Mahalanobis distances for ecological niche modelling and outlier detection: implications of sample size, error, and bias for selecting and parameterising a multivariate location and scatter method

The Mahalanobis distance is a statistical technique that has been used in statistics and data science for data classification and outlier detection, and in ecology to quantify species-environment relationships in habitat and ecological niche models. Mahalanobis distances are based on the location and scatter of a multivariate normal distribution, and can measure how distant any point in space is from the centre of this kind of distribution. Three different methods for calculating the multivariate location and scatter are commonly used: the sample mean and variance-covariance, the minimum covariance determinant, and the minimum volume ellipsoid. The minimum covariance determinant and minimum volume ellipsoid were developed to be robust to outliers by minimising the multivariate location and scatter for a subset of the full sample, with the proportion of the full sample forming the subset being controlled by a user-defined parameter. This outlier robustness means the minimum covariance determinant and the minimum volume ellipsoid are highly relevant for ecological niche analyses, which are usually based on natural history observations that are likely to contain errors. However, natural history observations will also contain extreme bias, to which the minimum covariance determinant and the minimum volume ellipsoid will also be sensitive. To provide guidance for selecting and parameterising a multivariate location and scatter method, a series of virtual ecological niche modelling experiments were conducted to demonstrate the performance of each multivariate location and scatter method under different levels of sample size, errors, and bias. The results show that there is no optimal modelling approach, and that choices need to be made based on the individual data and question. The sample mean and variance-covariance method will perform best on very small sample sizes if the data are free of error and bias. At larger sample sizes the minimum covariance determinant and minimum volume ellipsoid methods perform as well or better, but only if they are appropriately parameterised. Modellers who are more concerned about the prevalence of errors should retain a smaller proportion of the full data set, while modellers more concerned about the prevalence of bias should retain a larger proportion of the full data set. I conclude that Mahalanobis distances are a useful niche modelling technique, but only for questions relating to the fundamental niche of a species where the assumption of multivariate normality is reasonable. Users of the minimum covariance determinant and minimum volume ellipsoid methods must also clearly report their parameterisations so that the results can be interpreted correctly.

Identifikasi Plant Growth Promoting Rhizobacteria pada Rizosfer Bambu Duri dengan Gram KOH 3%

<p class="Abstract">Plant Growth Promoting Rhizobacteria is a group of microorganism that is able to increase plant growth and yield through reactions in the soil, but the large number of microorganisms contained in PGPR's rhizosphere from thorn bamboo make it difficult to know which bacteria are the most dominant and most active in influencing plants. This study aimed to determine the effect of using the 3% gram KOH test method in identifying PGPR bacteria from the thorn bamboo rhizosphere. This test was carried out at the Biofertilizer and Potential Microbial Laboratory, Faculty of Agriculture, Universitas Hasanuddin from October-December 2019. The testing methods include making microorganism growing media, pouring media, planting bacteria with the scatter and scratch methods, also the gram reaction test using KOH 3%. The results obtained the use of the 3% gram KOH test method in the scatter method showed there were 2 samples that have mucus with a percentage of 40%, while in the scratch method showed all samples have mucus with a percentage of 100% so that the use of the 3% gram KOH test method has an optimum effect in detecting microorganisms especially in identifying plant growth promoting rhizobacteria.</p>

IDENTIFIKASI BAKTERI PATOGEN PENYEBAB PENYAKIT PURPLE SYNDROME PADA KARANG FUNGIA DI PULAU HARI SULAWESI TENGGARA

IDENTIFIKASI BAKTERI PATOGEN PENYEBAB PENYAKIT PURPLE SYNDROME PADA KARANG FUNGIA DI PULAU HARI SULAWESI TENGGARA Nowadays coral disease is one of the causes of damage to coral reefs in Indonesia. Causative agents were found for some types of coral disease. This study aims to identify the type of pathogenic bacteria that cause purple syndrome which attacks Fungia corals. The study was conducted using descriptive exploratory methods. Corals infected with purple syndrome were collected on Pulau Hari, Southeast Sulawesi, through scuba diving. Then, microbiological analysis was carried out which included isolation using the scatter method, purification using a scratch method, a challenge test (antagonistic), a Koch Postulate test, and DNA analysis of putative bacterial isolates. Results showed that 5 bacterial isolates lived in symbiosis with the corals infected with purple syndrome (PSMH1, PSMH2, PSMH3, PSMH4, and PSMH5). Based on the Koch postulate test, 2 bacterial isolates which were pathogenic were obtained, namely PSHM2 and PSHM4 isolates. These bacteria infected the test corals with the characteristics of coral skeleton damage and coral bleaching (dead). Based on biomolecular testing, the two isolates were members of Enterobacter cloacae with a 99% similarity level.Keywords: Coral disease; Enterobacter cloacae; Fungia coral; Hari island; Purple syndromeABSTRAKSaat ini penyakit karang menjadi salah satu penyebab kerusakan terumbu karang di Indonesia. Penyebab pembawa untuk beberapa jenis penyakit karang sudah ditemukan. Penelitian ini bertujuan untuk mengidentifikasi jenis bakteri patogen penyebab penyakit purple syndrome yang menyerang karang Fungia. Penelitian dilakukan menggunakan metode deskriptif eksploratif. Sampel karang yang terinfeksi purple syndrome diambil di Pulau Hari, Sulawesi Tenggara, melalui scuba diving. Selanjutnya, analisis mikrobiologi dilakukan yang meliputi isolasi menggunakan metode sebar, purifikasi menggunakan metode gores, uji tantang (antagonistik), uji Postulat Koch, dan analisa DNA isolat bakteri yang diduga bersifat patogen. Hasil penelitian menemukan 5 isolat bakteri yang bersimbiosis dengan karang yang terinfeksi penyakit purple syndrome (PSMH1, PSMH2, PSMH3, PSMH4, dan PSMH5). Berdasarkan uji postulat Koch, 2 isolat bakteri yang bersifat patogen didapatkan, yaitu isolat PSHM2 dan PSHM4. Bakteri tersebut menginfeksi karang uji dengan ciri kerusakan skeleton karang dan pemutihan karang (mati). Berdasarkan uji biomolekuler kedua isolat tersebut merupakan anggota Enterobacter cloacae dengan tingkat kemiripan 99%.

Measurement of the Cellular Hemoglobin Concentration by Laser Scatter Method from Excessive Lipemic Sample: CASE REPORT

A 33-month old female child presented at a pediatric clinic with acute tonsillitis, and it was subsequently discovered that she had familial hyperlipidemia. Measurement of the patient’s whole blood tests was performed by a multiparameter automated hematology analyzer, the CELLDYN Ruby System&#174; (Abbott, Lake Forest, USA) using venous blood extracted from a tube containing 3.0 mL of EDTA. Although her hematocrit levels were within normal limits, the hemoglobin (Hgb) level, mean corpuscular volume (MCH) and mean corpuscular Hgb concentration (MCHC) could not be determined using the spectrophotometric method. The results of these tests could not be measured when repeated using dilution. When the sample was left to rest for several minutes, it was observed to be excessively lipemic. The measurements were repeated using the Alinity HQ Analyzer&#174; (Abbott), which determines Hgb concentration using laser scatter and spectrophotometry. Hgb cellular concentration was incorrectly measured as being 21.9 mg/dL using routine spectrophotometry (denoted by a flag indicating Hgb interference) and correctly found to be 10.8 mg/dL. Thus, in samples of excessive lipemia, Hgb, MCH, and MCHC levels cannot be measured accurately using spectrophotometry. Hematology analyzers that can measure cellular hemoglobin (cHGB) and average erythrocyte hemoglobin concentration (cHCM) by laser scatter method may be recommended when analyzing a blood sample that contains excessive lipemia.

Isolasi bakteri probiotik Lactobacillus sp dari usus ikan mas (Cyprinus carpio)

The objective of research was to isolate the probiotic bacteria from intestine of carp. Isolation was performed by weighing 1 g of intestine, crushed and inserted in a reaction tube containing 9 mL of NaCl then centrifuged. Supernatant was taken and spread over the agar medium by scatter method. The bacteria-stocked medium was then incubated in an incubator at 28°C for 24-48 hours. The growing colonies were re-isolated on the agar medium to obtain pure colonies. The bacteria were then identified by morphological observation, resulting pigment and gram staining. Five nile tilapia (sized 8 – 10 cm) were used in pathogenicity test and placed in the aquarium. Fish were injected with 0.2 ml of Lactobacillus solution containing 1x107 CFU/mL via intraperitoneal injection. The results showed that the bacteria Lactobacillus sp had rod-shaped characteristics, white pigment and gram positive and not pathogenic, which means it can be used as probiotic for aquaculture.Keywords : Lactobacillus sp, carp, probiotic, pathogenicity test