Miracle-dz/UniFAR-FTUs huggingface dataset:
Probing connectivity between transcriptional and post-transcriptional gene networks

The foundation for much of our current understanding of eukaryotic cell biology stems from studies exploiting the combined power of this yeast’s genetic tractability and its simple growth requirements. Furthermore, access to an early complete genome in 1996 allowed yeast researchers to spearhead the move toward genome-wide studies that underpin our thinking about systems-level biology today. Indeed, the last decade has been so rich in these studies that it has become close to impossible for most biologists to interrogate the data in an unbiased fashion. The challenge for the next decade is to generate the informational tools to sort the multidimensional datasets for underlying networks.
A novel meta-heuristic algorithm for numerical function optimization: Blind, naked mole-rats (BNMR) algorithm

Optimization algorithms inspired by the world of nature have turned into powerful tools for solving the complicated problems. However, they have still some drawbacks need the investigation of new and better optimization algorithms. In this paper, we propose a new meta-heuristic algorithm called blind naked mole-rats (BNMR) algorithm. This algorithm has been developed based on the social behavior of the blind naked mole-rats colony in searching the food and protecting the colony against invasions. By introducing this algorithm, we have tried to overcome many disadvantages of the usual optimization algorithms including getting trapped in local minimums or having low rate of convergence. Using several benchmark functions, we demonstrate the superior performance of the proposed algorithm in comparison with some other well-known optimization algorithms.
List of Phytoplankton of the Sea of Marmara

Abstract In this work, a list of the phytoplankton species in the Sea of Marmara is presented in the light of the previously conducted research. It was seen that totally 168 species, eight at the generic level, had been recorded from this region. Diatoms and Dinoflagellates were dominant in terms of species number, with 76 and 73 species, respectively. Diatoms represented the majority of the population (45.2%), followed by dinoflagellates (43.5%).
Genetic Similarities Among Geographic Isolates of Lysiphlebus testaceipes (Hymenoptera: Aphidiidae) Differing in Cold Temperature Tolerances

Abstract Lysiphlebus testaceipes (Cresson) is a solitary endoparasitoid of aphids and is the primary parasitoid attacking cereal aphids in the Great Plains, especially Schizaphis graminum (Rondani). In a previous study, it was found that a Lincoln, NE, isolate of L. testaceipes had a much higher survivorship at cold temperatures than isolates from Stillwater, OK, and Corpus Christi, TX. This suggested that the Nebraska isolate was locally adapted to the northern environment and perhaps genetically divergent from southern populations. We tested for genetic differentiation of the above isolates by sequencing portions of the COI and 16S mtDNA genes. We also examined a Florida isolate reared from Toxoptera citricida (Kirkaldy) and L. fabarum Marshall as an outgroup. The Great Plains isolates (Nebraska, Oklahoma, and Texas) were homogeneous with 0% and 0–0.2% sequence divergence in the COI and 16S gene fragments, respectively. The Florida isolate differed from the Great Plains isolates in nucleotide sequence by 1.4% (COI) and 0.5–0.7% (16S). Phylogenetic analysis placed the Florida isolate of L. testaceipes basal to the Great Plains isolates with L. fabarum, suggesting a possible species complex within L. testaceipes.
THE ROLE OF BMP SIGNALING AND ENDOGLIN IN REGULATION OF HEMATOPOIESIS

Hematopoiesis, the formation of blood cells, ultimately depends on a rare population of hematopoietic stem cells (HSCs), which can both self-renew to maintain the HSC pool, and differentiate into all mature blood lineages. HSC fate decisions are governed by a complex combination of numerous signals, although the molecular mechanisms are not fully understood. This thesis describes the role of two important regulatory candidates, Bone Morphogenetic Proteins (BMP) and Endoglin in adult hematopoiesis. Several publications have described the importance of BMP signaling in specification of hematopoietic tissue in developing embryos. In Article I and II, we investigate the full role of BMP signaling in adult mice, using single and double Cre-based conditional knockout mice for the BMP signaling mediators Smad1 and Smad5. We demonstrate that BMP signaling deficient bone marrow (BM) competes normally with wild-type cells and display unperturbed self-renewal and differentiation capacity when transplanted into lethally irradiated recipients. Thus, despite its crucial role in initial patterning of hematopoiesis, BMP signaling is not required to maintain adult hematopoiesis. Endoglin is a TGF-β accessory receptor recently demonstrated to identify functional long-term HSCs, although little is known regarding its function in these cells. We have investigated the role of endoglin in hematopoiesis by both knocking down, and over-expressing its levels using viral vectors. Interestingly, our study suggests a pivotal role for endoglin in adult erythropoietic development. However, transplantation of transduced BM stem and progenitor cells reveals that neither endoglin suppression nor over-expression affects the ability of HSCs to long-term repopulate recipient marrow.
Nutrient budget for the Eastern Mediterranean: Implications for phosphorus limitation

The eastern Mediterranean has a high nitrate to phosphate (N : P) ratio (~28 : 1) in the deep water and a highly unusual P limitation of the primary productivity. We present a detailed nutrient budget of inputs to the basin, which shows that there is a high N: P ratio (>16 : 1) in all the input sources, particularly from the atmospheric source, where the N: P ratio was 117 : 1. The high N: P ratio is retained within the system because there is no significant denitrification in either the sediments or intermediate water. This is because of the extreme oligotrophic nature of the system, which is caused by the unusual anti‐estuarine flow at the Straits of Sicily. Support for this conclusion is provided by the observation that the only area of the eastern Mediterranean where the N: P ratio in deeper water is ~16 : 1 is the northern Adriatic, which is also the only area with significant denitrification. The N budget (total input to basin vs. net output at the straits of Sicily) balances closely. This N balance suggests that N fixation is an insignificant process in this P‐limited system. The unusually light 15N values in the deep water nitrate and particulate organic nitrogen can be explained by processes other than nitrogen fixation. These processes include a lack of significant denitrification in the basin and by particulate organic matter exported from surface waters during the Plimited winter plankton bloom.
STATUS OF BACTERIAL WILT CAUSED BY RALSTONIA SOLANACEARUM IN PAKISTAN

Field and laboratory investigations for distribution of bacterial wilt (BW) caused by Ralstonia solanacearum in different vegetable growing areas of Pakistan (during April-September 2008-09) revealed that sweet pepper was highly susceptible with overall incidence percentage of 21.9% followed by hot pepper (16.6%), tomato (13.3%), potato (10.5%) and brinjal (5.5%). Aggregate incidence in the whole country was 13.8%. Most of the isolates were obtained from soil (17.2%) and plant samples (18.8%). The disease was mainly distributed in Islamabad Capital Territory and Punjab with BW incidence of 19.2% and 13.9% respectively. Along with bacterial wilt a number of other diseases i.e. Verticillium and Fusarium wilt, Root knot nematodes (Meloidogyne spp.), Phytophthora rot (Phytophthora capsici), stem rot/Southern blight of tomato (Sclerotium rolfsii), Chilli leaf curl virus, bacterial blights (Xanthomonas compestris and Pseudomonas syringae) were found to be associated with the wilt syndrome of solanaceous crops. Most of the farmers were not certain about bacterial wilt symptomology and management. Mean values in BW affected areas were 9.9 soil pH, 29.5 oC, 71.59% RH and 71.86 mm rainfall. The tests further revealed that biovar 2 and 3 were more prevalent in Pakistan with 80 % majority of strains belonging to biovar 3. Predominant biovar in potato was biovar 2 (mostly in Northern territory of the country). Studies further revealed that rest of strains obtained from tomato, sweet pepper, hot pepper and brinjal were mainly biovar 3. In addition, some biovar 3 strains were also found to be associated with sweet pepper and
Phylogenetic Analyses of Molecular Data and Reconstruction of Morphological Character Evolution in Asian Impatiens Section Semeiocardium (Balsaminaceae)

Abstract Phylogenetic analyses have revealed extensive evolutionary lability of morphological characters in the large genus Impatiens. This potentially complicates taxonomic classifications, especially if these are based on analyses which include a limited number of characters and taxa. In this study we focus on the systematics of previously poorly represented Impatiens from Southeast Asia, a hotspot of species diversity, using an expanded taxon sampling. Specifically we implement phylogenetic analyses of DNA sequences from the nuclear ITS and plastid atpB-rbcL intergenic spacer and reconstruct the evolution of several morphological characters to study Semeiocardium, a taxon which has been recognized as a distinct genus, subgenus, and section in previous taxonomic treatments. Both Bayesian and Parsimony analyses demonstrated that Impatiens subg. Semeiocardium is not monophyletic. Thirteen representatives are part of a large clade, which also includes many other Southeast Asian taxa. Connate lateral united petals are a synapomorphy of this clade, while a four-locular ovary and connate outer lateral sepals are not. Impatiens muscicola and I. santisukii, which were previously classified under I. subg. Semeiocardium, do not belong to the clade with connate lateral united petals or to I. sect. Semeiocardium. Due to ambiguous combinations of morphological characters we could not determine whether sampled species belonged to I. sect. Semeiocardium. In addition to the characters that were used to diagnose I. sect. Semeiocardium, we identify connate lateral united petals as a taxonomically useful character to distinguish an additional monophyletic clade in I. sect. Semeiocardium. Further research is needed to identify diagnostic characters for the sister clade comprising I. stenosepala and its allies.
INVESTIGATION OF THE 35delG MUTATION IN THE GJB2 (CONNEXIN 26) GENE-RELATED FAMILY IN MANISA AND VICINITY IN TURKEY Türkiye'de Manisa ve Yöresinde Akraba Evlilii Yapmõ Ailelerde GJB2 (Connexin 26) Genindeki 35delG Mutasyonunun Aratõrõlmasõ

Summary : Mutations in connexin 26 gene (GJB2) lead to a significant proportion of non-syndromic autosomal recessive congenital hearing loss in all populations studied so far . Eight patients with nonsyndromic hearing loss out of 14 related family (marriage couple) were screened to determine hearing loss attributed to connexin 26 gene and the types of mutations living in Manisa and vicinity, Turkey. The 35delG mutations were detected by Polymerase Chain Reaction (PCR) with Competitive Amplification Refractory Mutation System (CARMS). Seven patients were detected as homozygous for the 35delG mutation and one patient detected as heterozygous. Our results indicate that 35delG mutation in the connexin 26 gene was the cause of non-syndromic congenital hearing loss of the patients in Manisa and vicinity in Turkey.
Immunochemical Quantification of Metallothioneins of a Marine Mollusc

Mercury-induced, low molecular weight, metal-binding proteins were isolated from the marine mussel Mytilus edulis and used as antigen in the development of antibodies and an enzyme-linked immunosorbent assay (ELISA) for quantification of the proteins. Partial characterization of the isolated protein indicated that its properties were consistent with those of metallothionein (MT). In contrast with most MTs, this protein occurred as an apparent dimer and contained glycine at high levels. Polyclonal antibodies against this protein were produced in goats and purified to an IgG fraction by ammonium sulfate precipitation and DEAE ion-exchange chromatography. Ouchterlony analysis and ELISA showed that these antibodies were cross-reactive with two other charge variants of mercury-induced, metal-binding proteins of M. edulis, but not with rabbit MT. The ELISA was based on an indirect, competitive procedure utilizing a rabbit anti-goat IgG–horseradish peroxidase conjugate as the second antibody. Application of this.
Production, purification and characterization of an antibacterial agent from an alkaliphilic bacteria

Background and Aims: The aim of this study was initiated in order to overcome antimicrobial resistance by evaluating the potential of alkaliphilic microorganisms as potential producers of new antimicrobial substances. Methods: At first, a range of around 40 alkaliphilic strains has been screened to determine if they have an antibacterial activity. Then, the strain that showed pronounce activity selected and has been tried to produce the bioactive compound in large enough amount using different strategies that has been led to Solid State Fermentation (SSF) as the best method, followed by manipulation the effective factors including: supplementation with media, different salt, Na content, moisture ratio and time of cultivation . Next, the active agents purified successfully by HIC column with a proper purity which its quality was confirmed by silverstaining and then later with liquid chromatography. After that, the bioactive compound identified using the LCMS and tandem MS/MS analyses . Finally, the synergistic effect of this bacteriocin with some antibiotics against different pathogens evaluated. Results: The highest production of bioactive compound from the selected producer strain using SSF method was achieved after two days cultivation in the presence of 2mg Mg2SO4/g bran, 10mg K2HPO4/g bran, 10% (w/w) Na2CO3 and at a wheat bran/moisture ratio of 1:1.8. The MS and MS/MS analyses showed that the bioactive compound belongs to the two-component lantibiotics of haloduracin type. It is composed of two peptides with molecular weight 3043.2578 and 2330.0296. Fortunately, it demonstrates a clear synergistic effect in combination with chloramphenicol against some Gram-positive genuses such as Enterococcus and Streptococcus. Conclusions: The production of the haloduracin under solid state fermentation and its synergy with chloramphenicol is encouraging to screen further alkaliphiles, optimize the production conditions more and further study on synergistic effect of this bacteriocin with other antibiotics to formulate very potent antimicrobial products.
Variation in Maize Consumption by Brown Bears (Ursus arctos) in Two Coastal Areas of Hokkaido, Japan

Abstract. We measured carbon and nitrogen stable-isotope ratios in the livers of 130 brown bears (Ursus arctos) killed by hunters in two coastal areas of Hokkaido, Japan, from 2003 to 2004 to analyze the diets of individual bears, particularly maize. In both study areas, bears suspected of damaging maize, whose diets were higher in the C4 plant component, were mainly observed during late summer and autumn. Wide variation in the C4 plant component indicated that individual bears have differing degrees of dependence on maize, suggesting differential foraging behavior among the individual bears. We found that a stable-isotope ratio analysis of individual Hokkaido brown bears can serve as a tool to review the effectiveness of control killing and to monitor trends in maize consumption by local populations of bears.
Use of CLIMEX modelling to identify prospective areas for exploration to find new biological control agents for prickly acacia

Selection of biocontrol agents that are adapted to the climates in areas of intended release demands a thorough analysis of the climates of the source and release sites. We present a case study that demonstrates how use of the CLIMEX software can improve decision making in relation to the identification of prospective areas for exploration for agents to control the woody weed, prickly acacia Acacia nilotica ssp. indica in the arid areas of north Queensland.
RESIDUES OF FOUR SYNTHETIC PYRETHROIDS AND AZINPHOS-METHYL ON APPLE FOLIAGE AND THEIR TOXICITY TO AMBLYSEIUS FALLACIS (ACARI: PHYTOSEIIDAE)

Abstract Residue analysis of apple foliage obtained from an orchard treated with the insecticides cypermethrin, fenvalerate, deltamethrin, permethrin, and azinphos-methyl revealed detectable residues on the leaves 8–9 weeks after the last treatment. Laboratory studies of foliage showed that of the synthetic pyrethroids, permethrin was initially as toxic as the other synthetic pyrethroids; however, its toxicity decreased considerably by the 5th and 6th week post-treatment. Azinphos-methyl was the least persistent and toxic insecticide evaluated. Unless new pest-management strategies are developed, the use of synthetic pyrethroids post-bloom in an integrated-pest-management program would not be desirable where Amblyseius fallacis (Garman) is the principal predator of phytophagous mites. Résumé Les analyses de résidus d'insecticides sur des feuilles de pommiers provenant d'un verger traité avec chacun des insecticides suivants : cyperméthrine, fenvalerate, deltaméthrine, perméthrine et azinphos-méthyl ont révélé des traces détectables sur les feuilles après huit et neuf semaines de la date du dernier traitement. Des études toxicologiques en laboratoire avec ces feuilles traitées ont montré que parmi les pyréthrinoïdes de synthèse, la perméthrine a été initialement aussi toxique que les autres pyréthrinoïdes de synthèse, mais sa toxicité a diminué considérablement cinq à six semaines après le dernier traitement. L'azinphos-méthyle a été le moins persistant et le moins toxique parmi les insecticides évalués. A moins que des nouvelles stratégies de lutte soient développées, l'emploi des pyréthrinoïdes de synthèse après la floraison ne serait pas souhaitable dans un programme de lutte intégrée où Amblyseius fallacis (Garman) est le prédateur principal des acariens phytophages.
Population dynamics of Japanese pink salmon (Oncorhynchus gorbuscha): are recent increases explained by hatchery programs or climatic variations?

Hatchery programs involving the mass release of artificially propagated fishes have been implemented worldwide. However, few studies have assessed whether hatchery programs actually increase the net population growth of the target species after accounting for the effects of density dependence and climatic variation. We examined the combined effects of density dependence, climatic variation, and hatchery release on the population dynamics of Japanese pink salmon (Oncorhynchus gorbuscha) from 1969 to 2003. The population trends were more closely linked to climatic factors than to the intensity of the hatchery programs. The estimated contributions of hatchery-released fry to catches during the past decade are small. We concluded that the recent catch increases of Japanese pink salmon could be largely explained by climate change, with increased hatchery releases having little effect.
Xylem Sap Tension in Three Woodland Oaks of Central California

In mid—August bottomland Quercus agrifolia and Q. lobata trees had low xylem sap tensions, as estimated by a pressure chamber. After a very dry winter, pre—drawn minimum tensions were less than 6 atm, suggesting that these rates were rooted to a water table. Widely spaced Q. lobata trees in upland savannas also had low pre—dawn tensions, presumably due to the lack of woody plant competition. In contrast, all strands of Q. douglasii had high pre—dawn tensions even after a very wet winter. They seem well adapted to dry slopes where the water table is usually unavailable. Quercus douglasii trees appear to drop their leaves when the water supply becomes critical. Trees in some north aspect stands had higher tensions in mid—August than trees in south aspect stands due to soil moisture supply and tree density interactions. During the dry season a size—class effect appeared with tension inversely correlated with crown size and probably root depth. See full-text article at JSTOR
Rapid identification of marine algae (Raphidophyceae) using three-primer PCR amplification of nuclear internal transcribed spacer (ITS) regions from fresh and archived material

The internal transcribed spacer region of the nuclear rRNA gene was used to discriminate among the marine raphidophyte species Chattonella antiqua, Chattonella subsalsa, Fibrocapsa japonica, Heterosigma akashiwo, and Olisthodiscus luteus. These microalgae can be difficult to identify from natural water samples, owing to their fragile nature and pleomorphic morphology. Several of these species have been associated with massive fin-fish kills throughout the world, and positive identification is therefore of great economic importance. Species-specific diagnostic polymerase chain reaction (PCR) fragment sizes resulting from three-primer amplification reactions can reproducibly detect as few as five cells per fixed sample and as few as one cell from fresh or frozen samples. Recently, an active area of ecological research has been retrospective studies from archival material to determine population dynamics and species diversity. The PCR primers were successfully used with archived material containing either formalin or Lugol's iodine, as well as with fresh cultures. Because of the existence of other techniques more conducive to monitoring for aquaculture, this assay was developed primarily as a research tool for identification of Raphidophyceae from both cultured and archived field samples where cell integrity has been compromised. It has proved to be a valuable technique for detection and discrimination among marine Raphidophyceae, especially when cells cannot be identified morphologically and fixation methods have destroyed cellular RNA content.
Superdads

In discussions about multiculturalism, migration, Islam, and law, migrant and especially Muslim fathers have predominantly been discussed in terms of their overall power over women and children. The recurring question seems to be how much room they should be granted to have a polygamous marriage, keep their daughters out of school, and marry them off. This contribution argues that the sociolegal position of migrant fathers is much more complex and possibly more vulnerable than often perceived, as a consequence of the workings of family law and immigration law. Using (black) feminist critiques of family law, the question is to what extent migrant fathers’ weaker legal position is being caused by ideologies about fatherhood in family law and immigration law that exclude them from being “good fathers. ” The argument is based on an analysis of European Court of Human Rights case law on affiliation, divorce, custody, visiting rights, and residence.