High Amino Research Articles

Physiological, metabolic and hormonal responses of two Pinus spp. with contrasting susceptibility to brown-spot needle blight disease.

Needle blights are serious fungal diseases affecting European natural and planted pine forests. Brown-spot needle blight (BSNB) disease, caused by the fungus Lecanosticta acicola, causes canopy defoliation and severe productivity losses, with consequences depending on host susceptibility. To gain new insights into BSNB plant-pathogen interactions, constitutive and pathogen-induced traits were assessed in two host species with differential disease susceptibility. Six-month-old Pinus radiata D. Don (susceptible) and Pinus pinea L. (more resistant) seedlings were needle inoculated with L. acicola under controlled conditions. Eighty days after inoculation, healthy-looking needles from symptomatic plants were assessed for physiological parameters and sampled for biochemical analysis. Disease progression, plant growth, leaf gas-exchanges and biochemical parameters were complemented with hormonal and untargeted primary metabolism analysis and integrated for a holistic analysis. Constitutive differences between pine species were observed. Pinus pinea presented higher stomatal conductance and transpiration rate and higher amino and organic acids, abscisic acid as well as putrescine content than P. radiata. Symptoms from BSNB disease were observed in 54.54% of P. radiata and 45.45% of P. pinea seedlings, being more pronounced and generalized in P. radiata. For both species, plant height, sub-stomatal CO2 concentration and water-use efficiency were impacted by infection. In P. radiata, total soluble sugars, starch and total flavonoids content increased after infection. No differences in hormone content after infection were observed. However, secondary metabolism was induced in P. pinea visible through total phenolics, flavonoids and putrescine accumulation. Overall, the observed results suggest that P. pinea constitutive and induced traits may function as two layers of a defence strategy which contributed to an increased BSNB resistance in comparison with P. radiata. This is the first integrative study linking plant physiological and molecular traits in Pinus-Lecanosticta acicola pathosystem, contributing to a better understanding of the underlying resistance mechanisms to BSNB disease in pines.

Blood and faecal biomarkers to assess dietary energy, protein and amino acid efficiency of utilization by growing and finishing pigs

BackgroundDiet evaluation and optimization is a slow and expensive process and it is not possible to do it at a farm level. This study aimed to use the blood serum metabolite (BSM) and faecal volatile fatty acid (VFA) profiles as potential biomarkers to identify changes in protein, amino acid and energy dietary content in growing and finishing pig diets at farm level.ResultsTwo studies were conducted. The first study (S1) included 20 pens of 11 pigs (87.0 ± 4.10 kg; 18 weeks old) assigned to 5 diets: control (C1), high or low crude protein (HP1 and LP1, respectively), and high or low net energy (HE1 and LE1, respectively). The second study (S2) included 28 pens of 11 pigs (41.3 ± 2.60 kg; 12 weeks old) assigned to 7 diets: control (C2), high or low crude protein (HP2 and LP2, respectively), high or low amino acid (HA2 and LA2, respectively), and high or low net energy (HE2 and LE2, respectively). Pigs were followed for 10 (S1) and 20 (S2) days, and blood and faecal samples were collected at 20 (S1) and 14 (S2) weeks of age. Data were analysed using general linear models and receiver operating characteristic curve analysis. Urea nitrogen showed the best results as a biomarker. Urea nitrogen was higher in pigs fed high protein diets, HP1 (13.6 ± 0.95 mg/dL) and HP2 (11.6 ± 0.61), compared to those fed low protein diets, LP1 (6.0 ± 0.95) and LP2 (5.2 ± 0.61; P < 0.001), showing good discrimination ability (Area under the curve (AUC) = 98.4 and 100%, respectively). These differences were not observed between diets LA2 (6.5 ± 0.61) and HA2 (8.7 ± 0.61; P > 0.05; AUC = 71.9%), which were formulated based on the ideal protein profile but with no excess of protein. Creatinine, triglycerides, branched-chain fatty acids, albumin, propionic acid, and cholesterol showed differences between at least 2 diets but only in one of the studies.ConclusionsUrea nitrogen showed high accuracy to detect excess of crude protein in growing and finishing pig diets. Other biomarkers like BCFA showed promising results and need to be further studied.

Expression of fatty acid synthase genes and their role in development and arboviral infection of Aedes aegypti

BackgroundFatty acids are the building blocks of complex lipids essential for living organisms. In mosquitoes, fatty acids are involved in cell membrane production, energy conservation and expenditure, innate immunity, development and reproduction. Fatty acids are synthesized by a multifunctional enzyme complex called fatty acid synthase (FAS). Several paralogues of FAS were found in the Aedes aegypti mosquito. However, the molecular characteristics and expression of some of these paralogues have not been investigated.MethodsGenome assemblies of Ae. aegypti were analyzed, and orthologues of human FAS was identified. Phylogenetic analysis and in silico molecular characterization were performed to identify the functional domains of the Ae. aegypti FAS (AaFAS). Quantitative analysis and loss-of-function experiments were performed to determine the significance of different AaFAS transcripts in various stages of development, expression following different diets and the impact of AaFAS on dengue virus, serotype 2 (DENV2) infection and transmission.ResultsWe identified seven putative FAS genes in the Ae. aegypti genome assembly, based on nucleotide similarity to the FAS proteins (tBLASTn) of humans, other mosquitoes and invertebrates. Bioinformatics and molecular analyses suggested that only five of the AaFAS genes produce mRNA and therefore represent complete gene models. Expression levels of AaFAS varied among developmental stages and between male and female Ae. aegypti. Quantitative analyses revealed that expression of AaFAS1, the putative orthologue of the human FAS, was highest in adult females. Transient knockdown (KD) of AaFAS1 did not induce a complete compensation by other AaFAS genes but limited DENV2 infection of Aag2 cells in culture and the midgut of the mosquito.ConclusionAaFAS1 is the predominant AaFAS in adult mosquitoes. It has the highest amino acid similarity to human FAS and contains all enzymatic domains typical of human FAS. AaFAS1 also facilitated DENV2 replication in both cell culture and in mosquito midguts. Our data suggest that AaFAS1 may play a role in transmission of dengue viruses and could represent a target for intervention strategies.Graphical

P215. Higher amino acid demand in portal drained viscera of post-wean piglets

P215. Higher amino acid demand in portal drained viscera of post-wean piglets

Molecular characteristics of the full-length genome of occult hepatitis B virus from blood donors in China

The characteristics of a large sample size of the full-length genome of occult hepatitis B virus (HBV) infection (OBI) have not been extensively explored in China. Voluntary blood donors who were HBsAg-negative/HBV NAT-positive (HBsAg−/HBV NAT+) were identified by blood screening and recruited. Blood samples were tested for HBV serologic markers, viral loads, and PCR to identify OBI. HBV full-length genomes were obtained by amplifying two fragments using nested PCR. The characterization of OBI strains was based on sequence analyses compared with HBsAg+ strains obtained from the same donor population. Of the 50 full-length genomes of 172 identified OBI strains, 33 were classified as genotype B (OBIB) and 17 strains as genotype C (OBIC). Significantly higher nucleotide variabilities were observed in the Pre-S2/S promoter region (SP2) and core upstream regulatory sequence (CURS) in OBIB than in their HBsAg+ controls (P < 0.05). Both OBIB and OBIC showed higher amino acid (aa) variabilities in Pol and Pre-S/S regions than their controls (P < 0.05). In addition, 19 novel OBI-related mutations were found spanning the four open reading frames (ORFs) of the HBV genome. Four novel deletions and one novel insertion were also found in OBIC strains. Several novel OBI-related mutations spanning the four ORFs of the virus were identified by characterizing a large sample size of the full-length OBI genome, which may affect the production of HBsAg and contribute to the occult infection of HBV.

Epidemiological Evidence for Fecal-Oral Transmission of Murine Kobuvirus.

BackgroundMurine Kobuvirus (MuKV) is a novel picornavirus of the genus Kobuvirus, and was first identified in the feces of murine rodents in the USA in 2011. There is limited information on the transmission route of MuKV. Thus, we conducted a study to investigate virus detection rates in fecal, serum, throat, and lung tissue samples from murine rodents.ResultsA total of 413 fecal samples, 385 lung samples, 269 throat swab samples, and 183 serum samples were collected from 413 murine rodents (Rattus norvegicus, Rattus tanezumi, and Rattus rattus) captured in urban Shenzhen. Kobuviruses were detected via RT-PCR. Only fecal samples were positive, with prevalence rates of 34.9% in Rattus norvegicus and 29.4% in Rattus tanezumi. Phylogenetic analysis based on partial 3D and complete VP1 sequence regions indicated that all of the MuKV sequences obtained belonged to Aichivirus A, and were genetically closely related to other MuKVs reported in China, Hungary, and the USA. Twenty-eight full-length MuKV sequences were acquired. Phylogenetic analysis of two sequences randomly selected from the two species (SZ59 and SZ171) indicated that they shared very high nucleotide and amino acid identity with one another (94.0 and 99.3%, respectively), and comparison with human Kobuvirus revealed amino acid identity values of ~80%. Additionally, a sewage-derived sequence shared high similarity with the rat-derived sequences identified in this study, with respective nucleotide and amino acid identity values from 86.5 and 90.7% to 87.2 and 91.1%.ConclusionThe results of the current study provide evidence that murine Kobuvirus is transmitted via the fecal-oral route.

Evaluation of Nutritional, Physico-Chemical and Function Properties of Cactus Pear Opuntia ficus-indica (L.) Pulp and Cladode: A Comparative Study

The objective of this research was to evaluation of chemical, functional, and nutritional components of both pulp and cladode. The results indicated that cladode had higher moisture content (90.7%) and ash content (1.54%) compared to the pulp. While the cladode showed higher amount of protein content (1.08%), crude fiber (3.03%), crude fat (0.63%) and total carbohydrate (17.2%) compared to cladode. The significantly (P ≤ 0.05) higher pH (6.96), TSS (18.45 °Brix) and titratable acidity (0.18%) were recorded in pulp of cactus pear compared to cladode. The range of mineral contents such as magnesium, potassium, calcium, copper and zink were recorded between (0.16–96.45), (2.34–16.23), (5.64–16.65), (27.16–33.55), and (50.56–65.94) (μg/100 g DW), respectively. It could be noticed that pulp of cactus pear had a higher content of vitamin C(75.07 mg/100 g FW) and lower content of carotenoids (2.41 μg/ml FW) as compared to cladode. The statically significant (P ≤0.05) and higher amino acids were found in cladode of cactus pear; the Valine (0.40–3.71 g/100 g) and Serine (1.74–3.34 g/100 g) were found higher in cladode. The high phenolic (2.2 g/100 g) and tannin content (2.55 g/100 g) compared to cladode extract 1.03 g/100 g (2.34 g/100 g) on dry basis, respectively. Phytic acid content was higher in cladode (0.55 g/100 g DW) than in the pulp (0.34 g/100 g DW). Pulp and cladode values were similar to each other for Sophisticated analytical Saponins contents 0.55 g/100 g DW. Sophisticated analytical approaches will promote the use of the cactus plants in foods, medicines, cosmetics and pharmaceutical industries.

Effect of Bacillus amyloliquefaciens and Bacillus subtilis on fermentation, dynamics of bacterial community and their functional shifts of whole-plant corn silage

BackgroundBacillus amyloliquefaciens (BA) and Bacillus subtilis (BS) are usually used as feed supplements directly or bacterial inoculants in biological feeds for animals. However, few research have reported the effects of BA and BS on fermentation characteristics and bacterial community successions of whole-plant corn silage during ensiling. If the BA and BS inoculants have positive effects on silages, then they could not only improve fermentation characteristics, but also deliver BA or BS viable cells to ruminants, which would play its probiotic effect. Therefore, the objectives of this study were to investigate the effects of BA and BS on the fermentation, chemical characteristics, bacterial community and their metabolic pathway of whole-plant corn silage.ResultsFreshly chopped whole-plant corn was inoculated without or with BA and BS, respectively, and ensiled for 1, 3, 7, 14 and 60 d. Results showed that BA and BS inoculations increased lactic acid concentrations of whole-plant corn silages compared with control, and BA inoculation decreased acetic acid concentrations, whereas BS inoculation decreased fiber contents and increased crude protein (CP) content. Higher water-soluble carbohydrate contents and lower starch contents were observed in BA- and BS-inoculated silages compared with that in control. The decreased CP content and increased non-protein nitrogen content were observed in BA-inoculated silage, which was consistent with the higher amino acid metabolism abundances observed in BA-inoculated silage. In addition, it was noteworthy that BA and BS inoculations increased the metabolism of cofactors and vitamins, and decreased the relative abundances of drug resistance: antimicrobial pathways. We also found that the bacterial metabolism pathways were clearly separated into three clusters based on the ensiling times of whole-plant corn silage in the present study. There were no significant differences in bacterial community compositions among the three groups during ensiling. However, BA and BS inoculations decreased the relative abundances of undesirable bacteria such as Acetobacter and Acinetobacter.ConclusionOur findings suggested that the BS strain was more suitable as silage inoculants than the BA strain in whole-plant corn silage in this study.

The Evaluation of Oyster Marinating (Crassostrea Gasar) and Pasteurization Process in Vacuum Packaging during Storage

ABSTRACT The evaluation of oyster marinating (Crassostrea gasar) and pasteurization process in vacuum packaging during storage. The aim of this study was to establish better conditions for marinating and pasteurization for oysters (Crassostrea gasar) and to evaluate their shelf life. Microbiological, physicochemical and sensory analyzes were carried out on the oysters and on the optimized product. In the vacuum-packed product, under refrigeration, pH, water activity (aw), total volatile bases (N-TVB) and texture analyzes were performed, every 7 days for 35 days. Oysters had a high protein, mineral and amino acid content and a low lipid content. Planning 23 and 221 hour, 2.5% acetic acid, 1% NaCl and pasteurization was 62°C/2 min. Sensory analysis achieved acceptability above 80%. Marinated oysters remained suitable for consumption for 21 days, being an alternative to extend the shelf life and add value.

BIOLOGICAL VALUE OF EDIBLE HEN EGGS SOLD ON THE MARKET OF THE REPUBLIC OF BELARUS

The article presents the results of studies on the biological value of chicken eggs of various weight categories, developed at one of the domestic poultry farms in accordance with two regulatory documents. It has been established that eggs from modern poultry crosses have a high biological value, since they do not contain essential amino acids limiting the biological value and a balanced composition of essential amino acids. INAC of food chicken eggs samples differs from the standard by 0.35-0.47 units. The utilitarian coefficient of the amino acid composition is in the range of 0.68–0.77, the indicator of comparable redundancy is quite close to the standard and is 0.1–0.16. Of the studied weight categories, eggs of the highest category have the highest amino acid balance.&#x0D; The high percentage of satisfaction of the daily requirement for essential amino acids (by 40.3–62.7 % with the consumption of 100 g of egg mass), as well as the high balance of the amino acid composition, allow us to conclude that modern chicken eggs sold on the market of the Republic of Belarus, are a valuable food product that provides consumers with all vital essential amino acids.

The Effect of L-Glutamine on Basal Albumen and Yolk Indices, and Albumen Amino Acids Composition

Simple SummaryAt present, with increased consumers’ focus on eating healthy, it is expected that egg protein content and amino acids profile are among the components of eggs that play critical roles in egg selection. Thus, this research investigated the effect dietary L-glutamine supplementation has on basal albumen and yolk indices as well as albumen protein amino acid profile. The study shows a potential role of L-glutamine supplementation for enhancing nutritional values of eggs by the decrease of albumen lipid content and the change of amino acid profile.The current study tested the hypothesis that 1.0% dietary inclusion of L-glutamine (Gln), an non-essential amino acid that influences protein synthesis, can improve internal egg quality, including amino acids profile. Thirty-week-old Bovans Brown laying hens in their middle laying period were assigned to one of the two experimental groups (12 replicate cages, 2 hens/cage) with Gln in the form of alpha-ketoglutarate (10 g/kg) or without Gln inclusion. The experimental period lasted for 30 wks, from the 31st to the 60th week of age of hens, when eggs were collected and selected egg quality indices were determined. Gln supplementation had no effect on albumen and egg yolk share, albumen and yolk basal indices and composition, including yolk cholesterol content. However, Gln decreased the lipid content of the egg albumen (p < 0.001), and influenced albumen amino acid profile, increasing content of asparagine (p < 0.05), phenylalanine (p < 0.05), proline (p < 0.001), tryptophan (p < 0.01), and tyrosine (p < 0.05). In conclusion, the study shows a potential role of Gln supplementation for enhancing nutritional values of eggs by lower lipid content and higher amino acid profile.

Multiple novel filamentous phages detected in the cloacal swab samples of birds using viral metagenomics approach

Members of the family Inoviridae (inoviruses) are characterized by their unique filamentous morphology and infection cycle. The viral genome of inovirus is able to integrate into the host genome and continuously releases virions without lysing the host, establishing chronic infection. A large number of inoviruses have been obtained from microbial genomes and metagenomes recently, but putative novel inoviruses remaining to be identified. Here, using viral metagenomics, we identified four novel inoviruses from cloacal swab samples of wild and breeding birds. The circular genome of those four inoviruses are 6732 to 7709 nt in length with 51.4% to 56.5% GC content and encodes 9 to 13 open reading frames, respectively. The zonula occludens toxin gene implicated in the virulence of pathogenic host bacteria were identified in all four inoviruses and shared the highest amino acid sequences identity (< 37.3%) to other reference strains belonging to different genera of the family Inoviridae and among themselves. Phylogenetic analysis indicated that all the four inoviruses were genetically far away from other strains belonging to the family Inoviridae and formed an independent clade. According to the genetic distance-based criteria, all the four inoviruses identified in the present study respectively belong to four novel putative genera in the family Inoviridae.

Walker-256 Tumour-Induced Cachexia Altered Liver Metabolomic Profile and Function in Weanling and Adult Rats.

Cancer cachexia occurs in up to 85% of advanced cancer patients, affecting different tissues and organs, mainly the liver, which plays a central role in body metabolism control. However, liver responses to cancer cachexia progression are still poorly understood. Considering the possible different challenges provided by the rodent’s phase of life and the cachexia progression, we evaluated the liver metabolic alterations affected by Walker-256 tumour growth in weanling and young-adult rats. For this, we applied a metabolomics approach associated with protein and gene expression analyses. Higher amino acid levels and impaired glucose metabolism were important features in tumour-bearing animals’ liver tissue. The weanling hosts had more pronounced cachexia, with higher carcass spoliation, liver lipid metabolism and impaired CII and CIV mitochondrial complexes. The liver alterations in young adult tumour-bearing rats were related to energy status and nucleotide metabolites, such as uridine, NAD+, xanthosine, hypoxanthine and inosine. In conclusion, the Walker-256 tumour-induced cachexia impaired liver metabolism, being more severe in the weanling hosts. Further studies are needed to correlate these changes in the preclinical model, which can be correlated to the clinical features of cancer cachexia, allowing for a translational potential involving the liver function and its responses to potential treatments.

Genomic characterization of silvergrass cryptic virus 1, a novel partitivirus infecting Miscanthus sinensis.

In the present study we report the identification of a novel partitivirus recovered from Miscanthus sinensis, for which the provisional name "silvergrass cryptic virus 1" (SgCV-1) is proposed. High-throughput sequencing (HTS) and rapid amplification of cDNA ends (RACE) allowed the assembly of the complete sequence of each double-stranded RNA genome segment of this novel virus. The largest dsRNA segment, dsRNA1 (1699 bp), was predicted to encode a viral RNA-dependent RNA polymerase protein (RdRp) with 478 aa, and dsRNA2 (1490 bp) and dsRNA3 (1508 bp) were predicted to encode putative capsid proteins (CPs) with 347 and 348 aa, respectively. SgCV-1 has the highest amino acid sequence identity (≤70.80% in RdPp and ≤34.5% in CPs) to members of the genus Deltapartitivirus, family Partitiviridae, especially to unclassified viruses related to members of this genus. Its genome segment and protein lengths are also within the range of those of deltapartitiviruses. Moreover, phylogenetic analysis based on RdRp amino acid sequences also showed clustering of this novel virus with the related unclassified deltapartitiviruses. An RT-PCR survey of 94 imported M. sinensis samples held in quarantine identified seven additional samples carrying SgCV-1. This new virus fulfils all ICTV criteria to be considered a new member of the genus Deltapartitivirus.

Immunolocalization of the EDWM-Protein Indicates a Matrix Role in Cornification of Lizard Epidermis

During epidermal differentiation in the scales of lizards and snakes, from the basal layer beta- and later alpha-keratinocytes are generated to form beta-and alpha-corneous layers. In the lizard Anolis carolinensis, minor proteins derived from the EDC (Epidermal Differentiation Complex) are added to the main constituent proteins, IFKs (Intermediate Filament Keratins) and CBPs (Corneous Beta Proteins, formerly indicated as beta keratins). One of these proteins that previous studies showed to be exclusively expressed in the skin, EDWM (EDC protein containing high GSRC amino acids) is rich in cysteine and arginine, amino acids that form numerous –S–S– and electro-static chemical bonds in the corneous material. Light and electron microscopy immunolbeling for EDWM show a diffuse localization in differentiating beta-cells and in some alpha-cells, in particular those of the clear-layer, involved in epidermal shedding. The study suggests that EDWM may function as a matrix protein that binds to IFKs and CBPs, contributing to the formation of the specific corneous material present in beta- and alpha-corneous layers. In particular, its higher immunolocalization in the maturing clear layer indicates that this protein is important for its differentiation and epidermal shedding in A. carolinensis and likely also in other lepidosaurian reptiles.

Identification and Characterization of a Novel Aminoglycoside 3''-Nucleotidyltransferase, ANT(3'')-IId, From Acinetobacter lwoffii.

A novel plasmid-encoded aminoglycoside 3''-nucleotidyltransferase ANT(3")-IId, was discovered in Acinetobacter lwoffi strain H7 isolated from a chick on an animal farm in Wenzhou, China. The whole-genome of A. lwoffii H7 consisted of one chromosome and five plasmids (pH7-250, pH7-108, pH7-68, pH7-48, and pH7-11). ant(3")-IId was identified as being encoded on pH7-250, sharing the highest amino acid identity of 50.64% with a function-known resistance gene, ant(3")-IIb (KB849358.1). Susceptibility testing and enzyme kinetic parameter analysis were conducted to determine the function of the aminoglycoside 3"-nucleotidyltransferase. The ant(3")-IId gene conferred resistance to spectinomycin and streptomycin [the minimum inhibitory concentration (MIC) levels of both increased 16-fold compared with the control strain]. Consistent with the MIC data, kinetic analysis revealed a narrow substrate profile including spectinomycin and streptomycin, with Kcat/Km ratios of 4.99 and 4.45×103M−1 S−1, respectively. Sequencing analysis revealed that the ant(3")-IId gene was associated with insertion sequences (IS) element [ΔISAba14-ΔISAba14-hp-orf-orf-orf1-ant(3")-IId], and ant(3")-IId were identified in plasmids from various Acinetobacter species. This study of the novel aminoglycoside 3"-nucleotidyltranferase ANT(3")-IId helps us further understand the functional and sequence characteristics of aminoglycoside 3"-nucleotidyltranferases, highlights the risk of resistance gene transfer among Acinetobacter species and suggests that attention should be given to the emergence of new aminoglycoside 3"-nucleotidyltranferase genes.

Impact of viral features, host jumps and phylogeography on the rapid evolution of Aleutian mink disease virus (AMDV)

Aleutian mink disease virus (AMDV) is one the most relevant pathogens of domestic mink, where it can cause significant economic losses, and wild species, which are considered a threat to mink farms. Despite their relevance, many aspects of the origin, evolution, and geographic and host spreading patterns of AMDV have never been investigated on a global scale using a comprehensive biostatistical approach. The present study, benefitting from a large dataset of sequences collected worldwide and several phylodynamic-based approaches, demonstrates the ancient origin of AMDV and its broad, unconstrained circulation from the initial intercontinental spread to the massive among-country circulation, especially within Europe, combined with local persistence and evolution. Clear expansion of the viral population size occurred over time until more effective control measures started to be applied. The role of frequent changes in epidemiological niches, including different hosts, in driving the high nucleotide and amino acid evolutionary rates was also explored by comparing the strengths of selective pressures acting on different populations. The obtained results suggest that the viral passage among locations and between wild and domesticated animals poses a double threat to farm profitability and animal welfare and health, which is particularly relevant for endangered species. Therefore, further efforts must be made to limit viral circulation and to refine our knowledge of factors enhancing AMDV spread, particularly at the wild-domestic interface.

3D structure of NT-3 Protein (Neurotropin 3) of Pigeon (Columba livia) using Server-Swiss Model

The NT-3 protein plays an important role in the development and differentiation of neurons, and is unique in the neurotropin family, that it can bind to 3 Trk receptors, namely TrkC, TrkA and TrkB. This study aimed to analyze the characteristics and three-dimensional structure of NT-3 protein in Columba livia. The target protein was obtained from Uniprot server with the access code of PKK30025.1 using template 3buk.1A (PDB-ID) analyzed in-silico through homology method using SWISS-MODEL server. The results showed that the three-dimensional structure of the target NT-3 protein with a template formed a β-sheet and loop structure, which was composed of 304 amino acids, with the highest amino acid composition was serine at 8.88 mol polar, and the lowest amino acid was tryptophan at 1.32. moles which was relatively nonpolar. The analysis results of the structural quality revealed an identity value of 98.20%, QMEAN of 0.8, QMQE of 0.25, and the analysis on the Ramachandran plot presented an outlier value of 0.92%; the most favored region value was 94.5%, with good structural quality. The results of the 3-dimensional structure of the NT-3 Columba livia protein are expected to be useful for further research to determine the active side and interactions of proteins in carrying out their functions.

The changes in the chemical and microbiological characteristics of lamtoro (Leucaena leucocephala) tempe from Pacitan with usar inoculum during continued fermentation

In addition to soybean, Leucaena leucocephala is one of the tempe raw materials usually used in Indonesia. These tempe is only made by peoples in a few areas in the southern part of Java such as Wonogiri, Gunungkidul and Pacitan. For some purposes, such as cooking ingredients, tempe is deliberately fermented longer than usual to obtain a savory taste. In a previous study, we had studied leucaena tempe or people known as lamtoro tempe that process in Wonogiri and reported that there had been a change in characteristic during fermentation until over-fermented tempe. Therefore, in this research, we analyzed the change in the chemical and microbiological characteristic of lamtoro tempe from Pacitan during continued fermentation. This research showed that during the fermentation process, mold, yeast, and lactic acid bacteria (LAB) persisted for up to 126 hrs of fermentation time. The growth of yeast and mold tend to decrease while LAB continued to increase until it reached 11 log CFU/mL. In addition, the moisture content, ash content, soluble protein levels, pH and titrated acid increased during continued fermentation time. Glutamic acid and aspartic acid were the highest amino acids by weight percentage. Both amino acids have an important role in the sensory characteristics of lamtoro tempe.

The interaction of intestinal bacteria and feed: a case study of intensive-duck husbandry in Central Java

This study was aimed to compare sugars and amino acid content in duck’s feed and the intestinal bacteria's effects to improve ducks' quality. This research was an observational exploration involving five duck husbandries from Semarang, Temanggung, Magelang, Pati, and Salatiga District, Central Java. A total of 5 g of intestinal contents were collected from each of the five ducks randomly selected from each husbandry. The feed and intestinal contents were then analyzed using high-performance liquid chromatography (HPLC). The highest amino acid types were glutamate, aspartate, lysine, valine, and isoleucine, while the lowest was asparagine found in all sample farms. Intestinal contents freshly extracted then placed in dark bottles sterile for microbiome analysis with primers 6S rRNA V3-V4 genome identification. The concentration of glucose, fructose, and galactose in the intestine has increased significantly caused by digested polysaccharides. The composition of bacteria plays a vital role in digesting polysaccharides, makes them quickly absorbed by duck’s intestine cells. The abundance of bacteria in all sample locations was dominated by the phylum Firmicutes, especially Lactobacilalles, Bacilalles, and Clostridialles. Over feeding may not effective in sugar and essential amino acid absorption, however, it may play an essential role in the diversity of gut bacteria to produce necessary component for duck’s physiology.