Comparing carbon footprints of sheep farming systems in semi-arid regions of India: A life cycle assessment study

Carbon foot prints (CFs) studies based on life cycle assessment between sheep farming systems and green house gases (GHG) emissions is one of the best indicators to quantify the amount of GHG emissions per kg of product. Therefore, a life cycle assessment (LCA) study was conducted for three different sheep farming systems i.e. intensive system (stall fed only), semi-intensive (grazing with supplementation) and extensive system (grazing only) under semiarid region of India to assess the carbon cost of sheep rearing. The total CFs were estimated to be 16.9, 15.8 and 17.1 kg CO2-eq in intensive, semi-intensive and extensive system of grazing indicating semi-intensive system to be most carbon (C) efficient. For 1kg mutton production in semi-intensive and intensive system, around 30% and 24% CFs were contributed from enteric fermentation and feed respectively, whereas, in extensive system, the contribution of enteric fermentation increased up to 50%. The carbon foot prints analysis gives an insight of carbon inputs used but the amount of CO2 sequestered in soil making LCA a holistic approach for estimating GHG emissions from livestock.

Feasibility and outcomes of Desarda vs Lichtenstein hernioplasty by local anesthesia for inguinal hernia: a noninferiority randomized clinical trial

INTRODUCTION

The Desarda autologous tissue repair is comparable to the Lichtenstein hernioplasty for inguinal hernia regarding recurrence, chronic groin pain, and return to work activities. This study was designed to establish the outcomes of Desarda's repair versus Lichtenstein's hernioplasty concerning post-operative recovery to normal gait and its feasibility under local anesthesia (LA).

MATERIALS AND METHODS

This study was a single-center, prospective, double-blinded, non-inferiority, randomized trial. Patients undergoing open hernia repair for primary inguinal hernia were included. Patients were randomly assigned and followed up for 2 years. The primary endpoint was the time to return to normal gait post-surgery with comfort (non-inferiority margin fixed as 0.5 days). The secondary outcomes studied were post-operative pain score, the time required to return to work (all previously performed activities), and surgical-site occurrences (SSO).

RESULTS

One hundred ten eligible patients were randomly assigned [56 patients (50.9%) in the Desarda group and 54 patients (49.1%) in the Lichtenstein group]. All the procedures were safely performed under LA. The median (interquartile range) time for resuming gait post-surgery with comfort was 5 days in the Desarda vs 4 days in Lichtenstein's arm (P = 0.16), thereby failing to demonstrate non-inferiority of Desarda against Lichtenstein hernioplasty. However, there were no significant differences in days to return to work, SSO, chronic groin pain, and recurrence within two years of surgery.

CONCLUSIONS AND RELEVANCE

This study could not demonstrate the non-inferiority of the Desarda repair versus Lichtenstein hernioplasty regarding the time taken to return to normal gait. Comparing the days to return to work, pain score, SSO, and chronic groin pain, including recurrence rate, Desarda repair faired equally with Lichtenstein hernioplasty, thereby highlighting its feasibility and efficacy under LA.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT03512366.

Intradermal but not intramuscular modified vaccinia Ankara immunizations protect against intravaginal tier2 simian-human immunodeficiency virus challenges in female macaques

Route of immunization can markedly influence the quality of immune response. Here, we show that intradermal (ID) but not intramuscular (IM) modified vaccinia Ankara (MVA) vaccinations provide protection from acquisition of intravaginal tier2 simian-human immunodeficiency virus (SHIV) challenges in female macaques. Both routes of vaccination induce comparable levels of serum IgG with neutralizing and non-neutralizing activities. The protection in MVA-ID group correlates positively with serum neutralizing and antibody-dependent phagocytic activities, and envelope-specific vaginal IgA; while the limited protection in MVA-IM group correlates only with serum neutralizing activity. MVA-ID immunizations induce greater germinal center Tfh and B cell responses, reduced the ratio of Th1 to Tfh cells in blood and showed lower activation of intermediate monocytes and inflammasome compared to MVA-IM immunizations. This lower innate activation correlates negatively with induction of Tfh responses. These data demonstrate that the MVA-ID vaccinations protect against intravaginal SHIV challenges by modulating the innate and T helper responses.

Drip irrigation and sulphur fertilization influenced fodder yield, quality and water use efficiency of groundnut in arid region

Availability of ample and nutritious fodder for livestock is always a challenge in arid region. Choice of crops such as groundnut that can fulfil the requirement of fodder with its crop residues along with human needs can be a viable option to bridge the gap between availability and requirement of fodder. The fodder yield and quality largely depend on soil moisture and nutrient supply especially sulphur (S), a key nutrient for improving groundnut fodder quality. However, no researchers have given emphasis on coupling effect of drip irrigation (DI) and sulphur on fodder yield, quality, digestibility and water use efficiency (WUE). Therefore, the study was conducted to determine the effects of different regimes of DI and S on productivity and quality of fodder. Results revealed that higher regimes of DI i.e. 0.8 +1.0 PE(pan evaporation) and 1.0 PE level of irrigation along with 40 kg S ha-1 significantly improved the yield, primary quality traits (crude protein, ether extract and ash), digestibility indices and significant reduction in Fibers which indicates improvement in quality of fodder. Fodder productivity was 27.0 and 25.6% higher in 1.0 PE and 0.8+1.0 PE level of irrigation, respectively, as compared to 0.6 PE level (lower water regime) of irrigation, although 0.6 PE level of irrigation recorded higher WUE and was at par with 0.8 PE and 0.6 +1.0 PE level of DI. By changing the levels of DI from 1.0 PE to 0.8+1.0 PE, considerable water can be saved without affecting the yield and quality of fodder. Similarly, crop responded to S up to 60 kg ha-1 but at par with 40 kg S ha-1 indicating that application of extra S after 40 kg did not warrant any extra benefit in terms of fodder yield, WUE and quality of fodder. Thus, adjusting the PE levels of DI for water saving and optimal S application can be a sustainable strategy to improve the productivity and quality of groundnut fodder in arid region.

A microbiota and dietary metabolite integrates DNA repair and cell death to regulate embryo viability and aneuploidy during aging

During aging, environmental stressors and mutations along with reduced DNA repair cause germ cell aneuploidy and genome instability, which limits fertility and embryo development. Benevolent commensal microbiota and dietary plants secrete indoles, which improve healthspan and reproductive success, suggesting regulation of germ cell quality. We show that indoles prevent aneuploidy and promote DNA repair and embryo viability, which depends on age and genotoxic stress levels and affects embryo quality across generations. In young animals or with low doses of radiation, indoles promote DNA repair and embryo viability; however, in older animals or with high doses of radiation, indoles promote death of the embryo. These studies reveal a previously unknown quality control mechanism by which indole integrates DNA repair and cell death responses to preclude germ cell aneuploidy and ensure transgenerational genome integrity. Such regulation affects healthy aging, reproductive senescence, cancer, and the evolution of genetic diversity in invertebrates and vertebrates.

V2 hotspot optimized MVA vaccine expressing stabilized HIV-1 Clade C envelope Gp140 delays acquisition of heterologous Clade C Tier 2 challenges in Mamu-A*01 negative Rhesus Macaques

Stabilized HIV envelope (Env) trimeric protein immunogens have been shown to induce strong autologous neutralizing antibody response. However, there is limited data on the immunogenicity and efficacy of stabilized Env expressed by a viral vector-based immunogen. Here, we compared the immunogenicity and efficacy of two modified vaccinia Ankara (MVA) vaccines based on variable loop 2 hotspot (V2 HS) optimized C.1086 envelope (Env) sequences, one expressing the membrane anchored gp150 (MVA-150) and the other expressing soluble uncleaved pre-fusion optimized (UFO) gp140 trimer (MVA-UFO) in a DNA prime/MVA boost approach against heterologous tier 2 SHIV1157ipd3N4 intrarectal challenges in rhesus macaques (RMs). Both MVA vaccines also expressed SIVmac239 Gag and form virus-like particles. The DNA vaccine expressed SIVmac239 Gag, C.1086 gp160 Env and rhesus CD40L as a built-in adjuvant. Additionally, all immunizations were administered intradermally (ID) to reduce induction of vaccine-specific IFNγ+ CD4 T cell responses. Our results showed that both MVA-150 and MVA-UFO vaccines induce comparable Env specific IgG responses in serum and rectal secretions. The vaccine-induced serum antibody showed ADCC and ADCVI activities against the challenge virus. Comparison with a previous study that used similar immunogens via intramuscular route (IM) showed that ID immunizations induced markedly lower SHIV specific CD4 and CD8 T cell responses compared to IM immunizations. Following challenge, MVA-UFO vaccinated animals showed a significant delay in acquisition of SHIV1157ipd3N4 infection but only in Mamu-A*01 negative macaques with an estimated vaccine efficacy of 64% per exposure. The MVA-150 group also showed a trend (p=0.1) for delay in acquisition of SHIV infection with an estimated vaccine efficacy of 57%. The vaccine-induced IFNγ secreting CD8 T cell responses showed a direct association and CD4 T cells showed an inverse association with delay in acquisition of SHIV infection. These results demonstrated that both MVA-150 and MVA-UFO immunogens induce comparable humoral and cellular immunity and the latter provides marginally better protection against heterologous tier 2 SHIV infection. They also demonstrate that DNA/MVA vaccinations delivered by ID route induce better antibody and lower CD4 and CD8 T cell responses compared to IM.

A clade C HIV-1 vaccine protects against heterologous SHIV infection by modulating IgG glycosylation and T helper response in macaques

The rising global HIV-1 burden urgently requires vaccines capable of providing heterologous protection. Here, we developed a clade C HIV-1 vaccine consisting of priming with modified vaccinia Ankara (MVA) and boosting with cyclically permuted trimeric gp120 (CycP-gp120) protein, delivered either orally using a needle-free injector or through parenteral injection. We tested protective efficacy of the vaccine against intrarectal challenges with a pathogenic heterologous clade C SHIV infection in rhesus macaques. Both routes of vaccination induced a strong envelope-specific IgG in serum and rectal secretions directed against V1V2 scaffolds from a global panel of viruses with polyfunctional activities. Envelope-specific IgG showed lower fucosylation compared with total IgG at baseline, and most of the vaccine-induced proliferating blood CD4⁺ T cells did not express CCR5 and α4β7, markers associated with HIV target cells. After SHIV challenge, both routes of vaccination conferred significant and equivalent protection, with 40% of animals remaining uninfected at the end of six weekly repeated challenges with an estimated efficacy of 68% per exposure. Induction of envelope-specific IgG correlated positively with G1FB glycosylation, and G2S2F glycosylation correlated negatively with protection. Vaccine-induced TNF-α⁺ IFN-γ⁺ CD8⁺ T cells and TNF-α⁺ CD4⁺ T cells expressing low levels of CCR5 in the rectum at prechallenge were associated with decreased risk of SHIV acquisition. These results demonstrate that the clade C MVA/CycP-gp120 vaccine provides heterologous protection against a tier2 SHIV rectal challenge by inducing a polyfunctional antibody response with distinct Fc glycosylation profile, as well as cytotoxic CD8 T cell response and CCR5-negative T helper response in the rectum.

Structure-guided changes at the V2 apex of HIV-1 clade C trimer enhance elicitation of autologous neutralizing and broad V1V2-scaffold antibodies

HIV-1 clade C envelope immunogens that elicit both neutralizing and non-neutralizing V1V2-scaffold-specific antibodies (protective correlates from RV144 human trial) are urgently needed due to the prevalence of this clade in the most impacted regions worldwide. To achieve this, we introduce structure-guided changes followed by consensus-C-sequence-guided optimizations at the V2 region to generate UFO-v2-RQH¹⁷³ trimer. This improves the abundance of well-formed trimers. Following the immunization of rabbits, the wild-type protein fails to elicit any autologous neutralizing antibodies, but UFO-v2-RQH¹⁷³ elicits both autologous neutralizing and broad V1V2-scaffold antibodies. The variant with a 173Y modification in the V2 region, most prevalent among HIV-1 sequences, shows decreased ability in displaying a native-like V1V2 epitope with time in vitro and elicited antibodies with lower neutralizing and higher V1V2-scaffold activities. Our results identify a stabilized clade C trimer capable of eliciting improved neutralizing and V1V2-scaffold antibodies and reveal the importance of the V2 region in tuning this.

SARS-CoV-2 RBD trimer protein adjuvanted with Alum-3M-052 protects from SARS-CoV-2 infection and immune pathology in the lung

There is a great need for the development of vaccines that induce potent and long-lasting protective immunity against SARS-CoV-2. Multimeric display of the antigen combined with potent adjuvant can enhance the potency and longevity of the antibody response. The receptor binding domain (RBD) of the spike protein is a primary target of neutralizing antibodies. Here, we developed a trimeric form of the RBD and show that it induces a potent neutralizing antibody response against live virus with diverse effector functions and provides protection against SARS-CoV-2 challenge in mice and rhesus macaques. The trimeric form induces higher neutralizing antibody titer compared to monomer with as low as 1μg antigen dose. In mice, adjuvanting the protein with a TLR7/8 agonist formulation alum-3M-052 induces 100-fold higher neutralizing antibody titer and superior protection from infection compared to alum. SARS-CoV-2 infection causes significant loss of innate cells and pathology in the lung, and vaccination protects from changes in innate cells and lung pathology. These results demonstrate RBD trimer protein as a suitable candidate for vaccine against SARS-CoV-2.

Utilization of fruit and vegetable waste as an alternative feed resource for sustainable and eco-friendly sheep farming

Globally, 10-20% of horticultural wastes are disposed in landfills leading to environmental pollution. Recycling these wastes as animal feedstuff will lessen food-feed competition and minimize environmental hazards. The present study was undertaken to determine the nutritional quality of fresh fruit and vegetable waste (F&VW) and their dietary inclusion on nutrient utilization, antioxidant status, greenhouse gases (GHG) emissions and potable water sparing efficacy in sheep. Three dietary combinations were formulated i.e. control (C):70% Cenchrus ciliaris hay +30% concentrate mixture (CM), diet with fruit waste (FWD):70% Cenchrus ciliaris hay +20% CM +10% FW and diet with vegetable waste (VWD):70% Cenchrus ciliaris hay +20% CM +10% VW for in vitro and in vivo evaluation of these wastes as potential livestock feed. Twenty-one adult ewes were allocated into 3 groups C, FWD and VWD and fed on the above three diets. Dry matter and crude protein digestibility were significantly enhanced by 5.5 and 7.2%; 7.3 and 7.6% in F&VW supplemented groups, respectively, without affecting feed intake. Plasma total antioxidant capacity (TAC) was improved by 32.2 and 26.3% in F&VW supplemented groups. Inclusion of F&VW biomass reduced annual methane (CH₄) and nitrous oxide (N₂O) emissions (kg CO₂eq/sheep) by 3.12 and 4.55%; 15.18 and 14.92% and thus contributed to lowering of global warming potential by 4.00 and 5.27%, respectively. Furthermore, there was a net reduction of potable water consumption by 21.78 and 13.92% in F&VW supplemented groups, respectively. Therefore, it can be concluded that F&VW can be a potential feedstuff for ruminants and its efficient reuse would minimize environmental impacts associated with disposal of such waste in the landfills.

A modified vaccinia Ankara vector-based vaccine protects macaques from SARS-CoV-2 infection, immune pathology, and dysfunction in the lungs

A combination of vaccination approaches will likely be necessary to fully control the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic. Here, we show that modified vaccinia Ankara (MVA) vectors expressing membrane-anchored pre-fusion stabilized spike (MVA/S) but not secreted S1 induced strong neutralizing antibody responses against SARS-CoV-2 in mice. In macaques, the MVA/S vaccination induced strong neutralizing antibodies and CD8⁺ T cell responses, and conferred protection from SARS-CoV-2 infection and virus replication in the lungs as early as day 2 following intranasal and intratracheal challenge. Single-cell RNA sequencing analysis of lung cells on day 4 after infection revealed that MVA/S vaccination also protected macaques from infection-induced inflammation and B cell abnormalities and lowered induction of interferon-stimulated genes. These results demonstrate that MVA/S vaccination induces neutralizing antibodies and CD8⁺ T cells in the blood and lungs and is a potential vaccine candidate for SARS-CoV-2.

Utilization of byproducts of sheep farming as organic fertilizer for improving soil health and productivity of barley forage

Wool is a biodegradable fiber, rich in nutrients and can be recycled in soil as a fertilizer for maximum benefits. The present study was planned with the hypothesis that waste wool could be used as a nutrient source or manure to forage crops and aim of this study was to identify practicable recycling options of sheep based wastes in agriculture. In our study, we have compared the effect of different sheep based organic wastes on soil health, crop productivity and water use. Application of waste wool in soil significantly improved the fertility status of soil, and considerable improvement was also observed in organic carbon and nitrogen, i.e. around 30.8 and 32.6% higher over control. The activities of soil enzymes were 10-30% and 3-20% higher in waste wool treatment as compared to control and sheep based manures, respectively. Application of waste wool not only improved soil health but produced 50% higher grain and dry fodder yield of barley over control. The improvement in physical properties of soil with waste wool resulted in higher water use efficiency of the system. Our study will help in distinguishing choices for safe use of organic wastes along with up gradation of soil health and crop water utilization, particularly in nutrient poor soils of arid and semi-arid region of India.

Protein model discrimination attempts using mutational sensitivity, predicted secondary structure, and model quality information

Structure prediction methods often generate a large number of models for a target sequence. Even if the correct fold for the target sequence is sampled in this dataset, it is difficult to distinguish it from other decoy structures. An attempt to solve this problem using experimental mutational sensitivity data for the CcdB protein was described previously by exploiting the correlation of residue depth with mutational sensitivity (r ~ 0.6). We now show that such a correlation extends to four other proteins with localized active sites, and for which saturation mutagenesis datasets exist. We also examine whether incorporation of predicted secondary structure information and the DOPE model quality assessment score, in addition to mutational sensitivity, improves the accuracy of model discrimination using a decoy dataset of 163 targets from CASP. Although most CASP models would have been subjected to model quality assessment prior to submission, we find that the DOPE score makes a substantial contribution to the observed improvement. We therefore also applied the approach to CcdB and four other proteins for which reliable experimental mutational data exist and observe that inclusion of experimental mutational data results in a small qualitative improvement in model discrimination relative to that seen with just the DOPE score. This is largely because of our limited ability to quantitatively predict effects of point mutations on in vivo protein activity. Further improvements in the methodology are required to facilitate improved utilization of single mutant data.

In vitro rumen fermentation kinetics, metabolite production, methane and substrate degradability of polyphenol rich plant leaves and their component complete feed blocks

Background

This experiment aimed at assessing polyphenol-rich plant biomass to use in complete feed making for the feeding of ruminants.

Methods

An in vitro ruminal evaluation of complete blocks (CFB) with (Acacia nilotica, Ziziphus nummularia leaves) and without (Vigna sinensis hay) polyphenol rich plant leaves was conducted by applying Menke’s in vitro gas production (IVGP) technique. A total of six substrates, viz. three forages and three CFBs were subjected to in vitro ruminal fermentation in glass syringes to assess gas and methane production, substrate degradability, and rumen fermentation metabolites.

Results

Total polyphenol content (g/Kg) was 163 in A. nilotica compared to 52.5 in Z. nummularia with a contrasting difference in tannin fractions, higher hydrolysable tannins (HT) in the former (140.1 vs 2.8) and higher condensed (CT) tannins in the later (28.3 vs 7.9). The potential gas production was lower with a higher lag phase (L) in CT containing Z. nummularia and the component feed block. A. nilotica alone and as a constituent of CFB produced higher total gas but with lower methane while the partitioning factor (PF) was higher in Z. nummularia and its CFB. Substrate digestibility (both DM and OM) was lower (P < 0.001) in Z. nummularia compared to other forages and CFBs. The fermentation metabolites showed a different pattern for forages and their CFBs. The forages showed higher TCA precipitable N and lower acetate: propionate ratio in Z. nummularia while the related trend was found in CFB with V. sinensis. Total volatile fatty acid concentration was higher (P < 0.001) in A. nilotica leaves than V. sinensis hay and Z. nummularia leaves. It has implication on widening the forage resources and providing opportunity to use forage biomass rich in polyphenolic constituents in judicious proportion for reducing methane and enhancing green livestock production.

Conclusion

Above all, higher substrate degradability, propionate production, lower methanogenesis in CFB with A. nilotica leaves may be considered useful. Nevertheless, CFB with Z. nummularia also proved its usefulness with higher TCA precipitable N and PF. It has implication on widening the forage resources and providing opportunity to use polyphenol-rich forage biomass for reducing methane and enhancing green livestock production.

Effects of Saccharomyces cerevisiae and rumen bypass-fat supplementation on growth, nutrient utilisation, rumen fermentation and carcass traits of lambs

Forty-eight weaned (3 months of age) lambs were randomly distributed in a 2 × 2 factorial design to assess the effect of rumen bypass-fat (RBF) feeding (with and without) and probiotic (Saccharomyces cerevisiae) supplementation (with and without) on growth, nutrient utilisation, rumen metabolic profile and carcass traits during the post-weaning phase (3–6 months of age) of life. The four experimental groups, each having 12 lambs (six male and six female), were thus designated as control (C, basic diet without RBF and probiotic), basic diet without RBF but with probiotic (C + P), basic diet with RBF but without probiotic (C + RBF) and basic diet with RBF and probiotic (C + P + RBF). The basic diet consisted of ad libitum concentrates and dry pala (Zizyphus nummularia) leaves. Additionally, each lamb received 500 g of green ardu (Ailanthus excelsa) leaves. The RBF was calcium salt of fatty acids (source: rice bran oil) and fed at 40 g per kg of concentrate and the probiotic was fed at 9.0 × 107 colony-forming units (CFU) per kg bodyweight. Weekly bodyweights were recorded to assess the growth performance of lambs and revealed significantly (P = 0.026) higher gain in weight and average daily gain in RBF-supplemented groups independent of probiotic supplementation. The intake of concentrate was higher (P = 0.025) in RBF-fed groups and lead to increased (P = 0.028) total daily dry-matter intake and higher (P < 0.05) plane of nutrition (more metabolisable energy and a higher digestible crude protein intake) irrespective of probiotic supplementation. The feed conversion ratio (FCR) was narrower (P < 0.05) in RBF- and probiotic-supplemented animals. Digestibility of organic matter, ether extract and acid detergent fibre increased and higher nitrogen balance was observed in lambs fed with RBF. Probiotic supplementation showed a positive effect (P < 0.05) on digestibility of acid detergent fibre. Ruminal metabolic profile was assessed at the end of the experimental feeding and it showed higher pH and ciliate protozoa population with RBF, independent of probiotic supplementation. Urinary purine derivatives were measured during the metabolic trial at the end of the experiment, which showed higher allantoin excretion leading to increased microbial nitrogen flow with RBF supplementation. Pre-slaughter weight, loin eye area and lean percentage were higher with a lower bone percentage and cooking loss, showing positive carcass attributes in RBF-fed groups, and the effect of probiotic was non-significant. It is concluded that RBF supplementation enhanced higher intake and utilisation of nutrients that supported improved weight gain, FCR and carcass traits, while Saccharomyces cerevisiae feeding had a positive effect on fibre digestibility and FCR, possibly by modifying the gut environment.

Replacement of mustard oil cake by urea in short-term strategic feeding of cull ewes to improve body condition and carcass traits

Strategic short-term feeding of culled Malpura ewes (age >6 years, average liveweight 26.8 ± 0.96 kg) was aimed at improving their body condition and increase marketability of their carcass following slaughter. Randomly, 8 out of 40 ewes were slaughtered to study initial (Day 0) carcass traits and the remaining ewes were equally divided into two groups: mustard cake (Control) and urea. They were stall fed with ad libitum guar straw (Cyamopsis tetragonoloba) and concentrate mixture at 25 g/kg liveweight after 4 h of morning grazing in the pasture. The Control group was offered concentrate with solvent extracted mustard cake whereas it was replaced on an equivalent nitrogen (N) basis with urea in the concentrate offered to the other group. Daily feed intake and weekly change in ewe liveweight and body condition score were measured during the 91 days of the experiment. There was no significant (P > 0.05) difference in digestibility of nutrients between the groups. Both groups had similar dry matter and metabolisable energy intake, but the mustard cake group recorded higher (P < 0.05) cumulative weight gain and body condition score. Ruminal fluid samples and blood biochemical measurements were analysed periodically (0, 45 and 91 days), with ruminal fluid samples during the post-feeding hours also analysed. There was periodic variation in rumen pH (P = 0.013), volatile fatty acid (P = 007), total N (P = 0.001) and ammonia-N (P = 0.025) concentration in both groups. Higher post-feeding volatile fatty acid (P = 0.031) and total N (P = 0.003) values were observed in the mustard cake group. Ruminal ciliate protozoal population showed a quadratic response over time after feeding with an initial decline post-grazing, but was not affected by treatment. Similar significant (P < 0.05) improvements in haemoglobin, glucose, total protein, urea and cholesterol levels were evident in both groups at 91 days. Both treatments showed similar improvement in carcass composition, distribution of fat and chemical composition of Longissimus dorsi after 91 days of realimentation compared with initial values. Short-term pre-slaughter feeding of cull ewes improved body condition, carcass traits and composition. Replacement of costly mustard cake with urea in the diet of cull ewes could be a means to improve profitability of this strategic feeding protocol, as well as enhancing their market value.

Reduced small world brain connectivity in probands with a family history of epilepsy

BACKGROUND AND PURPOSE

The role of inheritance in ascertaining susceptibility to epilepsy is well established, although the pathogenetic mechanisms are still not very clear. Interviewing for a positive family history is a popular epidemiological tool in the understanding of this susceptibility. Our aim was to visualize and localize network abnormalities that could be associated with a positive family history in a group of patients with hot water epilepsy (HWE) using resting-state functional magnetic resonance imaging (rsfMRI).

METHODS

Graph theory analysis of rsfMRI (clustering coefficient γ; path length λ; small worldness σ) in probands with a positive family history of epilepsy (FHE+, 25) were compared with probands without FHE (FHE-, 33). Whether a closer biological relationship was associated with a higher likelihood of network abnormalities was also ascertained.

RESULTS

A positive family history of epilepsy had decreased γ, increased λ and decreased σ in bilateral temporofrontal regions compared to FHE- (false discovery rate corrected P ≤ 0.0062). These changes were more pronounced in probands having first degree relatives and siblings with epilepsy. Probands with multiple types of epilepsy in the family showed decreased σ in comparison to only HWE in the family.

CONCLUSION

Graph theory analysis of the rsfMRI can be used to understand the neurobiology of diseases like genetic susceptibility in HWE. Reduced small worldness, proportional to the degree of relationship, is consistent with the current understanding that disease severity is higher in closer biological relations.

Residue proximity information and protein model discrimination using saturation-suppressor mutagenesis

Identification of residue-residue contacts from primary sequence can be used to guide protein structure prediction. Using Escherichia coli CcdB as the test case, we describe an experimental method termed saturation-suppressor mutagenesis to acquire residue contact information. In this methodology, for each of five inactive CcdB mutants, exhaustive screens for suppressors were performed. Proximal suppressors were accurately discriminated from distal suppressors based on their phenotypes when present as single mutants. Experimentally identified putative proximal pairs formed spatial constraints to recover >98% of native-like models of CcdB from a decoy dataset. Suppressor methodology was also applied to the integral membrane protein, diacylglycerol kinase A where the structures determined by X-ray crystallography and NMR were significantly different. Suppressor as well as sequence co-variation data clearly point to the X-ray structure being the functional one adopted in vivo. The methodology is applicable to any macromolecular system for which a convenient phenotypic assay exists.

DOI:http://dx.doi.org/10.7554/eLife.09532.001

Common techniques to determine the three-dimensional structures of proteins can help researchers to understand these molecules’ activities, but are often time-consuming and do not work for all proteins. Proteins are made of chains of amino acids. When a protein chain folds, some of these amino acids interact with other amino acids and these contacts dictate the overall shape of the protein. This means that identifying the pairs of contacting amino acids could make it possible to predict the protein’s structure.

Interactions between pairs of contacting amino acids tend to remain conserved throughout evolution, and if a mutation alters one of the amino acids in a pair then a 'compensatory' change often occurs to alter the second amino acid as well. Compensatory mutations can suggest that two amino acids are close to each other in the three-dimensional shape of a protein, but the computational methods used to identify such amino acid pairs can sometimes be inaccurate.

In 2012, researchers generated mutants of a bacterial protein called CcdB with changes to single amino acids that caused the protein to fail to fold correctly. Now, Sahoo et al. – who include two of the researchers involved in the 2012 work – have developed an experimental method to identify contacting amino acids and use the CcdB protein as a test case. The approach involved searching for additional mutations that could restore the activity of five of the original mutant proteins when the proteins were produced in yeast cells. The rationale was that any secondary mutations that restored the activity must have corrected the folding defect caused by the original mutation. Sahoo et al. then predicted how close the amino acids affected by the secondary mutations were to the amino acids altered by the original mutations. This information was used to select reliable three-dimensional models of CcdB from a large set of possible structures that had been generated previously using computer models.

Next, the technique was applied to a protein called diacylglycerol kinase A. The structure of this protein had previously been inferred using techniques such as X-ray crystallography and nuclear magnetic resonance, but there was a mismatch between the two methods. Sahoo et al. found that the amino acid contacts derived from their experimental method matched those found in the crystal structure, suggesting that the functional protein structure in living cells is similar to the crystal structure. In the future, the experimental approach developed in this work could be combined with existing methods to reliably guide protein structure prediction.

DOI:http://dx.doi.org/10.7554/eLife.09532.002

Effects of calcium soap of rice bran oil fatty acids supplementation alone and with DL-α-tocopherol acetate in lamb diets on performance, digestibility, ruminal parameters and meat quality

Thirty-six Malpura lambs (28 day old and 6.7 ± 0.25 kg BW) were distributed equally in three groups having six males and six female. They were ad libitum fed individually three different experimental diets containing calcium soap of fatty acids (CA-FA) at 0 (T1 ) and 40 (T2 and T3 ) g/kg concentrate up to six months of age. Animals in T3 were supplemented additionally with 40 mg DL-α-tocopherol acetate/kg of concentrate. The roughage moiety included ad libitum dry Prosopis cineraria and fresh Azadirachata indica leaves. All the lambs were allowed to suckle from their dam up to weaning (90 day of age). Supplementation of Ca-FA improved weight gain and feed conversion ratio during both pre- (28-90 days) and post-weaning (91-180 days) phases; however, no effect of DL-α-tocopherol was observed. Metabolic parameters during post-weaning phase revealed non-significant effect on digestibility but improved nitrogen balance in the test groups. The effect on biochemical attributes did not show any significant alteration in ruminal parameters, blood biochemicals and urinary purine derivatives. Carcass traits revealed higher (p < 0.05) dressing yield and loin eye area with Ca-FA supplementation. The value of thiobarbituric reactive substances for nuggets prepared from frozen carcasses revealed significant (p < 0.05) reduction in T3 compared to the other dietary groups. Fatty acid profile of adipose tissue revealed higher (p < 0.001) 9-octadecanoic, 9-12-octadecadienoic, polyunsaturated fatty acids (PUFA), higher ratio of PUFA/saturated fatty acids (SFA), ω-6/ω-3 and lower SFA in Ca-FA-supplemented groups. It is concluded that supplementation of 40 g/kg calcium soap prepared from industrial grade rice bran oil in lamb ration provided additional energy intake, improved N utilization, gain and feed conversion ratio besides improving dressing yield and meat quality with CLA enriched fatty acid profile. DL-α-tocopherol acetate when supplemented at 40 mg/kg feed reduced lipid oxidation of meat products thus improving its keeping quality.

Effect of calcium salt of fatty acids supplementation on performance of Malpura lambs

Twenty-four Malpura lambs (28 days old) were distributed into three equal groups (four each from either sexes). They were fed ad libitum on three experimental diets containing graded levels of calcium salt of fatty acids (source: rice bran oil; Ca-FA) at 0 (T1), 20 (T2) and 40 (T3) g per kg of concentrate and dry roughage (Prosopis cineraria leaves) up to 6 months of age along with suckling of mother till weaning (3 months). Effect of Ca-FA supplementation on liveweight gain, feed and nutrient intake was not observed during pre-weaning (28–90 days), which however increased (P < 0.05) in T3 during post-weaning (90–180 days). There was an increase in organic matter intake and digestibility as well as metabolisable energy intake in Ca-FA-supplemented groups. Rumen ammonia-N and ciliate protozoa population was increased (P < 0.05) in T2 and T3 with a positive shift in rumen fermentation (increased propionate and decreased acetate). Blood biochemical analysis revealed effect of treatment and age (P < 0.05) for free fatty acids and cholesterol concentration. Ca-FA supplementation improved (P < 0.05) dressing percentage both at 2% and 4% CA-FA inclusions levels with no change in fat yield and composition. It is concluded that supplementation of Ca-FA prepared from industrial-grade rice bran oil in growing lamb rations improved gain, organic matter intake and digestibility during the post-weaning period and a linear response to the level of supplementation recommends Ca-FA at 40 g/kg for improved lamb performance.

Growth performance of lambs fed diet supplemented with rice bran oil as such or as calcium soap

Forty two Malpura lambs (21 d old) were divided into three groups of 14 each consisting of 8 females and 6 males. Lambs were allowed to suckle their respective dams twice daily up to weaning (13 wks) and offered free choice concentrate and roughage in a cafeteria system. The lambs in control group were fed conventional concentrate mixture, in RBO group concentrate mixture fortified with 4% industrial grade rice bran oil and in Ca-soap rice bran oil (as in RBO group) was supplemented in the form of calcium soap. The concentrate intake decreased(p≤0.05) in RBO group as a result total dry matter, crude protein and metabolizable energy intake decreased compared to control whereas Ca-soap prepared from the same rice bran oil stimulated the concentrate intake leading to higher total dry matter, crude protein and energy intakes. The digestibility of dry matter (p≤0.05), organic matter (p≤0.05) and crude protein (p≤0.05) was higher in RBO group followed by Ca-soap and control whereas no effect was observed for ether extract digestibility. Higher cholesterol (p≤0.05) content was recorded in serum of oil supplemented groups (RBO and Ca-soap) while no effect was recorded for other blood parameters. Rice bran oil as such adversely affected and reduced the body weight gain (p≤0.001) of lambs in comparison to control whereas the Ca-soap of rice bran oil improved body weight gain and feed conversion efficiency in lambs. Fat supplementation decreased total volatile fatty acids (p≤0.05) and individual volatile fatty acid concentration which increased at 4 h post feeding. Fat supplementation also reduced (p≤0.05) total protozoa count. Ca-soap of rice bran oil improved pre slaughter weight (p≤0.05) and hot carcass weight (p≤0.05). It is concluded from the study that rice bran oil in the form of calcium soap at 40 g/kg of concentrate improved growth, feed conversion efficiency and carcass quality as compared to rice bran oil as such and control groups.

Effect of mineral mixture and antioxidant supplementation on growth, reproductive performance and adaptive capability of Malpura ewes subjected to heat stress

This study was conducted to evaluate the effect of mineral and antioxidant supplementation on growth, reproductive performance and physiological adaptability of heat-stressed Malpura ewes. The study was conducted for a period of 21 days in 21 adult Malpura ewes. The ewes were randomly divided into three groups with seven animals each viz. GI (control; n = 7), GII (heat stress; n = 7) and GIII (heat stress + mineral and antioxidant supplementation; n = 7). The animals were stall fed ad libitum with the diet consisting of 70% roughage and 30% concentrate. GI ewes were maintained under normal controlled condition in the shed, while GII and GIII ewes were subjected to heat stress by exposing them to 42 °C in the climatic chamber. The parameters studied were feed intake (FI), water intake (WI), body weight, body condition score (BCS), physiological, biochemical and endocrine responses. Heat stress significantly altered FI, water intake, BCS, respiration rate and rectal temperature in the afternoon, oestrus duration, estradiol, progesterone, Hb, PCV, plasma glucose, total protein, cortisol, T3 and T4 levels while mineral and antioxidant supplementation ameliorated this heat stress effect on the parameters studied. Further, the adverse effect of heat stress on the productive and reproductive efficiency of Malpura ewes was reduced considerably by mineral mixture and antioxidant supplementation. This is evident from the non-significant difference in BCS, oestrus duration and plasma estradiol between GI and GIII in this study. Hence, it is very pertinent to conclude from this study that mineral mixture and antioxidant supplementation were able to protect Malpura ewes against heat stress.