Miracle-dz/UniFAR-FTUs huggingface dataset:
Molecular phylogenies of fig pollinating and non‐pollinating wasps and the implications for the origin and evolution of the fig‐fig wasp mutualism

Figs host three ecologically distinct groups of wasps: pollinators, non-pollinators (parasitic wasps) and parasitoids. Both pollinators and non-pollinators complete their life cycles using fig tissue, while parasitoids appear to attack some groups of non-pollinators. We used nucleotide sequence data to address a series of questions concerning genealogical associations, host specificities and degree of strict-sense co-evolution exhibited by members of these groups. We used the relatively conserved 12S rRNA gene of the mitochondria to estimate high level relationships among pollinator, parasitic and parasitoid taxa by sampling species collected from host figs representing five sections (three subgenera) from Asia, Africa, Europe and Central America. We found that all pollinators formed a clear monophyletic group. However, we could not resolve whether or not all of the non-parasitoid wasps associated with figs (Agaonidae, sensu Boucek) formed a single monophyletic group. Further, we used the more variable COII mitochondrial gene to attempt to determine relationships among closely related species of pollinators within two New World genera. Using sequences from the same gene we estimated the phylogenetic relationships among the parasites collected from the same New World host fig species and compared them with those of the pollinators. At fine taxonomic scale, we found that for both pollinator and parasites, species were generally specific to a given fig host. Moreover, the phylogenies of the non-pollinators are largely congruent with those of the pollinators, suggesting the predominance of strict-sense co-evolution on shared host fig species. The implications of these findings and opportunities for future research are discussed.
Epithelial-Mesenchymal Transition: NF-κB Takes Center Stage

Activation of the transcription factor NF-? B occurs in many human tumors, and studies have shown that NF-κB can promote cell proliferation and oncogenesis, possibly by protecting cells from apoptosis. Little is known, however, about whether NF-κB is involved in tumor progression including epithelial-mesenchymal transition (EMT), a central process governing both morphogenesis and carcinoma progression in multicellular organisms. In a combined in vitro/in vivo model of mammary carcinogenesis, NF-κB was essential both for the induction and maintenance of EMT and for in vivo metastasis. NF-κB and the signaling pathways that are involved in its activation should therefore receive attention as potential targets for the development of novel anti-metastatic cancer treatments.
EXCLUDING PESTS AND PATHOGENS: Plant health: How diagnostic networks and interagency partnerships protect plant systemsfrom pests and pathogens

Early detection and rapid response are crucial in any effort to reduce the risk of new and emerging biological threats to crops and other plant resources. This underscores the importance of having the necessary diagnostic expertise, infrastructure and resources in place. Three programs — the National Plant Diagnostic Network, the National Clean Plant Network and the Citrus Clonal Protection Program — illustrate how accurate and rapid diagnosis plays a critical role in providing healthy plants for growers and in securing production systems for food and fiber. These three programs depend on statewide, regional and national networking among university, state and federal scientists, regulatory officials and industry members to help mitigate the impacts of plant pests and diseases.
Shoot Regeneration from Leaf Explants of Withania somnifera (L.) Dunal

Regeneration from leaf explants of Withania somnifera (L.) for mass propagation was studied on Murashige and Skoog’s medium supplemented with Kinetin (Kn) and 6-benzylaminopurine (BAP) alone or in combination. Shoot buds were induced from the midrib on the abaxial side in presence of Kn and BAP (4 µM). These shoot buds developed into shoots on the same medium. Rooting of these shoots was achieved in 0.5 µM of IBA.
Association of the α-Adducin Locus With Essential Hypertension

Abstract Previous studies on genetic rat hypertension have shown that polymorphism within the α-adducin gene may regulate blood pressure. Adducin is a cytoskeletal protein that may be involved in cellular signal transduction and interacts with other membrane-skeleton proteins that affect ion transport across the cell membrane. There is a high homology between rat and human adducin and pathophysiological similarities between the Milan hypertensive rat strain and a subgroup of patients with essential hypertension. Thus, we designed a case-control study to test the possible association between the α-adducin locus and hypertension. One hundred ninety primary hypertensive patients were compared with 126 control subjects. All subjects were white and unrelated. Four multiallelic markers surrounding the α-adducin locus located in 4p16.3 were selected: D4S125 and D4S95 mapping at 680 and 20 kb centromeric, and D4S43 and D4S228/E24 mapping at 660 and 2500 kb telomeric. Alleles for each marker were pooled into groups. Comparisons between control subjects and hypertensive patients were carried out by testing the allele-disease association relative to the marker genotype. The maximal association occurred for D4S95 (χ12 13.33), which maps closest to α-adducin. These data suggest that a polymorphism within the α-adducin gene may affect blood pressure in humans.
Parasitoids of the Bean Leaf Beetle (Coleoptera: Chrysomelidae) Found in Nebraska Soybean Fields

The bean leaf beetle, Cerotoma trifurcata (Forster) (Coleoptera: Chrysomeli dae), is the major insect pest of soybean in Nebraska and throughout much of the midwest ern United States. Natural enemies of the bean leaf beetle have been reported in other states, but none have been reported in Nebraska. In this study, bean leaf beetle adults were obtained by aspirating those found on soybean plants early in the season and by sweep net once plants were in the V4 stage (approximately 0.33 meter tall). Sampling was done in 1997 and 1998 in soybean fields at the University of Nebraska Agricultural Research and Development Cen ter in Saunders County in east-central Nebraska. Beetles were taken to the laboratory and reared to monitor for parasitoid emergence or preserved in ethyl alcohol for later examina tion for external parasitic mites. Nine tachinid parasitoids emerged from nine of the beetles that were collected in 1997 and identified as Celatoria sp. (species undescribed) (Diptera: Ta chinidae). Percentage of beetles infested with the parasitoid ranged from zero to 1.1. Ec toparasitic mites, identified as Trombidium hyperi Vercammen-Grandjean, Van Driesche, and Gyrisco (Acari: Trombidiidae), were found under the elytra on six of the preserved beetles from 1997 and 16 of the beetles from 1998. A total of 8 mites were found in 1997 and 55 were found in 1998. Percentage of beetles infested with the mites ranged from 0-4 in 1997 and from 0-40 in 1998. This is the first report of natural enemies of the bean leaf beetle from Nebraska. This information may be useful to those developing integrated pest management strategies for the bean leaf beetle in the future.
Adaptative Response of Shewanella Putrefaciens and Pseudomonas Aeruginosa to Toxic Organic Solvents

ABSTRACT Organic solvents are compounds with high toxicity for the bacterial cells, and, as a result of their partition in lipid bilayer, they produce considerable modifications in the structure and functions of the membranes. Two bacterial strains, Shewanella putrefaciens IBBCt4 and Pseudomonas aeruginosa IBBCt5 which are tolerant to organic solvents (alkanes, aromatics) were isolated from Constanta harbor. Alkanes (i.e., n-hexane, n-decane) with logarithm of partition coefficient between n-octanol and water mixture (log POW) between 3.86 and 5.98, were less toxic for Shewanella putrefaciens IBBCt4 and Pseudomonas aeruginosa IBBCt5, compared to aromatics (i.e., toluene, styrene, xylene isomers, ethylbenzene, propylbenzene) with log POWbetween 2.64 and 3.69. Cell tolerance, cells viability, adhesion and β-galactosidase activity of Shewanella putrefaciens IBBCt4and Pseudomonas aeruginosa IBBCt5 in the presence of 1% (v/v) organic solvents (alkanes, aromatics) depends not only on their physicochemical properties, but also on the specific response of the cells, and the cellular response is not the same for these two Gamma-Proteobacteria. The lipolytic and proteolitic enzymes were produced in higher quantity by Pseudomonas aeruginosa IBBCt5 cells in the presence of 1% (v/v) organic solvents, compared with the enzymes produced by Shewanella putrefaciens IBBCt4. The results indicated that Pseudomonas aeruginosa IBBC5 is more tolerant to organic solvents than Shewanella putrefaciens IBBct4, although both bacterial strains posses HAE1 transporter genes and harbor plasmids.
Changes in pH and organic carbon were minimal in a long-term field study in the Western District of Victoria

Changes in soil pH from a long-term experiment at Hamilton, Vic. , associated with time, fertiliser application, and stocking rate were assessed. The pH was measured in a 1 :5 suspension of soil in water (pHW) from 1980 onwards and in a 1:5 suspension of soil in 0.01 M CaCl2 (pHCa) from 1984 onwards. Topsoils (0–10 cm) were sampled regularly from 1980 to 1999, and the soil profile to a depth of 80 cm in 1994. The site was sown to perennial ryegrass, phalaris, and subterranean clover in 1977. Treatments fertilised with different amounts of superphosphate were grazed by sheep at stocking rates of 7–19 dry sheep equivalents (DSE)/ha. Average applications of phosphorus (P) ranged from 0.5 to 38.7 kg P/ha.year. The pHCa of the topsoil in 1984 was 4.9. It decreased at an average rate of 0.005 pHCa or 0.008 pHW units/year, with little variation due to fertiliser or stocking rate. Measurements in 1994 revealed subtle but statistically significant (P < 0.01) trends in soil pHCa that were associated with grazing pressure, inputs of fertiliser, and whether or not areas sampled were used by the sheep for camping. The top 0–5 cm of soil was slightly less acidic (+0.07 pHCa units) in the camp areas compared with non-camp areas. Below 5 cm to a depth of 80 cm, camp areas were more acidic (–0.19 pHCa units). At the highest stocking rates, heavier applications of superphosphate were associated with greater subsoil acidity: –0.06 pHCa units per 100 kg phosphorus (P) applied. There was no relationship at medium stocking rates. At low stocking rates, higher P applications were associated with more alkaline subsoils. Net removal of product from 1979 to 1994 (wool and meat removed from plots and excreta transferred to camps) was estimated to be equivalent to 140–380 kg/ha of lime over this 15-year period. The organic carbon (OC) content of the topsoil did not change over 20 years of records from 1979, and was unaffected by inputs of P. In 1994, the OC content of the 0–5 cm layer of topsoil was greater than the 5–10 cm layer (mean values 5.5% and 3.8% respectively; P < 0.001). The OC content of camp areas was higher than that of non-camp areas, this difference being more pronounced in the 0–5 cm layer (P < 0.01). It was concluded that the rate of change of pH was slow because of the high pH buffering capacity of the soil, the small amount of alkalinity removed in product, and the generally high perennial grass content of the pastures. Soils shown to be at greatest risk of acidification from this study were those under camp areas, and where high fertiliser rates were applied to pastures with a low perennial grass content. Rotational grazing should diminish these problems by reducing the concentration of excreta in camp areas, and favouring perennials over annuals in both camp and non-camp areas. Inputs of lime may eventually be needed to compensate for the acidifying effect of product removal.
Scaleup and Optimization of Oxygen Transfer in Fermentors

The basic function of scaleup is to determine the operating conditions in equipment of different size and mass transfer characteristics so as to achieve the same process yield. A typical problem is the determination of operating conditions in existing large-scale equipment that will provide similar oxygen transfer as observed in laboratoryscale fermentors. In most fermentations of industrial importance, the critical substrate is oxygen due to its low solubility in water. For good process productivity, it is important to supply sufficient oxygen to satisfy the needs of the microorganism. However, supplying excessive oxygen is wasteful of power and may even lead to poor performance due to oxygen toxicity in some unusual cases. One way of ensuring adequate oxygen availability is to determine operating conditions that keep the dissolved oxygen concentrations above predetermined critical levels in all parts of the fermentor. In order to minimize power consumption, these operating conditions should be such that the dissolved oxygen levels are not kept higher than necessary. The work here will be restricted to geometrically similar stirred-tank fermentors. These units are common in the industry because of their versatility and somewhat standardized design. The main operating conditions that must be optimized are the agitator speed and the aeration rate. Suitable methods for the design of equipment for both Newtonian as well as nowNewtonian fermentation broths will be discussed. On-line techniques will be developed for the continuous optimization of oxygen transfer efficiency.
Internationalization of the forest industry: A corporate-level analysis

With far-reaching impacts of economic globalization, the internationalization process of the forest industry has been accelerated. Particularly since the 1990s, internationalization has progressed intensively through industry consolidation and production relocation. Within the wood and wood products sector, for example, world inward foreign direct investment (FDI) stocks increased from 20 billion US dollars in 1990 to more than 120 billion US dollars in 2011. Forest industry firms have geographically shifted their operations from traditional production bases in developed countries to emerging Asian and Latin American countries. The share of FDI flows into developing and transition economies has grown from 18.8% in 1990–1992 to 73% in 2009–2011. The internationalization process of the forest industry has induced multifaceted concerns from economic, strategic, and environmental perspectives at both country and corporate level. However, the actual consequences of such expansion are still largely unknown. It is therefore important to study the current status of the forest industry’s internationalization process and to explore drivers and goals of this process. The theoretical background of this thesis is mainly based on the internationalization and FDI theories portrayed in international business literature. A systematic literature review, a qualitative case study and cross-sectional regression analysis have been applied methodologically. China is used as an example in two of the empirical studies, as it is the most attractive FDI destination in the global forest sector. This thesis conceptually depicts a framework of the systematic internationalization process of the forest industry. Empirically, three themes are identified as focal topics; namely corporate financial performance, corporate sustainability, and corporate entry mode choice. Managerial implications derived from this thesis indicate that (1) firms could aim for either internationalized or domesticoriented operational strategies to pursue higher financial performance; (2) firms should implement social and environmental assessment to maintain sustainable overseas operations; and (3) firms ought to accumulate operational experience and familiarity with local culture before investing in a wholly owned subsidiary. In general, this thesis concludes that internationalization is a dynamic process of pursuing sustainable development to tackle physical forest resource constraints, socio-economic challenges, and corporate operational risks at the global operations scale. Topics related to the analysis of new innovative products, collaboration with supporting industries, and the consideration of sustainability as corporate core competitive advantages are worthy of future research aiming to analyze the further internationalization process of the forest industry.
Investigation of mammalian and viral Interleukin-10 family members during cytomegalovirus infection

Human cytomegalovirus (HCMV) infection in newborns and immunocompromised individuals with immature or deficient immune systems can cause life-threatening diseases. The clinical and subsequent economical burden of HCMV infection led the US Institute of Medicine designating a vaccine for HCMV as the highest level of priority. Complex virus-host interactions have developed over millions of years of co-evolution, making the understanding of the pathogenesis of HCMV disease particularly challenging. Consequently, a crucial factor in aiding the development of effective vaccinations and therapies to significantly reduce morbidity and mortality associated with HCMV infection is elucidating what immune mechanisms contribute to/impede protection against infection. For example, is the induction of immunomodulatory agents such as cytokines beneficial or harmful to the host during infection? Given the known immunosuppressive properties of one such cytokine, interleukin-10 (IL-10), in conjunction with the evolutionary acquisition by HCMV of its own IL-10 homologue, I hypothesised that mammalian- and viral-IL-10 suppress protective immunity during acute CMV infection. Utilising a mouse model of CMV infection, I revealed a surprising antiviral role for IL-10 during acute infection in vivo, which was achieved via limitation of activation-induced death of NK cells. The IL-10-related cytokine interleukin-22 (IL-22) provides critical protection against certain infectious agents and I therefore hypothesised that IL-22 provides protective immunity during acute CMV infection. Utilising the murine infection model once more, I discovered a tissue-specific antiviral role for IL-22 during acute infection in vivo and made the surprising finding that neutrophils play a protective role during infection. I also demonstrated that neutrophils can directly inhibit viral replication in vitro. Thus, novel insights into cytokine biology in the context of viral infections in vivo revealed by these studies highlighted important considerations for future research into herpesvirus infections, and has major implications for the treatment of this important infectious disease.
Establishing the Selection Method for the Lentinula edodes Strains Resistant to Trichoderma spp

Trichoderma inoculation tests for cultures of 89 different shiitake (Lentinula edodes) strains showed that the resistance of shiitake in a wood-powder medium correlated positively to that in 28-month-old bedlogs when T. harzianum was inoculated. Mycelial growth rate of shiitake in an agar medium or in the wood-powder medium also was correlated with the resistance of shiitake bedlogs, although the interaction in the agar medium appeared to be irrelevant. The amount of damage to shiitake caused by T. harzianum had a positive correlation with that by T. polysporum both in the wood-powder medium and in bedlogs. Strains having a high wood-rotting ability in bedlogs tended to have the ability to reject Trichoderma in the wood-powder medium. The inhibition rates of shiitake mycelial growth by trichopolyn proved not to correlate to the rate of damage by T. polysporum.
Kinetic and thermodynamic properties of hydrolases in Northeastern China soils affected by temperature

With incubation test, the kinetic and thermodynamic parameters of urease, phosphatase, and arylsulphatase in the black (phaeozem), albic (albic luvisols), brown (cambisols) and cinnamon soil (chromic luvisol) of Northeastern China at 10, 20 and 30 °C were studied. Soil temperature increased kinetic parameters (K m , V max and V max /k m distinctly, with more distinct variation at 20°C-30°C than at 10°C-20°C. The temperature-dependence of the affinity and the rate of substrate hydrolysis varied depending on the enzyme and soil. The values of the activation energy (E a ) and temperature coefficient (Q 10 ) for each enzyme did not differ much among soils. Less difference was observed in Ea and Q 10 values than in kinetic parameters within the studied range of temperature suggesting that, the fluctuation of temperature affected more kinetic rather than thermodynamic behaviors of soil hydrolases.
Environmental and economic analysis of the fully integrated biorefinery

Cellulosic biofuel systems have the potential to significantly reduce the environmental impact of the world's transportation energy requirements. However, realizing this potential will require systems level thinking and scale integration. Until now, we have lacked modeling tools for studying the behavior of integrated cellulosic biofuel systems. In this paper, we describe a new research tool, the Biorefinery and Farm Integration Tool (BFIT) in which the production of fuel ethanol from cellulosic biomass is integrated with crop and animal (agricultural) production models. Uniting these three subsystems in a single combined model has allowed, for the first time, basic environmental and economic analysis of biomass production, possible secondary products, fertilizer production, and bioenergy production across various regions of the United States. Using BFIT, we simulate cellulosic ethanol production embedded in realistic agricultural landscapes in nine locations under a collection of farm management scenarios. This combined modeling approach permits analysis of economic profitability and highlights key areas for environmental improvement. These results show the advantages of introducing integrated biorefinery systems within agricultural landscapes. This is particularly true in the Midwest, which our results suggest is a good setting for the cellulosic ethanol industry. Specifically, results show that inclusion of cellulosic biofuel systems into existing agriculture enhances farm economics and reduces total landscape emissions. Model results also indicate a limited ethanol price effect from increased biomass transportation distance. Sensitivity analysis using BFIT revealed those variables having the strongest effects on the overall system performance, namely: biorefinery size, switchgrass yield, and biomass farm gate price.
Comparative Phylogenetic Study of Four Genes of Mitochondrial Genome in Tenpounder Fishes (Order: Elopiformes)

The Elopiformes represent a group of seven known species of fishes found in marine and estuarine ecosystem and many of them are endemic to East Asia. To date published morphological and molecular phylogenetic hypothesis of Tenpounder fishes are part congruent and there are some areas of significant disagreement with respect to species relationships. The present study analyzed the sequence data from four genes (Cytb, CO1, 16S and 12S rRNA) of mitochondrial genome for the attempt to estimate the relationships among five species such as Elops saurus, E. affinis, E. smithi, E. machnata and E. hawaiensis and to assess the phylogenetic utility of these markers. The Kimura 2- parameter (K2P) genetic distance, average nucleotide frequencies, nucleotide substitution patterns and phylogenetic trees were reconstructed using neighbour joining (NJ) method. The interspecies K2P genetic distance was 0.0158 and intraspecies distance was 0.0042 based on the barcoding gene, CO1 sequence data. Whereas the interspecies K2P genetic distance was 0.6140 and intraspecies genetic distance was 0.0020 based on the Cytb data. The four mitochondrial marker genes used in this study showed different type of cluster and we could not confirm the relationship between the five Elops species. This is due to the independent mutation rate of each mtDNA genes. However, this problem can be overcome by analysing in parallel other gene markers.