Search results for: Iddo Weiner

Authors: Tamar Lin, Nufar Buchshtab, Yifat Elharar, Julian Nicenboim, Rotem Edgar, Iddo Weiner, Lior Zelcbuch, Ariel Cohen, Sharon Kredo-Russo, Inbar Gahali-Sass, Naomi Zak, Sailaja Puttagunta, Merav Bassan

Abstract:

Background: Atopic dermatitis (AD) is a chronic, relapsing inflammatory skin disorder that is characterized by dry skin and flares of eczematous lesions and intense pruritus. Multiple lines of evidence suggest that AD is associated with increased colonization by Staphylococcus aureus, which contributes to disease pathogenesis through the release of virulence factors that affect both keratinocytes and immune cells, leading to disruption of the skin barrier and immune cell dysfunction. The aim of the current study is to develop a bacteriophage-based product that specifically targets S. aureus. Methods: For the discovery of phage, environmental samples were screened on 118 S. aureus strains isolated from skin samples, followed by multiple enrichment steps. Natural phages were isolated, subjected to Next-generation Sequencing (NGS), and analyzed using proprietary bioinformatics tools for undesirable genes (toxins, antibiotic resistance genes, lysogeny potential), taxonomic classification, and purity. Phage host range was determined by an efficiency of plating (EOP) value above 0.1 and the ability of the cocktail to completely lyse liquid bacterial culture under different growth conditions (e.g., temperature, bacterial stage). Results: Sequencing analysis demonstrated that the 118 S. aureus clinical strains were distributed across the phylogenetic tree of all available Refseq S. aureus (~10,750 strains). Screening environmental samples on the S. aureus isolates resulted in the isolation of 50 lytic phages from different genera, including Silviavirus, Kayvirus, Podoviridae, and a novel unidentified phage. NGS sequencing confirmed the absence of toxic elements in the phages’ genomes. The host range of the individual phages, as measured by the efficiency of plating (EOP), ranged between 41% (48/118) to 79% (93/118). Host range studies in liquid culture revealed that a subset of the phages can infect a broad range of S. aureus strains in different metabolic states, including stationary state. Combining the single-phage EOP results of selected phages resulted in a broad host range cocktail which infected 92% (109/118) of the strains. When tested in vitro in a liquid infection assay, clearance was achieved in 87% (103/118) of the strains, with no evidence of phage resistance throughout the study (24 hours). A S. aureus host was identified that can be used for the production of all the phages in the cocktail at high titers suitable for large-scale manufacturing. This host was validated for the absence of contaminating prophages using advanced NGS methods combined with multiple production cycles. The phages are produced under optimized scale-up conditions and are being used for the development of a topical formulation (BX005) that may be administered to subjects with atopic dermatitis. Conclusions: A cocktail of natural phages targeting S. aureus was effective in reducing bacterial burden across multiple assays. Phage products may offer safe and effective steroid-sparing options for atopic dermatitis.

Keywords: atopic dermatitis, bacteriophage cocktail, host range, Staphylococcus aureus

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Authors: Sushmita Chaudhuri, Parthiba Basu

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Urbanization leads to habitat degradation and is responsible for the fast disappearance of native butterfly species. Random sampling of rural, suburban and urban sites in an around Kolkata metropolis revealed the presence of 28 species of butterfly belonging to 5 different families in winter (February-March). Butterfly diversity, species richness and abundance decreased with increase in urbanization. Psyche (Leptosia nina of family Pieridae) was the most predominant butterfly species found everywhere in Kolkata during the winter period. The most dominant family was Nymphalidae (11species), followed by Pieridae (6 species), Lycaenidae (5 species), Papilionidae (4 species) and Hesperiidae (2 species). The rural and suburban sites had butterfly species that were unique to those sites. Vegetation cover and flowering shrub density were significantly related to butterfly diversity.

Keywords: butterfly, Kolkata metropolis, Shannon-Weiner diversity index, species diversity

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Authors: Abdullah M. Alzahrani

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The unicellular alga Chlorella vulgaris was isolated from Al-Asfar Lake, which is located in the Al-Ahsa province of Saudi Arabia. Two different isolates were sub-cultured under laboratory conditions. The wild type was grown under a regular concentration of copper, whereas the other isolate was grown under a progressively increasing copper concentration. An Inter Simple Sequence Repeats (ISSR) analysis was performed using DNA isolated from the wild type and tolerant strains. The sum of the scored bands of the wild type was 155, with 100 (64.5%) considered to be polymorphic bands, whereas the resistant strain displayed 147 bands, with 92 (62.6%) considered to be polymorphic bands. The sum of the scored bands of a mixed sample was 117 bands, of which only 4 (3.4%) were considered to be polymorphic. The average Nei's genetic diversity (h) and Shannon-Weiner diversity indices (I) were 0.3891 and 0.5394, respectively. These results clearly indicate that the adaptation to a high level of copper in Chlorella vulgaris is not merely physiological but rather driven by modifications at the genomic level.

Keywords: chlorella vulgaris, copper tolerance, genetic diversity, green algae

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Authors: D. L. David, J. A. Wahedi, Q. T. Zaku

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A study was conducted at River Mayo Ranewo and River Lau, Taraba State Nigeria. The two rivers empty into the Upper Benue Basin. A visual encounter survey was conducted within the two wetlands from June to August, 2014. The fish record was based entirely on landings of fishermen, number of canoes that land fish was counted, types of nets and baits used on each sampling day. Fish were sorted into taxonomic groups, identified to family/species level, counted and weighed in groups. The relative species abundance was determined by dividing the number of species from a site by the total number of species from all tributaries/sites. Fish was preserved in 2% formaldehyde solution and taken to the laboratory, where they were identified. Shannon-Weiner index of species diversity indicated that the diversity was highest at River Mayo Ranewo than River Lau. In the result showed at River Mayo Ranewo, the family Mochokidae recorded the highest (23.15%), followed by Mormyridae (2.64%) and the least was the family Lepidosirenidae (0.04%). While at River Lau the family Mochokidae recorded the highest occurrence of (24.1%), followed by Bagridae (20.20%), and then Mormyridae, which also was the second highest in River Lau, with 18.46% occurrence. There was no occurrence of Malapteruridae and Osteoglossidae (0%) in River Lau, but the least occurrence was the family Gymnarchidae (0.04%). These results indicated that the fish composition were not significantly (p ≤ 0.05) different based on t-test.

Keywords: conservation, diversity index, Lau, Mayo Ranewo, wetlands

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Authors: Naomi Weiner-Levy

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The Mofet Institute of Research, established a School of Professional Development, the only one of its kind in Israel and throughout the world. It offers specialized programs for teacher educators, providing them with the professional knowledge and skills. The studies aim at updating teachers about rapidly changing knowledge and skills. Teacher educators are conceptualized as shifting from first order practitioners (school teachers) to second order practitioners. Those who train teachers are referred to as third order practitioners. The instructors in the School of Professional Development are third-order practitioners – teacher educators specializing in teaching their colleagues. Collegial guidance by teachers’ college staff members is no simple task: Tutors must be expert in their field of specialization, as well as in instruction. Moreover, although colleagues, they have to position themselves within the group as authoritative figures in terms of instruction and knowledge. To date, the role and professional identity of these third-order practitioners, has not been studied. To understand the nature and development of professional identity, a qualitative study was conducted in which 12 tutors of various subjects were interviewed. These were analyzed by categorical content analysis. The findings, assessed professional identity through a post-modern prism, while examining the interplay among events that tutors experienced, the knowledge they acquired and the structuring of their professional identity. The Tutors’ identity transformed through negotiating with ‘self’ and ‘other’ in the class, and constructed by their mutual experiences as tutors and learners. Understanding the function and identity of tutors facilitates comprehension of this unique training process for teacher educators.

Keywords: professional development, professional identity, teacher education, tutoring

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Authors: Lucky Dartsa Wakawa, Friday Nwabueze Ogana, Temitope Elizabeth Adeniyi

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Timely and reliable information on the status of a forest is essential for assessing the extent of regeneration and degradation. However, when such information is lacking effective forest management practices becomes impossible. Therefore, this study assessed the tree species composition, richness, diversity, structure of Oluwa forest reserve with the view of ascertaining it conservation status. A systematic line transect was used in the laying of eight (8) temporary sample plots (TSPs) of size 50m x 50m. Trees with Dbh ≥ 10cm in the selected plots were enumerated, identified and measured. The results indicate that 535 individual trees were enumerated cutting across 26 families and 58 species. The family Sterculiaceae recorded the highest number of species (10) and occurrence (112) representing 17.2% and 20.93% respectively. Celtis zenkeri is the species with the highest number of occurrence of tree per hectare and importance value index (IVI) of 59 and 53.81 respectively. The reserve has the Margalef's index of species richness, Shannon-Weiner diversity Index (H') and Pielou's Species Evenness Index (EH) of 9.07, 3.43 and 0.84 respectively. The forest has a mean Dbh (cm), mean height (m), total basal area/ha (m2) and total volume/ha (m3) of 24.7, 16.9, 36.63 and 602.09 respectively. The important tropical tree species identified includes Diospyros crassiflora Milicia excels, Mansonia altisima, Triplochiton scleroxylon. Despite the level of exploitation in the forest, the forest seems to be resilience. Given the right attention, it could regenerate and replenish to save some of the original species composition of the reserve.

Keywords: forest conservation, forest structure, Lowland tropical forest, South-west Nigeria

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Authors: I. Agboola Julius, Christopher A. Kumolu-Johnson, O. Kolade Rafiu, A. Saba Abdulwakil

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This work elucidates on mangrove diversity, trends of change, factors responsible for loss over the years and implications for sustainable livelihoods of locals in four villages (Ajido (L1), Tarkwa bay (L2), University of Lagos (L3), and Ikosi (L4)) along the coast of Lagos, Nigeria. Primary data were collected through field survey, questionnaires, interviews, and review of existing literature. Field observation and data analysis reveals mangrove diversity as low and varied on a spatial scale, where Margalef’s Diversity Index (D) was 0.368, 0.269, 0.326, and 0.333, respectively for L1, L2, L3, and L4. Shannon Weiner’s Index (H) was estimated to be 1.003, 1.460, 1.160, 1.046, and Specie Richness (E) 0.913, 0.907, 0.858, and 0.015, respectively, for the four villages. Also, The Simpson’s index of diversity was analyzed to be 0.632, 0. 731, 0.647, 0.667, and Simpson’s reciprocal index 2.717, 3.717, 3.060, and 3.003, respectively, for the four villages. Chi-square test was used to analyze the impact of mangrove loss on the sustainable livelihood of coastal communities. Calculated Chi-square (X2) value (5) was higher than tabulated value (4.30), suggesting that loss of mangrove wetlands impacted on local communities’ livelihood at the four villages. Analyses of causes and trends of mangrove wetland loss over the years suggest that urbanization, fuel wood and agricultural activities are major causes. Current degradation observed in mangrove wetlands on the Lagos coast suggest a reduction in mangroves biodiversity and associated fauna with potential cascading effects on higher trophic levels such as fisheries. Low yield in fish catch, reduction in income and increasing cases of natural disaster has culminated in threats to sustainable livelihoods of local communities along the coast of Lagos.

Keywords: Mangroves, lagos coast, fisheries, management

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Authors: Kishor Prasad Bhatta, Suman Ghimire, Durga Prasad Joshi

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Invasive Alien Species (IAS) are considered waste forest resources in Nepal. The rapid expansion of IAS is one of the nine main drivers of forest degradation, though the extent and distribution of this species are not well known. Further, the knowledge of the impact of IAS removal on forest plant diversity is hardly known, and the possibilities of income generation from them at the grass-root communities are rarely documented. Systematic sampling of 1% with nested circular plots of 500 square meters was performed in IAS removed and non-removed area, each of 30 hectares in Udayapur Community Forest User Group (CFUG), Chitwan, central Nepal to observe whether the removal of IAS contributed to an increase in plant diversity. In addition, ten entrepreneurs of Udaypur CFUG, involved in the charcoal production, briquette making and marketing were interviewed and interacted as well as their record keeping booklets were reviewed to understand if the charcoal production contributed to their income and employment. The average annual precipitation and temperature of the study area is 2100 mm and 34 degree Celsius respectively with Shorea robusta as main tree species and Eupatorium odoratum as dominant IAS. All the interviewed households were from the ̔below-poverty-line’ category as per Community Forestry Guidelines. A higher Shannon-Weiner plant diversity index at regeneration level was observed in IAS removed areas (2.43) than in control site (1.95). Furthermore, the number of tree seedlings and saplings in the IAS harvested blocks were significantly higher (p < 0.005) compared to the unharvested one. The sale of charcoal produced through the pyrolysis of IAS in ̔ Bio-energy kilns’ contributed for an average increased income of 30.95 % (Nepalese rupees 31,000) of the involved households. Despite above factors, some operational policy hurdles related to charcoal transport and taxation existed at field level. This study suggests that plant diversity could be increased through the removal of IAS, and considerable economic benefits could be achieved if charcoal is substantially produced and utilized.

Keywords: briquette, economic benefits, pyrolysis, regeneration

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Authors: Sarah E. Nelson, Casey Weiner, Alexander Sigmon, Jun Hua, Haris I. Sair, Jose I. Suarez, Robert D. Stevens

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Graph-theoretical information from structural connectomes indicated significant connectivity changes and improved acute prognostication in a Random Forest (RF) model in aneurysmal subarachnoid hemorrhage (aSAH), which can lead to significant morbidity and mortality and has traditionally been fraught by poor methods to predict outcome. This study’s hypothesis was that structural connectivity changes occur in canonical brain networks of acute aSAH patients, and that these changes are associated with functional outcome at six months. In a prospective cohort of patients admitted to a single institution for management of acute aSAH, patients underwent diffusion tensor imaging (DTI) as part of a multimodal MRI scan. A weighted undirected structural connectome was created of each patient’s images using Constant Solid Angle (CSA) tractography, with 176 regions of interest (ROIs) defined by the Johns Hopkins Eve atlas. ROIs were sorted into four networks: Default Mode Network, Executive Control Network, Salience Network, and Whole Brain. The resulting nodes and edges were characterized using graph-theoretic features, including Node Strength (NS), Betweenness Centrality (BC), Network Degree (ND), and Connectedness (C). Clinical (including demographics and World Federation of Neurologic Surgeons scale) and graph features were used separately and in combination to train RF and Logistic Regression classifiers to predict two outcomes: dichotomized modified Rankin Score (mRS) at discharge and at six months after discharge (favorable outcome mRS 0-2, unfavorable outcome mRS 3-6). A total of 56 aSAH patients underwent DTI a median (IQR) of 7 (IQR=8.5) days after admission. The best performing model (RF) combining clinical and DTI graph features had a mean Area Under the Receiver Operator Characteristic Curve (AUROC) of 0.88 ± 0.00 and Area Under the Precision Recall Curve (AUPRC) of 0.95 ± 0.00 over 500 trials. The combined model performed better than the clinical model alone (AUROC 0.81 ± 0.01, AUPRC 0.91 ± 0.00). The highest-ranked graph features for prediction were NS, BC, and ND. These results indicate reorganization of the connectome early after aSAH. The performance of clinical prognostic models was increased significantly by the inclusion of DTI-derived graph connectivity metrics. This methodology could significantly improve prognostication of aSAH.

Keywords: connectomics, diffusion tensor imaging, graph theory, machine learning, subarachnoid hemorrhage

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Authors: Sean E. Gregory P. Igano, Ranz Brendan D. Gabor, Baron Arthur M. Cabalona, Numeriano Amer E. Gutierrez

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Distribution patterns and abundance of butterflies respond in the long term to variations in habitat quality. Studying butterfly populations would give evidence on how vegetation types influence their diversity. In this research, the Rhopalocera diversity of PC Hills was assessed to provide information on diversity trends in varying vegetation types. PC Hills, located in Palo, Leyte, Philippines, is a relatively undisturbed area having forests and rivers. Despite being situated nearby inhabited villages; the area is observed to have a possible rich butterfly population. To assess the Rhopalocera species richness and diversity, transect sampling technique was applied to monitor and document butterflies. Transects were placed in locations that can be mapped, described and relocated easily. Three transects measuring three hundred meters each with a 5-meter diameter were established based on the different vegetation types present. The three main vegetation types identified were the agroecosystem (transect 1), dipterocarp forest (transect 2), and riparian (transect 3). Sample collections were done only from 9:00 A.M to 3:00 P.M. under warm and bright weather, with no more than moderate winds and when it was not raining. When weather conditions did not permit collection, it was moved to another day. A GPS receiver was used to record the location of the selected sample sites and the coordinates of where each sample was collected. Morphological analysis was done for the first phase of the study to identify the voucher specimen to the lowest taxonomic level possible using books about butterfly identification guides and species lists as references. For the second phase, DNA barcoding will be used to further identify the voucher specimen into the species taxonomic level. After eight (8) sampling sessions, seven hundred forty-two (742) individuals were seen, and twenty-two (22) Rhopalocera genera were identified through morphological identification. Nymphalidae family of genus Ypthima and the Pieridae family of genera Eurema and Leptosia were the most dominant species observed. Twenty (20) of the thirty-one (31) voucher specimen were already identified to their species taxonomic level using DNA Barcoding. Shannon-Weiner index showed that the highest diversity level was observed in the third transect (H’ = 2.947), followed by the second transect (H’ = 2.6317) and the lowest being in the first transect (H’ = 1.767). This indicates that butterflies are likely to inhabit dipterocarp and riparian vegetation types than agroecosystem, which influences their species composition and diversity. Moreover, the appearance of a river in the riparian vegetation supported its diversity value since butterflies have the tendency to fly into areas near rivers. Species identification of other voucher specimen will be done in order to compute the overall species richness in PC Hills. Further butterfly sampling sessions of PC Hills is recommended for a more reliable diversity trend and to discover more butterfly species. Expanding the research by assessing the Rhopalocera diversity in other locations should be considered along with studying factors that affect butterfly species composition other than vegetation types.

Keywords: distribution patterns, DNA barcoding, morphological analysis, Rhopalocera

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