bluuebunny/crossref_metadata_2025 huggingface dataset:
Future Outlook of Fresh Water Supply and Demand in Selangor
Authors: Ruslan Nur Iffika , Abbas Ahmad Rosly , Salleh Munirah Stapah , Alias Masitah , Rahim Nurfaziera
Published: December 2022

Water is an essential resource for the well-being of humans as well as for ecosystems. In this regard, the increasing water scarcity areas has become one of the major problems faced by humanity. In Malaysia, Selangor is considered a water-stressed area due to the increase in water demand and limited suitable fresh water resources for treatment and distribution. The increase in population as well as urbanization and industrialization made the rivers in Selangor arguably the most polluted compared to other states. These situations result in a series of unscheduled water supply interruption over the years and negatively impact the majority of consumers. Projected water demand also indicates that the existing water supplies are not sufficient in the long run, therefore, it is deemed required to study the water demand and supply gap in Selangor to ensure the current water management is sustainable for the remote future. This paper mainly discusses on the current water production from Water Treatment Plants as well as projection of water demand which also foresee the future water deficit in Selangor. The method used in this study was based on review of secondary data acquired from available published report and website, while the assessment of water demand conducted comprise of calculation of projected population, projected domestic water demand, projected total water demand and water deficit up to year 2050. According to the result obtained, the existing water demand and supply in Selangor is 4,967 MLD, meanwhile, the projection of water demand in Selangor up to year 2050 is 7,011 MLD with the projected water deficit of 2,044 MLD. The findings of this paper are essential in water resources planning and management, particularly in terms of additional raw water supply that will be required to cater to the future water demand in Selangor.
Antioxidant Properties and Antimicrobial Effect of Zingiber officinale Extract towards Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa
Authors: Zainal Annur Ashyqin , Salleh Nur Fatien Muhammad , Ahmad Wan Amir Nizam Wan , Rasudin Nur Syahmina , Zaabar Wan Razlin Wan , Ghafar Noraini Abdul
Published: December 2022

Bacterial infection and emergence of multi-drug resistant bacteria have been a great obstacle in today’s medicine development. Emergence of multi-drug resistant bacteria strains reduces the efficiency of currently available antimicrobial agents. Besides, oxidative stress, which is commonly correlated to numerous amounts of diseases also need to be tackled. Previous studies found that consumption of food containing natural antioxidant may help in reducing the risk of death-threatening diseases. Therefore, this study aimed to discover potential antioxidant and antimicrobial activity of Zingiber officinale against pathogenic bacteria strains such as E. coli, S. aureus and P. aeruginosa. Z. officinale rhizome ethanol extract was tested for antimicrobial activity through well diffusion method. Antioxidant property of the extract was tested using 2,2-Diphenyl-1-picrylhydrazyl (DPPH) method. According to the findings on antimicrobial assay, Z. officinale able to inhibit S. aureus and P. aeruginosa while E. coli remain resistant against ginger extract. At the concentration of 80 to 100mg/ml of ginger extract, the mean zone of inhibition against S. aureus ranged from 11mm to 15mm. Meanwhile, at concentration of 5 to 100mg/ml of extract, the inhibition zone of P. aeruginosa, ranged from 40mm to 64mm (±9mm). Additionally, IC50 value for Z. officinale extract is 0.4623μg/ml compared to ascorbic acid with IC50 value of 4.1602μg/ml. It is evident that Z. officinale has higher antioxidant property than ascorbic acid. Present findings and data gained through this study can be used to boost the application of natural or plant-based products in medicine to combat the emergence of drug-resistant bacteria.
The Level of Buying Behaviour Towards Organic Food Among Malays Consumers
Authors: Abdullah F A , Saidi S F S , Bakar T H S T Abu , Young L J
Published: December 2022

Globally, the demand for organic food rapidly rises and exceeds domestic supplies. Many are aware of the benefits of organic food, and it may guarantee a good lifestyle among the world’s populations. However, in most developing countries, including Malaysia, the supply growth of organic food cannot keep up with demand growth due to the slow transition from conventional to organic farming. To date, consumers are more preferred to choose food products that are naturally grown, good for health and may not harm the environment. This study examines the level of buying behaviour towards organic food among Malay consumers. Two hundred respondents were selected in this study by using the purposive sampling technique. The data were then analysed using descriptive analysis and measured using the mean score. The results showed high mean scores for all dependent and independent variables: consumer buying behaviour, attitude, subjective norm, and perceived behavioural control. Hence, this study can be concluded that Malay consumers would also like to consume organic food, but their socio-economic background may not permit them to have it frequently. The price of organic food is also known as pricey compared to non-organic. Hence, this study is significant for all stakeholders, including the farmer, policymaker, retailer and supplier, to ensure a good and sound organic food chain in Malaysia.
Analysis of NDVI and NDRE Indices Using Satellite Images for Crop Identification at Kelantan
Authors: Naguib N S , Daliman S
Published: December 2022

In Malaysia, the expansion of rubber trees, oil palm, and paddy plantations has become widely increased because of economic demands. Crop identification or monitoring is one of these applications since remote sensing provides precise, up-to-date, and cost-effective data on a range of crop kinds at various temporal and geographic resolutions. This study recommended integrating multispectral images, a tree canopy segmentation algorithm, and vegetable indicators to measure the attributes and spectral properties of crops and plants in a Kelantan region. Normalised difference vegetation index (NDVI) and normalised difference red edge (NDRE) were obtained from five spectral band images (red, green, blue, infrared (NIR), and red edge 2 (REDGE) that were processed by software into a full image map. NDVI is based on a plant’s characteristic reflection of a mix of visible red and near-infrared (NIR) light. NDVI function is to calculate the percentages of canopy cover, whereas the NDRE index is to assess leaf chlorophyll concentration or nitrogen content. The Red Edge sensors detected fluctuations in chlorophyll content within the leaf and throughout the plant canopy. Based on Landsat 8 and Sentinel 2A data, this study determined the NDVI and NDRE values for the crops in paddy fields, oil palm plantations and rubber tree plantations from different locations in Kelantan. The data was then analysed, the bar graphs and an emerging analysis of the differences between NDVI and NDRE maps for crop identification were used to present the results, respectively.
Consumption pattern of dairy products in Sabah, Malaysia during Covid-19
Authors: Seriger N S S B M J , Rahman M M , Umami N , Mat K , Nor M M , Rosli N D , Khalif R I A B R
Published: December 2022

Dairy production has a considerable effect on climate change due to emissions of greenhouse gases, but dairy products are meals that are well-known for their pleasant taste and nutritional value. During the Covid-19 outbreak, there were shortages of dairy goods on the shelves of grocery stores. This study investigated the consumption patterns of dairy products in Sabah. Using a pre-tested questionnaire, data were collected through online survey during Covid-19 outbreaks from 64 households comprising 16 from rural, 25 from town and 23 from city areas. The surveyed households were classified into 5 groups based on monthly household income: (i) ≤RM2000, (ii) RM2001-RM3000, (iii) RM3001-RM4000 and (iv) >RM4000. Among the participated households, 75% of respondents were female and 25% were male. There was a significant relationship among household income groups for fresh milk consumption. Regardless of areas and household incomes, the average monthly consumption for evaporated milk, fresh milk, condensed milk, powder milk, sweetmeats, yogurt, butter and ice cream per household were 1018g, 1425ml, 978g, 815g, 527g, 468g, 522g, and 650g, respectively. 28% of respondents monthly consumed 0.5-1.0 L fresh milk per household. 42%, 39%, 39%, 63%, 58%, 64% and 50% of respondents-- respectively-- monthly consumed evaporated milk, condensed milk, powder milk, sweetmeats, yogurt, butter and ice cream, where the amount of each component was not more than 500g per household. Results showed that 38% of respondents liked more on butter followed by cheese (30%), yogurt (20%), cream (9%) and condensed milk (3%). The 25% and 45% of respondents had reduced their consumption and expenditure behaviour, respectively. Results indicated that individual of city areas consumed more dairy products. Although cows add methane to our environment, organic dairy farming and husbandry methods can significantly reduce greenhouse gas emission.
Re-assessing Pollution Haven Hypothesis (PHH): corruption, FDI and CO2 emission
Authors: Huay Chong Siew , Li Tun Yin , Shah Said Zamin
Published: December 2022

In recent years, studies on the impact of international trade on environment been extensively debated. Stiff international trade market becomes a push factor for the firms to engage in race to bottom activity and therefore, firms reallocate their production plant overseas in the form of foreign direct investment (FDI). The reallocation of the production plants of firms into developing countries has causing the environment of the host countries depleting. The environmentalist claimed this scenario as Pollution Haven Hypothesis (PHH). In this study, System Generalized Method of Moments (S-GMM) is employed to address the gap in the literature with the focus on the role of corruption in PHH. With the focus of developing countries during 2002 to 2018, our result finds that PHH valid in a more corrupted country. Countries with higher level of corruption are attracting polluted FDI than less corrupted countries. The present study is imperative as it provides an opportunity to advance knowledge on the significant theoretical insights into the relationships between corruption and PHH in developing countries.
Benthic Macroinvertebrates Assemblages in the Fish Pond
Authors: Aida M Z , Aisyah S O S , Zamzani I M , Salam M A , Liyana A A , Aweng E R
Published: December 2022

Overall, small holder of fish farmers in Kelantan in particular does not monitor their pond water quality to maintain fish health due to tedious and expensive work. Hence, this study was proposed to identify the assemblages of benthic macroinvertebrates at the fish pond for potential as a tool for water quality assessment via biological indicator. The study area was in one of the small holder fish pond at Gua Musang, Kelantan, Malaysia. Benthic macroinvertebrates were collected monthly from March to August 2021. Benthic macroinvertebrates were collected by using a heavy-duty D-frame dip net combined with a bag-shaped. The ecological indices were calculated (Shannon diversity index, Margelef’s richness index, Pielou’s evenness index, and Simpson’s dominance index). Results showed a total of 356 individuals from 27 taxa of aquatic insects were collected. Corixidea (Hemiptera) recorded high abundance in July 2021. Even though there were differences in the abundance of benthos for monthly sampling, the season was only a part of the factors that might contribute, however the other factors cannot be neglected such as food availability, water quality and substrates composition conditions. Hopefully the findings could be used by the small holders to assess their pond water quality effectively with minimum cost.
Foxtail Palm Fruits as Potential Activated Carbon for Metamifop Removal
Authors: Yusoff N R Nik , Layli N N Mohd , Ghazi R Mohd , Jani M , Yusuf N N A N
Published: December 2022

The growing demand for rice as a staple food by the expanding human population forces farmers to use substantial pesticide pest control on their crops. Water pollution is a serious problem as a result of overuse of agrochemical pesticides. Nominee-M, a recently created post-emergence formulation herbicide that has been investigated, contains the active component metamifop. Herbicides that protect crops from weed infestation frequently contain this chemical. The purpose of this study was to examine the effectiveness and potential of foxtail palm fruits as a potential source of activated carbon for the elimination of metamifop. Nitric acid (HNO3) was used in the chemical process of chemical activation to create the activated carbon from the foxtail palm fruits. The effect of adsorbent dose used (2 g, 3 g, 4 g and 5 g), contact time (60 mins, 90 mins, 120 mins and 150 mins) and initial metamifop concentration (10 mg/L, 12 mg/L, 14 mg/L, 16 mg/L and 18 mg/L) toward the efficiency of the prepared activated carbon in removing metamifop was studied in this research. The highest percentage removal was 86.65%, obtained at optimized value of 3 g of activated carbon used at 60 minutes of contact time and 10 ppm of initial concentration of metamifop. The study has proven that activated carbon produce from foxtail palm fruit potentially reduce metamifop in water resources that has been contaminated.
Assessing the distribution of Piper porphyrophyllum (Sireh rimau) using species distribution model (SDM) in Kelantan, Peninsular Malaysia
Authors: Zulkeflee N H , Adek N B Nek , Norzin M A F , Awang A , Ismail N A , Daliman S , Amaludin N A
Published: December 2022

Piper porphyrophyllum (Lindl.) N.E.Br. is one of the genera from the family Piperaceae. The local names for Piper porphyrophyllum are Sireh Rimau, Kerakap Rimau or Akar Bugu. P. porphyrophyllum was recorded in Machang and Jeli, Kelantan. and very common in the forests of Peninsular Malaya, but flowers are scarcely ever found. However, limited information on its distribution occurred in Kelantan. The objective of this study is to map the potential distribution of P. porphyrophyllum that occurs in Kelantan using the Species Distribution Model (SDM). During the survey, a total of five individuals and twelve individuals of P. porphyrophyllum were recorded respectively at Pulai Chondong, Machang and Lata Cuit, Jeli, Kelantan. The potential distribution of P. porphyrophyllum that occurred in Kelantan was mapped using the species distribution model (SDM) to predict their occurrence in Kelantan and mostly distributed in Jeli and Gua Musang. According to the Malaysia Plant Red List P. porphyrophyllum is listed as Not Evaluated (NE).
Examining the Anatomical Characteristics of Rafflesia kerrii in Lojing Highlands, Peninsular Malaysia
Authors: Asfarina I , Siti-Munirah M Y , Susatya A , Norhazlini M Z , Zulhazman H
Published: December 2022

Rafflesia kerrii is an endemic species to Peninsular Malaysia and Southern part of Thailand. The genus grows without the vegetative components such as, leaves, stems and true roots, where the only visible structure is the flower itself. It is easy to identify R. kerrii by its large dull red flowers, perigones covered by numerous small white pinkish warts and a wide diaphragm opening. However, there is a scarcity of knowledge about the species’s anatomical traits. Herein, this study is aimed to evaluate the anatomical characteristics of R. kerrii in Lojing Highlands by using micro techniques analysis. The results were compared to those of a similar species found in Thailand. Four main components of flower were analysed, these are; the perigone lobe, window, processes and ramenta. The anatomical analysis of R. kerrii collected in Lojing Highlands have revealed that all the four components had simple and uncomplicated structures. Both upper and bottom layers of the plant have epidermal cell layers. The ground tissues also have an undeveloped vascular bundle. Based on the findings, the anatomical characteristics of R. kerrii found in Lojing Highlands and in Khao Sok National Park in Thailand were identical and shared similar types of main tissues. However, there are minor differences such as in the presence of starch grains, distance between vascular bundles in perigone lobe, and the presence of trichome in the compartment of windows.
Understanding the Socio-cultural Sustainability of Kedah Royalty and the Influences on the Palace’s Architecture
Authors: Muhammad S A , Rosdi N M
Published: December 2022

Socio-culture is a fundamental and common rule of a society that influences, controls, and directs the lives of individuals and societies. As the rulers with the most significant social status in a particular community, the Royals’ socio-culture is more sophisticated than commoners and heavily affected by royal customs and traditions. The royals’ socio-culture then affected the architecture of the palaces, notably the space arrangement, supporting the idea that socio-culture influences the constructed environment. This study aims to explicit the Kedah royalty’s socio-culture characteristics and influences in terms of traditional palace design in general and space arrangement. Qualitative approaches employ an analytical assessment of literature, historical and documentary sources, measured drawings and photos, site observation, and personal interviews to fulfill the study aims. The availability of secondary material and the absence of references limit the scope of the inquiry. According to the findings, the Kedah royalty’s socio-culture, including the activity system, privacy, family structure, the role and status of women, and social interaction, affected the characteristics of the residence palace architecture, notably the space arrangement. The case study demonstrates the Malay royal’s socio-cultural sustainability and relationship to palace architecture. Socio-cultural sustainability is a social development resilience component that shapes society’s future and the environmental aspects. The socio-cultural sustainability of the royal decree and ceremony is the essence of the hierarchical status between the royalty and the people that must be preserved as the civilization acknowledgment. The environmental aspects, such as the location of the dedicated palace influenced by the natural features like the mountain, river, and the sea, has definite practical meaning as the future references.
Importance - performance analysis of destination quality for ecotourism site in Tasik Puteri, Terengganu, Peninsular Malaysia
Authors: Hamid M A , Fuza Z I M , Mahmood R , Ahmad Z , Sinaga E K
Published: December 2022

The aim of this study was to investigate the destination qualities (activities and facilities) at Malaysian ecotourism locations between January and March 2022 using Importance and Performance Analysis. (IPA). Those who have visited Tasik Puteri in Dungun Terengganu are the respondents. The data were analysed and interpreted using the SPSS programme including reliability analysis, importance-performance analysis, and frequency analysis. The findings highlight the Tasik Puteri in Dungun Terengganu ecotourism areas’ destination quality. The result showed that ATV activities and public facilities, such as surau, convenience stores, parking, and waqaf, are found in quadrant 1 for continuing the good work. Facilities in Quadrant 2 should receive special attention, including restrooms, security guards, shower rooms, rental equipment, restaurants, and BBQ areas. Trekking, tubing, river cruises, fishing, and paddle boating are among the low priority pursuits in quadrant 3. While other activities such as camping, swimming, jogging, waterfall, kayaking, and playground facilities make up Quadrant 4’s potential overkill. The destination management company (DMC) will use the study’s findings to improve and strategically plan the short- and long-term development of this and future ecotourism sites. The growing understanding of destination qualities for ecotourism products is highlighted in this paper, along with the academic application of IPA analysis to destination attributes.
Comparison of common air pollutants, meteorological parameters, and cardio-respiratory hospitalization between urbanized areas in Kelantan
Authors: Sahar Nurul Najwa Mat , Ya’acob Siti Hajar , Awang Norrimi Rosaida , Ling Wong Hie , Nawawi Siti Aisyah
Published: December 2022

A high concentration of air pollution is relational to meteorological conditions and the consequences can lead to health problems which are cardiovascular and respiratory-related diseases. This study aimed to compare air pollution, meteorological reading, and hospitalization in urbanized areas in Kelantan. The secondary data for this study were obtained from DOE and MOH for descriptive and trend analysis from the year 2000 until 2015 at three different locations: Tanah Merah, Pengkalan Chepa, and Kota Bharu Kelantan. The mean concentration for SO2, O3, CO, NO2, and PM10 were 0.001 ± 0.001 μg/m3, 0.014 ± 0.004 μg/m3, 0.657 ± 0.145 mg/m3, 0.007 ± 0.002 μg/m3 and 45.195 ± 11.229 μg/m3 respectively. Overall, the concentration of all the criteria air pollutants was lower than the MAAQS except for PM10. The trend analysis shows the concentration of air pollutants, and the meteorological parameter were fluctuating and influenced by the monsoon. High wind speed and temperature were observed during the NE and SW monsoon, respectively. Tanah Merah showed a higher concentration of PM10 compared to the other two locations. In contrast, Kota Bharu and Pengkalan Chepa has higher gasses concentration than Tanah Merah. The gasses result in consistent with cardio and respiratory-related hospitalization which showed higher hospitalization recorded in Kota Bharu than Tanah Merah. In conclusion, the urbanized areas have different dominant air pollutants due to the potential major sources that exist differently.
Assessment of Risk Perception on Microplastics Pollution in Drinking Water Sources
Authors: Mahmod N A I , Saipolbahri N , Subki N S , Fauzi N M
Published: December 2022

Degradation of plastic debris in the marine environment has become a global issue. Microplastics may affect the human health and aquatic life. Therefore, a survey has been conducted on higher institutional students towards the risk perception of microplastics pollution in drinking water sources to increase awareness regarding microplastic pollution. On top of that, this study aims to measure the level of risk perception and the relationship between risk perception, concern and behavioural intentions of the respondents towards microplastics pollution in drinking water sources. In this study, questionnaires are distributed through an online platform to conduct the survey involving 320 respondents. Analysis of independent t-test, ANOVA, correlation and multiple linear regression has been used to analyse the data. It shows that the factor gender does not influencing the risk perception, concern and behavioural intentions of the respondents on microplastics pollution in drinking water sources. The results show a positive correlation between each variable. However, multiple linear regression analysis shows that the behavioural intentions do not significantly affect the level of respondents’ risk perceptions.
Solid Waste Disposal Practices Among Rural Community in Pasir Mas, Kelantan, Malaysia
Authors: Lukman N L M M , Halim N S A , Ling W H , Wee S T , Abas M A
Published: December 2022

Nowadays, improper solid waste disposal is a severe issue due to its impacts on environment, social, and economic sustainability. This manuscript aims to identify the knowledge and awareness of the rural community in Kg Tok Uban, Pasir Mas, Kelantan about solid waste disposal. Besides that, the socio-demographic factors that influence the knowledge and awareness of respondents have also been explored. The data was collected using an online survey questionnaire. A total of 232 respondents participated in this study through the convenience sampling method. The findings indicated that most respondents have good knowledge of proper solid waste disposal. Besides that, this study also revealed that most respondents have a good awareness of the impact of improper solid waste disposal. However, this study found that the respondents have moderate solid waste disposal practices. Even though people have good awareness and knowledge, it doesn’t lead them to good practices in solid waste disposal. Different gender, age, and income of respondents are significantly influence the knowledge and awareness of respondents. The findings of this study are significant for local governments to strive toward effective solid waste management in rural areas.
Characterization Effect of Polysulfone Membranes with Different Molecular Weight of Polyethylene Glycol Additives
Authors: Ismail Nurul Qistina , Azmi Nur Aina , Shoparwe Noor Fazliani , Ameram Nadiah , Yusoff Abdul Hafidz
Published: December 2022

Nowadays, membrane technology has gaining popularity in biotechnology, food processing, water treatment, pharmaceutical and semiconductor industries. It been reported as a potential technique for separation due to their low-cost process, does not used many chemical and energy sufficient. However, there is less study about polysulfone (PSF) used as a polymer based in membrane filtration with polyethylene glycol (PEG) as additives in different molecular weight (Mw: 400, 600, 1500, and 4000 Da). Therefore, this study has been conducted to investigate the effect of different molecular weight of PEG in terms of thermal stability, hydrophilicity, and porosity. For methodology, PSF polymer was fabricated with PEG and Dimethylacetamide (DMAc) act as solvent via wet phase inversion method. The physical, thermal and chemical characterization were analysed using Fourier transform infrared spectroscopy (FTIR), thermogravimetric analysis (TGA), and laboratory testing of contact angle, water uptake, and porosity. The result showed improvement in fabricated membranes hydrophilicity than pure membrane. PEG with high molecular weight demonstrated the higher membrane hydrophilicity, good thermal stability (38.40%), contact angle (54°), higher water uptake (385.23%), and higher porosity (82.72%). As conclusion, PSF with addition of the high molecular weight of PEG (PEG4000) can improve the performance of membrane filtration.
Group Outcomes for Time-Weighted Averaging in WBGT-Based Heat Stress Exposure Assessment
Authors: Bernard Thomas E , Flach John W , Ashley Candi D
Published: December 2022

The wet bulb globe temperature (WBGT)-based occupational exposure limits (OELs) were developed from steady exposures to heat stress at constant WBGT and metabolic rate (M). The exposure limits were based on compensable heat stress exposures at the upper limit of the prescriptive zone for most healthy people. Professional practice allows for using time-weighted averages (TWAs) of WBGT and M to account for heterogeneous heat stress exposures. The purpose of the current paper was to report on the effectiveness of time-weighted averaging to assess occupational heat stress using published studies. Our hypothesis was using TWA-WBGT and TWA-M was as protective as the recommended OELs for steady exposures. The current paper reports on 62 observations of work that alternate between at least two heat stress conditions (usually work and recovery) reported in 16 papers. The TWA-WBGT and TWA-M were determined for all observations. ΔLimit was the observed TWA-WBGT minus the exposure limit at the TWA-M based on acclimatization state. The observations were then classified as above or below ΔLimit = 0. Each observation was also classified as uncompensable if the mean core temperature for the group was greater than 38°C or a less tolerant individual was above 38.5°C. When comparing exposure classifications to outcome classifications using 2 × 2 tables, the sensitivity and specificity for all observations were 0.72 and 0.73, respectively. The sensitivity was much less than the expected value near 1.0, and the large difference called into question the ability of TWAs to represent actual heat stress. There was some suspicion that there were differences between acclimatized and unacclimatized observations. Before any of these findings are embedded in policy or practice, a more careful evaluation of TWAs is required. In conclusion, we believe that the use of TWAs for heat stress analysis was not fully evaluated, and we proposed a framework for evaluation.
Transitioning between ‘Outside’ and ‘Inside’ Knowledge in an Online University EMI Chemistry Course
Authors: Bozbiyik Merve , Morton Tom
Published: December 2022

Recent studies in applied linguistics research have focused on how teachers draw on ‘outside’ knowledge relating to students’ everyday life for the purpose of teaching subject matter content. This study focuses on such practices in the context of English-medium instruction (EMI) higher education in an online undergraduate chemistry module. Adopting an interdisciplinary perspective, the study combines multimodal Conversation Analysis (CA) and the Autonomy dimension of Legitimation Code Theory (LCT) to examine how one lecturer shifts between ‘inside’ knowledge of chemistry and ‘outside’ knowledge for a range of different purposes. Multimodal CA is used to carry out micro-analyses of epistemics and identity-related positioning in interaction, while LCT ‘autonomy codes’ are used to trace knowledge-building trajectories in which knowledge is positioned inside or outside the target topic and is used for different purposes. The analyses highlight how the lecturer skilfully deployed a range of semiotic resources in transitioning between ‘inside’ and ‘outside’ knowledge, and how these resources were leveraged for the building of disciplinary knowledge. Implications of this interdisciplinary approach for research and practice in university EMI contexts are discussed.
A realist approach to understanding alliancing within Local Government public health and social care service provision
Authors: Redgate S , Spencer L , Adams E A , Arnott B , Brown H , Christie A , Hardy C , Harrison H , Kaner E , Mawson C , McGovern W , Phillips P , Rankin J , McGovern R
Published: December 2022

Background

Within the current context of continued austerity and post-pandemic recovery, it remains important that Local Government services address the increasing needs of residents as cost-effectively as possible. Alliancing, whereby services work collaboratively focusing on the ‘whole-system’, has gained popularity as a tool with the potential to support collaborative whole systems approaches. This synthesis aims to identify how alliancing can be successfully operationalised in the commissioning of public health, wider National Health Service (NHS) and social care-related services.

Methods

A realist literature synthesis was undertaken in order to identify underlying generative mechanisms associated with alliancing, the contextual conditions surrounding the implementation and operationalisation of the alliancing approach mechanisms, and the outcomes produced as a result. An iterative approach was taken, using a recent systematic review of the effectiveness of Alliancing, online database searches, and grey literature searches.

Results

Three mechanistic components were identified within the data as being core to the successful implementation of alliances in public health and social care-related services within Local Government: (i) Achieving a system-level approach; (ii) placing local populations at the heart of the system; and (iii) creating a cultural shift. Programme theories were postulated within these components.

Conclusions

The alliancing approach offers an opportunity to achieve system-level change with the potential to benefit local populations. The realist synthesis approach taken within this study has provided insights into the necessary contextual and mechanistic factors of the Alliancing approach, above and beyond effectiveness outcomes typically collected through more conventional evaluation methodologies.
Development and applications of a CRISPR activation system for facile genetic overexpression in Candida albicans
Authors: Gervais Nicholas C , La Bella Alyssa A , Wensing Lauren F , Sharma Jehoshua , Acquaviva Victoria , Best Madison , Cadena López Ricardo Omar , Fogal Meea , Uthayakumar Deeva , Chavez Alejandro , Santiago-Tirado Felipe , Flores-Mireles Ana L , Shapiro Rebecca S
Published: December 2022

For the fungal pathogen Candida albicans, genetic overexpression readily occurs via a diversity of genomic alterations, such as aneuploidy and gain-of-function mutations, with important consequences for host adaptation, virulence, and evolution of antifungal drug resistance. Given the important role of overexpression on C. albicans biology, it is critical to develop and harness tools that enable the analysis of genes expressed at high levels in the fungal cell. Here, we describe the development, optimization, and application of a novel, single-plasmid-based CRISPR activation (CRISPRa) platform for targeted genetic overexpression in C. albicans, which employs a guide RNA to target an activator complex to the promoter region of a gene of interest, thus driving transcriptional expression of that gene. Using this system, we demonstrate the ability of CRISPRa to drive high levels of gene expression in C. albicans, and we assess optimal guide RNA targeting for robust and constitutive overexpression. We further demonstrate the specificity of the system via RNA sequencing. We highlight the application of CRISPR activation to overexpress genes involved in pathogenesis and drug susceptibility, and contribute toward the identification of novel phenotypes. Consequently, this tool will facilitate a broad range of applications for the study of C. albicans genetic overexpression.
Genetics of tibia bone properties of crossbred commercial laying hens in different housing systems
Authors: Johnsson Martin , Wall Helena , Lopes Pinto Fernando A , Fleming Robert H , McCormack Heather A , Benavides-Reyes Cristina , Dominguez-Gasca Nazaret , Sanchez-Rodriguez Estefania , Dunn Ian C , Rodriguez-Navarro Alejandro B , Kindmark Andreas , de Koning Dirk-Jan
Published: December 2022

Osteoporosis and bone fractures are a severe problem for the welfare of laying hens, with genetics and environment, such as housing system, each making substantial contributions to bone strength. In this work, we performed genetic analyses of bone strength, bone mineral density, and bone composition, as well as body weight, in 860 commercial crossbred laying hens from 2 different companies, kept in either furnished cages or floor pens. We compared bone traits between housing systems and crossbreds and performed a genome-wide association study of bone properties and body weight. As expected, the 2 housing systems produced a large difference in bone strength, with layers housed in floor pens having stronger bones. These differences were accompanied by differences in bone geometry, mineralization, and chemical composition. Genome scans either combining or independently analyzing the 2 housing systems revealed no genome-wide significant loci for bone breaking strength. We detected 3 loci for body weight that were shared between the housing systems on chromosomes 4, 6, and 27 (either genome-wide significant or suggestive) and these coincide with associations for bone length. In summary, we found substantial differences in bone strength, content, and composition between hens kept in floor pens and furnished cages that could be attributed to greater physical activity in pen housing. We found little evidence for large-effect loci for bone strength in commercial crossbred hens, consistent with a highly polygenic architecture for bone strength in the production environment. The lack of consistent genetic associations between housing systems in combination with the differences in bone phenotypes could be due to gene-by-environment interactions with housing system or a lack of power to detect shared associations for bone strength.
Differences in homologous recombination and maintenance of heteropolyploidy between Haloferax volcanii and Haloferax mediterranei
Authors: Dattani Ambika , Sharon Itai , Shtifman-Segal Ella , Robinzon Shachar , Gophna Uri , Allers Thorsten , Altman-Price Neta
Published: December 2022

Polyploidy, the phenomenon of having more than one copy of the genome in an organism, is common among haloarchaea. While providing short-term benefits for DNA repair, polyploidy is generally regarded as an “evolutionary trap” that by the notion of the Muller's ratchet will inevitably conclude in the species' decline or even extinction due to a gradual reduction in fitness. In most reported cases of polyploidy in archaea, the genetic state of the organism is considered as homoploidy i.e. all copies of the genome are identical. Here we demonstrate that while this is indeed the prevalent genetic status in the halophilic archaeon Haloferax volcanii, its close relative H. mediterranei maintains a prolonged heteroploidy state in a nonselective environment once a second allele is introduced. Moreover, a strong genetic linkage was observed between two distant loci in H. mediterranei indicating a low rate of homologous recombination while almost no such linkage was shown in H. volcanii indicating a high rate of recombination in the latter species. We suggest that H. volcanii escapes Muller's ratchet by means of an effective chromosome-equalizing gene-conversion mechanism facilitated by highly active homologous recombination, whereas H. mediterranei must elude the ratchet via a different, yet to be elucidated mechanism.
Pleiotropic fitness effects of a Drosophila odorant-binding protein
Authors: Mokashi Sneha S , Shankar Vijay , Johnstun Joel A , Mackay Trudy F C , Anholt Robert R H
Published: December 2022

Insect odorant-binding proteins (OBPs) are members of a rapidly evolving multigene family traditionally thought to facilitate chemosensation. However, studies on Drosophila have shown that members of this family have evolved functions beyond chemosensation, as evident from their expression in reproductive tissues and the brain. Previous studies implicated diverse functions of Obp56h, a member of the largest gene cluster of the D. melanogaster Obp repertoire. Here, we examined the effect of CRISPR/Cas9-mediated deletion of Obp56h on 2 fitness phenotypes, on resistance to starvation stress and heat stress, and on locomotion and sleep phenotypes. Obp56h−/− mutants show a strong sexually dimorphic effect on starvation stress survival, with females being more resistant to starvation stress than the control. In contrast, Obp56h−/− females, but not males, are highly sensitive to heat stress. Both sexes show changes in locomotion and sleep patterns. Transcriptional profiling of RNA from heads of Obp56h−/− flies and the wildtype control reveals differentially expressed genes, including gene products associated with antimicrobial immune responses and members of the Turandot family of stress-induced secreted peptides. In addition, differentially expressed genes of unknown function were identified in both sexes. Genes encoding components of the mitochondrial electron transport chain, cuticular proteins, gene products associated with regulation of feeding behavior (Lst and CCHa2), ribosomal proteins, lncRNAs, snoRNAs, tRNAs, and snRNAs show changes in transcript abundances in Obp56h−/− females. These differentially expressed genes are likely to contribute to Obp56h-mediated effects on the diverse phenotypes that arise upon deletion of this OBP.
The Gossypium herbaceum L. Wagad genome as a resource for understanding cotton domestication
Authors: Ramaraj Thiruvarangan , Grover Corrinne E , Mendoza Azalea C , Arick Mark A , Jareczek Josef J , Leach Alexis G , Peterson Daniel G , Wendel Jonathan F , Udall Joshua A
Published: December 2022

Gossypium herbaceum is a species of cotton native to Africa and Asia that is one of the 2 domesticated diploids. Together with its sister-species G. arboreum, these A-genome taxa represent models of the extinct A-genome donor of modern polyploid cotton, which provide about 95% of cotton grown worldwide. As part of a larger effort to characterize variation and improve resources among diverse diploid and polyploid cotton genomes, we sequenced and assembled the genome of G. herbaceum cultivar (cv.) Wagad, representing the first domesticated accession for this species. This chromosome-level genome was generated using a combination of PacBio long-read technology, HiC, and Bionano optical mapping and compared to existing genome sequences in cotton. We compare the genome of this cultivar to the existing genome of wild G. herbaceum subspecies africanum to elucidate changes in the G. herbaceum genome concomitant with domestication and extend these analyses to gene expression using available RNA-seq. Our results demonstrate the utility of the G. herbaceum cv. Wagad genome in understanding domestication in the diploid species, which could inform modern breeding programs.
Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli
Authors: Breckell Georgia L , Silander Olin K
Published: December 2022

DNA methylation in bacteria frequently serves as a simple immune system, allowing recognition of DNA from foreign sources, such as phages or selfish genetic elements. However, DNA methylation also affects other cell phenotypes in a heritable manner (i.e. epigenetically). While there are several examples of methylation affecting transcription in an epigenetic manner in highly localized contexts, it is not well-established how frequently methylation serves a more general epigenetic function over larger genomic scales. To address this question, here we use Oxford Nanopore sequencing to profile DNA modification marks in three natural isolates of Escherichia coli. We first identify the DNA sequence motifs targeted by the methyltransferases in each strain. We then quantify the frequency of methylation at each of these motifs across the entire genome in different growth conditions. We find that motifs in specific regions of the genome consistently exhibit high or low levels of methylation. Furthermore, we show that there are replicable and consistent differences in methylated regions across different growth conditions. This suggests that during growth, E. coli transiently differentiate into distinct methylation states that depend on the growth state, raising the possibility that measuring DNA methylation alone can be used to infer bacterial growth states without additional information such as transcriptome or proteome data. These results show the utility of using Oxford Nanopore sequencing as an economic means to infer DNA methylation status. They also provide new insights into the dynamics of methylation during bacterial growth and provide evidence of differentiated cell states, a transient analog to what is observed in the differentiation of cell types in multicellular organisms.
Comparative genomics of five Valsa species gives insights on their pathogenicity evolution
Authors: Sun Guangchao , Xie Shichang , Tang Lin , Zhao Chao , Zhang Mian , Huang Lili
Published: December 2022

Valsa is a genus of ascomycetes within the Valsaceae family. This family includes many wood destructive pathogens such as the well known Valsa mali and Valsa pyri which cause canker diseases in fruit trees and threaten the global fruit production. Lack of genomic information of this family is impeding our understandings about their evolution and genetic basis of their pathogenicity divergence. Here, we report genome assemblies of Valsa malicola, Valsa persoonii, and Valsa sordida which represent close relatives of Valsa mali and Valsa pyri with different host preferences. Comparative genomics analysis revealed that segmental rearrangements, inversions, and translocations frequently occurred among Valsa spp. genomes. Gene families that exhibited gene copy expansions tended to be associated with secondary metabolism, transmembrane transport, and pyrophosphatase activities. Orthologous genes in regions lost synteny exhibited significantly higher rate of synonymous substitution (KS) than those in regions retained synteny. Moreover, among these genes, membrane transporter families associated with antidrug (MFS, DHA) activities and nutrient transportation (SP and APCs) activities were significantly over-represented. Lineage specific synonymous substitution (KS) and nonsynonymous substitution (KA) analysis based on the phylogeny constructed from 11 fungal species identified a set of genes with selection signatures in Valsa clade and these genes were significantly enriched in functions associated with fatty acid beta-oxidation, DNA helicase activity, and ATPase activity. Furthermore, unique genes that possessed or retained by each of the five Valsa species are more likely part of the secondary metabolic (SM) gene clusters. SM gene clusters conserved across five Valsa species showed various degrees of diversification in both identity and completeness. All 11 syntenically conserved SM clusters showed differential expression during the infection of apple branch with Valsa mali suggesting involvements of secondary metabolism in the pathogenicity of Valsa species.
Envirome-wide associations enhance multi-year genome-based prediction of historical wheat breeding data
Authors: Costa-Neto Germano , Crespo-Herrera Leonardo , Fradgley Nick , Gardner Keith , Bentley Alison R , Dreisigacker Susanne , Fritsche-Neto Roberto , Montesinos-López Osval A , Crossa Jose
Published: December 2022

Linking high-throughput environmental data (enviromics) to genomic prediction (GP) is a cost-effective strategy for increasing selection intensity under genotype-by-environment interactions (G × E). This study developed a data-driven approach based on Environment–Phenotype Association (EPA) aimed at recycling important G × E information from historical breeding data. EPA was developed in two applications: (1) scanning a secondary source of genetic variation, weighted from the shared reaction-norms of past-evaluated genotypes and (2) pinpointing weights of the similarity among trial-sites (locations), given the historical impact of each envirotyping data variable for a given site. These results were then used as a dimensionality reduction strategy, integrating historical data to feed multi-environment GP models, which led to the development of four new G × E kernels considering genomics, enviromics, and EPA outcomes. The wheat trial data used included 36 locations, 8 years, and three target populations of environments (TPEs) in India. Four prediction scenarios and six kernel models within/across TPEs were tested. Our results suggest that the conventional GBLUP, without enviromic data or when omitting EPA, is inefficient in predicting the performance of wheat lines in future years. Nevertheless, when EPA was introduced as an intermediary learning step to reduce the dimensionality of the G × E kernels while connecting phenotypic and environmental-wide variation, a significant enhancement of G × E prediction accuracy was evident. EPA revealed that the effect of seasonality makes strategies such as “covariable selection” unfeasible because G × E is year-germplasm specific. We propose that the EPA effectively serves as a “reinforcement learner” algorithm capable of uncovering the effect of seasonality over the reaction-norms, with the benefits of better forecasting the similarities between past and future trialing sites. EPA combines the benefits of dimensionality reduction while reducing the uncertainty of genotype-by-year predictions and increasing the resolution of GP for the genotype-specific level.