Rhizobium leguminosarum inoculation decreases damage to faba bean (Vicia faba) caused by broad bean mottle bromovirus and bean yellow mosaic potyvirus

Faba bean (Vicia faba) plants were inoculated with rhizobia and then their sap was infected with broad bean mottle bromovirus (BBMV) or bean yellow mosaic potyvirus (BYMV) in a field experiment. Both viral infections significantly decreased shoot and root dry weight, number of nodules, nodule dry weight, numbers of flowers and pods/plant, total plant N, grain yield and N₂ fixation. However, inoculation withRhizobium leguminosarum significantly increased all these parameters, both in healthy and virus-infected plants. Although BYMV was more destructive than BBMV, inoculation with rhizobia could be used, with other control measures, to limit damage by both viruses.The authors are with the Department of Biochemistry and Soil Science, Faculty of Agriculture, Shambat, Sudan.     

Dye free automated cell counting and analysis

We have developed an automated cell counting method that uses images obtained at multiple focal heights to enumerate cells in confluent culture. By taking the derivative of image intensity with respect to focal height using two complementary images, we are able to count high‐density monolayers of cells over a large image area. Our method resists errors arising from variability in the focal plane caused by flatness or tilt non‐uniformities with a minimal amount of focal plane alignment, allowing the automated collection of images across a large area. Biotechnol. Bioeng. © 2013 Wiley Periodicals, Inc.     

Cold-induced vasodilation and vasoconstriction in the finger of tropical and temperate indigenes

While heat acclimatization reflects the development of heat tolerance, it may weaken an ability to tolerate cold. The purpose of this study was to explore cold-induced vasodilation (CIVD) responses in the finger of tropical indigenes during finger cold immersion, along with temperate indigenes. Thirteen tropical male indigenes (subjects born and raised in the tropics) and 11 temperate male indigenes (subjects born and raised in Japan and China) participated. Subjects immersed their middle finger at 4.3±0.8 °C water for 30 min. Rectal temperature, skin temperatures, finger skin blood flow, blood pressure and subjective sensations were recorded during the test. The results showed that: (1) the tropical group demonstrated a lower minimum (T_min), maximum (T_max) and mean finger temperature (T_mean) compared to those of the temperate group (P<0.05); (2) seven tropical indigenes demonstrated a late-plateau type of CIVD pattern, which is characterized by a pronounced 1st vasoconstriction and a single CIVD with a faint and weak 2nd vasoconstriction, whereas no temperate indigene demonstrated the late-plateau type; and (3) the hand temperature at the end of finger immersion was 3 °C lower in the tropical than the temperate group (P<0.05). These results indicate that tropical indigenes have less active responses of arterio-venous anastomoses in the finger and weaker vasoconstrictions after the first CIVD response during finger cold immersion, which can be considered as being more vulnerable to cold injury of the periphery in severe cold.     

Prevalence of Helicobacter pylori infection and the incidence of ureA and clarithromycin resistance gene 23S rRNA genotypes status in Saudi Arabia

ObjectivesTo determine the prevalence of Helicobacter pylori ureA and clarithromycin resistance gene 23S rRNA genotypes among H. pylori in Saudi Arabia.MethodsA total of 100 serum and fecal samples from 70 patients and 30 healthy volunteers, from patients who presented with symptoms suggestive of gastritis or peptic ulcer disease, were taken from the main hospital in the Southern region of Saudi Arabia from September 2010 C.E. to March 2011 C.E. corresponding to Shawwal 1431 A.H. to Rabi Al-Thani 1432 A.H. We cultured the samples for H. pylori and a polymerase chain reaction was carried out to check for the presence or absence of ureA gene and clarithromycin resistance gene 23S rRNA genotypes.ResultsAmong the 70 suspected patients, the suspected bacteria isolated from the fecal samples of 60, (85.7%) were positive using the culture techniques. The presence of ureA gene and clarithromycin resistance gene 23S rRNA was determined by using the polymerase chain reaction, Among the 100 fecal specimens, 65 fecal specimens from 70% patients showed positive results to clarithromycin resistance gene 23S rRNA (sensitivity, 93%; Specificity, 100% and Accuracy, 95%), Only 60 fecal specimens were positive with ureA gene (sensitivity, 86%; Specificity, 100% and Accuracy, 90%).Conclusion23S rRNA gene was associated with clarithromycin resistance in H. pylori. There was a high prevalence of H. pylori resistance to clarithromycin in Saudi Arabia. H. pylori is a neutrophilic bacteria that has been able to colonize the human stomach by using a variety of acid-adaptive mechanisms as Urease activity that hydrolyzed the Urea producing 2 NH₃ and H₂CO₃.     

Molecular and xylanolytic variation identified among strains of <Emphasis Type="Italic">Pyrenophora graminea</Emphasis>

The inter-retrotransposon amplified polymorphism (IRAP) was used to confirm the genetic variation among 22 strains of Pyrenophora graminea differing in their xylanase production. A total of 162 bands were scored of which 151 (93.21%) were polymorphic. The molecular parameter used showed that P. graminea strains reside in four phylogenetic groups. There was observed the resolution between clustering strains and their xylanase production. Hence, the described approach presented here constitutes no prior assumption about the characterization of P. graminea strains differing in xylanase production.     

Cutaneous thermal thresholds of tropical indigenes residing in Japan

The purpose of this study was to examine the deacclimatization of the cutaneous thermal sensations of tropical indigenes residing in temperate climates. Tropical indigenes (n=13) who were born and raised in tropics but had resided in Japan for 5–61 months participated in this study, along with temperate indigenes (n=11). Their cutaneous thermal thresholds for warm, cool, hot, and cold sensations were measured in 12 body regions using a thermal stimulator controlled by a Peltier element and a push button switch. Subjects pressed the button-switch as soon as they perceived a feeling of being ‘slightly warm’, ‘slightly cool’, ‘hot’, or ‘cold’ from a neutral thermal state. Our results showed that: (1) among the tropical indigenes, no significant relationship was found between the duration of their stay in Japan and their cutaneous thermal thresholds; (2) the tropical indigenes were, on average, 3.3, 3.5, 4.2, and 7.3 °C less sensitive to warm, hot, cool, and cold sensations, respectively, than the temperate indigenes (P<0.05); and (3) the inter-threshold sensory zones between cutaneous warmth and coolness, and hot and cold sensations were wider among the tropical indigenes than among the temperate indigenes. It was concluded that the nature of the heat acclimatization of the cutaneous thermal thresholds for the tropical indigenes was retained despite their residence in a temperate climate for up to 61 months, indicating that they had more blunted perceptions of both warming and cooling than the temperate indigenes.     

Rhizobia and bradyrhizobia under salt stress: possible role of trehalose in osmoregulation

Seven rhizobium fredii strains and seven Bradyrhizobium japonicum strains were grown in defined medium with or without 20m m trehalose in the presence or absence of NaCl. Trehalose had no effect on the growth rate of the strains in the absence of NaCl, but increased the growth rate of some strains in the presence of NaCl. Bradyrhizobium japonicum strain RCR 3827 was completely inhibited by 0·08 m NaCl in absence of trehalose, but multiplied when trehalose was added. The results indicate that trehalose may act as an osmoregulator in these strains of Rhizobium and Bradyrhizobium .     

Inference of link among diabetes,obesity, and thyroid dysfunction in data from a clinic at Saudi Arabia

The clinical link among diabetes, obesity, and thyroid dysfunction is of interest. Hence, medical records of 601 patients with diabetes, obesity, and thyroid dysfunctions at the Abha Specialist Center and Military Diabetic Endocrine Center we used in this analysis. Approximately 28% of diabetic patients had thyroid dysfunction, and 12.4% were vitamin D deficient. The patients with thyroid dysfunction had significantly elevated triglyceride levels compared to the patients without thyroid dysfunction (173.6 vs. 128. p=0.009). Vitamin D deficient obese patients were significantly younger (33.99±10.69 vs. 43.68±14.42; p<0.001) and had significantly lower levels of HbA1c (5.73±1.16 vs. 6.83±2.08; p=0.014) and lower systolic BP (120.26±11.75 vs. 124.58±13.63; p=0.049) than non-vitamin D deficient obese patients. Vitamin D deficient thyroid patients had significantly lower diastolic BP (71.4±9.9 vs. 74.9±9.7; p=0.040) and higher HbA1c (8.7±3.6 vs. 6.4±1.7; p=0.003) in comparison to non-vitamin D deficient thyroid patients. Hence, analysis of metabolic disorders in these patients will help combat complications in these cases.     

Sandflies (Diptera: Psychodidae) in a focus of visceral leishmaniasis in White Nile, Sudan

Visceral leishmaniasis (VL) has been known to occur since the 1980s on the western bank of the White Nile River (Central Sudan), 150 km south of Khartoum, and has resulted in high mortality. The most recent outbreak of the disease in this area began in 2006. Entomological surveys were carried out during May 2008, June 2010 and May and July 2011 in the White Nile area. Sandflies were collected using Centers for Disease Control light traps and sticky oil traps in the village of Kadaba and the nearby woodland. Phlebotomus females were dissected for the presence of Leishmania promastigotes. A total of 17,387 sandflies, including six species of Phlebotomus and 10 species of Sergentomyia, were identified. The Phlebotomus species recorded were Phlebotomus orientalis, Phlebotomus papatasi, Phlebotomus bergeroti, Phlebotomus duboscqi, Phlebotomus rodhaini and Phlebotomus saevus. P. orientalis was collected in both habitats. The relative abundance of P. orientalis in the woodland habitat was higher than that recorded in the village habitat. In the woodland habitat, there was a notable increase in the relative abundance of P. orientalis during the surveys conducted in 2008 and 2010 compared to 2011. None of the 311 P. orientalis females dissected were infected with Leishmania promastigotes, although relatively high parous rates were recorded in both habitats. Based on the distribution of P. orientalis recorded in this study, this species is the most likely vector of VL in the endemic focus in the White Nile area. Further investigation is required to elucidate the seasonal abundance and distribution of the vector, as well as the transmission season of VL in both habitats so that appropriate control strategies for the vector can be designed.     

Skip the alignment: degenerate, multiplex primer and probe design using K-mer matching instead of alignments

PriMux is a new software package for selecting multiplex compatible, degenerate primers and probes to detect diverse targets such as viruses. It requires no multiple sequence alignment, instead applying k-mer algorithms, hence it scales well for large target sets and saves user effort from curating sequences into alignable groups. PriMux has the capability to predict degenerate primers as well as probes suitable for TaqMan or other primer/probe triplet assay formats, or simply probes for microarray or other single-oligo assay formats. PriMux employs suffix array methods for efficient calculations on oligos 10-∼100 nt in length. TaqMan® primers and probes for each segment of Rift Valley fever virus were designed using PriMux, and lab testing comparing signatures designed using PriMux versus those designed using traditional methods demonstrated equivalent or better sensitivity for the PriMux-designed signatures compared to traditional signatures. In addition, we used PriMux to design TaqMan® primers and probes for unalignable or poorly alignable groups of targets: that is, all segments of Rift Valley fever virus analyzed as a single target set of 198 sequences, or all 2863 Dengue virus genomes for all four serotypes available at the time of our analysis. The PriMux software is available as open source from http://sourceforge.net/projects/PriMux.