Effects of feeding different dietary rates of mixed fodder beet tops-wheat straw silage on the performance of Holstein lactating cows.

Rations containing different rates of the mixed fodder beet tops-wheat straw silage (BS), instead of corn silage (CS), were given to 30 mid-lactation Holstein cows (all in parity 2) to measure the effects on feed consumption, milk production efficiency, milk chemistry, urinary purine derivatives (PD), blood chemistry, antioxidant levels, and in vitro methane (CH4) emission. The BS was prepared by mixing the fodder beet tops with wheat straw at a ratio of 9:1 based on fresh weight. The experimental design was completely randomized (one 28-d period with 21-d adaptation) using 30 cows (10 animals/treatment) and 3 treatments. The treatments were 1) a diet containing CS only (25 g/100 g DM) (CSD), 2) a diet containing 50% CS (12.5 g/100 g DM) and 50% BS (12.5 g/100 g DM) (CBSD), and 3) diet containing BS only (25 g/100 g DM) (BSD). Each animal (as an experimental unit) was housed individually in the tie stall and had ad libitum access to its diet. Dietary replacing 50% of CS with BS showed no significant differences in milk production, fat-corrected milk, fat and protein yields, feed efficiency, and apparent digestibility, however, these variables were less (P < 0.05) in the cows fed with BSD. Cows fed on BSD had less intakes of DM, organic matter, crude protein, and neutral detergent fiber but greater oxalic acid intake and blood urea-N, as compared to the other cows. Milk percentages of fat, protein, lactose, urea N, blood serum glucose, triglyceride, cholesterol, total protein, albumin, globulin, Ca, and P, as well as in vitro ruminal pH, were not affected by the diets. Saturated fatty acids concentration was less and monounsaturated FA and polyunsaturated FA (PUFA) was greater in the milk of cows receiving CBSD, compared to the other groups. The inclusion of both BS rates in the diet decreased the in vitro gas production, protozoa number, and CH4 emission in comparison to the control. Cows fed BSD had decreased levels of urinary allantoin, PD excreted or absorbed, and estimated microbial-N synthesis than the control and CBSD-fed groups. The milk and blood total antioxidant capacity (TAC) of the animals fed CBSD was the maximum among the cows. Overall, under the current experimental conditions, replacing 50% of dietary CS with BS did not affect milk production, but increased milk PUFA, as well as blood and milk TAC, and decreased in vitro CH4 emission, so it's feeding to lactating Holstein cows is recommended.

The effects of dietary replacing corn silage (CS) with a mixed fodder beet tops-wheat straw silage (BS) on feed consumption and milk production efficiency, milk chemistry, estimated microbial-N synthesis, blood chemistry, and the blood and milk antioxidant status of lactating Holstein cows were assessed. Replacing 50% of CS with BS increased milk polyunsaturated fatty acids (PUFA) concentration, and antioxidant capacity in blood and milk, but decreased in vitro methane production. There were no negative effects of partially feeding BS on intake, nutrient digestibility, animal performance, and blood metabolites. Therefore, replacing 50% of CS with BS is recommended in the diet of lactating Holstein cows.

Femtosecond thin-flap laser assisted in situ keratomileusis for correction of post-penetrating keratoplasty ametropia: long-term outcome.

PURPOSE: To evaluate the long-term clinical outcomes of femtosecond thin-flap LASIK (femto-LASIK) for correction of refractive error after penetrating keratoplasty in keratoconus-affected eyes. SETTING: a private ophthalmology clinic. DESIGN: Prospective interventional case series. METHODS: This prospective interventional case series enrolled 22 eyes of 22 patients who underwent femto-LASIK for the management of post-penetrating keratoplasty ametropia. The refractive error, uncorrected (UDVA), and corrected (CDVA) distance visual acuities and vector analysis were reported in short-term and long-term period after surgery. RESULTS: The mean age was 32.7 ± 7.5 years (range, 23 to 47 years) at the surgery time. The average time between PK and femto-LASIK was 42.5 ± 31.7 months. The average follow-up duration after femto-LASIK was 81.2 ± 18.6 months. The mean preoperative UDVA significantly improved from 0.47 ± 0.15 logMAR to 0.35 ± 0.14 logMAR at 12 months (P = 0.048) and 0.4 ± 0.17 at final follow-up exam (P = 0.007). CDVA was 0.22 ± 0.1 at baseline which improved to 0.18 ± 0.15 and 0.15 ± 0.1 logMAR at 12 and 81 months, respectively. (Ps = 0.027, 0.014). The mean cylinder before surgery was - 5.04 ± 1.4D which significantly decreased to -1.5 ± 0.8 D at 12 months postoperatively. (P < 0.001). There was a significant increase in refractive astigmatism from 12 months to 81 months postoperatively (-3.1 ± 2.0, P = 0.002). At the final visit, the efficacy index was 0.83, and the safety index was 1.16. CONCLUSIONS: Despite the short-term outcome indicated that femo-LASIK was effective for correction of post-keratoplasty ametropia during short-term period, a notable regression in its effect was observed in the long-term follow-up. Therefore, the predictability of this technique might decrease in the long-term.

The nutritional quality of a fresh orange pulp-wheat straw mixture ensiled with either sugar beet pulp, wheat bran, or urea compared to corn silage (Zea mays) in sheep.

This study compares corn silage (CS) with an orange pulp-wheat straw mixture (OW) ensiled with either sugar beet pulp (SBP), wheat bran (WB), or urea in terms of intake, chemical composition, phenolic compounds, silage fermentation characteristics, digestibility, in vivo rumen variables and biochemical blood variables in 48 Shall male sheep, and in vitro methane (CH4) production. In addition to CS, five other silages: OW (i.e., 87.5% fresh orange pulp + 12.5% wheat straw); OWU (OW + 1% urea); OWS (87.5% fresh orange pulp + 8.6% wheat straw + 3.9% SBP); OWSU (87.5% fresh orange pulp + 8.6% wheat straw + 1% urea + 3.9% SBP); and OWB (87.5% fresh orange pulp + 8.6% wheat straw + 3.9% SBP) were ensiled for 90 days. All diets, which contained a mineral-vitamin premix (10 g/kg of dry matter [DM]), were each randomly assigned to five sheep (live weight 40 ± 2.5 kg) using a completely randomized design, and the SAS software MIXED method was used for data analysis. Among all silages, OWU and OWSU had the highest (P < 0.01) ammonia-N concentration, but there were no differences in other fermentation characteristics. Animals fed on the CS diet had higher DM intake (P = 0.01) and DM (P = 0.01), organic matter (P = 0.01), and neutral detergent fiber (P = 0.02) digestibilities compared with other diets. However, sheep receiving OWU and OWSU diets had higher (P < 0.01) crude protein digestibility than those fed on other diets. The OWU and OWSU-fed sheep had the highest (P = 0.04) ruminal ammonia-N concentration. Sheep fed on CS had higher (P = 0.03) ruminal total short-chain fatty acids, acetate concentration (P = 0.02), total protozoa (P < 0.01), and cellulolytic bacteria numbers (P < 0.01), but had a lower (P = 0.03) propionate concentration compared with the other sheep. In vitro CH4 production was higher (P = 0.01) with the CS diet compared to the orange pulp diets. Estimated microbial protein supply was lower (P = 0.05) with CS compared to all orange silages. In conclusion, the variation in the nutritive quality among the OWS, OWSU, and OWB is relatively small, and the OWB, which is most comparable to CS, was judged to be nutritionally the best among the diets.

Comparing the yield and nutritional value of ensiled amaranth (Amaranthus hypochondriacus) cultivars with corn silage (Zea mays) in doublecropping condition.

Yield, chemical composition, and fermentation variables were compared for amaranth silages (AMS) from five cultivars (A5, A12, A14, A28, and Maria) and corn (Zea mays; CS). In vitro methane production, organic matter disappearance, microbial protein, ammonia-N concentration, volatile fatty acid levels, cellulolytic bacteria and protozoa populations, and in situ dry matter (DM) and crude protein (CP) degradability were evaluated. All crops were harvested when the plant was at the mid-milk line stage, then chopped, placed in sealed 5 L plastic bags and stored for 60 days. Data analysis was carried out using the PROC MIXED method of SAS with a randomized complete block design. The mean DM forage yield of CS was higher than the average DM yield of the amaranth cultivars (P < 0.001). In comparison with CS, the AMS had higher CP, lignin, ether extract, ash, calcium, phosphorus, magnesium, total phenolics and metabolizable protein (P < 0.001), but had lower DM, neutral detergent fiber, non-fiber carbohydrates, organic matter disappearance, lactic acid (P < 0.01) and in vitro methane production (P = 0.001). The AMS had higher (P < 0.01) pH, ammonia-N concentration, in vitro microbial protein, in situ digestible undegradable protein, and metabolizable protein compared to CS. Overall, in comparison to CS, the amaranths produced a silage of medium-quality.

Nutritive value of sorghum silage for sheep.

This study compared ensiled sorghum (ES) from two varieties (first and second cuts) with corn silage (CS) for chemical analysis, total-tract nutrient digestibility, ruminal variables and blood biochemistry metabolites in sheep. Five experimental silages representing first cut ES var. Pegah (PS1), second cut ES var. Pegah (PS2), first cut ES var. Speedfeed (SS1), second cut ES var. Speedfeed (SS2) and CS were assessed for chemical analysis, silage fermentation and anti-quality compounds. Diets consisted of lucerne hay, silage and a premix (at the ratio of 53.5:46:0.5 on a dry matter [DM] basis). Feed consumption, total-tract nutrient digestibility, microbial nitrogen supply (MNS), ruminal variables and blood biochemistry metabolites were determined in a Latin square design of five periods with five male sheep. Compared to sorghum, CS had lower (p < 0.01) concentrations of ash, water-soluble carbohydrates and crude protein, but higher starch, lignin (sa), non-structural carbohydrates and apparent nutrient digestibility. The measurements of pH, lactic acid, NH3 -N and volatile fatty acids (VFA) confirmed that all silages were well-preserved. The anti-quality compound levels in the silages were below the safe limits for ruminants. No differences were observed in feed consumption (p > 0.05) and total-tract digestibility of DM and nutrients (p > 0.05). Rumen pH, NH3 -N, VFA concentrations and acetate to propionate ratio showed no difference among treatments (p > 0.05). Sheep fed on sorghum silage showed a decrease (p < 0.01) in total protozoa, and particularly in the Entodiniae population. There were no differences in cellulolytic bacteria counts (p > 0.05) among treatments. Urinary N, MNS and blood biochemistry metabolites showed no difference among treatments (p > 0.05). Silages from both cuts of sorghum had comparable total-tract nutrient digestibility to CS, therefore, these varieties could be used as a more drought resilient silage source in the feeding of sheep.

Broccoli byproduct-wheat straw silage as a feed resource for fattening lambs.

The effect of feeding broccoli byproduct-wheat straw silage [BBWS; 69:31 ratio, dry matter (DM) basis] on performance, microbial N synthesis (MNS), rumen, and blood parameters in Fashandy lambs were evaluated. Three diets, with equal metabolizable energy and crude protein (CP) with a forage to concentrate ratio of 27:73 (DM basis), were formulated in which forage (lucerne and wheat straw) was replaced by BBWS (0, 100, or 200 g/kg of diet DM). These were assigned to three groups (n = 15/group) in a completely randomized block design for a 70-d period in which diets were offered as a total mixed ration. For each animal, dry matter intake (DMI), average daily gain (ADG), in vivo apparent digestibility, MNS, N retention, rumen, and blood parameters were measured. The BBWS diets had no influence on DMI, ADG, feed conversion efficiency, in vivo apparent digestibility coefficients of DM, organic matter, CP, and ash-free neutral detergent fiber. Neither MNS and N retention nor serum concentrations of glucose, triglycerides, creatinine, cholesterol, urea N, triiodothyronine, thyroxine, total protein, albumin, and globulin were affected. Rumen pH, NH3-N, short-chain fatty acid concentrations, the ratio of acetic to propionic acid, and protozoa numbers were, also, not influenced. In summary, BBWS may be fed to Fashandy lambs up to 200 g/kg of diet DM without any adverse impacts on growth performance.

Colostrum and milk performance, and blood immunity indices and minerals of Holstein cows receiving organic Mn, Zn and Cu sources.

Effects of supplementing the basal diets with Mn, Zn and Cu, as sulphate, glycine or methionine salts, on colostrum and milk performance, some blood immunity indices and blood minerals of pre- and post-partum Holstein cows were accessed. Forty cows in different groups received: 1) a diet without supplementary Mn, Zn and Cu (control), 2) a diet containing Mn, Zn and Cu sulphates, 3) a diet containing Mn, Zn and Cu glycine, or 4) a diet containing Mn, Zn and Cu methionine with 10 cows per group from d 60 before calving (dry period) to d 100 of lactation. Dry matter intake (DMI), dry matter digestibility (DMD), colostrum and milk performance, milk somatic cell count (SCC), blood and milk total antioxidant capacity (TAC), immunoglobulin M (IgM) and immunoglobulin A (IgA), and blood Mn, Zn and Cu were determined. Dietary supplementation with Mn, Zn and Cu as methionine, glycine or sulphate salts had positive effects on DMD, DMI, colostrum and milk performance, milk SCC, and blood Mn and Zn. Addition of Mn, Zn and Cu in diets could increase (P < 0.05) blood and milk TAC and blood IgA and IgM in the cows and their new-born calves. There were no differences in DMI, DMD, colostrum and milk yields, milk SCC, blood Mn (except d 50 postpartum), Zn and Cu and TAC (except d 50 postpartum) among the organic and inorganic minerals-supplemented groups (P > 0.05), however, the blood concentrations of IgA (except d 1 postpartum) and IgM in the cows supplemented with organic Mn, Zn and Cu were higher (P < 0.05) than those in the cows receiving the sulphate sources of minerals. Overall, dietary supplementation of Mn, Zn and Cu as methionine, glycine or sulphate salts can improve colostrum and milk performance, blood Zn and Mn and immunity indices in Holstein cows and their new-born calves. Moreover, the organic sources of Mn, Zn and Cu have advantage over the sulphate forms in terms of the blood immunoglobulins.

Yield, chemical composition, fermentation characteristics, in vitro ruminal variables, and degradability of ensiled amaranth (Amaranthus hypochondriacus) cultivars compared with corn (Zea mays) silage.

Silages from four amaranth varieties (A5, A12, A14, and A28) were compared with corn silage (CS) in terms of their yield, chemical composition, phenolic compounds, oxalic acid and nitrate levels, silage fermentation characteristics, in vitro methane production, organic matter disappearance (OMD), microbial crude protein (MCP), ruminal ammonia (NH3-N), pH, volatile fatty acids, cellulolytic bacteria numbers, protozoa counts, and in situ dry matter (DM) and crude protein (CP) degradability were determined. Forages were harvested 93 d after planting, chopped, and ensiled in plastic buckets for 60 d. The study was based on a randomized complete block design, and data were analyzed using SAS, general linear model (GLM) procedure for normal distribution. Compared with CS, amaranth silages (AMS) had lower ash-free neutral detergent fiber nitrate, OMD (P < 0.001), phosphorus (P = 0.003), and metabolizable energy (ME) (P = 0.043) but higher (P < 0.001) CP, calcium, non-fiber carbohydrates (NFC), acid detergent lignin, ether extract, ash, total phenolics, pH, NH3-N concentration, MCP, digestible undegradable protein (DUP), and metabolizable protein (MP). Fresh, OM, OMD, ME (P < 0.001), and DM (P = 0.032) yields of AMS from different varieties were higher than CS, with the exception of A5. Overall, amaranth made good quality silage, with some variation, and A28 had the highest yield and nutritional value (CP, NFC, MCP, DUP, and MP). The yield, CP concentration, and nutritional value of A28 silage were higher than CS. Although these in vitro results are promising, they also need to be validated with future in vivo research.

Performance, rumen fermentation, blood minerals, leukocyte and antioxidant capacity of young Holstein calves receiving high-surface ZnO instead of common ZnO.

This study was conducted to assess the effect of feeding high-surface ZnO instead of common ZnO on the performance, rumen fermentation, blood minerals, leukocytes and antioxidant capacity of pre- and post-weaning calves. Thirty male suckling Holstein calves were allotted to one of three experimental groups (10 replicates) in a completely randomised design. Calves received: (1) a low Zn diet without Zn supplementation (control diet), (2) a high Zn diet containing 50 mg supplementary Zn/kg dry matter (DM) as common ZnO or (3) a high Zn diet containing 50 mg supplementary Zn/kg DM as high-surface ZnO (nano-ZnO). The control diet contained a native Zn content of 35.5, 34.7 or 33.7 mg/kg DM for the age periods of 7 to 30, 31 to 70 and 71 to 100 d, respectively. Supplementation of the diet with Zn did not change the dry matter intake (DMI) of calves during d 7 to 30 but increased the ADG in this period (p < 0.05). During age periods of 31 to 70 and 71 to 100 d, DMI and ADG of the Zn supplemented calves were higher (p < 0.05) than the control animals. The nutrient digestibility and the concentration of rumen volatile fatty acids were positively affected (p < 0.05) and the rumen ammonia-N concentration decreased (p < 0.05) by dietary Zn supplementation. Furthermore, the incidence of diarrhoea and pneumonia was lower in calves receiving the Zn supplemented diets. Irrespective of ZnO source, the blood total antioxidant capacity, leukocyte and haematocrit levels significantly increased (p < 0.05) with the ZnO supplemented diets. The post-weaning DMI, nutrient  digestibility and blood haematocrit levels were higher in calves receiving high-surface ZnO, compared to those supplemented with common ZnO. With inclusion of the Zn sources in pre- and post-weaning diets, the blood Zn concentration increased (p < 0.05), but the blood Cu, Fe, Ca, P and Mg levels remained unchanged. Regardless of source, dietary supplementation of young calves with ZnO improved the performance and decreased rumen ammonia-N and the incidence of diseases. Moreover, high-surface ZnO had advantages over common ZnO in increasing the post-weaning feed intake, digestibility and blood Zn concentration.

The effect of lactic acid bacteria inoculation, molasses, or wilting on the fermentation quality and nutritive value of amaranth (Amaranthus hypochondriaus) silage1.

This study assessed the influence of wilting, lactobacillus (LAB), and/or molasses on the chemical composition, phenolic compounds, in situ degradability, and in vitro ruminal fermentation parameters of amaranth (var. Maria) silage using a randomized complete block design with 6 replicates. Treatments were fresh amaranth forage (FAF), ensiled amaranth without additive (EA), EA inoculated with LAB (EAB), EA + 5% of molasses (EAM), EA inoculated with LAB + 5% of molasses (EABM), and 24-h wilted EA (WEA). The ensiled materials were stored anaerobically for a period of 45 d. Chemical composition, oxalic acid and nitrate levels, silage fermentation characteristics, DM disappearance (DMD), OM disappearance (OMD), in vitro ruminal ammonia-N, volatile fatty acids, cellulolytic bacteria and protozoa counts, and in situ DM and CP degradability were determined. Compared with FAF, EA had lesser values of water-soluble carbohydrates (P = 0.023), nitrate (P = 0.001), total phenolics (P = 0.04), total tannins (P = 0.01), DMD (P = 0.01), ruminal cellulolytic bacteria (P = 0.02), soluble and very rapidly degradable fraction (P = 0.014), and effective degradability (P = 0.01). The EA had lesser OMD and CP degradability compared with FAF (P < 0.05). Adding molasses to EA resulted in increased ash and lactate concentrations and decreased ammonia (P < 0.05), but had no effect on OMD. The WEA had lesser ammonia and greater lactate compared with EA (P < 0.05). Overall, fresh amaranth var. Maria can be preserved as a valuable silage to feed ruminants. Ensiling amaranth var. Maria decreased the antiquality compounds, and molasses addition improved the fermentation quality of the silage.

Femtosecond laser implantation of a 340-degree intrastromal corneal ring segment in keratoconus: Short-term outcomes.

PURPOSE: To evaluate the short-term outcomes of femtosecond laser-assisted implantation of a 340-degree intracorneal ring (ICR) (Keraring) in patients with keratoconus. SETTING: Four centers in Iran. DESIGN: Prospective case series. METHODS: All cases had implantation of the 340-degree ICR after tunnel creation with a femtosecond laser. The uncorrected (UDVA) and corrected (CDVA) distance visual acuities, sphere, cylinder, manifest refraction spherical equivalent (MRSE), mean keratometry (K), steep K, and flat K were evaluated preoperatively and 1, 3, and 6 months postoperatively. RESULTS: Eighteen eyes of 17 patients were included. The mean follow-up was 4.33 months (range 1 to 6 months). The mean UDVA improved from 0.95 logarithm of the minimum angle of resolution (logMAR) ± 0.33 (SD) to 0.53 ± 0.35 logMAR (P = .001) and the mean CDVA from 0.39 ± 0.22 logMAR to 0.26 ± 0.21 logMAR (P = .09). The mean sphere decreased from -5.08 ± 3.74 diopters (D) to -1.67 ± 2.59 D, the mean cylinder from -5.83 ± 2.02 D to -2.72 ± 1.81 D, and the mean MRSE from -8.03 ± 3.88 D to -3.01 ± 2.82 D (P < .001). The mean K decreased from 51.43 ± 3.59 D to 47.42 ± 3.59 D (P < .001). All patients with a preoperative mean K greater than 55.0 D had worse CDVA. CONCLUSIONS: Implantation of a 340-degree ICR using femtosecond laser improved the visual, refractive, and topographic parameters in keratoconic patients. The findings indicate that patients with severe keratoconus (mean K >55.0 D) are not good candidates for this type of ICR.

Clinical Evidence of Decreased Iris Resistance in Patients With Keratoconus.

PURPOSE: To compare the total energy required for producing patent neodymium:yttrium-aluminum-garnet laser peripheral iridotomy in patients with or without keratoconus (KC). METHODS: In this case-control study, 36 eyes from 36 patients with KC and 24 eyes from 24 patients with myopia with or without astigmatism (as control group) who were scheduled for phakic intraocular lens implantation underwent neodymium:yttrium-aluminum-garnet laser peripheral iridotomy 1 week before surgery. The total laser energy was recorded and compared between the 2 groups. RESULTS: Mean total laser energy was significantly lower in patients with KC compared with the control group (114.7 ± 41.0 mJ and 263.9 ± 79.6 mJ, respectively, P < 0.01). Total laser energy was not correlated with patients' age, sex, race, refraction, maximum keratometry, or corneal thickness. CONCLUSIONS: Lower tissue resistance may be present in other ocular structures, such as iris, in patients with KC. Our findings supported a generalized abnormality in patients with KC rather than a localized corneal disease, at least in some cases.

Selection of Single Chain Antibody Fragments for Targeting Prostate Specific Membrane Antigen: A Comparison Between Cell-based and Antigen-based Approach.

Prostate cancer (PCa) is the most frequently diagnosed cancer and the second most common cause of cancer related mortality in United States male population. ScFv fragments have different usefulness. For example they have small size, high perfusion rate, high yield of production and are non-immunogenic, thus they can be used for therapeutic purposes. In this project we used a synthetic human ScFv library for isolation of ScFv monoclonal antibodies against prostate specific membrane antigen. For this purpose, after five rounds of cell-panning, and also five rounds of antigen-panning with rPSMA specific anti- PSMA ScFv-phage particles were isolated. Phages with high affinity toward PSMA were selected and used for further analysis. Specificity and affinity of both ScFv to PSMA and LnCaP cell line examined by ELISA. Recombinant ScFv antibody isolated from cell-panning had higher specificity and affinity for both the antigen and LNCaP cell line. Our result demonstrated that ScFv antibody obtained by cell-panning can target PSMA antigen and cell lines.

Measurement of Central Corneal Thickness Using Ultrasound Pachymetry and Orbscan II in Normal Eyes.

PURPOSE: To compare ultrasound pachymetry and Orbscan II for measurement of central corneal thickness (CCT) in normal eyes. METHODS: The current study was performed at Labbafinejad Medical Center (LMC), Tehran, Iran. Three hundred eyes from 150 healthy individuals referred for keratorefractive surgery were assessed first by Orbscan II and then by ultrasound pachymetry, and CCT values were recorded and compared. RESULTS: Overall, Orbscan II overestimated CCT as compared to ultrasound pachymetry by about 2.4% (mean values 547.6 ± 34.7 versus 534.8 ± 34.7, respectively, P < 0.001). The difference was more significant when CCT was less than 500 microns (mean values 493.2 ± 16.9 versus 479.9 ± 15.6, mean overestimation: 2.6%, P < 0.001). There was good linear correlation between the two methods (Pearson's correlation r = 0.968, P < 0.0001). CONCLUSION: Orbscan II has good correlation with ultrasound pachymetry for measurement of CCT in normal eyes; however Orbscan II should not be used to evaluate corneal thickness before keratorefractive surgeries, as it tends to overestimate corneal thickness and may result in undesirable, low residual stromal thickness.

Stringent DDI-based prediction of H. sapiens-M. tuberculosis H37Rv protein-protein interactions.

BACKGROUND: H. sapiens-M. tuberculosis H37Rv protein-protein interaction (PPI) data are very important information to illuminate the infection mechanism of M. tuberculosis H37Rv. But current H. sapiens-M. tuberculosis H37Rv PPI data are very scarce. This seriously limits the study of the interaction between this important pathogen and its host H. sapiens. Computational prediction of H. sapiens-M. tuberculosis H37Rv PPIs is an important strategy to fill in the gap. Domain-domain interaction (DDI) based prediction is one of the frequently used computational approaches in predicting both intra-species and inter-species PPIs. However, the performance of DDI-based host-pathogen PPI prediction has been rather limited. RESULTS: We develop a stringent DDI-based prediction approach with emphasis on (i) differences between the specific domain sequences on annotated regions of proteins under the same domain ID and (ii) calculation of the interaction strength of predicted PPIs based on the interacting residues in their interaction interfaces. We compare our stringent DDI-based approach to a conventional DDI-based approach for predicting PPIs based on gold standard intra-species PPIs and coherent informative Gene Ontology terms assessment. The assessment results show that our stringent DDI-based approach achieves much better performance in predicting PPIs than the conventional approach. Using our stringent DDI-based approach, we have predicted a small set of reliable H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies. We also analyze the H. sapiens-M. tuberculosis H37Rv PPIs predicted by our stringent DDI-based approach using cellular compartment distribution analysis, functional category enrichment analysis and pathway enrichment analysis. The analyses support the validity of our prediction result. Also, based on an analysis of the H. sapiens-M. tuberculosis H37Rv PPI network predicted by our stringent DDI-based approach, we have discovered some important properties of domains involved in host-pathogen PPIs. We find that both host and pathogen proteins involved in host-pathogen PPIs tend to have more domains than proteins involved in intra-species PPIs, and these domains have more interaction partners than domains on proteins involved in intra-species PPI. CONCLUSIONS: The stringent DDI-based prediction approach reported in this work provides a stringent strategy for predicting host-pathogen PPIs. It also performs better than a conventional DDI-based approach in predicting PPIs. We have predicted a small set of accurate H. sapiens-M. tuberculosis H37Rv PPIs which could be very useful for a variety of related studies.