Immediate impacts of COVID-19 pandemic on bean value chain in selected countries in sub-Saharan Africa

Africa's agriculture and food systems were already grappling with challenges such as climate change and weather variability, pests and disease, and regional conflicts. With rising new cases of COVID 19 propelling various African governments to enforce strict restrictions of varying degrees to curb the spread. Thus, the pandemic posed unprecedented shocks on agriculture and food supply chains in Sub Saharan Africa. In this study, we use survey data collected from nine countries in Central, Eastern, and Southern, Africa to understand the immediate impact of COVID-19 on production, distribution, and consumption of common beans, and possible food security implications. Descriptive analysis of data collected from bean farmers, aggregators, processors, bean regional coordinators, and mechanization dealers reveal that COVID-19 and government restrictions had impacted the availability and cost of farm inputs and labour, distribution, and consumption of beans in Eastern and Southern Africa. The immediate impacts were dire in Southern Africa with Central Africa slightly impacted. The production and distribution challenges negatively impacted on frequency and patterns of food consumption in households in Africa. Thus, the pandemic poses a greater risk to food security and poverty in the region. Governments could play a significant role in supporting the needs of smallholder farmers, traders and other actors through provision of subsidized agricultural inputs.

Loss of imprinting of insulin-like growth factor-II in Wilms' tumor commonly involves altered methylation but not mutations of CTCF or its binding site

Loss of imprinting (LOI) is the most common molecular abnormality in Wilms' tumor (WT), other embryonal cancers, and most other tumor types. LOI in WT involves activation of the normally silent maternal allele of the insulin-like growth factor-II (IGF2) gene, silencing of the normally active maternal allele of the H19 gene, and aberrant methylation of a differentially methylated region (DMR) upstream of the maternal copy of H19. Recently, the transcription factor CTCF, which binds to the H19 DMR, has been implicated in the maintenance of H19 and IGF2 imprinting. Here, we show that mutations in the CTCF gene or in the H19 DMR do not occur at significant frequency in WT, nor is there transcriptional silencing of CTCF. We also confirm that methylation of the H19 DMR in WT with LOI includes the CTCF core consensus site. However, some WTs with normal imprinting of IGF2 also show aberrant methylation of CTCF binding sites, indicating that methylation of these sites is necessary but not sufficient for LOI in WT.

Sequence and comparative analysis of the mouse 1-megabase region orthologous to the human 11p15 imprinted domain

A major barrier to conceptual advances in understanding the mechanisms and regulation of imprinting of a genomic region is our relatively poor understanding of the overall organization of genes and of the potentially important cis-acting regulatory sequences that lie in the nonexonic segments that make up 97% of the genome. Interspecies sequence comparison offers an effective approach to identify sequence from conserved functional elements. In this article we describe the successful use of this approach in comparing a approximately 1-Mb imprinted genomic domain on mouse chromosome 7 to its orthologous region on human 11p15.5. Within the region, we identified 112 exons of known genes as well as a novel gene identified uniquely in the mouse region, termed Msuit, that was found to be imprinted. In addition to these coding elements, we identified 33 CpG islands and 49 orthologous nonexonic, nonisland sequences that met our criteria as being conserved, and making up 4.1% of the total sequence. These conserved noncoding sequence elements were generally clustered near imprinted genes and the majority were between Igf2 and H19 or within Kvlqt1. Finally, the location of CpG islands provided evidence that suggested a two-island rule for imprinted genes. This study provides the first global view of the architecture of an entire imprinted domain and provides candidate sequence elements for subsequent functional analyses.

Molecular cloning and expression analysis of five novel genes in chromosome 1p36

The human chromosome 1p36 region displays frequent nonrandom chromosomal deletions and translocations in a number of human malignancies; these are thought to inactivate tumor suppressor genes. To identify these putative tumor suppressors we employed exon trapping, cDNA selection, and zoo blot analysis to clone five new genes located in 1p36. Two of these represent novel genes and were designated C1orf1 and xylan 1,4-beta-xylosidase 1 (XBX1). Two further genes represented new members of known gene families: PTPRZ2 was a tyrosine phosphatase and FRAP2 represented a FKBP12-rapamycin-associated protein. The fifth gene identified, ENO1L1, was significantly homologous to c-myc promoter binding protein, MBP-1, and to enolase 1 (ENO1). It colocalized with alpha enolase (ENO1) on a single P1 clone. ENO1L1 differed from both ENO1 and MBP-1 in the organization of its 5' untranslated sequences. Second, MBP-1 contained two single-base insertions not present in either ENO1 or ENO1L1 sequences, which led to a shift in the MBP-1 reading frame. Expression analysis revealed two brain-specific transcripts of 7.9 and 6.5 kb for PTPRZ2. In contrast, C1orf1, FRAP2, ENO1L1, and XBX1 appeared to be expressed ubiquitously in the tissues tested, with transcript sizes of 4.5, 8.7, 1.75, and 4.5 kb, respectively. Using fluorescence in situ hybridization, we mapped the five novel genes relative to chromosome 1p36 breakpoints present in three established tumor cell lines and one nontumor cell line. The karyotypic abnormalities in these cell lines were exploited as chromosomal landmarks; we could thus show that the telomere to centromere gene order was PTPRZ2-(MBP-1/ENO1/ENO1L1)-(C1orf1/XBX1)-+ ++FRAP2. The localization of these genes to a chromosomal region that is prone to deletions in human cancers makes them potential candidate tumor suppressors.

Determination and regional assignment of grouped sets of microclones in chromosome 1pter-p35

In an approach to mapping physically the most distal 30 Mb of human chromosome 1p, region-specific clone libraries were generated by microdissection and microcloning. PFGE blot hybridization of single or low-copy microclones against rare-cutter digests of genomic DNA revealed physical linkage for groups of markers. Supplementary PFGE analysis of 31 1p36-p35-specific probes for genetically mapped loci established a total of 15 grouped sets, consisting of altogether 69 markers. Twelve of the grouped sets were located in 1pter-p36.12, as revealed by microcell hybrid mapping; the remaining three were localized proximal to 1p36.12. Regional assignment and ordering of most grouped sets was achieved either by evaluating the included genetic markers or by fluorescence in situ hybridization of representative probes. The genomic extent of individual grouped sets encompassed between 1100 and 2100 kb, covering a total of approximately 22 Mb of the distal chromosome 1p region. One particular grouped set was shown to contain seven polymorphic marker loci that were previously suggested to be distributed across the entire 1pter-p35 region. The increase in the number of hybridization marker probes in 1p36 and their physical mapping is expected to facilitate positional cloning experiments in this region; in particular, the construction of clone contigs may be greatly facilitated.

A prokaryotic dnaA sequence in Drosophila melanogaster: Wolbachia infection and cytoplasmic incompatibility among laboratory strains

Using oligonucleotide primers derived from the aligned polypeptide sequences of several prokaryotic dnaA genes, we amplified from Drosophila melanogaster DNA a 557 bp fragment containing a single open reading frame. The predicted peptide sequence shows a significant similarity to previously characterized protein sequences that are encoded by the dnaA genes of several prokaryotes. The dnaA sequences are also detectable by PCR in DNA from Drosophila simulans and Nasonia vitripennis flies which are infected by a symbiotic bacterium assigned to the type species Wolbachia pipientis. A tetracycline treatment that eradicates bacterial parasites from insects, abolishes the dnaA sequences from Drosophila and Nasonia DNA. In addition, dnaA-positive Drosophila melanogaster contain numerous rod-shaped bacteria in embryos, which are abolished in subsequent generations after treatment with tetracycline. Combined with phylogenetic analysis of DnaA and 16S rRNA sequences, these results show that the dnaA cognate comes from Wolbachia. A survey of Drosophila stocks using PCR amplification of dnaA and 16S rRNA sequences showed that Wolbachia is widely spread among D. melanogaster laboratory strains but absent from several established strains of the Mediterranean fruit fly Ceratitis capitata. Evidence is also presented that presence of the bacterium can cause partial cytoplasmic incompatibility between infected and non-infected D. melanogaster strains.

Large-scale isolation of human 1p36-specific P1 clones and their use for fluorescence in situ hybridization

A series of 80 microclone probes derived from the chromosomal region 1p36 was used to isolate corresponding clones from the ICRF human P1 library (see Francis et al., this issue). Hybridization screenings were performed using probe pools on high-density filter grids. A total of 87 P1 clones specific for 1p36 were isolated. This large-scale approach allowed a detailed evaluation of the complexity, quality, and utility of this library. The isolated P1 clones were used both for size determination by pulsed-field gel electrophoresis and as probes for fluorescence in situ hybridization (FISH) analysis. FISH of P1 clones is shown to be both easy and efficient to perform on metaphase chromosomes and interphase nuclei. This observation is expected to reveal new avenues for diagnosis of disease-related chromosomal changes. The use of P1 clones as a tool in clinical and tumor interphase cytogenetics is discussed and compared with FISH data of other long insert clones such as cosmids and YAC clones.

Inhibition of Glossina morsitans midgut trypsin activity by D-glucosamine

The effect of the amino sugar D-glucosamine on trypsin in crude midgut homogenates of Glossina morsitans morsitans was studied in vitro. The results showed that the midgut trypsin was specifically and competitively inhibited by D-Glucosamine. Glucose, fructose, mannose, inositol, galactose, galactosamine, N-acetyl-D-glucosamine, and methyl-alpha-D-glucosamine were ineffective as inhibitors, even at concentrations exceeding 600 mM. D-glucosamine also had a similar inhibitory effect on bovine pancreatic trypsin. In both cases, the inhibition was incomplete as shown by nonlinear Dixon plots. The Michaelis and inhibition constants estimated for the midgut trypsin were 41 +/- 2 microM and 68 +/- 3 mM, respectively. These results suggest that the susceptibility of tsetse flies to trypanosome infection, which is associated with high midgut glucosamine levels, could be due to inhibition of trypsin or trypsin-like enzymes by this sugar.

Increased sensitivity to a natural pyrethrum extract of Trypanosoma-infected Glossina morsitans

Topical application of a natural pyrethrum extract on male and pregnant female Glossina morsitans morsitans resulted in higher mortality for flies infected with Trypanosoma brucei brucei than for uninfected control flies. Infected males showed a significantly higher mortality while infected pregnant females showed a marginally significant increase in mortality. Results support the hypothesis that infected flies are less healthy than uninfected flies. Results also parallel previous findings using endosulfan as the topical applicant and exclude the likelihood that the results were because of a peculiar effect of endosulfan.

Some observations on factors associated with the development of Trypanosoma brucei brucei infections in Glossina morsitans morsitans

The susceptibility of Glossina morsitans morsitans to Trypanosoma brucei brucei infection was shown to be age-dependent during the first 12 h: the youngest age group (1-8 h after emergence) being more susceptible than the older ones. The susceptibility was enhanced by cooling the young flies to a temperature of 0-5 degrees C for 30 min. Male flies were found to be more susceptible than females. The number of trypanosomes ingested did not influence the subsequent salivary-gland infection rates observed in G.m. morsitans; however, there was a relationship between the number ingested and subsequent T.b. brucei midgut infections in the flies.

Trypanosoma brucei-cultivation in vitro of infective forms derived from the midgut of Glossina morsitans

Infective forms of Trypanosoma brucei derived from the midgut of Glossina morsitans, have been propagated in vitro for 61 days on a bovine embryonic spleen (BESP) feeder layer using RPMI 1640 medium. It was reproducibly shown that only parasites cultured from the midgut of tsetse flies 12-14 hr after feeding on infected animals could be established in vitro. Cultures thus established were infective to rats and tsetse flies. Only midgut vector types of the parasites were identified by light and electron microscopic techniques.