bluuebunny/crossref_metadata_2025 huggingface dataset:
Different Nitrogen Sources to Improve the Quality of Spirulina platensis Culture in Mass Scale
Authors: Ruliaty L , Amalia I R , Sari R I , Aulia R
Published: December 2022

The research aimed to determine the effect of adding different sources of nitrogen to mass culture of Spirulina platensis. Materials needed for this test was culture media volume 1000 m3, fertilizer were SP-36 (40 ppm), ZA (10 ppm), EDTA (5 ppm) dan FeCl3 (1 ppm), Vitamin B-12 (0,001 ppm) and initial density of S. platensis was 10x103 sinusoid/ml. The test was carried out in two steps, firstly was the addition of nitrogen source from urea with doses of 80 ppm, 150 ppm and 200 ppm. Secondly, concurrent use of the best urea concentration from first treatment and potassium nitrate addition with doses of 50 ppm, 100 ppm and 150 ppm. Spirulina platensis was cultured on mass scale for 5 days until harvest. The first test showed that the dose of urea 80 ppm gave the highest growth rate (1,15 sinusoid/day) and the fastest generation time (0,60 hours) compared to doses of 150 ppm and 200 ppm. Protein content of Spirulina platensis added with 80 ppm of urea was also the highest (58,04%) compared to 150 ppm and 200 ppm. The results from second test showed concurrent use of urea 80 ppm and potassium nitrate 100 ppm to Spirulina platensis culture gave the highest growth rate (0,45 sinusoid/day) and the fastest generation time (1,54 hours) compared to those which added with 150 ppm and 50 ppm of potassium nitrate. Protein content of S. platensis with concurrent addition of urea 80 ppm and potassium nitrate 100 ppm was also the highest at 67,30%, compared to 150 ppm and 50 ppm.
Reproductive Performance of Osteochillus vittatus Outside of the Natural Environment
Authors: Pamungkas W , Arifin O Z , Subagja J , Imron  , Anggraeni F , Astuti D N , Palimirmo F S , Marnis H
Published: December 2022

Osteochilus vittatusis a species of bonylip barb in the Cyprinidae family of freshwater fish. Reproductive performance ofO. vittatusoutside of the natural environment is one of the important aspects to be observed. This study’s goal was to assess O. vittatus’s reproductive activity outside of its natural habitat. The research was carried out at the Research Institute for Fish Breeding, Subang, West Java from August to December 2021. Fifty females and thirty males were kept in concrete ponds. The fish were fed a 38 percent protein diet, and their gonad development was monitored monthly. Fish that had matured gonads were spawned and their reproductive performance was observed. The sperm motility and velocity ofO. vittatusmales were analyzed using a sperm analyzer (CASA). The ovi somatic index was 29.671±98.14 percent, total fecundity was 167,167±7371,11 eggs/100 g female, fertilization rate was 43.97±31.70 percent and hatching rate was 57.50±38.62 percent. The sperm volume was 12.42±4.19 mL, with percent motility and velocity of 93.50±4.36 and 84.00±3.83 respectively. The percentages of static, non-progressive motile, and progressive motile of fish sperm were 4.075±3.88, 103.28±19.02, and 29.85±16.32 percent respectively. Based on the study, we can conclude thatO. vittatushas the ability to reproduce outside of its natural habitat.
Potential of Single Cell Protein Production Using Waste as Growth Medium
Authors: Feliatra F , Hendra M , Batubara U M , Effendi I , Adelina A , Feliatra V A
Published: December 2022

Feed is an important factor affecting the growth of cultured fish. Around 86.5% of the production cost of aquaculture is allocated for the purchase of feed. Good quality and efficient feed is a determinant of the success of aquaculture business. Single Cell Protein (SCP) is a dry cell product of single cell microorganisms. SCP production is generally not only protein but also free amino acids, lipids, carbohydrates, vitamins and minerals. The purpose of this study was to analyze the growth media of Bacillus Cereus which will be used as a source of SCP by using some easy-to-use waste. The research method used is an experimental method using 2 isolates of Bacillus cereus bacteria, namely B. cereus strain SN7 and a consortium of bacterial isolates. Both isolates were grown in tofu liquid waste media, sago liquid waste media, and molasses waste media as a carbon source added with egg white as a nitrogen source with 3 replications in each treatment. The results showed that the most optimal growth medium for B. cereus strain SN7 and the consortium was molasses waste modified media which was incubated for 24 hours, compared to modified media for sago waste and tofu waste. For comparison, the isolates of B. cereus and consortium still had a higher growth potential than the isolates of strain SN7 which had been incubated for 24 hours.
Determination of Anoxygenic Photosynthetic Bacteria from Water and Sediment in Dumai Coastal Water, Indonesia
Authors: Batubara U M , Sibagariang R D , Siregar S S , Maelina T , Ginting T Y , Pratama MR , Jaboro M R
Published: December 2022

Dumai is one of the coastal waters of Indonesia that has the potential for the biodiversity of microorganisms including anoxygenic photosynthetic bacteria (APB). Anoxygenic photosynthetic bacteria are bacteria that carry out decomposition activities even though oxygen levels in water and sediment are very little or even absent. This study aims to determine anoxygenic photosynthetic bacteria from aquatic and sedimentary ecosystems in the coastal waters of Dumai, Indonesia. This research was conducted by an experimental method using modified mineral media. The APB was isolated from six different places in sequence, namely Dumai sea station, river prayer room, harbor, shrimp pond area, fish auction place, and, Purnama tour. All bacteria obtained were then characterized by their morphological and physiological characteristics. The isolation results showed that 15 different bacterial isolates were obtained after being determined based on Bergey’s Manual of Determinative Bacteriology. All isolates contained different pigments such as carotenoids, xanthophylls, and, chlorophylls. Thus, further utilization of APB bacteria can be carried out in various microbiological applications such as bioremediation, aquaculture, biofuel, food, and medicines.
Total Amino Acids and Protein Concentrate of Sea Cucumber (Stichopus vastus) From Natuna Waters, Riau Islands
Authors: Sukmiwati M , Sari N I , Edison E
Published: December 2022

Sea cucumbers haven’t been utilized optimally, and have a high economic value, due to high protein content of meat. This research aims to know the proximate content and total amino acids of sea cucumber flour, and total amino acids of protein concentrate of sea cucumber. The result showed that different ratios of flour and solvent have a significant effect on protein concentrate. Proximate content and protein concentrate with the ratio of flour and solvents (1:3) are protein 74.25%, moisture 10.58%, ash 7.25%, carbohydrate 6.47%, crude fiber 2.66%, and fat 0.16%. Total amino acids protein concentrate (1:3) is 53.59%. The major amino acids protein concentrate are glutamic acid, glycine, alanine, and aspartic acid. Ratios of flour and solvent (1:4) are protein content 76.13%, moisture 10.35%, ash 7.17%, carbohydrate 6.03%, crude fiber 2.51% and fat 0.13%. Total amino acids protein concentrate (1:4) is 56.74%. The major amino acids in protein concentrate are glycine, glutamic acid, alanine, and arginine. Ratios of flour and solvent (1:5) are protein 77.35%, moisture 9.14%, ash 6.67%, carbohydrate 6.00%, crude fiber 2.45%, and fat 0.10% respectively. Total amino acids protein concentrate (1:5) is 61.63%. The major amino acids protein concentrate are glycine, glutamic acid, aspartic acid, and alanine.
Characteristics of Fresh Water Lobster Carapaces Flour (Cherax quadricarinatus)
Authors: Desmelati  , Suparmi  , Leksono T
Published: December 2022

This study aims to determine the organoletic and chemical characteristics of freshwater crayfish carapace flour. The treatment was drying in an oven at a temperature of 80°C for 24 hours. The parameters analyzed were the amount of yield, organoleptic value and proximate value. Based on the results of the study, the yield was 92.45%. The organoleptic value is based on the percentage of consumer acceptance test that likes color 98.25%, taste 95%, aroma 90%, and texture 95%, with the characteristics of bright reddish color, savory taste, not too fishy aroma, and dry and smooth texture. The chemical characteristics are: water content (4.24%), protein (15.37.%), fat (2.07%), ash (4.2%), non-nitrogen extract material 1.63% and crude fiber 19.86%. From the data From these results it can be concluded that freshwater carapace flour can be used as a fortification material in processed products.
The Community Structure and Diversity of Sungai Bersejarah Mangrove in Sungai Apit District, Siak Regency
Authors: Efriyeldi E , Amin B
Published: December 2022

Mangroves are plants that live in the intertidal zone of the tropics and some sub-tropics. Mangrove ecosystems have many functions, which can be grouped into ecological and economic functions. The Sungai Bersejarah mangrove area is an educational tourism location managed by the conservation group Laskar Mandiri. The objective of the study was to analyze the structure and diversity of the mangrove community in the Sungai Bersejarah Mangrove area, which includes species, density, frequency, coverage, and importance value index. The environmental parameters measured were temperature, salinity and pH. The research was carried out from June to August 2021 using the quadrant line transect method. A total of five line transects were established in the mangrove area, each of which was placed in three plots measuring 10 m x 10 m (tree group) and 5 m x 5 m (sapling group). The study result indicate that there are 11 species of mangrove for the tree group and 9 species for the sapling group. Species Rhizophora apiculata was found to have the highest density, frequency, cover and important value index values, both for tree groups and sapling groups. The index values obtained are diversity (H′) 2.8626 and 2.1821, dominance index (C) 0.1835 and 0.3416 and eveness index (E) 0.8275 and 0.6884 for trees and saplings, respectively.
Macrozoobenthic diversity and heavy metals (Pb and Hg) accumulation in Bone River Gorontalo Indonesia
Authors: Kadim M K , Herawati E Y , Arfiati D , Hertika A M S
Published: December 2022

The heavy metal pollution on benthic macroinvertebrate communities in Bone River has not been studied. This present study determined to investigate the diversity of the macrozoobenthic trough the length of Bone River concerning the heavy metals leads and mercury at eight sampling stations. The samples were taken in July 2021. A sample of four representative macro zoobenthic families (Hydropsychidae, Baetidae and Elmidae) was also used to analyze metal bioaccumulation. The macrozoobenthic recorded in this study comprise of ten orders and 35 families with a total of 3146 individuals. Diptera, Ephemeroptera, Coleoptera, and Trichoptera dominate the population size of benthic. The diversity indices show the low and medium categories but favour a better macrozoobenthic development. Monitoring studies show that the concentration of Pb in sediments is much higher than that of mercury. Metal accumulation in sediments showed fluctuations but did not reflect macrozoobenthic metal concentrations. The bioconcentration factor (BCF) value generally indicates that the three taxa are categorized in the low accumulative category.
The Abundance of Micro plastics (MPs) in the Sediment of Pantai Carocok in Pesisir Selatan Regency, West Sumatra
Authors: Nedi S , Elizal  , Mulyadi L A
Published: December 2022

Micro plastics (MPs) are small fractions of plastid compound, which takes a long time to decompose in waters. The MPs can accumulate in seawaters, and in aquatic biota’s gut; and it harmful to human health. This study was done to know the abundance of MPs in the sediment in Pantai Carocok beach; it was in Pesisir Selatan regency, West Sumatra Province. Samples were collected from three stations, at HWL and LWL with two different depths. The findings showed that fragment type of MPs more dominant than fibre and film types; these figures were ±70%, ±16%, and ±13% consecutively. The abundance of MPs was higher at station 3 than the other two stations; the lowest was at station 1. The abundance of MPs ranged from 70.84-109.16 particles/kg of sediment. The abundance of MPs was varied between zone 1 in HWL and in the zone 2 in LWL for each station, and it was tended increase to deeper depth of samples; however, the different were not significant.
Genetic characterization of Ceratoglanis scleronema
Authors: Elvyra Roza
Published: December 2022

Ceratoglanis scleronema is an important fish species in the Riau Province, Indonesia. The fish of C. scleronema are distributed in several rivers of Riau Province. Research on the genetic characterization of C. scleronema is needed to complete its morphological data. Very little research has been done on the genetic characteristics of C. scleronema. This study analyzed the genetic characterization based on the cytochrome b gene of C. scleronema fish. The cytochrome b gene of C. scleronema fish from Riau Province has been successfully amplified. The result of the research showed that nucleotide transition substitutions were more common than transversion substitutions in the cytochrome b gene of C. scleronema. The range of genetic distance between C. scleronema from Kampar and Tapung rivers are 0.00-0.01. The genetic distance between C. scleronema from Riau Province and C. scleronema from GenBank data are 0.01-0.02. The phylogenetic tree showed the closest relationship C. scleronema from Riau Province with C. scleronema from Genbank data with 100% bootstrap value. The conclude of the research that cytochrome b gene can be used to differentiate species of C. scleronema with other fish species. The genetic characteristics of these fish are basic data that can be used for the development of fishery genetic resources in the future.
On the Salinity Distribution Induced Mixing at the Mouth of the Estuary
Authors: Mubarak M , Rifardi R , Riyadi A , Sulaiman A , Yoswati D , Wibowo M A
Published: December 2022

Salinity is an essential parameter in estuaries because it determines the mixing process and distribution of biota in the estuary ecosystem. In the paper, we investigate the dynamics of salinity distribution in the Dumai estuary. Salinity and tidal data observation were carried out during the transitional season around the mouth of the estuary. We get the salinity time series data in a tidal cycle. We observed that the Formzhal number is about 0.239, indicating that the tidal type in Dumai estuary waters is mixed directional, tending to double a day, with the highest and lowest tides in the Dumai estuary being 1.26 and 0.47 m, respectively. The salinity variability due to tides was studied by harmonic analysis, while the spatiotemporal distribution was studied using an analytical solution developed by previous researchers. The results show the presence of time lag between tidal elevation and salinity variation. Low tide and salinity, which indicate the effect of river discharge, are significant. This study further indicated that high salinity occurs during strong mixing conditions. It implied that the high salinity from the offshore entrance to shallower waters allowed for mixing processes. This paper ends with a comprehensive discussion of the vertical distribution of salinity at the mouth of the estuary.
Understanding the Mechanism of Currents through the Malacca Strait Study Case 2020 – 2022 : Mean state, Seasonal and Monthly Variation
Authors: Wibowo M A , Tanjung A , Rifardi  , Elizal  , Mubarak  , Yoswaty D , Susanti R , Muttaqin A S , Fajary F R , Anwika Y M
Published: December 2022

The Malacca Strait is the importance waters for international shipping routes and more 200 cases of ship collisions in the period 1970-2015 in this strait. That is related to some a shallow depth waters with many small islands and strong current which is making this strait have a highest risk in certain seasons. The CMEMS data used to understanding of mechanism of current, illustrate the pattern and tranport volume. The research uses descriptive and the statistical methods to understanding of mechanism and variability of current. The analysis of current patterns and water level shows that during the monsoon winds active, the current always moves to the Andaman Sea, we called the southeast current system. The Northeast (NE) and Southwest (SW) monsoon wind is strongly influence to the mechanism of formation southeast current system, which causes the varition in sea level hight in eastern and western of Malacca Strait. During the NE monsoon season, the water masses of the South China Sea are push away into the Karimata Strait, causing the sea level in the eastern part to be higher than the western part and will increase the current speed. On the other hand, during the SW monsoon season, the water masses from the Karimata Strait is pushed away from the eastern part of the Malacca Strait which causes the sea level decrease and causes the current speed to weaken. Numbers eddies phenomenon were found at the Malacca Strait each season. The anticyclonic eddies occurred almost every season centered at 3° - 5° N, 97° - 100° E. Meanwhile anticyclonic eddies appear around the northern part of Sumatra centered at 4° - 5°N, 99° - 101°E during SW Monsoon season and the eddies formation also existed during the second transition monsoon season.
Income Contribution Based on Fishing Gear of The Duano Tribe, Indragiri Hilir, Riau
Authors: Yanti C W , Metalisa R , Bathara L , Saragih V B
Published: December 2022

The Duano Tribe are fishermen that run fishing businesses traditionally. Generally, they use longlines and drift gill nets equipment for fishing. The purpose of this research is to analyze the income of fishermen that use longlines and drift gill nets based on the main catch of Belanak and Senangin fish and the contribution of fishing business income to the total fisherman income. The descriptive method that the author used to analyze where data were collected from 29 fishermen of Duano Tribe. This research was conducted in Tanjung Pasir village, Indragiri Hilir, Riau, in May 2021. The result shows that the average fishing income of Duano Tribe that use longlines is IDR.51,782,948.-year-1 and the average fishing income of Duano Tribe that uses drift gill nets is IDR.26,931,235.-year-1. The income of the Duano tribe using longlines is higher than drift gill nets, even with the same average duration of fishing. The contribution of income using longlines to the income of the Duano Tribe fishermen is 85 percent, and the contribution of income using drift gill nets to the income of the Duano Tribe fishermen is 78 percent. The income contribution using longline is higher than the income contribution using drift gill nets. Based on the contribution criteria, both income from fishing with drift gill nets and longlines provide a high contribution.
Analysis of the Fisheries Business Orientation of the Duano Tribe Based on Socio-Culturalism in Tanah Merah Subdistrict, Indragiri Hilir, Indonesia
Authors: Metalisa R , Yanti C W , Bathara L , Arief H , Novikarumsari N D
Published: December 2022

Business in the fisheries sector is the only business run by the duano tribes from their predecessors. Initially, the duano tribes was a cultural community whose lives moved according to the direction of the sea breeze and schools of fish. As the duano tribes community developed, they began to occupy an area to live permanently, build a family, and carry out business to meet the necessities of life. The business is offered by the duano tribe in the fisheries sector. The purpose of this study was to analyze the orientation of the fishery business carried out by the duano tribe based on social and culture. The research uses a survey with an explanatory research approach. The analysis technique uses quantitative and qualitative descriptive with as many as 54 respondents. The fishery business carried out by the duano tribe is still oriented to the subsystem, namely fishery products produced only to meet the family’s daily needs, so the category of duano fishermen is still classified as traditional fishermen. The categorization of duano fishermen is based on the use of fishing gear, utilization of labor, and productivity.
Preliminary Study Of Marine Debris Composition From Fisherman Activities : A Case Study On Cikidang Fishing Port, Pangandaran
Authors: Prasetiawan N R , Sudirman N , Salim H L , Ati R N A , Kepel T L , Daulat A , Kusumaningtyas M A , Permana S M , Setiawan A , Pranowo W S , Rustam A , Suryono D D , Jayawiguna M H , Sukoraharjo S S
Published: December 2022

Marine debris pollution has become an important issue in recent years. It has an impact on marine environment and marine life, as well as effecting human health. The objective of this study was to identify the composition of waste that was produced from the fishermen’s activities. The research was conducted in Cikidang Fishing Port, Pangandaran. The data of waste types from fishing vessel were grouped based on the vessel’s dimension. The result show that plastics dominated the waste composition, and based on the vessel dimension when compared the amount of waste generated, the amount of waste from one day fishing (small vessel) was greater than the ten days fishing (big vessel). The amount of waste generated from small vessel was 0.009 tons-1.vessel-1.year-1, meanwhile from big vessel was 0.09 tons-1.vessel-1.years-1. This indicates that the fishers habit to dispose waste not in the right place can become a potential source of marine debris pollution. Maintaining the quality of fishery products is very important starting from improving the fisherman behaviour to the fishing port facilities to achieve the sustainability fishery product.
Degradation of chlorobenzene by non-thermal plasma coupled with catalyst: influence of catalyst, interaction between plasma and catalyst
Authors: SHI Xiujuan , LIANG Wenjun , YIN Guobin , LIU Jia
Published: December 2022

Non-thermal plasma (NTP) is considered to be a promising technology for the removal of volatile organic compounds; however, its application is limited by low CO2 selectivity and undesirable by-products. To overcome these issues, this paper discusses the degradation of chlorobenzene (CB) in systems of NTP coupled with catalysts, and the influence of catalyst locations in the NTP was investigated. In addition, the interaction between plasma and catalyst was also explored. The results indicated that the degradability of CB was remarkably improved through the combination of NTP with catalysts, and the formation of ozone was effectively inhibited. The degradation efficiency increased from 33.9% to 79.6% at 14 kV in the NTP-catalytic system, while the ozone concentration decreased from 437 to 237 mg m−3, and the degradation efficiency of in plasma catalysis (IPC) systems was superior to that of the post plasma catalysis system, while the inhibition ability of ozone exhibited an opposing trend. In the IPC system, the degradation efficiency was 87.7% at 14 kV, while the ozone concentration was 151 mg m−3. Besides, the plasma did not destroy the pore structure and crystal structure of the catalyst, but affected the surface morphology and redox performance of the catalyst. Thus, NTP coupled catalytic system could improve the degradation performance of CB. Furthermore, the plasma discharge characteristics played a major role in the NTP synergistic catalytic degradation of CB. Finally, based on the experiment analysis results, the general reaction mechanism of CB degradation in an IPC reaction system was proposed.
Daylight entanglement-based quantum key distribution with a quantum dot source
Authors: Basso Basset F , Valeri M , Neuwirth J , Polino E , Rota M B , Poderini D , Pardo C , Rodari G , Roccia E , Covre da Silva S F , Ronco G , Spagnolo N , Rastelli A , Carvacho G , Sciarrino F , Trotta R
Published: December 2022

Entanglement-based quantum key distribution can enable secure communication in trusted node-free networks and over long distances. Although implementations exist both in fiber and in free space, the latter approach is often considered challenging due to environmental factors. Here, we implement a quantum communication protocol during daytime for the first time using a quantum dot source. This technology presents advantages in terms of narrower spectral bandwidth—beneficial for filtering out sunlight—and negligible multiphoton emission at peak brightness. We demonstrate continuous operation over the course of three days, across an urban 270 m-long free-space optical link, under different light and weather conditions.
Learning single-cell chromatin accessibility profiles using meta-analytic marker genes
Authors: Kawaguchi Risa Karakida , Tang Ziqi , Fischer Stephan , Rajesh Chandana , Tripathy Rohit , Koo Peter K , Gillis Jesse
Published: December 2022

Motivation

Single-cell assay for transposase accessible chromatin using sequencing (scATAC-seq) is a valuable resource to learn cis-regulatory elements such as cell-type specific enhancers and transcription factor binding sites. However, cell-type identification of scATAC-seq data is known to be challenging due to the heterogeneity derived from different protocols and the high dropout rate.

Results

In this study, we perform a systematic comparison of seven scATAC-seq datasets of mouse brain to benchmark the efficacy of neuronal cell-type annotation from gene sets. We find that redundant marker genes give a dramatic improvement for a sparse scATAC-seq annotation across the data collected from different studies. Interestingly, simple aggregation of such marker genes achieves performance comparable or higher than that of machine-learning classifiers, suggesting its potential for downstream applications. Based on our results, we reannotated all scATAC-seq data for detailed cell types using robust marker genes. Their meta scATAC-seq profiles are publicly available at https://gillisweb.cshl.edu/Meta_scATAC. Furthermore, we trained a deep neural network to predict chromatin accessibility from only DNA sequence and identified key motifs enriched for each neuronal subtype. Those predicted profiles are visualized together in our database as a valuable resource to explore cell-type specific epigenetic regulation in a sequence-dependent and -independent manner.
GSCA: an integrated platform for gene set cancer analysis at genomic, pharmacogenomic and immunogenomic levels
Authors: Liu Chun-Jie , Hu Fei-Fei , Xie Gui-Yan , Miao Ya-Ru , Li Xin-Wen , Zeng Yan , Guo An-Yuan
Published: December 2022

Cancer initiation and progression are likely caused by the dysregulation of biological pathways. Gene set analysis (GSA) could improve the signal-to-noise ratio and identify potential biological insights on the gene set level. However, platforms exploring cancer multi-omics data using GSA methods are lacking. In this study, we upgraded our GSCALite to GSCA (gene set cancer analysis, http://bioinfo.life.hust.edu.cn/GSCA) for cancer GSA at genomic, pharmacogenomic and immunogenomic levels. In this improved GSCA, we integrated expression, mutation, drug sensitivity and clinical data from four public data sources for 33 cancer types. We introduced useful features to GSCA, including associations between immune infiltration with gene expression and genomic variations, and associations between gene set expression/mutation and clinical outcomes. GSCA has four main functional modules for cancer GSA to explore, analyze and visualize expression, genomic variations, tumor immune infiltration, drug sensitivity and their associations with clinical outcomes. We used case studies of three gene sets: (i) seven cell cycle genes, (ii) tumor suppressor genes of PI3K pathway and (iii) oncogenes of PI3K pathway to prove the advantage of GSCA over single gene analysis. We found novel associations of gene set expression and mutation with clinical outcomes in different cancer types on gene set level, while on single gene analysis level, they are not significant associations. In conclusion, GSCA is a user-friendly web server and a useful resource for conducting hypothesis tests by using GSA methods at genomic, pharmacogenomic and immunogenomic levels.
Protein engineering via Bayesian optimization-guided evolutionary algorithm and robotic experiments
Authors: Hu Ruyun , Fu Lihao , Chen Yongcan , Chen Junyu , Qiao Yu , Si Tong
Published: December 2022

Directed protein evolution applies repeated rounds of genetic mutagenesis and phenotypic screening and is often limited by experimental throughput. Through in silico prioritization of mutant sequences, machine learning has been applied to reduce wet lab burden to a level practical for human researchers. On the other hand, robotics permits large batches and rapid iterations for protein engineering cycles, but such capacities have not been well exploited in existing machine learning-assisted directed evolution approaches. Here, we report a scalable and batched method, Bayesian Optimization-guided EVOlutionary (BO-EVO) algorithm, to guide multiple rounds of robotic experiments to explore protein fitness landscapes of combinatorial mutagenesis libraries. We first examined various design specifications based on an empirical landscape of protein G domain B1. Then, BO-EVO was successfully generalized to another empirical landscape of an Escherichia coli kinase PhoQ, as well as simulated NK landscapes with up to moderate epistasis. This approach was then applied to guide robotic library creation and screening to engineer enzyme specificity of RhlA, a key biosynthetic enzyme for rhamnolipid biosurfactants. A 4.8-fold improvement in producing a target rhamnolipid congener was achieved after examining less than 1% of all possible mutants after four iterations. Overall, BO-EVO proves to be an efficient and general approach to guide combinatorial protein engineering without prior knowledge.
Computational analyses reveal fundamental properties of the AT structure related to thrombosis
Authors: Lopes Tiago J S , Rios Ricardo A , Rios Tatiane N , Alencar Brenno M , Ferreira Marcos V , Morishita Eriko
Published: December 2022

Blood coagulation is a vital process for humans and other species. Following an injury to a blood vessel, a cascade of molecular signals is transmitted, inhibiting and activating more than a dozen coagulation factors and resulting in the formation of a fibrin clot that ceases the bleeding. In this process, antithrombin (AT), encoded by the SERPINC1 gene is a key player regulating the clotting activity and ensuring that it stops at the right time. In this sense, mutations to this factor often result in thrombosis—the excessive coagulation that leads to the potentially fatal formation of blood clots that obstruct veins. Although this process is well known, it is still unclear why even single residue substitutions to AT lead to drastically different phenotypes. In this study, to understand the effect of mutations throughout the AT structure, we created a detailed network map of this protein, where each node is an amino acid, and two amino acids are connected if they are in close proximity in the three-dimensional structure. With this simple and intuitive representation and a machine-learning framework trained using genetic information from more than 130 patients, we found that different types of thrombosis have emerging patterns that are readily identifiable. Together, these results demonstrate how clinical features, genetic data and in silico analysis are converging to enhance the diagnosis and treatment of coagulation disorders.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.
Tracing weak neuron fibers
Authors: Liu Yufeng , Zhong Ye , Zhao Xuan , Liu Lijuan , Ding Liya , Peng Hanchuan
Published: December 2022

Motivation

Precise reconstruction of neuronal arbors is important for circuitry mapping. Many auto-tracing algorithms have been developed toward full reconstruction. However, it is still challenging to trace the weak signals of neurite fibers that often correspond to axons.

Results

We proposed a method, named the NeuMiner, for tracing weak fibers by combining two strategies: an online sample mining strategy and a modified gamma transformation. NeuMiner improved the recall of weak signals (voxel values <20) by a large margin, from 5.1 to 27.8%. This is prominent for axons, which increased by 6.4 times, compared to 2.0 times for dendrites. Both strategies were shown to be beneficial for weak fiber recognition, and they reduced the average axonal spatial distances to gold standards by 46 and 13%, respectively. The improvement was observed on two prevalent automatic tracing algorithms and can be applied to any other tracers and image types.

Availability and implementation

Source codes of NeuMiner are freely available on GitHub (https://github.com/crazylyf/neuronet/tree/semantic_fnm). Image visualization, preprocessing and tracing are conducted on the Vaa3D platform, which is accessible at the Vaa3D GitHub repository (https://github.com/Vaa3D). All training and testing images are cropped from high-resolution fMOST mouse brains downloaded from the Brain Image Library (https://www.brainimagelibrary.org/), and the corresponding gold standards are available at https://doi.brainimagelibrary.org/doi/10.35077/g.25.

Supplementary information

Supplementary data are available at Bioinformatics online.
igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
Authors: Robinson James T , Thorvaldsdottir Helga , Turner Douglass , Mesirov Jill P
Published: December 2022

igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has no external dependencies. The viewer runs completely in the web browser, with no backend server and no data pre-processing required.

Availability and implementation

The igv.js JavaScript component can be installed from NPM at https://www.npmjs.com/package/igv. The source code is available at https://github.com/igvteam/igv.js under the MIT open-source license. IGV-Web, the end-user application built around igv.js, is available at https://igv.org/app. The source code is available at https://github.com/igvteam/igv-webapp under the MIT open-source license.

Supplementary information

Supplementary information is available at Bioinformatics online.
Nanocrystalline fluorapatite mineralization in the calciphile rock-boring bivalve Lithophaga: functional and phylogenetic significance
Authors: Taylor John D , Glover Emily A , Ball Alexander D , Najorka Jens
Published: December 2022

Phosphate mineralization as a skeletal material is uncommon in invertebrate animals and rare in Mollusca. Remarkably, apatite minerals were first reported more than 30 years ago in the periostracum of two species of the mytilid bivalve Lithophaga where shells are mostly constructed of calcium carbonate. This discovery extended the range of biominerals secreted by molluscs but has attracted no subsequent research. In this study we review the occurrence of phosphate mineralization in Lithophaga and putatively allied taxa. Lithophagine bivalves, particularly Lithophaga and the more diverse Leiosolenus species, are well known for their endolithic chemical dissolution of calcareous rocks and corals with calcium-binding lipoproteins secreted by mantle glands. Fluorapatite was identified by X-ray diffraction in an outer layer of the periostracum in six species of Lithophaga. Morphological study by scanning electron microscopy of four species showed the fluorapatite crystals embedded in periostracal material in a layer 10–20 µm thick. Dilute bleach treatment revealed the crystals as densely packed euhedral prisms 250–400 nm in size. The succeeding inner layers of the periostracum were unmineralized. Observations of the developing periostracum of Lithophaga teres suggest that the initial mineralization is in the form of amorphous granules that coalesce and transform into euhedral crystals. Periostracal phosphate was not recorded in other members of the Lithophaginae – Leiosolenus, Botula or Zelithophaga species. Leiosolenus species characteristically have extraperiostracal aragonitic encrustations that can be thick and structurally complex. Published molecular phylogenies of Mytilidae bivalves show a division into two major clades with Lithophaga species in one clade and Leiosolenus species in the other, indicating that the subfamily Lithophaginae as presently understood is polyphyletic. This result implies that the two genera have independent evolutionary pathways to endolithic occupation of calcareous substrates although using similar mantle gland secretions to excavate their crypts. Because fluorapatite is considerably less soluble and harder than calcium carbonate, it is suggested that the phosphate layer of Lithophaga is a functional adaptation to protect their shells from self-dissolution from their rock-dissolving glandular secretions and may also act as defence against other shell-eroding organisms.
Automatic Multi-Plug Filtration Cleanup Tip-Filtration with Ultra-Performance Liquid Chromatography/Tandem Mass Spectrometry Detection For 22 Pesticide Residues in Typical Vegetables
Authors: Ma Lili , Cao Lihua , Feng Yuechao , Jia Li , Liu Cong , Ding Qi , Liu Jia , Shao Peng , Pan Canping
Published: December 2022

An automatic multi-plug filtration cleanup (m-PFC) tip-filtration method was developed to reduce the manual operation workload in sample preparation. In this work, m-PFC was based on multi-walled carbon nanotubes mixed with primary secondary amines and anhydrous magnesium sulfate (MgSO4) in a packed column for analysis of pesticide residues followed by ultra-performance liquid chromatography coupled with tandem mass spectrometry. Method validation was performed on 22 pesticide residues in carrot, spinach and leek, at spiked levels of 5, 10 and 50 μg/kg, respectively. The average recoveries were between 70.1 and 119.5% with associated relative standard deviations <20% (n = 6) indicating satisfactory accuracy and repeatability. Matrix-matched calibration curves were performed with the correlation coefficients (R2) higher than 0.9903 within a linearity range of 5–100 ng/mL. The limits of quantification were 5 μg/kg for all the pesticides in carrot, spinach and leek matrices. The developed method was successfully used to determine pesticide residues in market samples.
The use of blended learning in postgraduate education in orthodontics: student versus teacher perception
Authors: Maes Désirée Martine , Zong Chen , Begnoni Giacomo , Verdonck Anna , Willems Guy , Cadenas de Llano-Pérula Maria
Published: December 2022

Objective

To investigate the use of blended learning (BL) in Postgraduate Education in Orthodontics.

Methods

A self-developed online questionnaire was sent to 244 teaching staff members of the European Orthodontic Departments. They were asked to answer it and share it with their postgraduate students. 18 questions for teaching staff and 27 for postgraduate students evaluated the use, perceptions, feedback options, learning outcomes, and teacher’s role in BL. The answers of teaching staff and students were statistically compared by Fisher’s Exact Test, Chi-Square Test, Unpaired t-test, and Mann–Whitney Test.

Results

124 completed questionnaires were received, 44 from teaching staff and 80 from postgraduate students. Teaching staff is more acquainted with BL than students (P = 0.001). Both groups found BL courses a good alternative to traditional courses (P = 0.654). The use of interactive multimedia was more appreciated by students (P = 0.015). Both groups found students’ results not to change with BL, but teaching staff had a more negative perception (P = 0.012). In general, teaching staff perceived feedback and interaction as less essential than postgraduates in BL. Teaching staff felt more like coaches when using BL, while postgraduates did not perceive any changes in teachers’ roles (P = 0.006). Limitations: Due to the General Data Protection Regulation it was not possible to directly contact the postgraduate students in Postgraduate Orthodontic Programs throughout Europe. Therefore, this study completely relied on the goodwill of the teaching staff being contacted.

Conclusion

The main differences in perception between teaching staff and postgraduate students were student results, teachers’ role, use, and importance of feedback and interactive multimedia. Although both groups found BL courses to stimulate students’ learning and to be a relevant cost-effective addition to traditional courses, they were hesitant to fully replace them with BL.
Change of pulmonary function tests in hospitalized COVID-19 patients at third and sixth month follow-up
Authors: Kafkas Meltem Karakulak , Tüzün Sabah , Hacıağaoğlu Nazlı , Çetin Hüseyin , Cömert Sevda Şener , Şimşek Engin Ersin
Published: December 2022

Background

The effect of COVID-19 infection on pulmonary function is unknown.

Objective

This study aimed to evaluate pulmonary function tests (PFTs) of patients hospitalized with the diagnosis of COVID-19 pneumonia at 3 and 6 months post-discharge.

Methods

Patients aged 18 years and over who had positive COVID-19 PCR test results and were hospitalized in the pandemic service between 1 May 2020 and 31 October 2020, were included in the study. All patients were evaluated with PFTs FVC, FEV1, FEV1/FVC, and FEF25–75 at 3 and 6 months after discharge.

Results

The mean age of 34 patients included in the study was 47.7 ± 12.7 years. The FVC, FEV1, FEV1/FVC, and FEF25–75 measurements at 3 and 6 months post-discharge showed no significant difference (P = 0.765, P = 0.907, P = 0.707, and P = 0.674, respectively). There was no significant difference in any PFT measurements at the third month follow-up, regardless of the pharmacological treatment protocols applied during hospitalization (P > 0.05). However, FEV1/FVC and FEF25–75 levels were 83.1 [3.4]% and 91.0 [10.0]%, respectively, in those who received systemic steroid treatment, and 78.3 ± 8.5% and 72.5 ± 25.7% in those who did not (P = 0.019 and P = 0.048, respectively). In addition, FVC and FEV1 levels increased significantly from the third to the sixth month follow-up in patients who received systemic steroid therapy (P = 0.035 and P = 0.018, respectively).

Conclusion

Although there is no significant difference in PFT measurements from 3 to 6 months in COVID-19 patients, systemic steroid therapy may have a beneficial effect on respiratory function in COVID-19 patients.
Illuminating the oral microbiome and its host interactions: tools and approaches for molecular microbiology studies
Authors: Merritt Justin , Kreth Jens
Published: December 2022

Advancements in DNA sequencing technologies within the last decade have stimulated an unprecedented interest in the human microbiome, largely due the broad diversity of human diseases found to correlate with microbiome dysbiosis. As a direct consequence of these studies, a vast number of understudied and uncharacterized microbes have been identified as potential drivers of mucosal health and disease. The looming challenge in the field is to transition these observations into defined molecular mechanistic studies of symbiosis and dysbiosis. In order to meet this challenge, many of these newly identified microbes will need to be adapted for use in experimental models. Consequently, this review presents a comprehensive overview of the molecular microbiology tools and techniques that have played crucial roles in genetic studies of the bacteria found within the human oral microbiota. Here, we will use specific examples from the oral microbiome literature to illustrate the biology supporting these techniques, why they are needed in the field, and how such technologies have been implemented. It is hoped that this information can serve as a useful reference guide to help catalyze molecular microbiology studies of the many new understudied and uncharacterized species identified at different mucosal sites in the body.
Long-range regulatory effects of Neandertal DNA in modern humans
Authors: Yermakovich Danat , Pankratov Vasili , Võsa Urmo , Yunusbayev Bayazit ,   Estonian Biobank Research Team, Metspalu Andres , Nelis Mari , Milani Lili , Mägi Reedik , Esko Tõnu , Dannemann Michael
Published: December 2022

The admixture between modern humans and Neandertals has resulted in ∼2% of the genomes of present-day non-Africans being composed of Neandertal DNA. Introgressed Neandertal DNA has been demonstrated to significantly affect the transcriptomic landscape in people today and via this molecular mechanism influence phenotype variation as well. However, little is known about how much of that regulatory impact is mediated through long-range regulatory effects that have been shown to explain ∼20% of expression variation. Here we identified 60 transcription factors (TFs) with their top cis-eQTL SNP in GTEx being of Neandertal ancestry and predicted long-range Neandertal DNA-induced regulatory effects by screening for the predicted target genes of those TFs. We show that the TFs form a significantly connected protein–protein interaction network. Among them are JUN and PRDM5, two brain-expressed TFs that have their predicted target genes enriched in regions devoid of Neandertal DNA. Archaic cis-eQTLs for the 60 TFs include multiple candidates for local adaptation, some of which show significant allele frequency increases over the last ∼10,000 years. A large proportion of the cis-eQTL-associated archaic SNPs have additional associations with various immune traits, schizophrenia, blood cell type composition and anthropometric measures. Finally, we demonstrate that our results are consistent with those of Neandertal DNA-associated empirical trans-eQTLs. Our results suggest that Neandertal DNA significantly influences regulatory networks, that its regulatory reach goes beyond the 40% of genomic sequence it still covers in present-day non-Africans and that via the investigated mechanism Neandertal DNA influences the phenotypic variation in people today.
Integrating complementary survey methods to estimate catches in Norway’s complex marine recreational hook-and-line fishery
Authors: Ferter Keno , Otterå Håkon , Christman Mary , Kleiven Alf Ring , Weltersbach Marc Simon , Gundersen Sofie , Djønne Christine , Bjelland Otte , Hartill Bruce , Lyle Jeremy , Hyder Kieran , Borch Trude , Vølstad Jon Helge
Published: December 2022

Marine recreational fishing is popular in Norway, but current estimates of the catches by resident and tourist anglers are lacking due to several challenges, in particular Norway’s long and intricate coastline with no defined access points and the large tourist fishery. To test methods for long-term monitoring of boat-based marine recreational anglers, estimate their catches, and characterize the fishery, we conducted a roving creel survey based on a novel spatial sampling frame and a survey of tourist fishing businesses in Troms and Hordaland County. These surveys showed that cod (Gadus morhua) and saithe (Pollachius virens) dominated the catches in Troms, while mackerel (Scomber scombrus) and saithe dominated the catches in Hordaland. The estimated total annual harvest of cod by all marine recreational anglers was 2 160 tonnes (relative standard error, or RSE 44%) in Troms and 73 tonnes (RSE 29%) in Hordaland, of which ∼40% (in weight) were landed in registered tourist fishing businesses, based on data from the tourist fishing survey. The results indicate that recreational anglers in Hordaland harvest more cod in coastal waters than commercial fishers. This study provides information for developing marine recreational fisheries monitoring in challenging survey situations to support science-based fisheries management.