Mixtures of AA with EMS were significantly more genotoxic than EMS alone. Mixtures of XU with EMS were less genotoxic than EMS, but not significantly, which made XU mildly anti-genotoxic to EMS GT. Mixtures of lower concentrations of HC with EMS were more genotoxic than EMS alone but not significantly. The most common aberrations among dividing cells were sticky chromosomes, c-metaphase, anaphase and telophase bridges, chromosome fragment and multipolar anaphase and telophase.
Identifying protein interaction partners for DEXI, encoded by the multiple sclerosis associated dexamethasone-induced gene, DEXI

Multiple sclerosis (MS) is a chronic demyelinating disorder of the central nervous system. The pathology of the disease is thought to be inflammation and demyelination, presumably caused by autoimmune T cells. The disease has a complex aetiology, affected by environmental factors as well as genetics. 200 MS-associated single nucleotide polymorphisms (SNPs) has been discovered through genome-wide association studies (GWAS). One interesting gene region, 16p13, was among the first to be discovered to contain MS associated SNPs. The gene region contains three genes associated with immune regulation: SOCS1, CIITA and CLEC16A, and one gene encoding a protein with unknown function, DEXI. Expression of CLEC16A has been shown to correlate with expression of DEXI in thymic tissue and an intron of CLEC16A that contains several MS-associated SNPs has been shown to interact with the promoter region of DEXI. These discoveries has led to the suggestion that DEXI may be an MS risk factor. We wanted to study the function of DEXI by investigating its protein interaction partners, by using a yeast two-hybrid system, in addition to investigating the protein subcellular localization in Jurkat cells. Through the yeast two-hybrid screening and subsequent in silico analysis of results we discovered five potential interaction partners for DEXI; CAMLG, MARCH2, MDK, SLTM, and SNAPIN. Subcellular localization of DEXI was investigated by overexpressing tagged DEXI in Jurkat cells, followed by immunostaining and confocal microscopy. From our experiment it appears as though DEXI is located in cytosol or plasma membrane.
IoT-Based Device for Indoor Premises Relative Humidity Control

The subject of this article is an electronic device based on IoT technology, for the control of relative humidity in a room. The IoT-based electronic device is part of a developed electronic system with implemented algorithms and criteria for providing comfortable conditions in a room. A mobile application has been developed through which remote control of relative humidity is carried out. Research has been done with a dehumidifier, which gives us reason to say that the correct choice of the dehumidifier in relation to the volume of a given room is essential. The obtained results show that the value of the relative humidity in the most severe mode "Long absence" can be reduced to the required values, according to the proposed criteria, within a twenty-four hours period of time.
Effect of variety and level of inclusion of barley varieties for silage selected to vary in neutral detergent fiber digestibility on performance and carcass characteristics of growing and finishing beef steers

Abstract Three ensiled barley varieties (‘CDC Cowboy’, ‘CDC Copeland’, and ‘Xena’) selected for differences in 30 h neutral detergent fiber digestibility (NDFD30h) were fed at two (LOW and HIGH) inclusion rates to study their effects on performance of crossbred steers (n = 288) in a 3 × 2 factorial design. Diets with the LOW inclusion level during backgrounding had a 1:1 barley silage:barley grain ratio, whereas HIGH diets had a 2:1 ratio (% DM basis). Respective ratios during finishing were 1:17 and 1:5. Actual NDFD30h averaged 37.6% ± 3.5%, 34.7% ± 3.8%, and 36.9% ± 3.0% for ‘CDC Cowboy’, ‘CDC Copeland’, and ‘Xena’, respectively. Backgrounding diets containing ‘CDC Cowboy’ as well as the HIGH diets had greater (P < 0.01) acid detergent fiber (ADF) and neutral detergent fiber (NDF) content. Steers fed ‘CDC Cowboy’ as well as the HIGH diets during backgrounding had lower (P < 0.01) dry matter intake (DMI), average daily gain (ADG), and end of backgrounding body weight. During finishing, ADG and DMI were greater (P < 0.01) for steers fed HIGH barley silage diets. The results indicate that barley variety and inclusion level had the greatest impact during backgrounding and highlight the difficulty in choosing barley varieties for silage based on a single nutritional parameter like NDFD30h.
Foraging behaviour of Carpenter bee (Xylocopa fenestrata) on Ridge gourd (Luffa acutangula) flowers

The foraging behaviour of Carpenter bee (Xylocopa fenestrata Fab.) was studied in ridge gourd, Luffa acutangula under field condition at University Apiary, Dr. Rajendra Prasad Central Agricultural University, Pusa, Samastipur (Bihar) during the year of 2016-17 in Kharif season. The results on foraging behaviour of Xylocopa fenestrata revealed that the bees started visiting ridge gourd flowers in early morning and ceased their activity later in the evening. It remained active throughout the flowering period. The minimum foraging rate of X. fenestrata was 3.9 flowers/minute in the morning hours (0700-h) and 3.2 flowers/minute in evening hours (1700-h) however, maximum was 7.3 flowers/minute during the mid day hours (1300-h). The maximum foraging speed was 17.6 sec. in morning hours (0700-h) and 23.5 sec. in evening hours (1700-h) while minimum 11.1 sec. in mid day hours (1300-h) and there was inverse relation between foraging rate and foraging speed. The heaviest pollen load carried by the Xylocopa was 28.54 mg in the evening hour (1700-h) while lightest pollen load was carried 9.75 mg in mid day hour (1300-h) which indicated that more pollen was collected by Xylocopa during morning and evening hours from ridge gourd flowers.
Projected regional forest plant community dynamics evidence centuries‐long effects of habitat turnover

Co-ordinating Editor: Hans Henrik Bruun Abstract Questions: Many Western European and North American countries have been experiencing strong reforestation in the last two centuries due to agricultural abandonment. Other landuse changes, such as urbanization, can simultaneously trigger forest erosion. In this context of habitat turnover, forest understorey plant dynamics depend on the balance between immigration credit in postagricultural forest and extinction debt in ancient forest. The transient and final community properties following concomitant habitat creation and destruction are poorly known. In this contribution, we study the projected transient regional forest plant dynamics and identify the determinants of the relaxation duration at both landscape and patch scales. Location: SeineetMarne region, France. Methods: Species’ incidences are projected in 9,208 patches of the SeineetMarne region characterized by strong development of postagricultural forests and a moderate erosion of ancient forests during the period 1840–2000. We use a metapopulation model with static biodiversity data and landscape history to project forest plant dynamics. We focus on 33 generalist forest species that are able to colonize both ancient and postagricultural forests. Results: Our analyses reveal that (1) extinction in ancient forests slows the colonization process, which lasts between 250 and 990 years after habitat turnover, depending on species characteristics; (2) the species incidence in postagricultural forests converges towards that in ancient forests long before the overall species incidence stabilizes at the landscape scale (i.e. long before the relaxation time); (3) landscapeand patchscale relaxation times depend on species colonization ability and patch functional connectivity; (4) the colonization process is rather slow for ancient forest species; and (5) the incidence of ancient forest species becomes larger than the incidence of other species at the end of the colonization dynamics thanks to their strong persistence. Conclusions: Ancient forest species may potentially benefit from a large immigration credit but need centuries to use it. On such time scales, many perturbations are likely to jeopardize the realization of this potential credit.
Ophrys fusca and Ophrys dyris (Orchidaceae) – constancy of tetraploidy amongst populations in Central Portugal

Ophrys is amongst the best known orchid genera and is an established system for the study of pollinator-mediated floral evolution. Two species, Ophrys fusca s.l. and Ophrys dyris (= O. omegaifera subsp. dyris) belonging to Ophrys section Pseudophrys are the focus of this study. In the context of an integrative study of morphological and genetic diversity of O. fusca and O. dyris, genome size (GS) and cytotype diversity were surveyed from Portuguese populations. Flow cytometry methods were used to assess GS, and subsequently determine the ploidy level of 67 specimens, including the species and putative hybrids. Cytotypes were also confirmed based on chromosome counts from the roots of two specimens, one of each species. Constancy of nuclear DNA content (1C = 11.19 pg) and ploidy level (2n = 4x = 72, 74) was documented among all the individuals analysed. Implications are considered, in terms of interpreting the origin and predicting the persistence of putative hybrids.
Genetics and Functions of Herpes Simplex Virus Type 1 (HSV-1) Glycoprotein K (gK) in Virus Envelopment and Egress.

HSV-1 (KOS)AgK, a virus lacking the UL53 gene coding for glycoprotein K(gK) was constructed, characterized and compared to the partially deleted gK-null virus HSV-1 (F)-gKp. AgK and F-gK(J viruses produced microscopic plaques on Vero cells at 48 hours post infection. F-gKp plaques at 72 hours post infection contained fused cells (syn), while AgK plaques resembled wild-type KOS plaques (syn*). AgK replicated efficiently in exponentially dividing Vero cells whereas F-gKp yields were 10 and 1000fold lower than AgK yields in HEp-2 or log-phase Vero cells, respectively. Electron micrographs of AgK-infected Vero cells revealed large numbers of capsids in the nuclei of Vero, but not HEp-2 cells, while a small number of enveloped virions were observed in the cytoplasm of infected Vero and HEp-2 cells that failed to translocate to the extracellular spaces. KOS and AgK replicated inefficiently in gK-transformed cells, with the exception of VK302 cells. Electron micrographs of the gK-transformed BL-1 cells infected with KOS revealed virions within perinuclear spaces, while there were no virions visualized in AgK infected BL-1 cells. VK302 cells were the only gKtransformed cells that supported the replication and cellular egress of both KOS and AgK To fine-map the functional domains of gK involved in membrane fusion, a longPCR site-directed mutagenesis system was developed that efficiently produced single base substitutions within larger than 4 kbp DNA fragments. Utilizing this system three different mutations were engineered and recombinant viruses containing one of the three mutations were isolated. The mutation at position 31 resulted in a syn* virus. This research revealed that gK is involved in nudeocapsid envelopment and cellular egress of infectious virions. Actively replicating cells can partially compensate for envelopment but not for the cellular egress defidendes of AgK Interference of viral replication in gK-transformed cells suggests that the cellular gK can function in-trans to inhibit egress by preventing certain cellular factors required for viral egress to function
Quantifying carbon fluxes from primary production to mesopelagic fish using a simple food web model

An ecosystem-based flow analysis model was used to study carbon transfer from primary production (PP) to mesopelagic fish via three groups of copepods: detritivores that access sinking particles, vertical migrators, and species that reside in the surface ocean. The model was parameterized for 40°S to 40°N in the world ocean such that results can be compared with recent estimates of mesopelagic fish biomass in this latitudinal range, based on field studies using acoustic technologies, of ∼13 Gt (wet weight). Mesopelagic fish production was predicted to be 0.32% of PP which, assuming fish longevity of 1.5 years, gives rise to predicted mesopelagic fish biomass of 2.4 Gt. Model ensembles were run to analyse the uncertainty of this estimate, with results showing predicted biomass >10 Gt in only 8% of the simulations. The work emphasizes the importance of migrating animals in transferring carbon from the surface ocean to the mesopelagic zone. It also highlights how little is known about the physiological ecology of mesopelagic fish, trophic pathways within the mesopelagic food web, and how these link to PP in the surface ocean. A deeper understanding of these interacting factors is required before the potential for utilizing mesopelagic fish as a harvestable resource can be robustly assessed.
Potential of insect proteins for food and feed : Effect of endogenous enzymes and iron-phenolic complexation

Insects have been identified as excellent alternative source of proteins due to their high protein content. The acceptance of insects increases when used as ingredient in an invisible manner and hence grinding is necessary. Off-colour formation occurs upon grinding larvae, which can hamper their potential use as ingredient for food and feed. The aim of this thesis was to investigate potential of insect larvae as protein source, the mechanisms responsible for the browning or blackening of larvae during grinding, and its impact on protein functionality. This was investigated for the larvae of three species: Tenebrio molitor, Alphitobius diaperinus and Hermetia illucens. The specific Kp factor of 4.76±0.09 was determined for the three species to determine protein content based on nitrogen, and 5.60±0.39 after protein extraction and purification. Thus, the general Kp factor of 6.25, used until now, overestimated the protein content in insects. Off-colour formation upon grinding was caused by both enzymatic and non-enzymatic browning. Phenoloxidase was found to be mainly responsible for browning in T. molitor and likely in A. diaperinus, whereas iron-phenolic complexation likely contributed to the black colour in H. illucens. A model system of L-DOPA and iron was used to elucidate the structures of the iron-L- DOPA complexes by mass spectrometry. Enzymatic browning did not influence the solubility of the proteins of all three species. Upon in-vitro hydrolysis by pepsin and trypsin, soluble proteins from H. illucens were more digestible compared to those of T. molitor and A. diaperinus. Phenoloxidase activity during processing negatively affected in-vitro pepsin hydrolysis. Besides phenoloxidase activity, also endogenous proteases remained active at pH 8 in extracts of insect larvae. Summarizing, endogenous enzyme activities and iron complexation should be taken into account for future application, as well as the specific Kp factor to prevent overestimation of the protein content of insects.
Incidence, Distribution, and Diversity of Citrus tristeza virus in the Hawaiian Islands

Citrus tristeza virus (CTV), the causal agent of tristeza quick decline and stem pitting in citrus, and its most effective vector, the brown citrus aphid (BrCA) ( Toxoptera citricida Kirk.), have been present together in Hawaii for over 50 yr. In this study the incidence, diversity, and population structure of Hawaiian CTV strains were examined. Citrus tissue samples collected on Kauai (8 sites, 91 trees), Oahu (13, 86), Molokai (4, 12), Maui (10, 87), and Hawaii (15, 129) were subjected to RT-PCR for the CTV coat protein gene as well as tissue blot immunoassays (TBIAs) using two CTV antibodies. Samples testing positive for either RT-PCR or TBIA were sub- jected to further RT-PCR using primers speciﬁc to CTV genotypes T3, T30, T36, and VT. The incidence of CTV on Kauai, Oahu, Molokai, Maui, and Hawaii was 59, 87, 58, 63, and 83% respectively, with an overall incidence of 74% (298/405). Strains with similarity to T3, T30, T36, and VT genotypes were identiﬁed in these samples, although their distribution was not uniform throughout the islands. Most infections, however, were composed of CTV strains that did not resemble any of these genotypes. The coat protein (CP) sequence was determined for over 100 Hawaiian strains. Phylogenetic analysis using these sequences as well as sequences of strains from other parts of the strains of the
Slime Gland Cytology and Mechanisms of Slime Thread Production in the Atlantic Hagfish (Myxine glutinosa)

Slime Gland Cytology and Mechanisms of Slime Thread Production in the Atlantic Hagfish (Myxine glutinosa) Timothy McEwen Winegard Advisor: University of Guelph, 2012 Dr. D.S. Fudge The multicellular slime glands of hagfish are functionally and structurally unique among cyclostomes. The holocrine release of cells from these glands results in the formation of a fibrous slime that viscously entraps seawater to discourage attacks by gill-breathing predators. Past research into the cytology of the slime gland, and processes of gland thread cell (GTC) and gland mucous cell (GMC) maturation, leads to a number of hypotheses on the mechanism of slime thread assembly in GTCs. Using a number of cell manipulation and imaging techniques, I reveal: (1) a previously undescribed cell in the hagfish slime gland, (2) the intermediate filament and microtubule distribution in hagfish gland cells, and (3) mechanisms of slime thread assembly. The findings test a number of hypotheses and provide the basis for further analysis of cytoskeletal element distribution and interaction in hagfish gland cell types.