bluuebunny/crossref_metadata_2025 huggingface dataset:
Programming and memory dynamics of innate leukocytes during tissue homeostasis and inflammation
Authors: Lee Christina , Geng Shuo , Zhang Yao , Rahtes Allison , Li Liwu
Published: May 2017

The field of innate immunity is witnessing a paradigm shift regarding “memory” and “programming” dynamics. Past studies of innate leukocytes characterized them as first responders to danger signals with no memory. However, recent findings suggest that innate leukocytes, such as monocytes and neutrophils, are capable of “memorizing” not only the chemical nature but also the history and dosages of external stimulants. As a consequence, innate leukocytes can be dynamically programmed or reprogrammed into complex inflammatory memory states. Key examples of innate leukocyte memory dynamics include the development of primed and tolerant monocytes when “programmed” with a variety of inflammatory stimulants at varying signal strengths. The development of innate leukocyte memory may have far-reaching translational implications, as programmed innate leukocytes may affect the pathogenesis of both acute and chronic inflammatory diseases. This review intends to critically discuss some of the recent studies that address this emerging concept and its implication in the pathogenesis of inflammatory diseases.
Caught in the act – protein adaptation and the expanding roles of the PACS proteins in tissue homeostasis and disease
Authors: Thomas Gary , Aslan Joseph E. , Thomas Laurel , Shinde Pushkar , Shinde Ujwal , Simmen Thomas
Published: May 2017

Vertebrate proteins that fulfill multiple and seemingly disparate functions are increasingly recognized as vital solutions to maintaining homeostasis in the face of the complex cell and tissue physiology of higher metazoans. However, the molecular adaptations that underpin this increased functionality remain elusive. In this Commentary, we review the PACS proteins – which first appeared in lower metazoans as protein traffic modulators and evolved in vertebrates to integrate cytoplasmic protein traffic and interorganellar communication with nuclear gene expression – as examples of protein adaptation ‘caught in the act’. Vertebrate PACS-1 and PACS-2 increased their functional density and roles as metabolic switches by acquiring phosphorylation sites and nuclear trafficking signals within disordered regions of the proteins. These findings illustrate one mechanism by which vertebrates accommodate their complex cell physiology with a limited set of proteins. We will also highlight how pathogenic viruses exploit the PACS sorting pathways as well as recent studies on PACS genes with mutations or altered expression that result in diverse diseases. These discoveries suggest that investigation of the evolving PACS protein family provides a rich opportunity for insight into vertebrate cell and organ homeostasis.
Mechanisms of regulation and diversification of deubiquitylating enzyme function
Authors: Leznicki Pawel , Kulathu Yogesh
Published: May 2017

Deubiquitylating (or deubiquitinating) enzymes (DUBs) are proteases that reverse protein ubiquitylation and therefore modulate the outcome of this post-translational modification. DUBs regulate a variety of intracellular processes, including protein turnover, signalling pathways and the DNA damage response. They have also been linked to a number of human diseases, such as cancer, and inflammatory and neurodegenerative disorders. Although we are beginning to better appreciate the role of DUBs in basic cell biology and their importance for human health, there are still many unknowns. Central among these is the conundrum of how the small number of ∼100 DUBs encoded in the human genome is capable of regulating the thousands of ubiquitin modification sites detected in human cells. This Commentary addresses the biological mechanisms employed to modulate and expand the functions of DUBs, and sets directions for future research aimed at elucidating the details of these fascinating processes.

This article is part of a Minifocus on Ubiquitin Regulation and Function. For further reading, please see related articles: ‘Exploitation of the host cell ubiquitin machinery by microbial effector proteins’ by Yi-Han Lin and Matthias P. Machner (J. Cell Sci. 130, 1985–1996). ‘Cell scientist to watch – Mads Gyrd-Hansen’ (J. Cell Sci. 130, 1981–1983).
Bigger is not better: cortisol-induced cardiac growth and dysfunction in salmonids
Authors: Johansen Ida B. , Sandblom Erik , Skov Peter V. , Gräns Albin , Ekström Andreas , Lunde Ida G. , Vindas Marco A. , Zhang Lili , Höglund Erik , Frisk Michael , Sjaastad Ivar , Nilsson Göran E. , Øverli Øyvind
Published: May 2017

Stress and elevated cortisol levels are associated with pathological heart growth and cardiovascular disease in humans and other mammals. We recently established a link between heritable variation in post-stress cortisol production and cardiac growth also in salmonid fish. A conserved stimulatory effect of the otherwise catabolic steroid hormone cortisol is likely implied, but has to date not been established experimentally. Furthermore, whereas cardiac growth is associated with failure of the mammalian heart, pathological cardiac hypertrophy has not previously been described in fish. Here we show that rainbow trout (Oncorhynchus mykiss) treated with cortisol in the food for 45 days have enlarged hearts with lower maximum stroke volume and cardiac output. In accordance with impaired cardiac performance, overall circulatory oxygen transporting capacity was diminished as indicated by reduced aerobic swimming performance. In contrast to the well-known adaptive/physiological heart growth observed in fish, cortisol-induced growth is maladaptive. Furthermore, the observed heart growth was associated with up-regulated signature genes of mammalian cardiac pathology, suggesting that signaling pathways mediating cortisol-induced cardiac remodeling in fish are conserved from fish to mammals. Altogether, we show that excessive cortisol can induce pathological cardiac remodeling. This is the first study to report and integrate the etiology, physiology and molecular biology of cortisol-induced pathological remodeling in fish.
Hindlimb muscle function in turtles: is novel skeletal design correlated with novel muscle function?
Authors: Mayerl Christopher J. , Pruett Jenna E. , Summerlin Morgan N. , Rivera Angela R. V. , Blob Richard W.
Published: May 2017

Variations in musculoskeletal lever systems have formed an important foundation for predictions about the diversity of muscle function and organismal performance. Changes in the structure of lever systems may be coupled with changes in muscle use and give rise to novel muscle functions. The two extant turtle lineages, cryptodires and pleurodires, exhibit differences in hindlimb structure. Cryptodires possess the ancestral musculoskeletal morphology, with most hip muscles originating on the pelvic girdle, which is not fused to the shell. In contrast, pleurodires exhibit a derived morphology, in which fusion of the pelvic girdle to the shell has resulted in shifts in the origin of most hip muscles onto the interior of the shell. To test how variation in muscle arrangement might influence muscle function during different locomotor behaviors, we combined measurements of muscle leverage in five major hindlimb muscles with data on muscle use and hindlimb kinematics during swimming and walking in representative semiaquatic cryptodires and pleurodires. We found substantial differences in muscle leverage between the two species. Additionally, we found that there were extensive differences in muscle use in both species, especially while walking, with some pleurodire muscles exhibiting novel functions associated with their derived musculoskeletal lever system. However, the two species shared similar overall kinematic profiles within each environment. Our results suggest that changes in limb lever systems may relate to changes in limb muscle motor patterns and kinematics, but that other factors must also contribute to differences in muscle activity and limb kinematics between these taxa.
Letters to anorexia. Narrative tools for working with anorectic patientsin a Dialogical Self context
Authors: Tokarska Urszula , Ryżanowska Dorota
Published: May 2017

Cel pracy

Pogłębienie rozumienia doświadczenia pacjentów z diagnozą anorexia nervosa w kontekście podejścia narracyjno-konstrukcjonistycznego wzbogaconego o psychologię Dialogowego Ja. Systematyczna eksploracja fenomenu wewnętrznych dialogów rozgrywających się w umysłach pacjentów pomiędzy walczącymi o wzajemną dominację zdrowymi i zaburzonymi aspektami Ja. Określenie możliwości diagnostycznych i aplikacyjnych bodźca narracyjnego w postaci „Listu do anoreksji”.

Metoda

Przyjęto, iż stanowiący objaw zdrowienia proces zdobywania/ odzyskiwania relatywnego dystansu wobec wewnętrznego głosu anoreksji może być zarówno diagnozowany, jak i wspomagany z wykorzystaniem tzw. technik eksternalizacyjnych. Opracowano autorskie narzędzie kategoryzacyjne łączące wymiar pozycjonowania własnego Ja w tzw. „pozycji nad” lub „pod” w odniesieniu do „głosu anoreksji” ze stopniem rozwinięcia przez osoby badane pełnego schematu autonarracyjnego.

Wyniki

Analizy statystyczne pozwoliły na wyodrębnienie dwu grup pacjentek: (1) „z dominującą pozycją pod” oraz (2) z tendencją do dominowania w wewnętrznych dialogach z własną chorobą. Z wykorzystaniem metodologii ilościowo-jakościowej (uwzględniającej analizy semantyczne) określone zostały również wieloaspektowe powiązania wewnątrz tych obu homogenicznych skupień, między innymi w zakresie rodzaju dominujących w nich dialogów wewnętrznych.

Wnioski

Postulowane w kontekście teorii dialogowego Ja wspieranie wewnętrznej aktywności dialogowej pacjentek z anorexia nervosa wydaje się współwystępować z kolejnymi etapami procesu leczenia, co znajduje m. in. odzwierciedlenie w listach terapeutycznych pisanych do własnej choroby. Można też potencjalnie założyć relację odwrotną, a mianowicie fakt pozytywnych efektów terapeutycznych intencjonalnego stymulowania wewnętrznej dialogowości oraz narracyjnej strukturyzacji doświadczenia również z wykorzystaniem bodźca narracyjnego w formie listu. Autorzy tekstu wskazują na kierunki dalszych pogłębionych badań w tym zakresie, określając jednocześnie aspekty aplikacyjne pozyskanych wyników, zarówno w aspekcie diagnostycznym, jak i psychoterapeutycznym oraz prewencyjnym.
Dynamics of mangrove community in revegetation area of Karangsong, north coast of Indramayu District, West Java, Indonesia
Authors: GUNAWAN HENDRA , SUGIARTI SUGIARTI , ISKANDAR SOFIAN
Published: May 2017

Gunawan H, Sugiarti, Iskandar S. 2017. Dynamics of mangrove community in revegetation area of Karangsong, north coast of Indramayu District, West Java, Indonesia. Biodiversitas 18: 659-665. Mangrove along the north coast of Java is heavily degraded due to the conversion of land into fish ponds and human settlement areas. A revegetation program has been initiated by the local community of Karangsong Village, Indramayu District, West Java, Indonesia, supported by PT. Pertamina RU VI Indramayu. Our research aimed to study the population dynamics of the mangrove revegetation in Karangsong. Secondary data was collected from the Fishery and Maritime Services of Indramayu and PT. Pertamina. We carried out on-location field observations and we interviewed key respondents. Data was analyzed to describe trends in the diversity index and population dynamics of the mangrove. It was observed that the revegetation effort in the shoreline of Karangsong had covered Â± 69.08 hectares which consisting of six species of mangrove and three tree species of coastal vegetation i.e. Rhizophora mucronata Lam., Rhizophora stylosa Griff., Rhizophora apiculata Blume, Avicennia marina (Forssk.) Vierh., Avicennia alba Blume, Sonneratia caseolaris (L.) Engl, Terminalia catappa L., Casuarina equisetifolia L., and Ziziphus mauritiana Lam. The mangrove population increased dramatically, from estimated 25,000 individuals in 2008 to 690,835 individuals in 2016. Rhizophora mucronata was the most dominant species (68.85%), followed by Rhizophora stylosa (18.33%) and Rhizophora apiculata (9.53%). The Shannon diversity index was fluctuated but tend to be increased from 0.80 to 0.95.
Short Communication: Diversity and prevalence of ectoparasites associated with cultured fish from coal ponds in East Kalimantan, Indonesia
Authors: SAPTIANI GINA , PEBRIANTO CATUR AGUS , AGUSTINA AGUSTINA , HARDI ESTI HANDAYANI , ARDHANI FIKRI
Published: May 2017

Saptiani G, Pebrianto CA, Agustina, Hardi EH, Ardhani F. 2017. Short Communication: Diversity and prevalence of ectoparasites associated with cultured fish from coal ponds in East Kalimantan, Indonesia. Biodiversitas 18: 666-670. In East Kalimantan, coal pits are used for fish culture. The most fish species cultured in the coal ponds were carp and tilapia. The study aimed to identify ectoparasites types, diversity, and prevalence of fish cultured in coal ponds. Sampling was carried out between January and March 2016 on coal ponds in Kutai Kartanegara District, East Kalimantan. Samples were taken from two different coal ponds, but both coal ponds cultivated the same species of fish samples (carp and tilapia). The number of fish samples taken from coal ponds was 40 samples for each fish types in each location of coal ponds with the body weight of the fish samples between, 20-30 g. The preparation of parasite identification was conducted by taking every fish's external organ which was then scraped for microscopical preparation and observation. The identification of parasites was determined based on the morphological characteristics including the shape performances, specific spots and also the type of environment and habitat. The results showed that ectoparasites found in carp and tilapia cultured in coal ponds were Ichtyopthirius multifilis, Trichodina, Oodonium, Dactylogyrus, and Gyrodactylus, while Epistylis was only found in carp. The average percentage of ectoparasites prevalence in carp was from 30.00 to 59.17% with the attacked intensity was between 2.47 to 4.43 parasites/fish, while in tilapia was from 27.5 to 40.83% with the attacked intensity between 1.04 to 2.83 parasites/fish. The highest prevalence and intensity of parasite attacks was Trichodina in carp from a pond which has been used for a long time for fish culture. The prevalence and attacked intensity of ectoparasites on fish were higher in the longer use of coal ponds rather than those in new ponds.
Genetic diversity of Pongamia pinnata (Millettia pinnata, aka. malapari) populations in Java Island, Indonesia
Authors: AMINAH AAM , SUPRIYANTO SUPRIYANTO , SURYANI ANI , SIREGAR ISKANDAR Z
Published: May 2017

Aminah A, Supriyanto, Suryani A, Siregar IZ. 2017. Genetic diversity of Pongamia pinnata (Millettia pinnata, aka. malapari) populations in Java Island, Indonesia. Biodiversitas 18: 677-681. One of the promising tree species to be utilized as biodiesel legume in Indonesia is malapari (Pongamia pinnata (L.) Pierre). The tree grows naturally along the North and South Coasts of Java Island. Malapari is now subjected to an initial breeding program, but its population diversity in Indonesia is not known yet. The objective of this study was to estimate genetic diversity in Java Island, namely populations of Carita, Batukaras, Kebumen, Alas Purwo National Park and Baluran National Park. RAPD markers were used to study the genetic diversity using the following DNA primers: OPL-11, OPAH-15, OPAO-01, OPAB-14 and OPAH-13. Results showed that DNA fragment lengths ranged from 250 to 1000 bp with a variable number of polymorphic bands, ranging between 13-24. Based on these RAPD markers, the population in Baluran was considered as a potential diversity center of malapari in Java, whereas the population in Kebumen was found to have the lowest genetic diversity. In general, the average genetic diversity within an population was lower than that among the populations. Cluster analysis of genetic similarity in five malapari population resulted in separation into two main clusters, the first group consisted of four populations (i.e., Carita, Batukaras, Kebumen and Alas Purwo). The other cluster was only one population only, namely Baluran.
Coral larvae spreading based on oceanographic condition in Biawak Islands, West Java, Indonesia
Authors: FITRIADI CANDRA A. , DHAHIYAT YAYAT , PURBA NOIR P. , HARAHAP SYAWALUDIN A. , PRIHADI DONNY J.
Published: May 2017

Fitriadi CA, Dhahiyat Y, Purba NP, Harahap SA, Prihadi DJ. 2017. Coral larvae recruitment based on oceanography condition in Biawak Islands, West Java, Indonesia. Biodiversitas 18: 681-688. This research aimed to know the recruitment pattern of planula in the Biawak Island. The dispersion of planula and corals recruitment as an important factor to determine the distribution of the adult corals. The spawning and brooding are the beginning processes of planula dispersion. Dispersion factors are highly influenced by water environment factors. The main factor in planula dispersion is sea currents, wind, tide, and bathymetry. The circulation of sea currents on Biawak Islands waters is influenced by the tidal movement. The results of research showed that Biawak Islands waters have mixed tide prevailing semidiurnal type of tidal movement. Currents of Biawak Islands waters moved from the northern toward the southern with a range of speed between 0.045-0.075 m/s on northeast and south and for west and north range of speed of sea currents are between 0.015-0.195 m/s, the sea currents movement of Biawak Islands waters was dominated by tidal movement. Biawak Islands have varying wind speed, the most direction of wind moved to northwestern toward southeastern by predominance speed 4.8-7.2 m/s. The results of research showed that planula on the Biawak Island moved to northern and northeastern at high tide and then moved to southern and southeastern at a low ebb with the furthest movement of planula on the Biawak Island was 2.2 km. The furthest movement of planula on the Gosong Island was 1.66 km and planula dispersed to the east and west region of Gosong Island, on the Cendikia Island planula dispersed to northern and eastern with the furthest movement of planula on the Cendikia Island was 0.44 km. Based on the movement of planula can be concluded that source of coral reefs on the Gosong Island derived from the coral reefs on the Biawak Island.
Abundance of corn planthopper (Stenocranus pacificus) (Hemiptera: Delphacidae) and the potential natural enemies in West Sumatra, Indonesia
Authors: NELLY NOVRI , SYAHRAWATI MY , HAMID HASMIANDY
Published: May 2017

Nelly N, Syahrawati M, Hamid H. 2017. Abundance of corn planthopper (Stenocranus pacificus) (Hemiptera: Delphacidae) and the potential natural enemies in West Sumatra, Indonesia. Biodiversitas 18: 696-700. A study about the abundance of corn planthopper Stenocranus pacificus and diversity of it's potential natural enemies in West Sumatra, Indonesia was conducted from July until October 2016 in Pasaman Barat, Limapuluh Kota and Tanah Datar. The method was purposive random technique sampling. Sampling Stenocranus pacificus Kirkaldy (Hemiptera: Delphacidae) and it's potential natural enemies were collected by using a modified d-vac vacuum. The Identification was done based on morphological differences between species. The result showed that corn planthopper was found in all study location, as well as natural enemies could be found in the vegetative and generative phase of corn. The distribution pattern of corn planthopper, S. pacificus generally was aggregated, except on the vegetative phase in Pasaman Barat that classified as uniform. The natural enemies that found consist of two class (Insects and Arachnids) and three ordo (Hymenoptera, Coleoptera and Araneae). Diversity index (H) of natural enemies in Pasaman Barat is higher than Tanah Datar and Limapuluh Kota district. Evenness index at all study locations showed low value (E<1).
Short Communication: Biocontrol activity of Phyllosphere fungi on mungbean leaves against Cercospora canescens
Authors: SUMARTINI SUMARTINI
Published: May 2017

Sumartini. 2017. Short Communication: Biocontrol activity of Phyllosphere fungi on mungbean leaves against Cercospora canescens. Biodiversitas 18: 720-726. Examination of biocontrol activity of phyllosphere fungi on mungbean leaves against Cercospora canescens, a causal agent of mungbean leaf spot disease, was conducted during February-July 2016. Samples of symptomatic mungbean leaves were collected from several production areas in East and Central Java. Symptomatic leaves with leaf spot were collected randomly by detaching the symptomatic leaves and kept in a plastic bag for laboratory studies. Fungi associated with leaf spot were isolated using surface sterilized technique on PDA medium. In vitro and in vivo antagonism assay was carried out in the laboratory and greenhouse, respectively. Fungi associated with leaf spot on mungbeans such as Fusarium spp., Curvularia spp., Aspergillus flavus, and Nigrospora sp. were tested against C. canescens in the antagonism assay. Highest inhibition activity against C. canescens was found on Fusarium sp. 2 (KH-KJP-1B) (in vitro = 61%, in vivo = 19.63%) and Curvularia sp.1 (KH-JBG-B) (in vitro = 66%, in vivo = 16.46%).
Short Communication: Phylogenetic analysis of mango (Mangifera) in Northern Sumatra based on gene sequences of cpDNA trnL-F intergenic spacer
Authors: FITMAWATI FITMAWATI , HARAHAP SANDI PRATIWI , SOFIYANTI NERY
Published: May 2017

Harahap SP, Fitmawati, Sofiyanti N. 2017. Short Communication: Phylogenetic analysis of mango (Mangifera) in Northern Sumatra based on gene sequences of cpDNA trnL-F intergenic spacer. Biodiversitas 18: 715-719. Northern Sumatra is an area with geographical variation. The environmental factors are affected on character plasticity such as found in Anacardiaceae family especially Mangifera genus. The character plasticity of Mangifera members raises a problem in determining clear boundaries between species based on morphological character. Therefore, a molecular approach is necessary to provide a specific character among Mangifera species. This study aimed to reconstruct the phylogeny among Mangifera members in Northern Sumatra based on the sequences of trnLF intergenic spacer. All of the sequences were aligned by using Clustal W and Cladogram was reconstructed by using PAUP by Maximum Parsimony (MP) and Neighbour-Joining (NJ) methods. The MP cladogram produced two in groups i.e., clade I consist of M. odorata1, M. odorata2, M. laurina1, M. laurina2, M. indica, M. zeylanica, M. quadrifida and Mangifera sp. and clade II consisted of M. foetida1 and M. foetida2. Based on the NJ method, it was obtained M. laurina2 which had the highest genetic distance among other members of Mangifera. The trnL-F intergenic spacer with a low sequences variation indicated that this region was highly conserved and had a low evolution rate in Mangifera.
Herpetofauna community establishment on the micro habitat as a result of land mines fragmentation in East Kalimantan, Indonesia
Authors: MUSLIM TEGUH
Published: May 2017

Muslim T. 2017. Herpetofauna community establishment on the microhabitat as a result of land mines fragmentation in East Kalimantan, Indonesia. Biodiversitas 18: 709-714. Herpetofauna community is established because of habitat suitability or adaptation process that forces a species to survive. In the mining region, herpetofauna habitat change has occurred. The loss of natural habitat and the creation of an artificial habitat result in severance of corridor as a connecting line between herpetofauna habitats so that only microhabitat remains. Microhabitats of herpetofauna survive on limited food resources. The process of surviving of herpetofauna in microhabitats is reflected on the phenomenon of the food chain i.e. reptiles act as predators (top) and amphibians are as preys and as insect predators (middle). In the mining area, an area with a source of water is the destination for all animals, especially herpetofauna, and it even becomes the microhabitat for certain species. The purpose of this study is to determine the species of herpetofauna, its communities and its domination on the water area its microhabitats within the mine area. The exploration is carried out by direct observation (visual encounter surveys). The survey location determination is done intentionally (purposive sampling) on the potential habitat in some locations of water sources, such as pit dam, settling pond, man-made lake (embung), rivers and swamps. Based on the similarity index, there are five species of herpetofauna dominating the life in microhabitats and playing role in the formation of food chain community. Enhydris enhydris and Dendrelaphis pictus are species of snake and act as predator of frog Fejervarya cancrivora and Polypedates leucomystax.
Short Communication: Fish fauna of Lake Lauik Tawar and Lake Laulo, Simeulue Island, Indonesia
Authors: MUCHLISIN ZAINAL A. , NURFADILLAH NURFADILLAH , ARISA IKO IMELDA , RAHMAH ALVI , PUTRA DEDI F. , NAZIR MUHAMMAD , ZULHAM ARMEN
Published: May 2017

Muchlisin ZA, Nurfadillah N, Arisa II, Rahmah A, Putra DF, Nazir M, Zulham A. 2017. Short Communication: Fish fauna of Lake Lauik Tawar and Lake Laulo, Simeulue Island, Indonesia. Biodiversitas 18: 752-757. The objectives of the present study were to evaluate the species composition and diversity index of fishes in Lake Lauik Tawar and Lake Laulo, Simeulue Island, Aceh Province, Indonesia. The survey was conducted from 17th to 21st of November 2015. The fishes were sampled using gillnets with mesh size 1-3 inches. The representative of each species was photographed and then preserved in 10% formalin and transported for taxonomic identification in the Laboratory of Ichthyology, Syiah Kuala University, Banda Aceh, Indonesia. The study showed that there were 11 species of fish recorded during the survey; where eight species were found in Lake Lauik Tawar and six species were found in Lake Laulo. Two species of alien fish were recorded in Lake Lauik Tawar, i.e. Osphronemus gouramy and Oreochromis niloticus and one species in Lake Laulo i.e. O. niloticus. In addition, Ambassis miops and Clarias batrachus were predominant species in Lake Lauik Tawar and Lake Laulo, respectively. In general, the two lakes were categorized as a low degree of fish diversity.
Agroforestry system biodiversity of Arabica coffee cultivation in North Toraja District, South Sulawesi, Indonesia
Authors: LISNAWATI ANDI , LAHJIE ABUBAKAR M. , SIMARANGKIR B.D.A.S. , YUSUF SYAHRIR , RUSLIM YOSEP
Published: May 2017

Lisnawati A, Lahjie AM, Simarangkir BDAS, Yusuf S, Ruslim Y. 2017. Agroforestry system biodiversity of Arabica coffee cultivation in North Toraja District, South Sulawesi, Indonesia. Biodiversitas 18: 741-751. Sustainable coffee plantation emphasizes the concept that is able to provide services that can improve the quality of the environment and the ecosystem as a conservation efforts. Arabica coffee plants do not need full sunlight that they are planted according to agroforestry system which covers simple mix system to complex system such as forest. Shade tree has a very big role in sustainable coffee agro-ecosystem and become one of the conditions in the world's coffee certification. This study aimed to analyze the role of shade trees lamtoro types (Leucaena glauca), and calliandra (Calliandra calothyrsus) used by companies as an agroforestry systems on coffee cultivation in North Toraja located at an altitude between 1050-1250 m above sea level, this study was conducted from January to December 2016. Result of the study suggests that the shade trees lamtoro and calliandra influence the amount of sunlight intensity that reaches coffee plant. The shaded and unshaded coffee plants received different sunlight intensity of every minute with a coefficient of determination R2 = 0.98 for unshaded and R2 = 0.89 for under the shade of calliandra, with a diameter growth increased 7.8% year-1, increase growth (riap) diameter decreased 2% year-1. Cherry increased growth of 13.5% year-1 with an average weight of 3.81 g beans-1,while for the effect of lamtoro, the coefficient of determination is R2 = 0.98 for unshaded and R2 = 0.91 for under the shade. The percentage of light intensity outside and under the shade obtained from a 17 year coffee plant is on average of 58% for the types of tree of calliandra, while for lamtoro the average is of 72.5%, diameter growth of coffee tree in under shade lamtoro by 7.4% year-1 and increase of growth (riap) diameter decreased by 2.5% year-1, cherry growth increased by 13.3% year-1 with an average weight of 3.92 g beans-1. In addition to that, shading also affect the surrounding nutrient soil and maximum production of coffee is achieved at the age 17 years i.e. an average of 1.50 kg tree-1 for a shaded tree calliandra species and 1.35 kg tree-1 for lamtoro species.
Effect of seed coating with biological agents on seed quality of rice
Authors: PALUPI TANTRI , ILYAS SATRIYAS , MACHMUD MUHAMMAD , WIDAJATI ENY
Published: May 2017

Palupi T, Ilyas S, Machmud M, Widajati E. 2017. Effect of seed coating with biological agents on seed quality of rice. Biodiversitas 18: 727-732. The research that consisted of two activities was performed at the Laboratory. Experiment 1 the aim to obtain biological agents that have high antagonistic potential against Xanthomonas oryzae pv. oryzae (Xoo) and two biological agents that are compatible to one another. Experiments 2 to determine the effect of rice (Oryza sativa L.) seeds coated with biological agents to improve seed quality and reduce levels of Xoo infection. In the first experiment, four isolates of bacterial antagonists, i.e: isolate Pseudomonas diminuta A6; isolate P. aeruginosa A54; isolate Bacillus subtilis 11/C, and isolate B. subtilis 5/B, were tested for their antagonism activities against Xoo on PSA plates using the method of growth inhibition zone with filter paper. Furthermore, the four antagonists were tested for their compatibility with each other on PSA plates. In the second experiment used a completely randomized design with a single factor (seed coating) consisting of seven levels, namely: negative control, healthy seed; positive control, the seeds contaminated with Xoo; P. diminuta A6 and B. subtilis 5/B; alginate 3% + 1% peat + P. diminuta A6 and B. subtilis % 5/B; arabic gum 3% + 1% gypsum + P. diminuta A6 and B. subtilis 5/B; CMC 1.5% + 1% talc + P. diminuta A6 and B. subtilis 5/B, and bactericide streptomycin sulfate 20%. Results of Experiment 1 showed that isolates P. diminuta A6 has the highest antagonistic potential against Xoo based on the diameter of inhibition zone on Xoo, followed by isolate B. subtilis 5/B. Isolate P. diminuta A6 and B. subtilis 5/B had a good growth compatibility with no antagonism. Therefore, isolates P. diminuta A6 and B. subtilis 5/B were selected and used as biocontrol agents in further studies. Results of Experiment 2 showed that treatment with P. diminuta A6 + B. subtilis 5/B gave the best of the increase of seed vigor, and the decrease of Xoo infection level in the seeds.
Seagrass community structure of Tayando-Tam Island, Southeast Moluccas, Indonesia
Authors: FITRIAN TYANI , KUSNADI AGUS , PERSILETTE ROSMI NUSLAH
Published: May 2017

Fitrian T, Kusnadi A, Persilette RN. 2017. Seagrass community structure of Tayando-Tam Island, Southeast Moluccas, Indonesia. Biodiversitas 18: 788-794. Seagrass bed is one of the marine ecosystem that having the highest productivity that could sustain coastal resources. The research purposes of this paper is to determine the community structure of seagrass at Tayando-Tam Island, Southeast Moluccas, Indonesia. The method of observation of seagrass bed using a line transect, transect ran perpendicular to the shore line for 100 meters. The field of observations include identification of seagrass species, counting the number of shoots and percentage (%) of seagrass cover. Seven species of seagrass had been found in Tayando-Tam island, i.e. Enhalus acoroides, Thalassia hemprichii, Cymodocea serrulata, Cymodocea rotundata, Halodule pinifolia, Halophila ovalis, Syringodium isoetifolium. Halodule pinifolia had the highest density in Tam Island with the number of 684.18 shoots/m2. The coverage in this area was between 4.64-43.1 %. Based on the number of species, diversity index and dominance index Tam Island had the most stable seagrass communities, with moderate value of diversity index (H'=1.26), high evenness Index (E=1.63), and low value of dominance index (D=0.34). Seagrass resources in the Tayando-Tam islands is good and the potential for biota the association, which is supported by the quality of water is good for the growth of seagrass.
The dominant species of herpetofauna in the coal mining area at East Kalimantan, Indonesia
Authors: MUSLIM TEGUH , SARI ULFAH KARMILA , YASSIR ISHAK
Published: May 2017

Muslim T, Sari UK, Yassir I. 2017. The dominant species of herpetofauna in the coal mining area at East Kalimantan, Indonesia. Biodiversitas 18: 773-779. Changing of habitat condition influences the variety of species including Herpetofauna. Herpetofauna is one of the components in the ecosystem that plays an important role, both from the ecological and economical aspect. From the ecological aspect, it has a specific role in the food chain, and it can also be used as a bio-indicator of the environmentâ€™s condition. Furthermore, herpetofauna found in reclamation area of coal mining not only stabilizes the ecosystem in the food chain, but also it can be used as a bioindicator of environment changes and the success rate of reclamation. The aim of this research was to find out the community of herpetofauna comprising and dominating the coal mining reclamation area, especially the wet and dry areas. The research location was located at PT. Singlurus Pratama Kalimantan Timur. The methods used in this research were visual encounter survey and patch sampling. This research found 10 species from 5 families of reptiles and 11 species from 6 families of amphibians. The highest dominant index score for reptile was 0.71, found in the fragmented forests. Meanwhile, the dominant reptile species were Eutropis multifasciata (20 individuals), Enhydris enhydris (4 individuals), and Dendrelaphis pictus (4 individuals). The highest dominant index score for amphibian was 1, found in the settling pond. Moreover, the dominant amphibian species were Polypedates leucomystax (42 individuals) and Fejervarya cancrivora (41 individuals). These two species were the ones able to survive in the degraded areas and they were easily found in the areas with disrupted habitats.
Short Communication: Population structure of mangrove crab Scylla oceanica in mangrove ecosystem of Tanjung Lesung, Banten, Indonesia
Authors: PUDIAWATI TITING , PATRIA MUFTI P.
Published: May 2017

Pudiawati T, Patria MP. 2017. Short Communication: Population structure of mangrove crab Scylla oceanica in mangrove ecosystem of Tanjung Lesung, Banten, Indonesia. Biodiversitas 18: 813-817. The mangrove crab Scylla oceanica is one of the dominant crabs in the mangrove ecosystem at Tanjung Lesung Beach, Banten, Indonesia. The aim of the study was to determine the temporal distribution, carapace width-weight relationship and condition factors of S. oceanica. The crabs were collected by using traps for four months from August to November 2015. It was observed that the carapace was larger in male crabs (9.97 cm) than in female crabs (9.34 cm) and the average weight of the males (206.08 g) was higher than that of the females (183.83 g). b value of male (1.955) and female (2.123) crabs were significantly different (P < 0.05). Both of them have a negative allometric growth pattern. The result of the distribution analysis was a Morisita spread index Id of 1.5176; this indicates the crabs have clustered distribution patterns and their distribution was allegedly associated with the reproductive cycle.
Short Communication: Diversity and abundance of soil insects at Jeruk Manis Protected Forest in East Lombok (Indonesia) using several trapping methods
Authors: ROHYANI IMMY SUCI , AHYADI HILMAN
Published: May 2017

Rohyani IS, Ahyadi H. 2017. Short Communication: Diversity and abundance of soil insects at Jeruk Manis Protected Forest in East Lombok (Indonesia) using several trapping methods. Biodiversitas 18: 809-812. Insects are the most successful organisms because it can live in almost all types of habitats, namely water (freshwater and sea), land, air, and even in both hot and cold climates. Identification of soil insects in a certain type of habitat requires practical, easy, inexpensive, and efficient collection methods so as to obtain high abundance and diversity of soil insects. This study aims to analyze the diversity and abundance of soil insects using several trapping methods in Jeruk Manis Protected Forest in East Lombok. There are five trapping methods applied in this study; (i) pitfall trap, (ii) pitfall traps with bait, (iii) yellow pan traps, (iv) soil sampling, and (v) forest floor collection. The findings show that the overall diversity of soil insects in Jeruk Manis Protected Forest is moderate (1.44), while its evenness level is low (0.48). Soil sampling method provides diversity value of 2.36 and evenness level of 0.89, which is also the highest one among the other methods. Pitfall traps with bait give high individual number of soil insects (10.577 individuals). The highest number of soil insect orders is obtained through forest floor collection with 11 orders, while the highest number of soil insect families is obtained through pitfall trap with 30 families. The taxa of soil insects with relatively highest abundance consecutively are Hymenoptera (Formicidae), Collembola (Isotomidae, Entomobryidae), Coleoptera (Hydrophilidae, Ptiliidae, Scarabeidae), and Diptera (Drosophilidae).
Dynamics expression of Osr40c1 gene and growth of maize (Zea mays) calluses in responding to salt stress
Authors: SAPUTRO TRIONO BAGUS , SHOLIHAH NUR FADLILLATUS , ERMAVITALINI DINI
Published: May 2017

Saputro TB, Sholihah NF, Ermavitalini D. 2017. Dynamics expression of Osr40c1 gene and growth of maize (Zea mays) calluses in responding to salt stress. Biodiversitas 18: 801-808. Maize (Zea mays L) is one of the most planted cereal plants worldwide. The demand of maize plant is increased over the years since its various usage in industry. Unfortunately, the production rate does not meet the demands caused by the significant reduction of plantation area for housing and the others building. The marginal saline soil area can be a promising area to grow the maize although contains a high amount of salt. The high concentration of salt can significantly reduce the plant growth and productivity. The aims of this study were to determine the tolerant level of Manding and Bluto varieties against salt stress. There were two main stages on this research. First, callus induction through in vitro culture (MS0 + 2,4-D 3 mg/L), then the calluses were subcultured on the selection medium (MS0 + 2,4-D 3 mg/L + NaCl concentrations (0, 2500, 5000 and 7500 mg/L)). Second, Q-PCR analysis was used to observe the differences of gene expression level. The result shows that NaCl stress can alter the color of callus, from yellow to brown. The percentage of surviving callus was 100% in both varieties, although the callus weight decreased along with the increment of NaCl concentrations. In 7500 mg/L, Manding has 0.023 g in fresh weight, while Bluto 0,027 gr. Interestingly, the expression of Osr40c1 gene showed different level between those two varieties. Manding had only 0.82 fold, while Bluto had 4.86 folds compared with the control. Taken together, Bluto has a better performance in high content of NaCl.
Genotype of Brahman and Brahman Cross Cattle based on SNP in Insulin-Like Growth Factor Binding Protein-3 (IGFBP-3) gene sequences
Authors: PRIYADI DWI AHMAD , PANJONO PANJONO , BINTARA SIGIT , HARTATIK TETY
Published: May 2017

Priyadi DA, Panjono, Bintara S, Hartatik T. 2017. The genotype of Brahman and Brahman Cross Cattle based on SNP in Insulin-Like Growth Factor Binding Protein-3 (IGFBP-3) gene sequences. Biodiversitas 18: 795-800. The IGFBP-3 gene is a potential marker of cattle growth, which is related to the functions that influence the growth, energy metabolism, reproduction and immunity. The genome was isolated from whole blood samples of 10 Brahman cattle and 16 Brahman Cross cattle. Cattle IGFBP-3 gene that targeted in this study was located in the part of intron 2, exon 3 and part of intron 3. The gene targets were amplified using specific primers by Polymerase Chain Reaction (PCR) technique, resulting 563 bp amplification product. As data comparison to reveal the SNP, the GenBank sequences (n = 14) from various breed and countries were used. The objective of this study was to reveal the SNP on the Brahman and Brahman Cross IGFBP-3 gene. The results obtained 3 genotypes from one SNP that spread in the sample population. The SNP was located in intron 2 at position 3,930 (Gïƒ A). The Polymorphism could be recognized by PvuII restriction enzymes. There was not enough evidence to associate the SNP with the phenotype (at pre-weaning age) of Brahman and Brahman Cross cattle. There was a genetic diversity in the population studied. Knowledgeable SNP could be used as genetic markers for further research on Brahman and Brahman Cross cattle.
Sequence variation among populations of sawfishes (Pristiformes: Pristidae) from Indonesia and Australia
Authors: SUTARNO SUTARNO , BUDIHARJO A. , SETYAWAN A.D. , LYMBERY A.J.
Published: May 2017

Sutarno, Budiharjo A, Setyawan AD, Lymbery AJ. 2017. Sequence variation among populations of sawfishes (Pristiformes: Pristidae) from Indonesia and Australia. Biodiversitas 18: 850-856. The sawfishes (Pristiformes: Pristidae) are very rare and critically endangered species globally, calling for conservation efforts around the world. This species is taxonomically interesting because molecular research in recent years has led to re-groupings in some species. The aim of this research was to sequence the control region (CR) of mitochondrial DNA of sawfishes from Indonesia and Australia, compare the sequences between samples, and construct phylogenetic trees to know the relationship of those samples. To achieve these aims, dried rostra of samples from both countries are collected, total DNA were purified and amplified using PCR, followed by sequencing reaction. The sequence data were then lined followed by constructing phylogenetic trees. The results of the BLASTN and phylogenetic tree analysis found two species, the all Australian samples belong to Pristis pristis (formerly P. microdon), one Indonesian sample also belongs to P. pristis, while the other Indonesian samples belong to Anoxypristis cuspidata.
The estimates spawning potential ratio of three dominant demersal fish species landed in Tegal, north coast of Central Java, Indonesia
Authors: NUGROHO DUTO , PATRIA MUFTI P. , SUPRIATNA JATNA , ADRIANTO LUKY
Published: May 2017

Nugroho D, Patria MP, Supriatna J, Adrianto L. 2017. The estimates spawning potential ratio of three dominant demersal fish species landed in Tegal, north coast of Central Java, Indonesia. Biodiversitas 18: 844-849. Java Sea is one of the important marine waters for fisheries purpose in Indonesia. The rich diversity of marine fish has been exploited for decades. Among them, demersal fish resource was commercially targeted by coastal fishers. The sustainability of demersal fishery is a crucial concern given the substantial economic contribution and its significant dependence of small-scale fishers for their livelihoods. The fishing intensity is considerable growing and tends to become threats their habitats. Three dominant species (Priacanthus tayenus, Scolopsis taeniopterus and Upeneus sulphureus) were selected in this study. To evaluate the vulnerability of these species to their bio-exploitation level, the spawning potential ratio (SPR) approach were applied. The calculation based on estimated length of first capture (Lc) indicates that SPR those demersal species occurred at less than 20%. These values indicate that existing fishery can be categorized as nearly fully exploited. Across broad range of species, 40% SPR is generally accepted as a proxy for Maximum Sustainable Yield (MSY) for recruitment overfishing in less resilience fish population.
Short Communication: Isolation of Actinomycetes from mangrove ecosystem in Torosiaje, Gorontalo, Indonesia
Authors: KATILI ABUBAKAR SIDIK , RETNOWATI YULIANA
Published: May 2017

Katili AS, Retnowati Y. 2017. Short Communication: Isolation of Actinomycetes from mangrove ecosystem in Torosiaje, Gorontalo, Indonesia. Biodiversitas 18: 826-833. Actinomycetes is a group of positive gram microorganism known to produce secondary metabolic compounds that work as antibiotics, anti-fungus, anti-virus, anti-cancer, and other important enzymes for the industry. This research aimed at discovering the potentials of Actinomycetes of the mangrove ecosystem in Torosiaje, Gorontalo, Indonesia. It focused on finding out the diversity of Actinomycetes at mangrove ecosystem in Torosiaje. Hence, various types of Actinomycetes that have potentials to create secondary metabolic compounds/bioactive compounds for industrial purposes can be found. This purpose can only be attained through isolation of actinomycetes. This isolation was conducted through characterization of morphological characteristics of the colony and the spore, molecular characterization through isolation of DNA genome of the actinomycetes, amplification of 16S rRNA through PCR, sequencing, and reconstruction of the phylogenetic tree. We were able to obtain the actinomycetes isolate from the sediment in rhizosphere area of Ceriops tagal, Bruguiera gymnorrhiza, Xylocarpus sp, Rhizophora apiculata, Avicennia sp, and Sonneratia alba species of mangrove. Each isolated actinomycetes has specific morphological characteristics. The density of isolated actinomycetes in Torosiaje mangrove area was very low with an average of 1 x 105 CFU gram-1 in each sediment.
Assessment of work ability in competing strands of social insurance: the German case
Authors: Aurich-Beerheide Patrizia , Brussig Martin
Published: May 2017

The article describes the system of social security in the case of incapacity in Germany and analyses how the pathway into incapacity benefits is structured. A special focus of the article is on conditionality as it is applied in different systems of social security in Germany today. A main result of the analysis is that incapacity benefits are embedded into a chain of different benefits and social services for persons with limited work ability. For the German case, this leads to a defensive reaction from both the Public Employment Service and pension insurers.
Gas chromatography-mass spectral structural analysis, phytochemical screening and antimicrobial activity of n-hexane leaf extract of Corymbia torelliana
Authors: Moses   Daben Janet , Albert Dashak Dayil , Uwhomagbejo Isaac Rahab
Published: May 2017

The chemical studies and antimicrobial activity of n-hexane leaf extract of Corymbiatorelliana was evaluated for medicinal importance. The phytochemical constituents present were steroids, tannins, cardiac glycosides alkaloids and terpenes. The result of sodium fussion test revealed the presence of Phosphorus Nitrogen and Chlorine. The Column Chromatography gave several fractions that were pulled together by Thin Layer Chromatography based on their Rf values, colours and resolutions on different solvent systems. GC-MS was used to identify compounds like: Hexadecanoic acid methyl ester, 9,12-Octadecadienoic acid methyl ester, 2,2,4,4-tetramethyl-1,3-cyclobutanediene, Pentadecanoic acid-14-methyl methyl ester, Hexadecanoic acid-2-hydroxyl propyl ester, 2(4H)-Benzofuranone-5,6,7,7a-tetrahydro-4,4,7a-trimethyl and many others. Antimicrobial screening was carried out on Escherichia coli, Staphylococcus aureus and Aspergillus niger using the agar well diffusion technique. The result shows that the extract exhibit antimicrobial activity with zones of inhibition in diameter. These results show that the plant exhibit antimicrobial activity and possess pharmacological characteristics, which could be applied in the production of potent drugs.