Attempt to silence genes of the RNAi pathways of the root-knot nematode, Meloidogyne incognita results in diverse responses including increase and no change in expression of some genes

Control of plant-parasitic nematodes (PPNs) via host-induced gene silencing (HIGS) involves rational selection of genes and detailed assessment of effects of a possible knockdown on the nematode. Some genes by nature may be very important for the survival of the nematode that knockdown may be resisted. Possible silencing and effects of 20 such genes involved in the RNA interference (RNAi) pathways of Meloidogyne incognita were investigated in this study using long double-stranded RNAs (dsRNAs) as triggers. Two of the genes, ego-1 and mes-2, could not be knocked down. Expression of six genes (xpo-1, pash-1, xpo-2, rha-1, ekl-4, and csr-1) were significantly upregulated after RNAi treatment whereas for 12 of the genes, significant knockdown was achieved and with the exception of mes-2 and mes-6, RNAi was accompanied by defective phenotypes in treated nematodes including various degrees of paralysis and abnormal behaviors and movement such as curling, extreme wavy movements, and twitching. These abnormalities resulted in up to 75% reduction in infectivity of a tomato host, the most affected being the J2s previously treated with dsRNA of the gfl-1 gene. For 10 of the genes, effects of silencing in the J2s persisted as the adult females isolated from galls were under-developed, elongated, and transparent compared to the normal saccate, white adult females. Following RNAi of ego-1, smg-2, smg-6, and eri-1, reduced expression and/or the immediate visible effects on the J2s were not permanent as the nematodes infected and developed normally in tomato hosts. Equally intriguing was the results of RNAi of the mes-2 gene where the insignificant change in gene expression and behavior of treated J2s did not mean the nematodes were not affected as they were less effective in infecting host plants. Attempt to silence drsh-1, mut-7, drh-3, rha-1, pash-1, and vig-1 through HIGS led to reduction in nematode infestation by up to 89%. Our results show that genes may respond to RNAi knockdown differently so an exhaustive assessment of target genes as targets for nematode control via RNAi is imperative

A Framework for Bioacoustic Vocalization Analysis Using Hidden Markov Models

Using Hidden Markov Models (HMMs) as a recognition framework for automatic classification of animal vocalizations has a number of benefits, including the ability to handle duration variability through nonlinear time alignment, the ability to incorporate complex language or recognition constraints, and easy extendibility to continuous recognition and detection domains. In this work, we apply HMMs to several different species and bioacoustic tasks using generalized spectral features that can be easily adjusted across species and HMM network topologies suited to each task. This experimental work includes a simple call type classification task using one HMM per vocalization for repertoire analysis of Asian elephants, a language-constrained song recognition task using syllable models as base units for ortolan bunting vocalizations, and a stress stimulus differentiation task in poultry vocalizations using a non-sequential model via a one-state HMM with Gaussian mixtures. Results show strong performance across all tasks and illustrate the flexibility of the HMM framework for a variety of species, vocalization types, and analysis tasks

A Framework for Bioacoustic Vocalization Analysis Using Hidden Markov Models

Using Hidden Markov Models (HMMs) as a recognition framework for automatic classification of animal vocalizations has a number of benefits, including the ability to handle duration variability through nonlinear time alignment, the ability to incorporate complex language or recognition constraints, and easy extendibility to continuous recognition and detection domains. In this work, we apply HMMs to several different species and bioacoustic tasks using generalized spectral features that can be easily adjusted across species and HMM network topologies suited to each task. This experimental work includes a simple call type classification task using one HMM per vocalization for repertoire analysis of Asian elephants, a language-constrained song recognition task using syllable models as base units for ortolan bunting vocalizations, and a stress stimulus differentiation task in poultry vocalizations using a non-sequential model via a one-state HMM with Gaussian mixtures. Results show strong performance across all tasks and illustrate the flexibility of the HMM framework for a variety of species, vocalization types, and analysis tasks

Heavy Metal Loading in Surface Sediments along the Kawere Stream, Tarkwa, Ghana

Sediment contamination by heavy metals resulting from anthropogenic activities is increasingly becoming a global concern due to the risk it poses to human well-being and ecological integrity at large. The purpose of this study was to assess the heavy metals loading in sediment along the Kawere stream. Ten sediment samples were collected, acid digested and analysed for copper (Cu), lead (Pb), cadmium (Cd), manganese (Mn), zinc (Zn), nickel (Ni), chromium (Cr), cobalt (Co) and iron (Fe) using a Varian AA240FS Atomic Absorption Spectrometer (AAS). The Australian and New Zealand Environment and Conservation Council (ANZECC) guidelines for freshwater sediment quality was used as the benchmark against which the measured metal concentrations were compared. Nemerow’s pollution and potential ecological risk indices were used to evaluate the pollution status and ecological risk levels of the heavy metals in the stream. The results obtained indicated that, except Cu which exceeded the ANZECC trigger value of 65 mg/kg at three sampling sites (K01=171.29 mg/kg, K05=170.83 mg/kg and K07=113.31 mg/kg), all other measured heavy metals concentrations were below their corresponding ANZECC values. Heavy metal pollution assessment showed that three samples (K01, K05 and K07) were slightly polluted, suggesting the likelihood of posing a health threat to the aquatic organisms and humans. Calculated Ecological Risk Index (RI) ranged from 3.229 to 19.750 (RI < 150), representing a low ecological risk. As such, the metals, Cu, Ni, Cd, Pb, Cr, and Zn pose a low ecological risk to the aquatic ecosystem. Although the ecological risk is low based on the current results, constant monitoring of the stream quality is recommended due to the increasing human activities along the stream as well as the sediments ability to accumulate and remobilise heavy metals back into the water column and possibly transferring them through the food chain.   Keywords: Heavy Metals, Sediment, Ecological Risk Assessment, Pollution, Strea

Prevalence of parasitic infections on cultured Nile tilapia, Oreochromis niloticus (Linnaeus, 1758) In Bong County, Liberia

This study investigated the prevalence rate, relative abundance and mean intensity of par­asites infecting cultured Nile tilapia Oreochromis niloticus L. in three fish farms, Gbarnga, Warta and CARI in Bong County, Liberia. Organs from thirty fish samples were exam­ined from September 2016 to February 2017, along with water quality parameters. Results showed the occurrence of seven parasites including protozoans, monogeneans, digeneans, cestodes, hirudineans, nematodes and crustaceans which were organ specific in terms of infection. The prevalence of the parasites varied seasonally, with the highest numbers oc­curring in November-January. The low prevalence rate, relative abundance and mean in­tensity of the parasites showed no threat to fish farmers in Liberia. All the water quality parameters were at desirable levels for the culture of the fish except nitrite, which was beyond the threshold for sustainable fish culture. It is therefore concluded that although parasitic infections in the three farms in the Bong County were low, best farm management practices are essential

Physicochemical influence on the spatial distribution of faecal bacteria and polychaetes in the Densu Estuary, Ghana

Coastal ecosystems are increasingly impacted by man-made disturbances including pollution from agriculture, aquaculture and municipal waste. This study employed multiple ecological indicators to assess environmental quality of the Densu Estuary and understanding of environmental controls on the spatial distribution of organisms. Physicochemical parameters were measured in situ. Water and sediment samples were collected from ten stations and analysed for nutrients, total suspended solids and organisms using standard methods. The water quality index for the Densu Estuary ranged from 359.5 to 484.4, suggesting an unhealthy ecosystem. The abundance of indicator species, e.g. faecal bacteria (Escherichia coli, Enterococcus species) and polychaetes (Capitella and Nereis species) varied significantly (p<0.05) among stations. Contaminated sites are located landwards with high human impacts. Faecal bacteria and polychaete abundance correlated significantly (p<0.05) with the respective physicochemical parameters. Canonical analysis (74.11%) showed the physicochemical influence on the spatial distribution of species. The pH significantly (p<0.05) controlled the spatial distribution of faecal bacteria and polychaetes in the Densu Estuary. The results suggest environmental pollution in the Densu Estuary, useful baseline information for effective legislation towards its sustainable management

Generating temperature cycle profile from in-situ climatic condition for accurate prediction of thermo-mechanical degradation of c-Si photovoltaic module

The use of climate specific temperature-cycling profile is critical to precisely quantifying the degradation rate and accurately determining the service fatigue life of crystalline silicon photovoltaic (c-Si PV) module operating in various climates. A reliable in-situ outdoor weathering database is pivotal to generating the required climate specific temperature cycle profile. This research utilizes high-resolution data obtained at five minutes interval from installed c-Si PV modules to generate a temperature cycle profile that is representative of a test site in sub-Saharan Africa climate. The study collected a three-year data from 2012 to 2014 on weathering of c-Si PV module located at College of Engineering, KNUST Ghana. The data site is on latitude 6° 40″ N and longitude 1° 37″ W at an elevation of 250 m above sea level. Analysis of the data on temperature variation and thermally induced stresses demonstrates that the region has a profile with a ramp rate of 8.996 °C/h, a hot dwell time of 228 min, cold dwell time of 369 min. Maximum and minimum module temperatures of 58.9 °C and 23.7 °C, respectively; and a cycle time of 86400 s. Comparison with the IEC 61215 standards for terrestrial PV modules qualification reveals percentage changes of – 91%, 2180%, 3590%, 747% for the ramp rate, dwell (hot and cold) and cycle times, respectively. The generated in-situ temperature cycle profile predicts to qualify accurately, c-Si PV modules operating in the sub-Saharan African test site. The systematic technique employed in this study to generate the in-situ temperature cycle profile would be useful to the thermo-mechanical reliability research community. In addition, photovoltaic design and manufacturing engineers may harness the information to create climate specific robust c-Si PV module. Keywords: Temperature cycling, Ramp rates, Temperature gradient, Accelerated Thermal Cycling (ATC), Co-efficient of Thermal Expansion (CTE), Rainflow counting, In-situ data generatio

Geochemistry of Pegmatites associated with the cape coast granite complex in the Egyaa and Akim Oda areas of southern Ghana

The Cape Coast granite complex, which is associated with  metasedimentary rocks of the Birirmian in Ghana, is characterised by various minor intrusions that include pegmatites. The pegmatites, which are feldspar-rich, occur within, and at the margins of the granite batholiths and the surrounding schists. The major and trace element compositions of the pegmatites sampled from Egyaa and Akim Oda areas have been determined. The data indicates that the pegmatites from these areas have granitic compositions. The rocks are medium-K to high-K, calc-alkaline, S-type granitoids that are peraluminous and magnesian. Lower values of molar CaO/ (MgO + FeO &lt;sub&gt;tot&lt;/tot&gt;) coupled with higher values of molar Al&lt;sub&gt;2&lt;/sub&gt;O&lt;sub&gt;3&lt;/sub&gt;/(MgO + FeO&lt;sub&gt;tot&lt;/sup&gt;) suggest their derivation from partial melting from metapelitic sources, with the Birimian metasedimentary rocks being the likely source material. The rocks are depleted in Rb, Ba, Nb, Ce and Ti but rich in U, K, La, Hf and Y relative to primitive mantle. The data suggest that the pegmatites from these areas are late orogenic, and were emplaced at upper to middle crustal levels in a volcanic arc geotectonic environment

Tah1 helix-swap dimerization prevents mixed Hsp90 co-chaperone complexes

Specific co-chaperone adaptors facilitate the recruitment of client proteins to the Hsp90 system. Tah1 binds the C-terminal conserved MEEVD motif of Hsp90, thus linking an eclectic set of client proteins to the R2TP complex for their assembly and regulation by Hsp90. Rather than the normal complement of seven α-helices seen in other tetratricopeptide repeat (TPR) domains, Tah1 unusually consists of the first five only. Consequently, the methionine of the MEEVD peptide remains exposed to solvent when bound by Tah1. In solution Tah1 appears to be predominantly monomeric, and recent structures have failed to explain how Tah1 appears to prevent the formation of mixed TPR domain-containing complexes such as Cpr6-(Hsp90)2-Tah1. To understand this further, the crystal structure of Tah1 in complex with the MEEVD peptide of Hsp90 was determined, which shows a helix swap involving the fifth α-helix between two adjacently bound Tah1 molecules. Dimerization of Tah1 restores the normal binding environment of the bound Hsp90 methionine residue by reconstituting a TPR binding site similar to that in seven-helix-containing TPR domain proteins. Dimerization also explains how other monomeric TPR-domain proteins are excluded from forming inappropriate mixed co-chaperone complexes

Genomic diversity of Escherichia coli isolates from backyard chickens and guinea fowl in the Gambia

Chickens and guinea fowl are commonly reared in Gambian homes as affordable sources of protein. Using standard microbiological techniques, we obtained 68 caecal isolates of Escherichia coli from 10 chickens and 9 guinea fowl in rural Gambia. After Illumina whole-genome sequencing, 28 sequence types were detected in the isolates (4 of them novel), of which ST155 was the most common (22/68, 32 %). These strains span four of the eight main phylogroups of E. coli, with phylogroups B1 and A being most prevalent. Nearly a third of the isolates harboured at least one antimicrobial resistance gene, while most of the ST155 isolates (14/22, 64 %) encoded resistance to ≥3 classes of clinically relevant antibiotics, as well as putative virulence factors, suggesting pathogenic potential in humans. Furthermore, hierarchical clustering revealed that several Gambian poultry strains were closely related to isolates from humans. Although the ST155 lineage is common in poultry from Africa and South America, the Gambian ST155 isolates belong to a unique cgMLST cluster comprising closely related (38-39 alleles differences) isolates from poultry and livestock from sub-Saharan Africa - suggesting that strains can be exchanged between poultry and livestock in this setting. Continued surveillance of E. coli and other potential pathogens in rural backyard poultry from sub-Saharan Africa is warranted