Candidate signatures of positive selection for environmental adaptation in indigenous African cattle: A review.

Environmental adaptation traits of indigenous African cattle are increasingly being investigated to respond to the need for sustainable livestock production in the context of unpredictable climatic changes. Several studies have highlighted genomic regions under positive selection probably associated with adaptation to environmental challenges (e.g. heat stress, trypanosomiasis, tick and tick-borne diseases). However, little attention has focused on pinpointing the candidate causative variant(s) controlling the traits. This review compiled information from 22 studies on signatures of positive selection in indigenous African cattle breeds to identify regions under positive selection. We highlight some key candidate genome regions and genes of relevance to the challenges of living in extreme environments (high temperature, high altitude, high infectious disease prevalence). They include candidate genes involved in biological pathways relating to innate and adaptive immunity (e.g. BoLAs, SPAG11, IL1RL2 and GFI1B), heat stress (e.g. HSPs, SOD1 and PRLH) and hypoxia responses (e.g. BDNF and INPP4A). Notably, the highest numbers of candidate regions are found on BTA3, BTA5 and BTA7. They overlap with genes playing roles in several biological functions and pathways. These include but are not limited to growth and feed intake, cell stability, protein stability and sweat gland development. This review may further guide targeted genome studies aiming to assess the importance of candidate causative mutations, within regulatory and protein-coding genome regions, to further understand the biological mechanisms underlying African cattle's unique adaption.

Genetic variation and demographic history of Sudan desert sheep reveal two diversified lineages.

More than 400 million sheep are raised on the African continent, the majority of which are indigenous and are primarily reared for sustenance. They have effectively adapted to various climatic and production environments, surviving and flourishing. The genetic relationships among these sheep populations remain understudied. Herein, we sequenced the entire mitochondrial DNA control region of 120 animals from Hamary and Kabashi and their crossbreed (Hamary x Kabashi) of Sudan desert sheep (SDS) to understand their maternal-inherited genetic variation and demographic history profiles and relate those to the history of sheep pastoralism on the African continent. The results show a diversified and predominant D- loop haplogroup B (n = 102, 85%), with all other sequences belonging to haplogroup A. Most of the maternal genetic variation was partitioned between haplogroup (76.3%) while within haplogroup accounted for 23.7% of the variation. However, little genetic differentiation was observed among the two breeds and their crosses, with our results supporting a Hamari maternal origin for the crossbreed. Bayesian coalescent-based analysis reveals distinct demographic history between the two haplogroups, two breeds and their crosses. Comparison of the two haplogroup showed that haplogroup B experienced an earlier expansion than haplogroup A. Unlike the breed-based comparison, the expansion of the two breeds started roughly at the same time, around 6500 years ago, with Kabashi having a slightly greater effective population size. The maternal ancestors of SDS may have diverged before their introduction to the African continent. This study provides novel insights into the early history of these two main breeds of Sudan desert sheep and their crosses.

BoLA-DRB3 gene haplotypes show divergence in native Sudanese cattle from taurine and indicine breeds.

Autochthonous Sudanese cattle breeds, namely Baggara for beef and Butana and Kenana for dairy, are characterized by their adaptive characteristics and high performance in hot and dry agro-ecosystems. They are thus used largely by nomadic and semi-nomadic pastoralists. We analyzed the diversity and genetic structure of the BoLA-DRB3 gene, a genetic locus linked to the immune response, for the indigenous cattle of Sudan and in the context of the global cattle repository. Blood samples (n = 225) were taken from three indigenous breeds (Baggara; n = 113, Butana; n = 60 and Kenana; n = 52) distributed across six regions of Sudan. Nucleotide sequences were genotyped using the sequence-based typing method. We describe 53 alleles, including seven novel alleles. Principal component analysis (PCA) of the protein pockets implicated in the antigen-binding function of the MHC complex revealed that pockets 4 and 9 (respectively) differentiate Kenana-Baggara and Kenana-Butana breeds from other breeds. Venn analysis of Sudanese, Southeast Asian, European and American cattle breeds with 115 alleles showed 14 were unique to Sudanese breeds. Gene frequency distributions of Baggara cattle showed an even distribution suggesting balancing selection, while the selection index (ω) revealed the presence of diversifying selection in several amino acid sites along the BoLA-DRB3 exon 2 of these native breeds. The results of several PCA were in agreement with clustering patterns observed on the neighbor joining (NJ) trees. These results provide insight into their high survival rate for different tropical diseases and their reproductive capacity in Sudan's harsh environment.

G1 point mutation in growth differentiation factor 9 gene affects litter size in Sudanese desert sheep.

BACKGROUND AND AIM: Sudanese desert sheep encompass different sheep breeds named according to the different Sudanese tribes that rear them such as the Dubasi, Shugor, and Watish sheep. The objectives of this study were to screen for G1 point mutation in the polymorphic growth differentiation factor 9 (GDF9) gene, investigate its association with litter size, and construct the phylogeny of the different tribal breeds that belong to the Sudanese Desert sheep tribal types. MATERIALS AND METHODS: Genomic DNA was extracted from whole blood of three tribal Desert sheep breeds (Dubasi, Watish, and Shugor) using the guanidine chloride method. Polymerase chain reaction-restriction fragment length polymorphism with HhaI restriction enzyme and sequencing techniques was used for genotyping the GDF9 locus for possible mutations associated with litter size in the three desert sheep tribal types. RESULTS: G1 mutation in GDF9 caused the replacement of Arginine by Histidine at residue 87. The wild type allele (A) had the highest frequency, whereas the mutant type allele (a) had the lowest in all the sequenced subtypes. The genotype frequencies of the wild type ewes (AA) were higher than the heterozygous (Aa) and the mutant type (aa) frequencies in the three studied desert sheep types. No significant differences were found in the allele frequency between the three tribal types. Litter size was significantly influenced by the genotypes of GDF9 gene, parities, and subtypes (p≤0.01, 0.01, and 0.05, respectively). In the Watish sheep type, heterozygous sheep in their second parity recorded the highest litter size. Sequence alignment of GDF9 gene samples with the database entry indicated that all three tribal types were similar and identical to the reference sequence. The phylogenetic tree revealed that Shugor is the common ancestor of the studied types and Watish is more closely related to Shugor than Dubasi. This result mi ght partly explain the lower reproductive performance of Dubasi compared to Watish and Shugor. CONCLUSION: The presence of one copy of GDF9 gene increased litter size in the studied Sudanese Desert sheep. This locus may be used as a biomarker for litter size improvement through genotypic selection and allele or gene introgression.

Genetic polymorphisms of fecundity genes in Watish Sudanese desert sheep.

BACKGROUND AND AIM: The Watish sheep is a strain of desert sheep of smaller size compared to other desert sheep ecotypes, and there is anecdotal evidence that it is endowed with high litter size. The present study was designed for screening for polymorphisms in the known fecundity genes (bone morphogenetic protein receptor type 1B A

Investigation of methicillin-resistant Staphylococcus aureus among clinical isolates from humans and animals by culture methods and multiplex PCR.

BACKGROUND: Staphylococcus aureus is responsible for large numbers of hospital-related and community-acquired infections. In this study, we investigated the presence of S. aureus and methicillin-resistant S. aureus (MRSA) in 100 samples from animals (55 cattle, 36 dogs, and 9 cats) and 150 samples from hospitalized human patients. The samples were collected from healthy and diseased animals and from diseased humans and included milk, wound swab, pus, exudates, nasal swab and diabetic ulcer. Initially, S. aureus was isolated and identified by colony morphology, Gram staining, and biochemical tests (catalase and coagulase tests). The S. aureus-positive samples were examined by polymerase chain reaction (PCR) to determine their MRSA status. RESULTS: Of the 100 animal samples, 29 were positive for S. aureus. Four samples (13.8%) from dogs were MRSA-positive, but samples from cattle and cats were MRSA-negative. Of the 150 human samples we collected, 64 were S. aureus-positive and, of these, 34 (53.1%) were MRSA-positive. Most (28%) of the MRSA samples were isolated from surgical wound swabs, followed by the pus from skin infections (11%), exudates from diabetic ulcers (6%), exudates from burns (4%), and aural swabs (3%). By contrast, a low MRSA detection rate (n = 4) was seen in the non-human isolates, where all MRSA bacteria were isolated from nasal swabs from dogs. The antimicrobials susceptibility testing results showed that S. aureus isolates with mecA genes showed resistance to penicillin (100%), oxacillin (100%), erythromycin (73.5%), ciprofloxacin (70.6%), and gentamicin (67.7%). The lowest resistance was found against ceftazidime, and no vancomycin-resistant isolates were obtained. CONCLUSIONS: We detected S. aureus and MRSA in both human and canine specimens. Isolates were found to be resistant to some of the antimicrobials available locally. MRSA carriage in humans and animals appears to be a great threat to effective antimicrobials treatment. The prudent use of antimicrobials will reduce the antimicrobial resistance. Our findings will help to find the most appropriate treatment and to reduce antimicrobial resistance in the future by implementing prudent use of antimicrobials. Further studies are required to better understand the epidemiology of MRSA human-animal inter-species transmission in Bangladesh.

Biomass accumulation and energy conversion efficiency in aromatic rice genotypes.

A field experiment was conducted to evaluate photosynthetic efficiency along with different growth parameters of aromatic rice genotypes. Forty genotypes including three non-aromatic checks exhibited enormous variations for leaf area index (LAI), crop growth rate (CGR), relative growth rate (RGR), net assimilation rate (NAR), grain yield, total dry matter, harvest index and photosynthetic efficiency or energy use efficiency (Emu) at panicle initiation and heading stages. Minimum LAI-value was 0.52 in Khazar at PI stage and maximum was 4.91 in Sakkor khora at heading stage. The CGR-value was in the range of 4.80-24.11 g m(-2) per day. The best yielder BR39 produced grain of 4.21 t ha(-1) and the worst yielder Khazar gave 1.42 t ha(-1). Total dry matter (TDM) yield varied from 4.04 to 12.26 t ha(-1) where genotypes proved their energy use efficiency a range between 0.58 to 1.65%. Emu showed a significant positive relation with TDM (r=0.80(**)), CGR (r=0.72(**)) and grain yield (r=0.66(**)). A negative correlation was established between TDM and harvest index and LAI and RGR. Path analysis result showed that NAR at heading stage exerted highest positive direct effect (0.70) on Emu.

Flowering response and crop duration of aromatic rices in diverse environments.

Crop duration of a rice plant, essentially dictated by flowering response, is an important selection criterion. It is determined by the interaction of genotype and environment. A field experiment was conducted with 40 rice genotypes to assess the fluctuation and/or stability of crop duration in a series of 16 environmental conditions. The effects of genotype, environment and all the components of G x E interaction were highly significant. Among the genotypes Benaful and Gandho kasturi were most sensitive to environmental changes, and indicating lower adaptability over the environments. Crop durations of 17 genotypes were comparatively stable against environmental changes. Four genotypes viz. Basmati PNR346, BR28, Neimat and Sarwati showed only nonlinear sensitivity and thus unpredictable fluctuation. Seventeen genotypes indicated average stability over the environments. The AMMI analysis identified Badshabhog, Basmati Tapl-90, Bhog ganjia, BR38, Elai, Jata katari and Radhuni pagal as most stable genotypes over the environment series. It also advocated three comparatively stable environments for all the genotypes.

A clinical review of large cerebello pontile angle tumors.

The study was designed as retro-prospective and the study period was 3.5 years. A total of 66 (42 prospective and 24 retrospective) consecutive patients were included in the study. The commonest tumor in CPA is the Schwannoma (76%) followed by Meningioma (13.3%) and Epidermoid (4.44%). Unusual forms are Ependymoma and Hemangiopericytoma. Amongst the troublesome clinical features headache, hearing loss, vertigo and imbalance, vomiting and tinnitus were more important besides visual failure and features of lower cranial nerve involvement. The objective of the study is to "Review the Large Cerebello Pontile Angle tumors clinically". In this study 66 large CPA tumors were included and analyzed. Analysis of variance (ANOVA) was implied for the test of significance. On the whole, n=66 Schwannoma represents 76.70% and Meningioma 15.38%. Of these there are 45 cases with histological verification. The most common presenting (average duration is 1.3 years) symptoms were Headache (94.54%) and Hearing loss of varying grade (85.45%). Vertigo or imbalance was present in 67.27% cases. Vomiting was found in 54.54% of the times and difficulties in deglutition or voice change were complained of in 29.09% cases. Tinnitus was found only in 27.27% cases and it was the complaint mostly in lower diameter tumors. By maximum diameter, there were 24 cases measuring 3-4 cm, 15 more than 4 cm and only one case <3 cm sized tumors. Volume-wise tumors with volume <10 cc were 5 cases, 10-20 cc were 10, 20-30 cc were 13, 30-40 cc were 6 and >40 cc were 6. Similarly tumor volume and posterior fossa volume ratio was as follows: <10% were 6 cases, 10-20% were 15 cases, 20-30% were 7 cases and >30% were 6 cases. Amongst the schwannomas, the consistency of the tumor has been shown to be important factor for LCN involvement. The softer variety involved LCN more often than the harder (p<0.05). The involvement of the different groups of lower cranial nerve ranged from 7% to 92%.

Does transurethral microwave thermotherapy have a different effect on prostate cancer than on benign or hyperplastic tissue?

OBJECTIVES: Transurethral microwave thermotherapy is useful for the treatment of benign prostatic hyperplasia, but its effect on cancer is not documented. We analyzed the pathologic changes occurring after microwave thermotherapy in whole mount radical prostatectomy specimens from patients with cancer. METHODS: Nine patients scheduled for radical prostatectomy for clinically localized prostate cancer were treated with transurethral microwave thermotherapy (Urologix Targis System). Patients ranged in age from 64 to 72 years (mean 68). Seven patients underwent prostatectomy 4 to 90 hours after thermotherapy, and 2 other patients underwent prostatectomy 12 months after thermotherapy. Whole mount totally embedded prostates were mapped for necrosis and cancer, and the volume of each was measured by the grid method. RESULTS: Pathologic stages were T2a (n = 4), T2b (n = 4), and T3b (n = 1). The prostates from patients who underwent radical prostatectomy within 4 to 90 hours of thermotherapy had a mean prostate weight of 47.4 g (range 19.5 to 70.3). Each consistently showed hemorrhagic necrosis and tissue devitalization without significant inflammation. Necrosis involved contiguous areas of benign epithelium, stroma, and cancer without skip areas. The mean volume of necrosis was 8.8 cc (range 1.4 to 17.8), and the mean percentage of the prostate involved by necrosis was 22% (range 3% to 39%). The necrosis was symmetric around the urethra in 6 of 7 cases. Urethral dilation was observed in 3 patients, and the mean maximum radial distance of necrotic tissue was 1.4 cm (range 0.6 to 1.8). Necrotic change was noted in 80% to 100% of the volume of cancer in 4 cases, 40% to 60% in 2 cases, and 5% in 1 case. The prostates from the 2 patients who underwent radical prostatectomy 12 months after thermotherapy had a mean weight of 88 g (55 and 121 g, respectively). Each showed periurethral fibrosis, nonspecific chronic inflammation, and squamous metaplasia of the urothelium. The mean volume of necrosis remaining was 0.2 cc. The mean percentage of the prostate involved by necrosis 1 year after thermotherapy was less than 1%. There was some reabsorption of dead tissue. The mean maximum radial distance of the necrotic tissue was 0.4 cm (0.2 and 0.7 cm, respectively). The prostatic urethra had viable and partially denuded urothelium in all cases. CONCLUSIONS: Microwave thermotherapy is clinically useful for ablation of benign prostate and cancer contiguous to the urethra, resulting in hemorrhagic necrosis with minimal damage to the urethra. There was no apparent differential morphologic sensitivity of benign prostatic tissue, hyperplastic tissue, or cancer to thermotherapy.

Medical termination of pregnancy at 63 to 83 days gestation.

OBJECTIVE: To assess the efficacy of a medical regimen for the termination of pregnancy within the gestational age range of 63 to 83 days. DESIGN: Prospective observational study. SETTING: Gynaecology department within a district general hospital. POPULATION: Women attending the pregnancy advisory clinic between June 1996 and December 1997. METHODS: The medical regimen used was mifepristone 200 mg orally followed after 36 to 48 h by misoprostol 800 microg administered vaginally. MAIN OUTCOME MEASURES: The success rate of the medical termination of pregnancy regimen, where success was defined as achieving complete abortion without the need for secondary intervention by either surgical or repeat medical means. RESULTS: Primary medical termination of pregnancy was chosen by 253 (80.8%) of the 313 women and was successful in 239 (94.5%). Repeat medical treatment achieved completion of the abortion in a further three women (1.2%) and surgical evacuation of the uterus was required in 10 (4.0%). One woman declined further intervention after failed medical treatment but subsequently miscarried. CONCLUSIONS: The combination of mifepristone and misoprostol is effective for the termination of pregnancy for gestations of 63 to 83 days.

A comparison of goserelin and danazol as endometrial thinning agents prior to endometrial laser ablation.

OBJECTIVE: To compare the effectiveness of goserelin and danazol prior to endometrial laser ablation and assess different dosage regimens. DESIGN: A prospective open randomised trial. SETTING: Specialist unit in minimal access gynaecological surgery in a district general hospital. PARTICIPANTS: One hundred and sixty premenopausal women with dysfunctional uterine bleeding. INTERVENTIONS: Randomisation into four groups receiving either one or two injections of goserelin acetate (3.6 mg subcutaneously) or 28 or 56 days of danazol (four 200 mg tablets daily), followed by endometrial laser ablation. MAIN OUTCOME MEASURES: Endometrial thickness pretreatment and, immediately prior to endometrial laser ablation, assessed by vaginal ultrasound and full thickness endometrial biopsy; appearance of the endometrium at surgery; duration of the operation; the amount of fluid absorbed during surgery; and the clinical outcome at 24 weeks after surgery. RESULTS: The two drugs were equally effective in thinning the endometrium. Compared with danazol, goserelin was better tolerated and resulted in a more satisfactory endometrial appearance at hysteroscopy, a greater reduction in cavity length (0.5 cm compared with 0.3 cm, P = 0.002), a shorter operation (16.4 min compared with 21.6 min, P < 0.001), less fluid absorption (0 ml compared with 200 ml, P = 0.001), and a higher rate of amenorrhoea or oligoamenorrhoea (77% compared with 54%, P < 0.001) at the six month check. The administration of goserelin for 8 weeks compared with 4 weeks produced greater thinning of the endometrium on ultrasound and on histological examination, a greater reduction in cavity length on ultrasound and an increase in reported vasomotor symptoms. In both treatment regimens, 95% of women reported a satisfactory reduction in menstrual flow at the six month check. CONCLUSIONS: Goserelin appears to be more effective and better tolerated than danazol for treatment prior to endometrial laser ablation. Eight weeks treatment with goserelin resulted in better operating conditions and more vasomotor side effect, compared with four weeks treatment, although there was no difference in clinical outcome.

A Prospective Randomized Trial Comparing a GnRH Analog, Zoladex, and Danazol as Agents for Priming the Endometrium Prior to Endometrial Laser Ablation

A randomized controlled trial of 160 patients undergoing endometrial laser ablation (ELA) was performed. Patients selected for ELA were randomized to receive either danazol or the GnRH analog Zoladex. Eighty patients were allocated to each group. Each group was also randomized to receive either 1 or 2 months of treatment prior to surgery The major end points for the study were patient compliance and drug-related side-effects, operative time and complications, effectiveness of endometrial thinning as judged by ultrasound, histologic measurements, and clinical response at 6 months assessment. Significant differences in the effectiveness of the two preparations were noted.