Miracle-dz/UniFAR-FTUs huggingface dataset:
Biogeography of major bacterial groups in the Delaware Estuary

We used fluorescence in situ hybridization to examine the spatial and temporal variation in the abundance of major bacterial groups in the Delaware Estuary. The abundance of alpha‐ and beta‐proteobacteria and Actinobacteria varied systematically in the estuary and mirrored the pattern seen in lakes and oceans. Beta‐proteobacteria and Actinobacteria were abundant in the Delaware River but were less so in the marine waters of the Delaware Bay. In contrast, alpha‐proteobacteria, including the SAR11 clade, were most abundant in the Bay and rare in the Delaware River. Actinobacteria were active in assimilating thymidine and leucine and appeared to contribute substantially to bacterial production in the Delaware River. Among the several biogeochemical parameters we examined, only salinity accounted for a substantial portion of the variation in abundance of these bacterial groups. However, relative abundance of these groups often varied independently of salinity. Cytophaga‐like bacteria were often abundant throughout the estuary, but they did not vary systematically over the estuarine gradient, unlike the other dominant bacterial groups. We hypothesize that this estuary‐wide high abundance occurs because Cytophaga‐like bacteria are very diverse, more so than other groups. Data on 16S rRNA sequences are consistent with this hypothesis. The consistent biogeographic patterns suggest that some bacterial groups, even at a broad phylogenetic level, operate as ecologically meaningful units for examining some processes, whereas the Cytophaga‐like bacteria as now defined might be too diverse to be useful for ecological studies.
Insight into microevolution of Streptomyces rimosus based on analysis of zwf and rex genes

Streptomyces rimosus has greatly influenced human history as a producer of many important secondary polyketide metabolites, such as oxytetracycline (OTC). The traditional screen and mutation program has resulted in a dramatic increase in OTC production. The availability of multiple semi-complete genome sequences of S. rimosus facilitates attempts to systematically address basic questions in genome evolution. We refer to such efforts as micro-evolutionary analysis. We report the results of comparative analysis of semi-complete genome sequences of three S. rimosus strains from the genealogy map (G7, M4018 and 23383) with different OTC production levels using genome comparison (single nucleotide polymorphisms, SNPs) method. These data were used to assess the influence of microevolution on the physiology, genetics and evolution of S. rimosus. Some SNPs were found in primary metabolism related genes which might affect the final OTC production. We further discussed the microevolution of primary metabolite genes (Glucose-6-phosphate dehydrogenase, zwf) and regulatory genes (redox regulator, rex) in S. rimosus. Using SOLEXA sequencing data, the phylogenetic trees of zwf and rex were constructed. The results indicate that S. rimosus is closely related with Streptomyces albus and represents a distinct evolutionary lineage compared with other Streptomyces. Our research cannot only provide important information for genotyping and evolutionary research of S. rimosus, but can also make possible the development of an informed view of genotype and phenotype.
HISTOPATHOLOGICAL TECHNIQUE

At the present time one hears of over-sanguine enthusiasts speaking glibly of the eradication of tuberculosis in fifteen, twenty or some other number of years: the warning against this ill-considered optimism is timely. This is in line with recent statistics relating to a number of countries having low death rates from tuberculosis, which indicate that during the years between 1940-1960 there was little correlation between the substantial fall in the death rate and the number of new cases notified, which in some countries showed an increase.
Agrobacterium-mediated transformation using gill tissue of Flammulina velutipes

Agrobacterium-mediated transformation was conducted in order to generate DNA insertional mutants of Flammulina velutipes. Agrobacterium tumefaciens AGL-1 harboring pBGgHg was transformed into gill tissues of Flammulina velutipes strain KACC42777. The transformants resistant on hygromycine (30 µg/ml) were confirmed by PCR. The targeted insertional sites were amplified by inverse PCR and sequenced. To find the phenotype variation of all generated transformants, bottle cultivation which followed by the standard cultivation protocol were conducted. Color variation was observed on the cultivated fruiting bodies. Futhermore, the transformant pool will be used as a good genetic resources for studying gene function.
In ovo feeding and its effects on performance of newly-hatched chicks

The broiler chick's gastrointestinal tract undergoes significant morphological and physiological changes during the first days after hatch. These changes occur mostly because birds switch from a diet based on fatty acids from the yolk sac to a diet based on carbohydrates, provided by commercial feeds, often formulated with corn and soya bean meal. In ovo feeding techniques enable the study of the early adaptation of the avian gastrointestinal tract, such as supplementation with carbohydrates during embryonic development. This procedure consists of inoculation into the amniotic fluid through a hole in the egg shell near the air-chamber during late embryonic growth. The hatching process requires large supply of energy to the muscles, and in ovo feeding has the objective of providing extra energy in order to avoid glycogen store reductions, which are needed during the first days after hatch. However, published reports have shown that in ovo manipulation can reduce incubation yield, mostly when applied during the beginning of embryonic development. The best results of in ovo feeding were found when supplementation was with carbohydrates.
New approach in diagnosis and treatment of Bovine Mycotic Mastitis in Egypt

In the present study, 123 collective milk samples from 71 cattle and 52 buffaloes suffering from clinical mastitis with no or poor response to treatment with conventional antibiotics were tested for mycotic mastitis using culture and multiplex PCR (m-PCR) methods. The overall positive percentage of Mycotic mastitis was 25.2 and 30.08% using culture and m-PCR respectively. Milk culture revealed 24 isolates of Candida albicans and 7 isolates of Aspergillus fumigatus. PCR succeeded to detect A. fumigatus from two samples and C. albicans out of four samples that were culturally negative. These yeast and fungi isolates were tested for their sensitivity toward different probiotic strains from different sources. Results revealed that Lactobacillus acidophilus isolated from goat colostrums followed by L. acidophilus isolated from mare colostrums showed the best antifungal activities against C. albicans followed by A. fumigatus, while, Lactobacillus plantarum and Bacillus subtilis had no effect. These results showed that Mycotic mastitis is an increasing problem due to the wide misuse of antibiotics as mastitis therapy. Antimicrobials should be used in mastitis in a careful way and effort most be encouraged to apply safe substitutes such as probiotics and bioactive natural compounds for prophylactic and therapeutic use.
Identification of the S3 self-incompatibility allele in almond by specific primers

To date, the identification of the S3 self-incompatibility allele in almond using PCR primers has been problematic, either because of its weak amplification in some allelic combinations, or because of a lack of polymorphism in comparison with the self-compatibility (Sf) allele. This paper describes the use of three new primers, one ‘forward’ (S3F) and two ‘reverse’ (S3R1 and S3R2), specifically designed to amplify the S3 allele. Primers S3F and S3R1 were designed from the sequence of the second intron of this allele, while S3R2 was designed from the sequence upstream of the RC4 conserved region. Four primer combinations (S3F/S3R2, S3F/ConR, ConF/S3R1 and ConF/S3R2) satisfactorily amplified the S3 allele. The use of consensus primers from the S-RNase intron sequences allows specific identification of the S-alleles, and indicates the expected size of the amplified fragment.
Antibiogram and heavy metal resistance pattern of Aeromonas spp. isolated from Asian seabass (Lates calcarifer) hatchery.

Summary. The paper was described antibiogram and heavy metal tolerance of Aeromonas spp. isolated from Asian seabass (Lates calcarifer) hatchery in Malaysia. Aeromonas spp. was recognized as causative agent of motile aeromonad septicemia (MAS) which attack in Asian seabass and caused tremendous loss to fish farmer. Therefore this study was carried out to help fish farmer in selecting the suitable antibiotic in controlling MAS due to Aeromonas spp. diseased Asian seabass fingerling and water sample from the fingerling tank were collected from a commercial farm. Aeromonas spp. was isolated using Glutamate Starch Pseudomonas (GSP). The isolated bacterial isolates were identified using conventional biochemical tests and confirmed with commercial identification kit. 150 bacterial isolates of Aeromonas spp. were randomly selected from antibiotic susceptibility and heavy metal tolerance test. All the bacterial isolates were found to be sensitive to nitrofuratoin, furazolidone, tetracycline, doxycycline, flumequine, oxolinic acid and florfenicol. Therefore, fish farmer may apply those antibiotics as prophylactive or treatment to against MAS due to Aeromonas spp. in Asian seabass culture.
MORPHOLOGIC EVOLUTION OF THE COCCOLITHOPHORID CALCIDISCUS LEPTOPORUS FROM THE EARLY MIOCENE TO RECENT

Abstract A detailed investigation of the morphological evolution of the coccolithophorids Calcidiscus leptoporus and C. macintyrei from the Early Miocene to the Quaternary shows that microevolutionary patterns were very complex. Speciation patterns such as cladogenesis and phyletic divergence were observed, but stasis also existed over prolonged time-intervals. Similar coccoliths developed repeatedly at stratigraphically distant intervals, leading to taxonomic uncertainies. On the basis of bivariate frequency diagrams of coccolith diameters and number of elements in the distal shields nine morphotypes S, I, L, F, A, B, C, D and E are distinguished. A tentative phylogeny was constructed for these morphotypes suggesting, that they belong to one extant species and several extinct species. The extant species is Calcidiscus leptoporus, which comprises the living morphotypes S, I, L, and F and one extinct morphotype E. Morphotype S is the most conservative one, which originated from an unknown ancestor during the Early Miocene or earlier, while morphotype I originated from S during the Early Miocene. Morphotypes L and E separated from I during the Late Miocene. An extinct lineage is proposed, including morphotypes C, D, A, and B, which all produced large coccoliths except morphotype B, which is small. Morphotypes C, D, and A are very similar to a coccolith that specialists call Calcidiscus macintyrei, but in the present phylogenetic model they may belong to separate species with similar morphology. Morphotype C developed from morphotype I during the Early Miocene and is the precursor of an extra large morphotype D, and two other morphotypes, A and B. All three forms separated from morphotype C by pronounced cladogenetic events during the Late Miocene and Pliocene, and hence may represent separate species. Morphotypes A and B are supposed to belong to an extinct morphocline and may thus be ecophenotypes of one species. Alternatively, due to the lack of paleoenvironmental and biogeographic observations in the past, it cannot be discounted that all morphotypes found in this investigation simply represent ecovariants of one species. With the present status of knowledge, it is not possible to propose a sound differential diagnosis in the plexus C. leptoporus-C. macintyrei, which would allow differentiation among species at each point in space and time. It is hoped that this study stimulates further morphometric and phylogenetical studies that will generate a more profound understanding of species in paleontology and biology in general.
SCREENING OF ANTIOXIDANT AND ANTIMICROBIAL POTENTIAL OF HAWTHORN (CREATAGUS MONOGYNA) FRUIT AND LEAVES EXTRACTS

In the present study, water and methanol extracts of hawthorn ( Creatagus monogyna ) were studied for antioxidant and antimicrobial properties. The antioxidant properties of fruits and leaves were evaluated by determining DPPH radical scavenging activity. The water and methanol extracts of both fruits and leaves have antioxidant potential, ranging from 3.7 %to 44 %. Antimicrobial activities of above extracts were also tested against clinical isolates of human pathogenic strains belonging to 4 bacteria, Enterobacter aerogenes, Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and 3 yeast species, Candida albicans, Candida glabrata and Candida parapisilosis, by disc-diffusion method. The minimal inhibition concentration (MIC) value of each active extracts was also determined. The most effective antibacterial activity was expressed by methanol extract of hawthorn leaves against Gram-positive bacteria Staphylococcus aureus with 12mm inhibition zone and 0.625 mg/ml MIC value. None of the extracts have antifungal activity against tested human pathogen clinic isolates. Keywords : Hawthorn ( Creatagus monogyna ), Antimicrobial activity, Antioxidant Activity
Response of soil surface CO2 flux in a boreal forest to ecosystem warming

Soil surface carbon dioxide (CO2) flux (RS) was measured for 2 years at the Boreal Soil and Air Warming Experiment site near Thompson, MB, Canada. The experimental design was a complete random block design that consisted of four replicate blocks, with each block containing a 15 m × 15 m control and heated plot. Black spruce [Picea mariana (Mill.) BSP] was the overstory species and Epilobium angustifolium was the dominant understory. Soil temperature was maintained (∼5 °C) above the control soil temperature using electric cables inside water filled polyethylene tubing for each heated plot. Air inside a 7.3‐m‐diameter chamber, centered in the soil warming plot, contained approximately nine black spruce trees was heated ∼5 °C above control ambient air temperature allowing for the testing of soil‐only warming and soil+air warming. Soil surface CO2 flux (RS) was positively correlated (P < 0.0001) to soil temperature at 10 cm depth. Soil surface CO2 flux (RS) was 24% greater in the soil‐only warming than the control in 2004, but was only 11% greater in 2005, while RS in the soil+air warming treatments was 31% less than the control in 2004 and 23% less in 2005. Live fine root mass (< 2 mm diameter) was less in the heated than control treatments in 2004 and statistically less (P < 0.01) in 2005. Similar root mass between the two heated treatments suggests that different heating methods (soil‐only vs. soil+air warming) can affect the rate of decomposition.
MOLECULAR SYSTEMATICS OF THE PEROMYSCUS TRUEI SPECIES GROUP

Abstract DNA sequences from the mitochondrial cytochrome-b gene were used to examine the composition and phylogenetic relationships of the Peromyscus truei species group. Thirty-one individuals from the southwestern United States and Mexico were examined. Results indicated that 6 Peromyscus species (attwateri, difficilis, gratus, nasutus, pectoralis, and truei) compose the P. truei species group and that the group should be divided into 2 species assemblages. The relationship of the P. truei species group to the P. boylii and P. aztecus species groups was unresolved, indicating a close association of these 3 groups. In addition, levels of sequence divergence between sister taxa were higher than those reported for other sister species of Peromyscus.
DETERMINATION OF MINIMUM INHIBITORY CONCENTRATION UTILIZING MICROTITREPLATE BIOASSAY FOR THREE MALAYSIAN HERBAL MEDICINES

Herbal medicine has a long history of being used for treating various ailments ranging in severity. The growing popularity of herbal medicine, termed the green boom, may be ascribed to people taking a more holistic approach to maintain their health.Traditional medicine is widely used on a regular basis by Malaysians . In this study three medicinal plants (Piper Sarmentosum, MoringaOleifera, MurrayaKoenigii) that are traditionally used in the Malaysians for treating infections, were collected for investigation. The bacteria used in this investigation are both Gram-positive and Gramnegative bacteria which is S. aureus, E.coli, P. aeruinosa and Bacillus Subtilis. The microtitre well plate and disc diffusion assay were used for determining the antibacterial activity of the traditional preparations and plants extracts against the different bacterial strains.Themicrotitre well plate was used for testing the antibacterial activity of the plants against the previously mentioned bacterial strains. Disc diffusion assay were also used as an alternative method for determining antibacterial activity of the plant extracts against the bacterial strains of these bacteria.Disc diffusion assay use uniform plant extractions concentrations which are 1mg, 10mg and 100mg. Two conventional antibiotic disc which is the broad spectrum antibiotics, Tetracycline and Erthromycin were used as positive control while alcohol 100% were was used as negative control. The results shows that extracts of Murrayakoenigii gave the highest antibacterial activity against S.aureus and P.aeruginosa followed by Piper sarmentosum and the extracts of Moringaoleifera inhibited the lowest number of bacterial strains. All extracts show minimal inhibitory or no inhibitory against E.coli and Bacillus Subtilis. The highest concentration that show highest antibacterial activity on disc diffusion assay were used as initial concentration in the microtitre well plate.Serial dilutions were made to produce highest concentration to lowest concentrations of extractions. Each bacterial of four bacteria strains were used as bacteria growth indicator. Uniform plant extract concentrations were tested for all extracts and bacteria strains. Lowest concentration that show no growth indicated as minimum inhibitory concentrations. P.aeruginosa and S.aureus shown MIC for plants extractions of MurrayaKoenigii.
Plant Regeneration of Pummelo cv. Cikoneng from Cotyledon and Epicotyl

In vitro conservation needs highly efficient micropropagation protocol. The objective of the research was to obtain an efficient and reproducible protocol for pummelo (Citrus maxima(Burm.) Merr. ) micropropagation through direct shoot formation. The experiment was arranged in a completely randomized design with two factors and 20 replications. The 1 stfactor was type of explant, i.e. cotyledon and epicotyl segments of Pummelo cv. Cikoneng, while the 2ndfactor was the media composition as follow (1) MS + 1.0 mg BAP L-1 + 0.5 mg Kinetin L-1 + 0.5 mg NAA L-1 ; (2) MS + 2.0 mg BAP L-1 + 0.5 mg Kinetin L-1 + 0.5 mg NAA L-1; (3) MS + 1.0 mg BAP L-1 + 1.0 mg Kinetin L-1 + 0.5 mg NAA L-1; (4) MS + 2.0 mg BAP L-1 + 0.5 mg Kinetin L-1+ 1.0 mg NAA L-1; (5) MS + 2.0 mg BAP L-1+ 1.0 mg Kinetin L-1 + 1.0 mg NAA L-1. Observation was conducted on days to shoot induction, number of explant forming shoots, shoot height, number of shoots, leaves, and roots. The results showed that adventitious shoots emerged from callus in epicotyl (6-8 WAP), but adventitious shoots could emerge directly without an intervening callus phase from cotyledon (4-5 WAP). Shoots emerged from epicotyl were weak and vitrous due to hyperhydricity, thus they can not be used for micropropagation. Cotyledons cultured in media MS + 1.0 mg BAP L-1 + 0.5 mg Kinetin L-1 + 0.5 mg NAA L-1or media MS + 1.0 mg BAP L-1 + 1.0 mg Kinetin L-1 + 0.5 mg NAA L-1gave the highest percentage of explant forming adventitious shoot (38.8 and 26.3%), highest efficiency of shoot formation (62.5 dan 72.5%), and highest numbers of leaves (value of 1.9 leaves shoot-1) and roots (1.1 roots shoot-1) compared to other media. Since shoot height and number of leaves and root were not significantly different in both media, thus cotyledon and media MS + 1.0 mg BAP L-1 + 0.5 mg Kinetin L-1+ 0.5 mg NAA L-1which was less in Kinetin is suggested to be used for pummelo micropropagation. Keywords: Citrus maxima, epicotyl, cotyledon, regeneration, pummelo
Simulating the effects of harvest and biofuel production on the forest system carbon balance of the Midwest, USA

Forests of the Midwestern United States are an important source of fiber for the wood and paper products industries. Scientists, land managers, and policy makers are interested in using woody biomass and/or harvest residue for biofuel feedstocks. However, the effects of increased biomass removal for biofuel production on forest production and forest system carbon balance remain uncertain. We modeled the carbon (C) cycle of the forest system by dividing it into two distinct components: (1) biological (net ecosystem production, net primary production, autotrophic and heterotrophic respiration, vegetation, and soil C content) and (2) industrial (harvest operations and transportation, production, use, and disposal of major wood products including biofuel and associated C emissions). We modeled available woody biomass feedstock and whole‐system carbon balance of 220 000 km2 of temperate forests in the Upper Midwest, USA by coupling an ecosystem process model to a collection of greenhouse gas life‐cycle inventory models and simulating seven forest harvest scenarios in the biological ecosystem and three biofuel production scenarios in the industrial system for 50 years. The forest system was a carbon sink (118 g C m−2 yr−1) under current management practices and forest product production rates. However, the system became a C source when harvest area was doubled and biofuel production replaced traditional forest products. Total carbon stores in the vegetation and soil increased by 5–10% under low‐intensity management scenarios and current management, but decreased up to 3% under high‐intensity harvest regimes. Increasing harvest residue removal during harvest had more modest effects on forest system C balance and total biomass removal than increasing the rate of clear‐cut harvests or area harvested. Net forest system C balance was significantly, and negatively correlated (R2 = 0.67) with biomass harvested, illustrating the trade‐offs between increased C uptake by forests and utilization of woody biomass for biofuel feedstock.
An Evaluation of the Use of Simulated Annealing to Optimize Thinning Rates for Single Even-Aged Stands

We evaluated the potential of simulated annealing as a reliable method for optimizing thinning rates for single even-aged stands. Four types of yield models were used as benchmark models to examine the algorithm’s versatility. Thinning rate, which was constrained to 0–50% every 5 years at stand ages of 10–45 years, was optimized to maximize the net present value for one fixed rotation term (50 years). The best parameters for the simulated annealing were chosen from 113 patterns, using the mean of the net present value from 39 runs to ensure the best performance. We compared the solutions with those from coarse full enumeration to evaluate the method’s reliability and with 39 runs of random search to evaluate its efficiency. In contrast to random search, the best run of simulated annealing for each of the four yield models resulted in a better solution than coarse full enumeration. However, variations in the objective function for two yield models obtained with simulated annealing were significantly larger than those of random search. In conclusion, simulated annealing with optimized parameters is more efficient for optimizing thinning rates than random search. However, it is necessary to execute multiple runs to obtain reliable solutions.