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Fulltext Gene co-expression networks from RNA sequencing of dairy cattle identifies genes and pathways affecting feed efficiency

Salleh SM, Mazzoni G, Løvendahl P, Kadarmideen HN

BMC Bioinformatics, 2018 Dec 17;19(1):513.
PMID: 30558534 DOI: 10.1186/s12859-018-2553-z

BACKGROUND: Selection for feed efficiency is crucial for overall profitability and sustainability in dairy cattle production. Key regulator genes and genetic markers derived from co-expression networks underlying feed efficiency could be included in the genomic selection of the best cows. The present study identified co-expression networks associated with high and low feed efficiency and their regulator genes in Danish Holstein and Jersey cows. RNA-sequencing data from Holstein and Jersey cows with high and low residual feed intake (RFI) and treated with two diets (low and high concentrate) were used. Approximately 26 million and 25 million pair reads were mapped to bovine reference genome for Jersey and Holstein breed, respectively. Subsequently, the gene count expressions data were analysed using a Weighted Gene Co-expression Network Analysis (WGCNA) approach. Functional enrichment analysis from Ingenuity® Pathway Analysis (IPA®), ClueGO application and STRING of these modules was performed to identify relevant biological pathways and regulatory genes.
RESULTS: WGCNA identified two groups of co-expressed genes (modules) significantly associated with RFI and one module significantly associated with diet. In Holstein cows, the salmon module with module trait relationship (MTR) = 0.7 and the top upstream regulators ATP7B were involved in cholesterol biosynthesis, steroid biosynthesis, lipid biosynthesis and fatty acid metabolism. The magenta module has been significantly associated (MTR = 0.51) with the treatment diet involved in the triglyceride homeostasis. In Jersey cows, the lightsteelblue1 (MTR = - 0.57) module controlled by IFNG and IL10RA was involved in the positive regulation of interferon-gamma production, lymphocyte differentiation, natural killer cell-mediated cytotoxicity and primary immunodeficiency.
CONCLUSION: The present study provides new information on the biological functions in liver that are potentially involved in controlling feed efficiency. The hub genes and upstream regulators (ATP7b, IFNG and IL10RA) involved in these functions are potential candidate genes for the development of new biomarkers. However, the hub genes, upstream regulators and pathways involved in the co-expressed networks were different in both breeds. Hence, additional studies are required to investigate and confirm these findings prior to their use as candidate genes.
The Distribution and Conservation Status of Green Turtles (Chelonia mydas) and Olive Ridley Turtles (Lepidochelys olivacea) on Pulau Pinang beaches (Malaysia), 1995-2009

Salleh SM, Yobe M, Sah SA

Trop Life Sci Res, 2012 May;23(1):63-76.
PMID: 24575226

The Green Turtle (Chelonia mydas) and Olive Ridley Turtle (Lepidochelys olivacea) are the only sea turtles with recorded landings in the Pulau Pinang coastal area. The Green Turtle has been the most abundant and widely distributed sea turtle in this area since it was first surveyed in 1995. Statistical analysis by the Pulau Pinang Department of Fisheries on the distribution of sea turtles from 2001 through 2009 has identified Pantai Kerachut and Telok Kampi as the most strongly preferred beaches for Green Turtle landings, with records for almost every month in every year. Green Turtle tracks and nests have also been found along the coast of Pulau Pinang at Batu Ferringhi, Tanjong Bungah, Pantai Medan, Pantai Belanda, Telok Kumbar, Gertak Sanggul, Moonlight Beach, Telok Duyung, Telok Aling, Telok Bahang and Telok Katapang. The Olive Ridley Turtle is present in smaller numbers; landing and nesting have only been recorded on a few beaches. There are no previous records of Olive Ridley landings at Pantai Kerachut and Telok Kampi, but tracks and nests have been found at Telok Kumbar, Tanjong Bungah, Pantai Medan, Telok Duyung and Gertak Sanggul. A Turtle Conservation Centre has been established at Pantai Kerachut to protect these species from extinction in Pulau Pinang. This paper presents details of the records and distribution of sea turtles in Pulau Pinang from 1995 through 2009.
Fulltext Study of sexual behaviours with different types of estrus synchronization protocols in Boer goats

Salleh SM, Basri AMH, Yaakub H

Anim Reprod, 2021;18(3):e20200038.
PMID: 34691262 DOI: 10.1590/1984-3143-AR2020-0038

There is still a lack of information on estrus synchronization in goats. Understanding the estrus synchronization protocols and the subsequent effects is important to improve the efficiency of assisted reproductive technologies (ARTs) and subsequently would improve the breeding procedures. This study will help in determining the most suitable estrus synchronization protocol and understand better the effect on the sexual behaviour and hormonal effects in goats. A total of 127 Boer does were used and divided into three groups with different duration of CIDR insertion intravaginally either for 14 (two groups) or 9 days (one group). Approximately 0.5 ml Estrumate® (PG) was administered intramuscularly to all groups at CIDR removal, and only groups PMSG14 and PMSG9 were administered with 200IU of Pregnant Mare Serum Gonadotropin (PMSG) intramuscularly. Estrus signs were observed at 4 h intervals and blood samples were collected for progesterone and luteinizing hormone determination. The percentage of does in estrus within 24 to 72 h post CIDR removal was significantly higher (P<0.05) in groups with PMSG compared to the group without the PMSG. The numbers of does display estrus signs within 24 to 28 h post CIDR removal were significantly higher (P<0.05) in group shorter period (9 days) compared to groups with 14 days CIDR. The P4 concentrations at 24 hours post CIDR removals and LH concentration was not significantly different (P>0.05) in all groups. The time of the LH peak in the group without the PMSG was significantly delayed (P<0.05) when compared to group 9 days CIDR and administered with PMSG. It is recommended to use the treatment for 9 days CIDR since the estrous cycle can be shortened.
Using machine learning methods to predict dry matter intake from milk mid-infrared spectroscopy data on Swedish dairy cattle

Salleh SM, Danielsson R, Kronqvist C

J Dairy Res, 2023 Mar 01.
PMID: 36855229 DOI: 10.1017/S0022029923000171

In this research communication we compare three different approaches for developing dry matter intake (DMI) prediction models based on milk mid-infrared spectra (MIRS), using data collected from a research herd over five years. In dairy production, knowledge of individual DMI could be important and useful, but DMI can be difficult and expensive to measure on most commercial farms as cows are commonly group-fed. Instead, this parameter is often estimated based on the age, body weight, stage of lactation and body condition score of the cow. Recently, milk MIRS have also been used as a tool to estimate DMI. There are different methods available to create prediction models from large datasets. The main data used were total DMI calculated as a 3-d average, coupled with milk MIRS data available fortnightly. Data on milk yield and lactation stage parameters were also available for each animal. We compared the performance of three prediction approaches: partial least-squares regression, support vector machine regression and random forest regression. The full milk MIRS alone gave low to moderate prediction accuracy (R2 = 0.07-0.40), regardless of prediction modelling approach. Adding more variables to the model improved R2 and decreased the prediction error. Overall, partial least-squares regression proved to be the best method for predicting DMI from milk MIRS data, while MIRS data together with milk yield and concentrate DMI at 3-30 d in milk provided good prediction accuracy (R2 = 0.52-0.65) regardless of the prediction tool used.
Fulltext A Preliminary Insight into an Islamic Mechanism for Neuroethics

Baharuddin A, Musa MN, Salleh SS

Malays J Med Sci, 2016 Jan;23(1):1-3.
PMID: 27540319 MyJurnal

Muslim relies on the structure or guideline of shari'ah or the maqasid al-shariah, which consist of five essential values, namely preservation/protection of faith, life, intellect, property, and dignity/lineage - to guide them in discovering guiding principles for new concerns such as posed by neuroscience. Like in the case of brain imaging technology, there is in need for proper explanation within Islamic and among the Muslim scientists/scholars on how Islamic beliefs, values, and practices might cumulatively provide 'different' meanings to the practice and application of this technology, or whether it is in line with the shari'ah - in the context of preservation of health and protection of disease. This paper highlights the Islamic mechanism for neuroethics as basis for a holistic ethical framework of neuroscience to cope with its new, modern, and emerging technologies in the globalised world, and how Muslim should response to such changes.
Enhanced rhamnolipid production by Pseudomonas aeruginosa USM-AR2 via fed-batch cultivation based on maximum substrate uptake rate

Noh NA, Salleh SM, Yahya AR

Lett Appl Microbiol, 2014 Jun;58(6):617-23.
PMID: 24698293 DOI: 10.1111/lam.12236

A fed-batch strategy was established based on the maximum substrate uptake rate (MSUR) of Pseudomonas aeruginosa USM-AR2 grown in diesel to produce rhamnolipid. This strategy matches the substrate feed rates with the substrate demand based on the real-time measurements of dissolved oxygen (DO). The MSUR was estimated by determining the time required for consumption of a known amount of diesel. The MSUR trend paralleled the biomass profile of Ps. aeruginosa USM-AR2, where the MSUR increased throughout the exponential phase indicating active substrate utilization and then decreased when cells entered stationary phase. Rhamnolipid yield on diesel was enhanced from 0·047 (g/g) in batch to 0·110 (g/g) in pulse-pause fed-batch and 0·123 (g/g) in MSUR fed-batch. Rhamnolipid yield on biomass was also improved from 0·421 (g/g) in batch, 3·098 (g/g) in pulse-pause fed-batch to 3·471 (g/g) using MSUR-based strategy. Volumetric productivity increased from 0·029 g l(-1) h(-1) in batch, 0·054 g l(-1) h(-1) in pulse-pause fed-batch to 0·076 g l(-1) h(-1) in MSUR fed-batch.
Fulltext Assessing Nesting Status of Green Turtles, Chelonia Mydas in Perak, Malaysia

Salleh SM, Sah SAM, Chowdhury AJK

Trop Life Sci Res, 2018 Mar;29(1):155-171.
PMID: 29644022 MyJurnal DOI: 10.21315/tlsr2018.29.1.11

The nesting of green turtle (Chelonia mydas) was monitored from 1998 untill 2013 along the beaches of Pasir Panjang, Segari, Perak. The objective of the study is to assess the nesting status of green turtles in Perak, Peninsular Malaysia in terms of total nests, eggs, survival hatchings, and density of visitors. A total number of green turtle nests found for 16 years were 1,019 nests and varied from 10 to 220 nests per year. Meanwhile, the sum of eggs collected for 16 years were 107,820 eggs, and varied from 553 to 20,881 eggs per year. The temporal pattern of nesting indicates year-round nesting in Perak in most years within the 16 years period. The peak season of nesting was estimated to occur between May and June. Survival hatchlings varied from 23.33% (2,071 hatchlings) to 55.03% (5,018 hatchlings) from 1998 to 2013. The density of visitors was not uniformly distributed among the years, and shows a sign of decline especially from 2006 onwards. This publication provides basic knowledge of green turtle nesting population in Perak, and would be helpful in upgrading the conservation program in Malaysia. In future, we hope 1) for an increase in manpower to obtain accurate nesting records along the nesting beaches during nocturnal survey and, 2) to include the breeding biology data such as nest placement, emergence hour, and morphological characteristics of green turtle.
Fulltext The Survival Rate from Splitting Clutch Design Method for Green Turtle's Relocated Nest in Penang Island, Malaysia

Salleh SM, Sah SAM, Chowdhury AJK

Trop Life Sci Res, 2022 Sep;33(3):107-127.
PMID: 36545050 DOI: 10.21315/tlsr2022.33.3.7

Ten nests were collected from Kerachut and Teluk Kampi, Penang Island between 2 August 2009 and 9 December 2009, and each one nest was split into three small clutch sizes for incubation at three nesting depths (45 cm, 55 cm and 65 cm), with a total of 30 modified nests for this experiment. Three important objectives were formulated; to observe on the survival hatchings among the three nesting depths, to study on the effects of sand temperature on incubation period among the three nesting depths, and to investigate the influence of sand temperature on hatchling's morphology. Main result shows that the mean survival of the hatchlings was 25.40% at 45 cm nesting depth, followed by mean 17.60% at 55 cm nesting depth, and lastly, the mean was 21.50% at 65 cm nesting depth. Overall, there are 56.63% survival hatchlings, 10.97% dead hatchlings and 32.40% unhatched eggs were produced. The incubation period was also found to be significantly correlated with sand temperature, p > 0.001, and nesting depth, p < 0.001. The hatchling's length and weight varies is sizes across the nesting depths, p < 0.001. However, the small difference in hatchling sizes per nesting depths are not strong enough to prove the significant correlation with sand temperature, p > 0.05. This article provides a basic knowledge from the splitting clutch design method. A sum of 50%-60% survivals hatchlings produced were incubating under small range of clutch sizes, 29 to 49 eggs. This article provides basic result on the survival hatchlings, eggs survivorship, incubation period, temperature, hatchling's morphology and discussion on implication of this method on conservation in Malaysia.
Effect of feeding Pleurotus pulmonarius-treated empty fruit bunch on nutrient digestibility and milk fatty acid profiles in goats

Zailan MZ, Salleh SM, Abdullah S, Yaakub H

Trop Anim Health Prod, 2023 Nov 10;55(6):402.
PMID: 37950132 DOI: 10.1007/s11250-023-03817-8

This study aimed to evaluate the effect of feeding P. pulmonarius-treated empty fruit bunch (FTEFB) on the nutrient intakes, digestibility, milk yield and milk profiles of lactating Saanen goats. A total of nine lactating Saanen goats were used in an incomplete cross-over experimental design. The balanced dietary treatments contain different replacement levels of Napier grass with FTEFB at 0% (0-FT), 25% (25-FT) and 50% (50-FT). The FTEFB contained crude protein (CP), neutral detergent fibre (NDF), acid detergent fibre (ADF) and acid detergent lignin (ADL) at 4.10, 94.6, 70.8 and 19.4% DM, respectively. The replacement of FTEFB in 25-FT did not alter dry matter, NDF, hemicellulose, ADL, ether extract and gross energy intakes when compared to the control fed group (0-FT). The ADF and cellulose intake was higher in 25-FT than in the others (P 0.05). There are no differences in milk fatty profiles between dietary treatments (P > 0.05), except for OCFA. Goat fed with 25-FT had the lowest OCFA (P
Fulltext Follow-up data on patent expiry and atorvastatin price: experiences in Brunei Darussalam, Malaysia, the Philippines and Thailand

Kemp-Casey A, Ceria-Perena J, Guerrero AM, Suchonwanich N, Salleh SM, Roughead EE

WHO South East Asia J Public Health, 2019 09;8(2):115-117.
PMID: 31441448 DOI: 10.4103/2224-3151.264857
Fulltext Transcriptomics analysis of differentially expressed genes in subcutaneous and perirenal adipose tissue of sheep as affected by their pre- and early postnatal malnutrition histories

Ahmad S, Drag MH, Salleh SM, Cai Z, Nielsen MO

BMC Genomics, 2021 May 11;22(1):338.
PMID: 33975549 DOI: 10.1186/s12864-021-07672-5

BACKGROUND: Early life malnutrition is known to target adipose tissue with varying impact depending on timing of the insult. This study aimed to identify differentially expressed genes in subcutaneous (SUB) and perirenal (PER) adipose tissue of 2.5-years old sheep to elucidate the biology underlying differential impacts of late gestation versus early postnatal malnutrition on functional development of adipose tissues. Adipose tissues were obtained from 37 adult sheep born as twins to dams fed either NORM (fulfilling energy and protein requirements), LOW (50% of NORM) or HIGH (110% of protein and 150% of energy requirements) diets in the last 6-weeks of gestation. From day 3 to 6 months of age, lambs were fed high-carbohydrate-high-fat (HCHF) or moderate low-fat (CONV) diets, and thereafter the same moderate low-fat diet.
RESULTS: The gene expression profile of SUB in the adult sheep was not affected by the pre- or early postnatal nutrition history. In PER, 993 and 186 differentially expressed genes (DEGs) were identified in LOW versus HIGH and NORM, respectively, but no DEG was found between HIGH and NORM. DEGs identified in the mismatched pre- and postnatal nutrition groups LOW-HCHF (101) and HIGH-HCHF (192) were largely downregulated compared to NORM-CONV. Out of 831 DEGs, 595 and 236 were up- and downregulated in HCHF versus CONV, respectively. The functional enrichment analyses revealed that transmembrane (ion) transport activities, motor activities related to cytoskeletal and spermatozoa function (microtubules and the cytoskeletal motor protein, dynein), and responsiveness to the (micro) environmental extracellular conditions, including endocrine and nervous stimuli were enriched in the DEGs of LOW versus HIGH and NORM. We confirmed that mismatched pre- and postnatal feeding was associated with long-term programming of adipose tissue remodeling and immunity-related pathways. In agreement with phenotypic measurements, early postnatal HCHF feeding targeted pathways involved in kidney cell differentiation, and mismatched LOW-HCHF sheep had specific impairments in cholesterol metabolism pathways.
CONCLUSIONS: Both pre- and postnatal malnutrition differentially programmed (patho-) physiological pathways with implications for adipose functional development associated with metabolic dysfunctions, and PER was a major target.
Fulltext A GNAS Gene Mutation's Independent Expression in the Growth of Colorectal Cancer: A Systematic Review and Meta-Analysis

Afolabi HA, Salleh SM, Zakaria Z, Ch'ng ES, Mohd Nafi SN, Abdul Aziz AAB, et al.

Cancers (Basel), 2022 Nov 08;14(22).
PMID: 36428574 DOI: 10.3390/cancers14225480

Globally, colorectal carcinoma CRC is the third most common cancer and the third most common reason for cancer-associated mortality in both genders. The GNAS mutations are significantly linked with poor prognosis and failed treatment outcomes in CRC. A systematic review and meta-analysis of multiple studies executed following Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) criteria and registered with PROSPERO (registration number: CRD42021256452). The initial search includes a total of 271 publications; however, only 30 studies that merit the eligibility criteria were eventually chosen. Data analysis via OpenMeta Analyst and comprehensive meta-analysis 3.0 (CMA 3.0) software were used to investigate the prevalence of GNAS gene mutation among CRC patients. The meta-analysis consisted of 10,689 participants with most being males 6068/10,689 (56.8%). Overall, prevalence of GNAS mutations was 4.8% (95% CI: 3.1−7.3) with I2 = 94.39% and (p < 0.001). In 11/30 studies, the frequency of GNAS gene mutations was majorly in codons R201C [40.7% (95% CI: 29.2−53.2%)] and in codon R201H [39.7% (95% CI = 27.1−53.8)]. Overall prevalence of GNAS mutations was highest among the male gender: 53.9% (95% CI: 48.2−59.5%: I2 = 94.00%, (p < 0.001), tumour location (colon): 50.5% (95% CI: 33.2−67.6%: I2 = 97.93%, (p < 0.001), tumour grade (Well): 57.5% (95% CI: 32.4−79.2%: I2 = 98.10%, (p < 0.001) and tumour late stage: 67.9% (95% CI: 49.7−84.3%: I2 = 98.%, (p < 0.001). When stratified according to study location, a higher prevalence was observed in Japan (26.8%) while Italy has the lowest (0.4%). Overall prevalence of GNAS gene mutations was 4.8% with codons R201C and R201H being the most mutated, and the results conformed with numerous published studies on GNAS mutation.
Fulltext The Prediction of Survival Outcome and Prognosis Factor in Association with Comorbidity Status in Patients with Colorectal Cancer: A Research-Based Study

Afolabi H, Salleh SM, Zakaria Z, Ch'ng ES, Mohd Nafi SN, Abdul Aziz AAB, et al.

Healthcare (Basel), 2022 Sep 05;10(9).
PMID: 36141305 DOI: 10.3390/healthcare10091693

Colorectal carcinoma (CRC) is rising exponentially in Asia, representing 11% of cancer worldwide. This study analysed the influence of CRC on patients’ life expectancy (survival and prognosis factors) via clinicopathology data and comorbidity status of CRC patients. Methodology: A retrospective study performed in HUSM using clinical data from the Surgery unit from 2015 to 2020. The demographic and pertinent clinical data were retrieved for preliminary analyses (data cleansing and exploration). Demographics and pathological characteristics were illustrated using descriptive analysis; 5-year survival rates were calculated using Kaplan−Meier methods; potential prognostic variables were analysed using simple and multivariate logistic regression analysis conducted via the Cox proportional hazards model, while the Charlson Comorbidity Scale was used to categorize patients’ disease status. Results: Of a total of 114 CRC patients, two-thirds (89.5%) were from Malay tribes, while Indian and Chinese had 5.3% each. The 50−69.9 years were the most affected group (45.6%). Overall, 40.4% were smokers (majorly male (95.7%)), 14.0% ex-smokers, and 45.6% non-smokers (p-value = 0.001). The Kaplan−Meier overall 5-year median survival time was 62.5%. From the outcomes, patients who were male and >70 years had metastasis present, who presented with per rectal bleeding and were classified as Duke C; and who has tumour in the rectum had the lowest survival rate. Regarding the prognosis factors investigated, “Gender” (adjusted hazard ratio (HR): 2.62; 95% CI: 1.56−7.81, p-value = 0.040), “Presence of metastases” (HR: 3.76; 95% CI: 1.89−7.32, p-value = 0.010), “Metastasis site: Liver” (HR: 5.04; 95% CI: 1.71−19.05, p-value = 0.039), “Lymphovascular permeation” (HR: 2.94; 95% CI: 1.99−5.92, p-value = 0.021), and “CEA-level” (HR: 2.43; 95% CI: 1.49−5.80, p-value = 0.001) remained significant in the final model for multiple Cox proportional hazard regression analyses. There was a significant mean association between tumour grades and the patient’s comorbidity status. Conclusions: Histopathological factors (gender, metastases presence, site of metastases, CEA level, and lymphovascular permeation) showed the best prognosis-predicting factors in CRC.
Molecular characterization of colorectal cancer (CRC) using next generation sequencing (NGS) in bridging the gap between research and clinical practice: from biomarker discovery to clinical implementation

Afolabi HA, Salleh SM, Zakaria Z, Seng CE, Nafi SNM, Aziz AABA, et al.

Discov Oncol, 2025 Mar 06;16(1):268.
PMID: 40048017 DOI: 10.1007/s12672-025-01960-2

BACKGROUND: Colorectal cancer (CRC) is the second most common cancer in men and third in females, a heterogeneous disease involving multistep mechanisms that represents 10% of all cancers globally. This study investigates gene mutation profiling in CRC using Next-Generation sequencing machine.
METHOD: Formalin-fixed paraffin-embedded tissues of 30 CRC patients were retrieved and reviewed. DNA was isolated from selected tissues. Desirable quality check using Qubit and Nanoquant machine was done, and desirable libraries prepared were loaded into the sequencer for sequencing. Using Illumina BaseSpace and Illumina Variant interpreter, generated FastQ data were treated for annotation, alignment, and mapping with reference genome. Sequencing-runs with Phred-score ≥ 30 were selected as desirable runs. Finally, the variants were validated on NCBI-dsSNP and Ensembl databases for clinical consequence interpretations.
RESULTS: Overall, patient distribution consists of 12(40%) females and 18 (60%) males with mean age (53.2 + 5.3). most patients were in TNM stage-3: 53.3% (15/30) and the least was Stage-4: 20%(6/30) respectively. Overall, 73.3%: (22/30) completed the sequencing, and 552 mutations involving 29 genes and 12 chromosomes were detected. The most upregulated variants are KIT:68(12.3%), FGFR4:61(11.1%), EGFR:60(10.9%), ALK:53(9.6%), DCUN1D1:41(7.4%), PDGFR:40(7.2%), KRAS:33(6.0%), CDK4:27(4.9%), FGFR3:26(4.7%), MTOR:14(2.6), while NRAS, CDK6, PIK3CA, and RET each has 13(2.4%) apiece. Chromosomes 4:134/55(24.2%), chr7:84/552(15.2%), chr12:71/552(12.9%), chr5:64/552(11.6%), chr2:61/552(11.1%), chr3:54/552(9.8%), and chr1:43/552(7.8%) are the most involved chromosomes. Nine genes (APC, NRAS, ALK, PIK3CA, KRAS, IDH1, FGFR1, ERBB2, and ESR1) are identified as pathogenic-causing variants in CRC.
CONCLUSION: This is the first NGS-based molecular study on FFPE-CRC tissues in hospital-USM that showed the most upregulated variants in CRC and identified nine genes as crucial pathogenic variants.

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