Miracle-dz/UniFAR-FTUs huggingface dataset:
Patterns and drivers of δ13C variation in the giant kelp, Macrocystis pyrifera

The giant kelp Macrocystis pyrifera is a major primary producer and supports species‐rich and productive marine communities on temperate coastlines. The δ13C signature of M. pyrifera tissue is an important potential tool for understanding species interactions within nearshore trophic networks. However, in macroalgae, δ13C can vary widely, and M. pyrifera can differ up to 6‰ within a single individual, greatly complicating the designation of a primary end member in isotope mixing models. Abiotic factors such as irradiance, dissolved inorganic carbon concentration, water motion, and water temperature can drive δ13C variation, either by altering the supply of total CO2 available to individual tissues, or by inducing facultative carbon concentrating mechanisms. In this study, we combine a controlled laboratory experiment with field sampling to better understand and predict the abiotic drivers of δ13C signatures in M. pyrifera tissues. In the field, data revealed strong correlations between δ13C signatures and depth, as well as season and location within a kelp bed. Experimental data demonstrated that the δ13C of incubated tissue was strongly driven by irradiance but not flow velocity, suggesting that enrichment in M. pyrifera tissue is the result of a light‐induced metabolic process. We also confirmed a physiological δ13C enrichment process associated with photosynthate transport. These results facilitate understanding and prediction of the variation in δ13C observed in the field, and inform interpretations of δ13C signatures in trophic analyses and community interaction studies.
Antifungal activity of fungicides and plant extracts against yellow sigatoka disease causing Mycosphaerella musicola

Mycosphaerella musicola causes yellow sigatoka disease in banana plantations, and affects overall yield and quality of the fruit. Synthetic fungicides are used to control disease. An integrated approach by using plant based extracts and synthetic fungicides can control the disease efficiently by reducing the usage of fungicides. In vitro studies were carried out to test methanolic extracts of ten plants belonging to seven different families having previous reports on antimicrobial activity against Mycosphaerella musicola, methanolic extracts of two plants showed significant antifungal activity as well as significant inhibition of spore germination in spore germination inhibition assay. All eight fungicides exhibited inhibitory action on M. musicola in poison food technique, where as MIC range of each fungicide varied significantly. The results revealed that integrated disease management by using efficient plant extracts and effective fungicides can control the disease and the pathogen in fields efficiently.
PERSISTENCE OF NEWCASTLE DISEASE VIRUS IN POULTRY FLOCKS: DIAGNOSTIC CHALLENGES -

Newcastle disease virus represents avian paramyxovirus -1 and is the most characterized among all avian paramyxovirus types. The fusion protein cleavage site sequence is a well characterized determinant of Newcastle disease virus pathogenicity in chickens. This study was conducted to characterize Newcastle disease virus from apparently healthy exotic, captive birds and local chicken in the southwestern region of Nigeria. A total of 250 birds from 18 farms were screened and Newcastle disease virus was detected in 3 fecal samples by reverse transcription polymerase chain reaction. The partial sequences of fusion protein gene of the three Newcastle disease virus strains detected were analyzed to determine the pathotype involved. Based on our results a proper diagnosis of Newcastle disease is necessary due to the persistence of the virus in poultry.
Antioxidant content and activity in different parts of pomelo [Citrus grandis (L.) Osbeck] by-products

This study aimed to investigate the total antioxidant content and activity in different parts of pomelo by-products, namely flavedo, albedo and segment membrane. Total phenolic content (TPC) was determined using Folin-Ciocalteu method while total flavonoid content (TFC) was determined using aluminium chloride colorimetric method. The total antioxidant activity was determined by performing DPPH free radical scavenging assay and ferric ion reducing antioxidant power (FRAP) assay. Albedo possessed the highest TPC and TFC while flavedo demonstrated the highest antioxidant activity in both assays as compared to other tissues. Pearson correlation tests revealed that there were no correlations between TPC and EC50 as well as FRAP value. There was also a lack of relationship between TFC and antioxidant activity as determined in DPPH and FRAP assays. The pomelo by-products of 'Ledang' possessed higher antioxidant properties than previous studies and therefore can be considered as a new source of natural antioxidants.
A review of feeding supplementary nitrate to ruminant animals: nitrate toxicity, methane emissions, and production performance

Lee, C. and Beauchemin, K. A. 2014. A review of feeding supplementary nitrate to ruminant animals: Nitrate toxicity, methane emissions, and production performance. Can. J. Anim. Sci. 94: 557-570. The purpose of this review is to discuss the risks and benefits of using supplementary nitrate to reduce enteric methane emissions in ruminants based on the results of a meta-analysis. The meta-analysis confirmed possible nitrate poisoning triggered by higher blood methemoglobin levels with increasing nitrate consumption of ruminants: methemoglobin (%)=41.3×nitrate [g kg-1 body weight (BW) d-1]+1.2; R 2=0.76, P<0.001. However, acclimatizing animals to nitrate reduced the toxicity of nitrate: methemoglobin (%)=4.2×nitrate (g kg-1 BW d-1)+0.4, R 2=0.76, P=0.002. Animals fed nitrate reduced enteric methane emissions in a dose-response manner: methane [g kg-1 dry matter intake (DMI)]=-8.3×nitrate (g kg-1 BW d-1)+15.2, R 2=0.80, P<0.001. The reduction of enteric methane emissions due to supplementary nitrate was effective and consistent in both in vitro and in vivo studies and also persistent in several long-term studies. Dry matter intake and live weight gain (LWG) of cattle were not affected by nitrate: DMI change, R 2=0.007, P=0.65; LWG change, R 2=0.03, P=0.31. It is anticipated that supplementary nitrate as a substitute for urea may change urinary nitrogen composition in a manner that increases ammonia and nitrous oxide emissions from manure. Furthermore, supplementary nitrate may have various physiological roles in nitric oxide metabolism in ruminants. In conclusion, supplementary nitrate is a viable means of mitigating enteric methane emissions due to its consistent and persistent efficacy. Risk of toxicity can be lowered by gradual acclimation of animals to nitrate. However, lowered methane production may not re-direct additional metabolizable energy towards animal production.
Characterization of Bosea sp. WAO and exploration of chemolithoautotrophic growth on lead and antimony

The aqueous concentration of lead [Pb] in geochemical environments is controlled by the solubility of Pb-bearing minerals and their weathering products. In contaminated soils, a common method for in situ stabilization of Pb is the addition of phosphate to convert more redox sensitive sulfide minerals into sparingly soluble pyromorphite [Pb5(PO4)3X]. In this study, I conducted experimental studies to investigate the fate of reduced sulfur during the conversion of galena [PbS] to chloropyromorphite [Pb5(PO4)3Cl]. Powder X-ray diffraction analysis indicated that the reaction of phosphate with galena resulted in the formation of elemental sulfur [S8]. Under abitoic conditions the S8 was retained in the solid phase, and negligible concentrations of sulfur as sulfide and thiosulfate was detected in the aqueous phase and only a small amount as sulfate. When PbS reacted in the presence of the chemoautotrophic organism Bosea sp. WAO, the S8 in the secondary mineral was oxidized to sulfate. Strain WAO produced significantly more sulfate from the secondary S8 than from the primary galena. Microscopic analysis of mineral-microbe aggregates on mineral embedded slide cultures showed that the organism was co-localized and increased in biomass over time on the secondary mineral surface supporting a
Analisis Hubungan Keragaman Gen SCD1 (Stearoyl CoA Desaturase) dengan Komposisi Asam lemak Daging Sapi Lokal di Ciamis

SCD1 merupakan kandidat gen yang berperan dalam mengkonversi asam lemak jenuh menjadi tidak jenuh, dan rasio keduanya menentukan kualitas daging. Single Nucleotide P o l y m o r ph i s m (SNP) V293A pada gen SCD1 yang mengubah asam amino Valina menjadi Alaninaberpengaruh terhadap komposisi asam lemak daging. Penelitian ini bertujuan mengidentifikasi keragaman gen SCD1 berdasarkan SNP V293A, dan hubungannya dengan kandungan asam lemak pada sapi lokal di Ciamis. Penelitian ini menggunakan 14 sampel daging dan DNA dengan genotipe yang berbeda. Metode PCR-RFLPdengan enzim Aci 1digunakan untuk mendeteksi SNP V293A pada exon 5. Hubungan keragaman gen SCD1 dengan komposisi asam lemak daging dianalisis dengan uji T. Hasil penelitian ini menunjukkan gen SCD1 pada sapi lokal Ciamis polimorfik, terdapat dua alel, yaitu alel T dan C dengan tiga genotipe, yaitu TT, CT dan CC. SNP V293A pada gen SCD1 tidak berpengaruh terhadap komposisi asam lemak daging sapi lokal di Ciamis Jawa Barat. K a t a kunci : asam lemak daging, PCR-RFLP, Sapi lokal Ciamis, SCD1.
Aberrant DNA Methylation of Ribosomal RNA Genes in Human Cancer

Aberrant regulation of rRNA genes has been reported in human cancers. The aim of this study was to analyze the epigenetic regulation of rRNA genes in lung cancer and to correlate methylation levels of the promoter, 18S and 28S regions with different chromatin states. Here we report, that methylation of rDNA ranged from 10% to 30% at individual CpG sites in the promoter region. In primary lung cancers a 1.2-fold increased rDNA methylation was observed at 19 analyzed CpGs (p < 0.001). Moreover, we report an increased methylation level of rDNA towards the 28S region of rRNA genes. This hypermethylation was more pronounced in cancer cell lines compared to primary tissue. To analyze the methylation status of protein-enriched rDNA, we utilized a technique that combines ChIP and bisulfite sequencing. Pol I- and CTCF-associated rDNA exhibited reduced methylation levels compared to global rDNA. Histone H1- associated promoter regions showed a 1.5-fold increase in methylation levels compared to H3-associated rDNA. In DNMT1 knock out cells a strong reduction of methylation of 18S and 28S regions was found in comparison to wild type HCT116 cells (2.7- and 1.4-fold reduction, respectively). In double DNMT1 and DNMT3B knock out cells no substantial rDNA methylation was detected. Independent of this hypomethylation, 28S level and number of rDNA repeats were constant in wild type, single knock out and double knockout HCT116 cells. Our data suggest that aberrant methylation of rDNA occurs in human cancer and that rRNA gene activity can be modulated in a constant manner independent of the level of methylated rDNA.
Regulatory responses to rifampicin exposure in Mycobacterium tuberculosis

The inherent drug susceptibility of microorganisms is determined by multiple factors, including growth state, the rate of drug diffusion into and out of the cell, and the intrinsic vulnerability of drug targets with regard to the corresponding antimicrobial agent. Mycobacterium tuberculosis, the causative agent of tuberculosis (TB), remains a significant source of global morbidity and mortality, further exacerbated by its ability to readily evolve drug resistance. It is well accepted that drug resistance in M. tuberculosis is driven by the acquisition of chromosomal mutations in genes encoding drug targets/promoter regions; however, a comprehensive description of the molecular mechanisms that fuel drug resistance in the clinical setting is currently lacking. In this context, there is a growing body of evidence suggesting that active extrusion of drugs from the cell is critical for drug tolerance. M. tuberculosis encodes representatives of a diverse range of multidrug transporters, many of which are dependent on the proton motive force (PMF) or the availability of ATP. This suggests that energy metabolism and ATP production through the PMF, which is established by the electron transport chain (ETC), are critical in determining the drug susceptibility of M. tuberculosis. In this review, we detail advances in the study of the mycobacterial ETC and highlight drugs that target various components of the ETC. We provide an overview of some of the efflux pumps present in M. Stellenbosch University https://scholar.sun.ac.za
A Promising Tool for Gene Therapy

Gene therapy is a promising tool for treatment of the human diseases that cannot be cured by rational therapies, and its primary success depends on suitable vectors to deliver therapeutic genes. Adenoviruses (Ads) are among the most commonly used vectors for gene therapy, second only to retroviruses. During the last decade, remarkable progress has been made in the development of Ad vectors and in the understanding of the toxicity related to the Ad vector system. Ad vector has certain advantages such as high transduction efficiency for different quiescent and dividing cell types and high levels of short-term expression to provide therapeutic benefits. However, researchers are facing the challenges associated with tissue-specific targeting of vectors and the vector-mediated immunogenicity. This review mainly focuses on the studies that have employed methods to improve Ad vectors and reduce viral toxicity for different applications. These methods include minimization or elimination of viral genes, retargeting of vector to the tissue of interest, and generation of immunocompromised recombinant vectors that lead to safer use of Ad vector systems that improve persistence of transgene expression. Moreover, the therapeutic applications of Ad vectors for liver-targeted gene therapy, suicide gene therapy, delivery of small interfering RNA, and production of recombinant vaccine under regulated conditions used in clinical trials are discussed. Index Entries: Adenovirus vector; inverted terminal repeat; small interfering RNA; Coxsackie and adenovirus receptor.
Acaricidal activity of plant essential oils against poultry red mite (Dermanyssus gallinae)

The main objective of the performed experiments was to monitor acaricidal activity of selected plant essential oils against poultry red mites (Dermanyssus gallinae) and the second objective was to define the lethal doses (LD50 a LD90) of selected essential oils. Effect of six plant essential oils as acaricides against poultry house-collected red mites was examined using direct contact method – by glass vial bioassay. All used essential oils caused mortality of poultry red mites in all their stages of development. Essential oils derived from clove buds and cinnamon have been shown to be effective acaricides against the poultry red mites at concentrations 0.5 and 0.25 µL/cm2, when tested over a 24h period. The average mortality in the negative control was 2%. Clove bud, lavender and cinnamon essential oils in merit further study as potential poultry red mites control agents.
Formulation of fish feed using ingredients from soyabean, radish, maize and beet

Currently, limited number of ingredients is used in the formulation of feeds used in intensive aquaculture. The choice of these ingredients should be based on the nutritional value taking into account potential anti-nutritional factors rather than merely on the basis of cost per unit weight alone. Taking into account these considerations, present formulation is undertaken by using plant origin sources of protein such as soyabean, maize, radish and beet root. They are used as base in feed formulation. Other ingredients used are of high nutritive and low economical value. The feeds formulated using soyabean, radish, maize and beet are well accepted and easily consumed by fishes particularly herbivorous fish Grass carp (Ctenopharangodon idella).
Molecular and physical interactions of human sperm with female tract secretions

To achieve fertilisation, human sperm have to navigate and interact with the female reproductive tract (FRT) on molecular and mechanical levels. The current knowledge of some aspects of both types of interactions are limited and they were examined in this research. Proteomic analysis of crude and depleted human follicular fluid (hFF) by three proteomic approaches identified 479 hFF-proteins of which 22% were novel. A table of hFF-proteins, compiled from twenty-four hFF proteomic studies, resulted in 1586 hFF proteins; a resource for folliculogenesis and discovery of hFF biomarkers. A comparative proteomic study of media-capacitated human sperm versus capacitated sperm in the presence of hFF revealed certain hFF proteins were acquired by sperm during capacitation. Comparative metabolomics revealed some elevated metabolites in the sperm capacitation-media following 6-hour incubation compared to 1-hour swim-up, which may have relevance to sperm energy metabolism and potentially to sperm signalling mechanisms in the FRT causing remodelling for fertilisation and preparation for implantation. Sperm micro-particle image-velocimetry revealed an average fluid velocity around the motile sperm of ≤ 25- 45 μm/s and ≤ 20-35 μm/s in low and high viscosity media respectively. The averaged fluid vorticity manifested a trail of spatially confined mixing of the fluid surroundings motile sperm. To the best of our knowledge, this work is the first to conduct a comparative proteomic analysis of human sperm versus sperm-hFF interaction and to perform metabolomics analysis of human sperm capacitation media at two time points. The novel perspective of mechanical aspects of sperm motility by studying fluid velocity and vorticity around motile sperm adds a new approach to the study of sperm motility and chemotaxis. In conclusion, sperm-FRT interactions involve complex molecular and physical interactions and regulatory events. Further research of these interactions may enhance our understanding of potential applications for improved assisted reproductive techniques’ outcome and possible diagnostic approaches of infertility.
Effects of unequal capture probability on stock assessment abundance and mortality estimates: an example using the US Atlantic sea scallop fishery

Most stock assessment models assume that the probability of capture for all individuals of the same size or age in the stock area is equal. However, this assumption is rarely, if ever, satisfied. We used spatially referenced simulations, based on the US Atlantic sea scallop (Placopecten magellanicus) fishery, to generate catch, survey index, fishing effort, and size structure data that we input into a (nonspatial) catch-at-size stock assessment model to estimate abundance and mortality rates. We show that spatial patterns in fishing mortality degrade model performance for sessile stocks. Fishing mortality tended to be overestimated and abundance underestimated because trends in fishing mortality were exaggerated and the model misestimated the numbers of larger individuals due to spatial fishing patterns. These results are particularly relevant to sedentary species such as scallops, but are applicable wherever strong spatial patterns exist in fishing mortality.
NUTRITIONAL AND HEALTH BENEFITS OF INULIN AND OLIGOFRUCTOSE

Inulin (I) and oligofructose (OF) are β(2-1)-fructans with different degrees of polymerization (DP). Oligofructose (DP 2-20) is usually produced from chicory inulin (DP 3-60) using chemical degradation or controlled enzymatic hydrolysis with endoglycosidase enzymes. Nowadays they are being recognized as important functional food ingredients due to their ability to affect numerous physiological and biochemical processes resulting in maintaining health and reduction of the risk of certain diseases. They primarily act as prebiotics by stimulating the growth of intestinal bifidobacteria. In addition, they also induce changes in colonic epithelium stimulating proliferation in the crypts, changing the profile of mucine and modulating endocrine and immune functions reducing in such ways colon cancer incidence. Depending on their DP and daily dose, I and OF also promote the absorption of certain nutritionally important minerals to various extent, especially Ca and Mg, acting as antiosteoporotic agents. Animal studies demonstrate that inulin-type fructans affect the metabolism of lipids, primarily by decreasing hypertriglyceridaemia probably by decreasing the synthesis of triglycerides and fatty acids in liver. In addition to their beneficial health protecting properties, I and OF also possess very specific technological characteristics that enable their use in food industry as fat or sugar replacers in development of novel functional food products with improved nutritional and organoleptic characteristics.
Generation of knockout human iPSCs to investigate genes associated with telomere length

Telomeres are repetitive sequences located at the ends of human chromosomes. During DNA replication, DNA polymerase is unable to fully replicate telomeric DNA causing a progressive reduction in telomere length with each cell division. Consequently, telomeres shorten with age and when telomere length reaches a critical length the cell becomes dysfunctional or senescent. Increasing numbers of senescent cells results in reduced organ function and telomere length has been associated with age-associated diseases including cardiovascular disease and cancer. Telomere length is highly heritable and genome-wide association studies have identified several loci that associate with telomere length. Interestingly, two of these loci do not contain genes with known roles in telomere maintenance. In this study, CRISPR/Cas9 genome editing was used to knockout telomere length associated genes in human induced pluripotent stem cells (hiPSCs) with the ultimate aim of definitively linking a novel telomere length associated gene to telomere maintenance. CRISPR/Cas9 was used to create hiPSCs with no telomerase activity by knocking out TERT, which encodes the catalytic subunit of telomerase. Telomere length was maintained in control iPSCs, but reduced by approximately 1% per day during extended culture of TERT knockout hiPSCs. Flow cytometric analysis of mutant hiPSCs revealed that they continued to express markers of pluripotency but had increased expression of a differentiation marker. Next, CRISPR/Cas9 was used to generate mutations in the candidate telomere maintenance genes ACYP2 and TSPYL6, however, no difference in telomere length was observed after extended culture of hiPSCs carrying mutations in either gene. In conclusion, CRISPR/Cas9 genome editing was successfully used to generate mutant hiPSCs for TERT, which resulted in telomere shortening and for two candidate telomere maintenance genes, which had no effect on telomere length. Further analysis will be required to determine which gene mediates the association with telomere length at the ACYP2 locus.