bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of the Environmental Factors Modulating Indole-3-acetic Acid (IAA) Production by Trichoderma harzianum InaCC F88
Authors: Napitupulu T P , Kanti A , Sudiana I M
Published: September 2019

Indole-3-acetic acid (IAA) is one of the most common plant hormones that regulate many aspects of growth and development of plants. Trichoderma harzianum, a plant growth promoting fungus, has the ability to produce IAA. However, various environmental factors influence the formation of the hormone. The objective of this study was to optimize the environmental condition for the production of IAA by Trichoderma harzianum InaCC F88 strain. The effects of L-tryptophan concentration, temperature, pH, salinity, and incubation time on IAA production and biomass were studied. The in vitro evaluations were carried out in the axenic condition of Luria-Bertani Medium. Supplementation of 1% L-tryptophan in the medium gives maximum IAA production. The most favourable initial pH and temperature for IAA production are 6.0 and 27°C, respectively. In the salinity test, the medium containing 1% NaCl yielded maximum IAA formation. After 4 days of incubation, the concentration of IAA reached equilibrium. Hence, optimum IAA production in liquid fermentation could be achieved by manipulating those factors.
Morphological characterization of different provenances of Teak (Tectona grandis L.)
Authors: Prasetyawati C A , A’ida N
Published: September 2019

Teak (Tectona grandis L.) is an important hardwood species in Indonesia. Morphological description of Indonesian teak remains inadequate. The purpose of this study was to determine the morphological traits of teak from the different provenances: Malabar, Java and Muna. The study was observed eight macroscopic morphology variables (anthocyanin color, intensity of anthocyanin color, leaf color, leaf size, edge of the leaf, base of blade, top surface texture of leaf, and veins color) and five microscopic morphology variables (adaxial epidermal density, abaxial stomatal density, abaxial stomatal size, trichomes density, and number of trichomes types). The leaf materials were collected from trees sample of each provenance. The Java and Muna provenance presented six similarities of macroscopic morphology of traits. The Malabar provenance materials were the least similar macroscopic morphology, with only one similar trait. Malabar provenance had the highest density of trichomes and stomata. The Malabar provenance had the lowest percentage of similarity coefficient among provenance.
Phenotypic performance of six interspecific carnation genotypes obtained from hybridization of Dianthus caryophyllus “Liberty” x Dianthus chinensis “SK 11-1”
Authors: Dewanti M , Rostini N , Karmana M H , Anas
Published: September 2019

Interspecific hybridization can be an effective strategy in ornamental plant breeding. Interspecific hybridization in the genus Dianthus is relatively easy to do. Therefore, the introduction of good character carriers from other Dianthus species into carnations will give prospect. The objective of this study was to produce new type interspecific carnation genotypes. The experiment was conducted at the Indonesian Ornamental Crops Research Institute experiment station in Cipanas – Cianjur, from November 2014 – July 2015. The experiment was conducted with an experimental method using randomized block design (RBD). The treatment consisted of six genotypes of interspecific carnation, female parent “Liberty” and male parent “SK 11-1” with four replications. The result showed that the flower color of the purplish red and red interspecific genotypes was different from the female parent yellow-flowered. The character of flower type, petal edges and leaf texture of the six progeny genotypes resemble male parent, while the flower shape character of the six interspecific carnation genotypes resemble female parent. Genotype D1 had a combination of the character of plant height, stem diameter and diameter of the appropriate flower as carnations of cut flowers, while genotype D5 had the character of plant height, the number of flowers blooming at one time, the diameter of the flower, the freshness of the flower suitable as garden carnations or pots.
Increasing resistance of chrysanthemum to white rust disease : the role of mutant genotypes and enzymes activities
Authors: Kurniasih D , Murdaningsih H K , Ruswandi D , Qosim W A
Published: September 2019

Chrysanthemum is an ornamental crop with high economic value and consistently received hight demand attributed to its amazing beautifulness. However, white rust disease has drastically suppressed the growth and production of chrysanthemum. The purpose of this study was to obtain genetic and phenotypic diversity characters of peroxidase (pod), polyphenol oxidase (ppo), phenylalanine ammonia lyase (pal) and their resistant component of enzymes activity. The eksperiment was conducted using a randomized block design. The treatments consisted of 37 mutants and 11 genotypes chrysanthemum parents with two replications. Observations were made for pod, ppo and pal enzyme activities. Results showed pod, ppo, and pal enzyme activities had narrow genetic and phenotypic variabilities. Further, chrysanthemum mutant obtained enzyme activities is better than the best control, namely 18.30.068, 10.10.010, 1.30.038, 20.35.056, 18.20.112, 18.25.079, 9.35.162, 18.20.089 and 16.35.086 genotypes. Pod, ppo and pal enzymes activity are more resistant to higher than the susceptible genotype chrysanthemum white rust disease. The other finding is as revealed by negative correlation between disease intensity character and pod, ppo and pal enzymes activity, while disease incidence and the rate disease development characters did not correlate with the third enzymes activity characters.
Accelerated rate storage and viability test of Basidiomycetous fungal strains were cryopreserved at - 80° C
Authors: Ilyas M , Soeka Y S
Published: September 2019

Maintaining and preserving microbes such as fungal cultures are essential elements in systematics and biodiversity studies, fundamental part in ex situ conservation and underpinning biotechnology. Majority of Basidiomycetous fungal strains and mushroom cultures in Indonesia are maintained and preserved by serial transfer. This short term active metabolism-based preservation was simple, but it can not be implemented for maintain and storage in the large numbers of fungal cultures due to time consuming and labour intensive. Recently, permanent long term and inactive metabolism-based preservation such as cryopreservation were introduced and implemented for resolved the problems. The objective of this study was to examine the effectiveness of cryopreservation at -80° C with 10% (v/v) glycerol and 5% (g/v) trehalose as cryoprotectant into the 50 strains of the Basidiomycetous fungi from Indonesian Culture Collection (InaCC). The Basidiomycetous fungal cultures were used consists of several taxa such as; Agaricus, Agrocybe, Auricularia, Coprinus, Ganoderma, Lentinula, Phanerochaete, Pleurotus and Trametes. The accelerated storage and viability tests were performed by thawed and revived the stored cultures after 2 weeks and 12 months storage at -80°C. The results showed there are no viability loss among the 50 strains were observed, however there is a distinct acclimatization time and growth rate between cultures were stored at -80°C for 48 hours and more than 3 years. Strains were stored for 48 hours at -80°C begin to grow after 3 days of incubation, whereas cultures were stored at -80°C for more than 3 years begin to grow optimally after 5 days of incubation. Nevertheless, significant differences in acclimatization time and growth rate in both storage periods were not seen in Ganoderma, Phanerochaete, Pleurotus, and Trametes cultures. In general, this long term inactive metabolism-based preservation method is effectively applied for maintain and keep the viability of Basidiomycetous fungal cultures in InaCC.
Pests and diseases on forest plant in burned peatlands in South Sumatra
Authors: Asmaliyah  , Hadi E E , Irianto R S B
Published: September 2019

At present most of the peatland in the OKI district, South Sumatra was damaged by forest fires. One way to restore the condition and function of peatlands as before is to rehabilitate by replanting suitable species on peatlands. One of the obstacles to the planting success on peatlands is the presence of pests and diseases. This study aims to determine pests and diseases of forest plants in several locations of burned peatlands in South Sumatra. The method used in this study was a survey method by direct observation of sample plants. Parameters observed were species of insect pests and pathogen, incidence and intensity of the attack. The results showed that several insect pests and diseases were found on burned peatland in Ogan Komering Ilir district, South Sumatra and identified asCycnotrachelussp.,Valanga nigricornis, bagworm,Daphnis hypothous, Macrophomasp.,Pestalotiopsissp., andCephaleurossp. The highest incidence of bagworm attacks was onShorea balangeranand categorized as very heavy damage. The highest intensity was occurred onDyera lowiithat were attacked byCephaleurossp. and was categorized as moderately heavy damage. Even though the pest and disease attacks brought no economic losses, they must be watched closely by continuous monitoring.
Mosses diversity from Lombok island, West Nusa Tenggara
Authors: Windadri F I
Published: September 2019

Lombok is a part of the Lesser Sunda Islands located in the West Nusa Tenggara Province. The diversity of mosses reported by Touw in 1992. The mosses research at surrounding Rinjani National Park was be conducted. The result reported 72 species of mosses including 46 genera and 21 families. The higher of mosses diversity is Meteoriaceae. More than 27% of mosses at the site is suggested as new records from Lombok.
Local people awareness towards social forestry program: a case study of Ogan Komering Ulu District, South Sumatra Province, Indonesia
Authors: Lestari S , Premono B T , Winarno B
Published: September 2019

Social forestry program is intended to improve people’s welfare and at the same time as an effort to conserve the forest. This paper examines the awareness of local communities toward social forestry programmes implemented by Ministry of Environment and Forestry of Republic Indonesia. This research was taken place in Bumi Kawa Village, Ogan Komering Ulu District. Survey, interview and focus group discussion methods were employed to collect the data. Descriptive qualitative method was used to analyze the data obtained during the research. Almost all of the people interviewed have a particularly favourable perception of the social forestry programmes implemented. Currently, the community has accessed the forest area and planted it with coffee. With the existence of social forestry program, community access to forests becomes a legal activity. The community can manage the land by implementing agroforestry system that is developing agricultural crops under forest trees. The type of tree that has been well known by the community is bambang lanang (Michelia champaca). This type of plant is suitable to grow in this region and has economic value. Based on the discussion, social forestry program is the best type of management for running the forests in this area. Communities were willing to further participate in tree planting activities. Moreover, women also had positive perception towards social forestry program although they were not fully involved in managing the forest. Some incentives were needed so that the local people will continue to participate in the long term environmental preservation.
The growth and yield of Calliandra Callothyrsus trees as biomass-based energy feedstock
Authors: Abdulah L
Published: September 2019

Calliandra callothyrsus is a woody plant that grows quickly and well in a wide range of natural conditions. C. callothyrsus is a tree species which easily cultivated and can be harvested in a short time (short-rotation wood crops). However, information about time and harvesting techniques that explain harvesting biomass is still needed. The aimed of this study is measured growth after trimming, the best time interval for harvesting and the results of cutting both biomass and the heating value contained. The method used is a destructive method. Observations are carried out repeatedly in a permanent plot. The permanent plot as treatment level cutting. So, this study evaluated the correlation between time and cutting level to growth and biomass harvested. The results showed that the best cutting limit was 50 cm above ground level. It is due to the high harvest biomass and the number of new stems that grow more. Meanwhile, to ensure business sustainability, the best harvest interval is 1 year. It will ensure adequate growth of new stems, large harvesting biomass and high calorific value of harvest. Harvesting potential can reach 25 m3.ha-1.yr1. While the heating value will be at an interval of 3016 - 3757 kcal.kg−1.
Isolation and preservation of microfungi from Indonesia islands
Authors: Wulandari N F
Published: September 2019

The research was aimed at utilizing more adequate methods of long-term preservation, cryopreservation (freezing at -80 °C). Samples obtained from three islands were used as sources of samples, i.e., Enggano, Riau, and Sumba. Direct isolation and single spore isolation were conducted to isolate the microfungi. All the cultures were grown on Potato Dextrose Agar (PDA). The growth rate of selected microfungi was calculated every day for a week. The growth rate for selected ten microfungi of each island, approximately 0.1-0.7 cm/day. All the cultures are maintained in InaCC (Indonesian Culture Collections), Cibinong, LIPI.
Carbon footprint of pesantren: the role of pesantren manager determining the food consumption
Authors: Hidayatullah A F , Della N V , Elfrida N , Haq D , Arikhah
Published: September 2019

Indonesia is a country with a large part of the population being Muslim with the characteristics of Islamic boarding schools. Islamic boarding schools are the oldest informal education institutions in Indonesia that influence the development of Indonesia. Santri, including pesantren people who have a higher mindset in understanding life than non-santri. The spiritual provision of the santri will be applied in the actions and behaviour of daily life starting from the smallest things like eating. Food consumption activities affect the environmental damage with carbon emissions produced. Carbon footprint can be used as a concept to calculate santri’s daily food consumption habits. The analytical method used to read data is the One-way Anova analysis program. Respondents of this research were Semarang Darul Falah Besongo’s Pesantren, who are 100% students of Walisongo State Islamic University Semarang. The spiritual knowledge of santri is the basis for optimally managing food. Pesantren with good food management principles, like food efficiency can minimize carbon emissions that damage the environment. The achievement of food safety will safeguard natural resources so that they remain sustainable.
Clustering analysis on interspesific hybrid of Paphiopedilum Maudiae x tonsum crossing
Authors: Rianawati S , Pramanik D , Kartikaningrum S , Dewanti M , Suryanah  , Budiarto K , Marwoto B
Published: September 2019

Paphiopedilum (Slipper Orchid/Venus orchid) is a genus belongs to subfamily of Cypripedioideae. All Paphiopedilum species are covered by the Convention on International Trade in Endangered Species (CITES). Cluster analysis has been used to grouping of plant variation. The aim of the research was to estimate the relationship between parents (Paph. Maudiae “Black” & Paph. tonsum) and their 19 progenies. 23 morphological Qualitative traits and 13 morphometrical/quantitative traits were used in multivariate analysis. The morphological qualitative data was scored numerically as present (1) and absent (0), and then analyzed using NTSYS PC (Rohlf, 1998). Similarity between accessions was estimated using Dice coefficient. Average taxonomic distance was used to group the quantitative data using Dist coefficient. Result showed that hierarchical clustering of 21 genotipes indicated two main groups based on qualitative data as well of quantitative data. Group 1 had 5 accessions (PH1-01, PH1-16, PH1-51, Ph1-73, PH1-78, and group 2 had 10 accessions. Four accessions were separated and stand alone. Group 1 had morphological resemblance with Paph. Maudiae and group 2 had morphological resemblance with Paph. Maudiae and Paph. tonsum. Based on quantitative data, group 1 (11 accessions) had quantitative trait resemblance with Paph. Tonsum. Group 2 (7 accessions) had quantitative trait resemblance with Paph. Maudiae. Morphological trait of Paph. Maudiae was dominant inherited to their progenies.
Rediscovery Sumatran endemic flora: towards the establishment of data of biodiversity loss
Authors: Mambrasar Y M , Damayanto I P G P , Atikah T D
Published: September 2019

The research of Sumatran endemic flora species for the establishment of a database of biodiversity loss has been conducted on March 2018 around Lake Toba areas. The exploration method was applied to collect the flora endemic and identified with specimen reference collection in Herbarium Bogoriense (BO) and related references. 28 species from six families were rediscovered as Sumatran endemic flora. Orchidaceae (15 species) and Ericaceae (5 species) were the most commonly families found. Meanwhile, Taman Eden 100 and Jangga Dolok were the most common location for the rediscovery of Sumatran endemic flora.
Effect of Formation Voltage on the Pore Size of Porous Anodic Aluminum Oxide
Authors: Sianturi Manogari , Juwono Ariadne L , Anawati Anawati
Published: September 2019

This work is aimed to clarify the effect of formation voltage on the pore size of porous anodic aluminum oxide (PAAO) layer formed on commercially pure aluminum. The PAAO layers were obtained by anodization process in 0.3 M sulfuric acid solution at constant voltages of 10, 15, 20, and 25 V at 10°C. The structure and morphology of PAAO layers were characterized by using FE-SEM. The pore diameters which were estimated by using ImageJ software were 19.61 + 15.35 nm, 20.03 +13.59 nm, 20.31 + 12.36 nm, 25.06 +12.10 nm, and the wall thicknesses were 33 nm, 49.99 nm, 74.97 nm, 83.33 nm for the PAAO formed at 10, 15, 20 and 25 V, respectively. The structure of the porous oxide layer became more uniform and organized, and the diameter of the pores increased linearly with applied voltage. High anodization voltage is known to cause Joule heating because of the fast movement of electrons and ions. It is believed that the Joule heat was transferred to the bulk electrolyte which results in larger pore diameter and interpore distance. The optimum condition to obtain high order PAAO is at 25 V.
Analysis of Damage Area of Fiberglass/Polyester Bi-Panel with Rice Husk Ash as a Filler Caused by the Impact of High-Speed Particles
Authors: Koto Nazarudin , Soegijono Bambang
Published: September 2019

Analysis of the damaged area of the composite bi-panel fiberglass/polyester with the addition of rice husk ash as a filler have been presented in this paper. The area of damage is caused by the impact of high-speed particles. Bi-panel composites were made by hand lay-up of S-glass and unsaturated polyester resin BTQN 157 ex with variations of 3, 5, 7, 9 %v rice husk ash as a filler. The impact test were carried out using a 9 mm caliber FN gun in accordance with NIJ level IIIA standards. The results show the area of damage caused by a projectile decrease with the increasing amount of Rice husk %v. There is a significant effect with the addition of rice husk ash filler on the composite of bi-panel fiberglass/polyester to the impact of high-speed particles. The rice husk ash could be used as an alternative for filler in Polyester/Fiberglass composite for body armor application.
Study on Heating Profile of Liquid-mixing-synthesized ZnTiO3
Authors: Ermawati F U , Imamah N A
Published: September 2019

The synthesis of monophasic ZnTiO3 powder has been reported as one of the challenges in material chemistry because under normal condition and as prepared by various synthesis methods, ZnTiO3 phase readily decomposes to Zn2TiO4 and TiO2 rutile phases. This is due to the temperature range of ZnTiO3 phase formation was very narrow, i.e. 600 - 800 °C; above that temperature, the decomposition of ZnTiO3 phase took place. This paper is intended to introduce a facile route, named liquid mixing method, to prepare ZnTiO3 powder from Zn and Ti metal powders as the raw materials and HCl as the solvent. Via this route, ZnTiO3 phase was formed at a temperature as low as 550 °C with particle size distributed homogeneously. The heating profile of ZnTiO3 phase from 440 to 900 °C was studied based on TG/DTA, XRD and FTIR data. However, when a ‘normal’ stoichiometric ratio of Zn: Ti = 1: 1 was applied, TiO2 rutile phase becomes dominant, while ZnTiO3 phase is only a secondary phase. This affects to the crystallinity of the ZnTiO3 phase. An effort to overcome the dominance of TiO2 phase was also demonstrated in this paper.
The Impact Resistance, Flammability, and Hardness of Polypropylene/Unidirectional Sumberejo Kenaf Fiber Composites
Authors: Maulana M I , Juwono A L
Published: September 2019

The use of natural fibers to substitute synthetic fibers on composites has been an interest to be developed. Kenaf is a plant that abundant in Indonesia because it‘s adaptive and its fiber has good strength. The purpose of this study was to determine the value of impact resistance, flammability, and hardness of polypropylene / unidirectional Sumberejo kenaf fiber composite boards in accordance with Standar Nasional Indonesia (SNI). Composites were fabricated by the variation of fiber, which were 30 wt%, 40 wt%, and 50 wt%. Pure polypropylene samples were also fabricated for comparison. The fabrication used a compression molding method. The best results were obtained from polypropylene / 50 wt% kenaf fiber composites with impact energy, flammability, and hardness values were (47.54 + 10.7) J / cm2, (7.1±5.1) mm / minute, and (66 + 0.8) HD respectively. Optical microscope observation on the impacted surface was a destruction of the matrix-fiber bonding and fiber breakage, in which showed the energy of impact was absorbed by kenaf fiber. The observation on the burned surface was burnt kenaf fibers and rest of PP that bonding with kenaf fiber, this indicated the kenaf fiber acted as an oxygen barrier.
The Effect of NaOH Immersion Time to Physical Properties of Purun Tikus (Eleocharis dulcis) Cement Board Composite
Authors: Haryanti Ninis Hadi , Wardhana Henry , Suryajaya
Published: September 2019

A research in cement board composite made from purun tikus (Eleocharis dulcis) has been conducted. The aims are to determine its physical properties as variations of purun tikus fibers mass and NaOH immersion time. The results were yielded 5.00 - 15.15%, 0.52 - 0.76 g / cm3 and 0.05 - 0.18%, respectively for water content, density and thickness development. For moisture content and density values, the results were not met the standard of SNI 03-2104-1991, while for thickness development of all samples met the standards. The results showed fluctuating changes in water content, density and thickness development, which were influenced by the immersion time and mass of purun tikus fibers. From the results, it can be concluded that shorter immersion time and less purun tikus fibers yielded a smaller value of water content and thickness development, while density was become higher.
Preparation and Characterization of Local Indonesian Chitosan-graft-Maleic Anhydride as Drug Carrier
Authors: Timotius Daniel , Rochmadi  , Kusumastuti Yuni
Published: September 2019

The modification of local Indonesian chitosan as a drug carrier is conducted by grafting with maleic anhydride (MA). The grafted film resulting in a negative charge of carboxyl group attach on chitosan backbone. Several ratio of MA/chitosan is conducted to evaluate the effect of MA on the drug release behavior. Chitosan and MA was dissolved and stirred in 1% (v/v) acetic acid for 24 hours. Tween 80 and curcumin are added to the solution as surfactant and drug model respectively. The homogeneous solution is casted into polyethylene petri dish and dried under room temperature. Chitosan-graft-MA is characterized by Fourier Transform Infra-Red (FTIR) in addition to gravimetric titration to characterize the existing of carboxyl groups of the films. The swelling and degradation ability in phosphate buffered saline (PBS) solution is showed an increasing trend as the addition of MA. The kinetic study of drug release is performed in Peppas and first order model. An optimum condition of grafting is achieved at 150% (w/w).
cdc37 is essential for JNK pathway activation and wound closure in Drosophila
Authors: Lee Chan-wool , Kwon Young-Chang , Lee Youngbin , Park Min-Yoon , Choe Kwang-Min
Published: September 2019

Wound closure in the Drosophila larval epidermis mainly involves nonproliferative, endocyling epithelial cells. Consequently, it is largely mediated by cell growth and migration. We discovered that both cell growth and migration in Drosophila require the cochaperone-encoding gene cdc37. Larvae lacking cdc37 in the epidermis failed to close wounds, and the cells of the epidermis failed to change cell shape and polarize. Likewise, wound-induced cell growth was significantly reduced, and correlated with a reduction in the size of the cell nucleus. The c-Jun N-terminal kinase (JNK) pathway, which is essential for wound closure, was not typically activated in injured cdc37 knockdown larvae. In addition, JNK, Hep, Mkk4, and Tak1 protein levels were reduced, consistent with previous reports showing that Cdc37 is important for the stability of various client kinases. Protein levels of the integrin β subunit and its wound-induced protein expression were also reduced, reflecting the disruption of JNK activation, which is crucial for expression of integrin β during wound closure. These results are consistent with a role of Cdc37 in maintaining the stability of the JNK pathway kinases, thus mediating cell growth and migration during Drosophila wound healing.
The mitochondrial intermembrane space–facing proteins Mcp2 and Tgl2 are involved in yeast lipid metabolism
Authors: Odendall Fenja , Backes Sandra , Tatsuta Takashi , Weill Uri , Schuldiner Maya , Langer Thomas , Herrmann Johannes M. , Rapaport Doron , Dimmer Kai Stefan
Published: September 2019

Mitochondria are unique organelles harboring two distinct membranes, the mitochondrial inner and outer membrane (MIM and MOM, respectively). Mitochondria comprise only a subset of metabolic pathways for the synthesis of membrane lipids; therefore most lipid species and their precursors have to be imported from other cellular compartments. One such import process is mediated by the ER mitochondria encounter structure (ERMES) complex. Both mitochondrial membranes surround the hydrophilic intermembrane space (IMS). Therefore, additional systems are required that shuttle lipids between the MIM and MOM. Recently, we identified the IMS protein Mcp2 as a high-copy suppressor for cells that lack a functional ERMES complex. To understand better how mitochondria facilitate transport and biogenesis of lipids, we searched for genetic interactions of this suppressor. We found that MCP2 has a negative genetic interaction with the gene TGL2 encoding a neutral lipid hydrolase. We show that this lipase is located in the intermembrane space of the mitochondrion and is imported via the Mia40 disulfide relay system. Furthermore, we show a positive genetic interaction of double deletion of MCP2 and PSD1, the gene encoding the enzyme that synthesizes the major amount of cellular phosphatidylethanolamine. Finally, we demonstrate that the nucleotide-binding motifs of the predicted atypical kinase Mcp2 are required for its proper function. Taken together, our data suggest that Mcp2 is involved in mitochondrial lipid metabolism and an increase of this involvement by overexpression suppresses loss of ERMES.
DNA damage triggers increased mobility of chromosomes in G1-phase cells
Authors: Smith Michael J. , Bryant Eric E. , Joseph Fraulin J. , Rothstein Rodney
Published: September 2019

During S phase in Saccharomyces cerevisiae, chromosomal loci become mobile in response to DNA double-strand breaks both at the break site (local mobility) and throughout the nucleus (global mobility). Increased nuclear exploration is regulated by the recombination machinery and the DNA damage checkpoint and is likely an important aspect of homology search. While mobility in response to DNA damage has been studied extensively in S phase, the response in interphase has not, and the question of whether homologous recombination proceeds to completion in G1 phase remains controversial. Here, we find that global mobility is triggered in G1 phase. As in S phase, global mobility in G1 phase is controlled by the DNA damage checkpoint and the Rad51 recombinase. Interestingly, despite the restriction of Rad52 mediator foci to S phase, Rad51 foci form at high levels in G1 phase. Together, these observations indicate that the recombination and checkpoint machineries promote global mobility in G1 phase, supporting the notion that recombination can occur in interphase diploids.
Longitudinal Changes in the Genital Hiatus Preceding the Development of Pelvic Organ Prolapse
Authors: Handa Victoria L , Blomquist Joan L , Carroll Megan , Roem Jennifer , Muñoz Alvaro
Published: September 2019

We aimed to explore relationships between changes in genital hiatus (GH) and development of pelvic organ prolapse using data from the Mothers’ Outcomes After Delivery (MOAD) Study, a Baltimore, Maryland, cohort study of parous women who underwent annual assessments during 2008–2018. Prolapse was defined as any vaginal segment protrusion beyond the hymen or reported prolapse surgery. For each case, 5 controls (matched on birth type and interval from first delivery to study enrollment) were selected using incidence sampling methods. We used a mixed model whose fixed effects described the initial size and slope of the GH as a function of prolapse status (case vs. control) and with nested (women within matched sets) random effects. Among 1,198 women followed for 1.0–7.3 years, 153 (13%) developed prolapse; 754 controls were matched to those women, yielding 3,664 visits for analysis. GH was 20% larger among the cases at enrollment (3.16 cm in cases vs. 2.62 cm in controls; P < 0.001), and the mean rate of increase in the size of the GH was more than 3 times greater (0.56 cm per 5-year period vs. 0.15 cm per 5-year period in controls; P < 0.001). Thus, to identify women at highest risk for developing prolapse, health-care providers could evaluate not simply the size of the GH but also changes in the GH over time.
High-Salt Intake Reduces Apomorphine-Induced Penile Erection and Increases Neurally Mediated Contractile Responses of the Cavernosal Smooth Muscle in Rats
Authors: Leitolis Amanda , Crestani Sandra , Linder Áurea Elizabeth , da Silva-Santos José Eduardo
Published: September 2019

BACKGROUND

This study was designed to evaluate whether overconsumption of NaCl, a well-known risk factor for hypertension, leads to erectile dysfunction in rodents.

METHODS

Male Wistar rats received regular chow (control group) or 4% NaCl chow for 24 weeks and were subjected to blood pressure measurement and apomorphine-induced erection. Moreover, cavernosal strips from both the control and 4% NaCl groups were evaluated in organ baths.

RESULTS

Animals subjected to 4% NaCl chow did not develop hypertension but presented a significant reduction in the total number of erections following apomorphine administration as compared with the control group. The addition of high KCl or phenylephrine resulted in similar contractile responses in the corpus cavernosal strips from both the control and 4% NaCl groups. However, electrical field stimulation-induced contraction was significantly enhanced in cavernosal strips from animals exposed to 4% NaCl. Incubation of Y-27632, but not of atropine and Nω-nitro-l-arginine methyl ester (L-NAME), entirely prevented the potentiation of the contractile responses evoked by electrical stimulation. The enhanced contractile responses evoked by electrical stimulation found in the high-salt group were also avoided in the absence of extracellular calcium. Concentration-response curves of CaCl2 revealed augmented contractility in response to extracellular calcium in cavernosal strips from the 4% NaCl-treated rats, compared with control samples.

CONCLUSIONS

A high-salt diet alone rendered the animals less responsive to apomorphine-induced penile erection and enhanced neurally mediated contractile responses in the corpus cavernosum, a clear indication that overconsumption of sodium can lead to erectile dysfunction even without the development of hypertension.
Reducing Attentional Bias in Individuals With Alcohol Use Disorders With a Tablet Application: A Randomized Controlled Trial Pilot Study
Authors: Flaudias Valentin , Zerhouni Oulmann , Chakroun-Baggioni Nadia , Pires Sylvie , Schmitt Audrey , De Chazeron Ingrid , Llorca Pierre Michel , Brousse Georges
Published: September 2019

Aims

Cognitive bias modification (CBM) training has been considered a promising and effective intervention tool for reducing cognitive biases toward alcohol. However, the link between the cognitive process and actual behavior remains statistically insignificant because computerized tasks do not have sufficient ecological validity and suffer from high dropout rates. The recent development of ‘serious games’ has shown encouraging results in maintaining adherence to health-related interventions. We aim to evaluate a CBM program using a gamified attentional bias (AB) training procedure on a touchpad for individuals with alcohol use disorders.

Methods

Forty-one patients were included in this study, 33 of whom displayed an AB and were randomly assigned into the ‘CBM group’ (N = 18, 16.7% women) or ‘Memory group’—which involved playing a memory game—(N = 15, no woman). Eight other participants (12.5% women) with no AB comprised the ‘Without AB group’. Efficacy was assessed for AB, craving, and inhibition and attentional capacities before and after the program.

Results

We observed that the reduction of AB was higher for the ‘CBM group’ (Mbefore = 153.61, SD = 172.21; Mafter = 18.00, SD = 77.71; t (17) = 4.21, P = 0.001) than for the ‘Memory group’ (Mbefore = 73.20, SD = 66.65; Mafter =42.47, SD = 113.77; ts < 1). The analysis showed that for the ‘Without AB group’, there was no significant difference in AB (t (7) = −2.15, P = .07) after the program.

Conclusions

This study demonstrated an increased reduction of AB for patients included in the CBM program on a touchpad than for patients playing only a memory game.
Towards a Green Applied Linguistics: Human–Sea Turtle Semiotic Assemblages in Hawai‘i
Authors: Lamb Gavin
Published: September 2019

This article argues that human–animal relationships are a key conceptual terrain for applied linguists to intervene in emerging interdisciplinary debates on how to address problematic human–environment relations in a time of growing ecological degradation. The scientific diagnosis of the Anthropocene has further generated critical discussion in the social sciences on the need to understand the diversity of local cultural responses to global environmental crises, ranging from climate change to species extinction. This article proposes that a ‘green applied linguistics’ can offer empirical insights into the role of language and discourse in mediating diverse human relationships with animals and nature. Taking human interactions with protected wildlife as one aspect of these wider socio-environmental debates, this article builds on recent embodied, materialist and posthumanist research in applied linguistics to suggest that nexus analysis offers a holistic methodology to examine the problematic ways people become caught up with threatened species through their semiotic practices. I illustrate these ideas through examples from my ethnographic research on the convergence of sea turtle conservation and ecotourism practices at Laniākea Beach, Hawai‘i.
A comparative study of multi-omics integration tools for cancer driver gene identification and tumour subtyping
Authors: Sathyanarayanan Anita , Gupta Rohit , Thompson Erik W , Nyholt Dale R , Bauer Denis C , Nagaraj Shivashankar H
Published: September 2019

Oncogenesis and cancer can arise as a consequence of a wide range of genomic aberrations including mutations, copy number alterations, expression changes and epigenetic modifications encompassing multiple omics layers. Integrating genomic, transcriptomic, proteomic and epigenomic datasets via multi-omics analysis provides the opportunity to derive a deeper and holistic understanding of the development and progression of cancer. There are two primary approaches to integrating multi-omics data: multi-staged (focused on identifying genes driving cancer) and meta-dimensional (focused on establishing clinically relevant tumour or sample classifications). A number of ready-to-use bioinformatics tools are available to perform both multi-staged and meta-dimensional integration of multi-omics data. In this study, we compared nine different integration tools using real and simulated cancer datasets. The performance of the multi-staged integration tools were assessed at the gene, function and pathway levels, while meta-dimensional integration tools were assessed based on the sample classification performance. Additionally, we discuss the influence of factors such as data representation, sample size, signal and noise on multi-omics data integration. Our results provide current and much needed guidance regarding selection and use of the most appropriate and best performing multi-omics integration tools.
Systematic evaluation of differential splicing tools for RNA-seq studies
Authors: Mehmood Arfa , Laiho Asta , Venäläinen Mikko S , McGlinchey Aidan J , Wang Ning , Elo Laura L
Published: September 2019

Differential splicing (DS) is a post-transcriptional biological process with critical, wide-ranging effects on a plethora of cellular activities and disease processes. To date, a number of computational approaches have been developed to identify and quantify differentially spliced genes from RNA-seq data, but a comprehensive intercomparison and appraisal of these approaches is currently lacking. In this study, we systematically evaluated 10 DS analysis tools for consistency and reproducibility, precision, recall and false discovery rate, agreement upon reported differentially spliced genes and functional enrichment. The tools were selected to represent the three different methodological categories: exon-based (DEXSeq, edgeR, JunctionSeq, limma), isoform-based (cuffdiff2, DiffSplice) and event-based methods (dSpliceType, MAJIQ, rMATS, SUPPA). Overall, all the exon-based methods and two event-based methods (MAJIQ and rMATS) scored well on the selected measures. Of the 10 tools tested, the exon-based methods performed generally better than the isoform-based and event-based methods. However, overall, the different data analysis tools performed strikingly differently across different data sets or numbers of samples.
Non-homogeneous dynamic Bayesian networks with edge-wise sequentially coupled parameters
Authors: Shafiee Kamalabad Mahdi , Grzegorczyk Marco
Published: September 2019

Motivation

Non-homogeneous dynamic Bayesian networks (NH-DBNs) are a popular tool for learning networks with time-varying interaction parameters. A multiple changepoint process is used to divide the data into disjoint segments and the network interaction parameters are assumed to be segment-specific. The objective is to infer the network structure along with the segmentation and the segment-specific parameters from the data. The conventional (uncoupled) NH-DBNs do not allow for information exchange among segments, and the interaction parameters have to be learned separately for each segment. More advanced coupled NH-DBN models allow the interaction parameters to vary but enforce them to stay similar over time. As the enforced similarity of the network parameters can have counter-productive effects, we propose a new consensus NH-DBN model that combines features of the uncoupled and the coupled NH-DBN. The new model infers for each individual edge whether its interaction parameter stays similar over time (and should be coupled) or if it changes from segment to segment (and should stay uncoupled).

Results

Our new model yields higher network reconstruction accuracies than state-of-the-art models for synthetic and yeast network data. For gene expression data from A.thaliana our new model infers a plausible network topology and yields hypotheses about the light-dependencies of the gene interactions.

Availability and implementation

Data are available from earlier publications. Matlab code is available at Bioinformatics online.

Supplementary information

Supplementary data are available at Bioinformatics online.
The Recovery Illusion: What Is Delaying the Rescue of Imperiled Species?
Authors: Ferreira Catarina C , Hossie Thomas J , Jenkins Deborah A , Wehtje Morgan , Austin Cayla E , Boudreau Melanie R , Chan Kevin , Clement Amy , Hrynyk Morgan , Longhi Jessica , MacFarlane Shawn , Majchrzak Yasmine N , Otis Josée-Anne , Peers Michael J L , Rae Jason , Seguin Jacob L , Walker Spencer , Watt Cristen , Murray Dennis L
Published: September 2019

With unprecedented losses in biodiversity, the need for stronger environmental policy has emerged as a conservation priority. Yet recovery planning for imperiled species remains a cumbersome, slow legislative process. In the present article, we examine features of recovery planning for species listed under Canada's Species at Risk Act to determine those influencing recovery planning duration. We found that the time to completion of recovery strategies increases with the number of jurisdictions concurrently listing the species, greater land tenure diversity, species population size, and road density. Species at risk in Canada with no listing status in the United States also suffered longer delays. To achieve a more efficient, timely, and defensible implementation of recovery planning, we recommend that governments prioritize recovery planning on the basis of risk level, promote transjurisdictional collaboration among listing agencies, anticipate and mitigate conservation challenges associated with multitenured and developed landscapes, and adopt procedures that enhance compliance with legislated timelines for recovery planning.
Exacerbation of C1q dysregulation, synaptic loss and memory deficits in tau pathology linked to neuronal adenosine A2A receptor
Authors: Carvalho Kevin , Faivre Emilie , Pietrowski Marie J , Marques Xavier , Gomez-Murcia Victoria , Deleau Aude , Huin Vincent , Hansen Jan N , Kozlov Stanislav , Danis Clément , Temido-Ferreira Mariana , Coelho Joana E , Mériaux Céline , Eddarkaoui Sabiha , Gras Stéphanie Le , Dumoulin Mélanie , Cellai Lucrezia ,   NeuroCEB Brain Bank, Landrieu Isabelle , Chern Yijuang , Hamdane Malika , Buée Luc , Boutillier Anne-Laurence , Levi Sabine , Halle Annett , Lopes Luisa V , Blum David
Published: September 2019

See Cunha (doi:10.1093/brain/awz335) for a scientific commentary on this article.

Carvalho et al. provide clues to the onset of immune dysregulation underlying early synaptic loss in Alzheimer’s disease and tauopathies, by linking overactivation of adenosine A2A receptors in tau pathology to a particular microglial signature (upregulation of C1q and TREM2) allied to the loss of glutamatergic synapses and cognitive deficits.
Ceftolozane/Tazobactam vs Polymyxin or Aminoglycoside-based Regimens for the Treatment of Drug-resistant Pseudomonas aeruginosa
Authors: Pogue Jason M , Kaye Keith S , Veve Michael P , Patel Twisha S , Gerlach Anthony T , Davis Susan L , Puzniak Laura A , File Tom M , Olson Shannon , Dhar Sorabh , Bonomo Robert A , Perez Federico
Published: September 2019

Background

Ceftolozane/tazobactam is a novel cephalosporin/beta-lactamase inhibitor combination that often retains activity against resistant Pseudomonas aeruginosa. The comparative safety and efficacy vs polymyxins or aminoglycosides in this setting remains unknown.

Methods

A retrospective, multicenter, observational cohort study was performed. Patients who received ceftolozane/tazobactam were compared with those treated with either polymyxin or aminoglycoside-based regimens for infections due to drug-resistant P. aeruginosa. Multivariate logistic regression was performed controlling for factors associated with treatment to assess the independent impact of ceftolozane/tazobactam on clinical cure, acute kidney injury (AKI), and in-hospital mortality.

Results

A total of 200 patients were included (100 in each treatment arm). The cohort represented an ill population with 69% in the intensive care unit, 63% mechanically ventilated, and 42% in severe sepsis or septic shock at infection onset. The most common infection type was ventilator-associated pneumonia (52%); 7% of patients were bacteremic. Combination therapy was more commonly used in polymyxin/aminoglycoside patients than those who received ceftolozane/tazobactam (72% vs 15%, P < .001). After adjusting for differences between groups, receipt of ceftolozane/tazobactam was independently associated with clinical cure (adjusted odds ratio [aOR], 2.63; 95% confidence interval [CI], 1.31–5.30) and protective against AKI (aOR, 0.08; 95% CI, 0.03–0.22). There was no difference in in-hospital mortality. The number needed to treat for a clinical cure with ceftolozane/tazobactam was 5, and the number needed to harm with AKI with a polymyxin/aminoglycoside was 4.

Conclusions

These data support the preferential use of ceftolozane/tazobactam over polymyxins or aminoglycosides for drug-resistant P. aeruginosa infections.
In Vitro Activity of Cefiderocol Against a Broad Range of Clinically Important Gram-negative Bacteria
Authors: Yamano Yoshinori
Published: September 2019

Carbapenem-resistant gram-negative bacteria including Enterobacteriaceae as well as nonfermenters, such as Pseudomonas aeruginosa and Acinetobacter baumannii, have emerged as significant global clinical threats. Although new agents have recently been approved, none are active across the entire range of resistance mechanisms presented by carbapenem-resistant gram-negative bacteria. Cefiderocol, a novel siderophore cephalosporin, has been shown in large surveillance programs and independent in vitro studies to be highly active against all key gram-negative causative pathogens isolated from patients with hospital-acquired or ventilator-associated pneumonia, bloodstream infections, or complicated urinary tract infections. The improved structure, the novel mode of entry into bacteria, and its stability against carbapenemases enables cefiderocol to exhibit high potency against isolates that produce carbapenemases of all classes or are resistant due to porin channel mutations and/or efflux pump overexpression. Resistance to cefiderocol is uncommon and appears to be multifactorial.