Indonesian Archipelago Research Articles

Whole genome sequence analysis of Salmonella Typhi in Papua New Guinea reveals an established population of genotype 2.1.7 sensitive to antimicrobials.

BackgroundTyphoid fever, a systemic infection caused by Salmonella enterica serovar Typhi, remains a considerable public health threat in impoverished regions within many low- and middle-income settings. However, we still lack a detailed understanding of the emergence, population structure, molecular mechanisms of antimicrobial resistance (AMR), and transmission dynamics of S. Typhi across many settings, particularly throughout the Asia-Pacific islands. Here we present a comprehensive whole genome sequence (WGS) based overview of S. Typhi populations circulating in Papua New Guinea (PNG) over 30 years.Principle findingsBioinformatic analysis of 86 S. Typhi isolates collected between 1980–2010 demonstrated that the population structure of PNG is dominated by a single genotype (2.1.7) that appears to have emerged in the Indonesian archipelago in the mid-twentieth century with minimal evidence of inter-country transmission. Genotypic and phenotypic data demonstrated that the PNG S. Typhi population appears to be susceptible to former first line drugs for treating typhoid fever (chloramphenicol, ampicillin and co-trimoxazole), as well as fluoroquinolones, third generation cephalosporins, and macrolides. PNG genotype 2.1.7 was genetically conserved, with very few deletions, and no evidence of plasmid or prophage acquisition. Genetic variation among this population was attributed to either single point mutations, or homologous recombination adjacent to repetitive ribosomal RNA operons.SignificanceAntimicrobials remain an effective option for the treatment of typhoid fever in PNG, along with other intervention strategies including improvements to water, sanitation and hygiene (WaSH) related infrastructure and potentially the introduction of Vi-conjugate vaccines. However, continued genomic surveillance is warranted to monitor for the emergence of AMR within local populations, or the introduction of AMR associated genotypes of S. Typhi in this setting.

Taxonomy, distribution, and conservation status of a rare arboreal lizard, Bronchocela hayeki (Mller, 1928) (Reptilia: Agamidae) from northern Sumatra, Indonesia.

Bronchocela hayeki (Mller, 1928) is one of the rarest species of the genus, known only from a handful of museum specimens from five locations in North Sumatra, and often confused with its similar congener, B. cristatella, which occurs widely throughout the Indonesian Archipelago and Peninsular Malaysia. Here, we examined the morphology of B. hayeki based on museum specimens, and redescribe the species based on a freshly collected series near the type locality, as the condition of its neotype is not in a good state. We studied the characters of B. hayeki with a morphometric comparison to its sympatric congener B. cristatella and allopatric congener, B. jubata from Sumatra Island, Indonesia. Based on the current distribution pattern and the apparent threats, we update the conservation status of B. hayeki using IUCN Red List Criteria and propose that it be considered as an Endangered (EN) species endemic of northern Sumatra including Aceh. We also provide a key to the recognized Bronchocela species, based on examined material and literature.

Efektivitas Farmakologi Senyawa Aktif Tumbuhan Mangrove Yang Hidup Di Indonesia

Mangroves are ecologically important plants in marine habitats that occupy the coastlines of several countries. Apart from their primary ecological importance, various parts of mangroves are widely used in traditional medicine and are claimed to be effective in treating various diseases. At present, no comprehensive effort has been made to compile and critically analyze the published literature in view of its ethnopharmacological utility. This review aims to provide a comprehensive overview of the biodiversity and distribution of mangrove plants, ethnopharmacology, phytochemical profiles, and pharmacological activities of mangrove plants used as traditional medicine in Indonesia. The method used is by using literature studies from the Science Direct, Pubmed, and Google Scholar database. Result show that In Indonesia, there are 33 types of mangrove species, all of which are traditionally used as medicine, which are spread throughout the archipelago in Indonesia. Bioactive compounds obtained from mangrove plants include polyphenols, flavonoids, alkaloids, carotenoids, tannins, saponins, steroids, amino acids, carbohydrates, proteins, vitamins etc. This review also shows that the pharmacological activities of mangrove plants in general include antimicrobials (such as antibacterial, antiviral and antifungal), anti-inflammatory, anti-ulcer, antidiarrheal, anticancer, antidiabetic, anti-HIV, antinociceptive, hepatoprotective, antiarthritis, analgesic, antioxidant and cytotoxic activities.

تنوع استخدام الحروف الهجائية كنظام كتابي جديد في كتابة الخط العربي الملايوي /الخظ العربي الجاوي

The progress of the civilization is considered to be the growth of their language, both between the mktaz and the written. The use of the Arabic alphabet has become in many Islamic civilizations, where it develops and diversifies its method in order to understand the Islamic religion. Such a civilization is the development of a new written system in the life of the Malay people, called the Malay Arabic script, which is a means of transmitting Islamic knowledge and knowledge by scholars to the Muslim community in the Indonesian archipelago. There are four letters added to the Arabic letters in the Jawi letters; The letter jim with an additional two-dot variation applies like the letter “c” in Indonesian, the letter “ain” with an additional three-dot difference above the letter and marked as “ng”, the letter fa with the additional two-dot variation reading “pa”, then the letter kaf with the addition of a dot The one on top reads “ga”, the letter nun with the addition of two dots reads “nya”, and finally the letter wawu with the addition of one dot at the top reading “Va”. What is the Arabic-Malay symbol? And how its develop? Is part of discussion in this article.

Sulawesi endemic tubers and perimedular flour properties an initial consideration for alternative sources for food starch ingredient

North Sulawesi is located in the North-Eastern regions of the Indonesian Archipelago. As it is with most parts of Indonesia, North Sulawesi is dependent on rice as their staple food. Not all islands within the North Sulawesi cluster of islands can grow paddy or corn for their carbohydrate needs or starch ingredients in their diet and must have them shipped from other places with the dire consequences of transportation costs. The endemic biodiversity of these islands also has many plants with the potential as an alternative food carbohydrate source. This study was to explore these endemic plants for potential food ingredients for starch replacements for rice and corn. The many diversities available for these starch ingredients amongst them are tuber sources (Taro – Colocasia esculenta, Dalugha – Cyrtosperma merkusii, Gembili – Discorea esculenta and Banggai – Discorea alata) and perimedular sources (Sago Tanah and Sago Baruk). Many studies have researched these plants individually in various originating from many other parts of the world, but not many have made a head-to-head comparison and explored the potentials of these underutilized plants as starch food ingredients. This study extracted starches of these plants in a standardized manner and compared the properties side-by-side. These plants were found to be potentially healthy alternatives to rice as functional food starch with lower digestibility which would lead to lower GI staples, especially for the livelihoods of North Sulawesi coastal dwellers.

HISTORICAL STAGES OF THE SPREAD OF ISLAM IN INDONESIA

Islam spread to a very large part of the world in the Middle Ages. Southeast Asia, especially Indonesia, did not remain aloof from these processes. The penetration and spread of Islam in the Indonesian archipelago dates back to the 9th-16th centuries. We can say that merchants, tourists, mystics, military men, and scientists also contributed to these historical processes. Indonesia is the most populous Muslim country in Southeast Asia. Indigenous peoples in this area practiced mainly Buddhism, Hinduism, Confucianism, and numerous other local polytheistic religions before Islam. The entry of Islam into the Indonesian archipelago and its transformation into one of the region’s major religions continued for several years. After the arrival of Islam in the region, the locals warmly welcomed the religion, seeing the culture and attitudes of Muslims towards other religions. Scholars have put forward several theories regarding the entry of Islam into the region. The article discusses in detail these theories and the views of their supporters. The most common of these theories is that Islam came to Indonesia through India, Arab traders, and China. Each of the above theories about the entry of Islam into the archipelago has its own evidence and historical sources. These views are also explored in the article. Scholars from Samarkand also played an important role in the spread of Islam in Indonesia. The article also examines the activities of these scholars.

Generation Expansion Planning Based on Local Renewable Energy Resources: A Case Study of the Isolated Ambon-Seram Power System

Energy sustainability has become one of the main issues in power system planning in the Indonesian archipelago system, which has many small, isolated systems. For that purpose, green and sustainable generation expansion planning (GEP) procedures based on local energy resources is required. GEP is a necessary procedure for fulfilling electricity demand, which determines the generating units to be installed within a specified time horizon with minimal total costs as the objective function. This study uses GEP considering the interconnection option among the existing small scattered generation systems in Maluku: the isolated Ambon, Seram, Haruku, and Saparua systems. With interconnection, the utilization of local renewable energy sources would be increased, especially biomass, which has abundant potential in these areas. The GEP was simulated in the PLEXOS environment using mixed-integer linear programming (MILP). For comparison purposes, there were interconnection and isolated system scenarios. The results showed that the interconnection system would have a high share of a renewable energy source (RES) of up to 54% in 2050, most of which is biomass as the primary local energy source. The interconnection system scenario met the LOLP criteria and had a lower reserve margin and total costs than the isolated scenario, with USD 773.7 million.

A crew-operated data recording system for length-based stock assessment of Indonesia's deep demersal fisheries.

Deep demersal fisheries in Indonesia yielded close to 90,000 metric tons of snapper and grouper in 2019, landed by a fleet of approximately 10,000 fishing boats. Prior to the present study, information on these multi-species, dispersed, small- to medium-scale fisheries was scarce, while reliable species-specific data on catch and effort were non-existent. This data-deficiency made stock assessments and design of harvest control rules impossible. We developed a new data collection method, the Crew Operated Data Recording System (CODRS), to collect verifiable species- and length-composition data from catches across all segments of the fleet. CODRS engaged crews of 579 fishing vessels to take pictures of each fish in their catch, in combination with the deployment of a tracking device on their boats. Furthermore, we also conducted a frame survey to map the fleet across the entire Indonesian archipelago. Using more than 2 million CODRS images, we aimed to understand the basic characteristics and challenges within the fishery. We updated life-history parameters for the top 50 species in the fishery based on the maximum observed length-frequency distribution of the catch (i.e., asymptotic length, size at maturity, optimum fishing length, total mortality, and spawning potential ratio). Length-based stock assessments using the updated life-history parameters showed high risks of overfishing for most of the major target species, especially for snapper species with large maximum sizes. Our results indicated that effective management and harvest strategies are urgently needed across Indonesia’s eleven Fishery Management Areas to prevent the collapse of these important fisheries.

Papua at the Crossroads: A Plea for Systematic Conservation Planning in One of the Largest Remaining Areas of Tropical Rainforest

Land-use change has progressed rapidly throughout the Indonesian archipelago and is now intruding into western New Guinea (Tanah Papua), one of the world’s last wilderness areas with extensive tracts of pristine and highly diverse tropical rainforests. Tanah Papua has reached a crossroads between accelerating environmental degradation and sustainable development policies entailing landscape-scale conservation targets, pledged in the Manokwari Declaration. We assessed the representation of ecoregions and elevational zones within Tanah Papua’s protected area network to identify its shortcomings at broad spatial scales. Lowland ecoregions are less protected than mountainous regions, with half of the western and southern lowlands designated for land-use concessions. Under the direct threat from land-use change, the political motivation in Tanah Papua toward conservation- and culture-centered land management provides a window of opportunity for scientifically guided, proactive conservation planning that integrates sustainable development for the benefit of Indigenous communities.

Human Trafficking on Illegal, Unreported and Unregulated Fishing Cases as Transnational Crime on Indonesia Coastal Boundary

Indonesian strategic archipelago allows rapid migration of goods and services to its neighbor countries. Along with goods and services, the wide coastal area also facilitates migrant worker to enter and exit Indonesia through several ports. First and foremost interference on the borderless coastal boundary is Illegal, Unreported and Unregulated (IUU) Fishing. The IUU foreign fishing vessels frequently transporting illegal migrant worker obtained through human trafficking, people smuggling, forced labor, child exploitation, torture, and discrimination. This practices can then be categorized as one of the transnational organized crime at sea. This paper focuses on the studies of notorious cases of human trafficking on IUU Fishing. This journal will also observe the lack of prevention measure of transnational crime on UNCLOS and utilization of bilateral and multilateral treaties on IUU Fishing.

Islam Nusantara and the Challenges of Political Islam in the Contemporary World

The purpose of this study is to investigate the most important challenges of Nusantara Islam with political Islam in the contemporary world. For this purpose, first the most important Islamic intellectual currents in Indonesia, namely traditional Islam, religious reformism and liberal Islam, are discussed. The religious reform movement in Indonesia has always been influenced by major Islamic centers in the Middle East such as Mecca, Medina and Cairo. The current of traditional Islam is in fact the heritage of Islamic culture of this region. Islam liberal is also influenced by modern Muslim thinkers such as Fadl al-Rahman. This article seeks to answer these questions of how the religious reform movement in the Malay world, especially in the pre-modern Indonesian archipelago, took shape and how the traditional movement reacted to it. Also, what are the most important features of Islamic thought and the current of religious reform and intellectualism in Indonesia? Finally, a picture of the situation of these three currents in Indonesia is drawn and the important role of Islam Nusantara in resolving the crises of the contemporary period is explained with emphasis on the thoughts of Abdul Rahman wahid.

Hexa Helix, participatory concept to support landslide early warning system

The Indonesian archipelago lies at triple junction between the world’s tectonic plates that have many natural disasters. Furthermore, Indonesia lies accross the equator which result in a tropical climate (dry and rainy seasons). During the rainy season, rainfall often triggers landslides. Landslides can be identified by the material type (soil, rock, or debris) and movement (slide, fall, flow, or combination). Landslide-prone areas can be influenced by lithology (rock type and weathering), slope (geomorphology), seismic vibrations (tectonic aspects), and human activities. In order to anticipate landslides, both structural and non-structural mitigation are required. Non-structural mitigation is required to determine the condition of rainfall, and the type of landslides. RAFLEWS (Rainfall Apparatus for Landslide Early Warning System) design model is a part of non-structural mitigation. Non-structural mitigation is also required to anticipate the possibility of landslides. Proposal of Hexa Helix participatory concept is a part for early warning system which will be useful in supporting non-structural mitigation. Hexa Helix consists of six participant elements, namely: Academia, Government, Society, Industry, Mass Media, and Laws/Regulations/Legislations. Combination of RAFLEWS model and Hexa Helix concept is expected to be influential in dealing with landslide disasters in the future.

THE URGENCY OF CULTURAL REVITALIZATION IN THE INDONESIA-MALAYSIA BORDER REGION

This study focuses on the cultural revitalization aspect as an urgent matter in the Indonesia-Malaysia border region, SajinganBesar Sub-district, Sambas Regency. The results of this study can be summarized that the main problem of cultural development in the border region is not only caused by globalization but also concerns on the condition of cultural resilience of the border communities themselves who have experienced stagnation which is from the conditions that are completely and inevitably marginal of Globalization, then it must be anticipated with cultural development that is characterized by the reinforcement of identity and local wisdom of the border community which is used as the basis for arranging strategies in preserving and developing culture. This study used a qualitative approach that was carried out by survey data, observation, analysis and FGD (Forum Group Discussion). This method is very effective for something that is urgent and important and will provide an increase in the welfare of the community whose life is generally less prosperous. Moreover, geopolitically, the cultural revitalization will further ensure the realization of the revitalization policy of the culture of the Indonesian Archipelago in the border region which can create nationalism, and maintain the border region from foreign infiltration as well as become a space for conflict resolution to create peace between countries.
 This study focuses on the cultural revitalization aspect as an urgent matter in the Indonesia-Malaysia border region, Sajingan Besar Sub-district, Sambas Regency. The results of this study can be summarized that the main problem of cultural development in the border region is not only caused by globalization but also concerns on the condition of cultural resilience of the border communities themselves who have experienced stagnation which is from the conditions that are completely and inevitably marginal of Globalization, then it must be anticipated with cultural development that is characterized by the reinforcement of identity and local wisdom of the border community which is used as the basis for arranging strategies in preserving and developing culture. This study used a qualitative approach that was carried out by survey data, observation, analysis and FGD (Forum Group Discussion). This method is very effective for something that is urgent and important and will provide an increase in the welfare of the community whose life is generally less prosperous. Moreover, geopolitically, the cultural revitalization will further ensure the realization of the revitalization policy of the culture of the Indonesian Archipelago in the border region which can create nationalism, and maintain the border region from foreign infiltration as well as become a space for conflict resolution to create peace between countries.

IMSS-BASED INDONESIAN DEFENSE CONCEPT MAP FOR THE SUNDA STRAIT REGION

The Indonesian Archipelago Seaway (ALKI) is a strategic area with heavy ship traffic. Starting with ships entering and exiting the Straits of Melaka (ALKI I), the Straits of Makassar (ALKI II) to the Papuaan waters (ALKI III).To protect and regulate seaway in Indonesian territorial waters, a centralized system is needed that can monitor all ships passing through Indonesian waters.Integrated Maritime Surveillance System (IMSS) is one of the latest technologies used by the militaries in many countries. Indonesia is one of the countries that has beganto implement IMSS in the marine defense system.In this paper, we conduct an evaluation of the IMSS concept in Indonesian waters to improve the seaway security. The results of the study conducted show thatthe implementation of monitoring systems using IMSS systems is important and needs to be implemented, especially in the ALKI I region, especially in the Sunda Strait. This requires good performance and coordination between the people and departments responsible for their respective responsibilities and functions. In practice, however, leadership in implementing information systems development and implementing IMSS-based oversight within the Navy still faces various hurdles.

The Spread of “Tradisi Mandi Uap” as a Track Identification of Spices in Indonesia

The presence of spices in the archipelago became one of the pioneers for various cultural manifestations that appeared in various regions of the Indonesian archipelago. One form of the presence of spices that is reflected in this cultural form is the traditional steam bath tradition. The aims of the study were to 1) describe the distribution of bathing habits using spice water in several regions in the Indonesian archipelago. 2) mapping the distribution plots of spices in the archipelago through local traditions that have existed and are still alive in the community in certain areas of the archipelago; 3) showing the traditional steam bath tradition which has become a habit and has the potential to become an intangible cultural heritage in Indonesia. In conducting the study, it was used to search for sources of information from literature studies related to the spice bath tradition. The method used is a qualitative method by describing a map of the distribution of the spice bath tradition in the regions of the archipelago. The results of the study show that traditional steam bathing is a spice bath tradition that is spread across the eight regions in Indonesia and is dominated by people who have a background of Malay cultural influence. The eight areas include North Sumatra (Batak Karo), Jambi (Tanjung Bajo Village), Palembang, Pontianak (Mempawah), West Kalimantan (Sintang Regency), Sambas Regency, North Kayong Regency (Pangkalan Buton Village), and East Belitung

Making impact: Towards discovering early projectile technology in Island South East Asian archaeology

Development of projectile hunting tools remains a significant tenant associated with modern humans' adaptive and migratory success. Technological innovations which accompanied the human odyssey between the now submerged ice-age shelves of Sunda and Sahul (the first major sea crossings by our species) are amongst the most decisive topics of human evolution today. With recent discoveries affirming the Indonesian archipelago's importance as a hub for these studies, technological records remain essential to reveal details of early human life across this strategic region. One such adaption, projectile technology, may appear quintessentially an early human technology, although this review shows projectile tools are poorly documented across Island South East Asia (ISEA), prior to the onset of major climatic change at the close of the last ice-age. Records of hunting and subsistence related to projectile technology, include flaked stone and osseous tools, rock art, and historical records – each reviewed here, to produce a vanguard methodological approach for identification of projectile tools in the early archaeological records of ISEA. Traceology backed by empirical data and contextualised within tool life histories, are found to be of dire need to advance the archaeological understanding of technological adaptations. Methodological advances elsewhere, outlay the latest techniques in recognising projectile tools, here adapted to the unique and globally relevant study area, spanning the extant lands and islands of Eastern Sunda, to Sahul.

The Tanah-Air Concept and Indonesia’s Maritime Nation Aspiration

This article analyses the Tanah-Air (Unity of Land-Water) concept conceived by Indonesian founding fathers during its independence period and its centrality in shaping the nation’s maritime outlook. Specifically, using descriptive historical analytical approach, it would like to emphasize the role of intersection of Indonesia’s political culture of national unity (Persatuan Nasional), strategic culture of turning of the ages of Nusantara (Cakra Manggilingan), and geopolitical outlook of archipelago’s heart seas (Segara Nusantara) as the three forming pillars of the Tanah-Air concept. Based on these intersections, it underlines unique contradictions within the Tanah-Air concept between need for unity and oneness of land-sea elements of the Indonesian archipelago and the concentric Javanese philosophy on the sea and its maritime power aspirations. Based on these contradictions and insight of the ‘Tanah-Air’ concept, the article provides a pragmatic view on Indonesia’s current aspiration of moving beyond archipelagic to maritime nation as stipulated in the 2014 Global Maritime Fulcrum Doctrine and 2017 Sea Policy Whitepaper.

Revealing Spanish mackerel’s diversity in Indonesian through local commodities in the fish market

Abstract. Widayanti R, Nugroho HA, Megarani DV, Widiasih DA, Pakpahan S. 2021. Revealing Spanish mackerel’s diversity in Indonesian through local commodities in the fish market. Biodiversitas 23: 624-630. The objective of this study was to explore the diversity of Spanish mackerel in Indonesian Archipelago based on commodities offered in local fish markets. Eighteen specimens were collected from six different fish markets around the Indonesian archipelago. According to Wallace Line, the cytochrome B sequence was used as a genetic marker to reveal diversity from West Indonesia to East Indonesia. Gene amplification was performed using the polymerase chain reaction followed by Sanger sequencing. Based on DNA sequence analysis, we identified three species of Spanish Mackerel available at various fish markets around the region. The first group is related to Scomberomorus commerson, which was sold in both Western and Eastern Indonesian fish markets; the second group is related to Scomberomorus semifasciatus, which was sold in Eastern Indonesian fish markets; and the third group is related to Scomberomorus koreanus, which was sold in Western Indonesian fish markets. The genetic differences amongst Spanish Mackerel populations ranged from 0 to 17% and the average evolutionary divergence in the overall populations was determined to be 4%. The data collected can be utilized to initiate map mackerel diversity based on CYT B sequence throughout the Indonesian Archipelago, as well as for further study and application in the identification of foods produced from mackerel.

Hyperendemic Dengue and Possible Zika Circulation in the Westernmost Region of the Indonesian Archipelago.

The transmission of dengue and other medically important mosquito-borne viruses in the westernmost region of Indonesia is not well described. We assessed dengue and Zika virus seroprevalence in Aceh province, the westernmost area of the Indonesian archipelago. Serum samples collected from 199 randomly sampled healthy residents of Aceh Jaya in 2017 were analyzed for neutralizing antibodies by plaque reduction neutralization test (PRNT). Almost all study participants (198/199; 99.5%) presented with multitypic profiles of neutralizing antibodies to two or more DENV serotypes, indicating transmission of multiple DENV in the region prior to 2017. All residents were exposed to one or more DENV serotypes by the age of 30 years. The highest geometric mean titers were measured for DENV-4, followed by DENV-1, DENV-2 and DENV-3. Among a subset of 116 sera, 27 neutralized ZIKV with a high stringency (20 with PRNT90 > 10 and 7 with PRNT90 > 40). This study showed that DENV is hyperendemic in the westernmost region of the Indonesian archipelago and suggested that ZIKV may have circulated prior to 2017.

Molecular ecology of a shallow water shrimp, Acetes sibogae sibogae Hansen 1919: Evidence for strongly limited gene flow across the western Pacific

AbstractThe shallow water shrimp Acetes sibogae sibogae is an ecological and economically important organism in the Asian region. We assessed the genetic diversity and population structure of this species based on samples obtained from eight sites in Japan, the Philippines and Indonesia. Nucleotide sequence analyses were performed based on PCR‐amplified mitochondrial DNA fragments comprising the control region and part of the 12S rRNA gene. In total, 656 bp nucleotide sequences were obtained from 377 individuals. The results show a low haplotype diversity value in shrimp from the Kokuba‐gawa River (0.5) in Japan and intermediate values (0.79–0.99) in other populations. While nucleotide diversity estimates in all sampled localities were lower (0.17%–0.86%) than those reported in other crustaceans, analysis of molecular variance revealed significant genetic differentiation (p < .001) among all sites. Furthermore, the mean fixation index estimate was very high (FST: 0.27), indicating that dispersal potential among sites was low and gene flow, therefore, was restricted. The mismatch distribution of pairwise differences between haplotypes indicated that A. s. sibogae did not fit a sudden population expansion model. Overall, the present study indicates that wild stocks of A. s. sibogae on Okinawa‐jima Island and the Philippine and Indonesian Archipelagos should be assigned high importance for conservation management of this species because adapted genotypes have significant evolutionary potential during environmental changes.[Correction added on 5th February 2022, after first online publication: Values have been corrected in the Abstract section.]