Effects of the Supplementation of Brewers’ Grain Silage or Wheat Bran with and without Urea on Meat Quantity and Quality in Mongolian Grazing Lambs

Natural open pastures occupy approximately 80% of the land in Mongolia and have traditionally supported the pastoral livestock production system. After the collapse of socialism and the introduction of a market economy more than two decades ago, the total number of animals, including sheep, goats, cattle, horses, camels, as well as grazing pressure on pastures has increased (National Statistical Office of Mongolia, 2014). Despite this, the number sharply decreased twice during the cold seasons of 2000/2001 and 2010/2011 by a dzud. The dzud is the Mongolian name for an abnormal winter weather condition in northeast Asia, characterized by snowy and cold winters so harsh that livestock are unable to graze through the snow cover, causing starvation and eventually death. The economy of the herder households was strongly affected by these weather events. The reasons for the overall increasing number of animals could be that herders do not want to sell their animals, the need to maintain breeding stock numbers, and the herders have limited access to markets. It is said that there are strong demands for meat in China and western Asian countries. However, actually, animal products occupy only 0.6% of the sum of exports, and most of these are wool, skin, and leather. Meat exports were only 3,000 tons in 2013. Besides sanitation problems such as foot-and-mouth disease, high transportation costs, and meat quality may contribute to low meat export. In addition, early fattening for domestic consumption itself has effects to reduce the grazing pressure on the pastures. It is, therefore, important that a diversified risk management and grassland conservation system together with an increase in herder income are established. We conducted a supplemental feeding experiment during the cold season using brewer grain (BG) silage, wheat bran, and urea and determined the effects on meat quantity and quality

Effects of Supplemental Feeding Using Different Nitrogen Sources on Body Weight Gain and Physiological Conditions on Grazing Castrated Lambs in the Steppe Zone of Mongolia

The pastoral livestock production system in Mongolia has traditionally been operated in natural open pastures, which occupies approximately 80% area of the country. The productivity of the system is extremely seasonal, and the nutritional values of pasture plants such as crude protein (CP) and total digestible nutrients (TDN) decrease until spring (Yamasaki et al., 2013), resulting in animals losing their live weight by spring. In recent years, the damage caused by disastrously snowy and cold conditions, termed dzud in Mongolian, has evidently worsened, thereby affecting farm management in the region. To overcome the dzud and establish a sustainable livestock production system, supplemental feeding during the cold seasons is required. Wheat bran is the most prevalent feed among the country’s herders. Brewers’ grain (BG) is one of the most important livestock feed resources because it is rich in energy, protein, fiber, and fat content (MAFF, 1995). The production of BG has been steadily increasing year by year (National Statistical Office of Mongolia, 2014), but the usage of BG in the country is restricted, particularly during summer. Then, ensilaging would be one of the key techniques to store and conserve the nutritional value of BG, as it is possible for even small-to-medium sized farmers and/or herders. In addition, the importation of urea into the country is beginning to accelerate and is expected to be a source of nitrogen (N) for ruminants. We then determined and compared the effects of the different N sources and the amounts on body weight gain and physiological conditions for animals, so as to contribute to the establishment of supplemental feeding technologies during the cold seasons in this region

Oncogenic FGFR1 mutation and amplification in common cellular origin in a composite tumor with neuroblastoma and pheochromocytoma

Neuroblastoma (NB) and pheochromocytoma (PCC) are derived from neural crest cells (NCCs); however, composite tumors with NB and PCC are rare, and their underlying molecular mechanisms remain unknown. To address this issue, we performed exome and transcriptome sequencing with formalin-fixed paraffin-embedded (FFPE) samples from the NB, PCC, and mixed lesions in a patient with a composite tumor. Whole-exome sequencing revealed that most mutations (80%) were shared by all samples, indicating that NB and PCC evolved from the same clone. Notably, all samples harbored both mutation and focal amplification in the FGFR1 oncogene, resulting in an extraordinarily high expression, likely to be the main driver of this tumor. Transcriptome sequencing revealed undifferentiated expression profiles for the NB lesions. Considering that a metastatic lesion was also composite, most likely, the primitive founding lesions should differentiate into both NB and PCC. This is the first reported case with composite-NB and PCC genetically proven to harbor an oncogenic FGFR1 alteration of a common cellular origin

Clonal hematopoiesis in adult pure red cell aplasia

Idiopathic pure red cell aplasia (PRCA) and secondary PRCA associated with thymoma and large granular lymphocyte leukemia are generally considered to be immune-mediated. The PRCA2004/2006 study showed that poor responses to immunosuppression and anemia relapse were associated with death. PRCA may represent the prodrome to MDS. Thus, clonal hematopoiesis may be responsible for treatment failure. We investigated gene mutations in myeloid neoplasm-associated genes in acquired PRCA. We identified 21 mutations affecting amino acid sequences in 11 of the 38 adult PRCA patients (28.9%) using stringent filtering of the error-prone sequences and SNPs. Four PRCA patients showed 7 driver mutations in TET2, DNMT3A and KDM6A, and 2 PRCA patients carried multiple mutations in TET2. Five PRCA patients had mutations with high VAFs exceeding 0.3. These results suggest that clonal hematopoiesis by stem/progenitor cells might be related to the pathophysiology of chronic PRCA in certain adult patients

The whole blood transcriptional regulation landscape in 465 COVID-19 infected samples from Japan COVID-19 Task Force

「コロナ制圧タスクフォース」COVID-19患者由来の血液細胞における遺伝子発現の網羅的解析 --重症度に応じた遺伝子発現の変化には、ヒトゲノム配列の個人差が影響する--. 京都大学プレスリリース. 2022-08-23.Coronavirus disease 2019 (COVID-19) is a recently-emerged infectious disease that has caused millions of deaths, where comprehensive understanding of disease mechanisms is still unestablished. In particular, studies of gene expression dynamics and regulation landscape in COVID-19 infected individuals are limited. Here, we report on a thorough analysis of whole blood RNA-seq data from 465 genotyped samples from the Japan COVID-19 Task Force, including 359 severe and 106 non-severe COVID-19 cases. We discover 1169 putative causal expression quantitative trait loci (eQTLs) including 34 possible colocalizations with biobank fine-mapping results of hematopoietic traits in a Japanese population, 1549 putative causal splice QTLs (sQTLs; e.g. two independent sQTLs at TOR1AIP1), as well as biologically interpretable trans-eQTL examples (e.g., REST and STING1), all fine-mapped at single variant resolution. We perform differential gene expression analysis to elucidate 198 genes with increased expression in severe COVID-19 cases and enriched for innate immune-related functions. Finally, we evaluate the limited but non-zero effect of COVID-19 phenotype on eQTL discovery, and highlight the presence of COVID-19 severity-interaction eQTLs (ieQTLs; e.g., CLEC4C and MYBL2). Our study provides a comprehensive catalog of whole blood regulatory variants in Japanese, as well as a reference for transcriptional landscapes in response to COVID-19 infection

DOCK2 is involved in the host genetics and biology of severe COVID-19

「コロナ制圧タスクフォース」COVID-19疾患感受性遺伝子DOCK2の重症化機序を解明 --アジア最大のバイオレポジトリーでCOVID-19の治療標的を発見--. 京都大学プレスリリース. 2022-08-10.Identifying the host genetic factors underlying severe COVID-19 is an emerging challenge. Here we conducted a genome-wide association study (GWAS) involving 2, 393 cases of COVID-19 in a cohort of Japanese individuals collected during the initial waves of the pandemic, with 3, 289 unaffected controls. We identified a variant on chromosome 5 at 5q35 (rs60200309-A), close to the dedicator of cytokinesis 2 gene (DOCK2), which was associated with severe COVID-19 in patients less than 65 years of age. This risk allele was prevalent in East Asian individuals but rare in Europeans, highlighting the value of genome-wide association studies in non-European populations. RNA-sequencing analysis of 473 bulk peripheral blood samples identified decreased expression of DOCK2 associated with the risk allele in these younger patients. DOCK2 expression was suppressed in patients with severe cases of COVID-19. Single-cell RNA-sequencing analysis (n = 61 individuals) identified cell-type-specific downregulation of DOCK2 and a COVID-19-specific decreasing effect of the risk allele on DOCK2 expression in non-classical monocytes. Immunohistochemistry of lung specimens from patients with severe COVID-19 pneumonia showed suppressed DOCK2 expression. Moreover, inhibition of DOCK2 function with CPYPP increased the severity of pneumonia in a Syrian hamster model of SARS-CoV-2 infection, characterized by weight loss, lung oedema, enhanced viral loads, impaired macrophage recruitment and dysregulated type I interferon responses. We conclude that DOCK2 has an important role in the host immune response to SARS-CoV-2 infection and the development of severe COVID-19, and could be further explored as a potential biomarker and/or therapeutic target

Cellulase–lactic acid bacteria synergy action regulates silage fermentation of woody plant

Abstract Background Feed shortage is an important factor limiting livestock production in the world. To effectively utilize natural woody plant resources, we used wilting and microbial additives to prepare an anaerobic fermentation feed of mulberry, and used PacBio single-molecule real-time (SMRT) sequencing technology to analyse the “enzyme–bacteria synergy” and fermentation mechanism. Results The fresh branches and leaves of mulberry have high levels of moisture and nutrients, and also contain a diverse range of epiphytic microorganisms. After ensiling, the microbial diversity decreased markedly, and the dominant bacteria rapidly shifted from Gram-negative Proteobacteria to Gram-positive Firmicutes. Lactic acid bacteria (LAB) emerged as the dominant microbial population, resulting in increased in the proportion of the carbohydrate metabolism and decreased in the proportion of the amino acid and “global and overview map” (GOM) metabolism categories. The combination of cellulase and LAB exhibited a synergistic effect, through which cellulases such as glycanase, pectinase, and carboxymethyl cellulase decomposed cellulose and hemicellulose into sugars. LAB converted these sugars into lactic acid through the glycolytic pathway, thereby improving the microbial community structure, metabolism and fermentation quality of mulberry silage. The GOM, carbohydrate metabolism, and amino acid metabolism were the main microbial metabolic categories during ensiling. The presence of LAB had an important effect on the microbial community and metabolic pathways during silage fermentation. A “co-occurrence microbial network” formed with LAB, effectively inhibiting the growth of harmful microorganisms, and dominating the anaerobic fermentation process. Conclusions In summary, PacBio SMRT was used to accurately analyse the microbial network information and regulatory mechanism of anaerobic fermentation, which provided a scientific basis for the study of woody silage fermentation theory. This study reveals for the first time the main principle of the enzyme–bacteria synergy in a woody silage fermentation system, which provides technical support for the development and utilization of woody feed resources, and achieves sustainable livestock production

Analysis of main factors affecting silage fermentation of sorghum prepared with whole crop and stover in semiarid West Africa

Sorghum (Sorghum bicolor L.) is widely cultivated in semiarid West Africa as a combined crop for human consumption and animal feed. In order to address the shortage of ruminant feed in Burkina Faso, we studied the potential of preparing silage from sorghum at  various growth stages and analysed the main factors affecting silage fermentation, including the microbial population, chemical  composition and ensiling characteristics of sorghum prepared with and without microbial additives at three stages of development  (soft dough; hard dough; physiological mature stover). After 90 d of ensiling, lactic acid bacteria (LAB) became the dominant  microorganisms in silages. The silage from soft dough sorghum exhibited the highest LAB counts, water-soluble carbohydrate (WSC) and crude protein content. In addition, silage presented greater quality with higher (p < 0.05) lactic acid content and lower (p < 0.05) pH and ammonia nitrogen levels than those at hard dough stage and stover. The WSC and LAB were the important factors affecting silage fermentation and the addition of LAB and cellulase improved fermentation quality. The combined additives displayed a synergistic effect and when silage is prepared with sorghum at soft dough stage, it has best potential for controlling spoilage microorganisms and preserving the silage quality for animal feed. Keywords: cellulase, ensiling, fermentation factor, growth stage, lactic acid bacteri